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1. 67 Setting Molecular Surface Colors 67 Setting Solvent Radius o ooo ooooooo 67 Setting Surface Mapping oocooooooo 68 Solvent Accessible Surface o o 68 Connolly Molecular Surface 69 Total Charge Density oooooooommmmo 69 Total Spin Density oooooooooommmoo 70 Molecular Electrostatic Potential 70 Molecular OtbitalS ooo oooooooo o o 70 Visualizing Surfaces from Other Sources 71 Chapter 4 Building and Editing Models Setting the Model Building Controls 73 Building with the ChemDraw Panel 74 Unsynchronized Mode 04 74 Namie Structse28 oemel a be caw as 75 Building with Other 2D Programs 13 Building With the Bond Tools 75 Creating Uncoordinated Bonds 76 Removing Bonds and Atoms 76 Building With The Text Tool 77 Using Labels init ins las 77 Changing atom types 0 20000 78 The Table Editor 03 2 iaa 78 Specifying Order of Attachment 78 Using Substructutes oooooooococccoo o 78 Building with Substructures 79 Example 1 Building Ethane with Substructures 79 Example 2 Building a Model with a Substructure and Several Other Elements 80 Example 3 Polypeptides o o 80 Example 4 Other Polymers 81 Replacing an Atom with a Substructure 81 Building From Tables
2. 81 Exam ples says Sa ihn acid aes tsetse ets ease oe 82 Changing an Atom to Another Element 82 Changing an Atom to Another Atom Type 83 Changing Bonds 83 Creating Bonds by Bond Proximate Addition 84 Adding Fragments 84 View HOCUS uta tado ql Sah eo aia eet 85 Setting Measurements 85 Setting Bond Lengths 04 86 Setting Bond Angles ooooooomommm 86 Setting Dihedral Angles oooommmmo o 86 Setting Non Bonded Distances Atom Pairs 86 Atom Movement When Setting Measurements 86 Setting Constraints saasaa seese 0 eee 87 Setting Charges 0 0 02 87 Setting Serial Numbers 88 Changing Stereochemistry 88 INVELSION ci cdi hades CERE E ae ee 88 Reflections io 89 Refining a Model 90 Rectifying Atoms eesi gete piau Siasii yk 90 Cleaning Up a Model ooooooommmo 90 Chapter 5 Manipulating Models Selecting oo opii mala 91 Selecting Single Atoms and Bonds 91 Selecting Multiple Atoms and Bonds 92 Deselecting Atoms and Bonds 92 Selecting Groups of Atoms and Bonds 92 Using the Selection Rectangle 92 Defining Groups 0 0 0c eee o 93 Selecting a Group or Fragment 93 Selecting Atoms or Groups by Distance 94 Showing and Hiding Atoms 94 Showing Hs and Lps
3. H6 0 05672 H7 0 05479 Example 7 UHF Spin Density for the Ethyl Radical To calculate the UHF spin density 1 Create the ethyl radical as described in Spin on page 189 Density 2 From the MOPAC Interface submenu of the Calculations menu choose Minimize Energy 3 On the Theoty tab select PM3 4 On the Properties tab select Open Shell Unrestricted and Spin Density 196 MOPAC Computations The Message window displays a list of atomic orbital spin densities The atomic orbitals are not labeled for each value however the general rule is shown in the table below MOPAC only uses s py py and p orbitals f Atomic Orbital Spin Density A O 0 07127 C1s 0 06739 C1 Py 0 08375 C1 py 0 94768 C1 pz 0 01511 C2 S 0 06345 C2 px 0 01844 C2 py 0 03463 C2 p 0 07896 H3 s 0 07815 H4 s 0 01046 H5 s 0 05488 H6 s 0 05329 H7 s You can reason from the result shown below that the unpaired electron in the ethyl radical is more localized at p orbital on C1 Generally this is a good indication of the reactive site CambridgeSoft Computing Properties Example 8 RHF Spin Density for the Ethyl Radical To calculate the RHF spin density 1 Create the ethyl radical as described in Spin Density on page 189 2 From the MOPAC Interface submenu of the Calculations menu choose Minimize Energy 3 On the Theory tab choose PM3 and Closed Shell Restricted 4 On the Properti
4. 0 0005 95 Showing All Atom os a ee 95 Moving Atoms or Models 95 Moving Models with the Translate Tool 96 Rotating Models 96 X Y or Z Axis RotatiO0NS 0o o oo o oo 97 Rotating Fragments 0 cee eee 97 Trackball Tooli scrie ceci Gut ed io ee tian 97 Internal Rotations 00 00 e eee eee eee 97 Rotating Around a Bond oooooo ooo 98 Rotating Around a Specific Axis 98 Rotating a Dihedral Angle 98 Using the Rotation Dial ooooo o 99 Changing Orientation 99 Aligning toan AWS daa 99 Aligning toa Plane ide 99 Resizing Models 100 Centering a SelectiON ooooooooo o 100 Using the Zoom Control ooooooo o o 101 Sealing a Model catas ips oa 101 Changing the Z matrix 101 The First Three Atoms in a Z matrix 101 Atoms Positioned by Three Other Atoms 102 Positioning Example 4 103 Positioning by Bond Angles 103 Positioning by Dihedral Angle 104 Setting Origin Atoms 0 04 104 Chapter 6 Inspecting Models Pop up Information 105 Non Bonded Distances o oooooo o 106 CambridgeSoft Measurement Table 106 Editing Measurements 06 107 Optimal Measurements 00 107 Non Bonded Distances in Tables
5. Minimize Energy To minimize the energy of the molecule based on MM2 Force Field NOTE You cannot minimize models containing phosphate groups drawn with double bonds For information on how to create a model with phosphate groups you can minimize see the Chem3D Drawing FAO at http www cambridgesoft com services fags cfm 1 Build the model for which you want to minimize the energy 2 To impose constraints on model measurements set Optimal column measurements in the Measurements table MM2 and MM3 Computations 151 Minimize Energy 3 From the Calculations menu point to MM2 4 Set the convergence criteria using the folowing and choose Minimize Energy options The Minimize Energy dialog box appears Minimize Energy Job Type Dynamics Properties General Job Type Minimize Energy v V Display Every Iteration Record Every Iteration Copy Measurements to Messages Move Only Selected Atoms Minimum RMS Gradient 0 100 Minimum RMS Gradi nt Summary Parameter Quality Some parameters are guessed Job Type Minimize Energy to Minimum AMS Gradient of 0 100 Display Each Iteration Properties If you want fo Then specify the convergence Enter a value for Minimum RMS Gradient criteria for the gradient of the potential energy surface If the slope of the potential energy surface becomes too small then the minimization has probably re
6. o oooooooo oo 20 The Model Display Toolbat 20 The Surfaces Toolbar o ooooooooo 21 The Movie Toolbar 21 The Calculation Toolbar 22 The ChemDraw Panel o oooooooooo 22 The Model Information Panel 23 The Output and Comments Windows 23 Model Building Basics 24 Internal and External Tables 24 The Model Setting Dialog Box 25 Model Display sito yl oon pees de 25 Model Data Labels ooooooooo o 26 ATOM TYPES ii ad a news 27 RECtACA ON di a 27 Bond Lengths and Bond Angles 27 The Model Explorers vis cso ties yes 27 Model Coordinates n nananana 28 LAMA dd a Na 28 Cartesian Coordinates o ooooooooooo 28 The Measurements Table 29 ChemOffice 2005 Chem3D Chapter 2 Chem3D Tutorials Tutorial 1 Working with ChemDraw 31 Tutorial 2 Building Models with the Bond Tools 0000 32 Tutorial 3 Building Models with the Text Building Tool 36 Replacing Atom io 1 o wena ees 37 Using Labels to Create Models 37 Using Substructures oooooccoooommmo 38 Tutorial 4 Examining Conformations 39 Tutorial 5 Mapping Conformations with the Dihedral Driver 42 Rotating two dihedrals oo ooo o oo 43 Customizing the Graph ooo oooooo o 43
7. Chem3D supports the Windows Metafile and Enhanced Metafile file formats These are the only graphic formats as opposed to chemistry modeling formats that can be used for import They may also be used for export EMF by using the Save As File menu command or the clipboard and WMF by using the clipboard only See Exporting With the Clipboard on page 127 for more information EMF files are exported with transparent backgrounds when this is supported by the operating system Windows 2000 and Windows XP The WMF and EMF file formats are supported by applications such as Microsoft Word for Windows NOTE Chem3D no longer embeds structural information in models exported as EMF files If you have EMF files produced with previous versions of Chem3D you can still open them in Chem3D and work with the structure However EMF files saved from Chem3D 8 0 contain graphic information only and cannot be opened in Chem3D 8 0 BMP The Bitmap file format saves the bitmapped representation of a Chem3D picture The Bitmap file format enables you to transfer Chem3D pictures to other applications such as Microsoft Word for Windows that support bitmaps Printing and Exporting Models 119 Exporting Models Using Different File Formats EPS The PostScript file format saves models as encapsulated postscript file EPS EPS files are ASCII text files containing the scaleable PostScript representation of aChem3D picture You can
8. Includes G O e Y m e aren A S Er SN o e PO Mom og Yy T ooy KA e Ses ng e Chem3D E Notebook Desktop BioAssay Desktop ChemDraw Excel O O 3 en O Ea 0 3 y m 2 E e 5 N ChemOffice WebServer E Notebook Workgroup Enterprise Registration Enterprise Inventory Workgroup Enterprise BioAssay Workgroup Enterprise ChemDraw Spottire ChemACX ChemSCX ChemINDEX NCI amp AIDS gt ES Se a Q a o J S E a a Structure Drawing Tips Importing SD Files Contents Introduction About CS MOPAC 9 About Gaussian 0 000000 9 About CS Mechanics 9 Whats New in Chem3D 9 0 10 What s New in Chem3D 9 0 1 10 For Users of Previous Versions of Chem3D 11 CambridgeSoft Web Pages o oooooo 11 Installation and System Requirements 11 Microsoft Windows Requirements 11 Site License Network Installation Instructions 12 Chapter 1 Chem3D Basics The Graphical User Interface 13 Model Window ccc cece cee e eens 13 Rotation Bats sana dan Gh oases oe eS 14 Menus and ToolbatS 0oo oooooooo o o 14 The File Met tud ina pa Res 14 Th Edit Ment saca ata de bate ace 15 The View Menu Model Display Toolbar 15 The Structure Menu caser emee o aa S 17 The Standard Toolbat o o ooooooooo 19 The Building Toolbar
9. Line 2 starts the block named DTCR The information in this line includes the name of the application that created the file and the date and time when the file was generated Line 3 starts the block named CT which contains the connection table of the compound s Also on this line is a 10 character description of the connection table This will be the same as the file name when the file is generated using Chem3D Pro Finally the number of records contained within the CT block is indicated 39 in the above example Line 4 of the CT Block contains four fields The first field is the number of atoms the second field is the number of bonds the third field is the FORTRAN format for the number of atoms and the fourth field is the FORTRAN format for the number of bonds 264 File Formats N number of hydrogens the stereo information and the formal charge fields are not used and will always contain Zeros Lines 24 42 of the CT Block each contains 3 fields describing a bond between the two atoms The first field is the serial number of the atom from which the bond starts the second field is the serial number of atom where the bond ends and the third field is the bond order Line 43 starts the block named CO The information in this block includes the Cartesian cootdinates of all the atoms from the CT block and indicates the type of coordinates used Angstroms in this example Also in this line is the number of
10. Locating global and local energy minima is often accomplished through energy minimization Locating a saddle point is optimizing to a transition state The ability of a geometry optimization to converge to a minimum depends on the starting geometry the potential energy function used and the settings for a minimum acceptable gradient between steps convergence criteria Geometry optimizations ate iterative and begin at some starting geometry as follows 1 The single point energy calculation is performed on the starting geometry 2 The coordinates for some subset of atoms are changed and another single point energy calculation is performed to determine the energy of that new conformation 134 Computation Concepts 3 The first or second derivative of the energy depending on the method with respect to the atomic coordinates determines how large and in what direction the next increment of geometry change should be 4 The change is made 5 Following the incremental change the energy and energy derivatives are again determined and the process continues until convergence is achieved at which point the minimization process terminates The following illustration shows some concepts of minimization For simplicity this plot shows a single independent variable plotted in two dimensions Potential Energy Variable The starting geometry of the model determines which minimum is reached For example starting at
11. To set the General settings 1 In the Minimize Energy dialog box click General Job Type Theory Properties General Solvation Model Kirkwood Onsager EA Solute Radius 1 400 Dielectric Constant 80 000 Additional Keywords Results In Browse Menu Item Name Create Input File Summary Job Type Compute Properties a Method Closed Shell Restricted Hartree Fock Basis Set STO 3G Orbital Guess Huckel Symmetry C1 z Save As Cancel 2 On the General tab set the following options e Select the Solvation model e Type the dielectric constant for the solvent The box does not appear for gas phase computations e In the Results In box type or browse to the path to the directory where results ate stored e If desired add GAMESS keywords to the Additional Keywords dialog box ChemOffice 2005 Chem3D Saving Customized Job Descriptions After you customize a job description you can save it as a Job Description file to use for future calculations For mote information see Job Description File Formats on page 126 To save a GAMESS job 1 On the General tab type the name of the file in the Menu ltem Name text box The name you choose will appear in the GAMESS menu 2 Click Save As The Save dialog box appears 3 Open the folder Chem3D C3D Extensions GAMESS Job NOTE You must save the file in the GAMESS Job folder for i
12. e On the Job amp Theory tab select COSMO in the Solvent field 188 MOPAC Computations e On the Properties tab check the COSMO Area and or COSMO Volume properties You must check each property you want to see in the results NOTE You can also use the Miertus S cirocco Tomasi solvation model which is available using the H20 keyword This method is recommended only for water as the solvent A discussion of this method can be found in the MOPAC online documentation Hyperfine Coupling Constants Hyperfine Coupling Constants are useful for simulating Electron Spin Resonance ESR spectra Hyperfine interaction of the unpaired electron with the central proton and other equivalent protons cause complex splitting patterns in ESR spectra ESR spectroscopy measures the absorption of microwave radiation by an unpaired electron when it is placed under a strong magnetic field Hyperfine Coupling Constants HFCs are related to the line spacing within the hyperfine pattern of an ESR spectra and the distance between peaks Species that contain unpaired electrons are as follows e Free radicals e Odd electron molecules Transition metal complexes e Rare earth ions e Triplet state molecules For mote information see the MOPAC online manual page 34 CambridgeSoft Computing Properties The following table contains the keywords automatically sent to MOPAC and those you can use to affect this property Keyword Descrip
13. mol MDL 118 124 mop 118 mop MOPAC 124 mpc MOPAC 124 msm MSI ChemNote 118 124 pdb Protein Data Bank 118 126 png 121 dl ROSDAL 118 126 sm2 SYBYL 118 126 smd Standard Molecular Data STN Express 118 126 sml SYBYL 118 126 xyz Tinker 126 zmt MOPAC 124 Alchemy 121 Bitmap 119 Gaussian Input 122 Postscript 120 QuickTime 121 TIFF 120 File menu 14 Filters property 215 Fock matrix 145 Force constant field 287 Force constants 200 Formal Charge ChemProp Std 206 Formal charge definition 52 Formats for chemistry modeling applica tions 121 FORTRAN Formats 242 246 249 250 253 257 259 260 267 Fragments creating 84 rotating 97 selecting 93 Fragments rotating 45 Fragments separating 44 Frame interval control 158 Free Energy ChemProp Pro 207 Freehand rotation 97 Fujitsu Ltd 293 G GAMESS Installing 211 installing 211 minimize energy command 211 overview 211 property server 210 server 210 specifying methods 211 Gaussian 03 199 about 9 Chem3D 9 0 1 checkpoint file format 122 compute properties command 202 copy measurements to messages con trol 200 create input file command 202 cube file format 122 display every iteration control 200 file formats 122 general tab 201 input file format 203 job type tab 199 minimize energy command 199 molecular surface types available 65 overview 199 properties tab 202 specifying basis sets 200 specifying keywords 201 s
14. oOo Oo OO Oo O0OoO0OOoOooo so O0OoO0OoOo0oOooo sos O0oo0Oo0oOoopo ys 5 0 Each line represents a data record containing one or more fields of information about the model Each field is delimited by space s or a tab The fields in the MacroModel format file used by Chem3D ate 1 Line 1 contains 2 fields the first field is the number of atoms and the second field is the name of the molecule The molecule name is the file name when the file is created using Chem3D 2 Lines 2 19 each contain 17 fields describing information about one atom and its attached bond The first field contains the atom type The second through thirteenth fields represent 6 pairs of numbers describing the bonds that this atom makes to other atoms The first number of each pair is the serial number of the other atom and the second number is the bond type The fourteenth field is the X coordinate the fifteenth field is the Y coordinate the sixteenth field is the Z coordinate and finally and the seventeenth field is the color of the atom Atom colors are ignored by Chem3D This field will contain a zero if the file was created using Chem3D NOTE Atom types are user definable See Editing File Format Atom Types on page 241 for instructions on modifying or creating an atom type 250 File Formats D On O GOG On ee O0oo0oOOo0oOooo ys O 1 972885 0 38063 0 679077 0 O 1 960663 0 413223 0 928909 0 O 0 981857 1 921463 0 9921
15. A model of ethane appears 2 View the Measurements table a From the Structure menu point to Measurements and then choose Bond Lengths Chem3D Tutorials 39 Tutorial 4 Examining Conformations b From the Structure menu point to Rotate the orientation of the model to obtain a Measurement and then choose Bond Angles Newman projection viewing the model along a bond This orientation helps clarify the conformations of ethane NOTE Ifthe Measurements table appears along side the Model Explorer you can stack the windows by locking the Model Explorer window open and dragging To rotate a methyl group on an ethane model the Measurements table on top of it 1 Click the Trackball too PM The information you chose appears in the When you mouse over the edges of the model Measurements table The measurements in the window the Rotation Bars appear Actual and Optimal columns are nearly Only the X and Y rotation bars ate active identical The Actual column represents the These Rotations bars ate always active because measurements for the model in the active they are not dependent on any atoms being window The Optimal measurements for bond selected tenet ne and hond angles Only represen 2 Click the X Axis rotation bar and drag to the standard measurements in the Bond Stretching right and Angle Bending parameter tables As you drag the status bar shows details about Measurement E the rotation Optimal H 8
16. FM Cut Copy Paste Replace with Text Tool ae Select gt Visibility Select Color Apply Fragment Color Display Mode y Show Atom Map Labels Atom Serial Number Atom Symbol Atom Dots rev vy Reset Children to Default Delete Fragment and Contents Rename Fragment New Group The icon on the fragment changes to a target ENS Model Explorer HH Epinephrine fe Methamphetamine 3 Select the Methamphetamine fragment TIP The check in the box next to Methamphetamine does not mean that it is selected it means that it is visible Try it This is bow you work with multiple overlays You must click on the fragment name for the Fast Overlay command to become active 4 Choose Fast Overlay from the Overlay submenu on the context menu The fragments are overlaid The numbers show the serial numbers of the target atoms that the matching overlay atoms correspond to TIP You can designate a group rather than the entire fragment as the target In some cases this will give more useful results To turn off the Fast Overlay mode Choose Clear Target Fragment from the Overlay submenu ChemOffice 2005 Chem3D Chem3D Tutorials 45 Tutorial 6 Overlaying Models Tutorial 7 Docking Models The Dock command enables you to position a fragment into a desired orientation and proximity relative to a second fragment Each fragment remains rigid du
17. XH2 Quality and Reference Angle Type The first field Angle Type contains the atom type numbers of the three atoms which describe the bond angle For example angle type 1 2 1 is a bond angle formed by an alkane carbon bonded to an alkene carbon which is bonded to another alkane carbon Notice that the alkene carbon is the central atom of the bond angle ChemOffice 2005 Appendix KB The KB or the angle bending constant contains a measure of the amount of energy required to deform a particular bond angle The larger the value of KB for a particular bond angle described by three atoms the more difficult it is to compress or stretch that bond angle XR2 XR2 the third field contains the optimal value of a bond angle where the central atom of that bond angle is not bonded to any hydrogen atoms In the XR2 notation X represents the central atom of a bond angle and R represents any non hydrogen atom bonded to X For example the optimal value of the 1 1 3 angle type for 2 2 dichloropropionic acid is the XR2 bond angle of 107 8 since the central carbon C 2 has no attached hydrogen atoms The optimal value of the 1 8 1 angle type for N N N triethylamine is the XR2 bond angle of 107 77 because the central nitrogen has no attached hydrogen atoms Notice that the central nitrogen has a trigonal pyramidal geometry thus one of the attached non hydrogen atoms is a lone pair the other non h
18. where N is the number of atoms In general molecular mechanical methods are computationally less expensive than quantum mechanical methods The suitability of each general method for particular applications can be summarized as follows Molecular Mechanics Methods Applications Summary Molecular mechanics in Chem3D apply to Systems containing thousands of atoms Organic oligonucleotides peptides and saccharides Gas phase only for MM2 Useful techniques available using MM2 methods include Energy Minimization for locating stable conformations Single point energy calculations for comparing conformations of the same molecule Searching conformational space by varying a single dihedral angle Studying molecular motion using Molecular Dynamics ChemOffice 2005 Chem3D Quantum Mechanical Methods Applications Summary Useful information determined by quantum mechanical methods includes Molecular orbital energies and coefficients Heat of Formation for evaluating conformational energies Partial atomic charges calculated from the molecular orbital coefficients Electrostatic potential Dipole moment Transition state geometries and energies Bond dissociation energies The semiempirical methods available in Chem3D and CS MOPAC apply to Systems containing up to 120 heavy atoms and 300 total atoms Organic organometallics and small oligomers peptide nucleotide saccharide Gas phase or i
19. 1 1236 0 177 0 059 3 2C3 0 26 0 856 1 0224 4 3 C3 1 01 0 0491 1 3267 5 4 C3 1 838 0 1626 0 0526 6 5 C3 0 9934 0 8543 1 0252 7 6C3 0 2815 0 0527 1 3275 8 703 2 1621 1 0585 0 3907 9 8H 1 4448 0 8185 0 3338 10 9H 0 8497 0 979 1 9623 11 10H 0 0275 1 8784 0 6806 12 11H 1 6239 0 5794 2 0941 13 12H 0 729 0 9408 1 7589 1 Alchemy III is a registered trademark of Tripos Associates Inc File Formats 241 Editing File Format Atom Types 40 13H 2 197 0 8229 0 3289 14H 2 7422 0 7763 0 282 15 H 1 5961 0 9769 1 9574 16 H 0 7156 1 8784 0 679 17 H 0 8718 0 6068 2 0941 18 H 0 004 0 9319 1 7721 19 H 2 7422 0 593 0 9688 1 1 2 SINGLE 2 1 6 SINGLE 3 1 7 SINGLE 4 1 8 SINGLE 5 2 3 SINGLE 6 2 9 SINGLE 7 2 10 SINGLE 8 3 4 SINGLE 9 3 11 SINGLE 10 3 12 SINGLE 11 4 5 SINGLE 12 4 13 SINGLE 13 4 14 SINGLE 14 5 6 SINGLE 15 5 15 SINGLE 16 5 16 SINGLE 17 6 17 SINGLE 18 6 18 SINGLE 19 7 19 SINGLE Each line represents a data record containing one or more fields of information about the molecule Each field is delimited by spaces or a tab The fields used by Chem3D are described below 1 Line 1 contains two fields The first field is the total number of atoms in the molecule and the second field is the total number of bonds Lines 2 20 each contain 5 fields of information about each of the atom in the molecule The first field is the serial number of the atom The second field is the atom type the thir
20. 135 The Force Field c oea sasao serant 136 MM2 a a IA Re ees 136 Bond Stretching Energy o oooo ooo 137 Angle Bending Energy o ooooooocmoo 137 Torsion Energy essee todeta eee 138 Non Bonded Energy o oooocooocmoo m oo 139 van der Waals Energy ooo oooooomooo 139 Cutoff Parameters for van der Waals Interactions 139 Electrostatic Energy o ooooooooo moo 140 charge charge contribution 140 dipole dipole contribution 140 dipole charge contribution 140 Cutoff Parameters for Electrostatic Interactions 140 OOP Bending ori Uat 141 Pi Bonds and Atoms with Pi Bonds 141 Stretch Bend Cross Terms o oooooo 142 User Imposed Constraints o o ooo o oo 142 Molecular Dynamics Simulation 142 Molecular Dynamics Formulas 143 Quantum Mechanics Theory in Brief 143 Approximations to the Hamiltonian 144 Restrictions on the Wave Function 145 Spin UNCUONS oi e 145 LCAO and Basis Sets oo ooooooo 145 The Roothaan Hall Matrix Equation 146 Ab Initio vs Semiempirical 146 The Semi empirical Methods 146 Extended H ckel Method 146 Methods Available in CS MOPAC 147 RHP im Grea dicey lee ad oles dls Snare gene whe 147 UHP aert A REY ERE he OER 147 Configuration Interaction 147 Approximate Hamiltonians in MOPAC 148 Choosing
21. All other trademarks are the property of their respective holders All specifications subject to change without notice www cam b r dg eso ft CcCOm DESKTOP CS ChemDraw W C hemical Structure D rawing Standard ChemDraw Ultra adds ChemD raw Excel ChemN MR Name Struct Beilstein s AutoN om CLogP and ChemFinder Word to ChemD raw Pro With rich polymer notation atom numbering BioArt templates and modern user interface ChenD raw is more powerful than ever before Create tables of structures identify and label stereochemistry estimate NMR spectra from a ChemDraw structure with structure to spectrum correlation obtain structures from chemical names assign names from structures and create multi page documents and posters ChemDraw Pro will boost your productivity more than ever Draw publication quality structures and reactions Publish on the web using the ChemD raw Plugin Create precise database queries by specifying atom and bond properties and include stereochemistry Display spectra structures and annotations on the same page Usethe Online M enu to query ChanACX Com by structure identify available vendors and order online E ka a rik h 1 1 x w gt Stereochemistry iA EA i nm Vio j pe pee Pree ly em Die he pim Fi pl Dato E lt a AA ig mar 7 pa Jai iy gt Structure to Spectrum NMR Correlation SOFTWARE ChemDraw Ultra Ultimate Drawing Query amp Analysis Adds Chem
22. Angstrom your model is scaled so that a distance of one ngstrom in the model is 1 centimeter in the printed image If you specify a value of 72 pixels angstrom a distance of one angstrom in the model is scaled to 1 inch on the printed image Scale To Full Page Always Print with White Background Printing and Exporting Models 117 If you want to Then select High Resolution Printing this can also be set with the OpenGL Preferences settings produce publication quality output print a footer at the Include Footer bottom left of the printed page containing the name of the model and the date and time changes wete last made Printing To print the contents of the active window From the File menu choose Print The Print dialog box appears The contents of the dialog box depend upon the type of printer you are using The picture of the model is scaled according to the settings in the Page Setup dialog box To print a table right click in the table and select Print Exporting Models Using Different File Formats The following table shows all of the chemistry file formats supported by Chem3D For more information about file formats see Appendix E File Formats 118 Printing and Exporting Models File Format Alchemy Cartesian Coordinate CCDB Chem3D Chem3D template ChemDraw Connection Table GAMESS Input Gaussian Checkpoint Gaussian Cube Gau
23. Detect Stereochemistry Scans the model and lists the stereocenters in the Output box Invert Inverts the isomeric form For example to invert a model from the cis form to the trans form select one of the stereo centers and use the Invert command Deviation from Plane When you select four or more atoms outputs the RMS deviation from the plane to the Output window Add Centroid Adds a centroid to a selected model or fragment At least two atoms must be selected The centroid and bonds to the selected atoms are displayed and bond lengths can be viewed in the tool tips To delete a centroid select it and press the Delete or Backspace key Rectify Fills the open valences for an atom usually with hydrogen atoms This command is only useful if the default automatic rectification is turned off in the Model Settings dialog box Clean Up Corrects unrealistic bond lengths and bond angles that may occur when building models especially when you build strained ring systems ChemOffice 2005 Chem3D e Overlay The Overlay submenu provides all of the commands to enable you to compare fragments by superimposing one fragment in a model window over a second fragment Two types of overlay are possible quick and minimization See Tutorial 6 Overlaying Models on page 43 and Comparing Models by Overlay on page 109 for information on each overlay type e Dock The Dock command enables you to positio
24. For a description and review of molecular dynamics see Dynamics of Proteins and Nucleic Acids J Andrew McCammon and Stephen Harvey Cambridge University Press Cambridge UK 1987 Despite its focus on biopolymers this book contains a cogent description of molecular dynamics and related methods as well as information applicable to other molecules Chem3D Changes to Allinger s Force Field The Chem3D implementation of the Allinger Force Field differs in these areas 1 A charge dipole interaction term 2 A quartic stretching term 3 Cutoffs for electrostatic and van der Waals terms with a fifth order polynomial switching function 4 Automatic pi system calculation when necessaty CambridgeSoft Editing Parameters Charge Dipole Interaction Term Allinger s potential function includes one of two possible electrostatic terms one based on bond dipoles or one based on partial atomic charges The addition of a charge dipole interaction term allows for a combined approach where partial charges are represented as bond dipoles and charged groups such as ammonium or phosphate are treated as point charges Quartic Stretching Term With the addition of a quartic bond stretching term troublesome negative bond stretching energies which appear when long bonds are treated by Allinger s force field are eliminated The quartic bond stretching term is required primarily for molecular dynamics it has little or no effect o
25. For many atom types that change bond order you must select all atoms attached to the bond so that the correct bond forms For example to change ethane to ethene 1 Select both carbons 2 Type C Alkene 3 Press the Enter key e Changing Bonds To change the bond order of a bond you can use the bond tools commands or the Text tool You can change the bond order in the following ways e One bond at a time e Several bonds at once By changing the atoms types on the bond To change the bond order with the bond tool 1 Select a bond tool of a different order 2 Drag from one atom to another to change To change the bond order using a command 1 Select a bond 2 From the Right click menu point to Set Bond Order and choose a bond order To change the bond order by changing the atom type of the atoms on either end of the bond 1 Click the Text tool 2 Shift click all the atoms that are attached to bonds whose order you want to change Building and Editing Models 83 Changing an Atom to Another Atom Type 3 Type the atom type to which you want to change the selected atoms 4 Press the Enter key The bond orders of the bonds change to reflect the new atom types To change several bonds at once 1 Open the ChemDraw panel and click in it to activate the ChemDraw control 2 Choose either selection tool Lasso or Marquee 3 Click the first bond to be changed then use Shift Click to select
26. Geneva M onaco and TrueType are trademarks of Apple Computer Inc The ChemSelect Reaction D atabase is copyrighted O by InfoChem GmbH 1997 AspTear is copyrighted O by Softwing Copyright O 1986 2004 C ambridgeSoft Corporation Cambridge Scientific Computing Inc All Rights Reserved Printed in the United States of America All other trademarks are the property of their respective holders CambridgeSoft End User License Agreement for Software Products Important T his CambridgeSoft Software License Agreement Agreement is a legal agreement between you the end user either an individual or an entity and C ambridgeSoft Corporation CS regarding the use of CS Software Products which may include computer software the associated media any printed materials and any online or electronic documentation By installing copying or otherwise using any CS Software Product you signify that you have read the CS End User License Agreement and agree to be bound by its terms If you do not agree to the Agreement s terms promptly return the package and all its contents to the place of purchase for a full refund CambridgeSoft Software License 1 Grant of License C ambridgeSoft CS Software Products are licensed not sold CS grants and you hereby accept a nonexclusive license to use one copy of the enclosed Software Product Software in accordance with the tems of this Agreement This licensed copy of the Software may o
27. MOPAC Computations 181 Minimizing Energy criteria to optimize to an excited state instead of the ground state or to calculate additional properties NOTE Other properties that you might specify through the keywords section of the dialog box may affect the outcome For more information see Using Keywords on page 170 Mopac Interface a Job amp Theory Properties General Keywords AM EF GEO OK GNORM 0 100 MMOK Results in C Documents and Settings zfrutkoFF CAMSOFT My Documents Mope Browse Set As Default Optimize to Transition State To optimize your model to a transition state use a conformation that is as close to the transition state as possible Do not use a local or global minimum because the algorithm cannot effectively move the geometry from that starting point 182 MOPAC Computations To optimize a transition state 1 Choose Optimize to Transition State from the MOPAC Interface submenu of the Calculations menu The MOPAC Interface dialog box appears Mopac Interface Job amp Theory Properties General Job Type Optimize to Transition State Method amt Wave Function Closed Shell Restricted Optimizer Solvent Move Which Minimum RMS i E E I Show Output in NotePad I Send Back Output Set As Default Cancel 2 On the Job and Theory tab select a Method and Wave Function NOTE Unless you are an experienced MOPAC user use the
28. The following table describes the elements of the Measurement table Table Element Description Column Heading Contains field names describing the information in the table Used to select an entire record Clicking a record selector highlights the corresponding atoms in the model window Recotd Selector Field Name Identifies the type of information in the cells with which it is associated Used to change the width of the column by dragging Column Divider Cell Contains one value of one field in a record All records in a given table contain the same number of cells The Output and Comments Windows The Output and Comments boxes are typically found at the bottom of the GUI window You can have them float if you wish or move them to another side of the window You can select Auto hide to minimize them Calculations on models and other operations produce messages that are displayed in the Output window You can save the information in the Output window either directly or using the clipboard To save information directly Chem3D Basics 23 The Graphical User Interface 1 Right click in the window and choose Export A Save As dialog box appears 2 Enter a name for the file select a file format html or txt and click Save To save information with the clipboard 1 Select the text you want to save 2 Right click in the window and choose Copy Alternately you can choose Select All from the rig
29. To show all hydrogen atoms and lone pairs in the model e From the Model Display submenu of the View menu choose Show H s and Lp s A check mark appears beside the command indicating that it has been selected When Show Hs and Lps is not selected hydrogen atoms and lone pairs ate automatically hidden Showing All Atoms If you are working with a large model it may be difficult to keep track of everything you have hidden To show all atoms or groups that are hidden 1 Select a level in the tree control above the hidden atoms or groups or Shiftt click to select the entire model 2 From the Right click menu point to Select and click Select All Children ChemOffice 2005 Chem3D 3 Right click again point to Show and choose Inherit Setting Moving Atoms or Models Use the Move Objects tool e to move atoms and other objects to different locations If the atom group of atoms bond or group of bonds that you want to move are already selected then all of the selected atoms move Using the Move Objects tool changes the view relative to the model coordinates The following examples use the visualization axes to demonstrate the difference between different types of moving To move an atom to a different location on the X Y plane 1 Click both the Model Axis and View Axis tools to visualize the axes NOTE The axes will only appear if there is a model in the window 2 Drag with the single bond tool
30. Type C Alkene Press the Enter key A The atom type and the bond order are changed to reflect the new model of ethyleneamine You can point at the atoms and bonds to display this new information 78 Building and Editing Models The Table Editor To use the Table Editor to enter text in a text box 1 From the View menu point to Parameter Tables and choose Atom Types Select the element or atom type in the table From the Edit menu choose Copy Double click in the Chem3D Model Window In Chem3D from the Edit menu choose Paste a A WwW N The copied text appears in the text box Specifying Order of Attachment In both the simple and complex forms for using the Text tool you can specify the order of attachment and repeating units by numbers and parentheses For example e Type CH3 3CNH2 into a text box with no atoms selected and press the Enter key A model of tert butylamine appears Using Substructures You can use pre defined functional groups called substructures to build models Some advantages for using substructures in your model building process are as follows e Substructures ate energy minimized e Substructutes have more than one attachment atom bonding atom pre configured For example the substructure Ph for the phenyl group has a single attachment point The substructure COO for the carboxyl group has attachment points at both the Carboxyl carbon and the Alcohol Oxygen Thes
31. a is amp Model XYZ Carte Showing the Deviation from Plane The Deviation from Plane command allows you to compute the RMS Deviation from the least squates plane fitted to the selected atoms in the model Inspecting Models 107 Measurement Table Example To examine the Deviation from Plane for five atoms in a penicillin molecule 1 Build a penicillin model as in the previous example 2 Using the Select tool click on the S 4 atom 3 Shift click the other atoms in the five membered penicillin ring The molecule should appear as follows 4 From the Structure menu choose Deviation from Plane When the deviation from plane calculation is complete the value appears in the Output window Output nx The RMS Deviation from the plane is 0 6534 108 Inspecting Models The result indicates that the atoms in the five membered ring of penicillin are not totally coplanar there is a slight pucker to the ring Removing Measurements from a Table You can remove information from the Measurements table without affecting the model To remove measurements from a table e From the Structure menu point to Measurements and choose Clear Displaying the Coordinates Tables You can view the internal coordinates or the Cartesian coordinates of your model by choosing Cartesian Table or Z Matrix Table from the View menu Internal Coordinates The Internal Coordinates table c
32. b minimization results in geometry a which is the global minimum Starting at d leads to geometry f which is a local minimum The proximity to a minimum but not a particular minimum can be controlled by specifying a minimum gradient that should be reached Geometry f rather than geometry e can be reached by decreasing the value of the gradient where the calculation ends Often if a convergence criterion energy gradient is too lax a first derivative minimization can result in a geometry that is near a saddle point This CambridgeSoft Computational Methods Overview occurs because the value of the energy gradient near a saddle point as neat a minimum is very small For example at point c the derivative of the energy is 0 and as far as the minimizer is concerned point c is a minimum First derivative minimizers cannot as a tule surmount saddle points to reach another minimum NOTE If the saddle point is the extremum of interest it is best to use a procedure that specifically locates a transition state such as the CS MOPAC Pro Optimize To Transition State command You can take the following steps to ensure that a minimization has not resulted in a saddle point e The geometry can be altered slightly and another minimization performed The new starting geometry might result in either a or in a case where the original one led to c e The Dihedral Driver can be employed to seatch the
33. number of atoms the second field is the number of bonds the third field is the number of atom lists the fourth field is an unused field and the fifth field is the stereochemistry NOTE Chem3D Pro ignores the following fields number of atom lists the unused field and stereochemistry These fields will always contain a zero if the file was created using Chem3D Pro 2520 File Formats 2 2 22 2 2 2 2d 2 2 0 0 0 6 0 0 0 0 0 10 0 6 0 0 10 0 6 0 0 0 0 0 0 0 0 1 0 0 6 0 0 5 Lines 5 23 the Atom block each contain 9 fields which describes an atom in the molecule The first field is the X coordinate the second field is the Y coordinate the third field is the Z coordinate the fourth field is the atomic symbol the fifth field is the mass difference the sixth field is the charge the seventh field is the stereo parity designator the eighth field is the number of hydrogens and the ninth field is the center NOTE Chem3D Pro ignores the following fields mass difference charge stereo parity designator number of hydrogens and center These fields contain zeros if the file was created using Chem3D Pro 6 Lines 24 42 the Bond block each contain 6 fields which describe a bond in the molecule the first field is the from atom id the second field is the to atom id the third field is the bond type the fourth field is the bond stereo designator the fifth field is an unused field and the sixth field i
34. process live at each iteration in the calculation NOTE Displaying or recording each iteration adds significantly to the time required to minimize the structure Gaussian Computations 199 Gaussian 03 If you want fo Then select record each iteration as a frame in a movie for later replay view the value of each measurement in the Measurement table calculate the second derivative matrix determined from atomic tadii and a simple valence force field This is the Gaussian default initial guess calculate the initial force constant at the current level of theory Corresponds to the Gaussian keyword Opt CalcFC calculate a new force constant at every point in the minimization Corresponds to the Gaussian keyword Opt CalcAll calculate using the equivalent to the Gaussian keyword Opt Tight Record Every Iteration Copy Measurements to Output Do Not Calculate Force Constants Calculate Initial Force Constants Calculate Force Constants At Each Point Use Tight Convergence Criteria 200 Gaussian Computations The Theory Tab Use the Theory tab to specify the combination of basis set and particular electronic structure theory referred to in Gaussian documentation as the model chemistry By default this tab is optimized for setting up ab initio computations Job Type Theory Properties General Method Hartree Fock X Wave Function MEN Basis Set
35. set the batrier to rotation 1 In the Measurements table type 0 in the Optimal column for the selected dihedral angle and press the Enter key 2 On the MM2 submenu of the Calculations menu choose Minimize The Minimize Energy dialog box appears 3 Click Run The model conforms to the following structure ChemOffice 2005 Chem3D Entering a value in the Optimal column imposes a constraint on the minimization routine You are increasing the force constant for the torsional term in the steric energy calculation so that you can optimize to the transition state When the minimization is complete the reported energy values ate as follows The energy for this eclipsed conformation is higher relative to the staggered form The majority of the energy contribution is from the torsional energy and the 1 4 VDW interactions NOTE The values of the energy terms shown here are approximate and can vary slightly based on the type of processor used to calculate them Output x Calculation started A Note All parameters used Iteration 196 Minimizat Stretch 0 0420 Bend 0 2009 Stretch Bend 0 0242 Torsion 2 1328 Non 1 4 VDW 0 0000 1 4 UDU 1 1527 Total 3 5526 Calculation ending e The dihedral angle in the Actual column becomes 0 corresponding to the imposed constraint The difference in energy between the global minimum Total previous calculation and the transition state Total this calcula
36. toolbar CambridgeSoft Rotating Models When you mouse over an edge of the model window the Rotation bars appear on the edges of the Model window Internal Rotation Bar Z Axis Rotation Bar Bie Edk View Sinxture Caladations Sigfoces Movin Qie Window Helo gt a ed a v DD Hi3 2 N A BN A 0 3 1l X Axis Rotation Bar X Y or Z Axis Rotations To perform a rotation about the X Y or Z axis Y Axis Rotation Bar 1 Point to the appropriate Rotation bar 2 Drag the pointer along the Rotation bar The number of degtees of rotation appears in the Status bar Rotating Fragments If more than one model fragment is in the model window you can rotate a single fragment or rotate all fragments in the model window To rotate only one fragment 1 Select an atom in the fragment you want to rotate 2 Drag a rotation bar To rotate all fragments do one of the following With an atom selected Shift drag a Rotation bar e With no atoms selected drag a rotation bar ChemOffice 2005 Chem3D Trackball Tool Use the Trackball tool to freely rotate a model e Starting anywhere in the model window drag the pointer in any direction The Status bar displays the X and Y axis rotation Internal Rotations Internal rotations alter a dihedral angle and create another conformation of your model You can rotate an internal angle using the Internal Rotation bar To perform internal rotations in a model you mu
37. 0 1 1 5 1 17 H 1 0 0 2 1 5 0 9 18 H 1 0 0 1 0 85 1 2 19 H 1 0 0 2 0 83 0 File Formats O0OoO0O0DOOOOOOoO O0o 0suonsoOoOoO0oomp onsso os OoO0O0OOOOOOoo o 0ocuonooOoOoO0oOooso os 0000000H 180 100 0000 H CambridgeSoft MSI MolFile 48 Bond List Bond bond_type atom1 atom2 cis trans length locked ring Sh_type Sh_nr Qorder Qtopol Qs 49 50 11120 0 000 0000 S 00 51 21160 0 000 0000 S 00 52 311180 0 000 0000 S 00 53 411190 0 000 0000 S 00 54 51230 0 000 0000 S 00 55 612160 0 000 0000 S 00 56 712170 0 000 0000 S 00 57 81340 0 000 0000 S 00 58 913140 0 000 0000 S 00 59 1013150 0 000 0000 S 00 60 111450 0 000 0000 S 00 61 1214110 0 000 0000 S 00 62 1314120 0 000 0000 S 00 63 141560 0 000 0000 S 00 64 151590 0 000 0000 S 00 65 1615100 0 000 0000 S 00 66 171670 0 000 0000 S 00 67 1816130 0 000 0000 S 00 68 191780 0 000 0000 S 00 69 Bond Angles 70 bond1 bond2 angle locked 71 Dihedral Angles 72 at1 cons at1 at2 at2 cons angle locked 73 Planarity data 74 User data area 75 End of File The MSI MolFile format is broken up into several sections Section headers ate preceded by a Blank lines also contain a Each line is either a blank line a header line or a data record containing one ot mote fields of information about the 1 Molecular Simulations MOLFILE ChemNote is a product of Molecular Simulations Inc ChemOffice 2005 Appendix structure Indivi
38. 0839 Bend 0 2638 1 3235 Stretch Bend 0 0163 0 0435 Torsion 1 4369 1 5366 Non 1 4 van der Waals 0 0193 0 3794 1 4 van der Waals 1 1742 1 1621 Dipole Dipole 0 0767 0 1032 Total 0 137 1 5512 The significant differences between the steric energy terms for cis and frans 2 butene are in the Bend and Non 1 4 van der Waals steric energy terms The Bend term is much higher in c s 2 butene because the C 1 C 2 C 3 and the C 2 C 3 C 4 bond angles had to be deformed from their optimal value of 122 0 to 127 4 to relieve some of the steric crowding from the interaction of hydrogens on C 1 and C 4 The interaction of hydrogens on C 1 and C 4 of trans 2 butene is ChemOffice 2005 Chem3D much less intense thus the C 1 C 2 C 3 and the C 2 C 3 C 4 bond angles have values of 123 9 much closer to the optimal value of 122 0 The Bend and Non 1 4 van der Waals terms for trans 2 butene are smaller therefore rans 2 butene has a lower steric energy than c s 2 butene Showing Used Parameters You can display all parameters used in an MM2 calculation in the Output window The list includes a quality assessment of each parameter Highest quality empirically derived parameters are rated as 4 while a lowest quality rating of 1 indicates that a parameter is a best guess value To show the used Parameters e From the MM2 submenu of the Calculations menu choose Show Used Parameters The parameters appear i
39. 1 8 1 5 2 3 1 6 2 9 1 ChemOffice 2005 Appendix FileFormats 265 Protein Data Bank Files 7 8 9 10 11 12 13 14 15 16 17 18 19 0 MOL NOOO TO an _A FP RWW WwW ON 10 6 11 12 5 13 14 6 15 16 17 18 19 The following illustration shows the components of the SYBYL Output File from Chem3D for C 6 and Bond 3 of Cyclohexanol Number of Aons Ss MOL Atom Atom ID Tipe Number of Bonds 19 MAL 3 1 Bond FromAtom Naber Number of Featwes 0 MAL 266 File Formats Molecule Name Gyclohexanol i X Y Coon onl 7 1 To Aom Bond Tipe Center 0 7768C f Cond 2 22222 2d 2 2 2 2 2d The format for SYBYL MOL files is as follows 1 The first record in the SYBYL MOL File contains the number of atoms in the model the word MOL the name of the molecule and the center of the molecule The atom records lines 2 20 in the cyclohexanol example contain the Atom ID in column 1 followed by the Atom Type in column 2 and the X Y and Z Cartesian coordinates of that atom in columns 3 5 The first record after the last atom records contains the number of bonds in the molecule followed by the word MOL The bond records lines 22 40 in the cyclohexanol example contain the Bond Number in column 1 followed by the Atom ID of the atom where the bond starts the From Atom in column 2 and the Atom ID of the atom where the bond stops the
40. 22 Line 75 is a header that indicates the End of File FORTRAN Formats The FORTRAN format for each record of the Molecular Simulations MolFile format is as follows Line Description FORTRAN Number Format Line 1 Line 2 Cyclohexanol Line 3 Line 4a Cc 0 0 0 Line 4b C 1 54152 1 0 Line 4c C 1 53523 1 Line 4d C 1 53973 1 ChemOffice 2005 Appendix 111 7747 109 7114 29 47 atom list field 1 1X A 3 1X 1 3F9 value 3 1X LF4 1 7 1X D 1X A 1 8 1X D EA oe 50 68 bond list field 1 4 1X D F9 3 4Q2X values D 1X A1 9 2 1X D MOPAC The specific format of the MOPAC files used by Chem3D is the MOPAC Data File format This format is described on pages 1 5 through 1 7 of the Description of MOPAC section and page 3 5 of the Geometry Specification section in the MOPAC Manual fifth edition For further details about the MOPAC Data File format please refer to the above publication The following is a sample MOPAC output file from Chem3D for cyclohexanol 0 0 000 0 0 0 0 10 0 1 0 0 2 1 0 1 55 6959 112 3 File Formats 257 MSI MolFile Line 4e C 1 53597 1 111 7012 Line 4f C 1 53424 1 110 7535 Line 4g O 1 40196 1 107 6989 Line 4h H 1 11739 1 107 8685 Line 4l H 1 11633 1 110 0751 Line 4j H 1 11566 1 109 4526 Line 4k H 1 11665 1 109 9597 Line 4l H 1 1161 1 109 5453 Line 4m H 1 11542 1 109 4316 Line 4n H 1 11499 1 110 549 Line 40 H 1 11671 1 109 93 Line 4p H 1 11615 1 109 4
41. Bank Files 268 Line 16 Line 17 Line 18 Line 19 Line 20 Line 21 Line 22 Line 23 Line 24 Line 25 Line 26 Line 27 Line 28 Line 29 Line 30 Line 31 Line 32 Line 33 Line 34 Line 35 Line 36 Line 37 Line 38 Line 39 Line 40 Line 41 Line 42 Line 43 Line 44 Line 45 Line 46 Line 47 Line 48 Line 49 File Formats CoN O 10 11 12 13 14 15 16 17 18 19 lt TRIPOS gt BOND ON DO BR WY 11 12 13 14 15 16 17 18 19 E LLO TETTE EE LO H 31 2 noonaa nua4arst A BP Y Y Y NNN AF 0 559 2 021 1 005 0 175 1 27 0 01 2 021 2 008 1 03 0 3 1 262 0 014 2 005 0 329 A OOO gt A N DN co Za a Oo 12 13 14 15 16 17 19 1 37 0 239 1 759 0 496 2 128 1 898 0 225 0 569 1 766 0 427 2 128 1 876 0 562 0 223 2 2 222 2 2d 2 ro Cn Cs 0 436 0 253 1 944 2 427 0 9 0 331 0 655 0 953 1 016 1 757 0 014 1 249 1 857 2 427 wm TIILO IIT ey mn jo on jo CambridgeSoft Protein Data Bank Files Each line is either a blank line a section header or a data record containing multiple fields of information about the compound The SYBYL MOL2 file is broken down into several sections of information Record type indicators RTT break the information about the molecule into sections RTT ate always preceded by an sign Individual fields are delimited by space s or a tab The fields in the SYBYL MOL2 format file used by
42. Bi Po At An in that the overall accuracy is considerably improved Specific improvements ate The following limitations apply to MNDO e The strength of the hydrogen bond in the water dimer is 5 5 kcal mol in accordance with experiment e Sterically crowded molecules are too unstable for example neopentane Four membered rings are too stable for mA i 8 e Activation barriers for reaction are markedly Sample cubane better than those of MNDO e Hydrogen bonds are virtually non existent for gt Fiyperealenipliosphomscompaundsare Scampi varer dinok veep considerably improved telative to MNDO nonbonding interactions between hydrogens and other atoms are predicted In particular simple H bonds are generally not predicted to exist using MNDO MNDO e AM1 phosphorus has a spurious and very sharp potential barrier at 3 0A The effect of this is to distort otherwise symmetric geometries and to introduce spurious e In general errors in AH obtained using AM1 ate about 40 less than those given by e Hypervalent compounds ate too unstable for example sulfuric acid e Activation barriers are generally too high ChemOffice 2005 Chem3D Computation Concepts 149 Approximate Hamiltonians in MOPAC activation barriers A vivid example is given by P Og in which the nominally equivalent P P bonds are predicted by AM1 to differ by 0 4A This is by far the most severe limitation of AM1 e Alkyl groups have a sy
43. Boiling Point ChemPropPro Paramet Parameter Best Estimate Method Best Estimate Best Estimate Literature Values 216 SAR Descriptor Computations 3 Edit the value or select the method 4 Click OK The new value is set Results To perform the calculation e Click OK Chem3D performs the calculation and displays the results in the Output window Chem3D Ultra Untitled 2 File Edit View Structure Calculations Surfaces Movie Online Window Help Os B o untitled 2 gt gt S e O 2 xs di gt aneiquiays Y daaojdx3 japOW 000 rties Broker r Parameters Method Best Estimate Boiling Point 237 189 K Critical Pressure 50 2993 bar Critical Temperature 388 569 K CambridgeSoft Setting Parameters Chapter 15 ULTRA ChemSAR Excel Overview ChemSAR Excel is a Chem3D Ultra addin for Microsoft Excel ChemSAR Excel enables you to calculate the physiochemical properties descriptors for a set of structures in an Excel worksheet ChemSAR Excel provides statistical tools to help identify trends in the calculated properties and cotrelate the data To run ChemSAR Excel you must have the following installed on your computer e Chem3D Ultra e ChemFinder e MS Excel 2000 2003 or XP Configuring ChemSAR Excel When you install Chem3D or ChemOffice the ChemSAR Excel add in is automatically installed To start ChemSAR Excel 1 Open MS Excel 2 F
44. C 2 1 1130 1 1130 H 7 C 2 1 1130 1 1130 H 6 C 2 1 1130 1 1130 H 5 C 1 1 1130 1 1130 H 4 C 1 1 1130 1 1130 3 Stop dragging when you have an end on view of ethane This staggered conformation where the HOC 411301 1 1130 hydrogens on adjoining carbons ate a C 1 C 2 1 5230 1 5230 HC8 C 2 H 7 108 8118 109 0000 maximum distance from one another which H 8 C 2 H 6 109 0000 109 0000 H 8 C 2 C 1 110 0000 110 0000 H 7 C 2 H 6 109 0000 109 0000 H 7 C 2 C 1 110 0000 110 0000 H 6 C 2 C 1 110 0000 110 0000 conformation of ethane H 5 C 1 H 4 108 8118 109 0000 H 5 C 1 H 3 109 0000 109 0000 H 5 C 1 C 2 110 0000 110 0000 HEH CC1 H 3 109 0000 109 0000 HEH CC1 C 2 110 0000 110 0000 H 3 C 1 C 2 110 0000 110 0000 XYZ Cartesian ZM Z Matrix HK Measure Chem3D shows the most common conformation of a molecule You can rotate parts of a molecule 4 such as a methyl group to see other conformations represents the global minimum on a potential energy plot represents the most stable 40 Chem3D Tutorials CambridgeSoft Tutorial 4 Examining Conformations To examine this result numerically calculate the steric energy of this conformation and then compare it to a higher energy eclipsed conformation 1 From the Calculations menu point to MM2 then choose Compute Properties The Compute Properties dialog box appears The Properties tab should show Pi Bond Orders and Ster
45. CHR Bending K for 22 22 22 angles in 3 membered rings The CHR Bending K for 1 1 1 angles allows more accurate force constants to be specified for Type 1 CHR and Type 2 CHR interactions The CHR Bending K for 1 1 1 angles in 4 membered rings and the CHR Bending K for 22 22 22 angles 22 is the atom type number for C Cyclopropane in 3 membered rings differ from the CHR Bending K for 1 1 1 angles and require separate constants for accurate specification Torsion Energy 2a T ISLAS This term accounts for the tendency for dihedral angles torsionals to have an energy minimum occurring at specific intervals of 360 n In Chem3D n can equal 1 2 or 3 The V 2 parameter is the torsional force constant It determines the amplitude of the curve The n signifies its periodicity n shifts the entire curve CambridgeSoft Molecular Mechanics Theory in Brief about the rotation angle axis The parameters are determined through curve fitting techniques Unique parameters for torsional rotation are assigned to each bonded quartet of atoms based on their atom types C C C C C O C N H C C H Chem3D provides three torsional parameters tables e Torsional parameters e 4 Membered ring torsions e 3 Membered ring torsions Non Bonded Energy The non bonded energy represents the pairwise sum of the energies of all possible interacting non bonded atoms i and j within a predetermined cut off di
46. Chem3D Pro are as follows 1 Line 1 is a comment field The pound sign preceding the text indicates a comment line Name is a field designating the name of molecule The molecule name is the file name when the file is created using Chem3D Pro 2 Line 2 is a blank line 3 Line 3 lt TRIPOS gt MOLECULE is a Record Type Indicator RTT which begins a section containing information about the molecule s contained in the file NOTE There are many additional RTs in the SYBYL MOL2 format Chem3D Pro uses only lt TRIPOS gt MOLECULE lt TRIPOS gt ATOM and lt TRIPOS gt BOND 4 Line 4 contains the name of the molecule The name on line 4 is the same as the name on line 1 5 Line 5 contains 5 fields describing information about the molecule The first field is the number of atoms the second field is the number of bonds the third field is the number ChemOffice 2005 Appendix of substructures the fourth field is the number of features and the fifth field is the number of sets NOTE Chem3D Pro ignores the following fields number of substructures number of features and number of sets These fields will contain zeros if the file was created using Chem3D Pro 6 Line 6 describes the molecule type This field contains SMALL if the file is created using Chem3D Pro 7 Line 7 describes the charge type associated with the molecule This field contains NO_CHARGES if the file is created using Chem3D
47. ChemFinder format Compatibility with M D L ISIS databases is provided by SD file and RD file import export ChemFinder provides network server workgroup functionality when used with Chem0 ffice WebServer ChemFinder Word is an extension of M icrosoft Excel and Word for Windows Create structure search able spreadsheets and index documents with embedded ChemD raw structures ChemDraw Excel adds chemical intelligence to M icrosoft Excel for Windows Show structures in spread sheet cells tabulate chemical calculations and analyze data with Excel functions and graphs Purchase Excel uses C hemD raw Excd to manage reagent lists and track purchasing information CombiChem Excel builds combinatorial libraries with embedded ChemDraw structures using ChemD raw Excd for Windows Find reagents with ChemFinder and design experiments gt ChemDraw Excel ye _ Re d e be ob Be per noi ne a Ff a ee ee ee 3 A Get a COMPOUNDS SYNTHESIZED BY Dr AMITABH JHA E Lima GELI Ai P e 5 a a os E 7 Ea Pe j bue Pee pasta Poe aora Pepa ippo rial rra bet m Pa a m En ae A j ae PRPA ip per eos rie Search Chemical oe ZA Databases j i LESE M e uns SOFTWARE ChemFinder Word e Search structures in documents folders ChemDraw Excel e Add chemical intelligence to spreadsheets Purchase Excel e Organize chemical purchasing information ChemFinder Pro Premier Searching Information e Advanced se
48. Click the Text Building tool click in the model window type PhOH in the text box and press the Enter key A molecule of phenol is created To compute Extended H ckel charges From the Calculations menu point to Extended Hiickel and choose Calculate Charges Messages are added to the Output box listing the partial charge of each atom CambridgeSoft Tutorial 10 Computing Partial Charges You can graphically display partial charges in the following ways e By coloring atoms By varying the size of atom spheres By varying the size of the dot surfaces To display partial charges 1 From the File menu choose Model Settings 2 Click the Model Display tab 3 Select the Color by Partial Charge radio button All of the atoms are colored according to a scale from blue to white to red Atoms with a large negative partial charge are deep blue Atoms with a large positive partial charge ate deep red As the magnitude of the charges approaches 0 the color of the atom becomes paler For phenol the greatest negative charge is on the oxygen atom The greatest positive charge is on the adjacent carbon atom with the adjacent hydrogen atom a close second The rest of the molecule has relatively pale atoms their partial charges are much closet to zero In addition to color you can vary the size of atom spheres or dot surfaces by partial charge 1 Select the Color By Element radio button in Model Display tab
49. Cube file which you can open in from Other Sources Chem3D You can use files from sources other than Chem3D to visualize surfaces From Windows sources you can open a Gaussian Formatted Checkpoint fchk ot Cube cub file ChemOffice 2005 Chem3D Displaying Models 71 Visualizing Surfaces from Other Sources 72 Displaying Models CambridgeSoft Visualizing Surfaces from Other Sources Chapter 4 Building and Editing Models Overview Chem3D enables you to build or change a model by three principal methods e Using the ChemDraw panel which utilizes ChemDraw to build and insert or copy and edit models e Using Bond tools which build using carbon exclusively e Using the Build from Text tool hereafter referred to as the Text tool which allows you to build or edit models using atom labels and substructures Usually a combination of methods yields the best results For example you might build a carbon skeleton of a model with ChemDraw or the bond tools and then change some of the carbons into other elements with the Text tool Or you can build a model exclusively using the Text tool In addition you can use Structure tools to change bond lengths and angles or to change stereochemistry Setting the Model Building Controls You control how you build by changing options in the Building control panel in the Model Settings dialog box The default mode is all options selected You can choose to build in a
50. DOUBLET TRIPLET QUARTET QUINTET SEXTET SINGLET DOUBLET TRIPLET QUARTET QUINTET SEXTET Keywords to Use OPEN n1 n2 ROOT n C l n 12 22 3 3 44 5 5 2 2 2 2 3 2 4 2 5 2 6 3 3 3 3 3 3 4 3 5 3 6 when the molecule has high symmetry such as molecular oxygen UHF Open Shell Electronic State Ground Spin State SINGLET DOUBLET MOPAC Computations Specifying the Electronic Configuration 173 TRIPLET QUARTET QUINTET SEXTET Even Electron Systems If a molecule has an even number of electrons the ground state and excited state configurations can be Singlet Triplet or Quintet not likely Normally the ground state is Singlet but for some molecules symmetry considerations indicate a Triplet is the most stable ground state Ground State RHF The Ground State RHF configuration is as follows e Singlet ground state the most common configuration for a neutral even electron stable organic compound No additional keywords are necessary e Triplet ground state Use the following keyword combination TRIPLET OPEN 2 2 e Quintet ground state Use the following keyword combination QUINTET OPEN 4 4 NOTE The OPEN keyword is normally necessary only when the molecule has a high degree of symmetry such as molecular oxygen The OPEN keyword increases the active Space available to the SCF calculation by including virtual orbitals This is necessary for attaining the higher
51. F dx dx The Hooke s Law potential function is quadratic thus the potential well created is symmetrical The real shape of the potential well is asymmetric and is 282 Parameter Tables defined by a complicated function called the Morse Function but the Hooke s Law potential function works well for most molecules V x f dV kp dis SS Certain molecules contain long bonds which are not described well by Hooke s Law For this reason the MM2 force field contains a cubic stretch term The cubic stretch term allows for an asymmetric shape of the potential well thereby allowing these long bonds to be handled However the cubic stretch term is not sufficient to handle abnormally long bonds Thus the MM2 force field contains a quartic stretch term to correct for problems caused by these abnormally long bonds Type 2 CHR Bending Force Parameters for C C C Angles CHR Bending K for 1 1 1 angles CHR Bending K for 1 1 1 angles in 4 membered rings CHR Bending K for 22 22 22 angles in 3 membered rings These constants are distinct from the force constants specified in the Angle Bending table The bending force constant K for the 1 1 1 angle 1 is the atom type number for the C Alkane atom type listed in the MM2 Angle Bending parameters table is for an alkane carbon with two non hydrogen groups attached Angle bending parameters for carbons with one or two attached hydrogens differ from those for carbons with no attached hydr
52. From the MOPAC Interface submenu of the Calculations menu choose a calculation 2 After all settings for the calculation are specified click Save As 178 MOPAC Computations To tun a MOPAC job from a jdf file 1 From the MOPAC Interface submenu of the Calculations menu click Run MOPAC Job The Open dialog box appears 2 Select the jdf file to run The dialog box corresponding to the type of job saved within the file appears 3 Click Run Repeating MOPAC Jobs After you perform a MOPAC calculation you can repeat the job as follows 4 From the MOPAC Interface submenu of the Calculations menu choose Repeat ame of computation The appropriate dialog box appears 5 Change parameters if desired and click Run The computation proceeds Creating Structures From arc Files When you perform a MOPAC calculation the results ate stored in an atc file in the Mopac Interface subfolder in your My Documents folder You can create a structute from the atc file as follows 1 Open the atc file in a text editor 2 Delete the text above the keywords section of the file as shown in the following illustration 3 Save the file with a mop extension 4 Open the mop file CambridgeSoft MOPAC Files SUMMARY OF Ani CALCULATION MOPAC2666 Version 1 11 EMPIRICAL FORMULA C2 H6 20007 7 5 SCF MMOK GEO OK AM1 MULLIK 1SCF WAS SPECIFIED SO BFGS WAS NOT USED SCF FIELD WAS ACHIEVED HEAT OF FORMATION 1
53. Interactions The use of cutoff distances for van der Waals terms greatly improves the computational speed for large molecules by eliminating long range and relatively insignificant interactions from the computation Chem3D uses a fifth order polynomial switching function so that the resulting force field maintains second order continuity The cutoff is implemented gradually beginning at 90 of the specified cutoff distance This distance is set in the MM2 Constants table Computation Concepts 139 Molecular Mechanics Theory in Brief The van der Waals interactions fall off as 1 1 and can be cut off at much shorter distances for example 10A This cut off speeds the computations significantly even for relatively small molecules NOTE To precisely reproduce the energies obtained with Allinger s force field set the van der Waals cutoff constants to large values in the MM2 Constants table Electrostatic Energy gt i j The electrostatic energy is a function of the charge on the non bonded atoms q their interatomic distance fij and a molecular dielectric expression D that accounts for the attenuation of electrostatic interaction by the environment solvent or the molecule itself In Chem3D the electrostatic energy is modeled using atomic charges for charged molecules and bond dipoles for neutral molecules There are three possible interactions accounted for by Chem3D e charge chatge e dipole dipole
54. KS field 278 L Lab supplies purchasing online 226 Chem3D 9 0 1 Labels 240 using 77 using for substructures 38 using to create models 37 LCAO and basis sets 145 Length field 278 LET keyword 171 183 Limitations 208 253 Local minima 133 LOCALIZE keyword 171 Localized orbitals 171 Locating the eclipsed transition state of ethane 183 Locating the global minimum 157 LogP ChemProp Pro 207 Lone pairs field 284 Lowest Unoccupied Molecular Orbital MOPAC 210 Lowest Unoccupied Molecular Orbital overview 70 Lowest Unoccupied Molecular Orbital viewing 49 LUMO see Lowest Unoccupied Molecular Orbital M MacroModel 249 FORTRAN format 250 MacroModel file format 123 Map Property control 69 Mapping properties onto surfaces 49 69 Maximum Ring Size field 275 MDL MolFile 250 251 MDL MolFile format 124 MDL MolFile FORTRAN format 253 Measurement table 106 Measurements actual field 29 deleting 108 editing 107 non bonded distances 106 107 optimal field 29 setting 85 table 29 39 106 Measuring coplanarity 107 Mechanics about 9 Melting Point ChemProp Pro 207 Menus edit 15 file 14 structure 17 view 15 Microstates 147 167 MINDO 3 148 168 200 Minimizations queuing 154 Minimize Energy 199 211 MOPAC 180 Minimize Energy command GAMESS 211 Gaussian 199 200 MM2 151 Minimize Energy dialog GAMESS 211 Gaussian 200 Minimizer 176 Minimizing example 154 Minimum RMS Gradient MM2 152 MOPAC 180 MM2 136 applying cons
55. Microsoft Excel add ins require Office 2000 2003 or XP e ChemDraw plugins ActiveX controls support Netscape 6 2 x and 7 x Mozilla 1 x and Microsoft IE 5 5 SP2 and 6 x The Chem3D ActiveX control supports IE 5 5 SP2 and 6 x only There is no Chem3D plugin available NOTE Windows XP Service Pack 2 includes security features that automatically block active content This means that by default Internet Explorer blocks ChemDraw and Chem3D ActiveX controls To activate them you must choose the option to allow blocked content from the bar appearing under the address bar notifying you that the security settings have blocked some of the content of the page IE does not remember this information so you must repeat Introduction 11 Installation and System Requirements the activation each time you access the page Site License Network If you visit a site frequently you can add it to the list of Installation Instructions trusted sites in LES security settings If you have purchased a site license please see the e Screen resolution must be 800 x 600 or higher following web site for network installation instructions http www cambridgesoft com services sl 12 Introduction CambridgeSoft Installation and System Requirements Chapter 1 Chem3D Basics Th e G ra ph ica U ser Comments boxes the Model Explorer and tables Cartesian coordinates Z Matrix and Inte rface Measurement and the ChemDraw P
56. Model Display toolbar 2 On the Model Display submenu of the View menu select Show Atom Labels or click the Atom Labelicon E on the Model Display toolbar NOTE The serial numbers that appear do not reflect a normal ordering because you started with a smaller model and built up from it You can teserialize the atoms as follows Select the Text Building tool Click the first atom A text box appears on the atom N ve Type the number you want to assign to this atom 1 for this example 4 Press the Enter key The first atom is renumbered as 1 ul Double click each of the atoms in the order you want them to be numbeted Each time you double click an atom to serialize it the new serial number is one greater than the serial number of the previously serialized atom a From the Model Display submenu of the View menu choose Show Hs and Lps and examine the model using the Trackball Tool sy The hydrogens appeat as far apart as possible 36 Chem3D Tutorials Because you built the structure by using bond tools you may have distorted bond angles and bond lengths To correct for distorted angles and lengths 1 From the Edit menu choose Select All All of the atoms in the model ate selected 2 From the Structure menu choose Clean Up Structure To locate an energy minimum for your structure which represents a stable conformation of your model click the MM2 Minimize En
57. Pro Struct N ame LabArt 3D Query GAMESS Client Tinker Chem3D ChemACX Ultra BioAssay Pro CombiC hem Excel ChemDraw Excel CLogP ChemDraw Structure Clean Up Win Mac Win Mac Win Mac Win Mac ChemM SDX ChemRXN Available Separately D esktop to Enterprise Solutions ChemOffice Ultra includes it all providing ChemD raw Ultra Chem3D Ultra E N otebook Ultra ChemFinder CombiC hem BioAssay and The M eck Index for a seamlessly integrated suite for chemists U se ChemD raw Excel and ChemFinder Word for M icrosoft O ffice integration Predict spectra use N ame Struct and visualize 3D molecular surfaces and orbitals with M OPAC Use the ChemD raw and Chem3D Plugins to publish your work or to query databases on the web ChemOffice WebServer enterprise solutions and databases help organizations collaborate on shared information with ChemD raw web based interface and O racle Cartridge security Knowledge Management with E N otebook Enterprise streamlines daily record keeping with rigorous security and efficient archiving Document M anager indexes chemical structure content of documents and folders Research Discovery efforts are improved with Registration System by organizing new compound information while Inventory M anager works with chemical databases for complete management of chemical inventories Applied Biolnformatics scientists u
58. Properties To remove properties from the Selected Properties list 1 Select the properties to delete or click Select All to select all the properties 2 Click Remove The properties are removed from the list o Property Filters Property filters allow you to select what properties appear in the Available Properties list The property filters ate e Class limits the list of available properties to types calculations that you specify SAR Descriptor Computations 215 Selecting Properties To Compute e Server limits the list of available properties to those properties computed by the servers you specify e Cost tepresents the maximum acceptable computational cost It limits the list of available properties to those which are less than or equal to the computational cost specified e Quality tepresents the minimum acceptable data quality It limits the list of available properties to those with quality greater than or equal to the quality specified Setting Parameters Ifa property has one or more parameters that affect the result of the calculation you can specify the values or calculation method of those parameters If several properties have the same parameters you can change the parameters simultaneously To change a parameter 1 Select the property or properties in the Selected Properties list 2 Click Parameters One of the following dialog boxes appears depending on the selected parameters
59. Proteins and several optimizers that alow fot more controlled molecular mechanics calculations The default optimizer used is the Truncated Newton Raphson method which Introduction 9 About CS MOPAC provides a balance between speed and accuracy Other methods are provided that are either fast and less accurate or slow but mote accurate What s New in Chem3D 9 0 Chem3D 9 0 is enhanced by the following features Redesigned GUI User customizable with new toolbars new layout for tables and subviews new menus and dialogs The GUI has been redesigned from the ground up to make it more usable New Model Hierarchy Tree Control Lets you open and close fragments chains or groups change display properties at different levels See Working With the Model Explorer on page 111 ChemDraw panel Building small molecules is easier than ever See Building with the ChemDraw Panel on page 74 New menu organization Important functions ate easier to locate Full screen mode Use Chem3D for demos or instruction New Dihedral Driver Do conformation analysis with graphical display of results See Tutorial 5 Mapping Conformations with the Dihedral Driver on page 42 Improved support for small molecule overlays compate different conformations or different structures See Tutorial 6 Overlaying Models on page 43 XML table editor easier to use better integration 10 Introduction W
60. SYBYL MOL2 File format is as follows Line Description FORTRAN Number Format 270 File Formats 11 29 31 49 Molecule name file 5X name Name AXA Number of 4 1X 12 atoms number of bonds Atom type name 14 6X A2 3X 3 coordinates and id F9 3 2X A5 Bond id from atom 314 3X A2 to atom bond type CambridgeSoft Protein Data Bank Files Appendix H Parameter Tables Parameter Table Overview Chem3D uses the parameter tables containing information about elements bond types atom types and other parameters for building and for analyzing your model The parameter tables must be located in the C3D Items ditectory in the same ditectory as the Chem3D application Parameter Table Use Chem3D uses several parameter tables to calculate bond lengths and bond angles in your model To apply this information select Apply Standard measurements in the Building Control panel Calculating the MM2 force field of a model requires special parameters for the atoms and bonds in your model The MM2 force field is calculated during Energy Minimization Molecular Dynamics and Steric Energy computations The use of the parameter tables are described in the following table Parameter Use Table Parameter Table Use 3 Membered Ring Bond angles for bonds in Angles xml 3 membered rings In force field analysis angle bending portion of the force field for bonds in 3 membered rings Ch
61. Table Fields Atom Type Numbets 00 Quality teow foams bars lips Reference suroriental parasitos 240 240 259 262 Estimating ParameterS 273 Creating Parameters 273 The Elements 4 274 Symbol ss cies aaa soles eects Bae 274 Covalent Radius caiga ds e 274 Colorado dh whe bee es 274 Atom Types 0 0 02000 08 274 Name ada erin Ds 274 Symbols nar a ae 274 van der Waals Radius o o oooo o o 275 Text Number Atom Type o ooooomomo 275 Characidae 275 Maximum Ring SiZC oooooooooomo o 275 Rectification Type ooooooooccommo mm 275 Geometry A ON 276 Number of Double Bonds Triple Bonds and Delocalized BondS o 0ooo ooooo oo o 276 Bound to Otdet o oocoioimmcacccc eas 276 Bound to Types sieis cerni es ds 276 Substructures 0000 000 00 cece 277 References 0 0 0 0 00 00 cece 277 Reference Number 00 00 0008 277 Reference Description 4 277 Bond Stretching Parameters 277 Bond Type sie taaan ence os 277 KS iene OAT Eee De 278 La e 278 Bond Dipole erotic pied das 278 Recotd Oteros da kora ees 278 Bendicion aaah 278 Angle Types soriana 279 KBr eG she taa 279 SRR 2 ete ira 279 ORs Sees cpg Cate i E daaihe des 279 TAD ote A aie hie waa 280 Record Order rr ina setae gain e 280 Pi Atoms ica a Es 280 ALOM TYPO rai Hoes behets RE Aas a
62. Transition State defaults 3 On the Properties tab select the properties you wish to calculate from the final optimized conformation 4 On the General tab type any additional keywords that you want to use to modify the optimization 5 Click Run The information about the model and the keywords are sent to MOPAC If you have selected Send Back Output the Output window appears CambridgeSoft Optimize to Transition State The Output window displays intermediate messages about the status of the minimization A message appears if the minimization terminates abnormally usually due to a poor starting conformation The following contains keywords automatically sent to MOPAC and some additional keywords you can use to affect convergence Keyword Description EF Automatically sent to MOPAC to specify the use of the Eigenvector Following minimizer GEO OK Automatically sent to MOPAC to override checking of the Z mattix MMOK Automatically sent to MOPAC to specify Molecular Mechanics correction for amide bonds Use the additional keyword NOMM to turn this keyword off RMAX n nn The calculated predicted energy change must be less than n nn The default is 4 0 RMIN n nn the calculated predicted energy change must be more than n n The default value is 0 000 PRECISE Runs the SCF calculations using a higher precision so that values do not fluctuate from run to run ChemOffice 2005 Chem3D Keyword Descr
63. Tutorial 6 Overlaying Models 43 Tutorial 7 Docking Models 46 Tutorial 8 Viewing Molecular Surfaces 48 Tutorial 9 Mapping Properties onto SUL ACES 3c o ida eve ea 49 Tutorial 10 Computing Partial Charges 52 Chapter 3 Displaying Models Structure DisplayS o 55 Model Types ter ino eau gee 56 Displaying Solid Spheres ooo oooooo 57 Setting Solid Sphere SizC ooooocooo 57 Displaying Dot Surfaces ooooooooooooo 58 Coloring Displays 0ooooooooommmo 58 Coloring by Element 000 58 Coloring by Group 06 0 0 ce eee eee 59 Coloring by Partial Charge o 59 Coloring by depth for Chromatek stereo viewers 59 Red blue Anaglyphs 0000 59 Depth Fading3D enhancement 60 Perspective Rendering 60 Coloring the Background Window 60 Coloring Individual Atoms 0 60 Displaying Atom LabelS ooo oooooo o 61 Setting Default Atom Label Display Options 61 Displaying Labels Atom by Atom 61 Using Stereo PAS serrer neren eee 61 Using Hardware Stereo Graphic Enhancement 62 Molecular Surface Displays 63 Extended Hiickel 00oo ooooooooo o o 63 Displaying Molecular Surfaces 64 Setting Molecular Surface Types 65 Setting Molecular Surface Isovalues 66 Setting the Surface Resolution
64. a sears EAER o ah 121 Cartesian Coordinates oo ooooooooo 121 Connection Tabla oag ass AE 122 Gaussian Input ts oF stn a al 122 Gaussian Checkpoint o ooooooocmoo o o 122 Gaussian Cube i ga nen triada aa 122 Internal CootrdinatesS oooooooo oo 123 MacroModel Files oo ooooooo 123 Molecular Design Limited MolFile MOL 124 MSI ChemNote 0000 cece nee eee 124 MOPAG Files canastas 124 MOPAC Graph Files o ooooooooo co 126 ChemOffice 2005 Chem3D Protein Data Bank Files 126 ROSDAL Files RDD 00ooocccccccoo 126 Standard Molecular Data SMD 126 SYBYL Pes a acid 126 Job Description File Formats 126 JDE Files merete erita eo aa A i 126 A says shes E yh rai seein reer 126 Exporting With the Clipboard 127 Transferring to ChemDraw 127 Transferring to Other Applications 127 Chapter 8 Computation Concepts Computational Methods Overview 129 Uses of Computational Methods 130 Choosing the Best Method 130 Molecular Mechanics Methods Applications UIA ALY aaa alse a tees dd sae EIET 131 Quantum Mechanical Methods Applications Summaya TE Soca R e oe a ou 131 Potential Energy Surfaces oo ooo o oo 132 Potential Energy Surfaces PES 133 Single Point Energy Calculations 133 Geometry Optimization 134 Molecular Mechanics Theory in Brief
65. about the chemical is available in these catenaries Finding Chemical Suppliers on ACX com The Find Suppliers on ACX Com menu item links your browser to the chemacx com database record of suppliers of the compound you have selected ChemACX Available Chemicals Exchange is a Webserver application that accesses a database of commercially available chemicals The database contains catalogs from research and industrial chemical vendors ChemACX allows the user to search for particular chemicals and view a list of vendors providing those chemicals Chem3D Appendix To use Find Suppliers on ACX Com menu access 1 In ChemOffice select a structure you want to look up 2 From the Online menu choose Find Suppliers on ACX com The ChemACX Com page opens in your browser with information on the selected structure For example the ChemACX com page for Benzene is shown below W SHOPHING CART LOGIN A ChemACX E room amp pL itt a 4 Your account HELP CambridgeSoft Print Preferences Hel About on Mew Query C4e Query J Refine Wass 2 Export Hee Substances matching your query 2 R Record 1 2 of 2 hts UU Re 22 NAMESY DETAILS MARK m NAMESY DETARS MARK Record 1 Record 2 CASH 71 432 CASA 27271662 For mote information on using the ChemACX website see the ChemOffice Enterprise Workgroup amp Databases Manual Finding ACX Structures and Numbers ChemOffice searches ACX and returns infor
66. are selected when you release the mouse button A bond is selected only if both atoms connected by the bond ate also selected To keep previously selected atoms selected e Hold down the Shift key while you make another selection If you hold down the Shift key and all of the atoms within the Selection Rectangle are already selected then these atoms are deselected Defining Groups You can define a portion of your model as a group This provides a way to easily select and to highlight part of a model such as the active site of a protein for visual effect To define a group 1 Select the atoms and bonds you want in the group Using the select tool select the first atom then use Shift click to select the other atoms and bonds 2 While still pointing at one of the selected atoms right click and choose New Group from the Context Sensitive menu If the groups in your model are substructures defined in the Substructures table substructures xml you can assign standard colors to them To assign or change a color 1 From the View menu point to Parameter tables and select Substructures 2 Double click in a cell in the Color field The Color dialog box appears 3 Select a color and click OK ChemOffice 2005 Chem3D 4 Close and Save the Substructures table Once colors are assigned in the Substructures table you can use them to apply color by group 1 From the File menu choose Model Settings 2 Select th
67. are sorted by the second atom type number in the Bond Type field For example the record for bond type 2 2 is listed before the record for bond type 2 3 Electronegativity Adjustments The parameters contained in the Electronegativity Adjustments table Electronegativity Adjustments xml are used to adjust the optimal Parameter Tables 281 Pi Bonds bond length between two atoms when one of the atoms is attached to a third atom which is electronegative For example the carbon carbon single bond length in ethane is different than that in ethanol The MM2 patameter set has only a single parameter for carbon carbon single bond lengths 1 523A The use of electronegativity correction parameters allows the C C bond in ethanol to be corrected The electronegativity parameter used in the Electronegativity Corrections table is the 1 1 6 angle type where atom type 1 is a C Alkane and atom type 6 is an O Alcohol The value of this parameter is 0 009A Thus the C C bond length in ethanol is 0 009A shorter than the standard C C bond length MM2 Constants The MM2 Constants table MM2 Constants xml contains patametets which Chem3D uses to compute the MM2 force field Cubic and Quartic Stretch Constants Integrating the Hooke s Law equation provides the Hooke s Law potential function which describes the potential energy of the ball and spring model The shape of this potential function is the classical potential well dv oY
68. as MOZYME and PM5 methods MOPAC Pro allows you to compute properties perform simple and some advanced energy minimizations optimize to transition states and compute properties The CS MOPAC Pro implementation supports MOPAC sparkles has an improved user interface and provides faster calculations It is included in some versions of ChemOffice 2005 Chem3D Chem3D or may be purchased as an optional addin Contact CambridgeSoft sales or your local reseller for details CAUTION Ifyou have CS MOPAC installed on your computer from a previous Chem3D or ChemOffice installation upgrading to version 9 0 1 will remove your existing MOPAC installation See the ReadMe for instructions on saving your existing MOPAC menu extensions See Chapter 10 MOPAC Computations on page 165 for more information on using CS MOPAC About Gaussian Gaussian is a cluster of programs for performing semi empirical and ab initio molecular orbital MO calculations Gaussian is not included with CS Chem3D but is available from SciStore com http scistore cambridgesoft com software When Gaussian is correctly installed Chem3D communicates with it and serves as a graphical front end for Gaussian s text based input and output Chem3D is compatible with Gaussian 03 for Windows and requires the 32 bit version About CS Mechanics CS Mechanics is an add in module for Chem3D It provides three force fields MM2 MM3 and MM3
69. as reference tools ChemACX Database however goes one step further by including the ability to collect products into an electronic shopping cart and export its con tents into electronic requisition forms or purchasing systems T his time saving feature has proven to be one of the most popular advantages of ChemACX among scientists and purchasing agents alike Users can readily export data from the shopping cart into Excel and Word templates used as departmental requisition forms EMAIL info cambridgesoftcom WWW _ www cambridgesoftcom TEL 1 800 315 7300 INTL 1 617 588 9300 FAX 1 617 588 9390 e MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge MA 02140 USA CambridgeSoft TTT Chemo ffice ChemDraw Chem3D ChemFinder Cheminfo are trademarks of CambridgeSoft 2002 5 All other trademarks are the property of their respective holders All specifications subject to change without notice www cam b T1 dg eso ft CcCOm CHEMICAL The Merck Index C hemistry s C onstant C ompanion Industry Standard Among printed chemical reference works one that stands out for its integrity detail and longevity is TheM erck Index This encyclopedia of chemicals drugs and biologicals has 10 250 monographs 446 named reactions and 23 additional tables Merck Co Inc the publisher of T he M eck Index has chosen C ambridgeSoft to pro duce the complete contents of the Ith edition in a fully searchable Chem0 ffice format Detailed M
70. as the name of the substructure is in the text box Replacing H 8 of the original structure would produce the following structure lt amp Ga Ga Notice that the carbon atom in the ester has replaced the hydrogen This is because when the ester was defined the carbon atom had a lower serial number 3 than the oxygen atom that formed the other attachment point in the substructure 5 NOTE When defining substructures with multiple attachment points it is critical to note the serial numbers of the atoms in the substructure so that you can correctly orient the substructure when it is inserted in the model See the rules for multiple attachment points discussed at the beginning of this section CambridgeSoft Defining Substructures Appendix D Atom Types Overview Chem3D assigns atom types when you build with Automatically Correct Atom Types turned on You can also create your own atom types Assigning Atom Types When you replace atoms Chem3D attempts to assign the best atom type to each atom by comparing the information about the atom such as its symbol and the number of bonds to the atom to each atom type record in the Atom Type table When you have selected the Automatically Correct Atom Types check box in the Building control panel atom types are corrected when you delete atoms ot bonds or when you add atoms or bonds In addition if this check box is selected then the atom types of pre existing
71. behind the atom at the other end of the bond Example 1 In Example 1 the two phenyl rings are trans about the cyclopentane tring The phenyl ring on the left is attached by a wedged hashed bond the phenyl ring on the right is attached by a wedged bond You can also use dashed hashed and bold bonds However you should be awate of potential ambiguity where these non directional bonds ate used A dashed hashed or bold bond must be between one atom that has at least three attachments and one atom that has no mote than two attachments including the dashed hashed ot bold bond Example 2 In Example 2 the nitrogen atom is placed behind the ring system and the two methyl groups are placed in front of the ring system Each of these three atoms is bonded to only one other atom so they ate presumed to be at the wide ends of the stereo bonds 2D to 3D Conversion 239 Stereochemical Relationships Example 3 K Y In Example 3 however the hashed bond is ambiguous because both atoms on the hashed bond are attached to more than two bonds In this case the hashed bond is treated like a solid bond Wavy bonds are always treated like solid bonds H Dots and H Dashes are also used to indicate stereochemistry H Dots become hydrogen atoms attached to carbon atoms by a wedged bond H Dashes become hydrogen atoms attached by a wedged hashed bond Example 4 HI tte tH H oot cis decalin trans decalin 240 2D to 3
72. bond order tutorial ex ample 33 conformations 39 dihedral angles tutorial example 34 Excited state RHF 174 175 Excited state UHF 175 Exporting models using different file formats 118 with the clipboard 127 Extended Htickel method 63 146 166 Extended Hiickel surfaces tutorial example 49 Extended Hiickel molecular surface types available 65 External tables 24 External tables overview 271 Extrema 133 F FAQ online accessing 224 Fast overlay tutorial 43 File format Alchemy 241 Cambridge Crystal Data Bank 246 Cartesian coordinates file 243 editing atom types 241 examples 241 internal coordinates file 246 MacroModel 249 MDL MolFile 251 MOPAC 257 MSI MolFile 253 Protein Data Bank file 259 ROSDAL 262 SYBYL MOL2 267 SYBYL MOL File 265 File formats 262 viiio CambridgeSoft 3dm 121 alc Alchemy 118 121 avi Movie 121 bmp Bitmap 119 ccl Cartesian coordinates 118 121 cc2 Cartesian coordinates 118 121 cdx 118 con connection table 122 ct connection table 118 122 cub Gaussian Cube 122 dat MacroModel 123 emf Enhanced Metafile 119 eps Encapsulated postscript 120 fch Gaussian Checkpoint 122 gif Graphics Interchange Format 121 gjc Gaussian Input 118 122 gjf Gaussian Input 122 gpt MOPAC graph 126 int Internal coordinates 118 123 jdf Job description file 126 jdt Job Description Stationery 126 mcm MacroModel 118 123 m2 SYBYL 126
73. charge is automatically sent to MOPAC when you do a calculation To specify the charge in MOPAC 1 From the Calculations menu point to MOPAC Interface and choose a computation The MOPAC Interface dialog box appears CambridgeSoft Specifying the Electronic Configuration 2 On the General tab in the Keywords box type the keyword CHARGE n where n is a positive or negative integer 2 1 1 2 Different combinations of spin up alpha electrons and spin down beta electrons lead to various electronic energies These combinations are specified as the Spin Multiplicity of the molecule The following table shows the relation between total spin S spin multiplicity and the number of unpaired electrons Spin Keyword unpaired electrons 0 SINGLET 0 unpaired 1 2 DOUBLET 1 unpaited 1 TRIPLET 2 unpaired 11 2 QUARTET 3 unpaired 2 QUINTET 4 unpaired 21 2 SEXTET 5 unpaired To determine the appropriate spin multiplicity consider whether e The molecule has an even or an odd number of electrons e The molecule is in its ground state or an excited state e To use RHF or UHF methods The following table shows some common permutations of these three factors ChemOffice 2005 Chem3D RHF Closed Shell Electronic State Ground 1st Excited 2nd Excited 2 The OPEN keyword is necessary only Spin State SINGLET DOUBLET TRIPLET QUARTET QUINTET SEXTET SINGLET
74. conformational space of the model For mote information see Tutorial 5 Mapping Conformations with the Dihedral Driver on page 42 e A molecular dynamics simulation can be run which will allow small potential energy barriers to be crossed After completing the molecular dynamics simulation individual geometries can then be minimized and analyzed For more information see Appendix 9 MM2 and MM3 Computations You can calculate the following properties with the computational methods available through Chem3D using the PES e Steric energy e Heat of formation e Dipole moment e Charge density e COSMO solvation in water ChemOffice 2005 Chem3D e Electrostatic potential e Electron spin density e Hyperfine coupling constants e Atomic charges e Polarizability e Others such as IR vibrational frequencies Molecular Mechanics Theory in Brief Molecular mechanics describes the energy of a molecule in terms of a set of classically derived potential energy functions The potential energy functions and the parameters used for their evaluation are known as a force field Moleculat mechanical methods are based on the following principles e Nuclei and electrons are lumped together and treated as unified atom like particles e Atom like particles are typically treated as spheres e Bonds between particles are viewed as harmonic oscillators e Non bonded interactions between these particles are treated u
75. connection cannot be made e If you have a model in the window but do not have anything selected a second fragment is added but is not connected to the model e When a text box is visible you can modify the selection by Shift clicking or Shift dragging across atoms Using Labels To use an element symbol in a text box 1 Select the Text tool 2 Click in the model window A text box appears 3 Type C 4 Press the Enter key A model of methane appears The atom type is automatically assigned as a C Alkane and the appropriate number of hydrogens ate automatically added Building and Editing Models 77 Building With The Text Tool To use the same text to add another methyl group 1 Point to the atom you want to replace in this example a hydrogen and click The text box appears with the previous label 2 Press the Enter key To add a different element 1 Click a hydrogen atom A text box appears over the atom 2 Type N 3 Press the Enter key A nitrogen is added to form ethylamine To build ethylamine in one step 1 Click in the model window A text box appears 2 Type CH3CH2NH 3 Press the Enter key A model of ethylamine appears Changing atom types You can use a text box to change the atom type and bonding characteristics To change the atom type of some atoms 1 Click a carbon atom A text box appears N Shift click the other carbon atom Both atoms ate selected 3
76. copyrighted by Fujitsu Ltd CS MOPAC is the licensed version that runs under Chem3D Potential Functions Parameters MOPAC provides five potential energy functions MINDO 3 MNDO PM3 AM1 and MNDO d All are SCF Self Consistent Field methods Each ChemOffice 2005 Appendix function represents an approximation in the mathematics for solving the Electronic Schr dinger equation for a molecule Historically these approximations were made to allow ab initio calculations to be within the reach of available computer technology Currently ab initio methods for small molecules ate within the teach of desktop computers Larger molecules however are still more efficiently modeled on the desktop using semi empirical or molecular mechanics methodologies To understand the place that the potential energy functions in MOPAC take in the semi empirical arena here is a brief chronology of the approximations that comprise the semi empirical methods The first approximation was termed CNDO for Complete Neglect of Differential Overlap The next approximation was termed INDO for Intermediate Neglect of Differential Overlap Next followed MINDO 3 which stands for Modified Intermediate Neglect of Differential Overlap Next was MNDO which is short for Modified Neglect of Differential Overlap which corrected MINDO 3 for various organic molecules made up from elements in rows 1 and 2 of the periodic table AM1 improved upon MNDO matk
77. d orbitals This method may be applied to the elements shaded in the table below Results obtained from MNDO d are generally superior to those obtained from MNDO The MNDO method should be used where it is necessary to compare or repeat calculations previously performed using MNDO The following types of calculations as indicated by MOPAC keywords are incompatible with MNDO d e COSMO Conductor like Screening Model solvation e POLAR polarizability calculation GREENF Green s Function e TOM Miertus Scirocco Tomasi self consistent reaction field model for solvation CambridgeSoft Approximate Hamiltonians in MOPAC Chapter 9 MM2 and MM3 Computations CS Mechanics Overview The CS Mechanics add in module for Chem3D provides three force fields MM2 MM3 and MM3 Proteins and several optimizers that allow fot mote controlled molecular mechanics calculations The default optimizer used is the Truncated Newton Raphson method which provides a balance between speed and accuracy Other methods ate provided that ate either fast and less accurate or slow but mote accurate The Chem3D atom types ate translated to the atom types required for the calculations implemented in CS Mechanics In some cases the translation is not quite correct since Chem3D has many more atom types than the standard MM2 and MM3 parameters and also has the ability to guess missing types In other cases the atom types ate correctly define
78. dForce dLength Quality and Reference Bond Type The Bond Type field is described by the atom type numbers of the two bonded atoms For example bond type 2 2 is a bond between two alkene carbons dForce The dForce field contains a constant used to decrease the bond stretching force constant of a particular conjugated double bond The force constant Kx for a bond with a calculated pi bond order x is ChemOffice 2005 Appendix K K3 1 x dForce where K is the force constant for a non conjugated double bond taken from the Bond Stretching table The higher the value of K for the bond between two pi atoms the mote difficult it is to compress or stretch that bond dLength The dLength field contains a constant used to increase the bond length of any conjugated double bond The bond length Ix for a bond with a calculated pi bond order x is 1 L 1 x dLength where 1 is the bond length of a non conjugated double bond taken from the Bond Stretching table The higher the value of l for the bond between two pi atoms the longer that bond is Record Order When sorted for Bond Type the order of the records in the Conjugated Pisystem Bonds table is as follows 1 Records are sorted by the first atom type number in the Bond Type field For example the record for bond type 2 2 is listed before the record for bond type 3 4 2 For records where the first atom type number is the same the records
79. data file 246 File Formats specifications of the Cambridge Structural Database Version 1 File Specifications from the Cambridge Crystallographic Data Centre For further details about the FDAT format please refer to the above publication or contact the Cambridge Crystallographic Data Centre As described in the specifications of the Cambridge Crystal Data Bank format bonds ate automatically added between pairs of atoms whose distance is less than that of the sum of the covalent radii of the two atoms The bond orders are guessed based on the tatio of the actual distance to the sum of the covalent radii The bond orders bond angles and the atom symbols are used to determine the atom types of the atoms in the model Bond Type Actual Distance Sum of Covalent Radii Triple 0 81 Double 0 87 Delocalized 0 93 Single 1 00 Internal Coordinates File Internal coordinates files INT Coords are text files that describe a single molecule by the internal coordinates used to position each atom The serial numbers are determined by the order of the atoms in the file The first atom has a serial number of 1 the second is number 2 etc CambridgeSoft File Format Examples The format for Internal coordinates files is as follows 1 Line 1 is a comment line ignored by Chem3D Each subsequent line begins with the atom type number of an atom type Line 2 contains the atom type number of the Origin atom Beginning with
80. deal with this explicitly by having non integral formal charges For example the two oxygen atoms in nitro 52 Chem3D Tutorials benzene each have charges of 0 500 because there is one electron that is shared across the two N O bonds However as shown above electrons in molecules actually occupy areas of the molecule that are not associated with individual atoms and can also be attracted to different atomic nucleii as they move actoss different atomic orbitals In fact bonds are a representation of the movement of these electrons between different atomic nucleii Because electrons do not occupy the orbitals of a single atom in a molecule the actual charge of each atom is not integral but is based on the average number of electrons in the model that are occupying the valence shells of that atom at any given instant By subtracting this average from the number of protons in the molecule the partial charge of each atom is determined Visualizing the partial charge of the atoms in a molecule is another way to understand the model s reactivity Typically the greater the partial charge on an atom the more likely it is to form bonds with other atoms whose partial charge is the opposite sign Using the theories in Extended H ckel MOPAC or Gaussian you can compute the partial charges for each atom In the following example the partial charges for phenol are computed by Extended H ckel 1 From the File menu choose New
81. deployed even within existing applications Since no manipulation of the data is needed new records are automatically added to the index for searching SL BCT EOS ITA FRM eya A HERT Dt arrak that ora m iat am gt Simple Client Server VE App racle ANO Architecture L E pi a Chemin CS po ir Actime M z Cartridge EEFT m a i CT lx Progeny hi EN Premas ro 4 E Fropmr Carma i errari Chalma Diada A A gt Web Based ee rr pemi e PAR e r E Par lan La E p Archi lea Ena alia ng aia SOLUTIONS e Adds chemical data types to O racle linking chemical applications to enterprise software systems without special programming Confers O racle s security and scalability simplifying large systems architectural considerations e Makes legacy chemical data such as M DL ISIS accessible to Chemo ffice W ebServer applications WebServer Enterprise Solutions Even if you re not developing your own applications or interested in the advanced data portability aspects of the Oracle Cartridge CambridgeSoft s strategy will have a positive benefit for your IT infrastructure CambridgeSoft s enterprise solutions are available in O racle Cartridge versions including E N otebook Enterprise Document M anager Registration System Inventory M anager and BioAssay HTS By utilizing O racle Cartridge you can deal with issues such as scalability and security entirely through the database layer simpl
82. e Increase the Virtual Memory VM Virtual memory extends RAM by allowing space on your hard disk to be used as RAM However the time for swapping between the application and the hard disk is slower than swapping with physical RAM Change the VM as follows e System control panel Performance tab System Crashes CambridgeSoft Desktop Applications should never crash but below are the steps you should go through to try to resolve issues that cause computer crashes while using a CS software product 1 Restart Windows and try to reproduce the problem If the problem recurs continue with the following steps 2 The most common conflicts concern Video Drivers Printer Drivers screen savets and virus protection If you do need to contact us be sure to determine what type and version of drivers you are using 230 Technical Support Video Driver related problems If you are having problems with the display of any CambridgeSoft Desktop Application try switching to the VGA video driver in the display Control Panel or System Setup and then retest the problems If using a different driver helps your original driver may need to be updated contact the maker of the driver and obtain the most up to date driver If you still have trouble contact us with the relevant details about the original driver and the resulting problem Printer Driver related problems Try using a different printer driver If using a different driver he
83. electrostatic potential is very high near each atom of a molecule and vanishingly small far away from it Chem3D generates a surface by connecting all the points in space that have the same value the isovalue Weather maps are a common example of the same procedure in two dimensions connecting locations of equal temperature isotherms or equal pressure isobars To set the isovalue 1 From the Surfaces menu choose Isocontour NOTE The exact name of this command reflects the type of isovalue in each window For example for Total Charge Density Surfaces it is Tsocharge The Isocontour slider appears Isocontour y 0 000 0 025 0 100 2 Adjust the slider to the new isovalue The new isovalue is the middle value listed at the bottom of the Isocontout tool CambridgeSoft Molecular Surface Displays Setting the Surface Resolution The Surface Resolution is a measure of how smooth the surface appears The higher the resolution the more points are used to calculate the surface and the smoother the surface appears However high resolution values can also take a long time to calculate The default setting of 30 is a good compromise between speed and smoothness To set the resolution 1 From the Surfaces menu choose Resolution The Resolution slider appears Resolution 2 Adjust the slider to the desired resolution The new tesolution is the middle value listed at the bottom of the Res
84. file 202 Gaussian Computations jdf Format The jdf format is a file format for saving job descriptions Clicking Save within the dialog box saves modifications without the appearance of a watning or confirmation dialog box Saving either format within the Gaussian Job folder adds it to the Gaussian submenu for convenient access Computing Properties To specify the parameters for computations to predict properties of a model e From the Calculations menu point to Gaussian and choose Compute Properties The Compute Properties dialog box appears and displays the Properties tab with the top property of the menu preselected Compute Properties Job Type Theory Properties General Properties Density Hyperfine Coupling Constants Polarizabilities vi Population Analysis Mulliken zi Summary Job Type Compute Properties Method Closed Shell Restricted Hartree Fock Basis Set STO 3G Spin Multiplicity 1 Solvation Model Gas Phase Save As Cancel Creating a Gaussian Input File A Gaussian Input file contains the coordinates and geometry of the model and the Gaussian keywords taken from the settings of the dialog box CambridgeSoft Job Description File Formats To create a Gaussian Input file 1 From the Gaussian submenu choose Create Input File The Create Input File dialog box appears Create Input File Job Type Theory Properties General J
85. fragments to specify an axis around which to totate Dummy atom n Axis of Rotation To rotate the model around an axis 1 Select any two atoms 2 Drag the pointer along the Internal Rotation bar Rotating a Dihedral Angle You can select a specific dihedral angle to rotate To rotate a dihedral 1 Select four atoms that define the dihedral 2 Drag the pointer along the Internal Rotation bat ethorybenzene crl UrtRled 3 apx x E ue amp CambridgeSoft Rotating Models Using the Rotation Dial The Rotation Dial offers a quick method of rotating a model or dihedral a chosen number of degrees with reasonable accuracy For more precision you can enter exact numbers into the degree display box The Internal Rotation icons are only available when atoms ot bonds have been selected in the model Rotation Dial x Internal Rotation free rotation bond axis rotation dihedral Changing Orientation Chem3D allows you to change the orientation of your model along a specific axis However your model moves the origin of the model 0 0 0 does not change and is always located in the center of the model window To change the origin see Centering a Selection on page 100 Aligning to an Axis To position your model parallel to either the X Y or Z axis 1 Select two atoms only 2 From the View menu point to View Position and then click Align View choose an axis With Sele
86. i hy IS r a i i H a F g aE iar iaj maaar a qm asa n aum kr nim e if Lp MANAGEMENT E N otebook Enterprise and Document Manager integrate corporate knowledge with regulatory compliance Consulting teams analyze and adapt existing procedures to comply with new regulations e Systems include authentication and digital signatures and adapt to changing regulations and demands Analysis As your enterprise develops the operating procedures that you will need to adopt for 21CFR11 Compliance CambridgeSoft s consulting team can provide invaluable assistance in analyzing your current operating proce dures adapting your existing procedures to comply with new regulations and validating the software and the operating procedures that you will use CambridgeSoft s consulting teams consist of individuals who have extended experience in deploying systems used by large pharmaceutical companies emerging biotechs and major enterprises worldwide Implementation Once you have determined how your enterprise will comply with these new regulations implementing those decisions needs to be done quickly efficiently and with the understanding that the rules for compliance are in flux In order to succeed you must be able to respond to change CambridgeSoft s 21CFR11 Compliance con sulting has both the tools and the expertise to provide complete solutions carry out integration with your exist ing systems
87. in Brief the same wave function and a constant The wave function is called an eigenfunction and the constant an eigenvalue e Exact solutions to the Schrodinger equation are possible only for the simplest 1 electron 1 nucleus system These solutions however yield the basis for all of quantum mechanics e The solutions describe a set of allowable states for an electron The observable quantity for these states is described as a probability function This function is the square of the wave function and when properly normalized describes the probability of finding an electron in that state ema 1 where r radius x y and z e There ate many solutions to this probability function These solutions ate called atomic orbitals and their energies orbital energies e Fora molecule with many electrons and nuclei the aim is to be able to describe molecular orbitals and energies in as analogous a fashion to the original Schr dinger equation as possible Approximations to the Hamiltonian The first apptoximation made is known as the Born Oppenheimer approximation which allows separate treatment of the electronic and nuclear energies Due to the large mass difference between an electton and a nucleus a nucleus moves so much mote slowly than an electron that it can be regarded as motionless relative to the electron In effect this approximation considers electrons to be moving with respect to a fixed nucleus This allow
88. installed on your computer other than a network server you may also use the Software on a portable or home com Software from one computer to another b distribute copies of the Software to others or c modify or translate the Software without the prior written consent of C ambridgeSoft d place the software on a server so that it is accessi ble via a public network such as the Internet e sublicense rent lease or lend any portion of the Software or Documentation or f modify or adapt the Software or merge it into another program T he Software may be placed on a file or disk server connected to a network provided that a license has been purchased for every computer with access to that server You may make only those copies of the Software which are necessary to install and use it as per mitted by this agreement or are for purposes of backup and archival records all copies shall bear C ambridgeSoft s copyright and proprietary notices You may not make copies of any accompanying written materials 4 Assignment Restrictions for CD DVD databases You may not rent lease or otherwise sublet the Software or any part thereof You may transfer on a permanent basis the rights granted under this license provided you transfer this Agreement and all copies of the Software including prior versions and all accompanying materials T he recipi ent must agree to the terms of this Agreement in full and register this transfer in writing with C ambridg
89. is more likely to exist NOTE As a rule steric energy values should only be used Jor comparing different conformations of the same model 42 Chem3D Tutorials Tutorial 5 Mapping Conformations with the Dihedral Driver The dihedral driver allows you to map the conformational space of a model by varying one or two dihedral angles At each dihedral angle value the model is energy minimized using the MM2 force field and the steric energy of the model is computed and graphed After the computation is complete you can view the data to locate the models with the lowest steric energy values and use these as starting points for further refinement in locating a stationery point To use the dihedral driver 1 Select the bond in your model that defines the dihedral angle of interest 2 Choose Dihedral Driver from the Calculations menu The Dihedral Driver window opens When the computation is completed a graph is displayed showing the energy kcal vs theta angle of rotation To view the conformation at any given point 1 Point to a location specific degree or energy setting inside the Dihedral Driver Window A dashed line box appears As you move the mouse the box moves to define a specific point on the graph Dihedral Driver Dihedral Driver Chart 45 90 135 180 225 270 315 360 theta degrees Output Comments Dihedral Driver 2 Click on the point of interest CambridgeSoft Tutor
90. is sent to MOPAC To perform the computation 1 From the MOPAC Interface submenu of the Calculations menu choose Minimize Energy 2 On the Theory tab choose AM1 3 On the Properties tab select Charges in the Properties list 4 Select Wang Ford from the Charges list 5 Click Run The results for the model appear in the Message window when the computation is complete The molecules are now planar reflecting sp hybridization of the central carbon The following table shows the results is used tri chloro cation di chloro cation mono chloro cation methyl cation C 1 0 03660 C 1 0 11255 C 1 0 32463 C 1 0 72465 Cll 0 31828 CI 0 33189 Cl 0 35852 HO 0 08722 C13 0 32260 CIB 0 33171 HA 0 15844 HA 0 09406 Cl 4 0 32253 H 4 0 22384 H 4 0 15841 H 4 0 09406 From these simple computations you can reason Example 3 that the charge of the cation is not localized to the centtal carbon but is rather distributed to different extents by the other atoms attached to the charged carbon The general trend for this group of cations is that the more chlorine atoms attached to the charged carbon the more stable the cation the decreasing order of stability is tri chloro gt di chloro gt mono chloro gt methyl ChemOffice 2005 Chem3D Analyzing Charge Distribution in a Series Of Mono substituted Phenoxy lons 1 From the File menu choose New Model 2 Click
91. line 3 the atom type number is followed by the serial number of the atom to which the new atom is bonded and the distance to that atom In an Internal coordinates file the origin atom is always the first distance defining atom in the file All distances are measured in Angstroms Beginning with line 4 the distance is followed by the serial number of the first angle defining atom and the angle between the newly defined atom the distance defining atom and the first angle defining atom All angles are measured in degrees 1 1 1 1 54146 1 2 1 53525 1 1 1 1 53967 2 1 4 1 53592 1 1 3 1 53415 2 6 1 1 40195 2 5 1 1 11742 2 5 2 1 11629 1 5 2 1 11568 1 5 3 1 11664 2 5 3 1 11606 2 5 4 1 11542 1 5 4 1 11493 1 5 5 1 11664 4 5 5 1 11617 4 5 6 1 11664 3 ChemOffice 2005 Appendix 5 Beginning with line 5 the serial number of a second angle defining atom and a second defining angle follows the first angle Finally a number is given that indicates the type of the second angle If the second angle type is zero the second angle is a dihedral angle New Atom Distance defining Atom First Angle defining Atom Second Angle defining Atom Otherwise the third angle is a bond angle New Atom Distance defining Atom Second Angle defining Atom If the second angle type is 1 then the new atom is defined using a Pro R Pro S relationship to the three defining atoms if the second angle type is 1 the relationship is Pro
92. menu NOTE For all discussions below all the Building control panel options in the Chem 3D Setting dialog box are assumed to be turned on Some general rules about using the Text Tool are as follows e Text is case sensitive For example the correct way to specify a chlorine atom is Cl The correct way to specify the phenyl group substructure is to type Ph PH or ph will not be recognized e Pressing the Enter key applies the text to the model e Typing a formal charge directly after an element symbol will set the formal charge for that atom For example PhO will create a model of a phenoxide ion instead of phenol ChemOffice 2005 Chem3D e Ifyou double click an atom the contents of the previous text box are applied to that atom If the atom is one of several selected atoms then the contents of the previous text box are applied to all of the selected atoms Ifa tool other than the Text tool is selected double clicking in the model window is equivalent to clicking with the Text tool selected Triple clicking in the model window is equivalent to double clicking with the Text tool selected The interpretation of the text in a text box depends on whether atoms are selected as follows e If the model window is empty a model is built using the text e If you have one or more atoms selected the text is added to the model at that selection if possible If the specifications for a selected atom are violated the
93. methods MNDO PM3 and AM1 This method is generally regarded to be of historical interest only although some sulfur compounds ate still more accurately analyzed using this method 168 MOPAC Computations The following table shows the diatomic paits that ate parameterized in MINDO 3 An x indicates parameter availability for the pair indicated by the row and column Parameters of dubious quality are indicated by x Na Ma Kica 2n Ga Gelas Se Br K Rb Sr Ca Snfsb re 1 fxe jes Ha T1 Pb Bi Pol at fin The following limitations apply to MNDO e Sterically crowded molecules are too unstable for example neopentane e Four membered rings ate too stable for example cubane e Hydrogen bonds are virtually non existent for example water dimer Overly repulsive nonbonding interactions between hydrogens CambridgeSoft MOPAC Semi empirical Methods and other atoms are predicted In particular simple H bonds are generally not predicted to exist using MNDO Hypervalent compounds ate too unstable for example sulfuric acid Activation barriers are generally too high Non classical structures are predicted to be unstable relative to the classical structure for example ethyl radical Oxygenated substituents on aromatic rings are out of plane for example nitrobenzene The peroxide bond is systematically too short by about 0 17 A The C O C angle in ethers is too large AM1
94. multiplicity configurations for even shell system The OPEN keyword also invokes the RHF computation using the 1 2 electron approximation method and a C I calculation to correct the final RHF energies To see the states used in a C I calculation type MECI as an additional keyword The information is printed at the bottom of the out file Ground State UHF For UHF computations all unpaired electrons are forced to be spin up alpha 174 MOPAC Computations e Singlet ground state the most common configuration for a neutral even electron stable organic compound No additional keywords are necessary e UHF will likely converge to the RHF solution for Singlet ground states e Triplet or Quintet ground state Use the keyword TRIPLET or QUINTET NOTE When a higher multiplicity is used the UHF solution yields different energies due to separate treatment of alpha electrons Excited State RHF First Excited State The first excited state is actually the second lowest state the toot 2 for a given spin system Singlet Triplet Quintet To request the first excited state use the following sets of keywords First excited Singlet ROOT 2 OPEN 2 2 SINGLET or specify the single keyword EXCITED First excited triplet ROOT 2 OPEN 2 2 TRIPLET C l n where n 3 is the simplest case First excited quintet ROOT 2 OPEN 4 4 QUINTET C l n where n 5 is the simplest case Second Excited State The second ex
95. numbers found 1001488 9 lt 1340581 9 Browsing SciStore com Browse ChemStore com opens the SciStote formerly ChemStore page of the CambridgeSoft web site http scistore cambridgesoft com To access Browse SciStore com e From the Online menu choose Browse ChemStore com The SciStore Com page opens in your browser Scientific Software Databases snw SOLUTIONS DATABASES SERVICIS ABOUT REOISTIR CONTACT Cateaore Product Neme freed Qomioads Tshirt Ains EREE e W raw caro Deo English Pesca France USS Kure 6 Swiss frans Browse O software Ashgate Drugs Masintash co ROM senption PREE wey fragshem com On Sale This ae O Databases Sh nf a us gt The Marck indt ARA so E E are E E CD ROM Edition Software Phea by C oft Sharnisal aisi Sharnical Office Suites List Price 1 290 00 CambridgeSoft Browsing SciStore com You can search SciStore Com fot chemicals lab supplies chemistry related software and other items you want to buy You can access ChemACX Com and other pages from SciStore Com Browsing CambridgeSoft com Browse CambridgeSoft com opens the Home page of the CambridgeSoft web site To access the CambridgeSoft Home Page e From the Online menu choose Browse CambridgeSoft com The CambridgeSoft web site in your browser sora SOLUTIONS DATABASES SERVICES SITES ABOUT REGISTER CONTACT ShemOffice ChemDraw hem3D ENoi
96. of the Model Settings dialog box 2 Click the Atom Display tab ChemOffice 2005 Chem3D 3 Click the Show by Default checkbox in the Solid Spheres section 4 Select the Partial Charges radio button In this representation the oxygen atom and its two adjacent atoms are large because they have relatively large partial charges of opposite signs The rest of the atoms are relatively small You can display dot surfaces whose size is specified by partial charge 1 Click the VDW Radius radio button in the Solid Spheres section 1 Select the Show By Default check box in the Dot Surfaces section 2 Click the Partial Charges radio button In this representation the oxygen atom and its two adjacent atoms have large dot surface clouds around them because they have relatively large partial charges of opposite signs The rest of the Chem3D Tutorials 53 Tutorial 10 Computing Partial Charges atoms are relatively small Their dot surfaces ate obscured by the solid spheres If another molecule wete to react with this molecule it would tend to react where the large clouds are near the oxygen atom 54 Chem3D Tutorials CambridgeSoft Tutorial 10 Computing Partial Charges Chapter 3 Displaying Models Overview You can display molecular models in several ways depending on what information you want to learn from them The atoms and bonds of a model can take on different appearances These appearances are generic
97. on page 32 Tutorial 3 Building Models with the Text Building Tool on page 36 Tutorial 4 Examining Conformations on page 39 Tutorial 5 Mapping Conformations with the Dihedral Driver on page 42 Tutorial 6 Ovetlaying Models on page 43 Tutorial 7 Docking Models on page 46 Tutorial 8 Viewing Molecular Surfaces on page 48 Tutorial 9 Mapping Properties onto Surfaces on page 49 Tutorial 10 Computing Partial Charges on page 52 Tutorial 1 Working with ChemDraw The following tutorial introduces model building with Chem3D It assumes that no defaults have been changed since installation If what you see is not like the description you may need to reset the defaults To reset defaults ChemOffice 2005 Chem3D From the File menu open the Model Settings dialog box Click the Reset button Open a new model window if one is not already opened To view models as shown in this tutorial select Cylindrical Bonds from the drop down menu of the Model Display mode tool on the Model Display toolbar Wire Frame Sticks Ball amp Stick Ei EREE Space Filling Ribbons Cartoons The installation default for the ChemDraw panel is activated hidden You should see a tab labeled ChemDraw on the upper right side of the GUL aces c 1 28 0 ChemDraw tab 41 x O a Z If you do not see the tab 1 From the View menu select ChemDraw Panel The ChemDraw Panel op
98. open EPS files using other applications such as PageMaker You can transfer EPS files among platforms including Macintosh Windows and UNIX TIF The Tagged Image File Format TIFF contains binary data describing a bitmap image of the model TIFF is a high resolution format commonly used for saving graphics for cross platform importing into desktop publishing applications TIFF images can be saved using a variety of resolution color and compression options As TIFF images can get large choosing appropriate options is important When you save a file as TIF an option button appears in the Save As dialog box To specify the save options 1 Click Options The TIFF Options dialog box appears TIFF Options Resolution ESUE v Mi Color RGB Indexed Compression PackBits v 2 Choose a resolution The size of the file increases as the square of the resolution 3 Choose a color option If you want to Then choose force objects to black Monochrome and white 120 Printing and Exporting Models If you want to Then choose store colors using RGB Indexed computer monitor style of color encoding use printing press CMYK Contiguous style of color encoding Stores colors non sequentially For example CMYKCMYK The PackBits compression type provides no compression for this type of file NOTE If objects in your document are black and white they are saved as black and white
99. or edit an atom type to the Atom Types table 1 From the View menu point to Parameter Tables and choose Atom Types The Atom Types table opens in a window 2 To edit an atom type click in the cell that you want to change and type new information 3 Enter the appropriate data in each field of the table Be sure that the name for the parameter is not duplicated elsewhere in the table 4 Close and Save the table You now can use the newly defined atom type CambridgeSoft Defining Atom Types Appendix E Keyboard Modifiers The following tables list the keyboard modifiers that allow you to manipulate your view of the model without changing tools Rotation Key Drag Shift Drag ALT Trackball rotate view Trackball rotate model selection B Rotate 1 2 of fragment around bond Vv Rotate view about selected axis Rotate model selection about axis x Rotate view about view X axis Rotate model about view X axis Y Rotate view about view Y axis Rotate model about view Y axis Z Rotate view about view Z axis Rotate model about view Z axis In addition to the keyboard shortcuts you can rotate a model by dragging with the mouse while holding down both the middle mouse button or scroll wheel and the left mouse button Tip The order is important press the middle button first Zoom and Translate Shift Drag CTRL Translate view Translate model selection A Zoom to center ChemOf
100. parameters are guessed Job Type Compute Properties Properties Pi Bond Orders 6 Click Run The Output window appears When the steric energy calculation is complete the individual steric energy terms and the total steric energy appear Use the Output window scroll bar to view all of the output The units are kcal mole for all terms At the beginning of the computation the first message indicates that the parameters are of Quality 4 meaning that they are experimentally determined verified parameters NOTE The values of the energy terms shown here are approximate and can vary slightly based on the type of processor used to calculate them The following values ate displayed The Stretch term represents the energy associated with distorting bonds from their optimal length e The second steric energy term is the Bend term This term represents the energy associated with deforming bond angles from their optimal values 162 MM2 and MM3 Computations e The Stretch Bend term represents the energy required to stretch the two bonds involved in a bond angle when that bond angle is severely compressed The Torsion term represents the energy associated with deforming torsional angles in the molecule from their ideal values e The Non 1 4 van der Waals term represents the energy for the through space interaction between pairs of atoms that are separated by more than three atoms For example in tran
101. principal torsional constants used to compute the total torsional energy in a molecule V1 derives its name from the fact that a torsional constant of 360 periodicity can have only one torsional energy minimum and one torsional energy maximum within a 360 period The period starts at 180 and ends at 180 A positive value of V1 means that a maximum occurs at 0 and a minimum occurs at 180 in a 360 period A negative value of V1 means that a minimum occurs at 0 and a maximum occurs at 180 in a 360 period The significance of V1 is explained in the example following the V2 discussion ChemOffice 2005 Appendix V2 The V2 or 180 Periodicity Torsional constant field contains the second of three principal torsional constants used to compute the total torsional energy in a molecule V2 derives its name from the fact that a torsional constant of 180 periodicity can have only two torsional energy minima and two torsional energy maxima within a 360 period A positive value of V2 indicates there are minima at 0 and 180 and there are maxima at 90 and 90 in a 360 period A negative value of V2 causes the position of the maxima and minima to be switched as in the case of V1 above The significance of V2 is explained in the following example A good example of the significance of the V1 and V2 torsional constants exists in the 1 2 2 1 torsional parameter of 2 butene The values of V1 and V2 in the To
102. regardless of which Color options you set If you import drawings from other applications and want them to print Black and White you must set the Color option to Monochrome 4 Choose a compression option If you want fo Then choose reduce file size by PackBits encoding repeating bytes of information as output For example for a line of color information such as CCCCCMMMMMYYYY YKKKKK the compression yields a smaller file by representing the information as C5M5Y5K5 fax transmissions of CCITT Group 3 or images CCITT Group 4 CambridgeSoft Exporting Models Using Different File Formats GIF and PNG and JPG Use the Graphics Interchange Format GIF Portable Network Graphics PNG file format or the JPEG format to publish a Chem3D model on the world wide web Each of these formats uses a compression algorithm to reduce the size of the file Applications that can import GIF PNG and JPG files include Netscape Communicator and Microsoft Internet Explorer The model window background color is used as the transparent color in the GIF format graphic NOTE The size of the image in Chem3D when you save the file will be the size of the image as it appears in your web page If you turn on the Fit Model to Window building preference in Chem3D you can resize the Chem3D window in Chem3D to resize the model to the desired size and then Save 3DM The QuickDraw 3D MetaFile 3DM file format contain
103. select the atoms which are bonded to the attachment points of the substructure To build a model using a substructure 1 Type the name of the substructure into a text box or copy and paste it from the Substructutes table 2 Press the Enter key ChemOffice 2005 Chem3D The substructute appears in the model window When you replace an atom or atoms with a substructure the atoms which were bonded to the replaced atoms are bonded to the attachment points of the substructure The attachment points left by the replaced atoms are also ordered by serial number Example 1 Building Ethane with Substructures To build a model of ethane using a substructure 1 Type Et or EtH into a text box with no atoms selected 2 Press the Enter key A model of ethane appears a NOTE When automatic rectification is on the free valence in the ethyl group is filled with a hydrogen If automatic rectification is off you need to type EtH to get the same result For substructures with more than one atom with an open valence explicitly specify terminal atoms for each open valence Building and Editing Models 79 Building With The Text Tool Example 2 Building a Model with a Substructure and Several Other Elements To build a model with substructures and other elements 1 Type PrNH2 into a text box with no atoms selected 2 Press the Enter key A model of ptopylamine appears The appropriate bonding site for t
104. summary 131 brief theory 135 force field 136 limitations 130 parameters 135 speed 131 uses 131 Molecular orbitals 70 Molecular orbitals calculation types re quired 65 Molecular orbitals definition 70 Molecular shape 70 Molecular surface displays 63 Molecular surfaces 188 calculation types 64 definition 188 dots surface type 66 grid 67 Chem3D 9 0 1 overview 63 smoothness 67 solid surface type 66 translucent surface type 66 types available from extended Hiickel 65 types available from Gaussian 65 types available from MOPAC 65 viewing 48 wire mesh surface type 66 Molecular Weight ChemProp Std 206 Moments of Inertia ChemProp Std 206 Monochrome 120 MOPAC 257 aaa file 176 about 9 approximations 147 background 293 compute properties command 184 create input file command 177 file formats 124 FORTRAN format 259 general tab 181 graph file format 126 Hamiltonians 148 167 history 293 Hyperfine Coupling Constants 181 methods choosing 148 167 minimizing energy 180 minimum RMS gradient 180 molecular surface types available 65 optimize to transition state 182 out file 176 overview 165 parameters editing 294 properties 185 property server 209 references 293 exiii repeating jobs 178 RHF 181 running input files 177 server 209 specifying electronic state 172 specifying keywords 170 181 troubleshooting 176 UHF 181 Move to X Y plane command 99 to X Z plane command 99 t
105. the ChemD raw Plugin for structure and substructure searches View live ChemD raw files on Windows and M acintosh clients gt ChemRXN database z on CD ROM AAA a AAA e Chemw ai a weet ee E NS ae aa a a a ic oe a A y gheni A ii Pymes e o ci imiu maam Agere i o H f F aS E j E E EENS CEA p erm gt ChemINDEX database on ChemFinder Com SOFTWARE The Merck Index Je Encyclopedic chemical reference ChemACX Pro oe ote e Chemical searching buying The Merck Index Chemistry s Constant Companion Over 10 000 monographs of chemicals drugs biologicals ChemACX Pro Chemical Searching amp Buying Database of commercially available chemicals 300 catalogs with 500 000 chemical products e ChemACX SC database with 500 000 structures from leading screening compound suppliers ChemACX Com WWW Chemical Searching amp Buying e Search by text structure or substructure and order online from major catalogs ChemINDEX Reference Searching amp Information NCI database of over 200 000 molecules with anti HIV anti cancer assay data ChemRXN Reaction Searching amp Information Includes ChemSelect with reactions from InfoChem GmbH ISI s ChemPrep ChemMSDX Safety Data Searching amp Information e Provides full M aterial Safety Data Sheets for over 7 000 pure compounds ChemFinder Com WWW Reference Searching amp I
106. the following e Select Reverse to rotate the right frame to the left If your left eye focuses on the right hand model and your right eye focuses on the left hand model the two stereo views can overlap 62 Displaying Models e Select Parallel to rotate the right view further to the right Using Hardware Stereo Graphic Enhancement Chem3D 9 0 provides stereo graphics rendering for hardwate that has stereo OpenGL capabilities There are now a variety of stereo graphics cards stereo glasses and 3D monitors that can be driven by Chem3D Hardware enhancement is enabled from the OpenGL tab in the Chem3D Preferences dialog which you can access from the File menu Chem3D Preferences Popup Info ChemDraw Dihedral Driver General OpenGL GUI Window Settings changes will only affect new windows V Use Hardware Acceleration when Available Use Hardware Stereo when Available Use Back Buffer for Refresh Global Settings changes will affect all open windows v Use Alpha for Blending High Resolution Printing slower Any 3D window opened after this mode is enabled will utilize hardware graphics capabilities if they are available and enabled NOTE You must enable stereo in OpenGL in the display adapter properties control as well as in Chem3D preferences and select the correct mode for the glasses monitor Jou are using CambridgeSoft Structure Displays You can use
107. to Internet and intranet applications User Friendly amp IT Ready User friendly and IT ready ChemO ffice WebServer and Browser enterprise solutions applications and databas es are easier and faster for users to learn and the IT staff to deploy Using ChemOffice WebServer technology along with familiar browser technology overall costs are lowered and less time is required for implementation Enterprise Solutions Enterprise solutions built upon ChemOffice WebServer including Oracle Cartridge help workgroups and organizations collaborate and share information just as ChemOffice supports the daily work of the scientist a a a cm a gt Browse Detailed Tee mere WE dean Bp Compound Information Ce a Easy Management OO of Search Results SOLUTIONS e Development and deployment platform for workgroup and enterprise chemical information applications e Webserver and browser components facilitate application deployment to desktops with minimal impact and training e Enterprise Solution applications address areas of Knowledge Management Research amp Discovery Applied Biolnformatics and Chemical Databases Knowledge Management Knowledge M anagement applications organize and distribute chemical information E N otebook Enterprise streamlines daily record keeping with rigorous security and efficient archiving and facilitates information retrieval by structure and text searching Document M anager indexes the chemical st
108. to enter relations between atoms by specifying angles and lengths You display the Z Matrix table by selecting it from the View menu You can edit the values within the table or move atoms within the model and use the Set Z matrix submenu of the Structure menu You can copy and paste tables to text txt files or Excel spreadsheets using the commands in the context right click menu 28 Chem3D Basics Below is an example of the internal coordinates Z matrix for ethane Z Matrix ax m Angle Dihedral Atom Dihedral S H Atom Bond Atom Bond Length c c t 1 5400 5 1 1220 c 1 109 5000 5 1 1220 c 1 109 5000 H 6 109 5000 cS 1 1220 c 1 109 5000 H 6 109 5000 ct 1 1220 c 5 109 5000 H 6 60 0000 cq 1 1220 c 5 109 5000 H 2 109 5000 cq 1 1220 c 5 109 5000 H 2 109 5000 AES EEEE aiolvlolulola gt rrrirzzo Cartesian Coordinates Cartesian coordinates are also commonly accepted as input to other computation packages They describe atomic position in terms of X Y and Z coordinates relative to an arbitrary origin Often the origin corresponds to the first atom drawn However you can set the origin using commands in the Model Position submenu of the Structure menu Instead of editing the coordinates directly in this table you can save the model using the Cartesian Coordinates file format ccl or cc2 and then edit that file with a text editor You can also copy and paste the table into a t
109. to them ate removed from the Measurements table Optimal Measurements Optimal values are used instead of the corresponding standard measurements when a measurement is required in an operation such as Clean Up Structure Optimal measurements are only used when the Measurements table is visible ChemOffice 2005 Chem3D When the Measurements table is not visible the standard measurements ate taken from the parameter tables To specify optimal values for particular measurements edit the value in the Optimal column Chem3D also uses the optimal values with the Dock command When you choose Dock from the Structure menu Chem3D reconciles the actual distance between atoms in two fragments to their optimal distances by rigidly moving one fragment relative to the other Non Bonded Distances in Tables To display non bonded atom measurements 1 Select the atoms 2 From the Structure menu point to Measurements and choose Set Distance Measurement The measurement between the selected atoms is added to the table Measurement AX Untitled 1 1 Atoms actual Optimal OGHA 08720 08720 HACIA 11130 1 1130 HOD 11130 1 1130 HAIC 14130 1 1130 C C 1 5230 1 5230 CHOO 14130 14130 CHG 14130 11130 H C 14130 14130 amp A C 15230 1 5230 ADH 14130 11130 O 6 C 1 1 3380 1 3380 O 5 C 1 1 2080 1 2080 So 5908 1 5090 H6 H 11 2 4876 Ru z Matrix OM meas non bonded distance jojo 0 02 o u
110. trajectory for a molecule or fragment in Chem3D A common use of molecular dynamics is to explore the conformational space accessible to a molecule and to prepare sequences of frames representing a molecule in motion For more information on Molecular Dynamics see Chapter 9 MM2 and MM3 Computations on page 151 Molecular Dynamics Formulas The molecular dynamics computation consists of a series of steps that occur at a fixed interval typically about 2 0 fs femtoseconds 1 0 x 10 seconds The Beeman algorithm for integrating the equations of motion with improved coefficients B R Brooks is used to compute new positions and velocities of each atom at each step Each atom i is moved according to the following formula x x v At 5a a9 At 8 Similarly each atom is moved for y and z where x y and z are the Cartesian coordinates of the atom v is the velocity a is the acceleration a is the acceleration in the previous step and At is the time between the current step and the previous step The potential energy and derivatives of potential energy g ate then computed with respect to the new Cartesian coordinates New accelerations and velocities are computed at each step according to the following formulas m is the mass of the atom veryold y old ayo aj apd aj a g m v v 3a 6a 4 a vervold At 8 ChemOffice 2005 Chem3D Quantum Mechanics Theo
111. used to describe the atomic connectivity The CONECT records contain the record name followed by the serial number of the atom whose connectivity is being described then the serial numbers of the first atom second atom third atom and fourth atom to which the described atom is connected Record Chem3D Name File Title COMPND Alanine pdb Record Serial Element Xx Y Z Name Number Symbol Coord Coord Coord HETATM 1 N 0 038 0 962 0 943 Record Serial Ist Atom 2nd Atom 3rd Atom 4th Atom Name Number Serial Serial Serial Serial Number Number Number Number CONECT 2 1 3 4 8 260 File Formats FORTRAN Formats The full description of the COMPND record format in Protein Data Bank files is as follows Column Number 1 6 7 10 11 70 Column Description Record Name COMPND UNUSED Name of Molecule Used by Chem3D Yes No Yes The full description of the ATOM and HETATM record formats in Protein Data Bank files is as follows Column Number 1 6 18 20 Column Used by Description Chem3D Record Name Yes HETATM or ATOM Atom Serial Number Yes UNUSED No Atom Name Yes Element Symbol Alternate Location No Indicator Residue Name Optional CambridgeSoft Protein Data Bank Files 21 UNUSED No 7 11 Atom Serial Number Yes 22 Chain Identifier No 12 16 Serial Number of First Yes Bonded Atom 23 26 Residue Sequence No Number 17 21 Serial Number of Yes Second Bonded Atom 27 Code for ins
112. using polarization functions The 6 31G basis set for example adds d functions to heavy atoms Computation Concepts 145 Quantum Mechanics Theory in Brief A variety of other basis sets such as diffuse function basis sets and high angular momentum basis sets are tailored to the properties of particular of models under investigation The coefficients C used for a given AO basis set o ate derived from the solution of the Roothaan Hall matrix equation with a diagonalized matrix of orbital energies E The Roothaan Hall Matrix Equation This equation shown below includes the Fock matrix F the matrix of molecular orbital coefficients C from the LCAO approximation the overlap matrix S and the diagonalized molecular orbital energies matrix E FSC Since the Fock equations are a function of the molecular orbitals they are not linearly independent As such the equations must be solved using iterative self consistent field SCF methods The initial elements in the Fock matrix are guessed The molecular coefficients are calculated and the energy determined Each subsequent iteration uses the results of the previous iteration until no further variation in the energy occurs a self consistent field is reached Ab Initio vs Semiempirical Ab initio meaning literally from first principles methods use the complete form of the Fock operator to construct the wave equation The semiempirical methods
113. values GEO OK Automatically sent to MOPAC to override checking of the Z matrix MMOK Automatically sent to MOPAC to specify Molecular Mechanics correction for amide bonds Use the additional keyword NOMM to turn this keyword off MOPAC Computations 187 Computing Properties Molecular Surfaces Molecular surfaces calculate the data necessary to render the Total Charge Density Molecular Electrostatic Potential Spin Density and Molecular Orbitals surfaces Polarizability The polarizability and hyperpolarizability property provides information about the distribution of electrons based on presence of an applied electric field In general molecules with more delocalized electrons have higher values for this property Polarizability data is often used in other equations for evaluation of optical properties of molecules For more information see the MOPAC online manual page 214 The polarizability and hyperpolarizability values reported are the first order alpha tensors xx yy ZZ XZ YZ Xy second order beta tensors and third order gamma tensors NOTE Polarizabilities cannot be calculated using the MINDO 3 potential function COSMO Solvation in Water The COSMO method is useful for determining the stability of various species in a solvent The default solvent is water For more information see the MOPAC online manual To run the COSMO method make the following selections in the MOPAC Interface
114. 0 6518 C 0 0 0 0 0 10 0 559 1 3696 0 4359 Cc 0 0 0 0 0 11 0 3007 0 4266 1 7567 O 0 0 0 0 0 12 2 0207 0 239 0 253 H O 0 0 0 0 13 2 0051 0 5617 1 8571 H 0 0 0 0 0 14 1 0054 1 7589 1 9444 H O0 0 0 0 0 15 0 1749 0 4961 2 4273 H O 0 0 0 0 16 1 27 2 1277 0 9014 H O 0 0 0 0 17 0 0103 1 8981 0 3309 H 0 0 0 0 0 18 2 0207 0 225 0 6551 H O 0 0 0 0 19 2 0084 0 5688 0 9529 H 0 0 0 0 0 20 1 0296 7659 1 0161 H 0 0 0 0 0 21 1 2615 2 1277 0 0139 H O 0 0 0 0 22 0 0143 1 8761 1 2488 H O0 0 0 0 0 23 0 3286 0 2227 2 4273 H 0 0 0 0 0 24 1 2 1 0 0 0 25 1 6 1 0 0 0 26 1 8 1 6 0 0 27 1 9 1 1 0 0 28 2 3 1 6 0 0 29 2 10 1 0 0 0 30 2 11 1 1 0 0 31 3 4 1 0 0 0 ChemOffice 2005 Appendx le Formats 251 File Format Examples 32 3 12 33 3 13 34 4 5 35 4 14 36 4 15 37 5 6 38 5 7 39 5 16 40 6 17 41 6 18 42 7 19 Each line represents either a blank line or a data record containing one or mote fields of information about the structure Each field is delimited by a space s or a tab The fields in the MDL MolFile format used by Chem3D Pro are discussed below 1 Line 1 starts the header block which contains the name of the molecule The molecule name is the file name when the file was created using Chem3D Pro 2 Line 2 continues the Header block and is a blank line 3 Line 3 continues the Header block and is another blank line 4 Line 4 the Counts line contains 5 fields which desctibes the molecule The first field is the
115. 0000 H 5 C 1 H 3 109 0000 109 0000 H 5 C 1 C 2 110 0000 110 0000 H 4 C 1 H 3 109 0000 109 0000 H 4 C 1 9 C 2 110 0000 110 0000 H 3 C 1 C 2 110 0000 110 0000 ChemOffice 2005 Chem3D If you edit the Actual field you change the value in the model and see atoms in the model move If you edit the Optimal value you apply a constraint These values are used only in Clean Up on the Structure menu and MM2 computations Deleting Measurement Table Data You can isolate the information you in the Measurements table by deleting the records that you do not want to view For example you could display bond lengths then delete everything except the carbon carbon bonds This would make them easier to compare To delete records e Select the records and click Delete on the right click menu Deleting records in a Measurements table does not delete the corresponding atoms To clear the entire table On the Measurement submenu of the Structure menu select Clear Chem3D Basics 29 Model Building Basics 30 Chem3D Basics CambridgeSoft Model Building Basics Chapter 2 Chem3D Tutorials Overview The following section gives detailed examples of some general tasks you can perform with Chem3D For examples of MOPAC calculations see Chapter 10 MOPAC Computations on page 165 In this section Tutorial 1 Working with ChemDraw on page 31 Tutorial 2 Building Models with the Bond Tools
116. 1 Chem3D adds the notion of view focus defined as the set of atoms that the user is interested in working on By default the view focus includes all of the atoms in the model ChemOffice 2005 Chem3D To change the view focus to include only those atoms and bonds you are working on 1 Select the fragment or set of atoms or bonds 2 Click Set Focus to Selection on the View Focus submenu of the View menu Once you have set the view focus the following things happen e When building with the bond tools Chem3D will resize and reposition the view so that all of the atoms in the view focus are visible e As new atoms ate added they become part of the view focus e When rotating or resizing the view manually the rotation ot resize will be centered around the view focus Setting Measurements You can set the following measurements using the Measurements submenu of the Structure menu Bond lengths e Bond angles e Dihedral angles e Close contacts NOTE When you choose Measurement from the Structure menu the display of the Set Measurement option will vary depending on what you have selected The grayed out option says Set Measurement when you select a bond it says Set Bond Length etc When you use the Clean Up Structure command the bond length and bond angle values are overridden by the standard measurements from the Optimal column of the Measurement table These optimal values are the standard measur
117. 107 Showing the Deviation from Plane 107 Removing Measurements from a Table 108 Displaying the Coordinates Tables 108 Internal Coordinates o oo ooooooooo 108 Cartesian Coordinates o ooooooooooo 109 Comparing Models by Overlay 109 Working With the Model Explorer 111 Model Explorer ObjectS ooooooomo 112 Creating Groups ici vn has eal es 113 Adding to Groups 0 000000 113 Pasting Substructures 00005 114 Deleting Groups 6 2 0 0 eee eee 114 Using the Display Mode 114 Coloring Gtoups 6 114 ResettingoDetanlis ciones 115 Animations oooooooooooo 115 Creating and Playing Movies 115 Spinning Models oooocoooommmm 115 Spin About Selected Axis oooo ooooo 115 Editing a Movie oooooococcommmm m 116 Movie Control Panel o oooooooo 116 Chapter 7 Printing and Exporting Models Specifying Print Options 0oooomoo 117 Pei ts da Scene ea 118 Exporting Models Using Different File Fotmats oir o carats 118 Publishing Formats ooooooooommoo 119 WIME And EME rote o ae ser 119 DMP aa ea bd ch be Hal bok he aay eee eee e 119 EPG 4 ce th Awaits Grace hb tas Rap hee aaa 120 TIP oe test nce A Reade Jacke 120 GIF and PNG and JPG 121 Mi to o dt ai ada 121 ANA A e ae a SSOP eE E ar EEEE 121 Formats for Chemistry Modeling Applications 121 Alchemy sa
118. 11 0 O 1 309372 2 283279 0 037933 0 O 0 033539 2 031708 1 272888 0 O 2 052933 0 717285 1 881104 0 O 0 275696 0 374954 2 411163 0 For example the following illustrates the atom and bond components for C6 and bond 3 of cyclohexanol Each pair of numbers represents art atom to which this atom is bondedAtorm Color 311511611 710000 O GOGBS250 AABEBOO p wee o f f gt nA f n Atom Typserial Ni t dpmet Ty pex Y Z Coordinates FORTRAN Formats The FORTRAN format for each record of the MacroModel format is as follows Line Description FORTRAN Number Format 1 number of 1X 15 2X A atoms and molecule name file name MDL MolFile The MDL MolFile format is defined in the article Description of Several Chemical Structure File Formats Used by Computer Programs Developed at Molecular Design Limited found in the Journal 1 MDL MACCS II is a product of MDL Information Systems Inc previously called Molecular Design Limited CambridgeSoft File Format Examples of Chemical Information and Computer Science using Chem3D Pro This file describes a model of Volume 32 Number 3 1992 pages 244 255 The cyclohexanol the line numbers ate added for following is a sample MDL MolFile file created reference only 1 cyclohexanol 2 3 4 19 19 0 0 0 5 1 3488 0 1946 1 0316 Cc 0 0 0 0 0 6 0 4072 0 8965 1 5632 Cc 0 0 0 0 0 7 0 5621 1 3777 0 4733 Cc 0 0 0 0 0 8 1 3507 0 2045 0 1277 C 0 0 0 0 0 9 0 4203 0 9011
119. 110 6903 13566 14061 808 4424 8880 7577 12182 14874 594 5270 10234 18551 4300 9815 18274 4047 17718 19321 5600 10636 19608 A 2 2222 22 2 2 2 2 2 2 2 2 2 2 20 OO O 4583 125 7132 1855 6240 13349 8725 9852 10879 2685 16168 ooo oO File Formats Protein Data Bank Files 263 Line 56 2794 21139 6600 Line 57 2876 15736 11820 Line 58 14029 20018 10310 Line 59 22477 3450 6965 Line 60 806 4365 16672 Line 61 14642 18918 3566 Line 62 23341 2014 13035 Line 63 1740 5536 22837 5 Lines 5 23 of the CT Block each contain 4 fields describing an atom The first field is the element symbol first letter uppercase second lowercase The second field is the total number of hydrogens attached to the atom the third field is the stereo information about the atom and the fourth field is the formal charge of the atom Each line is either a blank line a block header line or a data record containing multiple fields of information about the structure The SMD file is broken down into several blocks of information The header for each block starts with a gt sign Individual fields are delimited by space s or a tab The fields in the SMD format file used by Chem3D Pro ate discussed below 1 Line 1 statts the block named STRT This NOTE Ifthe file is created using Chem3D Pro the block contains the molecule name The molecule name is the file name when the file was created using Chem3D Pro
120. 3D Pi Bonds and Atoms with Pi Bonds For models containing pi systems MM2 performs a Pariser Parr Pople pi orbital SCF computation for each system A pi system is defined as a sequence of three or more atoms of types which appear in the Conjugate Pi system Atoms table Because of this computation MM2 may calculate bond orders other than 1 1 5 2 and so on NOTE The method used is that of D H Lo and M A Whitehead Can J Chem 46 2027 1968 with heterocycle parameter according to G D Zeiss and M A Whitehead J Chem Soc A 1727 1971 The SCF computation yields bond orders which are used to scale the bond stretching force constants standard bond lengths and twofold torsional barriers The following is a step wise overview of the process 1 A Fock matrix is generated based on the favorability of electron sharing between pairs of atoms in a pi system 2 The pi molecular orbitals are computed from the Fock matrix 3 The pi molecular orbitals are used to compute a new Fock matrix then this new Fock matrix is used to compute better pi molecular orbitals Step 2 and 3 are repeated until the computation of the Fock matrix and the pi molecular orbitals converge This method is called the self consistent field technique or a pi SCF calculation 4 A pi bond order is computed from the pi molecular orbitals 5 The pi bond order is used to modify the bond length BL and force constant K res for each bond
121. 5 Spinning models 115 xviii CambridgeSoft Standard Gibbs free energy ChemProp Pro 207 Standard measurement 271 Standard measurements bond angle 29 bond length 29 Standard measurements applying 27 Standard measurements bond angle 279 Standard measurements bond length 277 Standard Molecular Data file format 126 Stationary point 133 Step Interval control 158 Stereo pairs 61 Stereochemistr Inversion 88 Stereochemistry changing 88 stereochemical relationships 239 Steric energy computing 161 equations 136 parameters 161 terms 162 tutorial example 41 Sticks display 56 STN Express 126 Stopping minimization 153 molecular dynamics 160 Stretch bend cross terms 142 Stretch bend energy MM2 209 Stretch bend parameters 283 Structure displays changing 55 displays overview 55 Structure menu 17 Structure activity relationships 205 Substructures 231 Substructures table 38 277 Substructures adding to model 81 Summary file see MOPAC out file Suppliers finding online 225 Surface types 64 Surfaces toolbar 21 Surfaces mapping properties onto 49 SYBYL file format 126 SYBYL MOL File 265 SYBYL MOL2 File 267 FORTRAN format 270 SYBYL MOLFile 265 FORTRAN format 267 SYBYL2 seeSYBYL MOL2 File Symbol 274 Symmetry MOPAC 210 Synchronizing ChemDraw and Chem3D 74 System requirements 11 T Table editor 78 Tables internal and external 24 Technical support 229 230 serial numbers 229 system crashes 230 troubl
122. 5 molecular surfaces 64 solid spheres 57 Distance defining atom 102 dLength field 281 Docking models 46 Documentation web page 224 Dot density 58 Dot surfaces 58 Dots surface type 66 Double bond tool tutorial example 34 Double bonds field 276 Dummy atoms 76 Dynamics settings 158 E Edit menu 15 Editing atom labels 77 Cartesian coordinates 28 display type 55 56 file format atom types 241 internal coordinates 28 measurements 107 models 73 movies 116 parameters 290 selections 92 Chem3D 9 0 1 Z matrix 101 EF keyword 176 Eigenvector following 176 Eigenvectors 171 Electron field 280 Electronegativity adjustments 281 Electronic energy 298 K MOPAC 210 Electrostatic and van der Waals cutoff parameters 283 and van der Waals cutoff terms 291 cutoff distance 283 cutoff term 291 cutoffs 140 energy 140 potential 187 potential derived charges 186 potential overview 187 Element symbols see Atom labels Elements color 58 Elements table 272 274 Enantiomers creating using reflection 89 Encapsulated postscript file 120 Energy components MOPAC 171 Energy correction table 271 282 Energy minimization 134 Enhanced metafile format 119 ENPART keyword 171 EPS field 284 EPS file format 120 Eraser tool 76 Error messages 208 Error messages ChemProp 208 ESR spectra simulation 188 Estimating parameters 273 Even electron systems 174 Exact mass ChemProp Std 206 eyii Examining angles tutorial example 34 bond length and
123. 567 0 271255 1 48999 21 NOOoanb BWwWwNHD BSB BWR ANY ADHD Following is an example of a Cartesian Coordinate file with Connection table by Position for Cyclohexanol 244e File Formats Elemert X YandzZ Positions of Other Atoms Symbol Coordinates to which CCD is Bonded A ee C 1 0 706696 0661 85088201 2 4 7 8 Serial Atom Type Nianber Text Number CambridgeSoft File Format Examples An example of a Cartesian Coordinate File with Connection Table by Serial Number for Cyclohexanol follows co On FR WD 01 9 10 11 12 13 14 15 16 17 18 19 102 TITTTITITITTTTITIOOOOOOO Components of a Cartesian coordinate File with Connection Table by Serial Number for C 1 of 0 706696 0 834732 1 409012 1 217285 0 639328 0 89444 1 192993 1 052597 1 211624 1 208969 2 524918 1 11557 0 937027 2 329758 1 003448 1 005798 1 295059 1 265137 2 127594 Cyclohexanol is shown below Element X Yand Z Symbol Coordinates wea 1 066193 1 075577 0 275513 0 38632 1 19154 1 1698 1 809631 1 559525 2 125046 0 640518 0 2816 0 762314 0 8781 0 41023 2 24631 0 76137 1 73161 1 68524 1 865631 Serial Numbers of Other Atoms to which C D is Bonded WA C 1 0 7066965 0661 K 508820 1 2 4 9 101 Serial Number Atom Type Text Number ChemOffice 2005 Appendix 0 50882 0 508789 0 668915 0 508865 0 664444 0 646652 1 59346 0 432266 0 457016 1 465607 0
124. 596 Line 4q H 1 11664 1 110 0104 Line 4r H 1 11604 1 109 6082 Line 4s H 0 94199 1 106 898 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 55 3112 57 03175 172 662 62 06751 177 17 65 43868 178 6209 63 9507 66 0209 176 0838 178 296 64 43501 178 325 64 09581 173 033 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 NOOO oO NO FPF RA OONN A a ORA 2 OU U A A a A NNa A NNN N NNa A NNa a A AOU N The following illustrates the components of the MOPAC Output File from Chem3D for C 1 Through C 4 of Cyclohexanol Element Bond Action Bond Action Dihedral Action Connectivity Symbol Lengths Integers Angles Integers Angles Integers Atoms re ee ee ae Ist Atom_ C 0 000000 O 0 000000 O 0 000000 O o o o 2nd Atom gt C 1 541519 1 0 000000 O 0 000000 O 1 o o 3rd Atom gt C 1 535233 0 000000 O 111 774673 1 4 4th Atonr gt C say a 1 109 711411 1 55 695877 1 1 pA 3 A The internal coordinates section of the MOPAC Data File format contains one line of text for each atom in the model Each line contains bond lengths bond angles dihedral angles action integers and connectivity atoms 2580 File Formats As shown in the illustration above C 1 is the origin atom C 2 is connected to C 1 with a bond of length 1 541519 A C 3 is connected to C 2 witha bond of length 1 535233 A and is at a bond angle of 111 774673 degrees from C 1 C 4 is connected to C 1 with a bond o
125. 6 0 1 122113 0 858973 0 923295 Example 2 ethane Cartesian table tab as separator 82 Building and Editing Models 0 49560 57820 0037 0 4956 0 57820 0037 H 0 05521 55570 0037 H 1 15170 52520 9233 H 1 15690 5248 0 9233 H 0 0552 1 55570 0037 H 1 1517 0 52520 9233 H 1 1569 0 5248 0 9233 Example 3 ethenol Z Matrix table tab as separator 133 2321 119 73 9782 1091 180 991 1193 180 9892 119 53 180 9882 1193 0 Changing an Atom to Another Element 1 2 3 2 1 zo re 2000 oO o o OF HF 1 To change an atom from one element to another 1 Click the Text tool 2 Click the atom to change A text box appears 3 Type the symbol for the element you want case sensitive 4 Press the Enter key As long as the Text tool is selected you can double click other atoms to make the same change CambridgeSoft Changing an Atom to Another Element For example to change benzene to pyridine 1 Click the atom to replace and type NH2 t a 2 Press the Enter key a a Changing an Atom to Another Atom Type To change a single atom 1 Click the Text tool 2 Click the atom to change A text box appears 3 Type the name of the atom type case sensitive 4 Press the Enter key ChemOffice 2005 Chem3D To change more than one atom 1 Use Shift click to select the atoms to change 2 Type the name of the atom type case sensitive 3 Press the Enter key
126. 6 31G Diffuse None Polarization Heavy Atom None ind Net Charge 0 Spin Multiplicity 1 A Summary Job Type Minimize Energy Display Each Iteration Method Closed Shell Restricted Hartree Fock Basis Set 6 31G Spin Multiplicity 1 Save As v Cancel To set the Theory specifications 1 Select the appropriate Method N A Q NOTE To use a Method or Basis Set that is not on the list type it in the Additional Keywords section on the General page For more information see The General Tab on page 201 Select the wave function to use Closed Shell Restricted Open Shell Unrestricted or Restricted Open Shell Select the Basis Set Select the Diffuse function to add to the basis set Select the Polarization Heavy Atom If you select a Heavy Atom function also choose an H option CambridgeSoft Minimize Energy 6 Select a Spin Multiplicity value between one and 10 The Properties Tab The Properties tab allows you to select the properties and charges to calculate from the minimized structute Compute Properties Job Type Theory Properties General Properties q RMS Force a Dipole Charges Electron Density Molecular Surfaces Spin Density 3 Hyperfine Coupling Constants Polarizabilities s Population Analysis Mulliken X Summary Job Type Compute Properties a Method Closed Shell Restric
127. 625809 1 629425 1 470062 0 437714 0 618286 1 627 1 524567 0 271255 1 48999 1 1 1 1 1 1 6 5 5 5 5 5 5 5 5 5 5 5 21 2 4 9 1 3 10 2 6 12 1 5 14 4 6 16 3 5 18 1 102 1 3 3 4 4 5 5 6 6 7 7 10 1 10 11 13 15 17 19 Components of a Cartesian coordinate File with Crystal coordinate Parameters for C 1 is shown below Number of Atoms c a Y Exponent AN 10 23 12 568 12 900 120 0 0 1 1578 2341 5643 1 20 VA Fractional Cell Coordinates File Formats File Format Examples 4 21 e 245 FORTRAN Formats The FORTRAN format for the records in a Cartesian coordinate file with a connection table by serial number or position and a Cartesian coordinate file with fractional crystal cell parameters are listed in the following tables Cartesian coordinate File Connection Table by Serial Number or Position Line Description FORTRAN Number Format 1 Number of 13 Atoms 2toEnd Atom coordinates A3 1X 14 3 1X F11 6 1X 14 10 1X 14 Cartesian coordinate File Fractional Crystal Cell Parameters Line Description FORTRAN Number Format 1 Number of 13 6 1X F I Atoms Crystal Cell Parameters 2toEnd Atom coordinates A3 1X 14 3 1X F11 6 1X 14 10 1X 14 Cambridge Crystal Data Bank Files The specific format of Cambridge Crystal Data Bank files CCDB used by Chem3D is the FDAT format described on pages 26 42 of the
128. 7 What s new in Chem3D 9 0 1 10 What s new in Chem3D 9 0 10 Wire frame display 56 Wire mesh surface type 66 WMF and EMF 119 X X Y or Z axis rotations 97 XH2 field 280 XR2 field 279 XRH field 279 Z Zero point energy 171 Z matrix 28 changing 101 overview 108 pop up information 105 Zwitterion creating a 80 Chem3D 9 0 1 exxi Prise Solutions afiche Didernchmen Ae Life Science A a Hq 4 Desktop Softw are Enterprise Solutions Y Research Discovery Applied Biolnformatics Know ledge Management E Chemical Databases SUOHNJOS HOS CAMBRIDGESOFT ChemOffice Desktop to RESEARCH amp DISCOVERY Chemo ffice E Notebook ChemDraw Chem3D ChemFinder Cheminfo Chemo ffice WebServer Oracle Cartridge E Notebook Enterprise Document Manager Discovery LIMS 21CFR11 Compliance KNOWLEDGE MANAGEMENT Desktop E Notebook Enterprise Inventory Manager WebServer Discovery Registration LIMS System 21CFR11 Formulations Compliance amp Mixtures DESKTOP SOFTWARE Success begins at the desktop where scientists use ChemDraw and ChemOffice to pursue their ideas and communicate with colleagues using the natural language of chemical structures models and information In the lab scientists capture their results by organizing chemical information documents and data with E Notebook Chem3D modeling and ChemFinder inform
129. 7 182949 KCAL 71 89346 KJ ELECTRONIC ENERGY 929 360221 EU CORE CORE REPULSION 590 227818 EU DIPOLE 6 66600 DEBYE SYMMETRY D3d NO OF FILLED LEVELS 7 IONIZATION POTENTIAL 11 847014 EU HOMO LUMO ENERGIES EU 11 847 4 187 MOLECULAR WEIGHT 30 069 SCF CALCULATIONS 1 Delete text through COMPUTATION TIME 6 63 SECONDS this line FINAL GEOMETRY OBTAINED SCF MMOK GEO OK AM1 MULLIK 0 000080 0 000808 0 000009 8 2137 1 523018 8 900686 6 900088 0 2137 Keywords 1 112976 109 998169 6 668686 6 0714 section 120 876691 0 0712 8 0712 6 0714 8 0712 6 0712 128 076691 179 999634 59 923813 59 923813 1 112976 109 998169 1 112976 109 998169 1 112976 109 998169 6 4 4 1 112976 1 109 998169 1 1 1 1 112976 1 109 998169 TITS b ab b ab d d O O i d dd ChemOffice 2005 Chem3D MOPAC Computations 179 MOPAC Files Minimizing Energy Minimizing energy is generally the first molecular computation performed on a model From the Calculations menu point to MOPAC Interface and choose Minimize Energy The MOPAC Interface dialog box appears with Minimize as the default Job Type Mopac Interface Job amp Theory Properties General Job Type minimization Method amy Wave Function Close Shell Restricted Optimizer EF Solvent None Move Which All atoms Minimum RMS p 1000 r IV Display Every Iteration Show Output in NotePad I Send Back Output Set A
130. 8 122 cub file format 122 dat file format 123 emf file format 119 eps file format 120 fch file format 122 g1f file format 121 gjc file format 118 122 gjf file format 122 203 gjt file format 203 gpt file format 126 Int file format 118 123 Jdf file format 126 202 jdf Format 202 jdt file format 126 202 jdt Format 202 mcm file format 118 123 m12 file format 126 mol file format 118 124 mop file format 118 124 mpc file format 124 msm file format 118 124 pdb file format 118 126 png file format 121 Chem3D 9 0 1 dl file format 118 126 sm2 file format 118 126 smd file format 118 126 sml file format 118 126 xyz file format 126 zmt file format 124 Numerics 1 2 electron approximation 147 166 2D programs using with Chem3D 75 2D to 3D conversion 239 3D enhancement depth fading 60 hardware 62 red blue 59 stereo pairs 61 3RINGANG TBL see Angle bending table 4 Membered Ring Torsionals 271 4RINGANG TBL see Angle bending table A Ab initio methods speed 130 uses 131 vs semi empirical methods 146 Activating the select tool 38 Actual field editing 107 Actual field measurements 29 ACX information finding 225 ACX number search 226 ACX structure search 225 Adding calculations to an existing worksheet 220 formal charges 77 fragments 84 parameters to MOPAC 294 serial numbers tutorial example 36 to groups 113 Alchemy 241 Alchemy file format 121 241 Alchemy FORTRAN forma
131. Applicability and Limitations cs ba Ha T Pe ei Pol at rn Important factors relevant to AM1 are AM1 is similar to MNDO however there ate changes in the core cote repulsion terms and reparameterization AM1 is a distinct improvement over MNDO in that the overall accuracy is considerably improved Specific improvements ate e The strength of the hydrogen bond in the water dimer is 5 5 kcal mol in accordance with experiment e Activation barriers for reaction are markedly better than those of MNDO e Hypervalent phosphorus compounds are considerably improved relative to MNDO ChemOffice 2005 Chem3D In general errors in AH obtained using AM1 ate about 40 less than those given by MNDO e AM1 phosphorus has a spurious and very sharp potential barrier at 3 0A The effect of this is to distort otherwise symmetric geometries and to introduce spurious activation barriers A vivid example is given by P4Og in which the nominally equivalent P P bonds are predicted by AM1 to differ by 0 4A This is by far the most severe limitation of AM1 e Alkyl groups have a systematic error due to the heat of formation of the CH fragment being too negative by about 2 kcal mol e Nitro compounds although considerably improved are still systematically too positive in energy e The peroxide bond is still systematically too short by about 0 17A PM3 Applicability and Limitations PM3 Parameterized Mo
132. C 13 are also used to position the atom ChemOffice 2005 Chem3D Because H 14 is positioned by two bond angles there ate two possible positions in space about C 5 for H 14 to occupy the Pro R designation determines which of the two positions is used C 1 H 14 13 Positioned By C 5 lt 1 C 13 Pro R If an atom is positioned by a dihedral angle the three atoms listed in the information about an atom would all be connected by dashes such as C 6 C 3 C 1 and there would be no Pro R or Pro S designation The commands in the Set Z Matrix submenu allow you to change the Z matrix for your model using the concepts described previously Because current measutements ate retained when you choose any of the commands in the Set Z Matrix submenu no visible changes in the model window occur Positioning by Bond Angles To position an atom relative to three previously positioned atoms using a bond distance and two bond angles 1 With the Select tool click the second angle defining atom 2 Shift click the first angle defining atom 3 Shift click the distance defining atom 4 Shift click the atom to position You should now have four atoms selected with the atom to be positioned selected last 5 From the Structure menu point to Set Z Matrix and then choose Position by Bond Angles Manipulating Models 103 Changing the Z matrix For example consider the following structure To p
133. C 2 C 33 distance ChemOffice 2005 Chem3D Compute Properties Compute Properties represents a single point energy computation that reports the total steric energy for the current conformation of a model the active frame if more than one exists NOTE The Steric Energy is computed at the end of an MM2 Energy minimization A comparison of the steric energy of various conformations of a molecule gives you information on the relative stability of those conformations NOTE In cases where parameters are not available because the atom types in your model are not among the MM2 atom types supported Chem3D will attempt an educated guess You can view the guessed parameters by using the Show Used Parameters command after the analysis is completed Compare the steric energies of cis and trans 2 butene To build trans 2 butene and compute properties 1 From the File menu choose New 2 Select the Text Building tool 3 Click in the model window A text box appears 4 Type trans 2 butene and press the Enter key A molecule of trans 2 butene appears in the model window 5 From the MM2 submenu of the Calculations menu choose Compute Properties MM2 and MM3 Computations 161 Compute Properties The Compute Properties dialog box appears Compute Properties a Job Type Dynamics Properties General Properties EPT Steric Energy Summary Steric Energy Detail Summary Parameter Quality Some
134. ChemOffice Technical Support also opens the Cambridgesoft Professional Services page There are a number of links on this page for Troubleshooting Downloads Q amp A the ChemOffice FAQ Contact and so forth Finding Information on ChemFinder com The Find Information on ChemFinder com menu item links your browser to the ChemFinder database record of the compound you have selected ChemFinder is the public access database on the ChemFinder com website It contains physical regulatory and reference data for organic and inorganic compounds To access ChemFindet com 1 In ChemOffice select a structure you want to look up 2 From the Online menu choose Find Information on ChemFinder com The ChemFinder com page opens in your browser with information on the selected structure In ChemFinder com you can search for chemical information by name including trade names CAS number molecular formula or molecular weight CambridgeSoft Accessing the Online ChemDraw User s Guide Follow the links to do substructure queries The following illustration shows part of the page for Benzene TALL NOW Benzene 71 43 2 CAS RN Lookup Formula CH Molecular Weight 70 1134 CAS AN 71 43 2 Helens PRC ss ACK Number 1001488 9 DUALES 90 1 Density 8786 Vapor Density REE TAGE 1 9023 Vapor Pressure Evaporation Rate Water Selubility Flash Point C EPA Code DOT Number Comments srece More information
135. Comment 19 cyclohexanol 2 A Own ND a A ON ChemOffice 2005 Appendix Se 2 2 22 a S O0OoO0OOoocqcqumxm0 1 h 0 O Description FORTRAN Format Ignored by Chem3D O O O O O a a a dsd oana O O O O O aa a na 2 2 y mn 18 11 13 15 17 oO Oo Oo O O O O O aa a na na n mn D O O S OGO GO O O T OG oO gt E e E e a e E e A gt E e E m E o y on o E On On on gt E Oe e E oe oe Origin Atom Second Atom Third Atom Fourth Atom to Last Atom Blank Line Ring Closure Atoms MacroModel MacroModel is produced within the Department of Chemistry at Columbia University New York N Y The MactoModel file format is defined in the 14 14 1X 13 1X F9 5 14 2 1X 13 1X F9 5 14 3 1X 13 1X F9 5 14 2 1X 14 MactoModel Structure Files version 2 0 documentation The following is a sample MacroModel file created using Chem3D The following file describes a model of cyclohexanol 1 396561 0 455032 0 514313 1 302856 0 372467 0 606857 2 068466 1 053284 0 127151 1 222366 0 058121 0 350174 1 055603 0 0 740891 1 587143 0 1 222107 0 49733 0 0 04895 0 103714 0 1 056656 0 627853 0 1 525177 0 4599 0 0 083405 0 277008 0 1 603394 1 96843 0 0 3405 2 451294 0 1 972153 0 925369 0 1 742569 0 306931 0 File Formats 249 File Format Examples 41 41 41 41 41 41 42 2 20002 RARA AA Sd O O O OGOGO D DO O C e on On On E eee
136. D Conversion Example 4 shows cis decalin on the left and trans decalin on the tight as they would be drawn in ChemDraw to be read in by Chem3D Of course you can specify a cis fusion with two H Dots instead of two H Dashes As a general rule the more stereo bonds you include in your model the greater is the probability that Chem3D will make correct choices for chirality and dihedral angles When converting two dimensional structures Chem3D uses standard bond lengths and angles as specified in the current set of parameters If Chem3D tries to translate strained ring systems the ting closures will not be of the correct length or angle Labels Chem3D uses the atom labels in a two dimensional structute to determine the atom types of the atoms Unlabeled atoms are assumed to be carbon Labels are converted into atoms and bonds using the same method as that used to convert the text in a text box into atoms and bonds Therefore labels can contain several atoms or even substructures CambridgeSoft Labels Appendix G File Formats Editing File Format Atom Types Some file formats contain information describing the atom types that the file format understands Typically these atom types are ordered by some set of numbers similar to the atom type numbers used in the Atom Types table If the file format needs to support additional types of atoms you can supply those types by editing the file format atom types Chem3D 9 0 us
137. D atabase Suppliers In no event shall CS M erck and or other Supplier be liable for any indirect special or consequential damages such as but not limited to loss of anticipated profits or other economic loss in connection with or arising out of the use of the software by you or the services provided for in this agreement even if CS Merck and or other Supplier has been advised of the possibility of such damages CS and or M erck s entire liability and your exclusive remedy shall be at CS s discretion a return of any pro rata portion of the subscription fee The failure of either party to assert a right hereunder or to insist upon compliance with any term or condition of this Agreement shall not constitute a waiver of that right or excuse a similar subsequent failure to perform any such term or condition by the other party This Agreement shall be construed according to the laws of the Commonwealth of M assachusetts United States of America SOFTWARE NO it s not okay to copy your colleague s software Software is protected by federal copyright law which says that you can t make such additional copies without the permission of the copyright holder By protecting the investment of computer software O IS IT OK TO COPY MY COLLEAGUE S companies in software development the copyright law serves the cause of promoting broad public availability of new creative and innovative products These companies devote large portions of their e
138. DW interactions in a molecule such as hydrogen bonding to provide better correspondence with experimental data in calculating the MM2 force field For example consider the VDW interaction between an Alkane carbon Atom Type 1 and a hydrogen Atom Type 5 Normally the VDW energy is based on the sum of the VDW radii for these atoms found for each atom in the Atom Types table 1 900A for Atom type number 1 1 400A for Atom type number 2 3 4004 However better correspondence between the computed VDW energy and experimental data is found by substituting this sum with the value found in the VDW Interactions table for this specific atom type pair Atom Types 1 5 3 3404 288 Parameter Tables Similarly an Eps parameter is substituted for the geometric mean of the Eps parameters for a pair of atoms if their atom types appear in the VDW Interactions table Record Order When sorted by Atom Type the order of the records in VDW Interactions table window is as follows Records are sorted by the first atom type number in the Atom Type field For example the record for Atom Type 1 36 is before the record for atom type 2 21 For records where the first atom type number is the same the records are sorted by the second atom type number in the Atom Type field For example the record for atom type 2 21 is before the record for atom type 2 23 CambridgeSoft VDW Interactions Appendix I MM2 Overview This appendix co
139. Default Model Type preview Reset Set As Default f OK Cancel 3 Set the new options Displaying Models 55 Structure Displays To change the structural display type of a model temporarily 1 Click the arrow on the Model Display tool and select the display type Model Types The following table describes the Chem3D model types Model Type Wire Frame Sticks 56 Displaying Models Description Wire Frame models are the most simple model type Bonds are displayed as pixel wide lines Atoms are not displayed explicitly but each half of a bond is colored to represent the element color for the atom at that end Wire Frame models are well suited for extremely large models such as proteins Stick models are similar to Wire Frame however the bonds are slightly thicker As this model type is also fairly fast it is another good choice for visualizing very large models such as proteins Model Type Description Ball and Stick Space Filling Ball and Stick models show bonds drawn as thick lines and atoms are drawn as filled spheres The atom spheres are filled with color that corresponds to the element or position of the atom Cylindrical Bond models are similar to Ball and Stick models except that all bond types are drawn as cylinders Space Filling models are more complex to draw and slowest to display Atoms are scaled to 100 of the van der Waals
140. Display tab of the Settings dialog box e Model Axes Displays or hides the Model axes e View Axes Displays or hides the view axes NOTE When both axes overlap and the Model axes are displayed the View axes are not visible e Background Color Displays the Background color select toolbar Dark backgrounds are best for viewing protein ribbon or cartoon displays Selecting red blue or Chromatek 3D display will automatically override the background color to display the optimal black background Background colors are not used when printing except for Ribbon displays When saving a model as a GIF file the background will be transparent if you have selected that option for Image Export in the Preferences dialog box e Chem3D Basics Color By Selects the model coloring scheme See Coloring Displays on page 58 for more information Toolbars Click the name of a toolbar to select it for display Click again to deselect You can attach a toolbar to any side of the GUI by dragging it to where you want it attached If you are using a floating toolbar you can change its shape by dragging any of its edges Standard toolbar Contains standard file edit and print tools The commands are duplicated on the File and Edit menus Building toolbar Contains the Select Translate Rotate and Zoom tools in addition to the model building tools bonds text building tool and eraser These tools are not duplicate
141. Draw Excel ChemN MR N ame Struct AutoN om ChemFinder W ord to ChemDraw Pro N ame Struct AutoN om creates structures from names amp vice versa ChemN MR predicts H C NMR line spectra with peak to structure correlation Polymer notation based on IUPAC standards e ChemDraw Excel brings chemistry to Excel ChemDraw Pro Premier Drawing amp Information Query Query databases precisely by specifying atom bond properties reaction centers substituent counts R groups substructure e Read ISIS files with Macintosh W indows cross platform compatibility e Structure Clean Up improves poor drawings Display spectra from SPC and JCAMP files e Chemical intelligence includes valence bonding atom numbering Rightbutton menus speed access to features ChemDraw Std Publication Quality Structure Drawing e Draw and print structures amp reactions in color and save as PostScript EPS GIF SMILES amp more e Collections of pre defined structure templates e Large choice of bonds arrows brackets orbitals reaction symbols LabA rt e Style templates for most chemical journals e Compatible with Chem3D ChemFinder Cheminfo E N otebook Microsoft O ffice ChemDraw Plugin Advanced WWW Structure Client Embed live ChemDraw documents in WWW pages e Works with Netscape Internet Explorer e Included with ChemDraw Ultra Pro SYSTEMS LANGUAGES Windows amp Macintosh English Japanese French G
142. Ford charges utilized in the previous example Mulliken charges give a quick survey of charge distribution in a molecule NOTE For more information see the MOPAC online manual page 41 and 121 The following table contains the keywords automatically sent to MOPAC Keyword Description MULLIK Automatically sent to MOPAC to generate the Mulliken Population Analysis GEO OK Automatically sent to MOPAC to override checking of the Z matrix MMOK Automatically sent to MOPAC to specify Molecular Mechanics correction for amide bonds Use the additional keyword NOMM to turn this keyword off Charges From an Electrostatic Potential The charges derived from an electrostatic potential computation give useful information about chemical reactivity The electrostatic potential is computed by creating an electrostatic potential grid Chem3D reports the point charges derived from such a grid In general these atomic point charges give a better indication of likely sites of attack when compated to atomic charges derived from the Coulson density CambridgeSoft Computing Properties matrix Charges or Mulliken population analysis Mulliken Charges The uses for electrostatic potential derived charges are generally the same as for atomic charges For examples see Charges on page 186 There are two properties available for calculating atomic point charges Wang Ford Charges and Electrostatic Potential Wang Ford C
143. If you want to Then Select remove the grouping Delete Group but leave the model intact 114 Inspecting Models If you want to Then Select delete the group from Delete Group and the model Contents Using the Display Mode One means of bringing out a particular part of a model is by changing the display mode The usual limitations apply see Model Types on page 56 The submenu will only display available modes The following illustration shows the effect of changing the HEM155 group of PDB 101M from Wireftame the default to Space Filling PHE 138 ARG 139 LYS 140 E ASP 141 ILE 142 E ALA 143 E ALA 144 LYS 145 TYR 146 LYS 147 GLU 148 LEU 149 GLY 150 TYR 151 M 112761 Coloring Groups Another means of visualization is by assigning different colors to groups Changing a group color in the Model Explorer overrides the standard color settings in the Elements table and the Substructutes table To change a group color 1 Select a group or groups 2 Choose Select Color on the Right click menu The Color Dialog box appears 3 Choose a color and click OK CambridgeSoft Working With the Model Explorer The Apply Group Color command is automatically selected To revert to the default color 1 Select a group ot groups 2 Right click point to Apply Group Color on the Context Sensitive menu and select Inherit Group Color The default group
144. Method 1 From the File menu choose New Model 2 Select the Text Building tool and click in the model window A text box appears 3 Type Epinephrine and press the Enter key A molecule of Epinephrine appears 4 Click in the model window below the Epinephrine molecule A text box appears 5 Type Methamphetamine and press the Enter key A molecule of Methamphetamine appears beneath the Epinephrine molecule 6 From the Model Display submenu of the View menu deselect Show Hs and Lps The hydrogen atoms and lone pairs in the molecule are hidden The two molecules should appear as shown in the following illustration You may need to move or rotate the models to display them as shown TIP To move only one of the models select an atom in it before rotating 110 Inspecting Models 7 From the Model Display submenu of the View menu select Show Atom Labels and Show Serial Numbers The atom labels and serial numbers appear for all the visible atoms To perform an overlay you must first identify atom pairs by selecting an atom in each fragment and then display the atom pairs in the Measurements table Atom Pair an atom in one fragment which has a distance specified to an atom in a second fragment 1 Select C 9 in the Epinephrine molecule 2 Shift click C 27 in the Methamphetamine molecule 3 From the Structure menu point to Measurements and choose Set Distance The Measurements table appe
145. Model Settings dialog box then the partial charges will appear as part of the pop up information when you point to an atom Displaying Molecular Surfaces To display a surface 1 Decide what surface type to display 2 Perform a suitable calculation using Extended Huckel CS MOPAC or Gaussian 03 Include the Molecular Surfaces property calculation whenever it is available NOTE W Ultra CS MOPAC and Gaussian 03 surfaces calculations are only available in Chem3D Ultra Different calculation types can provide different results If you have performed mote than one calculation on a model for example both an Extended Hiickel and an AM1 calculation you must choose which calculation to use when generating the surface 3 From the Calculations menu point to Choose Result and select one of your calculations 64 Displaying Models 4 From the Surfaces menu point to Choose Surface and select one of the surface types NOTE The Choose Surface commands are toggle switches click once to display click again to turn off the display You can display more than one surface at a time When a surface is displayed its icon is highlighted with a light blue background Solvent 4 le e Connolly ar Total Charge Density Displayed surfaces E Molecular Orbital 5 Adjust the display using the surface display tools TIP If you are making a lot of adjustments to the display activate the Surfaces toolb
146. NORM property is not the same as the MOPAC keyword GNORM For more information see the MOPAC manual pages 31 and 180 MOPAC Computations 185 Computing Properties Dipole Moment The dipole moment is the first derivative of the energy with respect to an applied electric field It measures the asymmetry in the molecular charge distribution and is reported as a vector in three dimensions The dipole value will differ when you choose Mulliken Charges Wang Ford Charges or Electrostatic Potential as a different density matrix is used in each computation NOTE For more information see the MOPAC manual page 119 The following table contains the keywords automatically sent to MOPAC Keyword Description GEO OK Automatically sent to MOPAC to override checking of the Z matrix MMOK Automatically sent to MOPAC to specify Molecular Mechanics correction for amide bonds Use the additional keyword NOMM to turn this keyword off Charges The property Charges determines the atomic charges using a vatiety of techniques discussed in the following sections In this example the charges are the electrostatic potential derived charges from Wang Ford because Wang Ford charges give useful information about chemical stability reactivity 186 MOPAC Computations Mulliken Charges This property provides a set of charges on an atom basis derived by reworking the density mattix from the SCF calculation Unlike the Wang
147. O Partial Charges Show solid spheres by default Size 25 J YDW Radius O Partial Charges To change the display of solid spheres in a model e From the Model Display submenu of the View menu select or deselect Show Atom Dots Setting Solid Sphere Size The maximum radius of the sphere that represents an atom can be based on the Van der Waals VDW Radius or Partial Charge To specify which property to use select the radio button below the slider The VDW Radius is specified using the atom type of the atom The Partial Charge is the result of a calculation Extended Htickel MOPAC or Gaussian If you have not performed a calculation the partial charge for each atom is shown as 0 and the model will display as a Stick model If you have performed more than one calculation you can specify the calculation to use from the Choose Result submenu on the Calculations menu Displaying Models 57 Structure Displays When sizing by partial charge the absolute value of the charge is used An atom with a partial charge of 0 500 will have the same radius as an atom with a partial charge of 0 500 Solid Spheres Size The value of the Size slider on the Atom Display tab represents a percentage of the Covalent radius specified for each atom in the Elements Table This percentage ranges from 0 small to 100 large Thus when the Atom Size is 100 the atoms ate scaled to their maximum r
148. Pro 8 Line 8 blank in the above example might contain internal SYBYL status bits associated with the molecule 9 Line 9 blank in the above example might contain comments associated with the molecule NOTE Four asterisks appear in line 8 when there are no status bits associated with the molecule but there is a comment in Line 9 10 Line 10 lt TRIPOS gt ATOM is a Record Type Indicator RTI which begins a section containing information about each of the atoms associated with the molecule 11 Lines 11 29 each contain 6 fields describing information about an atom the first field is the atom id the second field is the atom name the third field is the X coordinate the fourth field is the Y coordinate the fifth field is the Z coordinate and the sixth field is the atom type NOTE Atom types are user definable See Editing File Format Atom Types on page 241 for instructions on modifying or creating an atom type File Formats 269 Protein Data Bank Files 12 Line 30 A lt TRIPOS gt BOND is a Record Type Indicator RTI which begins a section containing information about the bonds associated with the molecule 13 Lines 31 49 each contain 4 fields describing information about a bond the first field is the bond id the second field is the from atom id the third field is the to atom id and the fourth field is the bond type FORTRAN Formats The FORTRAN format for each record of the
149. S NOTE You cannot position an atom in terms of a later positioned atom The following is a sample of an Internal coordinates output file for cyclohexanol which was created from within Chem3D 111 7729 109 7132 3 55 6959 0 111 703 2 55 3112 0 110 7535 1 57 0318 0 107 6989 3 172 6532 0 109 39 4 109 39 1 109 41 3 109 41 1 109 41 3 109 41 1 109 41 6 109 41 1 109 41 6 109 41 1 109 41 5 109 41 1 109 41 5 109 41 1 109 41 6 109 41 1 109 41 6 109 41 1 109 41 5 109 41 1 e 247 File Formats File Format Examples 5 6 1 11606 3 21 7 0 942 1 Bonds Bonds ate indicated in Internal coordinates files in two ways First a bond is automatically created between each atom except the Origin atom and its distance defining atom Second if there ate any rings in the model ring closing bonds are listed at the end of the file If there are ring closing bonds in the model a blank line is included after the last atom definition For each ring closure the serial numbers of the two atoms which comprise the ring closing bond are listed on one line The serial number of the first atom is 1 the second is 2 etc In the prior Internal coordinates output example of cyclohexanol the numbers 5 and 6 ate on a line at the end of the file and therefore the ring closure is between the fifth atom and the sixth atom Ifa bond listed at the end of an Internal coordinates format file already exists because one of the atoms on t
150. S 0 Q R A S o 3 me to y A TH _ ANARD T Cambridgetott E Moteback Y 0 CambridgeSoft Life Science Enterprise Solutions L sungen fiir biowissenschaftliche Unternehmen Solutions d entreprise Life Science BAT le Ae IT NAZI RA CS LU oe eeeeeeere CambridgeSoft Life Science Enterprise Solutions L sungen fiir biowissenschaftliche Unternehmen Solutions d entreprise Life Science ATILIR III XA YU 1 User s Guide Revision 9 0 1 12 22 04 CS Chem3D 9 0 for Windows Chem3D is a stand alone application within ChemoOffice an integrated suite including ChemDraw for Chemical Structure Drawing ChemFinder for searching and information integration BioAssay for biological data retrieval and visualization Inventory for managing and searching reagents E Notebook for electronic journal and information and ChemInfo for chemical and reference databases Chem3D Molecular Modeling and Analysis Standard License Information ChemOffice ChemD raw Chem3D ChemFinder and Cheminfo programs all resources in the ChemOffice ChemD raw Chem3D ChemFinder and Cheminfo application files and this manual are Copyright 1986 2004 by CambridgeSoft Corporation CS with all rights reserved worldwide MOPAC 2000 and MOPAC 2002 are Copyright O 1993 2004 by Fujitsu Limited with all rights reserved Information in this document is subject to change without notice and does not represent a commitment o
151. Select the atom in the Explorer ae The atom is selected in the model Any Preview previously selected atoms or bonds are Reset Set As Defaut ok cancel deselected To select an atom or bond in the display window Selecting Single Atoms and 1 Click the Select tool Bonds 2 Click the atom or bond Any previously selected atoms and bonds are deselected When you click a bond both atoms on the bond are selected You can select atoms and bonds in the model window or by using the Model Explorer If the Model Explorer is not active open it from the View menu ChemOffice 2005 Chem3D Manipulating Models 91 Selecting Selecting Multiple Atoms and Bonds To select multiple individual atoms and bonds do one of the following e Shift click atoms or bonds in the display window to select them e Ctrl click atoms in the Model Explorer to select them e Shift click atoms in the Model Explorer to select all atoms between and including the two selected NOTE Selecting two adjacent atoms will also select the bond between them To quickly select all atoms and bonds in a model e From the Edit menu choose Select All NOTE If the last action performed was typing in a text box all of its text is selected instead of the atoms in the model Deselecting Atoms and Bonds When you deselect an atom you deselect all adjacent bonds When you deselect a bond you deselect the atoms on either en
152. Soft TTT Chemo ffice ChemDraw Chem3D ChemFinder Cheminfo are trademarks of CambridgeSoft 2002 5 All other trademarks are the property of their respective holders All specifications subject to change without notice www cam b T1 dg eso ft CcCOm RESEARCH amp BioSAR Browser Biological and C hemical M eta D ata C atalog BioSAR Browser BioSAR Browser a strategic must for any discovery organization interested in serious data mining is a data dic tionary driven structure activity analysis program U sers may choose among assays registered in the dictionary or search for assays of interest Providing Catalog Capabilities The power of BioSAR Browse lies in the researcher s freedom from dependence on IT support Once an assay is registered into the data dictionary it is automatically included in the powerful analysis framework By reduc ing the time between question and answer BioSAR Browse gives researchers the freedom to explore new ideas the bottom line for discovery information systems Systems that provide answers after questions have become irrelevant are of no use BioSAR Browse avoids this by placing application development in the researcher s control Forms amp Tables in a Unified Interface While most SAR tools provide only a table based interface BioSAR Browse provides a forms based interface in addition to a tabular view Researchers have demonstrated that both form and tabular views are essential Forms prov
153. Soft believes that successful technology utilization begins with the assessment and decision making process O ur experts can assist clients with Readiness Assessment Identify the scope requirements and deliverables for your project Assure critical IP is incorporated Allow end users to capitalize on existing scientific and technology resources Strategic Planning Conduct formal analysis of scientific technical operational and process environments to determine the necessary approach to customization and deployment Prototypes and Proof of Concept Prototypes allow you to test the technical feasibility of solutions This activity can provide a baseline for the future roll out of the solution and can also gather user feedback so requirements can be refined DECISION CUSTOM DEPLOYMENT amp MANAGE MAKING DEVELOPMENT TRAINING THE PROCESS Readiness Custom Application Assessment Application Development Development Strategic Beta amp Plannin ama cae Integration Prototype or Proof of Concept Controlled Installation amp Pilots Business Case Customization Development of Applications SERVICES Busnes Cas D evdopment Business cases help define a clear and purposeful solution based on well defined and documented business needs H aving a business case helps to justify good projects stop bad projects before they are started and provides the basis for ongoing measurements after project completion to make sure t
154. Sphere Isodensity as appropriate NOTE No value entry boxes appear for gas phase computations 3 Type Gaussian keywords in the Additional Keywords text box for access to less common ot more advanced functionality Gaussian Computations 201 Minimize Energy In the Results In text box specify the path to the directory where results are stored by typing or browsing Save a customized job to appear as a Gaussian submenu item as follows 1 In the Menu ltem Name text box type the name of the job description 2 Click Save As The Save dialog box appears 3 Browse to the Gaussian Job folder in the Chem3D CS3D Extensions folder NOTE The file must be saved in the Gaussian Job folder in order for it to appear in the menu 4 Select the file type to save For more information see Job Description File Formats on page 202 5 Click Save Job Description File Formats Job description files are like Preferences files they store the settings of the dialog box You may save the file as either a jdf or a jdt type You modify and save jdf files more easily than jdt files jdt Format The jdt format is a template format intended to serve as a foundation from which other job types may be derived The Minimize Energy and Compute Properties job types supplied with Chem3D are examples of these To discourage modification of these files the Save button is deactivated in the dialog box of a template
155. TE Rotation bars are only available when you are using the Trackball tool 2 Drag on one of the bars to rotate the model on that axis One of the bats is labeled Rotate About Bond You won t be able to select that one You ll cover rotating around bonds later TIP Once you start dragging you dont have to stay within the rotation bars boundaries Your model will only rotate around the chosen axis no matter where you drag your mouse ChemOffice 2005 Chem3D 3 Release the mouse button when the model is orientated approximately like this Examine the atoms and bonds in the model using the Select tool 1 Click the Select tool k 2 Move the pointer over the far left carbon NOTE Depending on how much you rotated the model the far left carbon might be C 2 An information box appears next to the atom you ate pointing at The first line contains the atom label In this case you are pointing to C 1 The second line contains the name of the atom type C Alkane Chem3D Tutorials 33 Tutorial 2 Building Models with the Bond Tools 3 Move the pointer over the C C bond to display its bond length and bond order C 1 C Length 1 5235 Order 1 000 To display information about angles select several atoms 1 Click C 1 then Shift click C 2 and H 7 2 Point at any of the selected atoms or bonds The angle for the selection appears To display information about contigu
156. To Atom in column 3 The last column in the bond records is the bond type Finally the last line in the file is the Number of Features CambridgeSoft Protein Data Bank Files record which contains the number of feature records in the molecule Chem3D does not use this information FORTRAN Formats The FORTRAN format for each record of the SYBYL MOL File format is as follows Line Description FORTRAN Format Number of Atoms File 14 1X MOL 20A2 11 Name X 4 Atom records 214 3F9 4 2A2 Number of Bonds record 14 1X MOL Bond records 314 9X 14 Line 1 Name CYCLOHEXANOL Line 2 Line 3 lt TRIPOS gt MOLECULE Line 4 CYCLOHEXANOL Line 5 1919000 Line 6 SMALL Line 7 NO_CHARGES Line 8 Line 9 Line 10 lt TRIPOS gt ATOM Line 11 1 C Line12 2 C Line 13 3 C Line14 4 C Line 15 5 C ChemOffice 2005 Appendix Number of Features record 14 1X MOL SYBYL MOL2 File The SYBYL MOL2 file format SYBYL2 is defined in Chapter 3 File Formats pages 3033 3050 of the 1991 SYBYL Programming Manual The following is a sample SYBYL MOL2 file created using Chem3D Pro This file describes a model of cyclohexanol the line numbers ate added for reference only 1 SYBYL is a product of TRIPOS Associ ates Inc a subsidiary of Evans amp Sutherland 1 349 0 195 1 032 C 3 0 407 0 896 1 563 C 3 0 562 1 378 0 473 C 3 1 351 0 205 0 128 C 3 0 42 0 9 0 652 C 3 File Formats 267 Protein Data
157. To begin the docking computation To have a reasonable dock you must specify at least four atom pairs Repeat steps 1 through 5 for matching atom pairs throughout the fragments For example if you choose one pair from each group your list might look like the following Atoms Actual Optimal C 1 C 93 21 2034 5 0000 C 98 C 6 21 1840 5 0000 C 104 C 12 21 2863 5 0000 C 108 C 16 21 1957 5 0000 C 22 C 114 20 6472 5 0000 C 28 C 120 20 7001 5 0000 ChemOffice 2005 Chem3D 1 From the Structure menu choose Dock The Dock dialog box appears Minimum RMS Error Minimum AMS Gradient Display Each Iteration C Record Each Iteration 2 Type 0 100 for the Minimum RMS Error value and 0 010 for the Minimum RMS Gradient The docking computation stops when the RMS Error or the RMS Gradient becomes less than the Minimum RMS Error and Minimum RMS Gradient value Click Display Every Iteration This allow you to see how much the fragments have moved after each iteration of the docking computation Chem3D Tutorials 47 Tutorial 7 Docking Models To save the iterations as a movie click Record Each Iteration iteration values Note that while the docking computation proceeds one molecule remains stationary and the second molecule moves To stop the docking computation before it reaches it s preset RMS values click Stop Calculation y on the Calculation toolbar Both docking and recording a
158. UMO energjes The out file contains the following information by default e Starting atomic coordinates e Starting Z matrix e Molecular orbital energies eigenvalues e Ending atomic coordinates The workings of many of the calculations can also be printed in the out file by specifying the appropriate keywords before running the calculation For example specifying MECI as an additional keyword will show the derivation of microstates used in an RHF 1 2 electron approximation calculation For more information see Using Keywords on page 170 NOTE Close the out file while performing MOPAC computations or the MOPAC application stops functioning Creating an Input File A MOPAC input file MOP is associated with a model and its dialog box settings ChemOffice 2005 Chem3D To create a MOPAC input file 1 From the MOPAC Interface submenu of the Calculations menu choose Create Input File Create Input File Job Type Theory Properties General Properties Gradient Norm Dipole Charges Cosmo Solvation in Water Electrostatic Potential Molecular Surfaces Spin Density Hyperfine Coupling Constants Y Charges Mulliken z Summary Save As Cancel 2 Select the appropriate settings and click Create Running Input Files Chem3D allows you to run previously created MOPAC input files To run an input file 1 From the MOPAC Interface submenu of the Calculations menu
159. VDW radii specified in the Atom Types table NOTE The VDW radii are typically set so that overlap between non bonded atoms in space filling models indicates a significant approximately 0 5 kcal mole repulsive interaction CambridgeSoft Structure Displays Model Type Description Ribbons models show large protein molecules in a form that highlights secondary and tertiary structure Ribbon models can be colored by Group to help identify the amino acid constituents Your model must have a protein backbone in order to display ribbons Ribbons Cartoon models like Ribbon models show large protein molecules in a form that highlights secondary and tertiary Cartoons structure The following caveats apply to the Ribbon and Cartoon model display types e They do not provide pop up information e They should be printed as bitmaps Displaying Solid Spheres In Ball and Stick Cylindrical Bond and Space Filling models you can display the solid spheres representing atoms and control their size in individual atoms or all atoms ChemOffice 2005 Chem3D To display solid spheres by default on all atoms 1 From the File menu select Model Settings 2 Select the Atom Display tab 3 In the Solid Spheres section click the Show By Default checkbox Atom Model Settings Display tab Colors amp Fonts Movie Model Display odel Building Atom Spheres Size By VDW Radius
160. View menu choose Model Explorer CambridgeSoft Working With the Model Explorer The Model Explorer window appears along the left side of the model Model Explorer m lx H F Fragment 1 F Fragment 2 H Chain A Chain B ChainC E o DPN 1 Se PRO 2 N 3389 CA 3390 e c 3391 O 3392 O CB 3393 CG 3394 CD 3395 Ho s ARGS He CH2 4 H 8 Chain A H20 Solvent NCC Backbone To view or change a property in a model 1 Select the object fragment group or atom you wish to change TIP To select multiple objects use Shift click if they are contiguous or Ctri click if they are not 2 Right click select the appropriate submenu and choose a command Cut Copy Paste Replace with Text Tool Select All Children Select Color Show Group Apply Group Color gt Hide Group Display Mode gt Atom Serial Numbers gt Atom Symbols Atom Dots gt Reset Children to Default ChemOffice 2005 Chem3D When you change an object property the object icon changes to green When you hide an object the icon changes to red Objects with default properties have a blue icon Model Explorer F Fragment 1 a F Fragment 2 2 Chain A D H HH gt 2 D 5 Creating Groups Some models PDB proteins for example have group information incorporated in the file For other models you will need to define the groups To do this in the Model Explor
161. W _ www cambridgesoftcom TEL 1 800 315 7300 INTL 1 617 588 9300 FAX 1 617 588 9390 e MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge MA 02140 USA CambridgeSoft TTT Chemo ffice ChemDraw Chem3D ChemFinder Cheminfo are trademarks of CambridgeSoft 2002 5 All other trademarks are the property of their respective holders All specifications subject to change without notice www cam b T1 dg eso ft CcCOm KNOWLEDGE Document Manager D esktop to Enterprise Document Searching Document Manager Everyone produces reports electronically but searching information located in these reports has always been difficult Thousands of M icrosoft Word Excel PowerPoint and other documents reside on file servers or indi vidual computers with no way to globally search them for information Certainly no easy way exists to search for the chemistry contained in these documents Document M anager solves this problem and requires no change in how you write and distribute reports Easy to Use Document M anager manages a repository of new documents T hese can be M icrosoft Word Excel PowerPoint or many other document types W hen a new document is added D ocument M anager automatically builds a free text index of the document and automatically extracts the chemical information into a chemically aware substructure searchable database Chemical information can be both ChemD raw and ISI S D raw Finding infor mation in report
162. a Hamiltonian 148 MINDO 3 Applicability and Limitations 148 MNDO Applicability and Limitations 149 AM1 Applicability and Limitations 149 PM3 Applicability and Limitations 150 MNDO d Applicability and Limitations 150 Chapter 9 MM2 and MM3 Computations Minimize Energy 151 Running a Minimization 153 Queuing Minimizations 153 Minimizing Ethane oooooooooomo o 154 Comparing Two Stable Conformations of Cyclohexane t 14 26 ea8 decree spaay estes 156 Locating the Global Minimum 157 Molecular Dynamics 158 Performing a Molecular Dynamics Computation 158 Dynamics Settings 000 0000 0 158 Job Type Settings 00 cc eee eee ens 159 Computing the Molecular Dynamics Trajectory for a Short Segment of Polytetrafluoroethylene PTFE 160 Compute Properties 161 Showing Used Parameters 163 Repeating an MM2 Computation 163 Using jdf Files 163 Chapter 10 MOPAC Computations MOPAC Semi empirical Methods 166 Extended Hiickel Method 166 RE Bes traits aaa ee ee ae e ean alee 166 DIR e Rimes then hae eee Ba 166 Configuration Interaction 167 Approximate Hamiltonians in MOPAC 167 Choosing a HamiltoniaN oo o oo 167 MINDO 3 Applicability and Limitations 168 MNDO Applicabil
163. a conformation run a force operation using the keyword FORCE The zero point energy is found at the bottom of the out file The heat of formation in MOPAC is the gas phase heat of formation at 298K of one mole of a compound from its elements in their standard state ChemOffice 2005 Chem3D The heat of formation is composed of the following terms Where e Ega is calculated from the SCF calculation elec e Enuc is the core core repulsion based on the nuclei in the molecule Ej and E potential function for the elements within your ate parameters supplied by the atoms molecule NOTE You can use the keyword ENPART and open the out file at the end of a run to view the energy components making up the heat of formation and SCF calculations See the MOPAC online manual reference page 137 for more information Gradient Norm This is the value of the scalar of the vector of derivatives with respect to the geometric variables flagged for optimization This property called GNORM in the MOPAC manual is automatically selected for a minimization which calculates the GNORM and compares it to the selected minimum gradient When the selected minimum is reached the minimization terminates Selecting this property for a Compute Properties operation where a minimization is not being performed will give you an idea of how close to optimum geometry the model is for the particular calculation NOTE The G
164. aa 280 Becton iaa Mare de Obed eee eens 280 TOnIZAHON ramas cated idenana is 280 Repulsiotiins gscscoanvetseney coiase seni eee 280 Pi Bonds iii oia ia 281 A tipeeds Bane d 281 Aten cita nta Goce see sila te dct seta tah 281 denota good tea es age adele 281 Record Order nanu see wie dis Hees aac 281 Electronegativity Adjustments 281 MM2 Constants 000 282 Cubic and Quartic Stretch Constants 282 CambridgeSoft Type 2 CHR Bending Force Parameters for CCC ANDES tall 282 Stretch Bend Parameters o o ooo ooo 283 Sextic Bending Constant 283 Dielectric Constants o ooooooommomo o 283 Electrostatic and van der Waals Cutoff Parameters shee raid s 283 MM2 Atom Types 283 Atom type number cis cca tas 283 Ruca usabessaty sanan data 284 EPS 284 Reduction e bate 284 Atomie Weight ali ida a 284 L ne Patt s 3285 25 sun Dt ts 284 Torsional Parameters 284 Dihedral Ipsos ado 285 A te gaeat aar i a A Ee tae 285 Ni ia a hr ieee 285 Mi A E a Reh cutee sate th ech cal a 286 Record Order pasear and Sued dk ees 287 Out of Plane Bending 287 Bond Type iy erer ahs as atte eas 287 ChemOffice 2005 Chem3D Force Constant 0 6 e806 6 o eh Ween 287 Record Ordet neeaae tte tr idea 287 VDW Interactions 288 Record Order iaa asia eas 288 MM2 MM2 Parametets 289 Other Parametet
165. ability properties biological activity organic reactions material safety data sheets and patent or development status e Developed by CambridgeSoft in partnership with the leading chemical database publishers Reactions Organic Syntheses is the electronic version of the annual and collective volumes of trusted peer reviewed syn thesis procedures published since 1921 by O rganic Syntheses Current Chemical Reactions CCR from ISI is both a current awareness and a data mining application used to design chemical syntheses Renowned for its quality CCR contains information from over 300 000 articles reporting the complete synthesis of molecules U pdated daily CC R isan excellent way to stay on top of recent developments ChemReact and ChemSynth from InfoChem are carefully selected from a database of over 25 million reac tions through an automated process of reaction classification With over 380 000 reaction types C hemReact is for expert synthetic chemists designing novel syntheses Entries in C hemSynth are further refined to those with over 50 yield and at least two literature references ChemRXN isa refined selection of over 29 000 fully atom mapped reactions Including carefully selected reactions from InfoC hem s C hemSelect database and 1SI s ChemPrep database ChemRXN isaterrific combination of utility Patents World Drug Alerts W DA from D erwent is a current awareness application providing information on patents new biolog
166. able can display internal measurements between atoms in your model in various ways To display internal measurements 1 From the View menu click Measurement Table A blank table appears in the Tables window 2 From the Structure menu point to Measurements and select a measurement to display Set Bond Angle Measurement Bond Lengths Bond Angles Dihedral Angles Close Contacts The measurement values appear in the table CambridgeSoft Measurement Table You can display several measurements sequentially in the table The following table shows the bond lengths and angles for Ethene Measurement ax Optimal H c 2 1 1000 11000 G H 14000 11000 bond H 3 C 1 11000 1 1000 lengths Cyc 13370 13370 C 1 H 4 1 1000 1 1000 H 5 C 2 H 6 118 9990 119 0000 H 5 C 2 C 1 120 4999 120 5000 bond J H B C 2 C 1 120 4987 120 5000 anges H 3 C 1 C 2 120 4999 120 5000 H 3 C 1 H 4 118 9990 119 0000 C 2 C 1 H 4 120 4987 120 5000 Editing Measurements If you select a measurement in the Measurements table the corresponding atoms are selected in the model window If you select atoms in your model any corresponding measurements are selected To change the value of a measurement 1 Select the text in the Actual column 2 Type a new measurement value in the selected cell 3 Press the Enter key The model reflects the new measurement When atoms are deleted any measurements that refer
167. ached a local minimum on the potential energy surface and the minimization terminates The default value of 0 100 is a reasonable compromise between accuracy and speed Reducing the value means that the calculation continues longer as it tries to get even closet to a minimum Increasing the value shortens the calculation but leaves you farther from a minimum Increase the value if you want a better optimization of a conformation that you know is not a minimum but you want to isolate for computing comparative data watch the minimization Select Display Every Iteration process live at each iteration in the calculation NOTE Displaying or recording each iteration adds significantly to the time required to minimize the structure 152 MM2 and MM3 Computations CambridgeSoft Minimize Energy If you want fo Then store each iteration as a frame in a movie for replay later view the value of each measurement in the Output window restrict movement of a selected part of a model during the minimization NOTE If you are planning to make changes to any of the MM2 constants such as cutoff values or other parameters used in the MM2 force field please make a backup copy of the parameter tables before making any changes This will assure that you can get back the values that are shipped with Chem3D in case you need them NOTE Chem3D guesses parameters if you try to minimize a structure containing atom type
168. ack a particular Copy Measurements to measurement Output 4 Click Run A new model window is created and the initial model appears The Gaussian job runs and the results will appeat All properties requested for the job appear in the out file Only iteration messages appear for Gaussian Input File jobs Gaussian Computations 203 Running a Gaussian Input File Repeating a Gaussian Job After you perform a Gaussian calculation you can repeat the job as follows 1 From the Gaussian submenu choose Repeat name of computation The appropriate dialog box appears 2 Change parameters if desired and click Run The computation proceeds Running a Gaussian Job Chem3D enables you to select a previously created Gaussian job description file jdf The jdf file can be thought of as a set of Settings that apply to a particular dialog box 204 Gaussian Computations You can create a jdf file from the dialog box of any of the Gaussian calculations Minimize Energy Optimize to Transition State by clicking Save As after all Settings for the calculation have been set For more information about jdf files see Job Description File Formats on page 126 To run a Gaussian job 1 From the Gaussian submenu choose Run Gaussian Job The Open dialog box appears 2 Select the file to run The dialog box corresponding to the type of job Minimize Energy Compute Properties and so on saved within the file appea
169. actually the second lowest state the root 2 for a given spin system Doublet Quartet Sextet To request the first excited state use the following sets of keywords First excited doublet ROOT 2 DOUBLET C l n where n 2 is the simplest case ChemOffice 2005 Chem3D First excited quartet ROOT 2 QUARTET C 1 n where n 4 is the simplest case First excited sextet ROOT 2 SEXTET C l n where n 5 is the simplest case Second Excited State The second excited state is actually the third lowest state the root 3 fora given system Singlet Triplet Quintet To request the second excited state use the following set of keywords Second excited doublet ROOT 3 DOUBLET C 1 n where n 3 is the simplest case Second excited quartet ROOT 3 QUARTET C l n where n 4 is the simplest case Second excited sextet ROOT 3 SEXTET C l n where n 5 is the simplest case NOTE Ifyou get an error indicating the active space is not spanned use C L gt n for the simplest case to increase the number of orbitals available in the active space To see the states used in a CI calculation type MECI as an additional keyword The information is printed at the bottom of the out file Excited State UHF Only the ground state of a given multiplicity can be calculated using UHF Sparkles Sparkles are used to represent pute ionic charges They are roughly equivalent to the following chemical entities Chemical Equivalent to
170. adii The value of this setting affects Ball and Stick and Cylindrical Bond models Displaying Dot Surfaces You can add dot surfaces to any of the model display types like the stick model shown below VN ad The dot surface is based on VDW radius or Partial Chatges as set in the Atom Display table of the Model Settings dialog box To display dot surfaces by default on all atoms 1 In the Chem 3D Model Settings dialog box click the Atom Display tab 2 In the Dot Surfaces atea click the Show By Default checkbox All atoms currently in the model window display the selected option 58 Displaying Models You can vary the number of dots displayed in a surface by using the density slider This is useful when dot surfaces are applied to a very small or very large models To change the display of dot surfaces in a model e From the Model Display submenu of the View menu select or deselect Show Atom Dots Coloring Displays You can change the default for the way colors are used to display your model in the Model Display tab of the Model Settings control panel To make a temporary change use the Color By command on the Model Display submenu of the View menu The choices are e Monochrome e Partial Charge e Chain e Element e Group e Depth Two of the choices Monochrome and Chain are only available for proteins displayed in the Ribbon or Cartoon mode Coloring by Element Color by element is the usua
171. ailable for all molecules e Some atom arrangements are not parameterized for the fragmentation methods used to calculate the properties Because of these limitations the property prediction fails for some molecules Error Messages If ChemProp Pro fails one of the following error messages appeats Error Message Cause Unparametrized A fragment in the molecule fragment is untecognized so no parameters exist for the property calculation Out of memory There is insufficient memory failure for the calculation 208 SAR Descriptors Data not in database Bad MDL Molfile format Invalid aggregate Too many molecules Too many atoms exceeded MDL Molfile size limit The literature values for this property are not in the database The molecule is too large or complex causing bad input data to be generated A fragment in the molecule is unrecognized or there is more than one disjointed molecule or fragment There is more than one molecule There ate more than 100 atoms The input data generated for this molecule exceeds the maximum size limit jurra MM2 Server The MM2 server computes property predictions using the methods of molecular mechanics For more information on MM2 see Molecular Mechanics Theory in Brief on page 135 and MM2 and MM3 Computations CambridgeSoft MM2 Server The MM2 server provides the following property calculations Property Bending Energ
172. al angles used to position atoms will also be negated Through YZ Plane Reflects the model through the YZ plane by negating X coordinates If the model contains any chiral centers this will change the model into its enantiomer Pro R positioned atoms will become Pro S and Pro S positioned atoms will become Pro R All dihedral angles used to position atoms will also be negated Invert Through Origin Reflects the model through the origin negating all Cartesian coordinates If the model contains any chiral centers this will change the model into its enantiomer Pro R positioned atoms will become Pro S and Pro S positioned atoms will become Pro R All dihedral angles used to position atoms will also be negated The Set Z Matrix submenu e Set Origin Atom s file Sets the selected atom s as the otigin of the internal coordinates Up to three atoms may be selected Setting Measurements on page 85 CambridgeSoft The Graphical User Interface e Position by Dihedrals Positions an atom relative to three previously positioned atoms using a bond distance a bond angle and a dihedral angle For more information on changing the internal coordinates see Setting Dihedral Angles on page 86 Position by Bond Angles Positions an atom relative to three previously positioned atoms using a bond distance and two bond angles For more information on changing the internal coordinates see Setting Bond Angles on page 86
173. al to show 55 Qo TIP To get exactly 55 you will probably have to edit the value in the number box After editing you must press the Enter key The value displayed in the right corner of the dial should be the same as in the number box The resulting model appears as shown in the following illustration the second model may appear in a different position on your computer D set optimal distances between atoms in the two fragments The Optimal distance determines how closely the molecules dock In this tutorial you will set the distance to 5A CambridgeSoft Tutorial 7 Docking Models In the Model Explorer select C 6 in Fragment 1 Hint It s in the AA mon 2 group Locate the C 98 atom in Fragment 2 AA mon 12 group and Ctrl click to select it also In the Structure menu point to Measurements and choose Set Distance Measurement The Measurements table opens if it is already open as a tabbed window it becomes active displaying the C 98 C 6 pair Click the Optimal cell Type 5 and press the Enter key The optimal distance between C 6 and C 98 is specified as 5 000A Atoms Actual Optimal C 34 C 126 20 1410 5 0000 C 133 C 41 20 3559 5 0000 C 45 C 137 20 3218 5 0000 C 60 C 142 20 4350 5 0000 Ignore the distances in the Actual cell because they depend on how the second polymer was positioned telative to the first polymer when the second polymer was created
174. ally termed rendering types and the term model display is used in Chem3D Depending on the type of molecule certain model displays may offer advantages by highlighting structural features of interest For example the Ribbons model display might be the option of choice to show the conformational folding of a protein without the distracting structural detail of individual atoms Model display options are divided into two general types e Structure displays e Molecular surface displays Structure Displays Structures ate graphical representations based on the traditional physical three dimensional molecular model types The following structure display types are available from Model Display view of the Chem 3D Setting dialog box e Wire Frame e Sticks Ball and Stick e Cylindrical Bonds e Space Filling ChemOffice 2005 Chem3D e Ribbons e Cartoons To change the default structural display type of a model 1 From the File menu choose Model Settings The Chem 3D Setting dialog box appears 2 Select the Model Display tab The Model Display control panel of the Chem 3D Setting dialog box appears Model Settings onts Movie Model Display Model Building Stereo amp Depth Atom Display Model Display Modes ddel i play Model Type Ball amp Stick v ap Ligand Model Type Wire Frame vj Solvent Model Type Not Displaying v Atom Labels show Element Symbols show Serial Numbers
175. also create a model by typing the name of a compound or a SMILES string into the Name Struc box When you finish editing add or teplace your Chem3D model by clicking the appropriate icon CambridgeSoft The Graphical User Interface The Model Information Panel The Model information panel contains information about the model in the top most tabbed window and its display You can display one or more of the following tables in the area e Model Explorer e Measurements e Cartesian Coordinates e Z Matrix table Tables are linked to the structure so that selecting an atom bond or angle in either will highlight both Numerical values in the tables can be edited or cut and pasted to from other documents text or Excel worksheets and the changes are displayed in the structure All of the tables have an Auto hide feature to minimize their display For more information on Model Tables see Model Coordinates on page 28 The Z Matrix table is shown below Column Field Name Cell Record F Heading Selector Column Divider e Matrix ax f S H Atom Bond Atom Bond Length An m Angle Dihedral Atom Dih dral z c t 1 5400 crs 1 1220 CK 103 5000 c5 1 1220 c 1 103 5000 H 6 109 5000 c5 1 1220 cq 109 5000 H 6 109 5000 ct 1 1220 c 5 109 5000 H 6 60 0000 cc 1 1220 c 5 109 5000 H2 109 5000 ca 1 1220 C 5 109 5000 H 2 109 5000 ABBE EERE sols olulo a rrzzizo0 ChemOffice 2005 Chem3D
176. ame Ag Delete Delete all Properties 4 For more information on Movies see Creating and Playing Movies on page 115 Chem3D Basics 21 The Graphical User Interface The Calculation Toolbar The Calculation toolbar provides a desktop icon for performing the most common calculation MM2 minimization It also provides a Stop button and a calculation running indicator that work with all calculations Calculation indicator MM2 minimization Stop button amp 4 The ChemDraw Panel Chem3D 9 makes it easier than ever to create or edit models in ChemDraw The ChemDraw panel is activated from the View menu By default it opens on the right side of the GUI but like the toolbars you can have it float or attach it anywhere you like 22 Chem3D Basics Close panel Auto Hide gt Synchronize 49 _ Draw gt 3D add N in p Draw gt 3D SR LA replace Yn 3D gt Draw gt A gt Clean up wa structure 1 gt Clear 8 a Lock i gt Name Struct Xa 5 ChemDraw ActiveX tool palette OR OO0RE 9 OQOO0V3 E Use the 3D gt Draw icon to drag a Chem3D model into the ChemDraw panel To create a model in ChemDraw click in the ChemDraw panel to activate the ChemDraw toolbar Use the Draw gt 3D Add or Draw gt 3D Replace icons to put the model in Chem3D or select the Synchronize icon to draw in both simultaneously You can
177. an open valence and is not attached to an atom that is unselected it goes after any atom that is attached to an unselected atom 2 If an atom is attached only to rectification atoms it goes after any atom that is attached to non rectification atoms 3 If two atoms ate the same according to the above criteria the atom with the lowest serial number goes first 4 If two atoms are the same according to the above criteria then the one which is attached to the atom with the lowest serial number goes first ChemOffice 2005 Appendix Angles and measurements In addition to the attachment points the measutements between the selected atoms and nearby unselected atoms ate saved with the substructure to position the substructure relative to other atoms when the substructure is used to convert labels into atoms and bonds For example Chem3D stores with the substructure a dihedral angle formed by two atoms in the substructure and two unselected atoms If mote than one dihedral angle can be composed from selected substructure and unselected non substructure atoms the dihedral angle that is saved with the substructure consists of the atoms with the lowest serial numbers Consider the following model to define a substructure for alanine Since polypeptides are specified beginning with the N terminal amino acid N 4 should have a lower serial number than the Carboxyl C 6 To ensure that a chain of alanine substructures is fo
178. anages daughter plate creation barcoding and freeze thaw cycle tracking Since it is integrated with your assay data you can instantly view compound information and visualize results plate wise to detect anomalies before they become a problem Automated Calculations amp Curve Fitting Once the database is configured for an assay calculations are performed automatically whenever new data is entered or imported Calculations can be quite complex built from multi step procedures For an 1C 50 assay in triplicate the software can average your triplicate results take control values into account and perform a sigmoidal dose response curve fit according to your specifications It is now as easy to do for 10 000 compounds as it is for ten Find Structure Activity Relationships Users can visualize data for multiple assays with BioSAR Browser which is specifically designed for viewing structures and alphanumerics side by side Other components of the ChenOffice product line provide additional ways to analyze structural and biological data and perform structure searches Both ChanFinder and Chem0 fficeWebServer make it easy to create customized forms for viewing data U sers can export data to Excel or Spotfire for further analysis and reporting EMAIL info cambridgesoftcom WWW _ www cambridgesoftcom TEL 1 800 315 7300 INTL 1 617 588 9300 FAX 1 617 588 9390 e MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge MA 02140 USA Cambridge
179. and devices by which infringing copies have been made or used in violation of the copyright owner s exclusive rights In cases of willful infringement criminal penalties may also be assessed against the infringer SHA also offers a number of other materials designed to help you comply with the Federal Copyright Law These materials include It s Just Not Worth the Risk video This 12 minute video available 10 has helped over 20 000 organizations dramatize to their employees the implications and consequences of software piracy Don t Copy that Floppy video This 9 minute rap video available for 10 is designed to educate students on the ethical use of software Other education materials including Software Use and the Law a brochure detailing the copyright law and how software should be used by educational institutions corporations and individuals and several posters to help emphasize the message that unauthorized copying of software is illegal To order any of these materials please send your request to SHA Anti Piracy Materials Software amp Information Industry Association 1090 Vermont Ave Sixth Floor Washington D C 20005 202 289 7442 We urge you to make as many copies as you would like in order to help us spread the word that unauthorized copying of software is illegal Software Desktop Applications Enterprise Solutions Databases Tips A Guide to CambridgeSoft Manuals
180. and help you execute the process as quickly as your organization demands Since ongoing moni toring is a part of business for regulated industries you can be confident that as regulations evolve and your requirements change your systems can adapt W ith C ambridgeSoft you can take advantage of the knowledge that has helped dozens of businesses large and small gain control over their business processes their intellectual capital and their material resources EMAIL info cambridgesoftcom WWW _ www cambridgesoftcom a a EU TEL 1 800 315 7300 INTL 1 617 588 9300 FAX 1 617 588 9390 o e MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge MA 02140 USA CambridgeSoft TTT Chemo ffice ChemDraw Chem3D ChemFinder Cheminfo are trademarks of CambridgeSoft 2002 5 All other trademarks are the property of their respective holders All specifications subject to change without notice www cam b T1 dg eso ft CcCOm RESEARCH amp Registration System Chemical and Biological Registration Registration System Registration Sytem includes a robust data model for pure compounds batches salt management automatic duplicate checking and uniquelD assignments Compounds may be entered individually or with SD files The data model resides entirely in Oracle and uses Oracles security and transaction framework For companies intending to modify or construct their own registration system Chen0 ffice WebServer includes a powerful Softwar
181. anel At the bottom of the GUI is a Status bar which displays The Graphical User Interface GUI is the part of information about the active frame of your model Chem3D that you interact with to perform tasks and about hidden atoms in your model The GUI is The GUI consists of a model window menus shown in Rotation mode with the dynamic toolbars and dialog boxes It can also include up to Rotation bars showing the ChemDraw panel open three optional panels that display Output and and the Tables panel set to Auto Hide Building Toolbar Computation Toolbar Model Display Toolbar ChemDraw Panel tab Title bar D Chem3D Ultra Untitled 1 Mex Menu bar S je e Standard Toolbar E Ela E E AS te a Active 65 Untitled Wide Untitled 1 Tab Model Explorer tab Model window CAP NUM SCRL Status bar Model Window the model it appears in the Output window or the f f Status bar The Model window is the work space where you do your modeling If there is textual information about ChemOffice 2005 Chem3D Chem3D Basics 13 The Graphical User Interface The following table describes the objects in the Model window Object Description Model area The workspace where a molecular model is viewed built edited or analyzed The origin of the Cartesian axes 0 0 0 is always located at the center of this window regardless of how the model is moved or scaled The Cartesian axes do not move relative to the wind
182. ant T his CambridgeSoft End U ser License Agreement is a legal agreement between you either an individ ual or a single entity and CambridgeSoft Corporation for the C ambridgeSoft supplied database product s and may include associated media printed materials and online or electronic documentation By using the database prod uct s you agree that you have read understood and will be bound by this license agreement Database Product License 1 Copyright Notice The materials contained in CambridgeSoft D atabase Products including but not limited to ChemACX Chemindex and The M erck Index are protected by copyright laws and international copyright treaties as well as other intellectual property laws and treaties Copyright in the materials contained on the CD and internet subscription products including but not limited to the textual material chemical structures representations artwork photographs computer software audio and visual elements is owned or controlled separately by CambridgeSoft Corporation CS CS is a distributor and not a publisher of information supplied by third parties Accordingly CS has no editorial control over such information D atabase Suppliers Supplier individually own all right title and interest includ ing copyright in their database and retain all such rights in providing information to Customers The materials contained in T he M erck Index are protected by copyright laws an
183. apter 13 ULTRA GAMESS Computations GAMESS Overview The General Atomic and Molecular Electronic Structure System GAMESS is a general ab initio quantum chemistry package maintained by the Gordon research group at Iowa State University It computes wavefunctions using RHF ROHE UHF GVB and MCSCE CI and MP2 energy corrections ate available for some of these GAMESS is a command line application which requires a user to type text based commands and data Chem3D serves as a front end graphical user interface GUD allowing you create and run GAMESS jobs from within Chem3D Installing GAMESS You must download and install the GAMESS application separately You can download the GAMESS application and documentation from the following web site http www msg ameslab gov GAMESS GAMESS html ChemOffice 2005 Chem3D Minimize Energy To perform a GAMESS Minimize Energy computation on a model 1 From the Calculations menu point to Gamess and choose Minimize Energy The Minimize Energy dialog box appears with the Theory tab displayed Minimize Energy Job Type Theory Properties General Method Hartree Fock X v Wave Function Closed Shell Restricted Symmetry None C1_y Basis Set E Huckel v Diffuse Polarization Heavy Atom Y Light Atom None y Exponent Pope Spin Multiplicity Summary Job Type Compute Propertie
184. ar and tear off the Specific tools you will be using often For a review of the surface display tools see The Surfaces Toolbar on page 21 Not all surfaces can be displayed from all calculations For example a Molecular Electrostatic Potential surface may be displayed only following a Gaussian ot MOPAC calculation If a surface is unavailable the command is grayed out in the submenu CambridgeSoft Molecular Surface Displays To generate surfaces from MOPAC or Gaussian you must choose Molecular Surfaces as one of the properties calculated by these programs The surface types and the calculations necessary to display them are summarized in the following table NOTE Spin Density map requires that MOPAC or Gaussian computations be performed with an open shell wavefunction Surface Extended MOPAC Gaussian Type H ckel Solvent NA NA NA Accessible Connolly Yes Yes Yes Molecular Total Yes Yes Yes Charge Density with Yes Yes Yes Molecular Orbital map with Spin No Yes Yes Density map ChemOffice 2005 Chem3D Surface Extended MOPAC Gaussian Type Hiickel with Partial Yes Yes Yes Charges with No Yes Yes Molecular Electrostatic Potential map Total Spin No Yes Yes Density Molecular No Yes Yes Electro static Potential Molecular Yes Yes Yes Orbitals Calculated automatically from parameters stored
185. arch and structure query features e Stores structures and reactions along with calculated data and associated information e Search by substructure including stereochemistry using ChemDraw e Import export MDL SD and RD files e Integration with ChemDraw and Chem3D ChemFinder Word Searching Word Excel amp More Searches documents for embedded structures Indexes structures and source locations Searches specified folders and whole hard drives ChemDraw Excel Searching amp Calculating in Excel Displays ChemDraw structures in spreadsheet cells e Adds chemical calculations to Excel functions e Useful for graphing and analyzing chemical data Purchase Excel High Throughput Purchasing e Finds vendor and price information from ChemACX Database or ChemACX Com Search for suppliers and purchase online e Maintains lists of compounds CombiChem Excel Combinatorial Chemistry in Excel Generate combinatorial libraries e Choose starting materials and reaction schemes e View structures and track plate well assignments SYSTEMS amp LANGUAGES English amp Japanese Windows 95 98 Me NT 2000 XP This software is W indows only iy All specifications subject to change without notice i qo ran EMAIL info cambridgesoftcom WWW _ www cambridgesoftcom ii a E pr o TEL 1800 315 7300 INTL 1617 588 9300 FAX 1 617 588 9390 e MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge MA 02140 USA am ri ge O C
186. ard Modifiers 237 238 Keyboard Modifiers CambridgeSoft Appendix F 2D to 3D Conversion Overview This section discusses how Chem3D performs the conversion from two to three dimensions when opening a ChemDraw or ISIS Draw document when pasting a ChemDraw ot ISIS Draw structure from the Clipboard or when opening a ChemDraw connection table file While Chem3D can read in and assimilate any ChemDraw structure you can assist Chem3D in the two to three dimensional conversion of your models by following the suggestions in this Appendix Chem3D uses the atom labels and bonds drawn in ChemDraw to form the structure of your model For every bond drawn in ChemDraw a corresponding bond is created in Chem3D Every atom label is converted into at least one atom Dative bonds are converted to single bonds with a positive formal charge added to one atom the atom at the tail of the dative bond and a negative formal charge added to the other the head of the dative bond He s S 0 Stereochemical Relationships Chem3D uses the stereo bonds and H Dot and H Dash atom labels in a ChemDraw structure to define the stereochemical relationships in the corresponding model Wedged bonds in ChemDraw indicate a bond where the atom at the wide end of the bond is in front of the atom at the narrow end of the bond Wedged hashed bonds ChemOffice 2005 Appendix indicate the opposite the atom at the wide end of a wedged hashed bond is
187. arnings to the creation of new software products and they deserve a fair return on their investment The creative teams who develop the software programmers writers graphic artists and others also deserve fair compensation for their efforts Without the protection given by our copyright laws they would be unable to produce the valuable programs that have become so important to our daily lives educational software that teaches us much needed skills business software that allows us to save time effort and money and entertainment and personal productivity software that enhances leisure time Q That makes sense but what do get out of purchasing my own software A When you purchase authorized copies of software programs you receive user guides and tutorials quick reference cards the opportunity to purchase upgrades and technical support from the software publishers For most software programs you can read about user benefits in the registration brochure or upgrade flyer in the product box Q What exactly does the law say about copying software A The law says that anyone who purchases a copy of software has the right to load that copy onto a single computer and to make another copy for archival purposes only or in limited circumstances for purposes only of maintenance or repair It is illegal to use that software on more than one computer or to make or distribute copies of that software for any other purpos
188. ars The Actual cell contains the current distance between the two atoms listed in the Atom cell 4 For an acceptable overlay you must specify at least three atom pairs although it can be done with only two pairs Repeat steps 1 to 3 to create at least three atom pairs 5 The optimal distances for overlaying two fragments ate assumed to be zero for any atom pair that appears in the Measurements table For each atom pait type 0 into the Optimal column and press the Enter key CambridgeSoft Comparing Models by Overlay Your measurements table should look something like this C 9 C 27 8 2774 0 0000 N 28 N 8 8 1075 0 0000 C 31 0 5 81876 0 0000 C 33 C 10 81936 0 0000 5 C 2 C 36 8 1933 Now perform the overlay computation NOTE To help see the two overlaid fragments you can color a fragment For more information see Working With the Model Explorer on page 111 1 From the Model Display submenu of the View menu deselect Show Atom Labels and Show Serial Numbers 2 From the Structure menu point to Overlay and click Minimize The Overlay dialog box appears Overlay Minimum RMS Error 10 100 Minimum RMS Gradient 0 010 Display Each Iteration C Record Each Iteration 3 Type 0 100 for the Minimum RMS Error and 0 010 for the Minimum RMS Gradient The overlay computation will stop when either the RMS Error becomes less than the Minimum RMS Error or the RMS Gradient becomes less than
189. art of the current selection Select Groups Selects all groups that contain within Distance of one or more atoms lying Selection within the specified distance from any part of the current selection Select Atoms within Radius of Selection Centroid Selects all atoms lying within the specified distance of the centroid of the current selection Select Groups within Radius of Selection Centroid Selects all groups that contain one of more atoms lying within the specified distance of the centroid of the current selection NOTE 1 Atoms or groups already selected are not included 2 The current selection will be un selected unless multiple selection is used Hold the shift key down to specify multiple selection Showing and Hiding Atoms You may want to view your models with different atoms visible or not visible You can temporarily hide atoms using the Model Explorer To hide atoms or groups CambridgeSoft Showing and Hiding Atoms e Right click at any level point to Visibility and click Hide Atom Group etc Hidden atoms or groups ate displayed in parentheses in the tree control By default all levels in the hierarchy are set to inherit the settings of the level above but you can reset the default to hide a group but show individual atoms in it To show an atom belonging to a hidden group e Right click on the atom in the tree control point to Visibility and choose Show Showing Hs and Lps
190. ata You can view information about an active model as a pop up or in measurement windows Pop up Information You can display information about atoms and bonds by pointing to them so that pop up information appears You specify what information appears by using the Pop up Info tab of the Preferences dialog box You can display the following information about an atom e Cartesian coordinates e Atom type e Internal coordinates Z matrix e Measurements e Bond Length Bond Order e Partial Charge Examples of pop up information are shown below C 1 C 2 Length 1 3375 Order 2 000 ChemOffice 2005 Chem3D NOTE Precise bond orders for delocalized pi systems are displayed if the MM2 Force Field has been computed The information about an atom or bond always begins with the name of that object such as C 12 for an atom or O 5 P 3 for a bond To set what pop up information appears If you want to Then Select display The three numerical Cartesian Coordinates values indicating the atom s position along the X Y and Z axes the atom type corresponding to the first column of a record in the Atom Types table Atom Type alist of the atoms used Z matrix to position the atom NOTE The Z matrix definition includes whether the second angle used to position the selected atom is a dibedral angle or a second bond angle If atoms other than the one at which you are pointi
191. ate After 10000 Steps 5 Enter the appropriate values 6 Click Run Dynamics Settings Use the Dynamics tab to enter parameter values for the parameters that define the molecular dynamics calculations Step Interval determines the time between molecular dynamics steps The step interval must be less than 5 of the vibration period for the highest frequency normal mode 10 fs for a 3336 cm H X stretching vibration Normally a step interval of 1 or 2 fs yields reasonable results Larger step intervals may cause the integration method to break down because higher order moments of the position are neglected in the Beeman algorithm Frame Interval determines the interval at which frames and statistics ate collected A frame interval of 10 or 20 fs gives a fairly smooth sequence of frames and a frame interval of 100 fs or more can be used to obtain samples of conformational space over a longer computation CambridgeSoft Molecular Dynamics e Terminate After causes the molecular dynamics run to stop after the specified dos Type Depenicellibiopeiiess Geneia number of steps The total time of the run is Job Type Molecular Dynamics Y the Step Interval times the number of steps y a Record Every Iteration Heating Cooling Rate dictates whether Copy Measurements to Messages A Move Only Selected Atoms temperature adjustments are made If the Heating Cooling Rate check box
192. ates in orthogonal or non orthogonal coordinate systems Atom Types in Cartesian Coordinate Files Two file formats are supplied with Chem3D that interpret Cartesian coordinate files The difference between the two file formats are the codes used to convert atom type numbers in the file into atom types used by Chem3D In Cartesian coordinates 1 atom types are numbered according to the numbering used by N L Allinger in MM2 These numbers are also generally followed by the program PC Model In Cartesian coordinates 2 the atom type number for all atom types is computed by multiplying the atomic number of the element by 10 and adding the number of valences as specified by the geometry of the atom type These numbers are also generally followed by the program MacroModel For example the atom type number for C Alkane a tetrahedral carbon atom is 64 To examine the atom types described by a file format see Editing File Format Atom Types on page 241 The Cartesian Coordinate File Format The format for Cartesian coordinate files is as follows 1 The first line of data contains the number of atoms in the model Optionally you can follow the number of atoms in the file with crystal cell parameters for the crystal structure a b c a B and y ChemOffice 2005 Appendix Following the cell parameters you can also include an exponent If you include an exponent then all of the fractional cell coordinates will b
193. ating the file Line 27 contains the header for the Atom Lists section Line 28 contains a listing of all the possible fields for the atom list section When the file is created using Chem3D Pro the following fields are used Atom Lbl Type and x y z File Formats 16 17 18 19 Lines 29 47 each contains 28 fields describing information about each of the atoms in the structure the first field is the atom number 6 the second field is the atom label C the third field is the atom type 10 the fourth field and fifth fields contain 2D coordinates and contain zeros when the file is created using Chem3D Pro the sixth field is the X coordinate 0 113 and the fifth field is the Y coordinate 1 005 the sixth field is the Z coordinate 0 675 the seventh through fifteenth fields are ignored and contain zeros when the file is created by Chem3D Pro the sixteenth field is again the atom label C the eighteenth field is again the atom number 6 the nineteenth field is the segment field the twentieth field is the coordination field the twenty first field is ignored the twenty second field is called the saturation field if the atom is attached to any single double or delocalized bonds this field is 1 not saturated otherwise this field is 0 The twenty third through the twenty sixth fields are ignored and contain zeros when the file is created using Chem3D Pro the twenty seventh field is again t
194. ation retrieval integrate smoothly with ChemOffice and Microsoft Office to speed day to day research tasks ENTERPRISE SOLUTIONS Document Manager Enterprise Just as ChemOffice supports the daily work of the individual scientist enterprise solutions and databases built on ChemOffice WebServer and Oracle Cartridge help organizations collaborate and share information KNOWLEDGE MANAGEMENT Research organizations thrive when information is easily captured well organized and available to others who need it E Notebook Enterprise streamlines daily record keeping with rigorous security and efficient archiving and facilitates searches by text and structure Document Manager organizes procedures and reports for archiving and chemically intelligent data mining Discovery LIMS tracks laboratory requests and 21CFR11 Compliance implements an organization s regulatory compliance processes SOLUTIONS Enterprise Solutions APPLIED BIOINFORMATICS CHEMICAL DATABASES CombiChem Enterprise Registration System Formulations amp Mixtures Inventory Manager CombiChem Enterprise BioAssay HTS BioSAR Browser ChemACX Database ChemSAR Properties The Merck Index Chemical Databases Consulting Development Support amp Training BioAssay ChemACX The Merck HTS Database Index BioSAR Browser ChemSAR Chemical Properties Databases RESEARCH amp DISCOVERY Managing the hug
195. ations are available to others on the network Finding Reagents Flexibility is the key when dealing with databases of chemical compounds CombiChen Enterprise can use reagent lists from a variety of different sources SD files ChemFinder databases ChemFinder hit lists ChemO ffice WebServer hit lists ChemACX Database or directly from the user via ChemD raw Regardless of the source CombiC hem Enterprise produces a list of reagents which match a particular generic reactant The chemist then chooses which of the compounds to use for generating products Getting Results Once the chemist has given CombiChem Enterprise a set of reagents for each of the generic reactants in the reaction scheme the software generates the set of products which would result from running the experiment CombiChen Enterprise evaluates the products using several in slico methods and the chemist can then choose which compounds to keep and which ones to reject After the products have been generated the software provides product information for each of the reagents T he chemist can use that information for example to trim away reagents having few or no products which pass the Lipinski Rule of Five test Finally the products are laid out on plates based on user definable plate layouts Integration with E Notebook Keeping track of compound library data can be a challenge which reagents led to this product which product goes with that spectrum what was in the mixture use
196. atoms may change when you replace other atoms with other atoms of a different type If the wrong atom type is assigned to an atom you can specify the correct atom type by selecting the Text Building Tool clicking the atom typing the name of the atom type into the text box and pressing the Enter key Atom Type Characteristics The characteristics of an atom must match the following atom type characteristics for Chem3D to assign the atom type to the atom e The symbol e The bound to type if specified for the atom type e The bound to order if the bound to type is specified ChemOffice 2005 Appendix The number of double triple and delocalized bonds NOTE For comparing bond orders an atom type that contains one double bond may be assigned to an atom that contains two delocalized bonds For example all six carbons in benzene are C Alkene If the maximum ring size field of an atom type is specified then the atom must be in a ring of that size or smaller to be assigned the corresponding atom type If an atom is bound to fewer ligands than are specified by an atom type geometty but the rectification type is specified then the atom can be assigned to that atom type Chem3D fills the open valences with rectification atoms For example consider the atom types for the following structure O O 3 matches the criteria specified for the atom type O Carbonyl Specifically it is labeled O it is boun
197. ay functions The Model type and Background color tools activate menus that let you choose one of the options All of the remaining tools are toggle switches click once to activate click again to deactivate y Model type E Brg Background Color Stereo Visualization Lal Rea Blue Stereo Gigi Chromatek Stereo Perspective Depth Fading Model Axes View Axes Bale oo AO Atom labels Atom numbers Full screen mode Spinning model demo CambridgeSoft The Graphical User Interface The Surfaces Toolbar The Surfaces toolbar controls the display of molecular surfaces In most cases you will need to do either an Extended Hiickel MOPAC or Gaussian calculation before you can display surfaces Surface Solvent radius Display mode Color Mapping Surface color Resolution HOMO LUMO selection Isovalues Color A Color B lo la Te 0 ES Bd 5 To b ChemOffice 2005 Chem3D For mote information on Sutfaces see Molecular Surface Displays on page 63 The Movie Toolbar The Movie toolbar controls the creation and playback of animations You can animate certain visualization operations such as iterations from a computation by saving frames in a movie Movies can be saved as Windows AVI video files b __ Play Stop 44 _ First frame 4 Previous Frame a HH Position k b Next frame b Last fr
198. bonds 76 Critical pressure ChemProp Pro 207 Critical temperature ChemProp Pro 207 Critical volume ChemProp Pro 207 Cubic and quartic stretch constants 282 Customizing calculations 221 dihedral graphs 43 Cutoff distances 283 Cutoff parameters electrostatic interac tions 140 Cutoff parameters for van der Waals inter actions 139 Cylindrical bonds display 56 vio CambridgeSoft D Data labels 26 Default minimizer 176 Define Group command 93 Defining atom types 234 groups 93 substructures 231 232 Deleting groups 114 measurement table data 29 Delocalized bonds field 276 Depth fading 60 Descriptive statistics 221 Descriptors ChemSAR Excel 220 Descriptors definition 205 Deselecting atoms and bonds 92 Deselecting changes in rectification 92 Deselecting description 92 Deviation from plane 107 dForce field 281 DFORCE keyword 171 Dielectric constants 283 Dihedral angles rotating 97 tutorial example 34 Dihedral angles setting 86 Dihedral Driver 42 Dihedral type field 285 Dipole moment 186 Dipole moment example 190 Dipole moment MM2 209 Dipole moment MOPAC Server 209 Dipole charge contribution 140 Dipole dipole contribution 140 Dipole dipole energy MM2 209 Display control panel 55 56 Display Every Iteration control GAMESS 212 Gaussian 200 MM2 152 199 203 Display types 55 Displaying atom labels 61 coordinates tables 108 dot surfaces 58 hydrogens and lone pairs 27 labels atom by atom 61 models 2
199. ce field depends on the parameters and the potential energy functions used to describe the total energy of a model Parameters must be optimized for a particular set of potential energy functions and thus ate not easily transferable to other force fields MM2 Chem3D uses a modified version of Allinger s MM2 force field For additional MM2 references see Appendix 9 MM2 and MM3 Computations The principal additions to Allinger s MM2 force field are e A charge dipole interaction term e A quartic stretching term CambridgeSoft Molecular Mechanics Theory in Brief e Cutoffs for electrostatic and van der Waals terms with 5th order polynomial switching function e Automatic pi system calculations when necessary Torsional and non bonded constraints Chem3D stores the parameters used for each of the terms in the potential energy function in tables These tables are controlled by the Table Editor application which allows viewing and editing of the patameters Each parameter is classified by a Quality number This number indicates the reliability of the data The quality ranges from 4 where the data are derived completely from experimental data or ab initio data to 1 where the data are guessed by Chem3D The parameter table MM2 Constants contains adjustable parameters that correct for failings of the potential functions in outlying situations NOTE Editing of MM2 parameters in the Table Editor should on
200. cel calculates the following statistics for every column in the data set e Mean e Minimum e Maximum e Range e Count e Sum e Standard deviation e Median To perform the statistical calculations ChemSAR Excel 221 Customizing Calculations From the ChemOffice menu point to ChemSAR then choose Descriptive Statistics or click the Statistics icon e The results are added as a separate worksheet Correlation Matrix ChemSAR Excel calculates scatter plots for each property to every other property To calculate the correlation matrix From the ChemOffice menu point to ChemSAR then choose Correlation Matrix The results are displayed on a separate worksheet correlating cells are colored 222 ChemSAR Excel Rune Plots Rune plots are used to compare data and visualize how normally the data is distributed The data is transformed on a scale of zero to one Each data set is then plotted next to each other You can then identify data sets that are not normally distributed and exclude them from any further calculation To create Rune plots From the ChemOffice menu point to ChemSAR then choose Rune Plots or click the Rune Plots icon HE The plot is added as a separate worksheet CambridgeSoft Calculating Statistical Properties Appendix A Accessing the CambridgeSoft Web Site Online Menu Overview The ChemOffice Online menu gives you quick access to the CambridgeSoft web site from with
201. charge chatge chatge dipole CambridgeSoft Molecular Mechanics Theory in Brief ot dipole dipole interactions are reached These cutoff values are located in the MM2 Constants parameter table Since the charge charge interaction energy between two point charges separated by a distance r is proportional to 1 t the charge charge cutoff must be rather large typically 30 to 40A depending on the size of the molecule The charge dipole dipole dipole interactions fall off as 1 17 1 1 and can be cutoff at much shorter distances for example 25 and 18A respectively To precisely reproduce the energies obtained with Allinger s force field set the cutoff constants to large values 99 in the MM2 Constants table OOP Bending Atoms that are arranged ina trigonal planar fashion as in sp hybridization tequire an additional term to account for out of plane OOP bending MM2 uses the following equation to describe OOP bending SS ESA The form of the equation is the same as for angle bending however the O value used is angle of deviation from coplanarity for an atom pair and 0 o is set to zero The illustration below shows the O determined for atom pairs DB The special force constants for each atom pair are located in the Out of Plane bending parameters table The sextic correction is used as previously described for Angle Bending The sextic constant SF is located in the MM2 Constants table ChemOffice 2005 Chem
202. chemistry definition 129 Computational methods choosing the best method 130 Chem3D 9 0 1 defined 129 limitations 130 model size 130 overview 129 parameter availability 130 potential energy surfaces 130 RAM 130 uses of 130 Compute Properties dialog box 215 Gaussian 202 MM2 161 MOPAC 184 removing properties 215 selecting properties 215 Compute Properties command 161 184 Computing partial charges 52 Computing properties 202 Computing steric energy tutorial example 41 Configuration interaction 147 167 Configuring ChemSAR Excel 217 Conformations examining 39 Conformations searching 43 Conjugated pi system bonds table 272 Connection table file format 122 Connection tables 122 Connolly accessible surface area descrip tion 205 Connolly molecular surface 69 ChemProp Std 206 displaying 69 overview 69 Connolly solvent excluded ChemProp Std 206 Constraining movement 95 Constraints setting 87 volume Copy As Bitmap command 127 Copy As ChemDraw Structure command 127 Copy command 127 Copy Measurements to Messages control GAMESS 212 Gaussian 200 Correlation Matrix 222 COSMO solvation 188 Covalent radius field 274 Create Input File command Gaussian 202 Creating and playing movies 115 atom pairs 46 atom types 234 bonds by bond proximate addition 84 Gaussian input files 202 groups 113 MOPAC input files 177 movies 115 parameters 273 structures from arc files 178 substructures 231 uncoordinated
203. ci Son apex ChemOffice 2005 Chem3D Coloring by depth for Chromatek stereo viewers Chem3D supports color by depth for Chromadepth stereo viewers When you select Color by Depth the model is colored so that objects nearer the viewer are toward the red end and objects further from the viewer toward the blue end of the spectrum This creates a stereo effect when viewed with a Chromadepth stereo viewer The effect is best viewed with a dark background If you use the Chromatek icon e on the Model Display toolbar to activate this viewing option rather than the Color By Depth menu the background color is set automatically to black Red blue Anaglyphs Chem3D supports viewing with red blue 3D glasses to create a stereo effect similar to that of the Chromatek viewer To activate red blue viewing 1 From the Stereo and Depth tab of the Model Settings dialog box select Render Red Blue Anaglyphs 2 Move the Eye Separation slider to adjust the effect Model Display Model Building Atom Display Colors amp Fonts Movie Stereo amp Depth General Stereo Settings O Disabled O Render Stereo Pairs Render Red Blue Anaglyphs Eye Separation 3 To toggle the effect on or off From the Model Display submenu of the View menu choose Red amp Blue Displaying Models 59 Structure Displays Depth Fading3D enhancement The depth fading feature in Chem3D creates a realistic depth effect by makin
204. cited state is actually the third lowest state the root 3 for a given system Singlet Triplet Quintet To request the second excited state use the following set of keywords Second excited Singlet OPEN 2 2 ROOT 3 SINGLET Second excited triplet OPEN 2 2 ROOT 3 TRIPLET C l n where n 3 is the simplest case Second excited quintet OPEN 4 4 ROOT 3 QUINTET C l n where n 5 is the simplest case CambridgeSoft Specifying the Electronic Configuration Excited State UHF Only the ground state of a given multiplicity can be calculated using UHE Odd Electron Systems Often anions cations or radicals are odd electron systems Normally the ground states and excited state configuration can be doublet quartet or sextet Ground State RHF Doublet ground state This is the most common configuration No additional keywords are necessary Quartet Use the following keyword combination QUARTET OPEN 3 3 Sextet ground state Use the following keyword combination SEXTET OPEN 5 5 Ground State UHF For UHF computations all unpaired electrons are forced to be spin up alpha Doublet ground state This is the most common configuration for a odd electron molecule No additional keywords are necessaty UHF will yield energies different from those obtained by the RHF method Quartet and Sextet ground state Use the keyword QUARTET or SEXTET Excited State RHF First Excited State The first excited state is
205. click Run Input File The Run MOPAC Input File dialog box appears Run MOPAC Input File File Browse I Display Each Iteration Copy Measurements to Messages Cancel 2 Type the full path of the MOPAC file or Browse to the file location 3 Select the appropriate options For more information about the options see Specifying the Electronic Configuration on page 172 MOPAC Computations 177 MOPAC Files 4 Click Run A new model window appears displaying the initial model The MOPAC job runs and the results appeat All properties requested for the job appear in the out file Only iteration messages appear for these jobs NOTE If you are opening a MOPAC file where a model has an open valence such as a radical you can avoid having the coordinates readjusted by Chem3D by turning off Automatically Rectify in the Building control panel NOTE MOPAC input files that containing multiple instances of the Z matrix under examination will not be correctly displayed in Chem3D This type of MOPAC input files includes calculations that use the SADDLE keyword or model reaction coordinate geometries Running MOPAC Jobs Chem3D enables you to select a previously created MOPAC job description file jdf The jdf file can be thought of as a set of Settings that apply to a particular dialog box For more information about jdf files see JDF Files on page 126 To create a jdf file 1
206. color is displayed Resetting Defaults To remove changes use the Reset All Children command Animations You can animate iterations from computations by saving frames in a movie You control the creation and playback of movies from the Movie menu ot toolbar Creating and Playing Movies To display the Movie toolbar e From the View menu point to Toolbars and choose Movies The Movie toolbar appears To create a movie select the Record Every Iteration checkbox when you set up the calculation To stop recording click Stop Calculations ho on the Calculation toolbar Movie or let the calculation terminate according to preset values ChemOffice 2005 Chem3D To view different frames of yout movie 1 Click the arrow on the Position button of the j ce Movie toolbar The Movie Process tool appears rH TIP You can tear the toolbar off by dragging the title bar 2 Drag the Slider knob to the frame you wish to view TIP You can also use the Previous and Next buttons to locate a frame in the movie To play back a movie you created e Click Start To stop playback of a movie e Click Stop Spinning Models You can spin models about a selected axis The number of frames created when you choose a Spin command is set using the Smoothness Slider in the Movies control panel Spin About Selected Axis To spin the model around an axis specified by a selection e Choose Spin About from the Movi
207. constant The values of V1 V2 and V3 in the Torsional Parameters table are 0 200 0 270 and 0 093 respectively Because a positive value of V3 indicates that there are minima at 60 60 and 180 and there ate maxima at 120 0 and 120 the minima at 60 signify the two conformations of n butane in which the methyl groups are gauche to one another The 180 minimum represents the conformation in which the methyl groups ate anti to one another The maximum at 0 represents the conformation in which the methyl groups are eclipsed The maxima at 120 conform n butane in which a methyl group and a hydrogen are eclipsed The V1 and V2 torsional constants in this example affect the torsional energy ina similar way to the V1 torsional constant for torsions about a carbon catbon double bond see previous example NOTE The results of MM2 calculations on hydrocarbons do not correspond well with the experimental data on hydrocarbons when only the V3 torsional constant is used when V1 and V2 are set to zero However including small values for the V1 and V2 torsional constants in the MM2 calculations for hydrocarbons dramatically improve the correspondence of the MM2 results with experimental results This use of V1 and V2 provides little correspondence to any particular physical property of hydrocarbons CambridgeSoft Torsional Parameters Record Order When sorted by Dihedral Angle the order of the records in t
208. containing other than an MM2 atom type NOTE Adding or changing parameter tables is not reconmended unless you are sure of the information your are adding For example new parameter information that is documented in journals NOTE A method for guessing at missing MM2 Parameters can be found in Development of an Internal Searching Algorithm for Parameterization of the MM2 MM3 Force Fieids Journal of Computational Chemistry Vol 12 No 7 844 849 1991 To add a new parameter to a parameter table 1 From the View menu point to Parameter Tables and choose the parameter table to open The parameter table appears 2 Right click on a tow header and choose Append Row from the context menu A blank row is inserted Parameter Tables 273 Estimating Parameters 3 Type the information for the new parameter 4 Close and Save the file The new parameter is added to the file NOTE Do not include duplicate parameters If duplicate parameters exist in a parameter table it is indeterminate which parameter will be used when called for in a calculation NOTE Ifyou do want to make changes to any of the parameters used in Chem3D we strongly recommend that you make a back up copy of the original parameter table and remove it from the C3DTABLE directory The Elements The Elements table Elements xml contains the elements for use in building your models To use an element in a model type its sy
209. created by all other electrons in the system which tends to overestimate the repulsion between electrons Repulsive interactions can be minimized by allowing the electrons to exist in more places i e more orbitals specifically termed virtual orbitals The multi electron configuration interaction MECI method in MOPAC addresses this problem by allowing multiple sets of electron assignments i e configurations to be used in constructing the molecular wave functions Molecular wave functions representing different configurations ate combined in a manner analogous to the LCAO approach For a particular molecule configuration interaction uses these occupied orbitals as a reference electron configuration and then promotes the electrons to unoccupied virtual orbitals These new states Slater determinants or microstates in MOPAC ate then linearly combined with the ground state configuration The linear combination of ChemOffice 2005 Chem3D microstates yields an improved electronic configuration and hence a better representation of the molecule Approximate Hamiltonians in MOPAC There are five approximation methods available in MOPAC e AM1 e MNDO e MNDO d e MINDO 3 PM3 The potential energy functions modify the HF equations by approximating and parameterizing aspects of the Fock matrix The approximations in semi empitical MOPAC methods play a role in the following ateas of the Fock operator e The basis set us
210. ct the atom or atoms to change 3 Type or followed by the number of the formal charge 4 Press the Enter key To set the formal charge of an atom in a molecular fragment as you build you can add the charge after the element in the text as you build To add the charge 1 Type PhO into a text box with no atoms selected 2 Press the Enter key The phenoxide ion molecule appears To remove the formal charge from an atom 1 Click the Text tool 2 Select the atom or atoms whose formal charge you want to remove 3 Type 0 4 Press the Enter key Building and Editing Models 87 Setting Charges Setting Serial Numbers Atoms are assigned serial numbers when they are created You can view the serial numbers in the following ways e Point to the atom to display the pop up information From the Model Display submenu of the View menu choose Show Serial Numbers e Inthe Chem 3D Model Settings dialog box choose the Atom Labels tab and then check the Show Serial Numbers checkbox e Click the Serial Number toggle 4 on the Model Display Toolbar Serial numbers are initially assigned based on the order in which you add atoms to your model To change the serial number of an atom 1 If you are using the Model Explorer select the atoms you want to re number and select Hide Atom Serial Number from the Atom Serial Numbers submenu of the context menu Pexprorer ty MD Cut Copy Paste Replace with Te
211. ction ChemOffice 2005 Chem3D The model rotates so that the two atoms you select are parallel to the appropriate axis NOTE This changes the view not the coordinates of the molecule To change the model coordinates use the Model Position submenu of the Structure menu For example to see an end on view of ethanol 1 Click the Select tool 2 Shift click C 1 and C 2 A a 3 From the View menu point to View Position and then click Align View Z Axis With Selection Aligning to a Plane You can align a model to a plane when you select three or more atoms When you select three atoms those atoms define a unique plane If you select more than three atoms a plane is computed that minimizes the average distance between the selected atoms and the plane Manipulating Models 99 Changing Orientation To position a plane in your model parallel to a plane of the Cartesian Coordinate system 1 Select three or more atoms 2 From the View menu point to View Position and then click Align View choose a plane With Selection The entire model rotates so that the computed plane is parallel to the X Y Y Z or X Z plane The center of the model remains in the center of the window To move three atoms to a plane and two of the atoms onto an axis 1 Select the two atoms 2 From the View menu point to View Position and then click Align View choose an axis With Selection 3 Shift click the third ato
212. culations You can use the ChemSAR Excel Options dialog box to customize a calculation by changing the default settings To change the defaults 1 From the ChemOffice menu point to ChemSAR then choose Options or click the Options icon The ChemSAR Excel Options dialog box appeats Before CAOS Descrgtors F Hydrogen FR Al Atoms T Cakculara Partisi Charges usa E Optimize 30 Geometry uan 2 To populate any unfilled valences with hydrogen atoms select Hydrogen Fill All Atoms 3 To customize the partial charge calculation click Calculate Partial Charges using d Select a type of method from the drop down list e To further customize the calculation click Options and then select a Charge Method and Theory to use f Click Use Custom Settings 4 To customize the how the 3D geometry is optimized select Optimize 3D Geometry using ChemOffice 2005 Chem3D g Select a type of method from the drop down list h To further customize the calculation click Options and then select a Optimization Method Theory and RMS Gradient to use i Click Use Custom Settings 5 Do one of the following To perform the calculation on Click a selected molecule Now the entire worksheet OK Calculating Statistical Properties ChemSAR Excel allows you to calculate the following statistical properties e Descriptive Statistics e Correlation matrix Rune Plot Descriptive Statistics ChemSAR Ex
213. cussion only 6 1X 12 File Formats 253 MSI MolFile 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 2540 3D displacement vector 0 000 0 000 0 000 3D rotation matrix 1 000 0 000 0 000 0 000 1 000 0 000 0 000 0 000 1 000 3D scale factor 0 2D scale factor 1 2D attributes 100000000000000 3D attributes 00000000000 Global display attributes 0 0 0000000C10 1000000I C 0000000C20 1000000 C 0000000C20 1000000 C 0000000C30 1000000 C 0000000C40 1000000 C 0000000C50 1000000 C 0000000C60 1000000 C 0000000070 1000000 0 0000000H70 1000000 H 0000000H80 1000000 H 0000000H90 1000000 H 0000000H 100 1 0 0 00 00 H 0000000H 110 100 0000 H 0000000 H 120 1 0 0000 0 H 0000000H 130 1 0 0 0000 H 0000000H 140 1 0 0 0 00 H 0000000H 150 1 0 0 0000 H 0000000H 160 1 0 0 0000 H 0000000H 17 0 1 0 0 0000 H 101 12256 Atom List Atom Lbl Type x y x y z bits chrg ichrg frag istp Ip chrl ring frad name seg grp FLAGS 1 C 10 0 0 1 0 46 0 2 2 C 10 0 0 1 2 1 1 0 2 2 C 10 0 0 1 2 1 1 0 2 3 C 10 0 0 0 1 1 6 0 7 4 C 10 0 0 1 3 1 1 0 5 C 10 0 0 1 2 0 48 0 6 C 10 0 0 0 1 01 1 7 O 45 0 0 0 2 42 1 8 H 8 0 0 0 6 2 72 1 9 H 1 0 0 2 1 0 86 1 10 H 1 0 0 1 4 0 86 0 8 11 H 1 0 0 1 1 1 4 1 12 H 1 0 0 2 2 1 4 0 2 13 H 1 0 0 0 0 72 2 14 H 1 0 0 0 1 2 7 0 7 15 H 1 0 0 0 3 1 3 1 7 16 H 1 0
214. d however the force field parameters may not be defined This will result in calculations failing due to missing atom types or parameters This problem can be resolved either by adding the missing patameters using the Additional Keywords section of the CS Mechanics interface or by creating an input file which can be corrected with a text editor The calculation can then be run by using the Run Input command in the Mechanics submenu of the Calculations menu Further details on how to define missing parameters can be found in the Tinker manual Tinker pdf on the ChemO ffice CDROM The behavior of the user interface closely matches that of the other add in modules such as MOPAC and Gaussian The calculations can be set up by ChemOffice 2005 Chem3D making selections of force field termination criteria etc Various properties can be computed as part of the single point or geometry optimization calculations These can be selected from the Properties panel The Chem3D MM2 submenu of the Calculations menu provides computations using the MM2 force field The MM2 procedures described assume that you understand how the potential energy surface relates to conformations of your model If you are not familiar with these concepts see Computation Concepts As discussed in the energy minimization routine performs a local minimization only Therefore the results of minimization may vary depending on the starting conformation in a model
215. d a fragment is added You can also define your own substructures and add them to the table The table below shows the substructure table window with the substructure records open triangles facing down Clicking a triangle closes the record The picture of the substructure is minimized References The References table References xml contains information concerning the source for other patameters Use of the References table does not affect the other tables in any way ChemOffice 2005 Appendix Two fields ate used for each reference record the reference number and the reference description Reference Number The reference number is an index by which the references ate organized Each measurement also contains a reference field that should contain a reference number indicating the source for that measutement Reference Description The reference description contains whatever text you need to describe the reference Journal references or bibliographic data are common examples of how you can describe your references Bond Stretching Parameters The Bond Stretching Parameters table Bond Stretching Parameters xml contains information about standard bond lengths between atoms of various atom types In addition to standard bond lengths are information used in MM2 calculations in Chem3D The Bond Stretching table contains parameters needed to compute the bond stretching and electrostatic portions of the force field for
216. d 3D gt draw Clear Lock e A TIP Use Cirl A to select the model you want to copy Tutorial 2 Building Models with the Bond Tools Draw ethane using a bond tool 1 Click the Single Bond tool gt 2 Point in the model window drag to the tight and release the mouse button A model of ethane appears When you rotate the model in a later step you will see the other hydrogen NOTE If you are using default settings hydrogens are displayed automatically To see the three dimensionality of your model you can perform rotations using the Trackball tool The Trackball Tool mimics a sphere in which your CambridgeSoft Tutorial 2 Building Models with the Bond Tools model is centered You can rotate your model by rotating the sphere You have a choice of free hand rotation or rotating around the X Y or Z axis To perform free hand rotation of the model with the Trackball tool 1 Click the Trackball tool 4 2 Point near the center of the model window and hold down the mouse button 3 Drag the cursor in any ditection to rotate the model CAUTION Users familiar with earlier versions of Chem3D should be aware of changed behavior the Trackball tool rotates the view only it does not change the atoms Cartesian coordinates To rotate around an axis 1 Move the cursor to the edge of the model window As you mouse over the edge of the window the rotation bars will appear NO
217. d Type The first field is the Bond Type which is described by the atom type numbers of the two bonded atoms For example Bond Type 2 3 is a bond between an alkene carbon and a carbonyl carbon Force Constant The Force Constant field or the out of plane bending constant field contains a measure of the amount of energy required to cause a trigonal planar atom to bend out of plane i e to become non planar The larger the value of Force Constant for a particular atom the mote difficult it is to coerce that atom to be non planar Record Order When sorted by Bond Type the order of the records in the Out of Plane Bending Parameters table is as follows 1 Records are sorted by the first atom type number in the Bond Type field For example the record for bond type 2 1 is before the record for bond type 3 1 2 For records where the first atom type number is the same the records are sorted by the second atom type number in the Bond Type field For example the record for bond type 2 1 is before the record for bond type 2 2 NOTE Out of plane bending parameters are not symmetrical For example the force constant for a 2 3 bond refers to the plane about the type 2 atom The force constant for a 3 2 bond refers to the plane about the type 3 atom Parameter Tables 287 Out ofPlane Bending VDW Interactions The parameters contained in the VDW parameters table VDW Interaction xml are used to adjust specific V
218. d but not confirmed 3 Parameter derived from experimental data 4 Parameter well confirmed Reference The reference for a measurement corresponds to a reference number in the References table References indicate where the parameter data was derived Estimating Parameters In certain circumstances Chem3D may estimate parameters For example during an MM2 analysis a non MM2 atom type is encountered in your model Although the atom type is defined in the Atom Types table the necessary MM2 parameter will not be defined for that atom type For example torsional parameters are missing This commonly occurs for inorganic complexes which MM2 does not cover adequately More parameters exist for organic compounds ChemOffice 2005 Appendix In this case Chem3D makes an educated guess wherever possible A message indicating an error in your model may appear before you start the analysis If you choose to ignore this you can determine the parameters guessed after the analysis is complete To view the parameters used in an MM2 analysis e From the Calculations menu point to MM2 and choose Show Used Parameters Estimated parameters have a Quality value of 1 Creating Parameters The MM2 force field parameters are based on a limited number of MM2 atom types These atom types cover the common atom types found in organic compounds As discussed in the previous section parameters may be missing from structures
219. d field is 242 File Formats the X coordinate the fourth field is the Y coordinate and the fifth field is the Z coordinate NOTE Atom types in the Alchemy file format are user definable See Editing File Format Atom Types on page 241 for instructions on modifying or creating an atom type Line Description Number Lines 21 40 each contain 4 fields describing information about each of the bonds in the molecule The first field is the bond number ranging from 1 to the number of bonds the second field is the serial number of the atom where the bond begins the third field is the serial number of the atom where the bond ends and the fourth field is the bond type The possible bond types are SINGLE DOUBLE TRIPLE AMIDE or AROMATIC Note that all the bond order names are padded on the right with spaces to eight characters FORTRAN Formats The FORTRAN format for each record of the Alchemy file is as follows FORTRAN Format number of atoms 15 1X number of bonds ATOMS 1X 15 1X BONDS 2 20 atom serial 16 A4 3 F9 4 number type and coordinates 2140 bond id from 16 15 16 2X A8 atom to atom bond type CambridgeSoft File Format Examples Cartesian Coordinate Files The Cartesian coordinate file format Cart Coords Cart Coords 2 interprets text files that specify models in terms of the X Y and Z coordinates of the atoms This file format can also interpret fractional cell coordin
220. d if they are not also connected to another selected bond To deselect a selected atom or bond do one of the following e Shift click the atoms or bonds in the display window e Ctrl click the atom in the Model Explorer 92 Manipulating Models If Automatically Rectify is on when you deselect an atom adjacent rectification atoms and lone pairs are also deselected NOTE A rectification atom is an atom bonded to only one other atom and whose atom type is the rectification type for that atom To deselect all atoms and bonds e Click in an empty atea of the Model window With the Model Explorer you can use different selection highlight colors for different fragments or groups To change the highlight color in the Model Explorer e Right click at any level and choose Select Color See Working With the Model Explorer on page 111 for information on other functions of the Model Explorer Selecting Groups of Atoms and Bonds You can define groups of atoms and fragments or large models and use the Model Explorer to select the entire group You can also select groups of atoms without defining them as a group with the selection rectangle Using the Selection Rectangle To select several atoms and bonds using the Selection Rectangle e Drag diagonally across the atoms you want to select s amp amp CambridgeSoft Selecting Any atoms that fall at least partially within the Selection Rectangle
221. d in this example 2 Point in the model window and drag in the direction you want the bond to be oriented 3 Release the mouse button to complete the bond Building and Editing Models 75 Building With the Bond Tools When Correct Atom Types and Rectify settings are selected in the Building control panel the atom type is set according to the bond tool used C Alkane in this example and the appropriate number of hydrogens are added To add bonds to the model 4 Point to an atom and drag in the direction you want to create another atom 1 Click and hold the 2 Drag in any direction and mouse button on an atom release the mouse button When the Rectify option is set in the Building control panel the hydrogen is replaced by a carbon amp amp a G 5 Repeat adding bonds until you have the model you want After you have the backbone you can change the carbons to different heteroatoms Creating Uncoordinated Bonds Use the Uncoordinated Bond tool to create an uncoordinated bond with a dummy atom labeled Du Uncoordinated Bonds and dummy atoms are ignored in all computations An uncoordinated 76 Building and Editing Models bond allows you to specify a connection between two atoms without a strict definition of the type of bond This bond is often used in coordination complexes for inorganic compounds where another element might be substituted Dummy atoms ate also useful for positioning atoms i
222. d in this thin layer chromatography C ombiC hem Enterprise provides ways to organize the data and navigation is simple W hen used with E N otebook Enterprise the data for a library of snared compounds and the entire experiment is automatically documented and made available to the entire organization EMAIL info cambridgesoftcom WWW _ www cambridgesoftcom iid TEL 1 800 315 7300 INTL 1 617 588 9300 FAX 1 617 588 9390 o e MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge MA 02140 USA CambridgeSoft TTT Chemo ffice ChemDraw Chem3D ChemFinder Cheminfo are trademarks of CambridgeSoft 2002 5 All other trademarks are the property of their respective holders All specifications subject to change without notice www cam b T1 dg eso ft CcCOm RESEARCH amp BioAssay HTS Biological Assay and High Throughput Screening BioAssay HTS BioAssay HTS provides scientists with an effective way of managing test results for biological and other kinds of experiments intended to assess the efficacy of compounds Suitable for both plate based high throughput screening assays and smaller scale lead optimization experiments BioAssay HTS provides researchers with simple tools for setting up their models in a database uploading data automating calculations and reporting on their findings User Friendly Assay Management Even for the most basic protein assays the independent and dependent variables used by the biologist to quan ti
223. d international copyright treaties as well as other intellectual property laws and treaties Copyright in the materials contained on the CD and internet subscription products including but not limited to the textual material chemical structures representations art work photographs computer software audio and visual elements is owned or controlled separately by the M erck amp Co Inc Merck and CambridgeSoft Corporation CS 2 Limitations on Use Except as expressly provided by copyright law copying redistribution or publication whether for commercial or non commercial purposes must be with the express permission of CS and or M eck In any copying redistribution or publication of copyrighted material any changes to or deletion of author attribution or copyright notice or any other proprietary notice of CS Merck or other D atabase producer are prohibited 3 Grant of License CD DVD Databases C ambridgeSoft Software Products are licensed not sold C ambridgeSoft grants and you hereby accept a nonexclusive license to use one copy of the enclosed Software Product Software in accordance with the terms of this Agreement This licensed copy of the Software may only be used on a single computer except as provided below You may physically transfer the Software from one computer to another for your own use provided the Software isin use or installed on only one computer at atime If the Software is permanently
224. d is restricted to even electron closed shell systems Further approximations are made to the RHF method when an open shell system is presented This approximation has been termed the 1 2 electron approximation by Dewar In this method unpaired electrons are treated as two 1 2 electrons of equal charge and opposite spin This allows the computation to be performed as a closed shell A CI calculation is automatically invoked to correct errots in energy values inherent to the 1 2 electron approximation For more information see Configuration Interaction on page 147 ChemOffice 2005 Chem3D With the addition of the 1 2 electron approximation RHF methods can be run on any starting configuration UHF The UHF method treats alpha spin up and beta spin down electrons separately allowing them to occupy different molecular orbitals and thus have different orbital energies For many open and closed shell systems this treatment of electrons results in better estimates of the energy in systems where energy levels are closely spaced and where bond breaking is occurring UHF can be run on both open and closed shell systems The major caveat to this method is the time involved Since alpha and beta electrons are treated separately twice as many integrals need to be solved As your models get large the time for the computation may make it a less satisfactory method Configuration Interaction The effects of electron electron rep
225. d on any menu This toolbar is divided into safe and unsafe tools The four safe tools on the left control only the view they do not affect the model in any way This includes the new safe select tool and the new translate tool The old s lect tool e is now called the Move tool Although 1t can also be used to select it s primary use is to move atoms and fragments Model Display toolbar Contains tools to control the display of the model These tools are duplicated on the View menu Surfaces toolbar Contains tools to calculate and display a molecular surface Molecular Surface displays provide information about entire molecules as opposed to the atom and bond information provided by Structure displays Movies toolbar Contains tools for the creation and playback of movies Chem3D movies are animations of certain visualization operations such as iterations from a computation They can be viewed in CambridgeSoft The Graphical User Interface Chem3D or saved in Windows AVI movie format The commands are reproduced on the Movie menu e Calculation toolbar Performs MM2 minimization from a desktop icon The spinning arrow icon shows when any calculation is running and the Stop icon can be used to stop a calculation before it s preset termination e Status bar Displays the Status bar which displays information about the active frame of your model e Customize Displays the Custom
226. d to a C Carbonyl by a double bond and it is attached to exactly one double bond and no triple bonds Atom Types 233 Assigning Atom Types If an atom can be assigned to more than one atom type atom types are assigned to atoms in the following order 1 Atom types whose bound to types are specified and are not the same as their rectification types 2 Atom types whose bound to types are specified and are the same as their rectification types 3 Atom types whose bound to types are not specified For example in the model depicted above O 4 could be one of several atom types First it could be an O Ether atom for which the bound to type is unspecified priority number 3 above Alternatively it could be an O Alcohol for which the bound to type is the same as the rectification type H Alcohol priority number 2 above A third possibility is O Carboxyl for which the bound to type is C Carbonyl and the rectification type is H Carboxyl priority number 1 Because the characteristic of a specified bound to type which is not the same as the rectification type number 1 in 234e Atom Types the priority list above is given precedence over the other two possibilities the O Carboxyl atom type is assigned to the oxygen atom Defining Atom Types If you need to define atom types whether to add to the atom types table for building or to add to a file format interpreter for importing here is the general procedure To add
227. del revision 3 may be applied to the elements shaded in the following table Rb S Cd In sn sb te 1 xe cs ba Hajm Pb Bi Po at rn The following apply to PM3 PM3 is a reparameterization of AM1 PM3 is a distinct improvement over AM1 Hypervalent compounds are predicted with considerably improved accuracy MOPAC Computations 169 MOPAC Semi empirical Methods e Overall errors in AH rare reduced by about 40 relative to AM1 e Little information exists regarding the limitations of PM3 This should be corrected naturally as results of PM3 calculations are reported e The barrier to rotation in formamide is practically non existent In part this can be corrected by the use of the MMOK option The MMOK option is used by default in CS MOPAC For mote information about MMOK see the online MOPAC Manual MNDO d Applicability and Limitations MNDO d Modified Neglect of Differential Overlap with d Orbitals may be applied to the elements shaded in the table below BEE o Oo A Pejs Cd tn Sn sb re x cs Ba Hol ri Pb i Po at frn MNDO d is a reformulation of MNDO with an extended basis set to include d orbitals This method may be applied to the elements shaded in the table below Results obtained from MNDO d are generally superior to those obtained from MNDO The MNDO method should be used where it is necessary to compare ot repeat calculations previously performed using MNDO Th
228. depth fading and perspective with hardwate enhancement but should not activate other stereo modes TIP The Eye Separation slider on the Stereo and Depth tab of the Model Settings dialog box can be used to control separation You should select the Disabled radio button when using hardware stereo Model Settings Model Display Model Building Atom Display Colors amp Fonts Movie Stereo amp Depth General Stereo Settings Disabled O Render Stereo Pairs O Render Red Blue Anaglyphs Eye Separation Stereo Pair Settings Parallel O Reversed Separation 5 0 Depth and Perspective Perspective C Depth Fading Field of view preview Molecular Surface Displays Molecular Surface displays provide information about entire molecules as opposed to the atom and bond information provided by Structure displays Surfaces show information about a molecule s physical and chemical properties They display aspects of the external surface interface or electron distribution of a molecule ChemOffice 2005 Chem3D Unlike atom and bond data Molecular Sutface information applies to the entire molecule Before any molecular surface can be displayed the data necessary to describe the surface must be calculated using Extended H ckel or one of the methods available in CS MOPAC or Gaussian Under MOPAC you must choose Molecular Surfaces as one of the properties to be calculated There is one exception to
229. dge MA 02140 USA CambridgeSoft TTT Chemo ffice ChemDraw Chem3D ChemFinder Cheminfo are trademarks of CambridgeSoft 2002 5 All other trademarks are the property of their respective holders All specifications subject to change without notice www cam b T1 dg eso ft CcCOm CHEMICAL Chemical Databases Reference C hemicals Reactions Patents and MSDS Databases Chemn0 ffice WebServer provides a full range of compound and reaction databases essential for research D atabases are available at ChemFinder Com or over corporate intranets Reference The Merck Index contains encyclopedic references for over 10 000 chemicals drugs and biologicals ChemI ND EX includes 100 000 chemicals public N Cl compounds and others World Drug Index WD from D erwent contains over 58 000 compounds with known biological activity W DI classifies compounds according to type of biological activity mechanism synonyms trade names references and more Chemicals ChemACX and ChemACX SC Available Chemicals Xchange is a large and growing source for information on compound availability It lists compounds from Alfa Aesar and Aldrich to TCI and Zeneca with hundreds in between including 500 000 products from 300 catalogs ChenACX SC is a library of screening compounds Derwent Patents DATABASES e Extensive collection of chemical reference information in fully searchable database format e Includes information on commercial avail
230. dual fields are delimited by space s or a tab The fields in the MSI MolFile format file used by Chem3D Pro are discussed below File Formats 255 MSI MolFile The field value for Carbon 6 from the example file is included in parentheses for reference 1 256 Line 1 is a standard header line for MSI MolFile format files Line 2 normally indicates the application which created the file Line 3 is the header for the File format version number section Line 4 indicates the file format version number The format for this field is YY MMDD Line 5 is the header for the File update version number section Line 6 indicates the file update version number The format for this field is YY MMDD Line 7 is the header for the molecule name section Line 8 contains the field molecule name This field contains either the file name or Undefined Name Line 9 is the header for the empirical formula Line 10 contains the empirical formula field This field contains either the empirical formula or Undefined Empirical Formula Lines 11 24 each contains information concerning conversions from 3D to 2D Line 25 is the header for the Global display attributes section Line 26 contains 5 fields describing the global display attributes Line thickness 1 font style 0 type face 1 type size 12 font 256 These values ate specific to the platform that is gener
231. e provide for insertion of this group within a model Similar multi bonding sites are defined for all amino acid and other polymer units CambridgeSoft Building With The Text Tool e Amino Acid substructures come in both alpha indicated by the amino acid name alone and beta indicated by a B preceding the name of the amino acid forms The dihedral angles have been preset for building alpha helix and beta sheet forms e You can use substructures alone or in combination with single elements or atom types e Using a substructure automatically creates a record in the Groups table that you can use for easy selection of groups or coloring by group e Substructures ate particularly useful for building polymers e You can define your own substructures and add them to the substructures table or create additional tables For mote information see Defining Substructures on page 232 To view the available substructures e From the View menu point to Parameter Tables and choose Substructures Building with Substructures You must know where the attachment points are for each substructure to get meaningful structures using this method Pre defined substructures have attachment points as defined by standard chemistry conventions For more information see Attachment point rules on page 231 To use a substructure as an independent fragment make sure there are no atoms selected To insert a substructure into a model
232. e D eveloper s Kit SDK to add custom functionality Instead of inventing a proprietary language Chem0 fficeWebServer SD K extends the M icrosoft and O racle platforms allowing information scientists to use the industry s most powerful development tools ChemDraw Plugin amp WebServer Registration System is easily adapted in almost any work environment Its web based industry standard ChemD raw interface makes Chemo fficeWebServer the best choice for your corporate scientific information User Friendly Chemical Registration New compounds are entered through a web form and chemical along with non chemical data is kept in a temporary storage area When the compound is registered it is compared for uniqueness via a configurable stereoselective duplicate check and assigned a registry number All information about the compound includ ing its test data and other syntheses is tracked by the registry number Search for a Compound DISCOVERY e Accessed through your favorite web browser the system uses O racle with robust data model to manage chemical products and their properties e Checks for uniqueness during registration and optionally registers duplicates as batches of existing substance e User administration and data entry are done through simple easy to learn web forms highly configurable system avoids tedious and expensive customization Duplicate Checking with Override W hen compounds are registered the struct
233. e Locating the Eclipsed Transition State of Ethane e The Dipole Moment of Formaldehyde e Comparing Cation Stabilities in a Homologous Series of Molecules e Analyzing Charge Distribution in a Series Of Mono substituted Phenoxy Ions e Calculating the Dipole Moment of meta Nitrotoluene e Comparing the Stability of Glycine Zwitterion in Water and Gas Phase e Hyperfine Coupling Constants for the Ethyl Radical e RHF Spin Density for the Ethyl Radical MOPAC Computations 165 The procedures assume you have a basic understanding of the computational concepts and terminology of semi empirical methods and the concepts involved in geometry optimization minimization and single point computations For mote information see Computation Concepts on page 129 For help with MOPAC see the online MOPAC manual at http Awww cachesoftware com mopac Mopac2002 manual MOPAC Semi empirical Methods The method descriptions that follow represent a very simplified view of the semi empirical methods available in Chem3D and CS MOPAC For more information see the online MOPAC manual Extended Huckel Method Developed from the qualitative H ckel MO method the Extended H ckel Method EH represents the earliest one electron semi empirical method to incorporate both o and p valence systems It is still widely used owing to its versatility and success in analyzing and interpreting ground state properties of organic organometal
234. e Model Display control panel 3 Select the Group radio button in the Color by section Each atom in your model appears in the color specified for its group NOTE Color by Group is only displayed when Ribbon or Cartoon display mode is selected Selecting a Group or Fragment There ate several ways to select a group or fragment The simplest is to use the Model Explorer and select the fragment Ch Ultra 1000 p49 You may also select a single atom or bond and use the Select Fragment command on the Edit menu NOTE If you want to select more than one fragment you must use the Model Explorer Manipulating Models 93 Selecting New in Chem3D version 9 0 1 is double click selection After you have selected a single atom or bond each successive double click will select the next higher level of hierarchy Selecting Atoms or Groups by Distance You can select atoms or groups based on the distance or radius from a selected atom or group of objects This feature is useful among other things for highlighting the binding site of a protein To select atoms or groups by distance 1 Use the Model Explorer to select an atom or fragment 2 Right click the selected object From the context menu point to Select and click the 94 Manipulating Models 3 appropriate option Option Result Select Atoms Selects all atoms lying within within Distance of the specified distance from Selection any p
235. e Properties tab select Molecular Surfaces and Spin Density use Shift click 2 Press Run The calculation toolbar appears Calculation When the calculation is finished select the Trackball tool and rotate the model back and forth It should be completely planar CambridgeSoft Tutorial 9 Mapping Properties onto Surfaces To complete this tutorial you will need to adjust a 5 On the Surfaces toolbar choose Isocharge number of surface settings For convenience activate the Surfaces toolbar The Isocharge tool appears 1 From the View menu point to Toolbars and choose Surfaces The Surfaces toolbar appears Drag it into the workspace for added convenience RR CRMC 6 Set the isocharge to 0 0050 The number in the Kes ds middle is the current setting a Solvent radius NOTE Isovalues are used to generate the surface gt You can adjust this value to get the display you want le Display mode The illustration below was made with the setting of 0 0050 3 Color Mapping gt Surface color E Resolution HOMO LUMO selection au Isovalues Color A a Color B 4 2 On the Surfaces toolbar point to Surface and select Total Charge Density Most of the surface is grey indicating that there is no contribution to it from unpaired electrons The areas of red centered over each of the terminal carbons is a visual representation of the expected The icon changes t
236. e Web www cambridgesoft com services mail USER INFORMATION Pes print tegib City State Zip Tel Fax DETAILS OF THE PROBLEM Submit this form via WWW www cambridgesoft com services mail EMAIL support cambridgesoft com 1 617 588 9360 MAIL CambridgeSoft 100 CambridgePark Dr Cambridge MA 02140 USA FAX SYSTEM CONFIGURATION SOFTWARE Application Name Version Number Serial Number SYSTEM Windows version MacOs version Web Browser s version us 1 617 588 9300 FAX 1617 588 9390 www EU 0080087520000 FAX 44 1223 464990 EMAIL MAIL 100 CambridgePark Drive Cambridge MA 02140 USA www cambridgesoft com info cambridgesoft com CambridgeSoft www cambridgesoft com CS ChemOffice Desktop to Enterprise Solutions eryjOurey gt SI A a A 4 3 0 3 a e ChemOffice Ultra desktop edition includes it all with ChemDraw Ultra Chem3D Ultra BioOffice Ultra Inventory Ultra E Notebook Ultra and ChemInfo Ultra for a seamlessly integrated suite Draw reaction mechanisms for publication and visualize 3D molecular surfaces orbitals and molecular properties Features include BioOffice The Merck Index ChemACX Database i CombiChem Excel ChemDraw Excel and BioViz Bring your work to the web or query online databases with the ChemDraw ActiveX Plugin ChemOffice Enterprise is a comprehensive know
237. e available to a model by storing iterations of the molecular dynamics run and later examining each frame Performing a Molecular Dynamics Computation To perform a molecular dynamics simulation 1 Build the model or fragments that you want to include in the computation NOTE The model display type you use affects the speed of the molecular dynamics computation Model display will decrease the speed in the following order Wire Frame lt Sticks lt Ball and Sticks lt Cylindrical Bonds lt Ribbons lt Space Filland VDW dot surfaces lt Molecular Surfaces 2 Minimize the energy of the model or fragments using MM2 or MOPAC 3 To track a particular measurement during the simulation choose one of the following e Select the appropriate atoms and choose Set Bond Angle or Set Bond Length on the Measurement submenu of the Structure menu 4 Choose Molecular Dynamics on the MM2 submenu of the Calculations menu of the Calculations menu 158 MM2 and MM3 Computations The Molecular Dynamics dialog box appears with the default values Molecular Dynamics Job Type Dynamics Properties General Step Interval 20 Frame Interval 10 Terminate After 110000 steps Heating Cooling Rate 1 000 Keal atom ps Target Temperature 300 Kelvin Summary Parameter Quality Some parameters are guessed Job Type Molecular Dynamics Step Interval 2 0 fs Frame Interval 10 fs Termin
238. e data streams of new lab technology is a key challenge Registration System organizes information about new compounds according to an organization s business rules while Inventory Manager works with Registration System and chemical databases for complete management of chemical inventories CombiChem Enterprise and Formulations amp Mixtures are also important parts of research data management APPLIED BIOINFORMATICS Finding structural determinants of biological activity requires processing masses of biological assay data Scientists use BioAssay HTS and BioSAR Browser to set up biological models and visualize information to generate spreadsheets correlating structure and activity and to search by structure CHEMICAL DATABASES Good research depends on reference information starting with the structure search able ChemACX Database of commercially available chemicals The Merck Index 13th Edition and other databases provide necessary background about chemicals their properties and reactions CONSULTING amp SERVICES CambridgeSoft s scientific staff has the industry experience and chemical and biological knowledge to maximize the effectiveness of your information systems Software Applications amp Features Databases Includes O ts O wy Sy e S CAs Oso x Se e a o e m Sa ChemDraw Pro Win Mac ChemDraw Plugin Pro Win Mac Chem3D Pro Chem3D Plugin Pro ChemFinder
239. e dipole charge Each type of interaction uses a different form of the electrostatic equation as shown below charge charge contribution Es Z J 4 where the value 332 05382 converts the result to units of kcal mole 140 Computation Concepts dipole dipole contribution where the value 14 388 converts the result from ergs mole to kcal mole is the angle between the two dipoles p and uj OL and q are the angles the dipoles form with the vector fij connecting the two at their midpoints and D is the effective dielectric constant dipole charge contribution EA Z J where the value 69 120 converts the result to units of kcal mole Bond dipole parameters u for each atom pair are stored in the bond stretching parameter table The charge q is stored in the atom types table The molecular dielectric is set to a constant value between 1 0 and 5 0 in the MM2 Atom types table NOTE Chem3D does not use a distance dependent dielectric Cutoff Parameters for Electrostatic Interactions The use of cutoff distances for electrostatic terms as for van der Waals terms greatly improves the computational speed for large molecules by eliminating long range interactions from the computation As in the van det Waals calculations Chem3D invokes a fifth order polynomial switching function in order to maintain second order continuity in the force field The switching function is invoked as minimum values for
240. e divided by 10 raised to the power of the exponent The first line of a Cartesian coordinate file is followed by one line of data for each atom in the model Each line describing an atom begins with the symbol for the atom This symbol must correspond to a symbol in the Elements table The symbol can include a charge such as N The symbol is followed by the serial number The serial number is followed by the three coordinates of the atom If you have specified crystal cell parameters in the first line of the file then these numbers are the fractional cell coordinates Otherwise the three numbers ate X Y and Z Cartesian coordinates Following the coordinates is the atom type number of the atom type for this atom This number must correspond to the code of an atom type record specified in the file format atom type table For more information see Editing File Format Atom Types on page 241 Following the atom type number is the connection table for the atom You can specify up to ten other atoms The connection table for a Cartesian coordinate file can be listed in one of two ways by serial number or by position Connection tables by serial number use the serial number of each atom to determine the number that appears in the connection table of other atoms All serial numbers must therefore be unique File Formats 243 File Format Examples Connection tables by position use the relative differen
241. e following types of calculations as indicated by MOPAC keywords ate incompatible with MNDO d e COSMO Conductor like Screening Model solvation e POLAR polarizability calculation 170 MOPAC Computations e GREENF Green s Function e TOM Miertus Scirocco Tomasi self consistent reaction field model for solvation Using Keywords Selecting parameters for a MOPAC approximation automatically inserts keywords in a window on the General tab of the MOPAC Interface You can edit these keywords or use additional keywords to perform other calculations or save information to the out file CAUTION Use the automatic keywords unless you are an advanced MOPAC user Changing the Reywords may give unreliable results For a complete list of keywords see the MOPAC online manual Automatic Keywords The following contains keywords automatically sent to MOPAC and some additional keywords you can use to affect convergence Keyword Description EF Automatically sent to MOPAC to specify the use of the Eigenvector Following EF minimizer BFGS Prevents the automatic insertion of EF and restores the BFGS minimizer GEO OK Automatically sent to MOPAC to override checking of the Z matrix CambridgeSoft Using Keywords Keyword Description MMOK RMAX n nn RMIN n nn PRECISE LET RECALC 5 Automatically sent to MOPAC to specify Molecular Mechanics correction for amide bonds Use the additional
242. e menu The Spin About command automatically activates the Record command Inspecting Models 115 Animations To stop spinning e On the Movie toolbar click the Stop button Spins are automatically recorded To replay the spins e Click Start Editing a Movie You can change a movie by removing frames To remove a frame 1 Position the movie to the frame you want to delete 2 Click the Remove Frame button x Movie Control Panel You can control how a movie is created by changing settings in the Movies control panel in the Model Settings dialog box You can specify the number of frames and at what increment they are captured To display the Movies control panel 1 From the Movies menu choose Properties 2 Take the appropriate actions If you want to Then set the movie toloop Click the Loop or Back or repeat backwards and Forth radio button and forwards 116 Inspecting Models If you want fo Then specify the speed at which the movie is replayed specify the number of degrees of rotation that is captured as a frame while recording Drag the Speed slider knob to the left to play your movie at a slower speed a smaller number of degrees per second Drag the Speed slider knob to the right to play your movie at a faster speed a larger number of degrees per second Drag the Smoothness slider knob to the left to capture more frames a smaller number of degrees of r
243. e notebook will do everything except calculate the experimental yield To do that you still have to run the experiment Microsoft Office amp Galactic Spectra E N otebook manages all the other kinds of data chemists store in their notebooks For free form data you can include M icrosoft Word or Excel documents For spectral data you can take advantage of the G alactic Spectral Control enbedded in the notebook that allows for analysis and storage of hundreds of kinds of spectra files Inventory Manager E N otebook includes an inventory of common reactants and reagents If you have one of these common com ponents loaded into the inventory application all you have to do is click the Add Reactant button in E N otebook From here you navigate to the desired compound and include it in your stoichiometry calcula tions The enterprise edition of E N otebook integrates with procurement and inventory management systems N ot only does this provide a useful way to know what compounds you have in stock and where they are locat ed it also saves time entering data Registration System E N otebook can be integrated into the entire chemical workflow of enterprise organizations For example once you record a reaction in your notebook you can click a button to forward the products of the reaction to your compound registration system These kinds of workflow enhancements increase productivity for the entire organization EMAIL info cambridgesoftcom WW
244. e properties of organic organometallic and inorganic compounds of biological interest Built into Chem3D EH is the default semiempirical method used to calculate data required for displaying molecular surfaces The EH method uses a one electron Hamiltonian with matrix elements defined as follows Ay Aa H 05K Ay Hy Syy psy where I is the valence state ionization energy VSIE of orbital u as deduced from spectroscopic data and K is the Wolfsberg Helmholtz constant CambridgeSoft Quantum Mechanics Theory in Brief usually taken as 1 75 The Hamiltonian neglects electron repulsion matrix elements but retains the overlap integrals calculated using Slater type basis orbitals Because the approximated Hamiltonian H does not depend on the MO expansion coefficient Cy the matrix form of the EH equations HAS CFE can be solved without the iterative SCF procedure Methods Available in CS MOPAC The approximations that MOPAC uses in solving the matrix equations for a molecular system follow Some areas requiting user choices are e RHF or UHF methods e Configuration Interaction CI e Choice of Hamiltonian approximation potential energy function RHF The default Hartree Fock method assumes that the molecule is a closed shell and imposes spin restrictions The spin restrictions allow the Fock matrix to be simplified Since alpha spin up and beta spin down electrons are always paired the basic RHF metho
245. e to insert into or link to the target application document Printing and Exporting Models 127 Exporting With the Clipboard 128 Printing and Exporting Models CambridgeSoft Exporting With the Clipboard Chapter 8 Computation Concepts Computational Chemistry Overview Computational chemistry extends beyond the traditional boundaries separating chemistry from physics biology and computer science It allows the exploration of molecules by using a computer when an actual laboratory investigation may be inappropriate impractical or impossible As an adjunct to experimental chemistry its significance continues to be enhanced by increases in computer speed and power Aspects of computational chemistry include e Molecular modeling e Computational methods e Computer Aided Molecular Design CAMD e Chemical databases e Organic synthesis design While a number of different definitions have been proposed the definition offered by Lipkowitz and Boyd of computational chemistry as those aspects of chemical research that are expedited or rendered practical by computers is perhaps the most inclusive Molecular modeling while often taken to include computational methods can be thought of as the rendering of a 2D or 3D model of a molecule s structure and properties Computational methods on the other hand calculate the structure and property data necessary to render the model Within a modeling program such as C
246. e unless specific permission has been obtained from the copyright owner If you pirate software you may face not only a civil suit for damages and other relief but criminal liability as well including fines and jail terms of up to one year Q So I m never allowed to copy software for any other reason A That s correct Other than copying the software you purchase onto a single computer and making another copy for archival purposes only or purposes only of maintenance or repair the copyright law prohibits you from making additional copies of the software for any other reason unless you obtain the permission of the software company Q At my company we pass disks around all the time We all assume that this must be okay since it was the company that purchased the software in the first place A Many employees dont realize that corporations are bound by the copyright laws just like everyone else Such conduct exposes the company and possibly the persons involved to liability for copyright infringement Consequently more and more corporations concerned about their liability have written policies against such softlifting Employees may face disciplinary action if they make extra copies of the companys software for use at home or on additional computers within the office A good rule to remember is that there must be one authorized copy of a software product for every computer upon which itis run Q Can take a p
247. e van der Waals parameters used to compute the force field for each atom in your model Each MM2 Atom Type record contains eight fields Atom type number R Eps Reduct Atomic Weight Lone Pairs Quality and Reference Atom type number The Atom Type number field is the atom type to which the rest of the MM2 Atom Type Parameter record applies The records in the MM2 Atom Type table window are sorted in ascending order of Atom Type Atom type number Parameter Tables 283 MM2 Atom Types R The R field is the van der Waals radius of the particular atom The larger the van der Waals radius of an atom is the larger that atom NOTE Chem3D uses the van der Waals radius R in the MM2 Atom Types table for computation It is not the same as the van der Waals radius in the Atom Types table which is used for displaying the model Eps The Eps or Epsilon field is a constant which is proportional to the depth of the potential well As the value of epsilon increases the depth of the potential well increases as does the strength of the repulsive and attractive interactions between this atom and other atoms NOTE For specific VDW interactions the R and Eps values from the VDW Interactions table are used instead of values in the MM2 Atom Types table See VDW Interactions later in the chapter for more information Reduct Reduct the fourth field is a constant used to orient the center of the electron cloud o
248. eM M 2 to perform rapid energy minimizations and molecular dynamics simulations ChemProp estimates physical properties such as logP boiling point melting point and more Visualize Connolly surface areas and molecular volumes a Vibration 11 Freqeency 3054 AMATA Heducad Megs be Ja Efecthe Masa 1 4407 a Tipe TESS gt Large Molecular Visualization SOFTWARE Chem3D Ultra Ultimate Modeling Visualization amp Analysis e Adds MOPAC CLogP Tinker ChemProp ChemSAR amp Chem3D Plugin to Chem3D Pro Includes GAMESS Gaussian client interfaces e ChemSAR Excel builds SAR tables Chem3D Pro Premier Modeling Visualization amp Analysis e Create 3D models from ChemDraw or ISIS Draw accepts output from other modeling packages e Model types space filling CPK ball stick stick ribbons VDW dot surfaces amp wire frame e Compute amp visualize partial charges 3D surface properties amp orbital mapping e Polypeptide builder with residue recognition e ChemProp Basic property predictions with Connolly volumes surface areas e MM2 minimization molecular dynamics extended H ckel MO calculations e Supports PDB MDL Molfile Beilstein RO SDAL Tripos SYBYL MOL EPS PICT GIF 3DMF TIFF PNG more MOPAC Chem3D Advanced Semi Empirical Computation Calculate AH solvation energy dipoles charges UHF amp RHF spin densities MEP charge densities amp more Optim
249. eSoft 5 Revocation of Subscription Access Any use which is commercial and or non personal is strictly prohibited and may subject the Subscriber making such uses to revocation of access to this Paid Subscription Service as well as any other applicable civil or criminal penalties Similarly sharing a Subscriber password with a non Subscriber or other wise making this Paid Subscription Service available to third parties other than the Authorized U ser as defined above is strictly prohibited and may subject the Subscriber participating in such activities to revocation of access to the Paid Subscription Services and the Subscriber and any third party to any other applicable civil or criminal penalties under copyright or other laws In the case of an authorized site license a Subscriber shall cause any employee agent or other third party which the Subscriber allows to use the Paid Subscription Service materials to abide by all of the terms and conditions of this Agreement In all other cases only the Subscriber is permitted to access the Paid Subscription Service materials Should CambridgeSoft become aware of any use that might cause revocation of the license they shall notify the Subscriber T he Subscriber shall have 90 days from date of notice to correct such viola tion before any action will be taken 6 Trademark Notice THE MERCK INDEX is a trademark of Merck Company Incorporated Whitehouse Station N ew Jersey USA and is registered
250. ea Angstroms probe sphere representing the solvent is rolled over the molecular model Connolly The volume contained Solvent Excluded within the contact Volume Angstroms molecular surface Exact Mass g mole The exact molecular mass of the molecule where atomic masses of each atom ate based on the most common isotope for the element Formal Charge electrons The net charge on the molecule The molecular formula showing the exact Molecular Formula number of atoms of each element in the molecule Molecular Weight atomic mass units The average molecular mass of the structure where atomic masses are based on the weighted average of all isotope masses for the element 206 SAR Descriptors to the Minimum Surface Area The Minimum Surface Area is the surface area of a sphere having a volume equal to the Solvent Excluded Volume of the molecule Computed from the Connolly Molecular Surface Area and Solvent Excluded Volume properties Principal Moments of The Moments of Inertia Inertia X Y Z grams mole Angstroms when the Cartesian cootdinate axes ate the principal axes of the molecule The surface area and volume calculations ate performed with Michael Connolly s program for computing molecular surface areas and volume M L Connolly The Molecular Surface Package J Mol Graphics 1993 11 For the latest information about the Connolly programs and definitions of the at
251. ea and volume properties see the following web site http connolly best vwh net NOTE The default Probe Radius used in the calculation is 1 4 angstroms You can change the Probe Radius value in the Parameters dialog box The Principal Moments of Inertia are the diagonal elements of the inertia tensor matrix when the Cartesian coordinate axes are the principal axes of the molecule with the origin located at the center of CambridgeSoft ChemProp Std Server mass of the molecule In this case the off diagonal elements of the inertia tensor matrix are zero and the three diagonal elements L ly and L correspond to the Moments of Inertia about the X Y and Z axes of the molecule ChemProp Pro Server ULTRA CS ChemProp Pro server allows you to predict the following physical and thermodynamic properties of molecules Property Description NOTE Fragmentation methods and literature values are used for these calculations Use the Full Report property to view references for the methods Property Description Boiling Point The boiling point for the Kelvin structure at 1 atm Critical Temperature Kelvin The temperature T3 above which the gas form of the structure cannot be liquefied no matter the applied pressure Critical Pressure bar The minimum pressure P that must be applied to liquefy the structure at the critical temperature Critical Volume The volume occupied V3 cm3 mo
252. ebook ChemFinder PDF literature seach Combrdpeson v co News O CombridgeSoft mm a Spring Acs een under Anahewn CA E Notebook Buy Software Academic Site License Don t miss out on traning y t Tuesday March 30th Live Classroom Training Chemap 9am 12pm amp ChemDrove gen Sp Regait posted 004 AAAI Oracle Cartridge J M View Product Demos d Seminars New Features Chemical Dorabases 100 Now erdu Ean ss Check the CambridgeSoft web site for new product information You can also get to SciStore Com ChemBioNews Com and other pages through CambridgeSoft Com Chem3D Appendix Using the ChemOffice SDK The ChemOffice Software Developer s Kit SDK enables you to customize your applications To browse the ChemOffice SDK e From the Online menu choose Browse ChemOffice SDK The CS ChemOffice SDK page opens in your browser TechnicalSupport CambridgeSoft Com Support CS ChemOffice Software Developer s Kit ChemDraw The ChemOffice SDK page contains documentation sample code and other resources for the Application Programming Interfaces APIs NOTE You must activate Javascript in your browser in order to use the ChemOffice SDK page Accessing the CambridgeSoft Web Site 227 Browsing CambridgeSoft com 228 Accessing the CambridgeSoft Web Site CambridgeSoft Using the ChemOffice SDK Appendix B Technical Support Ove
253. echanics correction for amide bonds Use the additional keyword NOMM to turn this keyword off Example 5 Comparing the Stability of Glycine Zwitterion in Water and Gas Phase To compare stabilities 1 From the File menu choose New Model 2 Click the Text Building tool 3 Click in the model window A text box appears 4 Type HGlyOH and press the Enter key A model of glycine appears A 5 From the MOPAC Interface submenu of the Calculations menu choose Minimize Energy 6 On the Theory tab choose PMS 194 MOPAC Computations 7 On the Property tab Ctrl click Heat of Formation and COSMO Solvation 8 Click Run The results appear in the Messages window 9 From the MOPAC Interface submenu of the Calculations menu choose Minimize Energy 10 On the Property tab deselect COSMO Solvation 11 Click Run The results appear in the Messages window To create the zwitterionic form 1 Click the Text Building tool 2 Click the nitrogen type then press the Enter key cc 3 Click the oxygen atom type Enter key then press the The glycine zwitterion is formed 4 Perform a minimization with and without the COSMO solvation property selected as performed for the glycine model The following table summarizes the results of the four analyses Form of AH Solvent glycine kcal mole Accessible Surface neutral H20 108 32861 52 36067 zwitterion H20 126 93974 52 37133 Ca
254. echniques and provide insight into which regions of a molecule ate more susceptible to electrophilic or nucleophilic attack You can visualize the relative MEP values by color when MEP is mapped onto another surface total charge density The most positive MEP value is red the most negative blue and neutral is white Molecular Orbitals Molecular orbital MO surfaces visually represent the various stable electron distributions of a molecule According to frontier orbital theory the shapes and symmetries of the highest occupied and lowest unoccupied molecular orbitals HOMO and LUMO are crucial in predicting the reactivity of a species and the stereochemical and regiochemical outcome of a chemical reaction To set the molecular orbital being displayed e From the Surfaces menu point to Molecular Orbital to see the HOMO LUMO options Select the orbital You can specify the isocontour value for any computed MO surface using the Isocontour tool on the Surfaces menu The default isocontout value for a newly computed surface is the value you last specified for a previously computed surface If you have not specified an isocontout value the default value is 0 01 NOTE The default isocontour value for an MO surface imported from a cube file is 0 01 regardless of any previously set isocontour value CambridgeSoft Molecular Surface Displays Vi sua izi n g S U rfa ces From sources other than Windows create a Gaussian
255. ecome Pro S and all of the Pro S positioned atoms become Pro R All dihedral angles used to position atoms are negated NOTE Pro R and Pro S within Chem3D are not equivalent to the specifications R and S used in standard chemistry terminology For example for the structure below when any atom is selected e From the Structure menu point to Reflect Model and choose Through X Z Plane do ee j Chem3D produces the following structute an enantiomer oe o9 Building and Editing Models 89 Changing Stereochemistry Refining a Model After building a 3D structure you may need to clean it up For example if your model was built without automatic rectification atom type assignment or standard measurements you can apply these as a refinement Rectifying Atoms To rectify the selected atoms in your model From the Structure menu choose Rectify Hydrogen atoms are added and deleted so that each selected atom is bonded to the correct number of atoms as specified by the geometry for its atom type This command also assigns atom types before rectification 90 Building and Editing Models The atom types of the selected atoms are changed so that they are consistent with the bound to orders and bound to types of adjacent atoms Cleaning Up a Model Normally Chem3D creates approximately correct structures However it is possible to create unrealistic structures especially when you bu
256. ecting graphical objects and menu items Chem3D serves as a front end GUI for Gaussian 03W enabling you to create and run Gaussian jobs in Chem3D The model in the Chem3D window transparently provides the data for Gaussian computations Menus and dialog boxes replace the many Gaussian commands although Chem3D preserves the option to use them for less common and advanced computations Minimize Energy To perform a minimize energy computation on a molecule From the Calculations menu point to Gaussian and choose Minimize Energy ChemOffice 2005 Chem3D The Minimize Energy dialog box appears Minimize Energy Job Type Theory Properties General Job Type Minimize Eneray IV Display Every Iteration Record Every Iteration Copy Measurements to Messages Do Not Calculate Force Constants Calculate Initial Force Constants Calculate Force Constants At Each Point Use Tight Convergence Criteria Summary Job Type Minimize Energy Display Each Iteration Method Closed Shell Restricted Hartree Fock Basis Set STO 3G Spin Multiplicity 1 L Save Save As The Job Type Tab The Job Type tab of the dialog box defaults to Minimize Energy when you select Minimize Energy from the menu Job Type can be changed to Compute Properties from within this tab v Cancel Select the appropriate options If you want to Then select watch the minimization Display Every Iteration
257. ed in consecutive records Hydrogen lone pair and dummy atoms are listed after heavy atoms To display the Cartesian Coordinates table do one of the following e If the Tables window has been activated click the XYZ tab at the bottom of the window e If the Tables window has not been activated choose Cartesian Table from the View menu The Cartesian Coordinates table appeats The Cartesian Coordinates table acts like the other tables you can select atoms or bonds either in the table or in the model Use the pin icon to collapse the window to save space Collapsed table tabs je Mouse over a tab to display the table The most recently used table displays the full name ugisaye5 Comparing Models by Overlay The Overlay submenu on the Structure menu is used to lay one fragment in a model window over a second fragment Each fragment remains rigid during the overlay computation Common uses of Overlay include e Comparing structural similarities between models with different composition e Comparing conformations of the same model Inspecting Models 109 Comparing Models by Overlay Chem3D provides two overlay techniques Tutorial 6 Overlaying Models on page 43 describes the Fast Overlay method This section uses the same example superimposing a molecule of Methamphetamine on a molecule of Epinephrine Adrenalin to demonstrate their structural similarities to describe the Minimization
258. ed in constructing the 1 electron atom orbitals is a minimum basis set of only the s and p Slater Type Orbitals STOSs for valence electrons The core electrons ate not explicitly treated Instead they ate added to the nucleus The nuclear charge is termed Neffective For example Carbon as a nuclear charge of 6 2 core electrons for a effective nuclear charge of 4 e Many of the 2 electron Coulomb and Exchange integrals are parameterized based on element Choosing a Hamiltonian Overall these potential energy functions may be viewed as a chronological progression of improvements ftom the oldest method MINDO 3 to the newest method PM5 However although the MOPAC Computations 167 MOPAC Semi empirical Methods improvements in each method were designed to make global improvements they have been found to be limited in certain situations The two major questions to consider when choosing a potential function are e Is the method parameterized for the elements in the model Does the approximation have limitations which render it inappropriate for the model being studied For mote detailed information see the MOPAC online manual MINDO 3 Applicability and Limitations MINDO 3 Modified Intermediate Neglect of Diatomic Overlap revision 3 is the oldest method Using diatomic pairs it is an INDO Intermediate Neglect of Diatomic Orbitals method where the degree of approximation is more severe than the NDDO
259. edly Finally the most recent PM3 is a reparameterization of AM1 The approximations in PM3 are the same as AM1 This sequence of potential energy functions represents a series of improvements to support the initial assumption that complete neglect of diatomic orbitals would yield useful data when molecules proved too resource intensive for ab initio methods MOPAC 293 Potential Functions Parameters Adding Parameters to MOPAC Parameters are in constant development for use with PM3 and AM1 potential functions If you find that the standard set of parameters that comes with CS MOPAC does not cover an element that you need for example Cu you can search the literature for the necessary parameter and add it at run time when performing a MOPAC job This flexibility greatly enhances the usefulness of MOPAC 294 MOPAC You can add parameters at run time using the keyword EXTERNAL name where name is the name of the file and its full path containing the additional parameters A description of the required format for this file can be found in Figure 3 4 page 43 of the MOPAC 2000 V 1 3 manual included on the CD ROM CambridgeSoft Adding Parameters to MOPAC Index Symbols CHR bending force parameters 282 3dm file format 121 alc file format 118 121 avi file formats 121 bmp file format 119 ccl file format 118 121 cc2 file format 118 121 cdx file format 118 con file format 122 ct file format 11
260. el and choose Clean Up from the Structure menu TIP You don t have to click the Select tool every time you want to select something Just hold down the letter on your keyboard while working with any building tool and you temporarily activate the Select tool You cannot specify stereochemistry when you build models with labels The structure of 1 2 dimethyl cyclopentane appears in the trans conformation To obtain the ws isomer 1 Click the Select tool kk 2 Select C 1 3 From the Structure menu choose Invert The cs isomer appears You can rotate the molecule to see the differences between the isomers after you invert the molecule Using Substructures Labels are useful to build simple structures However if you make larger more complex structures you will find it easier to use a combination of labels and pre defined substructures Over 200 substructures are pre defined in Chem3D These substructures include the most commonly used organic structures TIP Pre defined substructures are listed in the substructures xml file You can view the list by pointing to Parameter Tables on the View menu and selecting Substructures Text typed in the text box is case sensitive You must type it exactly as it appears in the Substructures table Build a model of nitrobenzene 1 From the File menu choose New 2 Click the Text Building tool A 3 Click the empty space in the model window CambridgeSoft Tutor
261. emOffice 2005 Appendix 4 Membered Ring Angles xml 4 Membered Ring Torsionals xml Angle Bending Parameters xml Atom Types xml Bond Stretching Parameters xml Conjugated Pisystem Atoms xml Bond angles for bonds in 4 membered rings In force field analysis angle bending portion of the force field for bonds in 4 membered rings Computes the portion of the force field for the torsional angles in your model for atoms in 4 membered rings Standard bond angles In force field analysis angle bending portion of the force field for bonds Contains atom types available for building models Standard bond lengths In force field analysis bond stretching and electrostatic portions of force field for bonds Bond lengths for bonds involved in Pi systems Pi system portion of the force field for pi atoms Parameter Tables 271 Parameter Table Use Parameter Use Parameter Use Table Table Conjugated Pi system portion of the force Torsional Computes the portion of the Pisystem field for pi bonds Parameters xml force field for the torsional Bonds xml angles in yout model Electronegativity Adjusts optimal bond length Adjustments xml between two atoms when one atom is attached to an atom that is electronegative Contains elements available for building models Elements xml MM2 Atom Type van der Waals parameters for Parameters xml computing force field for each atom MM2 Constants used for Co
262. ements in the Bond Stretching and Angle Bending parameter tables For all other measurements performing a Building and Editing Models 85 Setting Measurements Clean Up Structure or MM2 computation alters these values To use values you set in these computations you must apply a constraint Setting Bond Lengths To set the length of a bond between two bonded atoms 1 Select two adjacent atoms 2 From the Structure menu point to Measurement and choose Set Bond Length Measurement The Measurements table appears displaying distance between the two atoms The Actual value is highlighted 3 Edit the highlighted text 4 Press the Enter key Setting Bond Angles To set a bond angle 1 Select three contiguous atoms for a bond angle 2 From the Structure menu point to Measurement and choose Set Bond Angle Measurement The Measurements table appears displaying the angle value The Actual value is highlighted 3 Edit the highlighted text 4 Press the Enter key Setting Dihedral Angles To set a dihedral angle Select four contiguous atoms N From the Structure menu point to Measurement and choose Set Dihedral Measurement The Measurements table appears displaying the angle value The Actual value is highlighted w Edit the highlighted text 86 Building and Editing Models 4 Press the Enter key Setting Non Bonded Distances Atom Pairs To set the distance between two non b
263. emicals on a lab by lab basis The moving of chemical inventories is greatly helped by this model For example if an entire refrigerator is relocated all of its containers move along with it There is no need to re catalog or reconcile which saves a great deal of time Mhp gt Substructure Search Form gt Viewing Information by Container DISCOVERY e Integrated with Registration System and ChemACX for procurement and life cycle chemical tracking Cascading location model allows different labs to track reagents at different levels stockroom refrigerators e Designed for tracking reagents high throughput discovery libraries and true HTS plate management at multiple levels Discovery Reagents amp Stockroom Inventory Manager integrates fully with CambridgeSoft s ChemACX Database of available chemicals and Registration System It also functions completely as a stand alone application Through this architecture CambridgeSoft s enterprise solutions are truly plug and play T here are no added system integration costs and the applications can live on different servers in different parts of the world Flex ibility The flexibility of the location model allows Inventory M anager to accommodate both reagent and discovery inventories in the same system Each container in the system can be configured to track quantities in increas ingly small values A reagent bottle for instance can be measured as full or e
264. ens in its default position attached to the right edge of the model window If the tab is visible Chem3D Tutorials 31 Tutorial 1 Working with ChemDraw 2 Click the ChemDraw tab to open the panel TIP The panel default is Auto hide If you want the panel to stay open push the pin on the upper right ChemDraw 995 LD YN pin E Click in the ChemDraw panel it A blue line appears around the ChemDraw Panel model window and the ChemDraw tools palette appeats 4 On the ChemDraw tools palette select the Benzene Ring tool on Click in the panel to place a benzene ring The ChemDraw structure is converted into a 3D representation e E Yew De E Eunet z i i i 4 0D a 2 A gt 3 Q 3ZBLIAISE 007 OO OEE RC 08 You can work with the model in Chem3D The 2D and 3D models are hot linked so any change in one changes the other 1 Double click one of the hydrogens in the 3D model A text box appears 2 Type OH in the text box then hit the Enter key 3 A phenol molecule is displayed in both the Chem3D model window and the ChemDraw window 32 Chem3D Tutorials You can turn off the hot linking by clicking the Synchronize button If you do this you will need to use the 3D gt Draw and Draw gt 3D buttons to copy models between the windows Synchronize Draw gt 3D replace Name Struct Cleanup text box ChemDraw wk v hagas 0 Draw gt 3D ad
265. entify the dihedral to track You should have a nearly coplanar four atom chain such as H 4 C 1 C 2 H 7 selected 9 From the Structure menu point to Measurements and choose Dihedral Angle The Measurements table appears and displays an actual value for the selected dihedral angle of about 3 degrees this will vary slightly between experiments Chem30 Ultra Untitled 3 BR mars DZ Cortos Me mol Zh zone totation tool Hot Key XIY Z Mouse About XY Axis CeMouse Track Gall Mouse About Local Bandidos NN 184 MOPAC Computations 10 From the MOPAC Interface submenu of the Calculations menu choose Optimize to Transition State 11 Click the Copy Measurements to Messages box on the Job Type tab 12 Click Run The ethane model minimizes so that the dihedral is 0 degrees corresponding to the eclipsed conformation of ethane a known transition state between the staggered minima conformations To see the Newman projection of the eclipsed ethane model 1 Select both carbon atoms 2 From View Position submenu of the View menu click Align View Z Axis With Selection NOTE If you perform an Energy Minimization from the same starting dihedral your model would optimize to the staggered conformation of ethane where the dibedral is 60 degrees instead of optimizing to the transition state Computing Properties To perform a single point calculation on the current conforma
266. enu choose Minimize Energy and click Run 3 When the minimization is complete reorient the model using the Rotation bars to see the final chair conformation NOTE The values of the energy terms shown here are approximate and can vary slightly based on the type of processor used to calculate them Note All parameters used are A Iteration 49 Minimizatior Stretch 0 3302 Bend 0 3551 Stretch Bend 0 0862 e Torsion 2 1527 La Non 1 4 VDW 1 0573 Y 1 4 vow 4 6922 Total 6 5591 Calculation ending 3 lt gt Output El Comments Dihedral Driver This conformation is about 5 5 kcal mole more stable than the twisted boat conformation For molecules more complicated than cyclohexane where you don t already know what the global minimum is some other method is necessary for locating likely starting geometries for minimization One way of accessing this conformational space of a molecule with large energy barriers is to perform molecular dynamics simulations This in effect heats the molecule thereby increasing the kinetic energy enough to surmount the energetically disfavored transition states MM2 and MM3 Computations 157 Minimize Energy Molecular Dynamics Molecular Dynamics uses Newtonian mechanics to simulate motion of atoms adding or subtracting kinetic energy as the model s temperature increases or decreases Molecular Dynamics allows you to access the conformational spac
267. er 1 Holding down the Ctrl key select the atoms in the group 2 Choose New Group from the Context Sensitive menu The group is created with the default name selected 3 Rename the group by typing a new name Adding to Groups You can add lower level objects to an existing group ot combine groups to form new groups Inspecting Models 113 Working With the Model Explorer To add to a group 1 Select the objects you want to combine using either Shiftt click contiguous or Ctrl click non contiguous 2 Select Move Objects to Group from the Right click menu 3 Rename the group if necessary NOTE The order of selection is important The group or chain you are adding to should be the last object selected Pasting Substructures You can cut and paste or copy paste any substructure into another structure either within or between model windows In addition to the usual methods using the Cut Copy and Paste commands on either the Edit or Context Sensitive menus or Ctrl X Ctrl C and Ctri V you can use the Text tool to paste substructures To paste a substructure with the Text tool 1 Select a fragment chain or group 2 Choose Replace with Text Tool from the Context Sensitive menu The substructure appears in a Text tool in the model window 3 Click the Text tool on the atom that you want to link to the substructure Deleting Groups When deleting groups you have two options
268. eraction Energy The first three terms given as 1 2 and 3 below are the so called bonded interactions In general these bonding interactions can be viewed as a strain energy imposed by a model moving from some ideal zero strain conformation The last term which represents the non bonded interactions includes the two interactions shown below as 4 and 5 The total potential energy can be described by the following relationships between atoms The numbers indicate the relative positions of the atoms 1 Bond Stretching 1 2 bond stretching between directly bonded atoms 2 Angle Bending 1 3 angle bending between atoms that are geminal to each other 3 Torsion Energy 1 4 torsional angle rotation between atoms that are vicinal to each other 136 Computation Concepts 4 Repulsion for atoms that are too close and attraction at long range from dispersion forces van der Waals interaction 5 Interactions from charges dipoles quadrupoles electrostatic interactions The following illustration shows the major interactions non bonded interactions a angle bending bond i stretching torsion Different kinds of force fields have been developed Some include additional energy terms that describe other kinds of deformations such as the coupling between bending and stretching in adjacent bonds in order to improve the accuracy of the mechanical model The reliability of a molecular mechanical for
269. ergy tool pale on the Calculation toolbar For more information about MM2 and energy minimization see MM2 on page 136 After the minimization is complete 1 From the File menu choose Save 2 Select a directory in which to save the file 3 Type tut1 in the text box at the bottom of the dialog box 4 Click Save 5 Click the model window to activate it 6 From the File menu choose Close Window Tutorial 3 Building Models with the Text Building Tool This tutorial illustrates alternative methods to build models using the Text Building Tool You will start by opening the file you saved in the first tutorial 1 From the File menu choose Open 2 Locate and select the file tut1 that you created in the previous tutorial 3 Click Open CambridgeSoft Tutorial 3 Building Models with the Text Building Tool Replacing Atoms To change one element into another 1 Click the Text Building tool A 2 Click a hydrogen atom attached to C 1 A text box appears 3 Type C NOTE Element symbols and substructure names are case sensitive You must type an uppercase C to create a carbon atom 4 Press the Enter key The hydrogen attached to C 1 is changed to a carbon The valence is filled with hydrogens to form a methyl group because Automatic Rectification is turned on You don t have to select the Text tool in order to use it Double clicking with any other tool selected has the same effect a
270. erman Windows 95 98 Me NT 2000 XP Macintosh MacOS 8 6 10 1 Some features are Windows only All specifications subject to change without notice OCA Lig Mhi im EMAIL info cambridgesoftcom WWW _ www cambridgesoftcom TEL 1800 315 7300 INTL 1 617 588 9300 FAX 1 617 588 9390 c gt Y ED Oo MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge MA 02140 USA CambridgeSoft P AAA Chemo ffice ChemDraw Chem3D ChemFinder Cheminfo are trademarks of CambridgeSoft 2002 All other trademarks are the property of their respective holders All specifications subject to change without notice www cam b r dg eso ft CcCOm DESKTOP CS Chem3D M olecular M odeling and Analysis Chem3D Ultra includes M OPAC Tinker and set up control interfaces for optional use of GAM ESS and Gaussian Estimate advanced physical properties with CLogP and ChemProp and create SAR tables using property servers to generate data for lists of compounds Use ChemSAR Exce to explore structure activity relationships and use add on Conformer for conformational searching Publish and view models on the web using the Chen3D Plugin Chem3D Pro brings workstation quality molecular visualization and display to your desktop Convert ChemD raw and ISIS D raw sketches into 3D models View molecular surfaces orbitals electrostatic potentials charge densities and spin densities Use built in extended H Uckel to compute partial atomic charges Us
271. ertions of No residues 22 26 Serial Number of Third Yes Bonded Atom 28 30 UNUSED No 27 31 Serial Number of Yes 31 38 X Orthogonal Yes Fourth Bonded Atom coordinates 32 36 Hydrogen Bonds No 39 46 Y Orthogonal Yes Atoms in cols 7 11 are coordinates Donors 47 54 Z Orthogonal A Yes 3741 Hydrogen Bonds No coordinates 42 46 Salt Bridge Atoms in No 55 60 Occupancy No cols 7 11 have Negative Charge 61 66 Temperature Factor No 47 51 Hydrogen Bonds No Atoms in cols 7 11 are 67 UNUSED No A cceptors 68 70 Footnote Number No 5256 Hydrogen Bonds No The full description of the CONECT record format in Protein Data Bank files is as follows 57 61 Salt Bridge Atoms in No cols 7 11 have Positive Charge Column Column Used by Number Description Chem3D The FORTRAN formats for the records used in the Protein Data Bank file format are as follows 1 6 Record Name Yes Canney Line Description FORTRAN Format ChemOffice 2005 Appendix File Formats 261 Protein Data Bank Files files are for export only The following is a sample Rosdal format file created using Chem3D Pro for cyclohexanol 1 2 3 4 5 6 1 6 2 7H 3 8H 4 9H 5 10H 6 11H 1 120 13H 1 14H 2 15H 3 16H 4 17H 5 18H 6 COMPND COMPND 4X 60A1 ATOM ATOM 2X 15 1X A4 1X A3 10X 3F8 3 16X 19H HETATM HETATM 15 1X A4 14X 3F8 3 16X SMD 2 CONECT CONECT 515 30X The Standard Molecular Data SMD file file format is defined in the SMD File Forma
272. es If you rename a group as a chain or vice versa the icon will change This is also the reason that only the work Group is used in the menus All Group commands also apply to chains Group objects can consist of other groups atoms and bonds Chem3D does not limit a group to contiguous atoms and bonds though this is the logical definition Bond objects do not appear by default in the Model Explorer If you want to display bonds select Show Bonds in the GUI tab of the Chem3D Preferences dialog box The Solvent object is a special group containing all of the solvent molecules in the model The individual molecules appear as child groups within the Solvent object A Solvent object should not be child of any other object NOTE When importing PDB models solvents will sometimes show up in chains While this is incorrect Chem3D preserves this structure in order to be able to save the PDB file again The Backbone object is a display feature that allows you to show the carbon nitrogen backbone structure of a protein It appears in the Model Explorer as a separate object with no children The atoms and bonds that make up the backbone belong to other chains and groups but are also virtual children of the Backbone object This allows you to select display properties for the backbone that override the display properties of the chains and groups above them in the hierarchy To display the Model Explorer From the
273. es XML tables for storing file formats You can edit these tables in any text editor ot in Chem3D by selecting the table you want to edit from the Parameter Tables list on the View menu TIP The xml files are in the path Chem3D C3D Items Name Each atom type is described by a name This name is a number found in files of the format described by the file format All names must be unique The records in the table window are sorted by name NOTE While names are similar to atom type numbers they do not have to correspond to the atom type numbers of atom types In some cases however they do correspond Description The second field contains a description of the atom type such as C Alkane This description is included for your reference only ChemOffice 2005 Appendix The remaining fields Symbol Charge Maximum Ring Size Rectification type Geometry Number of Double Bonds Number of Triple Bonds Number of Delocalized Bonds Bound to Order and Bound to Type contain information corresponding to the information in an Atom Types table File Format Examples The following sections provide examples of the files created when you save Chem3D files using the provided file formats Alchemy File The following is a sample Alchemy file Alchemy created using Chem3D for a model of cyclohexanol The numbers in the first column are line numbers that are added for reference only 1 19 19 ATOMS BONDS 2 1 C3
274. es have changed in Chem3D 9 0 Please note the following e The rotation bars are now dynamic rather than permanently displayed See Rotation Bars on page 14 for details e Internal rotations have changed See Rotating Models on page 96 for details on how to perform internal rotations e The Measurements table has been augmented by three other tables the Model Explorer the Cartesian Coordinates table and the Z Matrix table See The Model Explorer on page 27 and Model Coordinates on page 28for more details e Menus and toolbars have changed Consult the relevant sections of the manual for details CambridgeSoft Web Pages The following table contains the addresses of ChemDraw related web pages For Access information about Technical http www cambridgesoft com Support services ChemDraw http products cambridgesoft c Plugin om ProdInfo cfm pid 278 http products cambridgesoft c om ProdInfo cfm pid 279 Software http sdk cambridgesoft com Developer s kit ChemOffice 2005 Chem3D For Access information about ActiveX control http sdk cambridgesoft com Purchasing http chemstore cambridgesoft CambridgeSoft com products and chemicals Installation and System Requirements Before installation see the ReadMeFirst and any other ReadMe documents on the installation CD ROM Microsoft Windows Requirements e Windows 2000 or XP e
275. es tab choose Spin Density The Message window displays the total spin densities for each atom spin densities for all orbitals are totaled for each atom NOTE You can look in the out file for a breakdown of the spin densities for each atomic orbital Total Spin Density 0 90744 C1 ChemOffice 2005 Chem3D Total Spin Density 0 00644 0 00000 0 00000 0 00001 0 04395 0 04216 C2 H3 H4 H5 H6 H7 You can reason from this result that the unpaired electron in the ethyl radical is more localized on C1 Generally this is a good indication of the reactive site MOPAC Computations Computing Properties 197 198 MOPAC Computations CambridgeSoft Computing Properties Chapter 11 ULTRA Gaussian Computations Gaussian Overview The following procedures describe the graphical user interface GUI Chem3D provides for users of Gaussian 03W For information about how to use Gaussian see the documentation supplied by Gaussian Inc makers of the application Gaussian 03W is not included with Chem3D but can be purchased separately from CambridgeSoft You can use the Online menu command Browse ChemStore com to link directly to the website Gaussian 03 Gaussian 03W is a powerful computational chemistry application including both ab initio and semiempirical methods Gaussian is a command line application that requires a user to type text based commands and data instead of sel
276. eshooting 229 Terminate After control 158 Text building tool 77 building tool tutorial example 36 number atom type 275 tool specifying order of attachment 78 Theory tab 200 211 Thermal Capacity ChemProp Pro 207 TIF file format 120 Tinker file formats 126 Toolbars Chem3D 9 0 1 building 20 calculation 22 model display 15 20 movie 21 standard 19 surfaces 21 Tools eraser 76 select 91 select hotkey 38 Tools palette see Building toolbar Torsion energy 138 Torsion energy constraints 142 Torsion energy MM2 209 Torsional parameters table 285 Torsional parameters table 4 membered ring 285 Torsionals table 272 Torsion stretch energy MM2 209 Total charge density 69 Total charge density surface calculation types required 65 Total charge density surface definition 69 Total spin calculation types required 65 definition 70 density 70 density surface dialog 70 Trackball tool overview 97 tutorial example 31 Z axis rotation 97 Transferring information to ChemDraw 127 to other applications 127 Transition state 133 Translate 96 235 Translate tool 96 exix Translucent surface type 66 Triple bonds field 276 Troubleshooting atoms shift on MOPAC input 177 background color 60 MOPAC quits 176 online 224 Type 2 CHR bending force parameters for C C C angles 282 U UHF 145 147 166 UHF spin density 189 UHF spin density example 196 Uncoordinated bonds creating 76 Unix Gaussian files 71 Use Cur
277. ext file or Excel worksheet using the commands in the context right click menu NOTE Ifyou do edit coordinates in the table remember to turn off Rectify and Apply Standard Measurements n the Model Build pane of the Model Settings dialog while you edit so that other atoms are not affected An example of the Cartesian coordinates for ethane is shown below Cartesian ax 0 7700 0 0000 0 0003 1 1445 0 5288 0 9163 1 1445 0 5277 0 9163 1 1445 1 0576 0 0010 0 7700 0 0000 0 0003 1 1445 1 0576 0 0003 1 1445 0 5299 0 9156 1 1445 0 5299 0 9150 TTT EE 1 2 3 4 5 6 7 3 CambridgeSoft Model Building Basics The Measurements Table The Measurements table displays bond lengths bond angles dihedral angles and ring closures When you first open a Measurements Table it will be blank To display data in a Measurements Table e From the Structure menu point to Measurements then select the information you wish to display The example shows the display of Bond Lengths and Bond Angles for ethane Measurement H 8 C 2 11130 1 1130 H 7 C 2 14130 11130 H B C 2 1 1130 1 1130 H 5 C 1 11130 11130 H 4 C 1 11130 11130 CD K 11130 11130 C 2 C 1 15230 1 5230 H 8 C 2 H 7 108 8118 109 0000 H 8 C 2 H 6 109 0000 109 0000 H 8 C 2 C 1 110 0000 110 0000 H 7 C 2 H B 109 0000 109 0000 H 7 C 2 C 1 110 0000 110 0000 H 6 C 2 C 1 110 0000 110 0000 H 5 C 1 H 4 108 8118 109
278. f length 1 539734 A and is at abond angle of 109 711411 degrees from C 2 C 4 also forms a dihedral angle of 55 695877 degrees with C 3 The action integers listed next to each measurement ate instructions to MOPAC which are as follows 1Optimize this internal coordinate ODo not optimize this internal coordinate 1Reaction coordinate or grid index When you create a MOPAC file from within Chem3D an action integer of 1 is automatically assigned to each non zeto bond length bond angle and dihedral angle for each atom record in the file CambridgeSoft MSI MolFile FORTRAN Formats The description of the MOPAC Data File format for each line is as follows Line Description Read by Written Number Chem3D by Chem3D 1 Keywords for No No Calculation Instructions 2 Molecule Title No Yes 3 Comment No No 4a s Internal Yes Yes coordinates for molecule 5 Blank line Yes Yes terminates geometry definition The FORTRAN format for each line containing internal coordinate data in the MOPAC Data File is FORMAT 1X 2A 3 F12 6 I3 1X 314 Protein Data Bank Files The Protein Data Bank file format Protein DB is taken from pages 3 14 15 and 17 18 of the Protein Data Bank Atomic coordinate and Bibliographic Entry Format Description dated January 1985 ChemOffice 2005 Appendix A Protein Data Bank file can contain as many as 32 different record types Only the COMPND ATOM HETATM and CONECT records are used b
279. faster mode with less built in chemical intelligence by turning off one or mote of the options ChemOffice 2005 Chem3D Intelligent mode yields a chemically reasonable 3D model as you build Fast mode provides a quick way to generate a backbone structure You can then turn it into a chemically reasonable 3D model by using the Structure menu Rectify and Clean Up tools To change the Building mode 1 From the File menu choose Model Settings The Model Settings dialog box appears 2 Select the Model Building tab Model Settings Colors amp Fonts Movie Stereo amp Depth Model Building Atom Display Model Display General Y Correct Atom Types C Rectify M Apply Standard Measurements Fit Model to Window M Detect Conjugated System Bond Proximate Addition 10 preview 3 Select or deselect the appropriate radio buttons Building and Editing Models 73 Setting the Model Building Controls The following table describes the Model Build controls Control Description Correct Atom Types are assigned to each atom as you build Atom types such as C Alkane specify the valence bond lengths bond angles and geometry for the atom Determines whether atom types Rectify Determines whether the open valences for an atom ate filled usually with hydrogen atoms Apply Standard Determines whether the Measurements standard measurements associated with an atom type ate app
280. fice 2005 Appendix Keyboard Modifiers 235 Q Zoom to rotation center Ww Zoom to selection center If you have a wheel mouse you may also use the scroll wheel to zoom Dragging with the middle button or scroll wheel translates the view Selection Standard Selection Key Click Shift Click Shift Drag Select atom bond Multiple select atom bond Box select atoms Multiple box select atoms bonds Notes e Double clicking a selected fragment selects the next higher fragment that is each double click moves you up one in the hierarchy until you have selected the entite model e Clicking a bond selects the bond and the two atoms connected to it e Double clicking an atom or bond selects the fragment that atom or bond belongs to Radial Selection Radial selection is selection of an object or group of objects based on the distance or radius from a selected object ot group of objects This feature is particularly useful for highlighting the binding site of a protein Radial selection is accessed through the Select submenu of the context menu in the Model Explorer or 3D display Cut Copy Paste Replace with Text Tool Select Atoms within Distance of Selection 4 Angstroms EA elect Groups within Distance of Selection 6 Angstroms Visibility q pa eet NR A ac chs a s a 8 Angstroms Select Color Select Atoms within Radius of Selection Centroid gt 10 Angstroms Apply Atom Color gt Select Group
281. formation sought e The availability of applicable experimentally determined parameters as required by some methods e Computer resources The three most important of the these criteria are e Model size The size of a model can be a limiting factor for a particular method The limiting number of atoms in a molecule increases by approximately one order of magnitude between method classes ftom ab initio to molecular mechanics Ab initio is limited to tens of atoms semiempirical to hundreds and molecular mechanics to thousands e Parameter Availability Some methods depend on experimentally determined parameters to perform computations If the model contains atoms for which the parameters of a particular method have not been derived that method may produce invalid predictions Molecular mechanics for example relies on parameters to define a force field Any particular force field is only applicable to the limited class of molecules for which it is parametrized e Computer resources Requirements increase relative to the size of the model for each of the methods Ab initio The time required for performing computations increases on the order of N4 where N is the number of atoms in the model CambridgeSoft Computational Methods Overview Semiempitical The time required for computation increases as N or N where N is the number of atoms in the model MM2 The time required for performing computations increases as N
282. fy efficacy can vary substantially from assay to assay The underlying requirement that follows from this vari ability is for a flexible data management system that can adapt quickly to different assays and biological mod els With BioAssay HTS researchers or IT support staff simply define the observables and calculations that make up the assay T he database does the rest Users can set up unlimited levels of drill down T his allows users for example to click an 1C 50 and see a graph of percent inhibition versus concentration Click again and the software displays the original triplicate results with outliers marked T he software even supports complex in vivo models ss e gt Automated Curve f Fitting amp Data Analysis gt Flexible Assay a Definition Tools DISCOVERY e Effectively manages data from complex biological assays involved with lead optimization e Adapts quickly and flexibly to different assays and biological models e Closely integrated with Microsoft Excel Chemo ffice and ChemDraw Easily Manage Large Volumes of Data BioAssay HTS offers an easy way to capture large volumes of data from automated laboratory equipment and store it securely in Oracle Scheduled data import means you can set up an import template once and all future data will appear in the system asit is gathered BioAssay H T S contains a complete plate inventory system that tracks plates and compound groups across plates It easily m
283. g Parameters xml and Angle Bending Parameters xml The Model Explorer The Model Explorer allows users to explore the hierarchical nature of a macromolecule and alter properties at any level in the hierarchy Display Chem3D Basics 27 Model Building Basics modes and color settings are easy to control at a fine grained level Properties of atoms and bonds ate easy to access and change The Model Explorer is designed as a hierarchical tree control that can be expanded collapsed as necessaty to view whatever part of the model you wish Changes are applied in a bottom up manner so that changes to atoms and bonds override changes at the chain or fragment level You can show hide highlight features at any level Hidden or changed features ate marked in the hierarchical tree with colored icons so you can easily keep track of your edits See Working With the Model Explorer on page 111 for more information Model Coordinates Each of the atoms in your model occupies a position in space In most modeling applications there ate two ways of representing the position of each atom internal coordinates and Cartesian coordinates Chem3D establishes internal and Cartesian coordinates as you build a model Z matrix Internal coordinates for a model are often referred to as a Z matrix although not strictly correct and are the most commonly used coordinates for preparing a model for further computation Changing a Z matrix allows you
284. g box The minimization and recording stops Queuing Minimizations You can start to minimize several models without waiting for each model to finish minimizing If a computation is in progress when you begin MM2 and MM3 Computations 153 Minimize Energy minimizing a second model the minimization of the second model is delayed until the first minimization stops If you are using other applications you can run minimization with Chem3D in the background You can perform any action in Chem3D that does not change the position of an atom or add or delete any part of the model For example you can move windows around during minimization change settings or scale your model Minimizing Ethane Ethane is a particularly straightforward example of minimization because it has only one minimum energy staggered and one maximum energy eclipsed conformation To minimize energy in ethane 1 From the File menu choose New An empty model window appears 2 Click the Single Bond tool 3 Drag in the model window A model of Ethane appears 4 Choose Show Serial Numbers on the Model Display submenu of the View menu You might also want to set the Model Display Mode to Ball and Stick or Cylindrical Bonds 5 On the Calculations menu point to MM2 and choose Minimize Energy 6 Click Run on the Minimize Energy dialog box The calculation is performed Messages appeat in the Output Window To view all the messages e Scr
285. g parts of the model further from the viewer fade into the background Depth shading is activated by selecting the Depth Fading checkbox on the Stereo and Depth tab of the Model Settings dialog box by selecting Depth Fading from the Model Display submenu of the View menu or by clicking the Depth fading icon ne on the Toolbar Perspective Rendering Chem3D supports true perspective rendering of models This results in a more realistic depiction of the model with bond lengths and atom sizes further from the viewer being scaled consistently The field of view slider adjusts the perspective effect Moving the slider to the right increases the effect Model Settings Model Display Model Building l Atom Display Colors amp Fonts Movie Stereo amp Depth General Stereo Settings Disabled O Render Stereo Pairs O Render Red Blue Anaglyphs o Eye Separation Depth Fading Perspective amp field of view slide Stereo Pair Settings Parallel O Reversed Separation 5 Y 0 100 eptbard Perspective Perspective Depth Fading Field of View CAUTION Moving the slider all the way to the left may make the model disappear completely Coloring the Background Window Chem3D allows you to select a color for the background of your models A black or dark blue background can be particularly striking for ribbon displays intended for full color viewing
286. ge without notice www cam b T1 dg eso ft CcCOm ENTERPRISE Oracle Cartridge E nterprise Infrastructure for D atabase Security WebServer Oracle Cartridge In scientific applications the ability to store and manipulate chemical information is essential By using CambridgeSoft s Oracle Cartridge you add chemical knowledge to your Oracle platform and automatically take advantage of O racles security scalability and replication without any other external software or programs You can search the chemical data by structure substructure and similarity including options for stereo selec tivity all through extensions to O racle s native SQ L language Tools like PowerBuilder Visual Basic and Visual C readily lend themselves as database clients W ith the addition of the ChemD raw ActiveX control in the client your end users can be structure searching in no time Chemical Data Formats CambridgeSoft recognizes that there is an enormous amount of legacy data out there in a myriad of formats and most users have no desire to make wholesale changes to their chemical data generation or storage To this end Oracle Cartridge supports all major data types without translation or modification In addition to CD X it supports C D XM L MolFile Rxn and SMILES formats M oreover there are built in extensions to SQ L that allow you to extract data in all supported formats Due to the variety of data formats supported Orade Cartridge is easily
287. gistical issues that must be addressed prior to alarge scale deployment When early release programs are enployed the success rate of large scale deployments is greatly increased and end users are more likely to adopt the new technology Controlled Pilots Controlled pilots involve deploying a pre production system to a small group of users to evaluate it s functional usability technical and operational characteristics in a real world environment prior to the completion of final system development A controlled pilot helps identify and correct show stopper technology or operational issues before a final roll out program is implemented Training D evelop customized training materials for users system administrators and help desk personnel If you choose to outsource training management C ambridgeSoft can schedule and conduct training for all users and stakeholders EMAIL info cambridgesoftcom WWW _ www cambridgesoftcom TEL 1800 315 7300 INTL 1 617 588 9300 FAX 1 617 588 9390 MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge MA 02140 USA CambridgeSoft P AAA Chemo ffice ChemDraw Chem3D ChemFinder Cheminfo are trademarks of CambridgeSoft 2002 m All other trademarks are the property of their respective holders All specifications subject to change without notice www cam b T1 dg eso ft CcCOm aBod Adosojoyd 10 asay nd aspajg Se CS Software Problem Report For faster response and accuracy use th
288. greement if you fail to com ply with its terms and conditions In such event you must destroy all copies of the Software Product and all of its component parts 8 Confidentiality The Software contains trade secrets and proprietary know how that belong to CS and are being made available to you in strict confidence ANY USE OR DISCLOSURE OF THE SOFTWARE OR USE OF ITS ALGORITHMS PROTOCOLS OR INTERFACES OTHER THAN IN STRICT ACCORDANCE WITH THIS LICENSE AGREEMENT MAY BE ACTIONABLE AS A VIOLATION OF OUR TRADE SECRET RIGHTS CS Limited Warranty Limited Warranty C S s sole warranty with respect to the Software is that it shall be free of errors in program logic or documentation attributable to CS which prevent the performance of the principal computing functions of the Software CS warrants this for a period of thirty 30 days from the date of receipt CS s Liability In no event shall CS be liable for any indirect special or consequential damages such as but not limited to loss of anticipated profits or other economic lossin connection with or arising out of the use of the soft ware by you or the services provided for in this agreement even if CS has been advised of the possibility of such dam ages C S s entire liability and your exclusive remedy shall be at CS s discretion either A return of any license fee or B correction or replacement of software that does not meet the terms of this limited warranty and that is returned to CS w
289. gths 86 bond order 83 changing structural display 55 56 charges 87 constraints 87 default atom label display options 61 dihedral angles 86 measurements 85 measurements atom movement 86 model building controls 73 molecular surface colors 67 molecular surface isovalues 66 molecular surface types 65 non bonded distances 86 origin atoms 104 parameters 216 serial numbers 88 solid sphere size 57 solvent radius 67 surface mapping 68 surface resolution 67 Sextic bending constant 283 Shift selecting 92 Show Internal Coordinates command 101 Show Surface button 65 Show Used Parameters command 161 163 273 Showing all atoms 95 atoms or groups 94 Hs and Lps 95 serial numbers 88 used parameters 163 Single point calculations definition 130 Single point calculations MOPAC 184 Single Point energy calculations 133 SM2 seeSYBYL MOL2 File SMD 262 SMD files 262 Solid spheres size by control 57 Solid spheres size 58 Solid surface type 66 Solubility ChemProp Pro 208 Solution effects 188 Solvent accessible surface calculation types required 65 definition 69 map property 69 mapping atom colors 69 mapping group colors 69 mapping hydrophobicity 69 solvent radius 68 Sorting properties 215 Space filling display 56 Specifying electronic configuration 172 general settings 213 print options 117 properties to compute 212 Speed control 116 Spin about selected axis 115 Spin density 189 Spin density tutorial example 49 Spin functions 14
290. harges This computation of point charges can be used with the AM1 potential function only For information about the elements covered using the AM1 potential function see and the MOPAC online manual page 223 NOTE For elements not covered by the AM1 potential function use the Electrostatic Potential property to get similar information on elements outside this properties range Below ate the keywords automatically sent to MOPAC Keyword Description PMEP Automatically sent to MOPAC to specify the generation of Point Charges from PMEP QPMEP Automatically sent to MOPAC to specify the Wang Ford electrostatic Potential routine GEO OK Automatically sent to MOPAC to override checking of the Z matrix ChemOffice 2005 Chem3D Keyword Description MMOK Automatically sent to MOPAC to specify Molecular Mechanics correction for amide bonds Use the additional keyword NOMM to turn this keyword off Electrostatic Potential Use the electrostatic potential property when the element coverage of the AM1 potential function does not apply to the molecule of interest For more information see the MOPAC online manual page 223 The following table contains the keywords automatically sent to MOPAC and those you can use to affect this property Keyword Description ESP Automatically sent to MOPAC to specify the Electrostatic Potential routine POTWRT Add this keyword if you want to print out the ESP map
291. hat s New in Chem3D 9 0 1 View translation tool translate pan the view without changing the model coordinates See Moving Models with the Translate Tool on page 96 Safer viewing new pure selection tool prevents unintentionally moving or rotating parts of the model while selecting See The Building Toolbar on page 20 Global keyboard modifiers advanced users can perform any action while in any mode using a global keyboard modifier See Keyboard Modifiers on page 235 Improved Zoom control zoom to center of screen center of selection or center of rotation See Zoom and Translate on page 235 Display axes display or hide axes centered at the origin of the model or at the origin of the view focus Middle mouse button and scroll wheel support use scroll wheel to zoom middle mouse button to rotate or translate See entries under Rotation and Zoom and Translate on page 235 New tools for large models e View focus selects a subset of the model for viewing and manipulation See View Focus on page 85 e Select higher group double click a selection to select the next higher group See Selecting a Group or Fragment on page 93 e Radial Selection select atoms or groups within a specified radius See Selecting Atoms or Groups by Distance on page 94 CambridgeSoft What s New in Chem3D 9 02 For Users of Previous Versions of Chem3D Many featur
292. hat the business is getting the results they wanted Operational Planning In order to effect change on complex environments it is necessary for organizations to develop operational plans T hese plans minimize the risks associated with large technology deployments Plans may incorporate key business processes and workflows and help to identify any operational constraints Custom Development Your organization requires solutions that meet you unique needs C ambridgeSoft consultants can assist with Custom Application Development Assess business needs document specifications and create custom web based solutions for your enterprise Data Integration Create interfaces with other data management systems to incorporate your data into an enterprise system Installation and Customization Customize your solution to your specifications M ake certain that all tech nical and logistical installation processes are managed Deployment amp Training D evelop a comprehensive road map for deployment of technology solutions across the enterprise O ur experts help you plan and deploy your solutions by Application D eployment Document define and execute all of the actions required to support end user acceptance M anage the deployment process to assure a smooth roll out to the end users Beta and PreRdease Programs Beta and prerelease programs involve a limited deployment to a small set of usersin order to identify deployment readiness or lo
293. he General tools toolbar for example will give you access to undo redo commands oO Build the structure The model appears simultaneously in both the ChemDraw and Chem3D model windows Unsynchronized Mode By default the ChemDraw panel works in synchronized mode In this mode your model appears simultaneously in the ChemDraw panel CambridgeSoft Building with the ChemDraw Panel and in Chem3D Editing either model changes the other automatically This affords maximum editing flexibility To turn off synchronized mode e Click the Synch button at the top left of the ChemDraw panel The button toggles synchronization on and off To copy a model to Chem3D click either the Add or Replace icon Name Struct The ChemDraw panel has a Name Struct window that allows you to build models by entering a chemical name or SMILES string You can also copy names or SMILES strings from other documents and paste them either into the Name Struct window or directly into the Chem3D model window TIP You can also paste chemical formulas into the Chem3D model window Be aware however that a formula may not represent a unique structure and the results may not be correct Building with Other 2D Programs You can use other 2D drawing packages such as ISIS Draw to create chemical structures and then copy them into Chem3D for automatic conversion to a 3D model To build a model with 2D drawings 1 In the source p
294. he Atom Display tab of the Model Settings dialog box or for individual atoms using the Right click Atom Dots submenu in the Model Explorer Text Number Atom Type Text numbers ate used to determine which measurements apply to a given group of atoms in other parameter tables For example C Alkane has an atom type number of land O Alcohol has an atom type number of 6 To determine the standard bond length of a bond between a C Alkane atom and an O Alcohol atom you should look at the 1 6 record in the Bond Stretching table Charge The charge of an atom type is used when assigning atom types to atoms in a model ChemOffice 2005 Appendix When the information about an atom is displayed the atom symbol is always followed by the charge Charges can be fractional For example the charge of a carbon atom in a cyclopentadienyl ring should be 0 200 Maximum Ring Size The maximum ring size field indicates whether the corresponding atom type should be restricted to atoms found in rings of a certain size If this cell is zero or empty then this atom type is not restricted For example the maximum ring size of C Cyclopropane is 3 Rectification Type Possible rectification types are e D H e H Alcohol e H Amide e H Amine e H Ammonium e H Carboxyl e H Enol e H Guanidine e H Thiol NOTE When you specify a rectification type the bound to type of the rectification type shouid not conflict with the atom
295. he Pr substructure is used for bonding to the additional elements NH2 a Example 3 Polypeptides Use substructures for building polymers such as proteins 1 Type HAlaGlyPheOH into a text box with no atoms selected The additional H and OH cap the ends of the polypeptide If you don t cap the ends and automatic rectification is on Chem3D tries to fill the open valences possibly by closing a ring 2 Press the Enter key Ring closing bonds appear whenever the text in a text box contains two or more open valences 80 Building and Editing Models The alpha form of the neutral polypeptide chain composed of Alanine Glycine and Phenylalanine appeats NOTE You can use the amino acid names preceded with a R to obtain the beta conformation for example HR amp Ala amp GlyR PheOH To generate the R character type AH 0223 using the number pad The appropriate bonding and dihedral angles for each amino acid ate pre configured in the substructure TIP To better view the alpha helix formation use the Trackball Tool to reorient the model to an end on view For more information see Trackball Tool on page 97 To change the polypeptide to a zwitterion 1 Select the Text tool Click the terminal nitrogen A text box appears over the nitrogen atom Type and press the Enter key The charge is applied to the nitrogen atom Its atom type changes and a hydrogen atom
296. he Torsional Parameters table and the 4 Membered Ring Torsional Parameters table is as follows 1 Records are sorted by the second atom type number in the Dihedral Type field For example the record for dihedral type 1 1 1 1 is listed before the record for dihedral type 1 2 1 1 2 For records where the second atom type number is the same the records are sorted by the third atom type number in the Dihedral Type field For example the record for dihedral type 1 1 1 1 is listed before the record for dihedral type 1 1 2 1 3 For multiple records where the second and third atom type numbers are the same the records ate sorted by the first atom type number in the Dihedral Type field For example the record for dihedral type 5 1 3 1 is listed before the record for dihedral type 6 1 3 1 4 For multiple records where the first second and third atom type numbers are the same the records are sorted by the fourth atom type number in the Dihedral Type field For example the record for dihedral type 5 1 3 1 is listed before the record for dihedral type 5 1 3 2 Out of Plane Bending The Out of Plane Bending table Out of Plane Bending Parameters xml contains parameters which are used to ensure that atoms with trigonal planar geometry remain planar in MM2 calculations ChemOffice 2005 Appendix There are four fields in records in the Out of Plane Bending Parameters table Bond Type Force Constant Quality and Reference Bon
297. he atom label C NOTE Atom types in the Molecular Simulations MolFile format are user definable For more information see Editing File Format Atom Types on page 241 Line 48 contains the header for the Bond List section Line 49 contains a listing of all the possible fields for the bond list section When the file is created by Chem3D Pro the following fields are used Bond Bond_type atom 1 atom 2 and cis trans and Qordet Lines 50 68 each contain 4 fields describing information about each of the bonds in the structure the first field is the internal bond number 6 the second field is the bond type 1 the third and fourth fields are the atom CambridgeSoft MSI MolFile serial numbers for the atoms involved in the bond atom 1 2 atom 2 16 the fifth field is the cis trans designator this is 0 if it does not apply the sixth through tenth fields are ignored and contain zeros if the file is created using Chem3D Pro the eleventh field contains the bond order S meaning single the twelfth and thirteenth fields are ignored and contain zeros if the file is created using Chem3D Pro 20 Lines 69 73 ate each a section header for 3D conversion use This section only contains the header name only as shown when the file is created using Chem3D Pro 21 Line 74 is a header for the section User data area This section contains the header name only as shown when the file is created using Chem3D Pro
298. he bond is used to position the other atom on 248 File Formats 5 109 41 1 106 8998 2 59 999 0 the bond the bond is removed from the model This is useful if you want to describe multiple fragments in an internal coordinates file Atom Type Text Numbers Bond Lengths Origin Atom First Angles Second Atom 1 1 154146 Second Angles Third Atom 1 2 153525 1 111 7729 Fourth Atom 1 1 53967 2 109 7132 3 55 6959 0 Distancedefining First Angle Second Angle Indicates Atoms defining Atoms defining Atoms Dihedral Components of an Internal coordinates File for C 1 through C 4 of Cyclohexanol In this illustration the origin atom is C 1 C 2 is connected to C 1 the origin and distance defining atom by a bond of length 1 54146 A C 3 is connected to C 2 with a bond of length 1 53525 A and at a bond angle of 111 7729 degrees with C 1 defined by C 3 C 2 C 1 C 4 is attached to C 1 with a bond of length 1 53967 A and at a bond angle of 109 7132 degrees with C 2 defined by C 4 C 1 C 2 C 4 also forms a dihedral angle of 55 6959 degrees with C 3 defined by C 4 C 1 C 2 C 3 CambridgeSoft File Format Examples This portion of the Internal coordinates file for C 1 through C 4 of Cyclohexanol can be represented by the following structural diagram FORTRAN Formats The FORTRAN formats for the records in an Internal coordinates file are as follows Line Number
299. he internal coordinates used to position each atom The serial numbers ate determined by the order of the atoms in the file The first atom has a serial number of 1 the second is number 2 and so on Internal Coordinates files may be both imported and exported You cannot use a Z matrix to position an atom in terms of a later positioned or higher serialized atom If you choose the second ot third options in the Internal Coordinates Options dialog box the nature of the serialization of your model determines whether a consistent Z matrix can be constructed If the serial numbers in the Z matrix which is about to be created are not consecutive a message appears You are warned if the atoms in the model must be reserialized to create a consistent Z matrix When you click Options in the Save As dialog box the following dialog box appears Internal Coordinate Options PR Use Current Z Matrix O Only Serial Numbers Bond and Dihedral Angles Only Serial Numbers Dihedral Angles Only ChemOffice 2005 Chem3D Select the appropriate options If you want fo Then click save yout model using the Z mattix described in the Internal Coordinates table of the model build a Z matrix in which the current serial number ordering of the atoms in the model is preserved in the Z matrix build a Z matrix in which the current serial number ordering of the atoms in the model is preserved in the Z matrix Mac
300. he structure Notes RMS The default value of 0 100 is a reasonable compromise between accuracy and speed Reducing the value means that the calculation continues longer as it tries to get even closer to a minimum Increasing the value shortens the calculation but leaves you farther from a minimum Increase the value if you want a better optimization ChemOffice 2005 Chem3D of a conformation that you know is not a minimum but you want to isolate it for computing comparative data NOTE Ifyou want to use a value lt 0 01 you must specify LET in the keywords section General Tab Wave Function Selecting a wave function from the drop down menu involves deciding whether to use RHF or UHF computations RHF is the default Hartree Fock method used for closed shell systems To use RHF select the Close Shell Restricted wave function UHF is an alternative form of the HF method used for open shell systems To use UHF select the Open Shell Unrestricted wave function If you wish to calculate Hyperfine Coupling Constants you must select the UHF wave function NOTE UHF computations take at least twice as long as RHF This may be the deciding consideration of method when large molecules are being studied Adding Keywords Click the General tab to specify additional MOPAC keywords This will tailor a calculation to more exacting requirements For example you might use additional keywords to control convergence
301. hem3D computational methods are referred to as computation engines while geometty engines and graphics engines render the model ChemOffice 2005 Chem3D Chem3D supports a number of powerful computational chemistry methods and extensive visualization options Computational Methods Overview Computational chemistry encompasses a variety of mathematical methods which fall into two broad categories e Molecular mechanics applies the laws of classical physics to the atoms in a molecule without explicit consideration of electrons e Quantum mechanics telies on the Schr dinger equation to describe a molecule with explicit treatment of electronic structure Quantum mechanical methods can be subdivided into two classes ab initio and semiempirical The generally accepted method classes are shown in the following chart Computational Chemistry Methods Molecular Mechanical Methods Quantum Mechanical Methods _ Semiempirical Ab Initio Methods Methods Chem3D provides the following methods e Molecular mechanical MM2 and MM3 method Computation Concepts 129 Computational Methods Overview e Semiempitical Extended H ckel MINDO 3 MNDO MNDO d AM1 and PM3 methods through Chem3D and CS MOPAC e Ab initio methods through the Chem3D Gaussian or GAMESS interface Uses of Computational Methods Computational methods calculate the potential energy surfaces PES of molecules The potential energy surface
302. hemo ffice ChemDraw Chem3D ChemFinder Cheminfo are trademarks of CambridgeSoft 2002 m _ _ _ All other trademarks are the property of their respective holders All specifications subject to change without notice www cam b r dg eso ft CcCOm DESKTOP CS ChemInfo Reference and C hemical D atabases The Merck Index is an encyclopedia of chemicals drugs and biologicals with over 10 000 monographs covering names synonyms physical properties preparations patents literature references therapeutic uses and more ChemACX Pro includes 500 000 chemical products from 300 supplier catalogs searchable with a single query by structure substructure name synonym partial name and other text and numeric criteria ChemACX SC is a compilation of searchable catalogs from leading screening compound suppliers ChemACX Com is the ChemACX web site with full search capabilities and convenient online ordering from major suppliers ChemINDEX includes 100 000 chemicals public N Cl compounds and more ChemRXN is a collection of 30 000 fully atom mapped reactions selected and refined from the chemical literature It includes reactions from InfoC hem s C hemSelect database and SI s ChemPrep database ChemMSDX provides material safety data sheets for 7 000 pure compounds ChemFinder Com is the award winning web site with information and WWW links for over 100 000 chemicals Search by name or partial name view structure drawings or use
303. hen click watch the Display Every Iteration minimization process live at each iteration in the NOTE Displaying or recording each iteration adds significantly to the time required to minimize the structure calculation 212 GAMESS Computations If you want to Then click record each iteration Record Every Iteration as a frame in a movie for later replay view the value of Copy Measurements to each measurement in Output the Measurement table calculate using the Use Tight Convergence equivalent to the Criteria Gamess keyword Opt Tight Specifying Properties to Compute Use the Properties tab to specify which properties ate computed The default Population Analysis type is Mulliken To specify properties 1 In the Minimize Energy dialog box click Properties Job Type Theory Properties General Properties Dipole Charges Electron Density Spin Density Polarizabilities RMS Force Population Analysis Mulliken ha Job Type Compute Properties Method Closed Shell Restricted Hartree Fock Basis Set STO 3G Orbital Guess Huckel Symmetry C1 Save As Summary Cance _ Create CambridgeSoft Minimize Energy 2 On the Properties tab set the following options e Select the properties to calculate e Select the Population Analysis type Specifying the General Settings Use the General tab to customize the calculation to the model
304. hereas a pytrole nitrogen atom type number 40 contributes 2 electrons to the pi system lonization The Ionization field contains the amount of energy required to remove a pi electron from an isolated pi atom The units of the ionization energy by electron volts eV The magnitude of the ionization energy is larger the more electronegative the atom For example an alkene carbon has an ionization energy of 11 160 eV and the more electronegative pyrrole nitrogen has an ionization energy of 13 145 eV Repulsion The Repulsion field contains a measure of CambridgeSoft Pi Atoms e The energy required to keep two electrons each on separate pi atoms from moving apart and e The energy required to keep two electrons occupying the same orbital on the same pi atom from moving apatt The units of the repulsion energy are electron volts eV The repulsion energy is more positive the more electronegative the atom For example an alkene carbon has an repulsion energy of 11 134 eV and the more electronegative pyrrole nitrogen has an repulsion energy of 17 210 eV Pi Bonds The Pi Bonds table Conjugated PI System Bonds xml contains parameters used to correct bond lengths and bond angles for bonds that are part of a pi system In Chem3D additional information is used to compute the pi system portions of the MM2 force field for the pi bonds in a model There are five fields in records in the Pi Bonds table Bond Type
305. hexanol 2 In Line 1 type the keywords for the computations you want MOPAC to perform blank in the example above Line 2 is where enter the name that you want to assign to the window for the resulting model However Chem3D ignores this line 3 Leave Line 3 blank 4 Line 4 through Ln were n is the last atom record include the internal coordinates optimization flags and connectivity information for the model e Column 1 is the atom specification e Column 2 is the bond distance for the connectivity specified in Column 8 e Column 3 is the optimization flag for the bond distance specified in Column 2 e Column 4 is the bond angle for the connectivity specified in Column 8 e Column 5 is the optimization flag for the bond angle specified in Column 4 ChemOffice 2005 Chem3D Line 3 Line 4 C 0 o JO o J0 0 0 0 0 Line 5 C 1 54152 1 0 o Jo 0 1 0 0 Line 6 C 1 53523 J1 111 7747 1 JO 0 2 1 0 L7 Ln C 1 53973 J1 109 7114 1 55 6959 1 1 2 3 Ln 1 e Column 6 is the dihedral angle for the connectivity specified in Column 8 e Column 7 is the optimization flag for the dihedral angle specified in Column 6 5 To specify particular coordinates to optimize change the optimization flags in Column 3 Column 5 and Column 7 for the respective internal coordinate The available flags in MOPAC are 1 Optimize this internal coordinate 0 Do not optimize this in
306. his procedure will be used instead of EF LBFGS For very large systems the LBFGS optimizer is often the only method that can be used It is based on the BFGS optimizer but calculates the inverse Hessian as needed rather than storing it Because it uses little memory it is preferred for optimizing very large systems It is however not as efficient as the other optimizers MOPAC Files CS MOPAC can use standatd MOPAC text files for input and creates standard MOPAC output files These are especially useful when running repeat computations Using the out file In addition to the Messages window MOPAC creates two text files that contain information about the computations Each computation performed using MOPAC creates a out file containing all information concerning the computation A summary arax file is also created where x increments from a to z after each run The out file is overwritten for each run but a new summary arax file is created after each computation araa arab and so on CambridgeSoft Optimizing Geometry The out and aax files are saved by default to the Mopac Interface subfolder in your My Documents folder You may specify a different location from the General tab of the Mopac Interface dialog box The following information is found in the summary file for each run Electronic Energy Estectronic Core Core Repulsion Energy Enuclear e Symmetry e Ionization Potential HOMO L
307. ht click menu 3 Paste into the document of your choice You must use Copy Paste to restore information from a saved file You can remove information from the Output window without affecting the model To remove messages 1 Select the text you want to delete 2 Do one of the following From the Right click menu choose Clear Press the Delete or Backspace key The Comments window gives you a place to add notes and comments about the model When you save a model comments are also saved Model Building Basics As you create models Chem3D applies standard parameters from external tables along with user selected settings to produce the model display There are several options for selecting your desired display settings you can change defaults in the Model Settings dialog box use menu or toolbar commands or use context sensitive menus right click menus in the Model Explorer You can also view and change model coordinates 24 Chem3D Basics Internal and External Tables Chem3D uses two types of parameter tables Internal tables Contain information about a specific model Examples of internal tables are e Measurements table e Z Matrix table Internal coordinates table External tables Contain information used by all models Examples of external tables are e Elements Atom Types and Substructutes tables that you use to build models e Torsional Parameters tables that are used by Che
308. i yde sons dades 183 Locating the Eclipsed Transition State of Ethane 183 Computing Properties 184 MOPAG Properties isere riuin ean 185 Heat of Formation DHf 185 Gradient NO esaa ieai ad a E e a E BAS 185 Dipole Moments a see eles 186 Charges se a RE emery ane eis 186 Mulliken Charges 0000005 186 Charges From an Electrostatic Potential 186 Wang Ford Charges 0oooooocococoomo 187 Electrostatic Potential 187 Molecular Surfaces o oooooooooomo 188 Polatizability wos seve tur e 188 COSMO Solvation in Watet 188 Hyperfine Coupling Constants 188 Spins Density 2 idas ad des 189 Example Livia ints Diaan 190 The Dipole Moment of Formaldehyde 190 Example Lista rs red aa do 191 Comparing Cation Stabilities in a Homologous Series of Molecules oo o oooooo 191 E ample Ji iii sneered etenaboee 191 Analyzing Charge Distribution in a Series Of Mono substituted Phenoxy Ions 191 Example dois a 193 Calculating the Dipole Moment of meta Nitrotoluene oooooomoomo o 193 Example isa a Ba 194 Comparing the Stability of Glycine Zwitterion CambridgeSoft in Water and Gas Phase o ooo 194 Example ride 195 Hyperfine Coupling Constants for the Ethyl Radical tacita daa doo io 195 Example Mur aa a a 196 UHF Spin Density for the Ethyl Radical 196 Example Biota cin dies cla ea a 197 RHF S
309. ial 3 Building Models with the Text Building Tool 4 Type Ph NO2 in the text box 5 Press the Enter key A model of nitrobenzene appears The substructure in this example is the phenyl group Substructures are defined with specific attachment points for other substituents For phenyl the attachment point is C 1 Build a peptide model 1 From the File menu choose New 2 Click the Text Building tool A 3 Click an empty space in the Model window A text box appears 4 Type H Ala 120H 5 Press the Enter key 6 Rotate this structure to see the alpha helix that forms Change the model display type 1 Click the arrow on the tight side of the Model Display Muue tool on the Model Display toolbar 2 Select Wire Frame as the Model Type TIP You can also click on the icon Successive clicks cycle through the Display Mode options ChemOffice 2005 Chem3D 3 Select the Trackball tool S v and rotate the model so you are viewing it down the center of the helix as shown below 4 Use the Model Display Mode tool to choose Ribbons as the Model Type to see an alternative display commonly used for proteins 4 Y y Be a gt Tutorial 4 Examining Conformations This tutorial uses steric energy values to compate two conformations of ethane The conformation with the lower steric energy value represents the more likely conformation Build ethane 1 Draw a single bond in the ChemDraw panel
310. ial 5 Mapping Conformations with the Dihedral Driver The model display rotates the dihedral to the selected conformation NOTE The dibedral is rotated in 5 degree increments through 360 degrees for a total of 72 conformations to produce the graph You can view the minimized energy values for each point in the Output window To rotate the other dihedral angle other end of the bond e Right click in the Dihedral Driver window and choose Exchange Rotating two dihedrals To rotate two dihedrals 1 Use Shift click to select two adjacent bonds In this case the middle atom s position remains fixed 2 Choose Dihedral Driver from the Calculations menu The Dihedral Driver window opens When the computation is completed a graph is displayed showing theta 1 vs theta 2 theta 2 degre 360 ma aon aa theta 1 degrees E Output El Comments Dihedral Driver NOTE The graph is the result of rotating one angle through 360 in 15 increments while holding the other constant The second angle is then advanced 15 and the operation is repeated To view the conformation at any given point e Click any block in the graph ChemOffice 2005 Chem3D The model display rotates both dihedrals to the selected conformation Customizing the Graph You can use the right click menu to set the rotation interval used for the computation You can also select display colors for the graph background co
311. ians in MOPAC There are five approximation methods available in MOPAC e AM1 MNDO e MNDO d e MINDO 3 e PM3 The potential energy functions modify the HF equations by approximating and parameterizing aspects of the Fock matrix The approximations in semiempirical MOPAC methods play a role in the following areas of the Fock operator e The basis set used in constructing the 1 electron atom orbitals is a minimum basis set of only the s and p Slater Type Orbitals STOs for valence electrons e The core electrons ate not explicitly treated Instead they are added to the nucleus The nuclear charge is termed N effective 148 Computation Concepts For example Carbon as a nuclear charge of 6 2 core electrons for a effective nuclear charge of 4 e Many of the 2 electron Coulomb and Exchange integrals are parameterized based on element Choosing a Hamiltonian Overall these potential energy functions may be viewed as a chronological progression of improvements from the oldest method MINDO 3 to the newest method PM3 However although the improvements in each method wete designed to make global improvements they have been found to be limited in certain situations The two major questions to consider when choosing a potential function are e Is the method parameterized for the elements in the model e Does the approximation have limitations which render it inappropriate for the model being studied Fo
312. ic Energy Summary selected as the default If it does not select them TIP Use Shift click to select multiple properties 2 Click Run The Output box appears beneath the model window with Steric Energy results displayed The last line displays the total energy NOTE The values of the energy terms shown are approximate and may vary slightly based on the type of processor used to calculate them To obtain the eclipsed conformation of ethane rotate a dihedral angle torsional angle Rotating a dihedral angle is a common way of analyzing the conformational space for a model To view dihedral angles 1 From the Structure menu point to Measurement and then choose Dihedral Angles All of the model s dihedral angles are added to the bottom of the Measurements table 2 Click the H 3 C 1 C 2 H 8 dihedral record to select the corresponding atoms in the model NOTE Although the serial numbers and element symbols are shown in the Measurements table they do not appear in your model ChemOffice 2005 Chem3D To help keep visual track of the atoms as you change the dihedral angle you can display the serial numbers and element symbols for the selected atoms From the Model Display submenu of the View menu select Show Serial Numbers and Show Element Symbols 1 Click the arrow next to the Trackball tool and tear off the rotation dial by dragging on the blue bar at the top trackball loca
313. ically active compounds new methods for synthesizing drugs and other data It is a requirement for effective decision making in all stages of drug design Investigational Drugs D atabase ID db from Current Drugs is the world s leading competitor intelligence service on drug R amp D Updated weekly it covers all aspects of drug development world wide from first patent to launch or discontinuation Safety MSDS ChemM SD X provides over 7 000 material safety datasheets 4 gi nu EMAIL info cambridgesoftcom WWW _ www cambridgesoftcom iid 2 Oo ie Eee eae Os Baen ds A CambridgeSoft Chemo ffice ChemDraw Chem3D ChemFinder Cheminfo are trademarks of CambridgeSoft 2002 5 All other trademarks are the property of their respective holders All specifications subject to change without notice www cam b T1 dg eso ft CcCOm CONSULTING amp Consulting amp Services D evelopment Installation amp Training Services Managing Information Today s businesses are facing many complex issues Among them are the overloads of disparate types of infor mation unmanaged proliferation of valuable research data virtual projects in many locations uncontrolled research data compliance certification and regulation Technological solutions to these issues require careful planning and management C ambridgeSoft now offers the following professional services to assist businesses in fully utilizing the power of technology Decision Making Cambridge
314. ide highly detailed information about one compound whereas tabular views make comparisons between Bem ee ee e i gt Form and Table Views Echa Minga ni If li uE gt Data Dictionary Organizes Reports DISCOVERY Catalog driven data mining and analysis operation e Both form and table views available within simple web interface ChemDraw for Spotfire e Role based security specifies operations allowed for administrators publishers and browsers compounds more feasible T here is often a tradeoff between power and simplicity and most SAR tools opt for the former at the expense of the latter BioSAR Browser however merges the sophistication of a powerful data catalog technique with knowledge gained through years of working closely with users The result is a SAR application that is as intuitive as it is powerful Security amp Convenience Security within BioSAR Browser is highly granular Different roles exist for administrators publishers and browsers Administrators may add assays to the data catalog engine publishers may create reports and publish them and browsers may use data query and analysis M ost data mining tools provide a mechanism to store queries but the interface for creating queries is too complex With BioSAR Browser each set of assays is a com plete report with a query form a view form and a table view combining the convenience of a ChemFinder or ISIS application with the power and flexibility
315. iece of software owned by my company and install it on my personal computer at home if instructed by my supervisor A A good rule of thumb to follow is one software package per computer unless the terms of the license agreement allow for multiple use of the program But some software publishers licenses allow for remote or home use of their software If you travel or telecommute you may be permitted to copy your software onto a second machine for use when you are not at your office computer Check the license care fully to see if you are allowed to do this Q What should do if become aware of a company that is not compliant with the copyright law or its software licenses A Cases of retail corporate and Internet piracy or non compliance with software licenses can be reported on the Internet at http www siia net piracy report asp or by calling the Anti Piracy Hotline 800 388 7478 Q Do the same rules apply to bulletin boards and user groups always thought that the reason they got together was to share software A Yes Bulletin boards and user groups are bound by the copyright law just as individuals and corporations However to the extent they offer shareware or public domain software this is a perfectly acceptable practice Similarly some software companies offer bulletin boards and user groups special demonstration versions of their products which in some instances may be copied In any event it
316. ifying large systems architectural considerations O rade Cartridge has the side benefit of providing a database level interface to key applications so developers can integrate C ambridgeSoft s solution platform with in house T solutions without tinkering with the business tie Communicating with O racle Cartridge is as simple as learning a few extensions to SQL Systems amp Support Support extends to include a variety of UNIX operating systems in addition to Windows servers Oracle Cartridge has been deployed by large pharmaceutical companies with O racle 8 and 9i EMAIL info cambridgesoftcom WWW _ www cambridgesoftcom TEL 1800 315 7300 INTL 1 617 588 9300 FAX 1 617 588 9390 MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge MA 02140 USA CambridgeSoft P AAA Chemo ffice ChemDraw Chem3D ChemFinder Cheminfo are trademarks of CambridgeSoft 2002 5 All other trademarks are the property of their respective holders All specifications subject to change without notice www cam b T1 dg eso ft CcCOm KNOWLEDGE E Notebook Enterprise D esktop to Enterprise Knowledge M anagement E Notebook E N otebook provides a smooth web based interface designed to replace paper laboratory notebooks with a fully configurable secure system for organizing the flow of information generated by your organization You can enter reactions M icrosoft Word documents spectra and other types of data and then search this data by text
317. ild strained ring systems To correct unrealistic bond lengths and bond angles use the Clean Up Structure command To clean up the selected atoms in a model From the Structure menu choose Clean Up The selected atoms are repositioned to reduce errors in bond lengths and bond angles Planar atoms are flattened and dihedral angles around double bonds are rotated to 0 or 180 degrees CambridgeSoft Refining a Model Chapter 5 Manipulating Models Overview Chem3D provides tools to manipulate the models File Edit you create You can show or hide atoms and select DELE groups to make them easier to manipulate ion Molecules can be rotated aligned and resized Sr xvz 9 DNA Selecting Most operations require that the atoms and bonds that ate operated on be selected Selected atoms and bonds ate highlighted in the model display You can change the default highlight color in the Model Model Explorer tab Settings dialog box Colors and Fonts Model Display Model Building Atom Display tab Colors amp Fonts Movie Stereo amp Depth z Color by al O Monochrome O Element Z O Partial Charge O Group m n O Chain O Depth E Set Highlight a Color Model Colors g Background ME v Alpha Helix Highlighted E na Beta Sheet oe Col RE mais S To select an atom using the Model Explorer Atom Label Font 1 Open the Model Explorer tn Y E 2
318. in ChemOffice With the Online menu you can e Register your software e Search for compounds by name or ACX number and insert the structure in a worksheet e Use ACX numbers or names or structures in the worksheet to search for chemical information e Browse the CambridgeSoft website for technical support documentation software updates and more To use the Online menu you must have internet access EN Window Help Find Suppliers on Chem CX Com Find Information on ChemFinder Com Find ACX Numbers from Structure Find Structure from ACX Number Find Structure from Name at ChemACX Com Browse ChemStore Com Browse CambridgeSoft Com Browse CambridgeSoft Documentation Browse CambridgeSoft Technical Support Browse CambridgeSoft Downloads Register Online Browse ChemoOffice SDK Registering Online Chem Office 2005 applications utilize a new security scheme In order to activate any ChemOffice application you must register with the CambridgeSoft website to receive a registration Chem3D Appendix code Upon filling out a registration form the registration code is sent to you by email This registration scheme does not apply to site licenses If your serial number is invalid for any reason or if you do not have an internet connection you will have to contact CambridgeSoft Support to receive a registration code You may use your ChemOffice application a limited number of times while waiting for the registrat
319. in the Chem3D parameters tables This surface is always available with no further calculation Setting Molecular Surface Types Chem3D offers four different types of surface displays each with its own properties These types are shown in the following table Displaying Models 65 Molecular Surface Displays Surface Type Description Solid The surface is displayed as an opaque form Solid is a good 4 choice when you are interested in the details of the surface itself and not particularly interested in the underlying atoms and bonds The surface is displayed as a connected net of lines Wire Mesh is a good choice when you want to focus on sutface features but still have some idea of the atoms and bonds in the structure Wire Mesh Dots The surface is displayed as a series of unconnected dots amp Dots atea good choice if you ate primarily interested in the underlying structure and just want to get an idea of the surface shape 66 Displaying Models Surface Type Description The surface is displayed in solid form but is partially A transpatent so you can also see the atoms and bonds within it X Translucent is a good compromise between surface display styles Translucent Setting Molecular Surface lsovalues Isovalues ate by definition constant values used to generate a surface For each surface property values can be calculated throughout space For example the
320. in the United States Patent and Trademark O ffice C ambridgeSoft and ChemACX are trademarks of C ambridgeSoft C orporation Cambridge M assachusetts USA and are registered in the United States Patent and Trademark O ffice the European Union CTM and Japan Any use of the marks in connection with the sale offering for sale distribution or advertising of any goods and ser vices including any other website or in connection with labels signs prints packages wrappers receptacles or advertisements used for the sale offering for sale distribution or advertising of any goods and services including any other website which is likely to cause confusion to cause mistake or to deceive is strictly prohibited 7 Modification of D atabases Websites or Subscription Services CS reserves the right to change modify sus pend or discontinue any or all parts of any Paid Subscription Services and databases at any time 8 Representations and Warranties The User shall indemnify defend and hold CS Merck and or other Supplier harmless from any damages expenses and costs including reasonable attorneys fees arising out of any breach or alleged breach of these Terms and Conditions representations and or warranties herein by the User or any third party to whom User shares her his password or otherwise makes available this Subscription Service T he User shall cooperate in the defense of any claim brought against C ambridgeSoft M erck and or other
321. in the pi system Computation Concepts 141 Molecular Mechanics Theory in Brief 6 The modified values of Kres and BL ate used in the molecular mechanics portion of the MM2 computation to further refine the molecule Stretch Bend Cross Terms Stretch bend cross terms are used when a coupling occurs between bond stretching and angle bending For example when an angle is compressed the MM2 force field uses the stretch bend force constants to lengthen the bonds from the central atom in the angle to the other two atoms in the angle a Sir The force constant K differs for different atom combinations The seven different atom combinations where force constants are available for describing the situation follow X B C N O Y B B C N O H e X AI S Y e X AI S H e X Si P Y e X Si P H e X Ga Ge As Se Y P Y where X and Y are any non hydrogen atom User Imposed Constraints Additional terms are included in the force field when constraints are applied to torsional angles and non bonded distances by the Optimal field in the Measurements table These terms use a harmonic potential function where the force constant has been set to a large value 4 for torsional constraints and 10 for non bonded distances in order to enforce the constraint 142 Computation Concepts For torsional constraints the additional term and force constant is described by E TES LOIS For non bonded distance cons
322. ing sites highlighting 94 Bitmap file format 119 BMP file format 119 Boiling point ChemProp Pro 207 Bond angles 27 angles setting 86 dipole field 278 length 27 length and bond order tutorial example 33 length pop up information 105 length setting 86 order matrix 171 order changing 83 order pi systems 141 order pop up information 105 proximate addition command 84 stretching energy 137 stretching force constant field 278 stretching parameters 277 stretching table 272 277 tools building with 75 tools tutorial example 31 type field 277 281 287 Bond Angles 29 Bond angles parameters 29 Bond lengths parameters 29 Bonds 248 creating between nearby atoms 84 creating uncoordinated 76 moving 95 removing 76 selecting 91 BONDS keyword 171 Born Oppenheimer approximation 144 Bound to order 276 Bound to type 276 Building controls see Model building controls Chem3D 9 0 1 modes 73 toolbar 20 with bond tools 75 with other 2D programs 75 with substructures 79 with substructures examples 79 80 81 with the ChemDraw panel 74 with the text building tool 77 Building models 24 73 from Cartesian or Z Matrix tables 81 order of attachment 78 with bond tools 31 with ChemDraw 39 with the text building tool 36 C C3DTABLE 274 Calculate Force Constants At Each Point control 200 Calculate Initial Force Constants control 200 Calculating statistical properties 221 Calculating the dipole moment of meta ni tro
323. ion process to be completed Once the application times out you must register to activate the software In addition to registering your software you can request literature or register for limited free access to ChemFinder com ChemACX com ChemClub com and the email edition of ChemBioNews from the Register Online link of the Online menu This link connects you to the Cambridgesoft Professional Services page From this page you can link to a registration form To register online 1 From the Online menu choose Register Online The Cambridgesoft Professional Services page opens in your browser Technical Seapect News MacOS 10 Accessing the CambridgeSoft Web Site 223 Registering Online Accessing the Online ChemDraw User s Guide The Online menu link Browse CS ChemDraw Documentation opens the Cambridgesoft Desktop Manuals page where you can access current and previous versions of the ChemOffice User s Guide To access the CambridgeSoft Manuals page 1 From the Online menu choose Browse CS ChemDraw Documentation The Desktop Manuals page appears PDF versions of the CambridgeSoft manuals can be accessed from this page NOTE If you do not have a CambridgeSoft User account you will be directed to a sign up page first 2 Click version of the manual to view 224 Accessing the CambridgeSoft Web Site Accessing CambridgeSoft Technical Support The Online menu link Browse CS
324. ional aspects of the model For cyclohexane there ate six equivalent local minima twisted boat two equivalent global minima chair and many transition states one of which is the boat conformation CambridgeSoft Minimize Energy Locating the Global Minimum Finding the global minimum is extremely challenging for all but the most simple molecules It requires a starting conformation which is already in the valley of the g oba minimum not in a local minimum valley The case of cyclohexane is straightforward because you already know that the global minimum is either of the two possible chair conformations To obtain the new starting conformation change the dihedrals of the twisted conformation so that they represent the potential energy valley of the chair conformation The most precise way to alter a dihedral angle is to change its Actual value in the Measurements table when dihedral angles are displayed An easier way to alter an angle especially when dealing with a ring is to move the atoms by dragging and then cleaning up the resulting conformation To change a dihedral angle e Drag C1 below the plane of the ring then drag C4 above the plane of the ring ChemOffice 2005 Chem3D During dragging the bond lengths and angles wete deformed To return them to the optimal values before minimizing 1 Select all Ctrlt A and run Clean Up Now tun the minimization 2 From the MM2 submenu of the Calculations m
325. ionship SAR of molecules Selecting Properties To Compute To select properties for computation 1 From the Calculations menu choose Compute Properties The Compute Properties dialog box appears Compute Properties Available Properties y Property Server Class Balaban Index Binds Topolog Steric BetaPolarizabilties BetaPol Mopac Electronic y Boiling Point BP ChemPro Thermody Cluster Count ClsC Topolog Steric Fiter Connolly Accessible Area SAS ChemPro Steric Connolly Molecular Area MS ChemPro Steric Connolly Solvent Excluded Volum ChemPro Steric Critical Pressure Pc ChemPro Thermady Critical Temperature Tc ChemPro Thermady k t F tical Volume Nel FhemPra Thermodo lt Defaults Cost Accuracy Remove Parameters 2 Set appropriate values for the Class Server Cost and Quality filters For more information see Property Filters on page 215 3 From the list of Available Properties select the properties to calculate ChemOffice 2005 Chem3D 4 Click Add The properties you select appear in the Selected Properties list NOTE Some properties may not be computed for a particular model because of the limitations of standard computational methods Sorting Properties To sort the properties in the Property and Method columns e Click the column heading The items in the columns are sorted Removing Selected
326. iption LET Overrides safety checks to make the job run faster or further RECALC 5 Use this keyword if the optimization has trouble convetging to a transition state For descriptions of error messages reported by MOPAC see Chapter 11 pages 325 331 in the MOPAC manual To interrupt a minimization that is in progress e Click Stop in the Movie Controller Example Locating the Eclipsed Transition State of Ethane Build a model of ethane 1 From the File menu choose New Model 2 Double click in the model window A text box appears 3 Type CH3CH3 and press the Enter key A model of ethane appears 4 Select the Rotation tool 5 Click the arrow next to the Rotation tool and drag down the Rotation dial S ae SOR click here to open the Rotation dial dihedral rotators MOPAC Computations 183 Optimize to Transition State 6 Hold down the S key and select the bond between the C 1 and C 2 atoms NOTE Holding down the S Rey temporarily activates the Select tool 7 Select one of the dihedral rotators then enter 57 in the text box and press the Enter key A nearly eclipsed conformation of ethane is displayed TIP To view this better rotate the model on the Y axis until the carbon atoms are aligned Use Mopac to create the precise eclipsed transition state 8 Holding down the S and shift keys click on any two nearly eclipsed hydrogen atoms such as H 4 and H 7 to id
327. is added Click the terminal oxygen A text box appears over the oxygen atom Type in the text box and press the Enter key CambridgeSoft Building With The Text Tool The charge is applied to the oxygen atom Its atom type changes and a hydrogen atom is removed For amino acids that repeat put parentheses around the repeating unit plus a number rather than type the amino acid repeatedly For example type HAla Pro 10GlyOH Example 4 Other Polymers The formation of a PET polyethylene terephthalate polymer with 4 units a k a Dacron Terylene Mylar ia shown below e Type OH PET 4H into a text box with no atoms selected and press the Enter key The H and OH are added to cap the ends of the polymer Replacing an Atom with a Substructure The substructure you use must have the same number of attachment points as the atom you ate replacing For example if you try to replace a carbon in the middle of a chain with an Ethyl substructure an error occurs because the ethyl group has only one open valence and the selected carbon has two To replace an individual atom with a substructure 1 Click the Text tool 2 Click the atom to teplace A text box appears 3 Type the name of the substructure to add case sensitive ChemOffice 2005 Chem3D 4 Press the Enter key The substructure replaces the selected atom For example to change benzene to biphenyl 1 Click the atom to replace A text b
328. is checked SaveStepDatalnn sid the Heating Cooling Rate slider determines the rate at which energy is added to or removed from the model when it is far from the target Summary Parameter Quality Some parameters are guessed Job Type Molecular Dynamics temp erature Step Interval 2 0 fs Frame Interval 10 fs gt A heating cooling rate of approximately 1 0 Terminate After 10000 Steps 3 kcal atom picosecond results in small corrections which minimally disturb the trajectory A much higher rate quickly heats up Select the appropriate options the model but an equilibration or stabilization petiod is required to yield statistically If you want to Then Click meaningful results To compute an isoenthalpic trajectory record each iteration Record Every constant total energy deselect as a frame in a movie Iteration Heating Cooling Rate for later replay e Target Temperature the final temperature to which the calculation will run Energy is track a particular Copy Measurements added to or removed from the model when the measurement to Output computed temperature vaties more than 3 from the target temperature 8 P restrict movement of Move Only Selected a selected part ofa Atoms model during the The computed temperature used for this purpose is an exponentially weighted average temperature with a memory half life of about minimization Constraint is not 20 steps imposed on any term in the ca
329. is the embodiment of the forces of interaction among atoms in a molecule From the PES structural and chemical information about a molecule can be derived The methods differ in the way the surface is calculated and in the molecular properties derived from the energy surface The methods perform the following basic types of calculations e Single point energy calculation The energy of a given spacial arrangement of the atoms in a model or the value of the PES for a given set of atomic coordinates e Geometry optimization A systematic modification of the atomic coordinates of a model resulting in a geometry where the net forces on the structure sum to zero A 3 dimensional arrangement of atoms in the model representing a local energy minimum a stable molecular geometry to be found without crossing a conformational energy barrier e Property calculation Predicts certain physical and chemical properties such as charge dipole moment and heat of formation Computational methods can perform more specialized functions such as conformational seatches and molecular dynamics simulations 130 Computation Concepts Choosing the Best Method Not all types of calculations are possible for all methods and no one method is best for all purposes For any given application each method poses advantages and disadvantages The choice of method depend on a number of factors including e The nature of the molecule e The type of in
330. is the responsibility of the bulletin board operator or user group to respect copyright law and to ensure that it is not used as a vehicle for unauthorized copying or distribution Q I ll bet most of the people who copy software don t even know that they re breaking the law A Because the software industry is relatively new and because copying software is so easy many people are either unaware of the laws governing software use or choose to ignore them It is the responsibility of each and every software user to understand and adhere to copyright law Ignorance of the law is no excuse If you are part of an organization see what you an do to initiate a policy statement that everyone respects Also suggest that your management consider conducting a software audit Finally as an individual help spread the word that users should be software legal Q What are the penalties for copyright infringement A The Copyright Act allows a copyright owner to recover monetary damages measured either by 1 its actual damages plus any additional profits of the infringer attributable to the infringement or 2 statutory damages of up to 150 000 for each copy righted work infringed The copyright owner also has the right to permanently enjoin an infringer from engaging in further infringing activities and may be awarded costs and attorneys fees The law also permits destruction or other reasonable disposition of all infringing copies
331. ith a copy of your purchase receipt NO OTHER WARRANTIES CS DISCLAIMS OTHER IMPLIED WARRANTIES INCLUDING BUT NOT LIMITED TO IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE AND IMPLIED WAR RANTIES ARISING BY USAGE OF TRADE COURSE OF DEALING OR COURSE OF PERFORMANCE NOTWITH STANDING THE ABOVE WHERE APPLICABLE IF YOU QUALIFY AS A CONSUMER UNDER THE MAGNUSON MOSS WARRANTY ACT THEN YOU MAY BE ENTITLED TO ANY IMPLIED WARRANTIES ALLOWED BY LAW FOR THE PERIOD OF THE EXPRESS WARRANTY AS SET FORTH ABOVE SOME STATES DO NOT ALLOW LIMITATIONS ON IMPLIED WARRANTIES SO THE ABOVE LIMITATION MIGHT NOT APPLY TO YOU THIS WARRANTY GIVES YOU SPECIFIC LEGAL RIGHTS AND YOU MAY ALSO HAVE OTHER RIGHTS WHICH VARY FROM STATE TO STATE No Waiver T he failure of either party to assert a right hereunder or to insist upon compliance with any term or con dition of this Agreement shall not constitute a waiver of that right or excuse a similar subsequent failure to perform any such term or condition by the other party Governing Law This Agreement shall be construed according to the laws of the Commonwealth of M assachusetts Export You agree that the Software will not be shipped transferred or exported into any country or used in any man ner prohibited by the United States Export Administration Act or any other export laws restrictions or regulations End User License Agreement for CambridgeS oft Database Products Import
332. ity and Limitations 168 AM1 Applicability and Limitations 169 PM3 Applicability and Limitations 169 MNDO d Applicability and Limitations 170 Using Keywords 170 Automatic Keywords oooooooccooooo oo 170 Additional Keywords ooooooooooo oo 171 Specifying the Electronic Configuration 172 Even Electron Systems 04 174 Ground State RHF 000000 174 Ground State UHF 0 00000 174 Excited State RAP ita 008 174 Excited State UAE oe coed ean eee eines 175 Odd Electron Systems oooooooomoo o 175 Ground State RHF 00 0000 175 Ground State UHE sac siso nusen creton 175 Excited State RHE so nanai a oe ae 175 Excited State UA Fic we pct on eG ene ews 175 Spatklessvs cay e Recs Eli lt i eens bhi 175 Optimizing Geometry 176 TIoni pad hee tl ne dete ened eae RSA 176 BEGSi33 t dese drea ee sa 176 BES Os Rete os 176 MOPAC Files 176 Using the out fileres ari ascessi isikie 176 Creating an Input File o oooooomoo o 177 Running Input Files oooooommmm o o 177 Running MOPAC Jobs oooomoom o 178 Repeating MOPAC Jobs ooooooooooo 178 Creating Structures From arc Files 178 Minimizing Energy 180 INES si aes FG da ao 181 Adding Keywords 0ooooocccccccommo 181 Optimize to Transition State 182 Examplen
333. ize dialog box Customizing toolbars is a standard MS Windows operation and is not described in Chem3D documentation Model Explorer Displays a hierarchical tree representation of the model Most useful when working with complex molecules such as proteins the Model Explorer gives you highly granular control over the model display ChemDraw Panel Displays the ChemDraw Panel Use the ChemDraw Panel to build molecules quickly and easily with familiar ChemDraw drawing tools You can import export edit or create small molecules quickly and easily using the ChemDraw ActiveX tools palette Cartesian Table Displays the Cartesian Coordinates table Cartesian Coordinates describe atomic position in terms of X Y and Z coordinates relative to an arbitrary origin Z Mattix Table Displays the internal coordinates or Z Matrix table Internal coordinates ate the most commonly used coordinates for preparing a model for further computation ChemOffice 2005 Chem3D Measurements Table Displays the Measurements table The Measurements table displays bond lengths bond angles dihedral angles and ring closures Parameters Tables Displays a list of external tables that are used by Chem3D to construct models perform computations and display results Output Box Displays the Output box which presents textual information about the model iterations etc Comments Box Displays the Comments box a place for user comments tha
334. ize transition state geometries AM1 PM3 MNDO MINDO 3 methods CAMEO ChemDraw Synthetic Reaction Prediction e Expert system predicts and displays products e ChemDraw creates starting materials when you choose reaction conditions sold separately Chem3D Plugin Advanced WWW Model Client e Works with Microsoft Internet Explorer e Visualize 3D molecules on ChemFinder Com SYSTEMS amp LANGUAGES Windows Macintosh English Japanese Windows 95 98 Me NT 2000 XP Macintosh MacOS 8 6 9 2 X Some features are Windows only All specifications subject to change without notice mee qo term EMAIL info cambridgesoftcom WWW _ www cambridgesoftcom TEL 1 800 315 7300 INTL 1 617 588 9300 FAX 1 617 588 9390 e MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge MA 02140 USA am ri geSofi O Chemo ffice ChemDraw Chem3D ChemFinder Cheminfo are trademarks of CambridgeSoft 2002 All other trademarks are the property of their respective holders All specifications subject to change without notice www cam b r idg eso ft CcCOm DESKTOP CS ChemFinder Searching and Information Integration ChemFinder Pro is a fast chemically intelligent relational database search engine for personal group or enterprise use Extended integration with M icrosoft Excel and Word adds chemical searching and database capability to spreadsheets and documents An ever increasing number of chemical databases are available in
335. keyword NOMM to turn this keyword off The calculated predicted energy change must be less than n nn The default is 4 0 The calculated predicted energy change must be more than n n The default value is 0 000 Runs the SCF calculations using a higher precision so that values do not fluctuate from run to run Overrides safety checks to make the job run faster Use this keyword if the optimization has trouble converging to a transition state For descriptions of error messages reported by MOPAC see Chapter 11 pages 325 331 in the MOPAC manual ChemOffice 2005 Chem3D Additional Keywords Keywords that output the details of a particular computation are shown in the following table Terms marked with an asterisk appear in the out file Keyword Data ENPART All Energy Components FORCE Zero Point Energy FORCE Vibrational Frequencies MECI Microstates used in MECI calculation none HOMO LUMO Energies none Ionization Potential none Symmetry LOCALIZE Print localized orbitals VECTORS Print final eigenvectors molecular orbital coefficients BONDS Bond Order Matrix MOPAC Computations 171 Using Keywords The following table contains the keywords that invoke additional computations Terms marked with an asterisk appear in the out file Keyword Description CIS UV absorption energies NOTE Performs C I using only the first excited Singlet states and does not include the grou
336. l ChemN MR N ame Struct AutoN om ChemFinder W ord to ChemDraw Pro e ChemN MR Stereochemistry Polymers amp BioArt ChemDraw Pro Premier Drawing amp Database Query e Define complex database queries ISIS Draw amp Base compatible via copy paste e Structure CleanUp and Chemical Intelligence Chem3D Ultra Ultimate Modeling Visualization amp Analysis e Adds MO PAC CLogpP Tinker ChemProp ChemSAR amp Chem3D Plugin to Chem3D Pro e Advanced modeling molecular analysis tool E Notebook Ultra Ultimate Journaling amp Information ENotebook ChemDraw Std Chem3D Std ChemDraw Excel amp CombiC hem Excel Includes ChemFinder ChemFinder W ord ChemiIN DEX amp ChemRXN databases Some features are W indows only All specifications subject to change without notice DESKTOP CS E Notebook Electronic Journal and Information E Notebook Ultra streamlines daily record keeping tasks of research scientists maintains live chemical structures and data and saves time documenting work and retrieving chemical information E N otebook com bines all of your notebooks into one and sets up as many project notebooks as you need organized the way you work Notebook pages include ChemD raw documents Excel spreadsheets Word documents and spectral data E N otebook automatically performs stoichiometry calculations on ChemD raw reaction pages Search by struc ture keyword dates and other types of data Maintain
337. l you can specify which calculation to use from the Choose Result submenu of the Calculations menu Solvent Accessible Surface The solvent accessible surface represents the portion of the molecule that solvent molecules can access When viewed in the ball and stick representation a molecule may appear to have many nooks and crannies but often these features CambridgeSoft Molecular Surface Displays are too small to affect the overall behavior of the molecule For example in a ball and stick representation it might appear that a water molecule could fit through the big space in the center of a benzene molecule The solvent accessible surface which has no central hole shows that it cannot The size and shape of the solvent accessible surface depends on the particular solvent since a larger solvent molecule will predictably enjoy less access to the crevices and interstices of a solute molecule than a smaller one To determine the solvent accessible surface a small probe sphere simulating the solvent molecule is rolled over the surface of the molecule van der Waals surface The solvent accessible surface is defined as the locus described by the center of the probe sphere as shown in the diagram below Solvent accessible surface eN Solvent probe van der Waals surface A Connolly Molecular Surface The Connolly surface also called the molecular surface is similar to the solvent accessible surface Using a sma
338. l Building Basics If you select four contiguous atoms the dihedral angle appears in the model label If you select two bonded or non bonded atoms the distance between those atoms appears To specify what information appears in atom bond and angle labels e In the Model Settings dialog box select the Pop up Info tab then select the information you want to display Atom Types Atom types contain much of the Chem3D chemical intelligence for building models with reasonable 3D geometries If an atom type is assigned to an atom you can see it in the model data when you point to it In the previous illustration of pointing information the selected atom has an atom type of C Alkane An atom that has an atom type assigned has a defined geometry bond orders type of atom used to fill open valences rectification and standard bond length and bond angle measurements depending on the other atoms making up the bond The easiest way to build models uses a dynamic assignment of atom types that occurs as you build For example when you change a single bond in a model of ethane to a double bond the atom type is automatically changed from C Alkane to C Alkene In the process the geometry of the carbon and the number of hydrogens filling open valences changes You can also build models without assigning atom types This is often quicker but certain tasks such as rectification or MM2 Energy Minimization will also correct a
339. l axis rotation dihedral rotation dihedral move other side The Rotation dial should show the angle of the selected dihedral approximately 60 and dihedral rotation should be selected 2 Grab the green indicator button and rotate the dial to 0 0 Chem3D Tutorials 41 Tutorial 4 Examining Conformations In the Measurements table notice that the dihedral for H 3 C 1 C 2 H 8 is now minus 0 degrees as shown in the model H 5 C 1 C 2 H 8 0 1551 H S C 1 C 2 H 7 120 0000 H 5 C 1 C 2 H 6 119 9224 H 4 C 1 C 2 H 8 120 0000 H 4 C 1 C 2 H 7 120 1551 H 4 C 1 C 2 H 6 0 0776 H 3 C 1 C 2 H 8 119 9224 H 3 C 1 C 2 H 7 0 0776 H 3 C 1 C 2 H 6 120 0000 lt gt E Mo XZca 242 HN Me To compute steric energy 1 From the Calculations menu point to MM2 then choose Compute Properties NOTE The property tab defaults should remain as in the previous calculation 2 Click Run The final line in the Output box appears as follows 1 4 VDU 1 7726 Total 3 9061 The steric energy for frame l 3 906 kcal mole Calculation completed NOTE The values of the energy terms can vary slightly based on the type of processor used to calculate them The steric energy for the eclipsed conformation 3 9 kcal mole is greater in energy than that of the staggered conformation 1 kcal mole indicating that the staggered configuration is the conformation that
340. l copies of the Software and accompanying written materials to CS You may not modify decompile reverse engineer or disassemble the Software 3 Assignment Restrictions You may not rent lease or otherwise sublet the Software or any part thereof You may transfer on a permanent basis the rights granted under this license provided you transfer this Agreement and all copies of the Software including prior versions and all accompanying materials The recipient must agree to the terms of this Agreement in full and register this transfer in writing with CS 4 Use of Included Data All title and copyrights in and to the Software product including but not limited to any images photographs animations video audio music text applets Java applets and data files and databases the Included D ata are owned by CS or its suppliers You may not copy distribute or otherwise make the Included D ata publicly available Licensed users of Chemo ffice Enterprise and Workgroup and the accompanying Plugin software products may access search and view the Included D ata and may transmit the results of any search of the Included D ata to other users of the licensed Chemo ffice Enterprise and Workgroup software products within your organization only provided that such transmission is via an internal corporate or university network and is not accessible by the public You may not install the Included Data on non licensed computers nor distribu
341. l default mode for small molecules The default colors are stored in the Elements Table To change the color of elements specified in the Elements table 1 From the View menu point to Parameter Tables and choose Elements The Elements Table opens 2 Double click the Color field for an element The Color dialog box appears 3 Select the color to use and click OK CambridgeSoft Structure Displays 4 Close and Save the table NOTE You must save the changes before they take effect Coloring by Group You may assign different colors to substructures groups in the model To change a color associated with a group in the active model 1 In the Model Explorer Right click on the group name and choose Select Color The Color dialog box appears 2 Select the color to use and click OK 3 Save the changes to the Model Coloring by Partial Charge When coloring by partial charge atoms with a highly negative partial charge ate deep blue Atoms with a highly positive partial charge are deep red As the partial charge gets closer to 0 the atom is paler Atoms with a 0 partial charge are white The Partial Charge is the result of a calculation Extended H ckel MOPAC or Gaussian If you have not performed a calculation the partial charge for each atom is 0 If you have performed more than one calculation you can specify the calculation to use in the Choose Result submenu of the Calculations menu Peri
342. l method Hydrophobicity mapping onto surfaces 69 Hydrophobicity scale 68 Hyperfine coupling constants 188 Hyperfine coupling constants example 195 Hyperpolarizability 188 I Ideal gas thermal capacity ChemProp Pro 207 Import file command 14 Importing Cartesian coordinates files 177 ISIS Draw structures 75 Inertia ChemProp Std 206 Installing GAMESS 211 Int Coords see Internal coordinates file INT see Internal coordinates file Internal coordinates 28 changing 101 file 246 file format 123 FORTRAN file format 249 pop up information 105 table 108 Internal coordinates file 246 Internal rotations see Dihedral angles ro tating Internal tables 24 Internet CambridgeSoft web site 227 Inverting a model 88 Inverting cis trans isomers 38 Ionization field 280 ISIS Draw 75 Isocharge 69 Isopotential 70 Isospin 70 Isovalues editing 66 Iterations recording 111 J Job description file format 126 202 Job description stationery file format 126 Job description template file format 202 Job type settings 159 Job Type tab GAMESS 212 Gaussian 199 molecular dynamics 159 Job type tab 199 212 K KB field 279 Keyboard modifiers table of 235 236 Keywords BFGS 176 BOND 171 DFORCE 171 EF 176 ENPART 171 LBFGS 176 LET 171 183 LOCALIZE 171 NOMM 172 PI 172 PRECISE 171 172 183 RECALC 171 183 RMAX 171 RMIN 171 TS 176 VECTORS 171 Keywords additional Gaussian 201 Keywords automatic 170 Keywords MOPAC 170
343. lculation and the Job Type Settings values of any results are Use the Job Type tab to set options for the not affected computation ChemOffice 2005 Chem3D MM2 and MM3 Computations 159 Molecular Dynamics Computing the Molecular Dynamics If you want to Then Click Trajectory for a Short Segment of Polytetrafluoroethylene PTFE save a file containing Click Save Step Data the Time in In and browse to choose To build the model picoseconds Total a location for storing this 1 From the File menu choose New Energy Potential file ate Pages aad 2 Select the Text Building tool Temperature data for The word heating or 3 Click in the model window each step cooling appears for A text box appears h step in which ee 4 Type F C2F4 6F and press the Enter key heating or cooling was A polymer segment consisting of six repeat performed A summary of this data appears in the units of tetrafluoroethylene appears in the Message window each model window time a new frame is To perform the computation created 1 Select C 2 the leftmost terminal carbon then To begin the computation Shift click C 33 the rightmost terminal e Click Run carbon The computation begins Messages for each iteration and any measurements you are tracking appear in the Output window A measurement for the overall length of the molecule appears in the Measurements table 2 Choose Set Distance from the Measurement
344. le at the compound s critical temperature and pressure ChemOffice 2005 Chem3D Full Report Heat of Formation kcals mole Henty s Law Constant unitless Ideal Gas Thermal Capacity J mole K LogP Melting Point Kelvin Molar Refractivity cm mole Standard Gibbs Free Energy kJ mole A detailed list of information used for performing the calculations including additional properties and literature references used Results for other fragmentation methods ate included The heat of formation AHp for the structure at 298 15 K and 1 atm The inverse of the logarithm of Henry s law constant log H The constant pressure 1 atm molar heat capacity at 298 15 K for an ideal gas compound The logarithm of the partition coefficient for n octanol water The melting point for the structure at 1 atm The molar refraction index The Gibbs free energy AG for the structure at 298 15 K and 1 atm SAR Descriptors ChemProp Pro Server 207 Property Description Error Message Cause The vapor pressure for the structure at 25 C Vapor Pressure Pa Prediction of the water solubility of the structure Water Solubility at 25 C mg L Limitations Property prediction using CS ChemProp Pro has following limitations e Single molecules with no more than 100 atoms e Literature values for Partition Coefficients LogP and Henry s Law Constant are not av
345. ledge management and informatics solution covering elextronic notebooks biological screening chemical registration and more over your intranet Enterprise Ultra includes E Notebook for record keeping BioAssay for low and high throughput screening integrated plate inventory Inventory for reagents BioSAR for SAR reports Registration system and ChemACX Database of available chemicals Technologies include ChemDraw ActiveX and Oracle Cartridge E Notebook US 1617 588 9300 FAX 1617 588 9390 WWW www cambridgesoft com CambridgeSoft EU 0080087520000 FAX 44 1223 464990 EMAIL _ info cambridgesoft com MAIL 100 CambridgePark Drive Cambridge MA 02140 USA www cambridgesoft com MAE 04980 0408
346. lic and inorganic compounds of biological interest Built into Chem3D EH is the default semi empirical method used to calculate data required for displaying molecular surfaces The EH method uses a one electron Hamiltonian with matrix elements defined as follows Hap ly Hy 0SK H A Syy ey where 1 u is the valence state ionization energy VSIE of orbital 1 as deduced from spectroscopic data and K is the Wolfsberg Helmholtz constant 166 MOPAC Computations usually taken as 1 75 The Hamiltonian neglects electron repulsion matrix elements but retains the overlap integrals calculated using Slater type basis orbitals Because the approximated Hamiltonian H does not depend on the MO expansion coefficient Cy the matrix form of the EH equations HS Cr can be solved without the iterative SCF procedure RHF The default Hartree Fock method assumes that the molecule is a closed shell and imposes spin restrictions The spin restrictions allow the Fock matrix to be simplified Since alpha spin up and beta spin down electrons are always paired the basic RHF method is restricted to even electron closed shell systems Further approximations ate made to the RHF method when an open shell system is presented This approximation has been termed the 1 2 electron approximation by Dewar In this method unpaired electrons are treated as two 1 2 electrons of equal charge and opposite spin This allows the computation
347. lication that can accept this format e Copy As Picture Puts the model on the Clipboard as a bitmap You may only paste the structure into an application that can accept bitmaps NOTE The application you paste into must recognize the format For example you cannot paste a ChemDraw structure into a Microsoft Word document e Paste Special Preserves coordinates when pasting a Chem3D model from one document to another e Clear Clears the model window of all structures e Select All Selects the entire model ChemOffice 2005 Chem3D e Select Fragment lIf you have selected an atom selects the fragment that atom belongs to The View Menu Model Display Toolbar Use the View menu to select the view position and focus as well as which toolbars tables and panels ate visible The Model Display submenu of the View menu duplicates all of the commands in the Model Display toolbar e View Position The View Position submenu gives you options for centering the view fitting the window and aligning the view with an axis e View Focus The View Focus submenus is used to set the focus See View Focus on page 85 e Model Display Duplicates the Model Display toolbar Contains tools to control the display of the model These tools are duplicated on the View menu e Show Atom Labels A toggle switch to display or hide the atom labels Show Serial Numbers A toggle switch to display or hide the ato
348. lick in the empty space in the model window A text box appears where you clicked 4 In the text box type CH3CH CH3 CH2CH OH CH3 You type labels as if you were naming the structure pick the longest chain of carbons as the backbone and specify other groups as substituents Enclose substituents in parentheses after the atom to which they are attached Chem3D Tutorials 37 Tutorial 3 Building Models with the Text Building Tool 5 Press the Enter key TIP The Text building tool will also accept structures in SMILES notation either typed in or cut and pasted from other documents Another simpler way of building this model is to type Pentane in the Name Struct text box and then modify the appropriate hydrogens Refine the model as follows 1 Click the Select tool k 2 Select the model by dragging diagonally across it 3 From the Structure menu choose Clean Up If you want a mote accurate representation of a low energy conformation optimize the geometry of the model by clicking the MM2 tool MM2 on the Calculation toolbar To specify text equivalent to the structure of 1 2 dimethyl cyclopentane shown below H2 c Ta Sai CH CH H3C CH From the File menu choose New Click the Text Building tool A Click in the empty space in the model window Type CH CH3 CH CH3 CH2CH2CH2 Press the Enter key me WN e The rans isomet appears 38 Chem3D Tutorials 6 Select the mod
349. lied as you build Fit Model to Determines whether the entire Window model is resized and centered in the model window after a change to the model is made Detect When selected all bonds in a Conjugated conjugated system are set at a System bond order of 1 5 When unselected bonds are displayed as drawn Does not affect previously drawn structures Bond Proximate Determines whether a bond is Addition created between a selection of atoms For more information see Creating Bonds by Bond Proximate Addition on page 84 74 Building and Editing Models NOTE For more information about atom types standard measurements and rectification see Model Building Basics on page 24 Building with the ChemDraw Panel Chem3D 9 makes it easier than ever to create or edit models in ChemDraw The ChemDraw panel is activated from the View menu Using ActiveX technology it puts the functionality of ChemDraw Pro at your fingertips To add a new structure to Chem3D 1 Open the ChemDraw Panel by selecting it from the View menu The ChemDraw panel appears on the tight of the model window 2 Click in the panel to activate it The Tools palette appears TIP If you don t see the Tools palette right click in the ChemDraw panel and check the View menu to see that it has been activated There should be a check mark next to Show Main Tools While you are at it you might want to activate other toolbars Activating t
350. lines in the block 20 in this example Line 44 contains two fields The first field contains the exponent used to convert the coordinates in the lines following to the CambridgeSoft Protein Data Bank Files coordinate type specified in line 43 The SYBYL MOL File second field is the FORTRAN format of the atom coordinates 9 Lines 45 65 each contains three fields describing the Cartesian coordinates of an The SYBYL MOL File format SYBYL is defined in Chapter 9 SYBYL File Formats pages 9 1 through 9 5 of the 1989 SYBYL Programming atom indicated in the CT block The first field pee is the X coordinate the second field is the Y The following is an example of a file in SYBYL coordinate and the third field is the Z format produced from within Chem3D This file coordinate describes a model of cyclohexanol 19 MOL CyclohexanolO 1 1 1 068 0 3581 0 7007C 2 1 0 207 1 2238 0 7007C 3 1 1 473 0 3737 0 5185C 4 1 1 1286 0 477 0 5913C 5 1 0 139 1 324 0 7800C 6 1 1 396 0 445 0 7768C 7 8 2 1708 1 2238 0 70070 8 13 1 0068 0 343 1 5689H 9 13 0 284 1 7936 1 6577H 10 13 0 147 1 9741 0 1228H 11 19 2 375 1 032 0 4983H 12 13 1 589 0 314 1 3895H 13 13 1 2546 0 202 1 4669H 14 13 2 0091 1 161 0 5742H 15 13 0 077 1 893 1 7389H 16 13 0 21 2 076 0 0419H 17 13 2 308 1 081 0 8816H 18 13 1 372 0 2442 1 6545H 19 13 2 9386 0 6891 0 8100H 19 MOL 1 1 2 1 2 1 4 1 3 1 7 1 4
351. ll spherical probe to simulate a solvent it is defined as the surface made by the center of the solvent sphere as it contacts the van der Waals sutface The volume enclosed by the Connolly ChemOffice 2005 Chem3D surface is called the solvent excluded volume These surfaces ate shown in the following illustration van Der Waals Sie airs verti cae ay The Connolly Surface of icrn is shown below ULTRA Total Charge Density The Total Chatge Density is the electron density in the space surrounding the nuclei of a molecule or the probability of finding electrons in the space around a molecule The default isochatge value of 0 002 atomic units a u approximates the molecule s van der Waals radius and represents about 95 of the entire three dimensional space occupied by the molecule The Total Charge Density surface is the best visible representation of a molecule s shape as determined by its electronic distribution The Total Charge Displaying Models 69 Molecular Surface Displays Density surface is calculated from scratch for each molecule The Total Charge Density is generally more accurate than the Space Filling display For Total Charge Density surfaces the properties available for mapping are Molecular Orbital Spin Density Electrostatic Potential and Partial Charges The color scale uses red for the highest magnitude and blue for the lowest magnitude of the property Neutral is white You can choose
352. ll to the worksheet 2 Select the appropriate option If you want to Then click create a new New ChemOffice ChemOffice worksheet Worksheet convert the current Convert Worksheet Excel worksheet to a ChemOffice worksheet NOTE Ifyou are already in a ChemOffice worksheet the Convert button is grayed out and you can immediately click Next 3 Click Next 218 ChemSAR Excel The Step 2 of 4 dialog box appears CS ChemSAR Wizard Step 2 of 4 Select a cell to label Structure molecules will be placed in this column below this cell column labels for calculated descriptors will be placed in this row to the right of this cell Structure Cell 01 Press Next gt to add structures to the worksheet Cancel lt Back Next gt 4 Click in the cell that will be the heading cell for the structure column or type in a cell reference 5 Click Next The Step 3 of 4 dialog box appears CS ChemSAR Wizard Step 3 of 4 Several tools are available to add chemical structures to a ChemOffice work sheet Pick the method you want to use The right hand buttons require a Cell Range to be selected before they are enabled Show Structures as 2D Pictures Get Current List from ChemFinder Import SD File Load From File Cell Range Cancel lt Back Next gt The buttons on the right are active when you use a range of cells in your worksheet To select a range of ce
353. ller or larger resize the model window accordingly before you copy it If the model windows for several models are the same size and Fit Model to Window is on then the models should copy as the same size Transferring to ChemDraw You can transfer information to ChemDraw as a 3D model or as a 2D model To transfer a model as a 3D picture 1 Select the model 2 From the Edit menu point to Copy As then choose Picture 3 In ChemDraw select Paste from the Edit menu NOTE The model is imported as an EMF graphic and contains no structural information To transfer a model as a 2D structure ChemOffice 2005 Chem3D 1 Select the model 2 From the Edit menu point to Copy As then choose ChemDraw Structure 3 Open ChemDraw 4 From the Edit menu choose Paste The model is pasted into ChemDraw Transferring to Other Applications To copy and paste a space filling model into a word processing desktop publishing presentation or drawing application such as Microsoft Word or PowerPoint 1 Select the model 2 From the Edit menu point to Copy As then choose Picture 3 Paste the model into the target application document TIP If you are pasting into MS Word or PowerPoint select Paste Special and choose the type of graphic you wish to import bitmap WME or EMF The EMF option will copy with a transparent background Alternatively you could use Save As Bitmap or EMF to create a fil
354. llowing property calculations ULTRA Property Description Alpha Coefficients First order polarizability coefficients Beta Coefficients Second order polarizability coefficients Dipole Debye Molecular dipole moment SAR Descriptors MOPAC Server 209 Property Description Electronic Energy 298 K eV at 0 Celsius Gamma Coefficients HOMO Energy eV LUMO Energy eV Repulsion Energy eV Symmetry Total Energy eV 210 SAR Descriptors The total electronic energy Third order polarizability coefficients Energy of the highest occupied molecular orbital Energy in of the lowest unoccupied molecular otbital Total core core internuclear repulsion between atoms Point group symmetry The sum of the MOPAC Electronic Energy and the MOPAC Repulsion Energy GAMESS Server ULTRA GAMESS uses ab initio computational methods to compute property predictions For more information see and The GAMESS server provides the following property calculations Property Description Dipole Moment Molecular dipole moment Debye HOMO Energy eV Energy of the highest LUMO Enetgy eV Repulsion Energy Energy eV Total Energy eV occupied molecular orbital Energy of the lowest unoccupied molecular otbital Total core core internuclear repulsion between atoms The total energy of the molecule CambridgeSoft GAMESS Server Ch
355. lls a Click the minus sign at the right end of the Cell Range box A selection box appears b Drag the range of cells you want to include CambridgeSoft The ChemSAR Excel Wizard c Click the icon at the right of the selection box ChemDraw1 A 2 4 13 The range is entered and the buttons are active as shown below CS ChemSAR Wizard Step 3 of 4 Several tools are available to add chemical structures to a ChemDraw work sheet Pick the method you want to use The right hand buttons require a Cell Range to be selected before they are enabled Import ChemFinder Database I Show Structures as 2D Pictures Get Current List from ChemFinder Convert From SMILES Import SD File Convert From Chemical Name Load From File Use Selected Range Cell Range ChemDraw1 4 2 4 13 Press Next gt to calculate descriptors Cancel 6 To display graphics of your structures in the worksheet choose Show Structures As 2D Pictures lt Back Next gt 7 Select the appropriate option If you want to Then If you want to Then use data from a ChemFinder database a Click Import ChemFinder Database b In the Import Table dialog box choose the database and click Open a Click Get Current List from ChemFinder use an active ChemFinder hit list b Click Yes ChemOffice 2005 Chem3D import a structure data file into the ChemFinder worksheet import a file of one of the following forma
356. lps your original driver may need to be updated contact the maker of the driver and obtain the most up to date driver If you still have trouble contact us with the relevant details about the original driver and the resulting problem Try reinstalling the software Before you reinstall uninstall the software and disable all background applications including screen savers and virus protection See the complete uninstall instructions on the CambridgeSoft Technical Support web page If the problem still occurs use our contact form at http www cambridgesoft com services mail and provide the details of the problem to Technical Support CambridgeSoft Troubleshooting Appendix C Substructures Overview You can define substructures and add them to a substructures table When you define a substructure the attachment points where unselected atoms are bonded to selected atoms ate stored with the substructure If a substructure contains more than one attachment point such as Ala the atom with the lowest serial number normally becomes the first attachment point The atom with the second lowest serial number becomes the second attachment point and so on However there ate situations where this general rule is not valid Attachment point rules The following rules cover all possible situations for multiple attachment points in substructures Rule 3 is the normal situation described above 1 If an atom has
357. lve fields comprise an atom type record name symbol van der Waals radius text number charge the maximum ring size rectification type geometry number of double bonds number of triple bonds number of delocalized bonds bound to order and bound to type Name The records in the Atom Types table are ordered alphabetically by atom type name Atom type names must be unique Symbol This field contains the element symbol associated with the atom type The symbol links the Atom Type table and the Elements table The element symbol is used in atom labels and when you save files in file formats that do not support atom types such as MDL MolFile CambridgeSoft The Elements van der Waals Radius The van der Waals VDW radius is used to specify the size of atom balls and dot surfaces when displaying the Ball amp Stick Cylindrical Bonds or Space Filling models The Close Contacts command in the Measurements submenu of the Structure menu determines close contacts by comparing the distance between pairs of non bonded atoms to the sum of their van der Waals radii The van der Waals radii specified in the Atom Types table do not affect the results of an MM2 computation The radii used in MM2 computations are specified in the MM2 Atom Types table NOTE The space filling model display is set in the Model Display tab of the Model Settings dialog box The appearance of VDW dot surfaces is specified for the entire model in t
358. ly be done with the greatest of caution by expert users Within a force field equation parameters operate interdependently changing one normally requires that others be changed to compensate for its effects Bond Stretching Energy TA D LS The bond stretching energy equation is based on Hooke s law The K parameter controls the stiffness of the spring s stretching bond stretching force constant while r defines its equilibrium length the standard measurement used in building models Unique K and r patameters are assigned to each pair of bonded atoms based on their atom types C C C H O C The parameters are stored ChemOffice 2005 Chem3D in the Bond Stretching parameter table The constant 71 94 is a conversion factor to obtain the final units as kcal mole The result of this equation is the energy contribution associated with the deformation of a bond from its equilibrium bond length This simple parabolic model fails when bonds are stretched toward the point of dissociation The Morse function would be the best correction for this problem However the Morse Function leads to a large increase in computation time As an alternative cubic stretch and quartic stretch constants are added to provide a result approaching a Motse function correction The cubic stretch term allows for an asymmetric shape of the potential well allowing these long bonds to be handled However the cubic stretch term is not s
359. m 4 From the View menu point to View Position and then click Align View choose a plane With Selection For example to move a cyclohexane chair so that three alternating atoms are on the X Y Plane 1 Select two non adjacent carbon atoms in the ring 2 From the View menu point to View Position and then click Align View X Axis With Selection 100 Manipulating Models The model moves to the position shown below 3 Select the third carbon atom such that no two selected atoms in the ring are adjacent 4 From the View menu point to View Position and then click Align View X Y Plane With Selection The model moves to the position shown below Resizing Models Chem3D provides the following ways to resize your model e Resizing Windows e Scaling a Model Centering a Selection When resizing a model or before doing computations it is often useful to center the model Chem3D allows you to select an atom or atoms to determine the center or performs the calculation on the entite model CambridgeSoft Resizing Models To center your model based on a particular selection 1 Select one or more atoms optional 2 Choose Center Model from the Model Position submenu of the Structure menu This command places the centroid of the selected atoms at the coordinate origin Chem3D calculates the centroid of the selected atoms by averaging their X Y and Z coordinates If you do not select any at
360. m Excel Combinatorial Chemistry in Excel e Generate combinatorial libraries e Choose starting materials amp reaction schemes e View structures amp track plate well assignments ChemFinder Pro Premier Searching amp Information Advanced search structure query features Stores structures reactions along with calculated data associated information e Search by substructure including stereochemistry using ChemDraw Integration with ChemDraw Chem3D Import export MDL SD RD files Cheminfo Std Reference amp Reaction Searching ChemIN DEX for small molecule information e ChemRXN for reaction databases BioAssay Pro Biological Assay Structure Activity Set up biological models visualize information e Search data by structure to isolate key structural determinants of biological activity e Tabulate analyze structure activity relationships with spreadsheet templates Available in Chemo ffice Ultra SYSTEMS LANGUAGES English Japanese Windows 95 98 Me NT 2000 XP This software is Windows only All specifications subject to change without notice A q 8 CA EN EMAIL info cambridgesoftcom WWW _ www cambridgesoftcom iii TEL 1800 315 7300 INTL 1617 588 9300 FAX 1 617 588 9390 Oo MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge MA 02140 USA CambridgeSoft P AAA Chemo ffice ChemDraw Chem3D ChemFinder Cheminfo are trademarks of CambridgeSoft 2002 m
361. m numbers e Show Atom Dots Displays or hides atom dot surfaces for the model The dot surface is based on VDW radius or Partial Charges as set in the Atom Display table of the Settings dialog box e Show Atom Spheres Displays or hides atom spheres for the model The radius is based on VDW radius or Partial Charges as set in the Atom Display table of the Settings dialog box e Show Hs and Lps A toggle switch to display or hide hydrogen atoms and lone pairs e Red and Blue glasses A toggle switch to set the display for optimal viewing with red blue 3D glasses to create a stereo effect Chem3D Basics 15 The Graphical User Interface 16 e Stereo Pairs A toggle switch to enhance three dimensional effect by displaying a model with two slightly different orientations It can also create orthogonal simultaneous front and side views The degree of separation is set on the Stereo View tab of the Settings dialog box e Perspective A toggle switch to create a perspective rendering of the model by consistent scaling of bond lengths and atom sizes by depth The degree of scaling is controlled by the Perspective Field of View slider on the Model Display tab of the Settings dialog box e Depth Fading A toggle switch to create a realistic depth effect where more distant parts of the model fade into the background The degree of fading is controlled by the Depth Fading Field of View slider on the Model
362. m3D when you perform an MM2 computation e Tables that store data gathered during Dihedral Driver conformational searches Standard Measurements Standard measurements are the optimal or equilibrium bond lengths and angles between atoms based on their atom type The values for each particular atom type combination are actually an average for many compounds each of which have that atom type for example a family of alkanes Standard measurements allow you to build models whose 3D representation is a fair approximation of the actual geometry when other forces and interactions between atoms are not considered For mote information on External Tables see Parameter Tables on page 271 To view an internal table e Choose the table from the View menu CambridgeSoft Model Building Basics To view an external table e Point to Parameter Tables on the View menu then choose the table to view TIP You can superimpose multiple tables if you attach them to an edge of the GUI One table will be visible and the others will display as selection tabs Attached tables have the Auto hide feature To auto hide a table e Push the pin in the upper right corner of the table The table minimizes to a tab when you ate not using it The Model Setting Dialog Box The Chem3D Model Settings dialog box allows you to configure settings for your model To open the Chem3D Model Settings dialog box From the File menu cho
363. mACX on CD ROM DATABASES Fully structuresearchable database of 500 000 products from 300 chemical catalogs separate ChemAC X SC database contains screening compounds e Search by name synonym partial name formula and other criteria as well as structure and substructure e Shopping cart system works with requisition forms and purchasing systems such as SAP Ariba and Commercel to streamline chemical purchasing Data Currency A premium is placed on the accuracy and currency of the ChemACX Database M any suppliers listed in the database are also currently selling their products online through the ChemACX Com web site and therefore have a vested interest in ensuring that their data remains complete accurate and up to date You wont find a sourcing database with more frequently updated content and current pricing than ChemACX Data Accessibility The same way that Internet users can publicly access C hemAC X Com enterprise users can access their private ChemACX Database via a standard web browser There is no need to configure or install any additional soft ware ChenD raw users can either use the ChemD raw Plugin to draw chemical structures directly in the brows er s search page or alternatively submit queries to the database server directly from ChenD raw ChemFinder users can access their own copy of the database right from their local hard drive Electronic Requisitions Traditional sourcing databases were conceived merely
364. mOffice 2005 Chem3D Sorting Properties 0 cece eee eee 215 Removing Selected Properties 215 Property Filters nesenai a eani 215 Setting Parameters 216 Results ia Aue nace ween 216 Chapter 15 ChemSAR Excel Configuring ChemSAR Excel 217 The ChemSAR Excel Wizard 217 Selecting ChemSAR Excel Descriptors 220 Adding Calculations to an Existing Worksheet ooooocccccccccccccco 220 Customizing Calculations 221 Calculating Statistical Properties 221 Descriptive StatiStiCS oooooommmm oo oo 221 Correlation Matrix 0ooooooccocooooo 222 Rune Plots sana 222 Appendixes Accessing the CambridgeSoft Web Site Registering Online 223 Accessing the Online ChemDraw User s Guida Maen ous 224 Accessing CambridgeSoft Technical SUPPOFt ei nosis ees dew ols eds 224 Finding Information on ChemFinder com 224 Finding Chemical Suppliers on ACX com 225 Finding ACX Structures and Numbers 225 ACX Structures sis seeds cad een ss ba ais 225 ACX Numbers opa 226 Browsing SciStore com 226 Browsing CambridgeSoft com 227 Using the ChemOffice SDK 227 Technical Support Serial Numbets 5 229 Troubleshooting 229 Performance oaeen bine os acne sere sen ta eed 230 Oyster Crashes ios eins scale omen cogent 230 Substructures OVERVIEW 5 a hss RU Se hn Sens 231 Attach
365. mat may be used to import a model Only the Molecule Specification section of the input file is saved For atoms not otherwise specified in Chem3D the charge by default is written as 0 and the spin multiplicity is written as 1 You can edit Gaussian Input files using a text editor with the addition of keywords and changing optimization flags for running the file using the Run Gaussian Input file within Chem3D ot using Gaussian directly Gaussian Checkpoint A Gaussian Checkpoint file FCHK FCH stores the results of Gaussian Calculations It contains the final geometry electronic structure including energy levels and other properties of the molecule Checkpoint files are supported for import only Chem3D displays atomic orbitals and energy levels stored in Checkpoint files If Cubegen is installed molecular surfaces ate calculated from the Checkpoint file Gaussian Cube A Gaussian Cube file CUB results from running Cubegen on a Gaussian Checkpoint file It contains information related to grid data and model coordinates Gaussian Cube files ate supported for import only CambridgeSoft Exporting Models Using Different File Formats Chem3D displays the surface the file describes If more than one surface is stored in the file only the first is displayed You can display additional sutfaces using the Surfaces menu Internal Coordinates Internal Coordinates INT files are text files that describe a single molecule by t
366. mation about related structures and numbers You can place the returned information in your document ACX Structures There ate two ways to find ACX structures by ACX number or by name Accessing the CambridgeSoft Web Site 225 Finding Chemical Suppliers on ACX com To find a structure that corresponds to an ACX number 1 From the Online menu choose Find Structure from ACX Number The Find Structure from ACX number dialog box appears Find Structure from ACX Number Enter the ACX number for which a structure is to be found Cancel 2 Type the ACX tegistry number 3 Click OK The Structure appears in your document To find a structure from a name 1 From the Online menu choose Find Structure from Name at ChemACX com The Find Structure from Name dialog box appears Find Structure from Name at ChemAc Enter the chemical name for which a structure is to be found Cancel 2 Type ina name As with ChemFindet com you can use a chemical name or a trade name 3 Click OK The Structure appears in your document 226 Accessing the CambridgeSoft Web Site ACX Numbers To Find an ACX number for a structure 1 In a ChemOffice document select the structure for which you want to find an ACX number 2 From the Online menu choose Find ACX Numbers from Structure The ACX number appears in the Find ACX Numbers from Structure dialog box Find ACX Numbers from Structure ES Here are the ACX
367. mber of independent variables Since each atom has three independent variables x y z coordinates visualizing a surface for a many atom model is impossible However you can generalize this problem by examining any 2 independent variables such as the x and y coordinates of an atom as shown below eth m Fi AT AN ARA AT e WASHED ih 2 BAN ane NN NE PIS NN Aaa Ws AN UE y Local Minimum Global Minimum The main areas of interest on a potential energy surface are the extrema as indicated by the arrows are as follows ChemOffice 2005 Chem3D Global minimum The most stable conformation appears at the extremum where the energy is lowest A molecule has only one global minimum Local minima Additional low energy extrema Minima are regions of the PES where a change in geometry in any direction yields a higher energy geometry Saddle point The point between two low energy extrema The saddle point is defined as a point on the potential energy surface at which there is an increase in energy in all directions except one and for which the slope first derivative of the surface is zero NOTE At the energy minimum the energy is not zero the first derivative gradient of the energy with respect to geometry 15 Xero All the minima on a potential energy surface of a molecule represent stable stationery points where the forces on atoms sum to
368. mbol in the Replacement text box or paste it after copying the cell in the Symbol field to the Clipboard and press the Enter key when an atom is selected or double click an atom If no atom is selected a fragment is added Four fields comprise a record in the Elements table the symbol the covalent radius the color and the atomic number Symbol Normally you use only the first column of the Elements table while building models If you are not currently editing a text cell you can quickly move from one element to another by typing the first letter or letters of the element symbol Covalent Radius The covalent radius is used to approximate bond lengths between atoms 274 Parameter Tables Color The colors of elements are used when the Color by Element check box is selected in the control panel To change the color of an element e Double click the current color The Color Picker dialog box appears in which you can specify a new color for the element Atom Types The Atom Types table Atom Types xml contains the atom types for use in building your models Normally you use only the first column of the Atom Types table while building models To use an atom type in a model type its name in the Replacement text box or paste it after copying the name cell to the Clipboard and press the Enter key when an atom is selected or when you double click an atom If no atom is selected a fragment is added Twe
369. mbridgeSoft Computing Properties Form of AH Solvent glycine kcal mole Accessible Surface A neutral gas 92 75386 zwitterion gas 57 83940 From this data you can reason that the glycine zwitterion is the more favored conformation in water and the neutral form is more favored in gas phase Example 6 Hyperfine Coupling Constants for the Ethyl Radical To build the model 1 From the File menu choose New Model 2 Click the Text Building tool Click in the model window oO A text box appears Type EtH and press the Enter key Click the Select tool Select H 8 7 Press the Backspace key Do oa A If you have automatic rectification on a message appears asking to turn it off to perform this Operation 8 Click Turn Off Automatic Rectification ChemOffice 2005 Chem3D The Ethyl Radical is displayed To perform the HFC computation 1 From the MOPAC Interface submenu of the Calculations menu choose Minimize Energy 2 On the Theory tab choose the PM3 potential function and the Open Shell Unrestricted wave function 3 On the Properties tab choose Hyperfine Coupling Constants 4 Click Run The unpaired electron in the ethyl radical is delocalized Otherwise there would be no coupling constants Hyperfine Coupling Constants C1 0 02376 C2 0 00504 H3 0 02632 H4 0 02605 H5 0 00350 MOPAC Computations 195 Computing Properties Hyperfine Coupling Constants
370. ment point rules o oo oo oo 231 Angles and measurements 4 231 Defining Substructures 232 Atom Types Assigning Atom Types 233 Atom Type CharacteristiCS oo o 233 Defining Atom Types Keyboard Modifiers Standard Selection o o oooooooooo o Radial Selection 0 o oooooooooo o 2D to 3D Conversion Stereochemical Relationships Example rapidas on ExampleiZ aaa tain bt eis aie ale dao dond Examples So cus seen Gases odia Example caen Labels cade File Formats Editing File Format Atom Types Name util baw Sears sole ee DESCHPUOR Lat do ets eS File Format Examples Alchemy Filetes s were hein te ehh deed FORTRAN Formats 00 0000 ee Cartesian Coordinate Files Atom Types in Cartesian Coordinate Files The Cartesian Coordinate File Format FORTRAN Formats ooooooooooo Cambridge Crystal Data Bank Files Internal Coordinates File Bos ia a ta AES FORTRAN Formats o o ooooooooooo MactoModel ici iden ea eee ieee FORTRAN Formats 0000 eee MDE MolPil sinss ccc pimru ceed pra LION dea dde das eb FORTRAN Formats oooooooooooo MSI MolFile 3 segs osa ows SYBYL MOL2 File ooooooooo FORTRAN Formats o oooooooooooo Parameter Tables Parameter Table Use Parameter
371. mmand infrequently you can save clutter by using the menu commands The File Menu In addition to the usual File commands you use the File menu to access the Chem3D Templates and Preferences and the Model Settings e Import File Import MOL2 and SD files into Chem3D a document The import utility accurately preserves model coordinates e Model Settings Displays the Settings dialog box Set defaults for display modes and colors model building atom and ligand display atom labels and fonts movie and stereo pair settings and atom bond popup label information CambridgeSoft The Graphical User Interface e Preferences Displays the Preferences dialog box Set defaults for image export calculation output path OpenGL settings and including hydrogens in CDX format files e Sample Files Accesses example models The Edit Menu In addition to the usual Edit functions you can use the Edit menu to copy the model in different formats to clear the model window and to select all or part of the model e Copy as Puts the model on the Clipboard in ChemDraw format as a SMILES string or in bitmap format e Copy As ChemDraw Structure Puts the model on the Clipboard in CDX format You may only paste the structure into an application that can accept this format for example ChemDraw ChemFinder or Chem3D e Copy As SMILES Puts the model on the Clipboard as a SMILES string You may only paste the structure into an app
372. mplicit solvent environment Ground transition and excited states Ab initio methods available through the Gaussian interface apply to Systems containing up to 150 atoms Organic organometallics and molecular fragments catalytic components of an enzyme Gas or implicit solvent environment Study ground transition and excited states certain methods The following table summarizes the method types Computation Concepts 131 Computational Methods Overview Method Type Advantages Disadvantages Best For Molecular Mechanics MM2 Uses classical physics Relies on force field with embedded empirical Least intensive computationally fast and useful with limited computer resources Can be used for molecules as large as Particular force field applicable only for a limited class of molecules Does not calculate electronic properties Requires experimental Large systems thousands of atoms Systems or processes with no breaking or forming of bonds Uses quantum physics Uses experimentally derived empirical parameters Uses approximation extensively computationally than ab initio methods Capable of calculating transition states and excited states data or data from ab initio for parameters Less rigorous than ab initio methods parameters enzymes data or data from ab initio for parameters Semiempitical MOPAC Less demanding Requires experimental Medium si
373. mpty while wells in a 96 well plate can be measured in microliters By moving such settings and preferences down to the container level rather than system wide or custom programming Inventory M anager can accommodate both worlds in a single instance Integration with Purchasing amp Registration Inventory records are created directly from ChemACX Database of available chemicals as well as from Registration System For substances that do not exist in either database Inventory M anager has its own chemi cally aware user interface By tightly coupling with ChemACX Database and Registration System the need for duplicate data entry is virtually eliminated O nce a product is ordered its chemical information is stored and it is given an on order status reducing duplicate ordering of popular reagents EMAIL info cambridgesoftcom WWW _ www cambridgesoftcom TEL 1 800 315 7300 INTL 1 617 588 9300 FAX 1 617 588 9390 e MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge MA 02140 USA CambridgeSoft TTT Chemo ffice ChemDraw Chem3D ChemFinder Cheminfo are trademarks of CambridgeSoft 2002 5 All other trademarks are the property of their respective holders All specifications subject to change without notice www cam b T1 dg eso ft CcCOm RESEARCH amp CombiChem Enterprise D esktop to Enterprise C ombinatorial C hemistry Benefits of Combinatorial Chemistry Combinatorial chemistry in particular the techni
374. mputed from the pi molecular orbitals MM2 10 The pi bond order is used to modify the bond length BL and force constant KS for each sigma bond in the pi system 11 The values of KS and BL are used in the molecular mechanics portion of the MM2 computation to further refine the molecule To examine the computed bond orders after an MM2 computation 1 In the Pop up Information control panel select Bond Order 2 Position the pointer over a bond The information box contains the newly computed bond orders for any bonds that are in a pi system CambridgeSoft Chem3D Changes to Allinger s Force Field Appendix J MOPAC Overview The appendix contains miscellaneous information about MOPAC You can find additional information about MOPAC by visiting the MOPAC home page at http www cachesoftware com mopac index shtml MOPAC Background MOPAC was created by Dr James Stewart at the University of Texas in the 1980s It implements semi empirical methodologies for analyzing molecular models MOPAC stands for Molecular Orbital PACkage Due to its complexity and command line user interface its use was limited until the mid 1990s Since version 3 5 1996 Chem3D has provided an easy to use GUI interface for MOPAC that makes it accessible to the novice molecular modeller as well as providing greater usability for the veteran modeller We are currently supporting MOPAC 2000 MOPAC 2000 is
375. n a Z matrix perhaps for export to another application for further analysis This is a common use when models become large and connectivities are difficult to specify To add an uncoordinated bond and dummy atom 1 Select the Uncoordinated Bond tool 2 Point to an atom and drag from the atom An uncoordinated bond and a dummy atom ate added to the model The atom created is labeled Du the Chem3D element symbol for Dummy atoms Dummy atom Removing Bonds and Atoms When you temove bonds and atoms e Click a bond to remove only that bond e Click an atom to remove the atom and all attached bonds To remove an atom or bond do one of the following e Click the Eraser tool and click the atom ot bond CambridgeSoft Building With the Bond Tools e Select the atom or bond and from the Edit menu choose Clear e Select the atom or bond and press Delete NOTE If automatic rectification is on you will not be able to delete hydrogen atoms Turn rectification off when editing a model Building With The Text Tool The Text tool allows you to enter text that represents elements atom types elements with specific hybridization substructures formal charges and serial numbers The text you enter must be found in either the Elements Atom Types ot Substructures tables The match must be exact including correct capitalization These tables can be found in the Parameter Tables list on the View
376. n a fragment into a desired orientation and proximity relative to a second fragment Each fragment remains rigid during the docking computation The Standard Toolbar The Standard toolbar contains tools for standard Windows functions including up to 20 steps of Undo and Redo D __ New File Y Open File El Save File To Copy an Cut B Eo ooo Paste MES Undo gt cas Redo c Print ____ About Chem3D 4 Chem3D Basics 19 The Graphical User Interface The Building Toolbar The Building toolbar contains tools that allow you to create and manipulate models The tools are shown below Rotation Dial activator Zoom tool me Trackball tool Tr a 13 r Move tool lt J Single Bond tool Double Bond tool _Triple Bond tool Uncoordinated Bond tool Text tool Eraser tool tol e 4 The Rotation Dial activated by clicking the arrow under the Trackball tool lets you rotate a model an exact amount Select an axis then drag the dial or type a number into the box Rotation Dial Ex 0 90 i fae 180 59 9 XYZO 20 Chem3D Basics For detailed descriptions of the tools see Building With the Bond Tools on page 75 Rotating Models on page 96 and Resizing Models on page 100 The Model Display Toolbar The Model Display toolbar contains tools for all of the Chem3D displ
377. n a hydrogen atom toward the nucleus of the carbon atom to which it is bonded by approximately 10 of the distance between the two atoms Any atom in a van der Waals potential function must possess a spherical electron cloud centered about its nucleus For most larger atoms this is a reasonable assumption but for smaller atoms such as hydrogen it is not a good assumption Molecular mechanics calculations based on spherical electron clouds centered about hydrogen nuclei do not give accurate results 284 Parameter Tables However it is a reasonable compromise to assume that the electron cloud about hydrogen is still spherical but that it is no longer centered on the hydrogen nucleus The Reduct constant is multiplied by the normal bond length to give a new bond length which represents the center of the repositioned electron cloud The value of the Reduct field for all non hydrogen atoms is zero Atomic Weight The fifth field Atomic Weight is the atomic weight of atoms represented by this atom type number NOTE The atomic weight is for the isotopically pure element i e the atomic weight for atom type number 1 is 12 000 the atomic weight of C Lone Pairs The Lone Pairs field contains the number of lone pairs around a particular atom type Notice that an amine nitrogen atom type number 8 has one lone pair and an ether oxygen atom type number 6 has two lone pairs Lone pairs are treated explicitly for atoms s
378. n low energy conformations To precisely reproduce energies obtained with Allinger s force field e Set the quartic stretching constant in the MM2 Constants table window to zero The quartic term is eliminated Electrostatic and van der Waals Cutoff Terms The cutoffs for electrostatic and van der Waals terms greatly improve the computation speed for large molecules by eliminating long range interactions from the computation To precisely reproduce energies obtained with Allinger s force field e Set the cutoff distances to large values greater than the diameter of the model Every interaction is then computed ChemOffice 2005 Appendix The cutoff is implemented gradually beginning at 50 of the specified cutoff distance for charge and charge dipole interactions 75 for dipole dipole interactions and 90 for van der Waals interactions Chem3D uses a fifth order polynomial switching function so that the resulting force field is second order continuous Because the charge charge interaction energy between two point charges separated by a distance r is proportional to 1 r the charge charge cutoff must be rather large typically 30 or 40A The charge dipole dipole dipole and van der Waals energies which fall off as 1 1 1 1 and 1 respectively can be cut off at much shorter distances for example 25A 18A and 10A respectively Fortunately since the van der Waals interactions are by far the most numero
379. n some versions of Chem3D or may be purchased as an optional addin MOPAC Ultra is the full MOPAC implementation and is only available as an optional addin The CS MOPAC Ultra implementation provides support for previously unavailable features such as MOZYME and PM5 methods In both cases you need a separate installer to install the MOPAC application Once installed either version of MOPAC will work with either version of Chem3D NOTE Ifyou have CS MOPAC installed on your computer from a previous Chem3D or ChemOffice installation upgrading to version 9 0 1 will NOT remove your existing MOPAC installation Chem3D will continue to support it even if the update version does not include CS MOPAC Installing either of the CS MOPAC 2002 versions will replace the existing MOPAC installation ChemOffice 2005 Chem3D CS MOPAC provides a graphical user interface that allows you to perform MOPAC computations directly on the model in the Chem3D model window As a computation progresses the model changes appearance to reflect the computed result In this section e A brief review of semi empirical methods e MOPAC Keywords used in CS MOPAC e Electronic configuration includes using MOPAC sparkles e Optimizing Geometry e Using MOPAC Properties e Using MOPAC files e Computation procedures with examples e Minimizing Energy e Computing Properties e Optimizing to a Transition State e Computing Properties e Examples
380. n the Chem3D Parameter tables is Hydrogen H The atom type numbers for these atom types range from 111 to 851 The atom type number for each of the non MM2 atom types in the MM2 Atom Type Parameters table is based on the atomic number of the element and the number of ligands in the geometty for that atom type To determine an atom type number the atomic number is multiplied by ten and the number of ligands is added For example Co Octahedral has an atomic number of 27 and six ligands Therefore the atom type number is 276 In a case where different atom types of the same element have the same number of ligands Iridium Tetrahedral Atom Type 774 and Iridium Square Planar Atom Type 779 the number nine is used for the second geometry Viewing Parameters To view the parameters used by Chem3D to perform MM2 computations From the View menu point to Parameter Tables and choose a table The table you chose opens in a window MM2 289 MM2 Parameters Editing Parameters You can edit the parameters that come with Chem3D Parameters that you add or change can be guesses or approximations that you make or values obtained from current literature In addition there are several adjustable parameters available in the MM2 Constants table For information on parameters and MM2 constants see The Force Field on page 136 NOTE Before performing any editing we strongly recommend that you create back up copie
381. n the Output window Repeating an MM2 Computation After you perform an MM2 computation you can repeat the job as follows 1 Choose Repeat MM2 Job from the MM2 submenu of the Calculations menu The appropriate dialog box appears 2 Change parameters if desired and click Run The computation proceeds Using jdf Files The job type and settings are saved in a jdf file if you click the Save As button on the dialog box before running a computation You can then run these computations in a different work session MM2 and MM3 Computations 163 Showing Used Parameters To run a pteviously created MM2 job The dialog box for the appropriate 1 Choose Run MM2 Job from the MM2 A submenu of the Calculations menu 2 Choose the file and click Open 3 Change parameters if desired and click Run 164 MM2 and MM3 Computations CambridgeSoft Using jdf Files Chapter 10 MOPAC Computations Overview MOPAC is a molecular computation application developed by Dr James Stewart and supported by Fujitsu Corporation that features a number of widely used semi empirical methods It is available in two versions Professional and Ultra MOPAC Pro allows you to compute properties and perform simple and some advanced energy minimizations optimize to transition states and compute properties The CS MOPAC Pro implementation supports MOPAC sparkles has an improved user interface and provides faster calculations It is included i
382. n the part of CS Both these materials and the right to usethem are owned exclusively by CS U se of these materials is licensed by CS under the terms of a software license agreement they may be used only as provided for in said agreement Chemo ffice ChemD raw Chem3D CS M OPAC ChemFinder Inventory E N otebook BioAssay and ChemInfo are not supplied with copy protection Do not duplicate any of the copyrighted materials except for your personal backups without written permission from CS To do so would be in violation of federal and international law and may result in criminal as well as civil penalties You may use ChemO ffice ChemD raw Chem3D CS MOPAC ChemFinder Inventory E Notebook BioAssay and ChemInfo on any computer owned by you however extra copies may not be made for that purpose Consult the CS License Agreement for Software and D atabase Products for further details Trademarks Chemo ffice ChemDraw Chem3D ChemFinder Cheminfo and ChemACX are registered trademarks of CambridgeSoft Corporation Cambridge Scientific Computing Inc The M erck Index is a registered trademark of Merck amp Co Inc 2001 All rights reserved MOPAC 2000 and MOPAC 2002 are trademarks of Fujitsu Limited Microsoft Windows Windows NT Windows 95 and M icrosoft Word are registered trademarks of M icrosoft Corp Apple Events M acintosh Laserwriter Imagewriter Q uickD raw and AppleScript are registered trademarks of Apple Computer Inc
383. nal groups and many others Q ueries can also be refined after an initial search extending the power of the query language Structured Document Support Structured documents including documents created with Word templates or XML are also supported Information in structured documents is extracted and stored in specific fields of the database for more precise searching ChemFinder Word ChenFinde Word the desktop version searches Word documents Excel spreadsheets ChemD raw files ChenFinde databases SD files MDL molfiles and more Unlike other Microsoft Find facilities ChemFinder Word lets you work with the results you ve located Once you have a hit list you can browse search refine or export it to any destination EMAIL info cambridgesoftcom WWW _ www cambridgesoftcom a e EN TEL 1 800 315 7300 INTL 1 617 588 9300 FAX 1 617 588 9390 o e MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge MA 02140 USA CambridgeSoft TTT Chemo ffice ChemDraw Chem3D ChemFinder Cheminfo are trademarks of CambridgeSoft 2002 5 All other trademarks are the property of their respective holders All specifications subject to change without notice www cam b T1 dg eso ft CcCOm KNOWLEDGE 21CFR11 Compliance Electronic Records and Signatures Regulations The Challenge Large and growing enterprises are facing a challenge to their core missions of developing and producing new products including food therapeutic pharmaceu
384. nd choose Delete from the right click menu The Model Position submenu Center Model on Origin Resizes and centers the model in the model window after a change to the model is made Center Selection on Origin Resizes and centers the selected portion of the model in the model window Align Model With X Axis When two atoms ate selected moves them to the X axis Align Model With Y axis When two atoms ate selected moves them to the Y axis Align Model With Z axis When two atoms ate selected moves them to the Z axis Align Model With XY Plane When three atoms ate selected moves them to the XY plane Align Model With XZ Plane When three atoms ate selected moves them to the XZ plane Align Model With YZ Plane When three atoms ate selected moves them to the YZ plane e Chem3D Basics The Reflect Model submenu e Through XY Plane Reflects the model through the XY plane by negating Z coordinates If the model contains any chiral centers this will change the model into its enantiomer Pro R positioned atoms will become Pro S and Pro S positioned atoms will become Pro R All dihedral angles used to position atoms will also be negated Through XZ Plane Reflects the model through the XZ plane by negating Y coordinates If the model contains any chiral centers this will change the model into its enantiomer Pro R positioned atoms will become Pro S and Pro S positioned atoms will become Pro R All dihedr
385. nd state Use MECI to print out energy information in the out file FORCE Vibrational Analysis NOTE Useful for determining zero point energies and normal vibrational modes Use DFORCE to print out vibration information in out file NOMM No MM correction NOTE By default MOPAC performs a molecular mechanics MM correction for CONH bonds Pl Resolve density matrix NOTE Resolve density matrix into sigma and pi bonds PRECISE Increase SCF criteria NOTE Increases criteria by 100 times This is useful for increasing the precision of energies reported 172 MOPAC Computations Keyword Description T n M H D Increase the total CPU time allowed for the job NOTE The default is 1h 1 hour or 3600 seconds Specifying the Electronic Configuration MOPAC must have the net charge of the molecule in order to determine whether the molecule is open or closed shell If a molecule has a net charge be sure you have either specified a charged atom type or added the charge CS MOPAC 2002 supports sparkles pure ionic charges that can be used as countet ions or to form dipoles that mimic solvation effects You can assign a charge using the Text Building tool or by specifying it in MOPAC To add the charge to the model 1 Click the Text Building tool 2 Click an atom in your model 3 Type a charge symbol For example click a carbon and type ina text box to make it a carbocation The
386. ned atom Atoms Positioned by Three Other Atoms In the following set of illustrations each atom D is positioned relative to three previously positioned atoms C B and A Three measurements are needed to position D a distance and two angles Atom C is the Distance Defining atom D is placed a specified distance from C Atom B is the First Angle Defining atom D C and B describe an angle Atom A is the Second Angle Defining atom It is used to position D in one of two ways e By a dihedral angle A B C D e By a second angle A C D 102 Manipulating Models In the left example atom D is positioned in terms of a dihedral angle thus the second angle is the dihedral angle described by A B C D This dihedral angle is the angle between the two planes defined by D C B and A B C In the right example if you view down the C B bond then the dihedral angle appears as the angle formed by D C A A clockwise rotation from atom D to atom A when C is in front of B indicates a positive dihedral angle oF q DEB Plane che paralld to I Z Cartesian plane ABC Pare er is ss When D is positioned using two angles there are two possible positions in space about C for D to occupy a Pro R position and a Pro S position nd Angie Lbtining Atan Distance Letining Ata A nd Ange t Aten Bang Fortinet st Ange Park a ist Angle NOTE The terms Pro R and Pro S used in Chem3D to positi
387. nergy 207 full report 207 Gibbs free energy 207 heat of formation 207 Henry s law constant 207 Ideal gas thermal capacity 207 LogP 207 melting point 207 molar refractivity 207 refractivity 207 server 207 solubility 208 standard Gibbs free energy 207 thermal capacity 207 vapor pressure 208 Water solubility 208 ChemProp Std server 205 ChemProp Std server properties 205 ChemProp error messages 208 ChemProp limitations 208 ChemSAR Excel descriptors 220 statistics 221 wizard 217 ChemSAR Excel wizard 217 ChemStore com see SciStore com Choosing a Hamiltonian 148 167 Choosing the best method see Computa tional methods Chromatek stereo viewers 59 CI microstates used 171 CIS 172 Cleaning up a model 90 Clipboard copying to 127 exporting with 127 Clipboard importing with 75 Close Contacts command 275 Closed shell system 174 CMYK Contiguous 120 Color applying to individual atoms 60 background 60 by depth 59 by depth for Chromatek stereo viewers 59 by element 58 by group 59 by partial charge 59 displays 58 field 274 settings 58 Coloring groups 114 Coloring the background window 60 Commands close contacts 275 compute properties 161 184 import file 14 Comments panel 23 Comparing cation stabilities in a homologous series of molecules 191 models by overlay 43 the stability of glycine zwitterion in wa ter and gas phase 194 two stable conformations of cyclohex ane 156 Compression 120 Computational
388. nfo e WWW links for over 100 000 compounds Enter text queries or use ChemDraw Plugin for structure amp substructure searching e Works with Netscape MS Internet Explorer SYSTEMS amp LANGUAGES English amp Japanese Windows 95 98 Me NT 2000 XP CD ROM software is Windows only All specifications subject to change without notice 2 o UN EMAIL info cambridgesoftcom WWW _ www cambridgesoftcom pik pr o TEL 1800 315 7300 INTL 1 617 588 9300 FAX 1 617 588 9390 e MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge MA 02140 USA am ri ge O Chemo ffice ChemDraw Chem3D ChemFinder Cheminfo are trademarks of CambridgeSoft 2002 m _ _ _ All other trademarks are the property of their respective holders All specifications subject to change without notice www cam b r dg eso ft CcCOm ENTERPRISE ChemOffice WebServer Enterprise Solutions Applications and D atabases ChemOffice WebServer Chem0 fficeWebServer is the leading solution platform for enterprise corporate intranet and Internet scientif ic information applications Compatible with major databases including O racle SQL Server and M icrosoft Access ChemOfficeWebServer is the development and deployment platform for custom applications and those listed below ChemOffice Browser Chem0O ffice Browser including ChemD raw Java ActiveX and the ChemD raw and Chem3D Plugins brings the power and chemical intelligence of ChemO ffice
389. ng are selected the Inspecting Models 105 Pop up Information If you want to display Then Select information relative to other selected atoms such as the distance between two atoms the angle formed by three atoms or the dihedral angle formed by four atoms the distance between the atoms attached bya bond in angstroms the bond orders calculated by Minimize Energy Steric Energy ot Molecular Dynamics the partial charge according to the currently selected calculation measurement formed by all the selected atoms appears Measurements Bond Length Bond Order Bond orders are usually 1 000 1 500 2 000 or 3 000 depending on whether the bond is a single delocalized double or triple bond Computed bond orders can be fractional Partial Charge See Displaying Molecular Surfaces on page 64 for information on how to select a calculation Non Bonded Distances To display non bonded atoms measurements 106 Inspecting Models e Select two non bonded atoms and point to one of them The interatomic non bonded distance appears in the last line of the pop up window For example in the cyclohexane model below when you select two non bonded atoms and point to one of them the interatomic non bonded distance appears in the last line of the pop up window Measurement Table Another way to view information about your model is to activate the Measurement Table This t
390. nly be used on a single computer except as provided below You may physically transfer the Software from one computer to another for your own use provided the Software isin use or installed on only one computer at a time If the Software is permanently installed on your com puter other than a network server you may also use the Software on a portable or home computer provided that you use the software on only one computer at a time You may not a electronically transfer the Software from one computer to another b distribute copies of the Software to others or c modify or translate the Software without the prior written consent of CS d place the software on a server so that it is accessible via a public network such as the Internet e sublicense rent lease or lend any portion of the Software or Documentation f modify or adapt the Software or merge it into another program g modify or circumvent the software activation or h reverse engi neer the software activation so as to circumvent it T he Software may be placed on a file or disk server connected to a network provided that a license has been purchased for every computer with access to that server You may make only those copies of the Software which are necessary to install and use it as permitted by this agreement or are for purposes of backup and archival records all copies shall bear CS s copyright and proprietary notices You may not make copies of any accompanying writ
391. ns that parents determine the properties of children until you choose to ChemOffice 2005 Chem3D Inspecting Models 111 Working With the Model Explorer change a property By changing some property of a lower level object you can better visualize the part of the model you want to study Use the Model Explorer to e Define objects e Add objects to groups e Rename objects e Delete objects with or without their contents The display properties of objects you can alter include e Changing the display mode e Showing or hiding e Changing the color At the atom level you can display or hide e Atom spheres e Atom dots e Element symbols e Serial numbers Model Explorer Objects The Model Explorer objects are e Fragments e Chains e Groups e Atoms e Bonds e Solvents e Backbone The Fragment object represents the highest level segment parent of a model Fragments represent separate parts of the model that is if you start at an atom in one fragment you cannot trace through a series of bonds that connect to an atom in another fragment If you create a bond between two such atoms Chem3D will collapse the hierarchical structure to create one fragment 112 Inspecting Models Fragment objects typically consist of chains and groups but may also contain individual atoms and bonds In Chem3D chains and groups are functionally identical Chains ate special groups found in PDB fil
392. nstants xml computing MM2 force field Parameters to assure atoms in trigonal planar geometry remain planar In force field Out of Plane Bending Parameters xml analysis parameters to assure atoms in trigonal planar geometry remain planar Contains information about where parameter information is derived References xml Substructures xml Contains predrawn substructures available for speeding up model building 272 Parameter Tables VDW Adjusts specific VDW Interactions xml interactions such as hydrogen bonding Parameter Table Fields Most of the tables contain the following types of fields e Atom Type Numbers e Quality e Reference Atom Type Numbers The first column in a parameter table references an atom type using an Atom Type number An Atom Type number is assigned to an atom type in the Atom Types table For example in Chem3D a dihedral type field 1 1 1 4 in the Torsional Parameters table indicates a torsional angle between carbon atoms of type alkane Atom Type number 1 and carbon atoms of type alkyne Atom Type number 4 In the 3 membered ring table the angle type field 22 22 22 indicates an angle between three cyclopropyl carbons Atom Type number 22 in a cyclopropane ring CambridgeSoft Parameter Table Fields Quality The quality of a parameter indicates the relative accuracy of the data Quality Accuracy Level 1 Parameter guessed by Chem3D 2 Parameter theorize
393. ntains miscellaneous information about the MM2 parameters and force field MM2 Parameters The original MM2 parameters include the elements commonly used in organic compounds carbon hydrogen nitrogen oxygen sulfur and halogens The atom type numbers for these atom types range from 1 to 50 The MM2 parameters were derived from three sources 1 Most of the parameters were provided by Dr N L Allinger 2 Several additional parameters were provided by Dr Jay Ponder author of the TINKER program 3 Some commonly used parameters that were not provided by Dr Allinger or Dr Ponder are provided by CambridgeSoft Corporation However most of these parameters are estimates which are extrapolated from other parameters The best source of information on the MM2 parameter set is Molecular Mechanics Burkert Ulrich and Allinger Norman L ACS Monograph 177 American Chemical Society Washington DC 1982 A method for developing reasonable guesses for parameters for non MM2 atom types can be found in Development of an Internal Searching ChemOffice 2005 Appendix Algorithm for Parameterization of the MM2 MM3 Force Fields Journal of Computational Chemistry Vol 12 No 7 844 849 1991 Other Parameters The rest of the parameters consist of atom types and elements in the periodic table which were not included in the original MM2 force field such as metals The rectification type of all the non MM2 atom types i
394. nts are used to lengthen the C C bonds in cyclobutane to 1 550A from a C C bond length of 1 536A in cyclohexane Sextic Bending Constant Sextic bending constant 10 8 Chem3D uses the sextic bending constant to increase the energy of angles with large deformations from their ideal value Dielectric Constants Dielectric constant for charges Dielectric constant for dipoles ChemOffice 2005 Appendix The dielectric constants perform as inverse proportionality constants in the electrostatic energy terms The constants for the charge and dipole terms ate supplied separately so that either can be partially or completely suppressed The charge dipole interaction uses the geometric mean of the charge and dipole dielectric constants For example when you increase the Dielectric constant for dipoles a decrease in the Dipole Dipole energy occuts This has the effect of reducing the contribution of dipole dipole interactions to the total steric energy of a molecule Electrostatic and van der Waals Cutoff Parameters Cutoff distance for charge chatge interactions Cutoff distance for charge dipole interactions Cutoff distance for dipole dipole interactions Cutoff distance for van der Waals interactions These parameters define the minimum distance at which the fifth order polynomial switching function is used for the computation of the listed interactions MM2 Atom Types The MM2 Atom Types table MM2 Atom Types xml contains th
395. o Y Z plane command 99 Movie control panel 116 Movie controller speed control 116 Movie file format 121 Movie toolbar 21 Movies editing 116 overview 115 Moving atoms 95 models see Translate MOZYME 180 MSI ChemNote file format 124 MSI MolFile 253 Mulliken charges 186 Multiple models 84 N Name field 274 Name Struct 75 Naming a selection 93 NOMM keyword 172 Non bonded distances constraints 142 Non bonded distances displaying 106 Non bonded distances displaying in tables 107 Non bonded energy 139 xive CambridgeSoft O Odd electron systems 175 Online Menu browse SciStore com 226 CambridgeSoft homepage 227 ChemOffice SDK 227 CS technical support 224 lookup suppliers on SciStore com 225 register online 223 Online menu ACX numbers 226 ACX structures 225 OOP see Out of Plane Bending Open shell 175 Optimal field 29 107 Optimal measurements 107 Optimizing to a transition state 134 182 Order of attachment specifying 78 Origin atoms Z matrix 101 Out of plane bending equations 141 Out of plane bending 287 Output panel 23 Ovality ChemProp Std 206 Overlays 43 Overlays hiding fragments 45 P Packbits compression 120 Page size 117 Pan see Translate Parameter table fields 272 Parameter tables overview 271 Parameters bond angle 29 bond length 29 creating 273 estimating 273 guessing 153 161 MM2 161 289 MOPAC 294 setting 216 Partial charge atom size control 57 definition 52 pop up informa
396. o denote the surface selected Ey 3 On the Surfaces toolbar point to Display Mode delocalization of the radical there is some radical and choose Translucent character simultaneously on both of these carbons 4 On the Surfaces toolbar point to Color Now hide this surface Mapping and choose Spin Density ii j ds Click the Surfaces icon to toggle the surface off ChemOffice 2005 Chem3D Chem3D Tutorials 51 Tutorial 9 Mapping Properties onto Surfaces Determine the raw spin density alone not mapped onto the charge density surface 1 On the Surfaces toolbar point to Surface and select Total Spin Density 2 From the Surfaces menu point to Surfaces and choose Wire Mesh 3 Set Isospin to 0 001 There is a large concentration of unpaired spin over each of the terminal carbons and a small concentration over the central hydrogen This extra little bit of spin density is not very significant you could not even see it when looking at the mapped display earlier but the calculations show that it is in fact there Tutorial 10 Computing Partial Charges To compute the charge of a molecule the number of electrons contributed by each of its atoms can be subtracted from the number of protons in the nucleus of each of its atoms Each atom of a molecule contributes an integral charge to the molecule as a whole This integral contribution is known as the formal charge of each atom Certain types of atoms in Chem3D
397. ob Type Compute Properties ind Summary Job Type Compute Properties Method Closed Shell Restricted Hartree Fock Basis Set STO 3G Spin Multiplicity 1 Solvation Model Gas Phase Save As 2 Click Create An input file saves in Gaussian s native GJF format Cancel NOTE The G F Gaussian Input File is not the same as the G C Gaussian Input File The GJC file stores only the model coordinates and not the Gaussian keywords specifying computational parameters Running a Gaussian Input File If you have a previously created GJF Gaussian input file you can run the file from within Chem3D ChemOffice 2005 Chem3D To run a Gaussian input file 1 From the Gaussian submenu choose Run Input File The Run Gaussian Input file dialog box appears Run Gaussian Input File File C Program Files CambridgeS oft Version Browse IV Display Each Iteration Record Each Iteration Copy Measurements to Messages Cancel 2 Type the full path of the Gaussian file or Browse to location 3 Select the appropriate options If you want to Then click watch the minimization process live at each iteration in the calculation Display Every Iteration NOTE Displaying or recording each iteration adds significantly to the time required to minimize the structure recotd each iteration Record Every Iteration as a frame in a movie for later replay tr
398. odel Building Basics e Inthe Model Settings dialog box select the Atom Labels tab and check the box next to Show Element Symbols and Show Serial Numbers The serial number for each atom is assigned in the order of building However you can reserialize the atoms For mote information see Setting Serial Numbers on page 88 The element symbol comes from the Elements table The default color used for an element is also defined in the Elements table For more information see Coloring by Element on page 58 and The Elements on page 274 Model Data Labels When you point to an atom information about the atom appeats in a model label pop up window By default this information includes the element symbol serial number atom type and formal charge The following illustration shows the model label for the C 1 atom of ethane The model data changes when you point to a bond instead of an atom 26 Chem3D Basics The following illustration shows the model label for the bond between C 1 and C 2 Order 1 000 The model data changes to reflect the atoms that are selected in the model For example when three contiguous atoms H 3 C 1 C 2 are selected the model label includes the atom you point to and its atom type the other atoms in the selection and the angle This is shown in the following illustration these atoms are selected they are displayed in yellow in Chem3D CambridgeSoft Mode
399. of a data catalog driven mining program ChemDraw for Spotfire ChemD raw for Spotfire is a powerful add in for the Spotfire DecisionSite software Spotfire makes industry standard applications for high dimensional visual data analysis and is used to explore large biological datasets ChemD raw for Spotfire adds chemistry to D ecisionSite providing structure visualization and searching servic es Highlight a spot in Spotfires D ecisionSite and a structure is displayed directly in the window If you draw a structure and click Search the matching records are displayed right in the Spotfire window T he structures are retrieved from a chemical database such as Registration System ChemFinder or Oracle Cartridge and are returned directly over the network In this way structures can be linked by registry number CAS number or EMAIL info cambridgesoftcom WWW _ www cambridgesoftcom a e EN TEL 1 800 315 7300 INTL 1 617 588 9300 FAX 1 617 588 9390 o e MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge MA 02140 USA CambridgeSoft TTT Chemo ffice ChemDraw Chem3D ChemFinder Cheminfo are trademarks of CambridgeSoft 2002 5 All other trademarks are the property of their respective holders All specifications subject to change without notice www cam b T1 dg eso ft CcCOm CHEMICAL ChemACX Database Available C hemicals and Screening C ompounds ChemACX Database Sifting through chemical catalogs is a poor use of time f
400. ogens Because carbons with one or two attached hydrogens frequently occut separate force constants are used for these bond angles The CHR Bending K for 1 1 1 angles allows more accurate force constants to be specified for the Type 1 CH2 and Type 2 CHR interactions In addition the CHR Bending K for 1 1 1 angles in CambridgeSoft MM2 Constants 4 membered rings and the CHR Bending K for 22 22 22 angles 22 is the atom type number for the C Cyclopropane atom type in 3 membered rings differ from the aforementioned CHR Bending K for 1 1 1 angles and thus require separate constants to be accurately specified Stretch Bend Parameters X B C N O Y Stretch Bend interaction force constant X B C N O H Stretch Bend interaction force constant X ALS Y Stretch Bend force constant X AI S H Stretch Bend force constant X Si P Y Stretch Bend force constant X Si P H Stretch Bend force constant X Ga Ge As Se Y Stretch Bend force constant The stretch bend parameters are force constants for the stretch bend interaction terms in the prior list of elements X and Y represent any non hydrogen atom When an angle is compressed the MM2 force field uses the stretch bend force constants to lengthen the bonds from the central atom in the angle to the other two atoms in the angle For example the normal C C C bond angle in cyclobutane is 88 0 as compared to a C C C bond angle of 110 8 in cyclohexane The stretch bend force consta
401. olecule fragment you must add that fragment to your worksheet To select descriptors 1 From the ChemOffice menu point to ChemSAR then choose Select Descriptors or click the Select descriptors icon y 220 ChemSAR Excel The Select Descriptors dialog box appears 2 Select the calculation type from the Class drop down list 3 Select the computational model from the Server drop down list 4 Use the Cost and Accuracy sliders to set the appropriate ratio The greater the cost number the greater the time it takes for the calculation The greater the accuracy number the greater the accuracy of method used to perform the calculations 5 Select the properties to calculate and click Add 6 To delete a property from the list click Remove 7 To view the calculation method of a property select it and click Parameters 8 Click OK The calculations are performed Adding Calculations to an Existing Worksheet When you add structures to a worksheet that already has calculated properties you can calculate the properties for only the added structures without recalculating the entire worksheet CambridgeSoft Selecting ChemSAR Excel Descriptors To calculate properties for added structures 1 In a worksheet with calculated properties add the structures for which you want to calculate properties 2 Click Calculate Now The properties are calculated and added to the worksheet Customizing Cal
402. oll in the Output Window 154 MM2 and MM3 Computations You can also tear off the window and enlarge it to make it easier to view Output x Calculation started Note All parameters used Iteration 4 Minimizat Stretch 0280 Bend Stretch Bend o 0 0998 0 0139 Torsion 0 0000 Non 1 4 VDW 0 0000 1 4 VDU 0 6764 Total 0 8181 Calculation ending e Iv The Total Steric Energy for the conformation is 0 8181 kcal mol The 1 4 VDW term of 0 6764 dominates the steric energy This term is due to the H H repulsion contribution NOTE The values of the energy terms shown are approximate and can vary slightly based on the type of processor used to calculate them To view the value of one of the dihedral angles that contributes to the 1 4 VDW contribution 1 Select the atoms making up the dihedral angle as shown below by Shift clicking H 7 C 2 C 1 and H 4 in that order G e 2 From the Structure menu point to Measurement and select Set Dihedral Measurement CambridgeSoft Minimize Energy The following measurement appears Measurement ax Atoms Actual Optimal 1 H 4 C 1 C 2 H 7 59 9441 The 60 degree dihedral represents the lowest energy conformation for the ethane model Select the Trackball tool 1 Reorient the model by dragging the X and Y axis rotation bars until you have an end on view To force a minimization to converge on the transition conformation
403. olution tool Setting Molecular Surface Colors How you set the color depends on what type of surface you ate working with For Solvent Accessible Connolly Molecular or Total Charge Density surfaces do the following 1 On the Surfaces menu choose Surface Color The Surface Color dialog box appears 2 Select the new color 3 Click OK For the other surface types where you must specify two colors do the following 1 On the Surfaces menu choose Alpha Color or Beta Color The Alpha or Beta Color dialog box appears 2 Select the new color 3 Click OK ChemOffice 2005 Chem3D Setting Solvent Radius The Solvent Radius can be set from 0 1 to 10 A using the slider The default solvent radius is 1 4 A which is the value for water Radii for some common solvents are shown in the following table Solvent Radius A Water 1 4 Methanol 1 9 Ethanol 2 2 Acetonitrile 2 3 Acetone 2 4 Ether 2 4 Pyridine 2 4 DMSO 2 5 Benzene 2 6 Chloroform 2 7 To set the solvent radius 1 From the Surfaces menu choose Solvent Radius The Radius slider appeats 0 1 1 4 10 0 Displaying Models 67 Molecular Surface Displays 2 Adjust the slider to the desired resolution The new radius is the middle value listed at the bottom of the Radius tool Setting Surface Mapping The Mapping Property provides color coded visualization of Atom Colors Group Colors Hydrophobicity Partial Charges or Electr
404. om services mail Email support cambridgesoft com Fax 617 588 9360 Mail CambridgeSoft Corporation ATTN Technical Support 100 CambridgePark Drive Cambridge MA 02140 USA Serial Numbers When contacting Technical Support you must always provide your serial number This serial number was on the outside of the original application box and is the number that you entered when you launched your CambridgeSoft application for the first time If you have thrown away your box and lost your installation instructions you can find the serial number in the following way e Choose About CS lt application name gt from the Help menu The serial number appears at the bottom left of the About box For more information on obtaining serial numbers and registration codes see http www cambridgesoft com services codes cfm Troubleshooting This section describes steps you can take that affect the overall performance of CambridgeSoft Desktop Applications as well as steps to follow if your computer crashes when using a CS software product Technical Support 229 Serial Numbers Performance Below are some ways you can optimize the performance of CambridgeSoft Desktop Applications e Inthe Performance tab in the System control panel allocate more processor time to the application e Install more physical RAM The more you have the less ChemOffice Desktop Applications will have to access your hard disk to use Virtual Memory
405. oms the command operates on the entite model NOTE This command affects all frames of your model not Just the active frame Using the Zoom Control You can reduce or enlarge a model using the Zoom tool NOTE The Zoom tool lets you resize the model by dragging This changes the view not the coordinates of the molecule Scaling a Model You can scale a model to fit a window If you have created a movie of the model you have a choice of scaling individual frames or the whole movie To scale a model to the window size do one of the following From the View menu point to View Position and click Fit To Window e From the View menu point to View Position and choose Fit All Frames To Window to scale an entire movie ChemOffice 2005 Chem3D The Model To Window command operates only on the active frame of a movie To scale mote than one frame you must repeat the command for each frame you want to scale NOTE The Fit command only affect the scale of the model Atomic radii and interatomic distances do not change Changing the Z matrix The relative position of each atom in your model is determined by a set of internal coordinates known as a Z matrix The internal coordinates for any particular atom consist of measurements bond lengths bond angles and dihedral angles between it and other atoms All but three of the atoms in your structure the first three atoms in the Z matrix which describe
406. on atoms bear no relation to the Cahn Ingold Prelog R S specification of the absolute stereochemical configuration of a chiral atom Pro R and Pro S refer only to the positioning of D and do not imply any stereochemistry for C C may be chiral or achiral The most convenient way to visualize how the Pro R Pro S terms are used in Chem3D to position D is described in the following examples CambridgeSoft Changing the Z matrix To position Atom D in Pro S Orientation left and Pro R Orientation right 1 Orient the Distance Defining atom C the First Angle Defining atom B and the Second Angle Defining atom A such that the plane which they define is parallel to the X Y plane 2 Orient the First Angle Defining atom B to be directly above the Distance Defining atom C such that the bond joining B and C is parallel to the Y axis and the Second Angle Defining atom A is somewhere to the left of C In this orientation D is somewhere in front of the plane defined by A B and C if positioned Pro R and somewhere behind the plane defined by A B and C if positioned Pro S When you point to or click an atom the information box which appears can contain information about how the atom is positioned Positioning Example If H 14 is positioned by C 5 C 1 C 13 Pro R then the position of H 14 is a specified distance from C 5 as described by the H 14 C 5 bond length Two bond angles H 14 C 5 C 1 and H 14 C 5
407. onded atoms an atom pair 1 Select two unbonded atoms 2 From the Structure menu point to Measurement and choose Set Distance Measurement The Measurements table appears displaying the distance The Actual value is highlighted 3 Edit the highlighted text 4 Press the Enter key Atom Movement When Setting Measurements When you change the value of a measurement the last atom selected moves Chem3D determines which other atoms in the same fragment also move by repositioning the atoms that are attached to the moving atom and excluding the atoms that are attached to the other selected atoms Tf all of the atoms in a measurement are within a ring the set of moving atoms is generated as follows e Only one selected end atom that describes the measurement moves while other atoms describing the measurement remain in the same position e If you are setting a bond length or the distance between two atoms all atoms bonded to the non moving selected atom do not move This set of non moving atoms is extended through all bonds From among the remaining atoms any atoms which are bonded to the moving atom move this set of moving atoms is also extended through all bonds CambridgeSoft Setting Measurements e Ifthe Automatically Rectify check box in the Building control panel is selected rectification atoms that ate positioned relative to an atom that moves may also be repositioned For example consider the following s
408. onographs T he subjects covered include human and veterinary drugs biologicals and natural products agricultural chem icals industrial and laboratory chemicals and environmentally significant compounds What makes The M eck Index so valuable is its extensive coverage T he information provided includes chemical common and generic names trademarks C AS registry numbers molecular formulas and weights physical and toxicity data therapeutic and commercial uses and literature citations In addition to the standard searches compound monographs can now be searched by ChemD raw structure as well as substructure M oving this information to the fully searchable Chemo ffice format makes it easier and faster to search and get results Instead of consult ing the auxiliary indices and then turning to the actual monograph all searching can be done from a single form Query Search Form DATABASES e Encyclopedic reference for over 10 000 chemicals drugs and biologicals e Fully searchable by ChemDraw structure substructure names partial names synonyms and other data fields e Available in desktop enterprise and online formats Integrated Information H aving The M eck Index in Chemo ffice format confers another valuable benefit integration with other infor mation sources For example after locating a substance in The M eck Index it is a simple matter to copy the name structure or other data elements to search ChemACX D atabase
409. ontains one entry for each atom The fields contain a description of how each atom in the model is positioned relative to the other atoms in the model The order of atoms in the Internal Coordinates table is determined by the Z matrix The origin atom is listed first and the rest of the atoms ate listed in the order that they are positioned For more information see Scaling a Model on page 101 CambridgeSoft Measurement Table To display the Internal Coordinates table 1 From the View menu choose Z Matrix Table The Internal Coordinates table appears Cartesian ax BrrrrrzrTrr7Tr7dseqcannanana NOTE The default condition is that all of the tables open in a tabbed window when you select any one When you select a record in the Internal Coordinates table the corresponding atom is selected in the model When you select atoms in the model the corresponding records are selected in the Internal Coordinates table To edit measurements in the Z matrix 1 Type a new measurement in the selected cell 2 Press the Enter key To change which atoms Chem3D uses to position each atom use the commands in the Set Z matrix submenu in the Structure menu Cartesian Coordinates The fields in the Cartesian Coordinates table contain the atom name and the X Y and Z coordinates for each atom The order of atoms is ChemOffice 2005 Chem3D determined by their serial numbers All of the atoms in a fragment ate list
410. oose Inherit Atom Color The custom colors are removed from the selected atoms Displaying Atom Labels You can control the appearance of element symbols and serial numbers using the Atom Labels tab in the Model Settings control panel and the corresponding commands in the Model Display submenu of the View menu Setting Default Atom Label Display Options To set the Element Symbols and Serial Numbers defaults 1 On the Colors and Fonts tab of the Model Settings dialog box select the font point size and color 2 Click the Set as Default button All atoms currently in the model window display the selected options ChemOffice 2005 Chem3D To toggle the Atom Labels or Serial Numbers at any time do one of the following e From the Model Display submenu of the View menu choose Show Atom Labels or Show Serial Numbers e Click the Atom Label or Serial Numbers icon Y on the Model Display Toolbar Displaying Labels Atom by Atom To display element symbols or serial numbers in individual atoms 1 In the Model Explorer select the atom to change 2 On the Right click menu point to Atom Serial Number or Atom Symbol and choose Show Using Stereo Pairs Stereo Pairs is a display enhancement technique based on the optical principles of the Stereoscope the late Nineteenth centuty device for 3D viewing of photographs By displaying two images with a slight displacement a 3D effect is created Stereo vie
411. or any researcher T he Available Chemicals Xchange database ChemACX Database provides a complete tool for research chemical sourcing and purchasing T he database can be accessed from both desktop and enterprise environments and boasts an impressive list of major suppliers from Alfa Aesar and Aldrich to TC and Zeneca with hundreds in between T he enterprise pro curement solution for ChemACX saves time by streamlining the entire purchasing process Use ChemACX to build an internal requisition print the form on your company template fill it out and submit it to purchasing ChemACX SC ChenACX SC is an additional fully structure searchable database containing the catalogs of leading screening compound suppliers including ChemBridge M aybridge Sigma Aldrich s Rare Chemical Library and others Data Quality O ver 500 000 products from 300 research chemical and biological catalogs have been selected to have their product catalogs prepared for electronic delivery T he data provided by the suppliers is enriched by editors who add searchable chemical structures physical and chemical properties and incorporate a comprehensive chemical synonym dictionary All substances and supplier catalog numbers are cross referenced making it easy to locate alternate sources for back ordered or discontinued items ChemACX on the Web pi MEGAS E See EE tl i 7 e at a ira oo n T oa ons a ct alee 5 Eo x E f gt Che
412. ordinates and labels You also use the right click menu to copy the graph or it s data set to other applications or to carra the Ata Tutorial 6 Overlaying Models Overlays are used to compate structural similarities between models or conformations of the same model Chem3D provides two overlay techniques e a Fast Overlay algorithm e the traditional do it by hand method based on minimization calculations This tutorial describes the Fast Overlay method For the Minimization Method see Comparing Models by Overlay on page 109 The Minimization Method is mote accurate but the Fast Overlay algorithm is more robust In both tutorial examples you will superimpose a molecule of Methamphetamine on a molecule of Epinephrine Adrenalin to demonstrate their structural similarities 1 From the File menu choose New Model Open the Model Explorer if it is not already open 2 Choose the Text tool from the Building Toolbar and click in the model window A text box appears 3 Type Epinephrine and press the Enter key Chem3D Tutorials 43 Tutorial 6 Overlaying Models A molecule of Epinephrine appears TIP If you leave out the upper case E Chem3D will display an Invalid Label error message 4 Click in the model window again to open another text box 5 Select the entire word Epinephrine replace it with Methamphetamine and press the Enter key The list of atoms in the Model E
413. ose Model Settings The Settings dialog box appears Model Settings Colors 8 Fonts Movie Stereo amp Depth Model Display Model Building Atom Display Model Display Modes Model Type Ball amp Stick Ligand Model Type Wire Frame Solvent Model Type Not Displaying Atom Labels C Show Element Symbols C Show Serial Numbers Preview Set As Default f ok Cancel ChemOffice 2005 Chem3D The settings are organized into tabbed panels To select a control panel click one of the tabs at the top of the dialog box Model Display The model of ethane shown below displays the cylindrical bonds display type rendering type with the element symbols and serial numbers for all atoms Atom serial numbers Element symbols e To specify the rendering type do one of the following From the View menu point to Model Display then Display Mode and select a rendering type e Activate the Model Display toolbar click the arrow next to the Model Display icon J and select a rendering type In the Model Settings dialog box choose Model Display and select a rendering type To specify the display of serial numbers and element symbols do one of the following e On the View menu point to Model Display then click Show Serial Number or Show Atom Label e Activate the Model Display toolbar and click the Atom Labels and Serial Numbers icons Chem3D Basics 25 M
414. osition atom C 7 by two bond angles select atoms in the following order C 5 C 1 C 6 C0 then choose Position by Bond Angles Positioning by Dihedral Angle To position an atom relative to three previously positioned atoms using a bond distance a bond angle and a dihedral angle 1 With the Select tool click the dihedral angle defining atom 2 Shift click the first angle defining atom 3 Shift click the distance defining atom 4 Shift click the atom to position 104 Manipulating Models You should now have four atoms selected with the atom to be positioned selected last 5 From the Structure menu point to Set Z Matrix and then choose Position by Dihedral For example using the previous illustration choose atoms in the following order C 7 C 6 C 1 C 10 to position C 10 by a dihedral angle in a ring Then choose Position by Dihedral Setting Origin Atoms To specify the origin atoms of the Z matrix for a model 1 With the Select tool click the first one two or three atoms to start the Z matrix 2 From the Structure menu point to Set Z Matrix and then choose Set Origin Atom or Set Origin Atoms The selected atoms become the origin atoms for the Z matrix and all other atoms are positioned relative to the new origin atoms Because current measurements are retained no visible changes to the model occur CambridgeSoft Changing the Z matrix Chapter 6 Inspecting Models Model D
415. ostatic Potential derived from partial charges superimposed upon the solvent accessible surface Surface Color is color you have chosen with the Surface Color tool Atom Color is based on the displayed atom colors which may ot may not be the default element colors Element Color is based on the default colors in the Elements Table Group Color is based on the colors if any you specified in the Model Explorer when creating groups Hydrophobicity is displayed according to a widely used color convention derived from amino acid hydrophobicities where the most hydrophobic lipophilic is red and the least hydrophobic lipophobic is blue The following table shows molecule hydrophobicity Amino Acid Hydrophobicity Phe 3 7 Most hydrophobic Red Met 3 4 Ile 3 1 Leu 2 8 Val 2 6 1 Engelman D M Steitz T A Goldman A Identifying nonpolar transbilayer helices in amino acid sequences of membrane proteins Annu Rev Bio phys Biophys Chem 15 321 353 1986 68 Displaying Models Amino Acid Hydrophobicity Cys 2 0 Trp 1 9 Ala 1 6 Thr 1 2 Gly 1 0 Ser 0 6 Middle White Pro 0 2 Tyr 0 7 His 3 0 Gln 4 1 Asn 4 8 Glu 8 2 Lys 8 8 Asp 9 2 Arg 12 3 Least hydrophobic Blue The Partial Charges and Electrostatic Potential derived from the partial charges properties are taken from the currently selected calculation If you have performed more than one calculation on the mode
416. otation capture a frame Drag the Smoothness slider knob to the right to capture fewer frames a larger number of degrees of rotation capture a frame CambridgeSoft Animations Chapter 7 Printing and Exporting Models Printing Models You can print Chem3D models to PostScript and non PostScript printers Before printing you can specify options about the print job Specifying Print Options To prepare your model for printing 1 From the File menu choose Print Setup The Print Setup dialog box appears The available options depend on the printer you use There are five options specific to Chem3D which are described in the following table Print Setup Printer Acrobat Distiller OK Form Letter v Cancel Orientation 2 Sided Printing More Portrait Al O Pota Network O Landscape Help Scale To Full Page O Scale To mm Angstrom v Always Print with White Background High Resolution Printing slower Include Footer ChemOffice 2005 Chem3D 2 Select the appropriate options If you want to Then select resize your model according to a scaling factor scale yout model so the printed image fills the printed page print with white background default Scale To and type a scaling value Scaling factors ate measured in pixels per angstrom A pixel is 1 72 of an inch or approximately 1 28 of a centimeter With a value of 28 pixels
417. ote documentation Both import and export ate supported MOPAC Files MOPAC data may be stored in MOP DAT MPC ot 2MT file formats Chem3D can import any of these file formats and can export MOP files You can edit MOPAC files using a text editor adding keywords and changing optimization flags and run the file using the Run MOPAC Input file command within Chem3D 124 Printing and Exporting Models When you click Options in the Save As dialog box the MOPAC options dialog box appeats MOPAC Options PR C Save All Frames Click the Save All Frames check box to create a MOPAC Data file in which the internal coordinates for each view of the model are included The initial frame of the model contains the first 3 lines of the usual MOPAC output file see the example file below Each subsequent frame contains only lines describing the Z matrix for the atoms in that frame NOTE For data file specifications see page 13 of the online MOPAC manual To edit a file to run using the Run MOPAC Input File command 1 Open the MOPAC output file in a text editor The output file below shows only the first four atom record lines The first line and column of the example output file shown below ate for purposes of description only and ate not part of the output file CambridgeSoft Exporting Models Using Different File Formats Col 1 Col 2 C3 Col 4 c5 Col 6 Col 7 Col 8 Line 1 Line 2 Cyclo
418. ou can adjust the value from 0 to 100 If the value is zero then two atoms ate considered proximate only if the distance between them is no greater than the standard bond length of a bond connecting them For example if the value is 50 then two atoms ate considered proximate if the distance between them is no greater than 50 mote than the standard length of a bond connecting them To create bonds between proximate atoms 1 Select the atoms that you want tested for bond proximity 2 From the Right click menu point to Bond s and choose Proximate If they ate proximate a bond is created Adding Fragments A model can be composed of several fragments If you are using bond tools begin building in a corner of the window CambridgeSoft Adding Fragments If you are using the Text tool 1 Click in an empty area of the window A text box appeats 2 Type in the name of an element atom type or substructure 3 Press the Enter key The fragment appears For example to add water molecules to a window containing a model of formaldehyde 1 Click the Text tool 2 Click in the approximate location you want a water molecule to appear A text box appears 3 Type H20 4 Press the Enter key The fragment appears 5 Double click in a different location to add another H2O molecule View Focus As models become large keeping track of the section you are working on becomes more difficult With version 9 0
419. ould be used and for 2 2 dimethylpropane the XR2 parameter would be used The effect of the K and 09 parameters is to broaden or steepen the slope of the parabola The larger the value of K the more energy is required to deform an angle from its equilibrium value Shallow potentials are achieved with K values less than 1 0 A sextic term is added to increase the energy of angles with large deformations from their ideal value The sextic bending constant SF is defined in the MM2 Constants table With the addition of the sextic term the equation for angle bending becomes TS EM US DIAZ SS NOTE The default value of the sextic force constant is 0 00000007 To precisely reproduce the energies obtained with Allinger force field set the sextic bending constant to 0 in the MM2 Constants tables There are three parameter tables for the angle bending parameters 138 Computation Concepts e Angle Bending parameters e 3 Membered Ring Angle Bending parameters e 4 Membered Ring Angle Bending parameters There are three additional angle bending force constants available in the MM2 Constants window These force constants ate specifically for carbons with one or two attached hydrogens The following force constants ate available The numbers refer to atom types which can be found in the Atom Types Table in Chem3D e CHR Bending K for 1 1 1 angles e CHR Bending K for 1 1 1 angles in 4 membered rings e
420. ound to type specified this field is not used Possible bond orders are e Single e Double e Triple e Delocalized NOTE The bound to order should be consistent with the number of double triple and delocalized bonds for this atom type If the bound to type of an atom type is not specified its bound to order is ignored Bound to Type Specifies the atom type that this atom must be bound to If there is no restriction this field is empty Used conjunction with the Bound to Order field Non blank Bound to Type values e C Alkene e C Carbocation e C Carbonyl e C Carboxylate e C Cyclopentadienyl e C Cyclopropene e C Epoxy e C Isonitrile e C Metal CO e C Thiocarbonyl e H Alcohol e H Thiol e N Ammonium e N Azide Center e N Azide End CambridgeSoft Atom Types e N Isonitrile e N Nitro e O Carbonyl O Carboxylate e O Epoxy O Metal CO e O Nitro e O Oxo O Phosphate e P Phosphate e S Thiocarbonyl Substructures The Substructure table Substructures xml contains substructures to use in your model To use a substructure simply type its name in the Replacement text box or paste it after copying the name cell to the Clipboard and press the Enter key when an atom s is selected or double click an atom You can also copy the substructures picture to the Clipboard and paste it into a model window The substructure is attached to selected atom s in the model window If no atom is selecte
421. ous atoms 1 Hold the Shift key and select four contiguous atoms 2 Point at any portion of the selection 34 Chem3D Tutorials The dihedral angle formed by those four atoms is displayed Change the ethane model to an ethylene model 1 Click the Double Bond tool Y 2 Drag the mouse from C 1 to C 2 3 Point to the bond The bond length decreases and the bond order increases Continue to build on this model to build cyclohexane 1 Click the Select tool k 2 Click the double bond 3 Right click point to Bond s then to Order and choose Single Bond The bond order is reduced by one Hide the hydrogens to make it easier to build CambridgeSoft Tutorial 2 Building Models with the Bond Tools On the Model Display submenu of the View Create a ting mena denon iaa lOs 1 Drag from one terminal carbon across to the The hydrogens are hidden othet Add more atoms to the model The pointing information appeats when you drag properly 1 Click the Single Bond tool N 2 Drag upward from the left carbon 3 Another C C bond appears 4 Continue adding bonds until you have 6 carbons as shown below 2 Release the mouse button to close the ring ChemOffice 2005 Chem3D Chem3D Tutorials 35 Tutorial 2 Building Models with the Bond Tools Add serial numbers and atom labels 1 On the Model Display submenu of the View menu select Show Serial Numbers or click the Serial Number icon 4 on the
422. ow Active Window Chem3D 9 can open multiple tab models simultaneously The tab selects the active window Rotation Bars Chem3D 9 introduces dynamic auto hide rotation bars The rotation bars only appear on your screen when you ate actually using them To view the dynamic rotation bars you must do two things e Activate rotation mode by selecting the Trackball tool e Mouse over the rotation bar atea Z axis X axis Bond axis Y axis 14 Chem3D Basics Click on a bar and drag to rotate a model around that axis The Rotate About a Bond bar is only active when a bond or dihedral is selected Freehand rotation is accomplished by dragging in the main window The cursor changes to a hand E when you ate in freehand rotation mode You can turn off the display but not the function of the bars with the Show Mouse Rotation Zones checkbox on the GUI tab of the Preferences dialog box File gt Preferences Menus and Toolbars All Chem3D commands and functions can be accessed from the menus or toolbars The toolbars contain icons that offer shortcuts to many commonly used functions You can activate the Toolbats you want from the Toolbars submenu of the View menu Toolbats can be attached to any side of the GUI or can be torn off and placed anywhere on the screen for convenience TIP Most Toolbar commands are duplicated from the menus and are intended as a convenience If you only use a co
423. ox appears c 2 Type Ph 3 Press the Enter key Building From Tables Cartesian Coordinate tables and Z Matrix tables can be saved as text files or in Excel worksheets See Z matrix on page 28 and Cartesian Coordinates on page 28 for mote information Likewise tables from text files or worksheets can be Building and Editing Models 81 Building From Tables copied into blank tables in Chem3D to create models Text tables can use spaces or tabs between columns For a Cartesian table there must be four columns not including the Serial Number column or five columns if the Serial Number column is included The relative order of the the X Y Z columns must be preserved otherwise column order is not important For a Z Matrix table there must be seven columns not including Serial Number column or eight columns if the Serial Number column is included The column order must NOT be changed To copy a Cattesian or Z Matrix table into Chem3D 1 Select the table in the text or Excel file 2 Use Ctrl C to transfer to the clipboard 3 Right click in a blank table in Chem3D and select Paste Examples Example 1 chloroethane Cartesian table space character as separator C 0 0 464725 0 336544 0 003670 C 0 0 458798 0 874491 0 003670 Cl 0 0 504272 1 818951 0 003670 H 0 1 116930 0 311844 0 927304 O 1 122113 0 311648 0 927304 O 0 146866 1 818951 0 003670 1 116883 0 859095 0 92332
424. pecifying methods 200 specifying path to store results 202 specifying population analyses 201 specifying solvation models 201 specifying spin multiplicities 201 specifying wave functions 200 theory tab 200 tutorial example 49 Unix visualizing surfaces 71 General tab GAMESS 213 tab Gaussian 201 General tab 181 201 Geometry field 276 Geometry optimization 134 Geometry optimization definition 130 Gibbs free energy ChemProp Pro 207 GIF file format 121 Global minimum 133 Gradient norm 185 Grid density 67 editing 67 settings dialog 67 Ground state 174 Ground state RHF 175 Ground state UHF 174 175 Groups defining 93 mapping colors onto surfaces 69 table 93 Guessing parameters 153 273 GUI see User interface H Hamiltonians 143 Hamiltonians approximate in MOPAC 167 Hardware stereo graphic enhancement 62 Heat of formation ChemProp Pro 207 Heat of formation definition 185 Heat of formation DHF 185 Heating cooling rate control 159 Henry s law constant ChemProp Pro 207 Hiding atoms or groups 94 hydrogens tutorial example 34 serial numbers 88 Highest Occupied Molecular Orbital MO PAC 210 Highest Occupied Molecular Orbital over view 70 Highest Occupied Molecular Orbital view ing 49 Home page CambridgeSoft 227 HOMO see Highest Occupied Molecular Orbital Hooke s law equation 282 Hotkeys select tool 38 Hickel method see Extended Hiickel meth xe CambridgeSoft od Hiickel see Extended Hiicke
425. pin Density for the Ethyl Radical 197 Chapter 11 Gaussian Computations Gaussian 03 199 Minimize Energy 199 The Job Type Tab venis driers tak 199 The Theory Tabies eriisos ccc dins omnia gis ence 200 The Properties Tab voor ero 201 The Genetal Tab ee cia eo is 201 Job Description File Formats 202 Jd Pormat a E 202 AGE POLA econo AAE EES ENE 202 Computing Properties 202 Creating a Gaussian Input File 202 Running a Gaussian Input File 203 Repeating a Gaussian Job 204 Running a Gaussian Job 204 Chapter 12 SAR Descriptors Chem3D Property Broker 205 ChemProp Std Server 205 ChemProp Pro Server 207 Limita its 208 Error Messages avprety eked esa 208 MM2 Servet 0 00 000008 208 MOPAC Servet 2 04 209 GAMESS Server 210 Chapter 13 GAMESS Computations Installing GAMESS 211 Minimize Energy 211 The Theoty Tabs cece ness darte acts 211 The Job Type Tabo tara ist 212 Specifying Properties to Compute 212 Specifying the General Settings 213 Saving Customized Job Descriptions 213 Running a GAMESS Job 213 Repeating a GAMESS Job 214 Chapter 14 SAR Descriptor Computations Selecting Properties To Compute 215 Che
426. pin orbital a or Boy are the only two possible for any single MO Spin orbitals are orthogonal LCAO and Basis Sets Rigorous solution of the Hartree Fock equations while possible for atoms is not possible for molecules Generally an approximation known as Linear Combination of Atomic Orbitals LCAO must be used to compute MOs This uses the sum of 1 electron atomic orbitals whose individual contributions to the MO is each weighted by a molecular orbital expansion coefficient Cy YS The set of atomic orbitals by being used to generate the sum is called the basis set Choice of an appropriate basis set is an important consideration in ab initio methods There are a number of functions and approaches used to derive basis sets Basis sets ate generally composed of linear combinations of Gaussian functions designed to approximate the AOs Minimal basis sets such as SIO 3G contain one contracted Gaussian function single zeta for each occupied AO while multiple zeta basis sets also called split valence basis sets contain two or more contracted Gaussian functions For example a double zeta basis set such as the Dunning Huzinaga basis set D95 contains twice as many basis functions as the minimal one and a triple zeta basis set such as 6 311G contains three times as many basis functions Polarized basis sets allow AOs to change shape for angular momentum values higher than ground state configurations by
427. ping Properties onto Surfaces The allyl radical CH CHCH is a textbook example of resonance enhanced stabilization A a Ds A aS a gt gt asi To examine Radicals with Spin Density surfaces 1 From the File menu choose New 2 Type 1 propene in the ChemDraw Name Struct text box A molecule of 1 propene appears Create a tadical Select the H9 hydrogen N Press Delete A dialog box appears asking if you want to turn off rectification Chem3D is chemically intelligent and knows that in most cases carbon atoms have four substituents Radicals are one of the rare exceptions Click Turn Off Automatic Rectification Qo The propene radical is displayed 4 From the Calculations menu point to Gaussian and choose Minimize Energy In the Theory tab set the Method to PM3 and the Wave Function to Open Shell Unrestricted on 50 Chem3D Tutorials 6 Also in the Theory tab set the Spin Multiplicity to 2 NOTE If you are doing this tutorial with CSMOPAC there is no Spin Multiplicity setting This molecule is intended to be a radical and setting the Spin Multiplicity ensures that it is One of the best ways to view spin density is by mapping it onto the Total Charge Density surface This allows you to see what portions of the total charge ate contributed by unpaired electrons or radicals To view Spin Density mapped onto Total Charge Density Surface 1 In th
428. ppears y a 5 From the MOPAC Interface menu of the Calculations menu choose Minimize Energy 6 On the Theory tab choose AM1 7 On the Properties tab select Dipole 8 Click Run The results shown in the Messages window indicate the electron distribution is skewed in the direction of the oxygen atom Xx Y Z Total Dipole 2 317 0 000 0 000 2 317 vector Debye If you rotate your model the X Y and Z components of the dipole differ However the total dipole does not In this example the model is oriented so that the significant component of the dipole lies along the X axis CambridgeSoft Computing Properties Example 2 Comparing Cation Stabilities in a Homologous Series of Molecules To build the model 1 From the File menu choose New Model 2 Click the Text Building tool 3 Click in the model window A text box appears 4 For tri chloro type CCI3 and press the Enter key 5 Repeat step 1 through step 4 for the other cations type CHCI2 for di chloro type CH2CI for mono chloro and CH3 for methyl cation NOTE The cations in this example are even electron closed shell systems and are assumed to have Singlet ground state No modifications through additional keywords are necessary The default RHF computation 6 For each model click the central carbon type and press the Enter key The model changes to a cation and insures that the charge
429. pplemented by terms CambridgeSoft Quantum Mechanics Theory in Brief that describe the interaction between 2 electrons These terms include a density matrix P and the Coulomb and exchange integrals The final equation for the Fock operator is represented by the Fock matrix EE pt bain o Intesrals The Fock matrix has two forms Restricted RHF Requires that spin up and spin down electrons have the same energy and occupy the same orbital U Unrestricted UHF Allows the alpha and beta spin electrons to occupy different orbitals and have different energies Restrictions on the Wave Function For a molecular orbital MO with many electrons the electronic wave function P is restricted to meeting these requirements e Y must be normalized so that flevPav n where n is the number of electrons cis a normalization coefficient and Y is interpreted as the probability density This ensures that each electron exists somewhere in infinite space e Y must be antisymmetric meaning that it must change sign if the positions of the electrons in a doubly occupied MO are switched This requirement accommodates the Pauli exclusion principle Spin functions Spin functions amp and f3 represent the allowed angular momentum states for each electron spin up and spin down J respectively The product of ChemOffice 2005 Chem3D the spatial function dy which represents the MO and the spin function is the s
430. que of parallel synthesis has become an essential element of the drug discovery process T his is true both at the point of finding new leads as well as optimizing a promising lead By using parallel synthesis techniques chemists are able to multiply their productivity by a factor of between 5and 100 T his increase in productivity creates data management challenges CombiC hen Enterprise has been developed to provide the software tools required by the combinatorial chemist to manage and document parallel synthesis experiments T he software models real world workflow as much as possible Starting Out To start the user simply draws a generic reaction step in a ChemD raw ActiveX control directly embedded in the notebook environment Multiple reactants and products are supported Points of variability on the mole cules are indicated by the traditional R designation Furthermore query features can be used to precisely define the intended molecules After drawing the reaction the software analyzes the generic reaction determines the role of each molecule and creates pages for managing the lists of real reagents to be used in the actual parallel synthesis experiment Reaction Based Library Generation Library in Spreadsheet View DISCOVERY e Reagent lists can be drawn from varied sources e Reaction based library generation allows for evaluation by product or reagent e Data management is simplified and library specific
431. r more detailed information see the MOPAC online manual MINDO 3 Applicability and Limitations MINDO 3 Modified Intermediate Neglect of Diatomic Overlap revision 3 is the oldest method Using diatomic pairs it is an INDO Intermediate Neglect of Diatomic Orbitals method where the degree of approximation is more severe than the NDDO methods MNDO PM3 and AM1 This method is generally regarded to be of historical interest only although some sulfur compounds are still more accurately analyzed using this method The following table shows the diatomic paits that are patameterized in MINDO 3 An x indicates patameter availability for the pair indicated by the row and column Parameters of dubious quality are indicated by x CambridgeSoft Approximate Hamiltonians in MOPAC e Non classical structures ate predicted to be unstable relative to the classical structure for example ethyl radical e Oxygenated substituents on aromatic rings ate out of plane for example nitrobenzene The peroxide bond is systematically too short by about 0 17 A The C O C angle in ethers is too large AM1 Applicability and Limitations Rb Sr cd in sn sbfre 1 fxe cs Ba Haji Po ei Po at rin Important factors relevant to AM1 are e AM1 is similar to MNDO however there are changes in the core core repulsion terms and reparameterization e AM1 is a distinct improvement over MNDO Csfea Ha Ti Pb
432. r online chemical database searching Both import and export are supported 1 ROSDAL is a product of Softron Inc 126 Printing and Exporting Models SYBYL Files Use the SYBYL SML SM2 ML2 file formats to interface with Tripos s SYBYL applications The SML and SM2 formats can be used for both import and export the ML2 format is supported for import only Tinker MM2 and MM3 Files Use the XYZ file format to interface with TINKER software tools Specify MM2 for most models MM3 for proteins Both import and export ate supported Job Description File Formats You can use Job description files to save customized default settings for calculations You can save customized calculations as a Job Description file JDF or Job Description Stationery JDT Saving either format in a Chem3D job folder adds it to the appropriate Chem3D menu JDF Files The JDF file format is a file format for saving job descriptions When you open a JDF file you can edit CSBR and save the settings JDT Files The JDT file format is a template format for saving settings that can be applied to future calculations You can edit the settings of a template file however you cannot save your changes CambridgeSoft Job Description File Formats Exporting With the Clipboard The size of the file that you copy to the clipboard from Chem3D is determined by the size of the Chem3D model window If you want the size of a copied molecule to be sma
433. rals 43 using trackball 97 with mouse buttons 235 X Y axis rotation 97 Z axis rotation 97 Rotating fragments 45 Rotation bars 14 Run GAMESS Input File command 213 Run Gaussian Input File command 203 Run Gaussian Job command 204 Rune plots 222 Running GAMESS jobs 213 Gaussian input files 203 Gaussian jobs 204 minimizations 153 MOPAC input files 177 MOPAC jobs 178 S Saddle point 133 Sample code SDK web site 227 SAR descriptors definition 205 Save All Frames checkbox 124 Save As command 119 Saving customized job descriptions 213 Scaling a model 101 SciStore com 226 SDK Online accessing 227 Searching for chemical information online 224 for conformations 43 Select Fragment command 93 Select tool 91 Select tool hotkey 38 Selecting 91 adding atoms to a selection 92 all children 95 atoms 91 atoms and bonds 91 bonds 91 by clicking 91 by distance 94 by double click 93 by dragging 92 by radius 94 ChemSAR Excel Descriptors 220 defining a group 93 fragments 93 moving 95 multiple atoms or bonds 92 properties to compute 215 selection rectangle 92 Selection rectangle 92 Self consistent field 146 Semi empirical methods 146 166 limitations 130 speed 131 uses 131 Chem3D 9 0 1 xvii Semi empirical methods brief theory 143 Separating fragments 44 Serial numbers see also Atom labels see also Serial numbers displaying 61 Serial numbers tutorial example 36 Set Z Matrix commands 103 Setting bond angles 86 bond len
434. ration 100 CambridgePark Drive Cambridge MA 02140 USA CambridgeSoft TTT Chemo ffice ChemDraw Chem3D ChemFinder Cheminfo are trademarks of CambridgeSoft 2002 5 All other trademarks are the property of their respective holders All specifications subject to change without notice www cam b T1 dg eso ft CcCOm RESEARCH amp Inventory Manager C hemical and Biological Inventory Integration Database Technology Inventory M anager isa ChenO fficeWebServer based application designed to manage the reagent tracking needs of chemical and pharmaceutical research centers The system manages data associated with both commercially and internally produced chemical substances Although Inventory M anager is a stand alone application it can be tightly integrated with C ambridgeSoft s Registration System and chemical procurement ChemACX D atabase Inventory M anager is designed for a range of sizes from large workgroups to enterprises and captures both stockroom and reagent needs as well as high throughput discovery Cascading Location Model Inventory M anager has a fully cascading location model T his means that laboratories can decide for themselves the granularity of their locations Some labs may define locations as wells on plates residing on shelves inside refrigerators which in turn are found in laboratories Another lab may decide to track reagents at the bench or cabinet level Still in other settings it may suffice to track ch
435. re stopped The Status bar displays the values describing each iteration of the docking computation The following illustration shows the docked polymer molecules 48 Chem3D Tutorials The following illustration shows the distances between atom pairs at the completion of the docking computation The distances in the Actual cell are close to the distances in the Optimal cell Measurement C 1 C 93 C 6 C 98 5 1445 5 0000 C 12 C 104 5 0399 5 0000 C 16 C 108 5 0804 5 0000 C 114 C 22 4 9278 5 0000 C 120 C 28 4 9188 5 0000 C 34 C 126 5 0133 5 0000 C 41 C 133 4 9953 5 0000 C 137 C 45 5 0634 5 0000 C 142 C 50 5 1013 5 0000 Your results may not exactly match those described here The relative position of the two fragments or molecules at the start of the docking computation can affect your results For more accurate results lower the minimum RMS gradient Tutorial 8 Viewing Molecular Surfaces Frontier molecular orbital theory says that the highest occupied molecular orbitals HOMO and lowest unoccupied molecular orbitals LUMO are the most important MOs affecting a molecule s reactivity This tutorial examines the reactivity of double bonds by looking at the simplest molecule containing a double bond ethene Create an ethene model 1 From the File menu choose New 2 Draw a double bond in the ChemDraw panel A molecule of ethene appears Before you can view the molecular orbital su
436. rent Z Matrix button 123 Use tight convergence criteria 200 212 User guide online 224 User interface 13 User imposed constraints 142 Using Jdf Files 163 bond tools tutorial example 31 ChemDraw to create models 39 display mode 114 double bond tool tutorial example 34 hardware stereo graphic enhancement 62 labels 77 labels for substructures 38 labels to create models 37 measurements table tutorial example 39 MM2 tutorial example 41 MOPAC keywords 170 Name Struct 75 rotation dial 99 selection rectangle 92 xxo CambridgeSoft stereo pairs 61 substructures 78 table editor to enter text 78 text building tool 77 text building tool tutorial example 36 trackball tool tutorial example 31 Using the zoom control 101 UV energies 172 Vv V1 field 285 V2 field 285 V3 field 286 van der Waals cutoff distance 283 cutoff term 291 cutoffs 139 energy 139 209 energy MM2 209 radius field 275 surface definition 69 Van der Waals radii atom size control 57 dot surfaces display 58 Vapor pressure ChemProp Pro 208 VDW interactions 288 VDW interactions table 272 VECTORS keyword 171 Vibrational energies 171 View focus 85 View menu 15 Viewing Highest Occupied Molecular Orbitals 49 Lowest Unoccupied Molecular Orbitals 49 molecular surfaces 48 parameters 289 Visualizing surfaces from other sources 71 W Wang Ford charges 187 Water solubility ChemProp Pro 208 Wave equations 144 Web site CambridgeSoft accessing 22
437. required hardcopy archives by printing out pages Information cannot be accidentally modified Spectral controls from T hermo Galactic are available CombiChem Excel builds combinatorial libraries with embedded ChenD raw structures using ChemD raw Excel for Windows Find reagents with ChemFinder and design experiments BioAssay Pro available in ChemOffice Ultra allows for flexible storage and retrieval of biological data It is designed for complex lead optimization experiments and supports almost any biological model El le lo me ls he 2 al al lija io la ja gt Automatic oa PA Stoichiometric ral Calculations ja sn A vam me en Ea ha s Wii mer A 1 Eo 35 Eh el bie aj Fi mmmn Ei amm er 155 7 jua zes E j Po Iisi is bD ha Hh iin Al TEA t l at Ll i La i wee BF pyre rors we JU te ie a lr ligt LA nome ithe a eee ae py aai a p ee Scanned Images in E y T e amam Notebook Pages sd feo l 4 SOFTWARE E Notebook Ultra Ultimate Journaling amp Information e Advanced search and structure query features e Stores structures and models for easy retrieval e Stores physical and calculated data e Search by substructure including stereochemistry using ChemDraw e Search and store chemical reaction data e CombiC hem Excel combinatorial libraries e Integration with ChemDraw and Chem3D e Import export MDL SD RD files a E f i F i E CombiChe
438. rface you must calculate it CambridgeSoft Tutorial 8 Viewing Molecular Surfaces 3 From the Calculations menu point to Extended Huckel and select Calculate Surfaces To view the Highest Occupied Molecular Orbital HOMO 4 From the Surfaces menu point to Choose Surface and select Molecular Orbital 5 From the Surfaces menu point to Molecular Orbital to see the HOMO LUMO options Select HOMO N 6 The pi bonding orbital surface appears NOTE You may need to rotate the molecule to view the orbitals ChemOffice 2005 Chem3D To view the Lowest Unoccupied Molecular Orbital LUMO 1 From the Surfaces menu point to Molecular Orbital to see the HOMO LUMO options Select LUMO N 7 The pi antibonding orbital surface appears These are only two of twelve different orbitals available The other ten orbitals represent various interactions of sigma orbitals Only the pi orbitals ate involved in the HOMO and the LUMO Because the HOMO and LUMO control the reactivity of a molecule you can conclude that it is the pi bonding interactions of ethene that control its reactivity This is a specific case of a more general rule pi bonds are more reactive than sigma bonds Tutorial 9 Mapping Properties onto Surfaces ULTRA NOTE This example is designed to demonstrate Gaussian minimization You can also do it using CS MOPAC or Extended Hiickel calculations Chem3D Tutorials 49 Tutorial 9 Map
439. ring the docking computation The Dock command is available when two ot more distances between atoms in one fragment and atoms in a second fragment are specified These distances are entered into the Optimal field in the Measurements table You can use docking to simulate the association of regions of similar lipophilicity and hydrophilicity on two proximate polymer chains There are four steps A Build a polymer chain 1 Open a new Model window and select the Text Building tool 2 Click in the model window A text box appears 3 Type AA mon 3 C2F4 4 AA mon 3H in the text box 4 Press the Enter key A polyacrylic acid polytetrafluoroethylene block copolymer appears in the model window The text AA mon 3 is converted to a polymer segment with three repeat units of acrylic acid The text C2F4 4 is converted to a polymer segment with four repeat units of tetrafluoroethylene B Build a copy of the chain Double click in the model window well above and to the right of the first polyacrylic acid polytetrafluoroethylene block copolymer molecule 46 Chem3D Tutorials A second polymer molecule appears above the first polyacrylic acid polytetrafluoroethylene block copolymer molecule C Orient the chains 1 Click in the empty space in the model window to deselect any atoms in the model window 2 Click the arrow on the Trackball tool to open the Rotation Dial tool Select the Y axis and drag the di
440. rmed correctly C 1 should have a lower serial number than O 3 so that the C C N C dihedral angle is used to position adjacent substructures within a label Substructures 231 Overview Defining Substructures To define a substructure 1 Build a model of the substructure You can use Chem3D tools ot build it in the ChemDraw panel 2 Select the atoms to define 3 From the Edit menu choose Copy To save the substructure definition 1 Open Substructures xml From the 2 View menu point to Parameter Tables and choose Substructures 3 Right click in the Substructures table and choose Append Row A new tow is added to the table 4 Select the cell in the Model column 5 Right click in the cell and choose Paste from the context menu The structure is pasted into the table cell Note that it will be not be visible until you move to another cell 6 Select the cell in the Name column 7 Type a name for the substructure 8 Close and save the Substructures table For example consider an ester substructure R COOR You can build this substructure as part of the following model 232 Substructures Select atoms 3 5 the two oxygens and the carbon between them and using the instructions above create a new record in the Substructures Table If you want to append an ester onto the end of the chain as a catboxylic acid you can simply double click a hydrogen to replace it with the ester as long
441. roModel Files Use Current Z matrix Only Serial Numbers Bond and Dihedral Angles Pro R Pro S and Dihedral angles are used to position atoms Only Serial Numbers Dihedral Angles Only The Pro R and Pro S stereochemical designations are not used in constructing the Z matrix from a model All atoms ate positioned by dihedral angles only The MacroModel MCM DAT OUT file formats are defined in the MacroModel Structure Files version 2 0 documentation Chem3D supports import of all three file types and can export MCM 1 MacroModel is produced within the Department of Chemistry at Columbia University New York N Y Printing and Exporting Models e 123 Exporting Models Using Different File Formats Molecular Design Limited MolFile MOL The MDL Molfile format saves files by MDL applications such as ISIS Draw ISIS Base MAACS and REACCS The file format is defined in the article Description of Several Chemical Structure File Formats Used by Computer Programs Developed at Molecular Design Limited in the Journal of Chemical Information and Computer Science Volume 32 Number 3 1992 pages 244 255 Use this format to interface with MDL s ISIS applications and other chemistry related applications Both import and export are supported MSI ChemNote Use the MSI ChemNote MSM file format to interface with Molecular Simulations applications such as ChemNote The file format is defined in the ChemN
442. rogram copy the structure to the clipboard 2 In Chem3D from the Edit menu choose Paste The 2D structure is converted to a 3D model ChemOffice 2005 Chem3D The standard measurements are applied to the structure For more information see Appendix D 2D to 3D Conversion NOTE Yon cannot paste from ISIS Draw into the ChemDraw panel only into the Chem3D model window You can however use the synchronize control to add the model to the ChemDraw panel You can also cut and paste or drag and drop models to and from ChemDraw to Chem3D or the ChemDraw panel See Transferring to Other Applications on page 127 for more information on pasting into other applications Non bond or atom objects copied to the clipboard arrows orbitals curves are ignored by Chem3D Superatoms in ISIS Draw are expanded if Chem3D finds a corresponding substructure If a corresponding structure is not found you must define a substructure For more information see Defining Substructures on page 232 Building With the Bond Tools Use the bond tools to create the backbone structure of simple models Bond tools always create bonds that terminate with carbon atoms Hydrogens display automatically by default You can hide them to reduce clutter You can change the carbons or hydrogens to other elements after you create the generic model To create a model using a Bond tool 1 Choose a bond tool The Single Bond tool is use
443. rom the Tools menu choose Add Ins ChemOffice 2005 Chem3D The Add Ins dialog box appears Add Ins available Analysis ToolPak Analysis ToolPak VBA PA chembraw for Excel aa V ChemSAR for Excel CombiChem for Excel Conditiomal Sum Wizard Euro Currency Tools Internet Assistant VBA Lookup Wizard Purchasing for Excel Solver Add in Browse Automation El ChemDraw For Excel Adds chemical capability to Excel 3 Click ChemDraw for Excel and ChemSAR for Excel 4 Click OK The ChemSAR Excel toolbar appeats Select Mark Dependent Rune Options Descriptors Columns Plots L i i at es Calculate Mark Independent Descriptive Now Columns Statistics The ChemSAR Excel Wizard The ChemSAR Excel wizatd leads you through the steps required to perform property calculations on a set of molecules Briley ChemSAR Excel 217 Configuring ChemSAR Excel To perform property calculations using the ChemSAR Excel Wizard 1 From the ChemOffice menu point to ChemSAR then choose Wizard The Step 1 of 4 dialog box appears CS ChemSAR Wizard Step 1 of 4 CS ChemSAR uses CS ChemOffice For Excel worksheets to display Manage and manipulate molecules Press Next gt to use the current ChemOffice for Excel worksheet or press New ChemoOffice Worksheet to create and use a new ChemOffice worksheet New ChemoOffice Worksheet Press Next gt to add the Structure ce
444. rs 3 Click Run 4 CambridgeSoft Repeating a Gaussian Job Chapter 12 SAR Descriptors SAR Descriptor Overview Chem3D provides a set of physical and chemical property predictors These predictors which help predict the structure activity relationship SAR of molecules ate referred to as SAR descriptors in this uset s guide These descriptors are also available in ChemSAR Excel Chem3D Property Broker The Chem3D Property Broker provides an interface in Chem3D and ChemSAR Excel that allows you to calculate properties using many calculation methods provided by various Property Setver components ChemOffice 2005 Chem3D The components of the Property Broker Server architecture are illustrated below Chem3D ChemSAR Excel A Property Broker Interface ChemProp Std m ChemProp Pro Property _ Servers MM2 TT MOPAC L__ GAMESS ChemProp Std Server The ChemProp Std Server enables you to calculate the following structural properties Property Description The locus of the center of a spherical probe Connolly Solvent Accessible Surface Area Angstroms representing the solvent as it is rolled over the molecular model SAR Descriptors 205 Chem3D Property Broker Property Description Property Description Connolly Molecular The contact surface Ovality The ratio of the Surface Area created when a spherical Molecular Surface Ar
445. rsional Parameters table are 0 100 and 10 000 respectively Because a positive value of V2 indicates that there are minima at 0 and 180 these minima signify cis 2 butene and trans 2 butene respectively Notice that V2 for torsional parameters involving torsions about carbon carbon double bonds all have values ranging from approximately V2 8 000 to V2 16 250 In addition V2 torsional parameters involving torsions about carbon carbon single bonds all have values ranging from approximately V2 2 000 to V2 0 950 The values of V2 for torsions about carbon carbon double bonds are higher than those values for torsions about carbon carbon single bonds A consequence of this difference in V2 values is that the energy barrier for rotations about double bonds is much higher than the barrier for rotations about single bonds Parameter Tables 285 Torsional Parameters The V1 torsional constant creates a torsional energy difference between the conformations represented by the two torsional energy minima of the V2 constant As discussed previously a negative value of V1 means that a torsional energy minimum occurs at 0 and a torsional energy maximum occurs at 180 The value of V1 0 100 means that cis 2 butene is a torsional energy minimum that is 0 100 kcal mole lower in enetgy than the torsional energy maximum represented by trans 2 butene The counterintuitive fact that the V1 field is negative can be understood by remembering tha
446. ructure content of docu ments Discovery LIM S tracks laboratory requests and 21CFR11 Complianceimplenents an organization s reg ulatory compliance processes Research amp Discovery Research and discovery applications include Registration System for managing proprietary compound informa tion Inventory M anager for reagent tracking needs and chemical databases for complete management of chem ical inventories Formulations amp Mixtures and CombiC hem Enterprise also provide tailored approaches to man aging chemical data Applied BioInformatics BioAssay HTS and BioSAR Browse applications process biological assay data to pinpoint the structural deter minants of biological activity BioAssay H TS supports low high and ultra high throughput workflow includ ing sample and plate management while BioSAR Browser probes structural details within assay data Chemical Databases TheM eck Index and ChemACX Database provide reference information property estimations and searchable compilations of commercially available chemicals EMAIL info cambridgesoftcom WWW _ www cambridgesoftcom TEL 1 800 315 7300 INTL 1 617 588 9300 FAX 1 617 588 9390 e MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge MA 02140 USA CambridgeSoft TTT Chemo ffice ChemDraw Chem3D ChemFinder Cheminfo are trademarks of CambridgeSoft 2002 5 All other trademarks are the property of their respective holders All specifications subject to chan
447. rview CambridgeSoft Corporation CS provides technical support to all registered users of this software through the internet and through out Technical Support department Our Technical Support webpages contain answers to frequently asked questions FAQs and general information about our software You can access our Technical Support page using the following address http www cambridgesoft com services If you don t find the answers you need on out website please do the following before contacting Technical Support 1 Check the ReadMe file for known limitations ot conflicts 2 Check the system requirements for the software at the beginning of this User s Guide 3 Read the Troubleshooting section of this appendix and follow the possible resolution tactics outlined there 4 Ifall your attempts to resolve a problem fail fill out a copy of the CS Softwate Problem Report Form at the back of the User s Guide This form is also available on line at http www cambridgesoft com services mail e Try to reproduce the problem before contacting us If you can reproduce the problem please record the exact steps that you took to do so e Record the exact wording of any error messages that appear e Record anything that you have tried to correct the problem Chem3D Appendix You can deliver your CS Software Problem Report Form to Technical Support by the following methods Internet http www cambridgesoft c
448. ry in Brief The following information is intended to familiarize you with the terminology of quantum mechanics and to point out the areas where approximations are made in semiempirical and ab initio methods For complete derivations of equations used in quantum mechanics you can refer to any quantum chemistry text book Quantum mechanical methods describe molecules in terms of explicit interactions between electrons and nuclei Both ab initio and semiempirical methods are based on the following principles e Nuclei and electrons are distinguished from each other e Electron electron usually averaged and electron nuclear interactions are explicit e Interactions are governed by nuclear and electron charges i e potential energy and electron motions e Interactions determine the spatial distribution of nuclei and electrons and their energies e Quantum mechanical methods are concerned with approximate solutions to Schr dinger s wave equation HY EY The Hamiltonian operator H contains information describing the electrons and nuclei in a system The electronic wave function Y describes the state of the electrons in terms of their motion and position E is the energy associated with the particular state of the electron NOTE The Schr dinger equation is an eigenequation where the H operator the Hamiltonian operates on the wave function to return Computation Concepts 143 Quantum Mechanics Theory
449. s 289 Viewing Parameters 289 Editing Parameters 290 The MM2 Force Field in Chem3D 290 Chem3D Changes to Allinger s Force Field 290 Charge Dipole Interaction Term 291 Quartic Stretching TerM oooooooo 291 Electrostatic and van der Waals Cutoff Terms 291 Pi Orbital SCF Computation 291 MOPAC MOPAC Background ooooocococccccoo 293 Potential Functions Parametets 293 Adding Parameters to MOPAC 294 CambridgeSoft Introduction About Chem3D Chem3D is an application designed to enable scientists to model chemicals It combines powerful building analysis and computational tools with a easy to use graphical user interface and a powerful scripting interface Chem3D provides computational tools based on molecular mechanics for optimizing models conformational searching molecular dynamics and calculating single point energies for molecules About CS MOPAC CS MOPAC is an implementation of the well known semi empirical modeling application MOPAC which takes advantage of the easy to use interface of Chem3D CS MOPAC currently supports MOPAC 2002 There ate two CS MOPAC options available with Chem3D 9 0 1 e MOPAC Ultra e MOPAC Pro MOPAC Ultra is the full MOPAC implementation and is only available as an optional addin The CS MOPAC Ultra implementation provides support for previously unavailable features such
450. s Method Closed Shell Restricted Hartree Fock Basis Set STO 3G Orbital Guess Huckel Symmetry C1 3 Save As Cancel 2 Use the tabs to customize your computation See the following sections for details 3 Click Run The Theory Tab Use the Theory tab to specify the combination of basis set and particular electronic structure theory By default this tab is optimized for setting up ab initio computations For more detailed information see the BASIS section of the GAMESS documentation GAMESS Computations 211 Installing GAMESS To specify the calculation settings 1 From the Method list choose a method 2 From the Wave Function list choose a function 3 From the Basis Set list choose the basis set NOTE To use a Method or Basis Set that is not on the list type it in the Additional Keywords section on the General tab For more information see Specifying the General Settings on page 213 4 From the Diffuse list select the diffuse function to add to the basis set 5 Set the Polarization functions If you select a function for Heavy Atom also select an H option 6 Select a Spin Multiplicity value between 1 and 10 The Job Type Tab Use the Job Type tab to set options for display and recording results of calculations To set the job type options 1 In the Minimize Energy dialog box click the Job Type tab 2 Select the appropriate options If you want to T
451. s 2 butene the Non 1 4 van det Waals energy term includes the energy for the interaction of a hydrogen atom bonded to C 1 with a hydrogen atom bonded to C 4 The 1 4 van der Waals term represents the energy for the through space interaction of atoms separated by two atoms For example in trans 2 butene the 1 4 van der Waals energy term includes the energy for the interaction ofa hydrogen atom bonded to C 1 with a hydrogen atom bonded to C 2 The dipole dipole steric energy represents the energy associated with the interaction of bond dipoles For example in trans 2 butene the Dipole Dipole term includes the energy for the interaction of the two C Alkane C Alkene bond dipoles To build a c s 2 butene and compute properties 1 From the Edit menu choose Clear to delete the model 2 Double click in the model window A text box appears 3 Type cis 2 butene and press the Enter key A molecule of c s 2 butene appears in the model window 4 From the MM2 submenu of the Calculations menu choose Compute Properties CambridgeSoft Compute Properties The steric energy terms for s 2 butene appears in the Output window Below is a comparison of the steric energy components for cis 2 butene and rans 2 butene NOTE The values of the energy terms shown here are approximate and can vary slightly based on the type of processor used to calculate them Energy Term trans 2 cis 2 butene butene Stretch 0 0627 0
452. s 3 dimensional object data describing the model You can import 3DM files into many 3D modeling applications You can transfer 3DM files between Macintosh and Windows platforms AVI Use this file format to save a movie you have created for the active model You can import the resulting movie file into any application that supports the AVI file format Formats for Chemistry Modeling Applications The following file formats are used to export models to chemistry modeling application other than Chem3D Most of the formats also support import ChemOffice 2005 Chem3D Alchemy Use the ALC file format to interface with TRIPOSO applications such as Alchemy This is supported only for input Cartesian Coordinates Use Cartesian Coordinates 1 CC1 or 2 CC2 to import or export the X Y and Z Cartesian coordinates for your model When you save a file as Cartesian Coordinates an option button appears in the Save As dialog box To specify the save options 1 Click Options The Cartesian Coordinates Options dialog box appears Cartesian Coordinates A Connection Table By Serial Number By Position O Missing Include Serial Numbers Include Atom Type Text Numbers C Save All Frames 2 Select the appropriate options If you want the file to Then click contain a connection table for By Serial Number each atom with serial numbers contain a connection table for By Position each a
453. s Default You may use the defaults or set your own parameters Option Function Option Function Job Type Sets defaults for different types of computations Method Selects a method See Choosing a Hamiltonian on page 167 for descriptions of the methods 180 MOPAC Computations Wave Function Optimizer Solvent Move Which Minimum RMS Use MOZYME Selects close or open shell See Specifying the Electronic Configuration on page 172 for more details gt Selects a geometty minimizer See Optimizing Geometry on page 176 for mote information Selects a solvent For more information on solvent effects see the online MOPAC manual Allows you to minimize part of a model by selecting it Specifies the convergence criteria for the gradient of the potential energy surface See also Gradient Norm on page 185 ULTRA For very large models alters the way the SCF is generated cutting memory requirements and running much faster CambridgeSoft Minimizing Energy Option Function Display Every Displays the minimization Iteration process live at each iteration in the calculation NOTE Adds significantly to the time required to minimize the structure Show Output in Sends the output to a text Notepad file Send Back Output Displays the value of each measurement in the Output window NOTE Adds significantly to the time required to minimize t
454. s a toggle When it is selected the number 1 displays in a frame 7 With the Text Building tool click H 11 and then type NO2 in the text box that appears 8 Press the Enter key A model of nitrotoluene appears ug Lo wz ao t p ChemOffice 2005 Chem3D Use MOPAC to find the dipole moment 1 From the MOPAC Interface submenu of the Calculations menu choose Minimize Energy 2 On the Theory tab choose AM1 3 On the Property tab select Polarizabilities 4 Click Run The following table is a subset of the results showing the effect of an applied electric field on the first order polarizability for m nitrotoluene Applied field eV alpha xx alpha yy alpha zz 0 000000 108 23400 97 70127 18 82380 0 250000 108 40480 97 82726 18 83561 0 500000 108 91847 98 20891 18 86943 The following table contains the keywords automatically sent to MOPAC and those you can use to affect this property Keyword Description POLAR Automatically sent to MOPAC E n1 n2 n3 to specify the polarizablity routine n is the starting voltage in eV The default value is E 1 0 You can reenter the keyword and another value for n to change the starting voltage MOPAC Computations 193 Computing Properties Keyword Description GEO OK Automatically sent to MOPAC to override checking of the Z matrix MMOK Automatically sent to MOPAC to specify Molecular M
455. s is now as simple as entering a query through your web browser Unattended Data Indexing As new documents are added they are automatically indexed and chemical information is extracted Similarly if a document is modified it is reindexed N o administration of the server is necessary other than routine back up A A y unattended Data gt gt Repository Indexing o Loe L AA po a WE m ep oes ai Sa ce A U a w Te a ls i 5 ee A ae ia WE f an A 3 wai ras de Tal Ta ae i al a he ae a i mae ae aL as Wii 7 3 Ta i a g al i E E gt Search Documents by Structure MANAGEMENT e Indexes chemical structure information in documents and compiles a structure searchable database e Monitors designated folders or drives and automatically indexes new documents as they appear e Documents are searchable by structure and free text Free Text Searching Documents are searchable by free text including Boolean expressions proximity operators or simple queries For example author near Saunders finds all Word documents where the word author appears near the word Saunders Advanced Chemical Searching Since the chemical information is automatically extracted documents can be queried by structure substruc ture similarity molecular weight and formula Chemical queries also support atom lists Boolean operations on structures superatoms functio
456. s not supported by MM2 Examples include inorganic complexes where known parameters are limited You can view all parameters used in the analysis using the Show Used Parameters command See Showing Used Parameters on page 163 Running a Minimization To begin the minimization of a model e Click Run TIP In all of the following minimization examples you can use the MM2 icon on the Calculation toolbar instead of the Calculations menu ChemOffice 2005 Chem3D Select Record Every Iteration Select Copy Measurements to Output Select Move Only Selected Atoms Constraint is not imposed on any term in the calculation and the values of any results ate not affected The Output window appears when the minimization begins if it was not already opened The data is updated for every iteration of the computation showing the iteration number the steric energy value at that iteration and the RMS gradient If you have not selected the Copy Measurements to Output option only the last iteration is displayed After the RMS gradient is reduced below the requested value the minimization ends and the final steric energy components and total appear in the Output window Intermediate status messages may appeat in the Output window A message appears if the minimization terminates abnormally usually due to a poor starting conformation To interrupt a minimization that is in progress e Click Stop in the Computing dialo
457. s of all the parameter files located in the C3D Table directory To add a new parameter to the Torsional parameters table 1 From the View menu point to Parameter Tables and choose Torsional Parameters The Torsional Parameters table opens in a window 2 Enter the appropriate data in each field of the parameter table Be sure that the name for the parameter is not duplicated elsewhere in the table 3 Close and Save the table The MM2 Force Field in Chem3D Chem3D includes a new implementation of Norman L Allinger s MM2 force field based in large measure on work done by Jay W Ponder of Washington University This appendix does not attempt to completely describe the MM2 force field but discusses the way in which the MM2 force field is implemented and used in Chem3D and the 290 MM2 differences between this implementation Allinger s MM2 program QCPE 395 and Ponder s TINKER system M J Dudek and J W Ponder J Comput Chem 16 791 816 1995 For a review of MM2 and applications of molecular mechanics methods in general see Molecular Mechanics by U Burkert and N L Allinger ACS Washington D C USA 1982 Computational Chemistry by T Clark Wiley N Y USA 1985 also contains an excellent description of molecular mechanics For a description of the TINKER system and the detailed rationale for Ponder s additions to the MM2 force field visit the TINKER home page at http dasher wustl edu tinket
458. s single clicking with the Text tool To demonstrate this let s replace two more hydrogens using an alternative method 1 Select the Trackball tool so that you can rotate your model to get a better view of what you ate building 2 Double click two more hydrogens to change them to methyl groups TIP Notice that the C you entered previously in the Text tool remains as the default until you change it You only have to double click and press the Enter Rey Now refine the structure to an energy minimum to take into account the additional interactions imposed by the methyl groups by clicking the MM2 tool HNE on the Calculation toolbar When the minimization is complete 1 From the File menu choose Save As 2 Type tut2a ChemOffice 2005 Chem3D 3 Select a directory in which to save the file 4 Click Save Save a copy of the model using a different name 1 From the File menu choose Save As 2 Type tut2b 3 Select a directory in which to save the file 4 Click Save We ll be using these two copies of your model in later tutorials Using Labels to Create Models You can also create models by typing atom labels element symbols and numbers into a text box a HH HCc Cc cCc C aH l CH To build the model of 4 methyl 2 pentanol shown above 1 From the File menu choose New or click the new file tool on the Standard toolbar 2 Click the Text Building tool A 3 C
459. s the electronic energy to be described separately from 144 Computation Concepts nuclear energy by an electronic Hamiltonian which can be solved at any set of nuclear coordinates The electronic version of the Schr dinger equation is Another approximation assumes that electrons act independently of one another or more accurately that each electron is influenced by an average field created by all other electrons and nuclei Each electron in its own orbital is unimpeded by its neighbors The electronic Hamiltonian is thus simplified by representing it as a sum of 1 electron Hamiltonians and the wave equation becomes solvable for individual electrons in a molecule once a functional form of the wave function can be derived Ha NA HY yw ew For a molecular system a matrix of these 1 electron Hamiltonians is constructed to describe the 1 electron interactions between a single electron and the core nucleus The following represents the matrix for two atomic orbitals gt and Oy We me However in molecular systems this Hamiltonian does not account for the interaction between electrons with 2 ot mote different interaction centets or the interaction of two electrons Thus the Hamiltonian is further modified This modification renames the Hamiltonian operator to the Fock operator Festa The Fock operator is composed of a set of 1 electron Hamiltonians that describe the 1 electron 1 center interactions and is su
460. s the topology code NOTE Chem3D Pro ignores the unused field and topology code These fields will contain zeros if the file was created using Chem3D Pro CambridgeSoft File Format Examples Limitations The MDL MolFile format does not support non integral charges in the same way as Chem3D Pro For example in a typical MDL MolFile format file the two oxygens in a nitro functional group NO contain different charges 1 and 0 In Chem3D models the oxygen atoms each contain a charge of 0 500 FORTRAN Formats The FORTRAN format for each record of the MDL MolFile format is as follows Line Description FORTRAN Number Format 1 Molecule name A file name 2 Blank line 3 Blank line 1 Polygen 133 2 Polygen Corporation ChemNote molecule file 2D 3 File format version number 4 90 0928 5 File update version number 6 92 0114 7 molecule name 8 cyclohexanol MSI 9 empirical formula 10 Undefined Empirical Formula 11 need 3D conversion 12 0 ChemOffice 2005 Appendix 4 Number ofatoms 513 Number of bonds 5 23 Atom 3F10 4 1X A2 513 coordinates atomic symbol 24 42 Bond id from atom to atom and bond type MSI MolFile The MSI MolFile is defined in Chapter 4 Chem Note File Format in the Centrum Chem Note Application documentation pages 4 1 to 4 5 The following is a sample MSI MolFile file created using Chem3D Pro for cyclohexanol the line numbers ate added for purposes of dis
461. s within Radius of Selection Centroid gt Display Mode no ES 12 Angstroms EE AP 14 Angstroms Atom Serial Number 16 Angstroms Atom Symbol Atom Dots Delete Atom New Group 236 Keyboard Modifiers CambridgeSoft In all cases multiple selection is specified by holding the shift key down while making the selections Submenu option Effect Select Atoms within Distance of Selects all atoms except for those already selected lying within the Selection specified distance from any part of the current selection The current selection will be un selected unless multiple selection is used Select Groups within Distance Selects all groups except for those already selected that contain one or of Selection more atoms lying within the specified distance from any part of the current selection The current selection will be un selected unless multiple selection is used Select Atoms within Radius of Selects all atoms except for those already selected lying within the Selection Centroid specified distance of the centroid of the current selection The current selection will be un selected unless multiple selection is used Select Groups within Radius of Selects all groups except for those already selected that contain one or Selection Centroid more atoms lying within the specified distance of the centroid of the current selection The current selection will be un selected unless multiple selection is used ChemOffice 2005 Appendix Keybo
462. s your model are positioned in terms of three previously positioned atoms To view the current Z matrix of a model e From the View menu choose Z Matrix Table The First Three Atoms in a Z matrix The first three atoms in a Z matrix are defined as follows e Origin atom The first atom in a Z matrix All other atoms in the model ate positioned either directly or indirectly in terms of this atom e First Positioned atom Positioned only in terms of the Origin atom Its position is specified by a distance from the Origin atom Usually the First Positioned atom is bonded to the Origin atom Manipulating Models 101 Changing the Z matrix e Second Positioned atom Positioned in terms of the Origin atom and the First Positioned atom There are two possible ways to position the Second Positioned atom as described in the following example a Positioved St Positioned o E Aran is Positicna Aam In the left example the Second Positioned atom is a specified distance from the First Positioned atom In addition the placement of the Second Positioned atom is specified by the angle between the Origin atom the First Positioned atom and the Second Positioned atom In the right example the Second Positioned atom is a specified distance from the Origin atom In addition the placement of the Second Positioned atom is specified by the angle between the First Positioned atom the Origin atom and the Second Positio
463. se BioAssay HTS and BioSAR Browse to set up biological models and visualize information to generate spreadsheets correlating structure and activity and to search by structure Chemical Databases include the ChamACX Database of commercial ly available chemicals TheM erck Index h edition and other databases Consulting amp Services includes consulting development technical support and education training for pharmaceutical biotechnology and chemical customers including government and education by Cambridgesoft s experienced staff ChemOffice WebServer Enterprise Solutions amp Databases e Oracle Cartridge amp Database W ebserver Knowledge Management E N otebook Enterprise Document M gr Discovery IMS 21CFR11 Compliance Research amp Discovery e Registration System Formulations amp Mixtures Inventory Manager amp CombiChem Enterprise Applied Biolnformatics e BioAssay HTS BioSAR Browser Chemical Databases The Merck Index ChemAC X amp ChemSAR Properties ChemOffice Ultra Ultimate Drawing Modeling amp Information Adds The Merck Index EN otebook CombiChem MOPAC BioAssay ChemACX to O ffice Pro ChemOffice Pro Premier Drawing Modeling amp Information 1 Includes ChemDraw Ultra Chem3D Pro ChemSAR Excel ChemFinder Pro ChemiN DEX ChemRXN databases Also Available Separately ChemDraw Ultra Ultimate Drawing Query amp Analysis Adds ChemDraw Exce
464. sed in MM2 Calculations in Chem3D Angle bending parameters are used when the central atom has four or fewer attachments and the bond angle is not in a three or four membered ring In three and CambridgeSoft Angle Bending 4 Membered Ring Angle Bending 3 Membered Ring Angle Bending four membered tings the parameters in the 3 Membered Ring Angles xml and 4 Membered Ring Angles xml are used The Angle Bending table contains the parameters used to determine the bond angles in your model In Chem3D Pro additional information is used to compute the angle bending portions of the MM2 force field for the bond angles in your model The 4 membered Ring Angles table contains the patameters that are needed to determine the bond angles in your model that are part of 4 membered rings In Chem3D additional information is used to compute the angle bending portions of the MM2 force field for any bond angles in your model which occur in 4 membered tings The 3 membered Ring Angles table contains the patameters that are needed to determine the bond angles in your model that are part of 3 membered rings In Chem3D additional information is used to compute the angle bending portions of the MM2 force field for any bond angles in your model which occur in 3 membered tings Each of the records in the Angle Bending table the 4 Membered Ring Angles table and the 3 Membered Ring Angles table consists of seven fields Angle Type KB XR2 XRH
465. sing potential functions derived using classical mechanics e Individual potential functions are used to describe the different interactions bond stretching angle bending and torsional bond twisting energies and through space non bonded interactions e Potential energy functions rely on empirically derived parameters force constants equilibrium values that describe the interactions between sets of atoms e The sum of interactions determine the spatial distribution conformation of atom like particles Computation Concepts 135 Molecular Mechanics Theory in Brief e Molecular mechanical energies have no meaning as absolute quantities They can only be used to compate relative steric energy strain between two or more conformations of the same molecule The Force Field Molecular mechanics typically treats atoms as spheres and bonds as springs The mathematics of spring deformation Hooke s Law is used to describe the ability of bonds to stretch bend and twist Non bonded atoms greater than two bonds apart interact through van der Waals attraction steric repulsion and electrostatic attraction and repulsion These properties are easiest to describe mathematically when atoms ate considered as spheres of characteristic radii The total potential energy E of a molecule can be described by the following summation of interactions Energy Stretching Energy Bending Energy Torsion Energy Non Bonded Int
466. ssian Input Internal Coordinates MacroModel Name Extension Alchemy calc mol Cart Coords 1 ccl Cart Coords 2 cc2 Cambridge ccd Crystallographic Database c3xml c3d C3t ChemDraw cdx cdxml Conn Table Ct con GAMESS Input inp fchk fch cub Gaussian Input gjc gjf Int Coords int MacroModel mcm dat out CambridgeSoft Exporting Models Using Different File Formats File Format Name Extension Molecular Design MDL MolFile mol Limited MolFile MSI ChemNote MSI ChemNote msm MOPAC input MOPAC mop dat file mpc 2mt MOPAC graph gpt file Protein Data Protein DB pdb ent Bank ROSDAL Rosdal tdl Standard SMD File smd Molecular Data SYBYL MOL SYBYL sml SYBYL MOL2 SYBYL2 sm2 ml2 Tinker MM2 MM3 XYZ To save a model with a different format name or location 1 From the File menu choose Save As The Save File dialog box appears 2 Specify the name of the file the folder and disk where you want to save the file 3 Select the file format in which you want to save the model 4 Click Save ChemOffice 2005 Chem3D When you save a file in another file format only information relevant to the file format is saved For example you will lose dot surfaces color and atom labels when saving a file as an MDL MolFile Publishing Formats The following file formats ate used to import and or export models as pictures for desktop publishing and word processing softwate WMF and EMF
467. st select at least two atoms or one bond Internal rotation is typically specified by a bond The fragment at one end of the bond is stationary while the fragment attached to the other end rotates The order in which you select the atoms determines which fragment rotates See the following examples For example consider ethoxybenzene phenetole ethonybenzene cenl apex To perform a rotation about the C O bond where the phenyl group moves 1 Select the Trackball tool 2 Hold down the S key and select the O atom Manipulating Models 97 Rotating Models 3 Hold down the Shift and S keys and select the Cl atom 4 Drag the pointer along the Internal Rotation bat ethorybenzene conl apex 1 selection 2 selection Anchor faded fragment is rotating To perform a rotation about the C O bond where the ethyl group moves 1 Reverse the order of selection first select C1 then O TIP To deselect the atoms hold down the S key and click anywhere in the model window 2 Drag the pointer along the Internal Rotation bat Rotating Around a Bond To rotate the model around a specific bond 1 Select a bond 2 Hold down the Shift key and drag the pointer along the Internal Rotation bar 98 Manipulating Models Rotating Around a Specific Axis You can totate your model around an axis you specify by selecting any two atoms in your model You can add dummy atoms as
468. stance The non bonded energy accounts for repulsive forces experienced between atoms at close distances and for the attractive forces felt at longer distances It also accounts for their rapid falloff as the interacting atoms move farther apart by a few Angstroms van der Waals Energy Repulsive forces dominate when the distance between interacting atoms becomes less than the sum of their contact radii In Chem3D repulsion is modeled by an equation which combines an exponential repulsion with an attractive dispersion interaction 1 R Eon der wa 2 20000 E2 AR where A RoR ChemOffice 2005 Chem3D The parameters include R and R the van der Waals radii for the atoms Epsilon determines the depth of the attractive potential energy well and how easy it is to push atoms together which is the actual distance between the atoms e fi At short distances the above equation favors repulsive over dispersive interactions To compensate for this at short distances R 3 311 this term is replaced with a BES The R and Epsilon parameters are stored in the MM2 Atom Types table For certain interactions values in the VDW interactions parameter table are used instead of those in the MM2 atom types table These situations include interactions where one of the atoms is very electronegative relative to the other such as in the case of a water molecule Cutoff Parameters for van der Waals
469. stematic error due to the heat of formation of the CH fragment being too negative by about 2 kcal mol e Nitro compounds although considerably improved are still systematically too positive in energy e The peroxide bond is still systematically too short by about 0 17A PM3 Applicability and Limitations PM3 Parameterized Model revision 3 may be applied to the elements shaded in the following table Zn rele lafin fsnfso te 1 fre esea Hajm Pb Bi Po at An The following apply to PM3 e PM3 is a reparameterization of AM1 e PM3 is a distinct improvement over AM1 e Hypervalent compounds are predicted with considerably improved accuracy Overall errors in AH are reduced by about 40 relative to AM1 e Little information exists regarding the limitations of PM3 This should be corrected naturally as results of PM3 calculations are reported 150 Computation Concepts e The barrier to rotation in formamide is practically non existent In part this can be corrected by the use of the MMOK option The MMOK option is used by default in CS MOPAC For more information about MMOK see the online MOPAC Manual Ultra MNDO d Applicability and Limitations MNDO d Modified Neglect of Differential Overlap with d Otbitals may be applied to the elements shaded in the table below ols cafe nse jes Ba Hal Tt Pb Bi Po at rn MNDO d is a reformulation of MNDO with an extended basis set to include
470. sub structure or meta data You can organize your electronic pages by projects experiments or any other classifi cation that conforms to your workflow Desktop to Enterprise E N otebook allows organization of notebook pages at either the personal or enterprise leve Enterprise groups can organize and store notebook pages in a central data repository allowing colleagues to take advantage of each others work All access to data is subject to granular security E N otebook works with Orade Cartridge and SQL Server for departments or entire enterprises and M icrosoft Access for individuals or small groups ChemDraw Stoichiometry Calculations W hile not quantum theory stoichiometric calculations remain long and tedious E N otebook tackles this trou blesome problem First draw your reaction directly in the page T hen imply enter the mass volume and den Automatic Stoichiometric Calculations Scanned Images in Notebook Pages j MANAGEMENT Custom organization of notebook pages at personal or enterprise levels with links to chemical registration e Notebook pages include ChemDraw reaction schemes Microsoft Word and Excel documents and spectral data using the Galactic Spectral Control e Oracle Cartridge provides detailed security and data integrity SQ L Server also available sity volume and molarity and other factors of the limiting reagent and specify the number of equivalents of the other reactants Th
471. submenu of the Structure menu If you have chosen to Record each iteration the Movie menu commands and Movie 3 Choose Molecular Dynamics from the MM2 toolbar icons will be active at the end of the submenu of the Calculations menu computation 4 Click the Job Type tab and click the checkbox for Copy Measurements to Output If you want to save the calculation as a movie select Record Every Iteration checkbox The simulation ends when the number of steps specified is taken To stop the computation prematurely 5 Click Run e Click Stop in the Computation dialog box When the calculation begins the Output Window appears To replay the movie e Click Start on the Movie menu The frames computed during the molecular dynamics calculation are played as a movie 160 MM2 and MM3 Computations CambridgeSoft Molecular Dynamics To review the results 1 View the Output window to examine the measurement data included in the molecular dynamics step data 2 Drag the Movie slider knob to the left until the first step appears Selected The C 2 C 33 distance for the molecule before the molecular dynamics calculation began is approximately 9 4A 3 Scroll down to the bottom of the Output window and examine the C 2 C 33 distance for the molecule at 0 190 picoseconds which corresponds to frame 20 in the Movie slider of the model window The C 2 C 33 distance is approximately 13 7A 42 greater than the initial
472. symbol tetramethyl ammonium potassium or cesium cation electron MOPAC Computations 175 Specifying the Electronic Configuration Chemical Equivalent to symbol barium di cation 2 electrons borohydride halogen or nitrate anion minus electron sulfate oxalate di anion minus 2 electrons Sparkles are represented in Chem3D by adding a charged dummy atom to the model TIP Dummy atoms are created with the uncoordinated bond tool You must add the charge after creating the dummy The output file shows the the chemical symbol as XX ATOH CHEMICAL X NUMBER SYMBOL 1 23440000 6 66666666 6 3646 6666 0 77340000 0 52830000 1 88750000 2 19333900 1 08280000 1 14516666 Optimizing Geometry Chem3D uses the Eigenvector Following EF routine as the default geometry optimization routine for minimization calculations EF is generally superior to the other minimizers and is the default used by MOPAC 2002 Earlier versions of MOPAC used BFGS as the default The other alternatives are desctibed below OOnN OM EF oh slaleanon 176 MOPAC Computations ANGSTROMS TS The TS optimizer is used to optimize a transition state It is inserted automatically when you select Optimize to Transition State from the MOPAC Interface submenu BFGS For large models over about 500 1 000 atoms the suggested optimizer is the Broyden Fletcher Goldfarb Shanno procedure By specifying BFGS t
473. t only the total energy can be compared to experimental results In fact the total energy of trans 2 butene is computed to be 1 423 kcal mole lower than the total energy of cis 2 butene This corresponds closely with experimental results The negative V1 term has been introduced to compensate for an overestimation of the energy difference based solely on van der Waals repulsion between the methyl groups and hydrogens on opposite ends of the double bond This example illustrates an important lesson There is not necessarily any correspondence between the value of a particular parameter used in MM2 calculations and value of a particular physical property of a molecule V3 The V3 or 120 Periodicity Torsional constant field contains the third of three principal torsional constants used to compute the total torsional energy in a molecule V3 derives its name from the fact that a torsional constant of 120 periodicity can have three torsional energy minima and three torsional energy maxima within a 360 period A positive value of V3 indicates there are minima at 286e Parameter Tables 60 60 and 180 and there are maxima at 120 0 and 120 in a 360 period A negative value of V3 causes the position of the maxima and minima to be reversed as in the case of V1 and V2 above The significance of V3 is explained in the following example The 1 1 1 1 torsional parameter of n butane is an example of the V3 torsional
474. t 242 Aligning parallel to an axis 99 parallel to plane 100 to center 101 Allinger s force field 290 AMI 200 AMI applicability and limitations 149 169 Angle bending energy 137 Angle bending force constant field 279 Angle bending table 271 279 Angle defining atom 102 Angle type field 279 Angles and measurements 231 Animations 115 Apply Standard Measurements bond angles 87 bond lengths 87 Approximate Hamiltonians in MOPAC 148 Approximations to the Hamiltonian 144 Assigning atom types 233 Atom labels 61 77 movement when setting measurements 86 pairs creating 46 pairs setting 86 replacing with a substructure 81 size by control 57 size control 58 spheres hiding and showing 57 CambridgeSoft type characteristics 233 type field 280 283 type number 283 type number field 272 275 Atom Labels 26 Atom types assigning automatically 27 creating 234 in cartesian coordinate files 243 pop up information 105 table 274 Atomic Weight field 284 Atoms aligning to plane 100 changing atom types 83 coloring by element 58 coloring individually 60 displaying element symbols 61 displaying serial numbers 61 mapping colors onto surfaces 69 moving 95 moving to an axis 99 positioned by three other atoms 102 removing 76 selecting 91 setting formal charges 87 size 57 58 Attachment point rules 231 B Background color 60 Ball amp stick display 56 Basis sets 145 148 167 Bending constants 282 Bending energy MM2 209 Bind
475. t coordinates Chem3D generates positions of the atoms in the file to determine independent views using the additional sets of the number for each atom that will appear in the connection table of other atoms The first atom is number 1 the second is 2 etc 6 To create multiple views of the same set of atoms you can flow the descriptions of the atoms with an equal number of lines corresponding to the same atoms with co 2 ODO 1020N 01 9 10 11 12 13 14 15 16 17 18 19 102 TITTTITITITITOOOOOO O x 0 706696 0 834732 1 409012 1 217285 0 639328 0 89444 1 192993 1 052597 1 211624 1 208969 2 524918 1 11557 0 937027 2 329758 1 003448 1 005798 1 295059 1 265137 2 127594 1 066193 1 075577 0 275513 0 38632 1 19154 1 1698 1 809631 1 559525 2 125046 0 640518 0 2816 0 762314 0 8781 0 41023 2 24631 0 76137 1 73161 1 68524 1 865631 coordinates Samples of Cartesian coordinate files with connection tables by position and serial number for a model of cyclohexanol are shown below To clearly illustrate the difference between the two formats the serial number of the oxygen has been set to 101 0 50882 0 508789 0 668915 0 508865 0 664444 0 646652 1 59346 0 432266 0 457016 1 465607 1 7 8 1 1 1 1 1 6 5 5 5 0 625809 5 5 5 5 5 5 5 5 11 12 13 14 15 16 17 18 2 0 oan dD wo Ff 1 629425 1 470062 0 437714 0 618286 1 627 1 524
476. t is stored with the file Dihedral Chart Opens the window displaying results of Dihedral Driver MM2 computation See Tutorial 5 Mapping Conformations with the Dihedral Driver on page 42 for more information Status Bar Displays or hides the Status Bar Start Spinning Model Demo Spins the model on the Y axis Use stop calculation ho on the Calculations toolbar to stop the demo Full Screen Activates the full screen display The Structure Menu The Structure menu commands populate the Measurements table and control movement of the model The Measurements submenu e Set Measurements Sets a measurement bond length angle or distance according to what is selected Bond Lengths Displays bond lengths in the Measurements Table The Actual values come from the model and the Optimal values come from the Bond Stretching Parameters external table Chem3D Basics 17 The Graphical User Interface Bond Angles Displays bond angles in the Measurements Table The Actual values come from the model and the Optimal values come from Angle Bending Parameters and other external tables Dihedral Angles Displays dihedral angles in the Measurements Table The Actual values come from the model and the Optimal values come from Angle Bending Parameters and other external tables Clear Clears the entire Measurement table If you only want to clear part of the table select the portion you want to clear a
477. t to appear in the menu 4 Select the jdf or jdt file type 5 Click Save Your custom job description appears in the GAMESS menu Running a GAMESS Job If you have a previously created an inp GAMESS job file you can run the file in Chem3D To run the job file 1 From the Calculations menu point to Gamess and choose Run GAMESS Job The Open dialog box appears 2 Type the full path of the GAMESS file or Browse to location GAMESS Computations 213 Saving Customized Job Descriptions 3 Click Open The appropriate dialog box appears 4 Change settings on the tabs if desired 5 Click Run A new model window is created and the initial model will appear The GAMESS job runs and the results appear Properties requested for the job appear in the out file Only iteration messages will appear 214 GAMESS Computations Repeating a GAMESS Job After a GAMESS computation has been performed you can repeat it using the GAMESS menu To repeat a GAMESS job 1 From the Calculations menu point to Gamess and choose Repeat ame of computation The appropriate dialog box appears 2 Change parameters if desired and click Run The computation proceeds CambridgeSoft Repeating a GAMESS Job Chapter 14 SAR Descriptor Computations Overview Chem3D performs property prediction calculations These computed properties are the descriptors that may be used to estimate the structure activity relat
478. t types CDX MOL SKC f1d lq or RXN use structutes entered as SMILES strings use structutes entered as text use specific structures in worksheet 8 Click Next a Click Import SD File b In the Importable dialog box choose the database and click Open a Click Load from File b In the Choose Molecule to Load dialog box choose the file a Select the strings to include b Click Convert From SMILES a Select the text to include b Click Convert From Chemical Name a Type the range of cells containing the structures to use b Click Use Selected Range ChemSAR Excel 219 The ChemSAR Excel Wizard The Step 4 of 4 dialog box appears CS ChemSAR Wizard Step 4 of 4 Press Select Descriptors to select specific descriptors to calculate for the structures in the worksheet Select Descriptors Cancel 9 Click Select Descriptors 10 In the Select Descriptors dialog box select the appropriate descriptors For more information on using the Select Descriptors dialog box see Selecting ChemSAR Excel Descriptors on page 220 11 Click Finish The calculations are performed and the results appear in the worksheet Selecting ChemSAR Excel Descriptors The Select Descriptors dialog box allows you to specify which physical properties to calculate for your worksheet Properties are calculated for entire molecules If you want to calculate the properties of a m
479. t version 4 3 documentation dated 04 Feb 1987 The ROSDAL following is a sample SMD file produced using Chem3D Pro for cyclohexanol the line numbers 1 The Rosdal Structure Language file format is cadde toe papa sof dienian defined in Appendix C Rosdal Syntax pages 91 108 of the MOLKICK User s Manual The Rosdal format is primarily used for query searching in the Beilstein Online Database Rosdal format 2 SMD format H Bebak AV IM AM 1 Rosdal is a product of Softron Inc Bayer AG Line 1 gt STRT Cyclohexane Line 2 DTCR Chem3D 00000 05 MAY 92 12 32 26 Line 3 gt CT Cyclohexan 00039 Line 4 19 19 A2 512 613 Line 5 C 0 0 0 Line 6 C 0 0 0 Line 7 C 0 0 0 Line 8 C 0 0 0 Line 9 C 0 0 0 Line 10 C 0 0 0 Line 11 H 0 0 0 Line 12 H 0 0 0 Line 13 H 0 0 0 Line 14 H 0 0 0 Line 15 H 0 0 0 Line 16 O 0 0 0 Line 17 H 0 0 0 Line 18 H 0 0 0 Line 19 H 0 0 0 262 File Formats CambridgeSoft Protein Data Bank Files Line 20 Line 21 Line 22 Line 23 Line 24 Line 25 Line 26 Line 27 Line 28 Line 29 Line 30 Line 31 Line 32 Line 33 Line 34 Line 35 Line 36 Line 37 Line 38 Line 39 Line 40 Line 41 Line 42 Line 43 Line 44 Line 45 Line 46 Line 47 Line 48 Line 49 Line 50 Line 51 Line 52 Line 53 Line 54 Line 55 ChemOffice 2005 Appendix H 0 H 0 H 0 H 0 1 2 1 6 1 12 1 14 2 2 2 15 3 4 3 8 3 16 4 5 4 9 4 17 5 6 5 10 5 18 6 11 6 19 12 13 gt CO ANGSTROEM 0020 4 3
480. te or otherwise make the Included Data publicly available You may use the Software to organize personal data and you may transmit such personal data over the Internet pro vided that the transmission does not contain any Included D ata All rights not specifically granted under this Agreement are reserved by CS 5 Separation of Components T he Software is licensed as a single product Its component parts may not be sepa rated for use on more than one computer except in the case of Chemo ffice Enterprise Chemo ffice Enterprise includes licenses for ChemD raw ActiveX and licenses for Chem3D ActiveX The ActiveX software products may be installed on computers other than that one on which Chem0 ffice Enterprise is installed H owever each copy of the ActiveX is individually subject to the provisions of Paragraphs 1 through 4 of this Agreement 6 Educational Use Only of Student Licenses If you are a student enrolled at an educational institution the CS License Agreement grants to you personally a license to use one copy of the enclosed Software in accordance with the terms of this Agreement In this case the CS License Agreement does not permit commercial use of the Software nor does it permit you to allow any other person to use the Software 7 Termination You may terminate the license at any time by destroying all copies of the Software and documenta tion in your possession Without prejudice to any other rights CS may terminate this A
481. ted Hartree Fock E Basis Set STO 3G Spin Multiplicity 1 Solvation Model Gas Phase To set the properties and charges 7 From the Properties list select the properties to calculate 8 From the Population Analysis list select the method to compute atomic charges e Mulliken population analysis e Electrostatic potential derived charges according to the CHelp CHelpG and Merz Singh Kollman schemes e Natural Bond Order analysis NBO e Analysis according to the Theory of atoms in molecules by Badet et al Atoms In Molecules The General Tab The General tab allows you to customize the calculation for the model ChemOffice 2005 Chem3D Job Type Theory Properties General Solvation Model Dipole amp Sphere y Dielectric Constant 1 000 Solute Radius 1 000 Additional Keywords Results In Browse Menu Item Name Minimize Energy Job Type Minimize Energy Display Each Iteration Method Closed Shell Restricted Hartree Fock Basis Set 6 31G Spin Multiplicity 1 Summary Save As Cancel To specify the general settings 1 From the Solvation Model list choose a solvation model Gas Phase Onsager Model Dipole amp Sphere Tomasi s PCM Model PCM Model Isodensity Model l PCM Model Self consistent Isodensity Model SCI PCM Model 2 Enter values fot Dielectric Constant e for the solvent Solute Radius Points per
482. ten materials With a fixed license the software cannot be installed on more than the number of computers equivalent to the num ber of fixed licenses purchased For example a 10 user fixed license means the software can be installed on no more than 10 different computers A fixed license cannot be installed on a server With a concurrent license the software can be installed on any number of computers at the organization but the number of computers using the software at any one time cannot exceed the number of concurrent licenses purchased For example a 10 user concurrent license can be installed on 20 computers but no more than 10 users can be using it at any one time If the number of users of the software could potentially exceed the number of licensed copies then Licensee must have a reasonable mechanism or process in place to assure that the number of persons using the software does not exceed the number of copies CambridgeSoft reserves the right to conduct periodic audits no more than once per year to review the implementation of this agreement at the Licensees site At C ambridgeSoft s request Licensee will provide a knowl edgeable employee to assist in said audit 2 Ownership T he Software is and at all times shall remain the sole property of CS T his ownership is protected by the copyright laws of the U nited States and by international treaty provisions U pon expiration or termination of this agreement you shall promptly return al
483. ternal 1 Reaction coordinate or grid index T Monitor turning points in DRC 6 Add additional information in line Ln 1 For example symmetry information used in a SADDLE computation Printing and Exporting Models 125 Exporting Models Using Different File Formats 7 Leave the last line in the data file blank to indicate file termination 8 Save the file in a text only format MOPAC Graph Files A MOPAC Graph GPT file stores the results of MOPAC calculations that include the GRAPH keyword It contains the final geometry electronic structure and other properties of the molecule Chem3D supports the MOPAC Graph file format for import only Protein Data Bank Files Brookhaven Protein Data Bank files PDB ENT are used to store protein data and ate typically large in size Chem3D can import both file types and exports PDB The PDB file format is taken from the Protein Data Bank Atomic Coordinate and Bibliographic Entry Format Description ROSDAL Files RDL The ROSDAL Structure Language RDI file format is defined in Appendix C ROSDAL Syntax of the MOLKICK User s Manual and in this manual in Appendix E File Formats on page 262 The ROSDAL format is primarily used for query searching in the Beilstein Online Database Chem3D supports the ROSDAL file format for export only Standard Molecular Data SMD Use the Standard Molecular Data SMD file format for interfacing with the STN Express application fo
484. the bonds in your model The Bond Stretching Parameters record consists of six fields Bond Type KS Length Bond Dpl Quality and Reference Bond Type The Bond Type field contains the atom type numbers of the two bonded atoms For example Bond Type 1 2 is a bond between an alkane carbon and an alkene catbon Parameter Tables 277 Substructures KS The KS or bond stretching force constant field contains a proportionality constant which directly impacts the strength of a bond between two atoms The larger the value of KS for a particular bond between two atoms the more difficult it is to compress or to stretch that bond Length The third field Length contains the bond length for a particular bond type The larger the number in the Length field the longer is that type of bond Bond Dipole The Bond Dpl field contains the bond dipole for a particular bond type The numbers in this cell give an indication of the polarity of the particular bond A value of zero indicates that there is no difference in the electronegativity of the atoms in a particular bond A positive bond dipole indicates that the atom type represented by the first atom type number in the Bond Type field is less electronegative than the atom type represented by the second atom type number Finally a negative bond dipole means that the atom type represented by the first atom type number in the Bond Type field is more electronegative than the atom
485. the Minimize Energy command to reach a minimum point 1 From the Edit menu choose Select All 2 From the Structure menu choose Clean Up NOTE The Clean Up command is very similar to the minimize energy command in that it is a preset short minimization of the structure To perform the minimization 156 MM2 and MM3 Computations e From the MM2 submenu of the Calculations menu choose Minimize Energy and click Run When the minimization is complete reorient the model so it appears as follows The conformation you converged to is not the well known chair conformation which is the global minimum Instead the model has converged on a local minimum the twisted boat conformation This is the closest low energy conformation to your starting conformation Had you built this structure using substructures that are already energy minimized or the ChemDraw panel you would be close to the chair conformation The minimizer does not surmount the saddle point to locate the global minimum and the closest minimum is sought The energy values in the Output window should be approximately as follows Output x A Note All parameters used are Iteration 34 Minimizatior Stretch 0 4250 Bend 0 7404 Stretch Bend 0 1276 Torsion 5 6021 Non 1 4 VDW 0 8821 1 4 UDU 5 9041 Total 11 9172 lt gt Output Comments Dihedral Driver The major contributions are from the 1 4 VDW and Tors
486. the Minimum RMS Gradient value 4 Click Display Every Iteration 5 Click Start How the fragments are moved at each iteration of the overlay computation is displayed To save the iterations as a movie click the Record Each Iteration check box To stop the overlay computation before it reaches the preset minima click Stop Calculation amp on the toolbar The Overlay operation stops Recording is also stopped The following illustration shows the distances between atom pairs at the completion of the overlay computation The distances in the Actual cells are quite close to zero C 9 C 27 0 4872 0 0000 N 28 N 8 0 6404 0 0000 C 31 C 5 0 0995 0 0000 C 33 C 10 0 1653 0 0000 5 c 2 C 36 0 1021 Your results may not exactly match those described The relative position of the two fragments or molecules at the start of the computation can affect the final results Working With the Model Explorer The Model Explorer displays a hierarchical tree representation of the model It provides an easy way to explore the structure of any model even complex macromolecules and alter display properties at any level The Model Explorer defines the model in terms of objects Every object has a set of properties including a property that defines whether or not it belongs to another object is a child of a higher level parent object The default setting for all properties is Inherit Setting This mea
487. the Text Building tool MOPAC Computations 191 Computing Properties 3 Click in the model window A text box appears 4 Type PhO and press the Enter key A phenoxide ion model appears e For the last two monosubstituted nitro phenols first select the nitro group using the Select Tool and press the Delete key Add the nitro group at the meta H9 or ortho H8 position and repeat the analysis The data from this series of analyses are shown below The substitution of a nitro group at pata meta and ortho positions shows a decrease in negative charge at the phenoxy oxygen in the order meta gt para gt ortho where ortho substitution shows the greatest reduction of negative charge on the phenoxy oxygen You can reason from this data that the phenoxy ion is stabilized by nitro substitution at the ortho position NOTE All the monosubstituted phenols under examination are even electron closed shell systems and are assumed to have Singlet ground state No modifications by additional keywords are necessary The default RHF computation is used 5 From the MOPAC Interface submenu of the Calculations menu choose Minimize Energy 6 On the Theory tab choose PMS This automatically selects Mulliken from the Charges list 7 On the Property tab select Charges 8 Click Run To build para nitrophenoxide ion 1 Click the Text Building tool 2 Click H10 type NO2 and then press the Enter key Para ni
488. the orbital to map onto the surface with the Molecular Orbital tool on the Surfaces menu The orbital number appears in parentheses in the HOMO LUMO submenu ULTRA Total Spin Density The total spin density surface describes the difference in densities between spin up and spin down electrons in any given region of a molecule s space The larger the difference in a given region the more that region approximates an unpaired electron The relative predominance of spin up or spin down electrons in regions of the total spin density surface can be visualized by color when total spin density is mapped onto another sutface total charge density Entirely spin up positive value electrons are red entirely spin down negative blue and paired electrons neutral are white The total spin density surface is used to examine the unpaited electrons of a molecule The surface exists only where unpaired electrons are present Viewing the total spin density surface requires that both Spin Density and Molecular Surfaces are calculated by MOPAC or Gaussian using an Open Shell Wavefunction ULTRA Molecular Electrostatic Potential The molecular electrostatic potential MEP represents the attraction or repulsion between a molecule and a proton Attraction is represented by 70 Displaying Models negative values and repulsion is indicated by positive values Experimental MEP values can be obtained by X ray diffraction or electron diffraction t
489. the others 4 Right click in the selected area and choose the bond type Align Distribute gt Add Frame Single PS v Plan Triple gt Bold Quadruple gt Double Either Query Tautomeric Bond Position Aromatic Topology gt Object Settings Reaction Center Color gt v Show Query Indicator v Show Reaction Indicator Atom Jv Show Stereochemistry Text Bracket gt Curve 5 Click in the Chem3D window to complete the action Creating Bonds by Bond Proximate Addition Atoms that are within a certain distance the bond proximate distance from one another can be automatically bonded Chem3D determines whether two atoms ate proximate based on their Cartesian coordinates and the standard bond length measurement 84 Building and Editing Models Pairs of atoms whose distance from each other is less than the standard bond length plus a certain percentage are considered proximate The lower the percentage value the closer the atoms have to be to the standard bond length to be considered proximate Standard bond lengths are stored in the Bond Stretching Parameters table To set the percentage value 1 From the File menu choose Model Settings The Chem 3D Model Settings dialog box appears 2 Select the Model Build tab 3 Use the Bond Proximate Addition arrows 2 to adjust the percentage added to the standard bond length when Chem3D assesses the proximity of atom pairs Y
490. the requirement that you must perform a calculation before a molecular surface can be displayed Solvent Accessible surfaces are automatically calculated from parameters stored in the Chem3D parameters tables Therefore no additional calculations ate needed and the Solvent Accessible command on the Choose Surface submenu is always active Extended Huckel Extended H ckel is a semi empirical method that can be used to generate molecular surfaces rapidly for most molecular models For this teason a brief discussion of how to perform an Extended Hiickel calculation is given here For more information see Appendix 8 Computation Concepts To compute molecular surfaces using the Extended Huckel method e From the Computations menu point to Extended Hiickel and choose Calculate Surfaces NOTE Before doing an Extended Hiickel calculation Chem3D will delete all lone pairs and dummy atoms You will see a message to this effect in the Output window At this point a calculation has been performed and the results of the calculation are stored with the model To compute partial charges using the Extended Huckel method Displaying Models 63 Molecular Surface Displays e From the Computations menu point to Extended Hiickel and choose Calculate Charges For each atom in the model a message is created listing the atom and its partial charge If you have selected Partial Charge in the Pop up Information tab of the
491. ticals medical devices cosmetics or other health enhancing items The complexity lies in complying with government regulations designed to protect public health and safety The most notable of these is Title 21 of the Code of Federal Regulations governing Electronic Records and Signatures 21C FR11 Although 21CFR11 has been in the draft stage for almost a decade final regula tions have recently been created Enforcement of these regulations is beginning to take place and enterprises are responding with a wide variety of initiatives both within individual organizations and across industry sectors Integrated Software CambridgeSoft applications such as E N otebook Enterprise and D ocument M anager are at the leading edge of the integration of corporate knowledge management with 21CFR11 Compliance T hese products are designed so that as your organization reviews its internal processes for 21C FR11 Compliance the software can be configured to support these internal processes M ajor requirements of 21C FR11 such as electronic signatures audit trails and long term archiving are incorporated within the routine workflow to generate the critical information required by research development and production In addition E N otebook Enterprise and D ocument M anager can be integrated with existing critical data systems Record Management Mm creo a 09 eee z y ART a A Hm pe pe pee i eye PR ae Sind bor a za a Ea n als A a ao
492. tion UHF Automatically sent to MOPAC if you choose Open Shell Unrestricted wave functions to specify the use of the Unrestricted Hartree Fock methods Hyperfine Automatically sent to MOPAC to specify the hyperfine computation GEO OK Automatically sent to MOPAC to override checking of the Z matrix MMOK Automatically sent to MOPAC to specify Molecular Mechanics cortection for amide bonds Use the additional keyword NOMM to turn this keyword off Spin Density Spin density arises in molecules where there is an unpaired electron Spin density data provides relative amounts of alpha spin electrons for a particular state Spin density is a useful property for accessing sites of reactivity and for simulating ESR spectra Two methods of calculating spin density of molecules with unpaired electrons are available RHF Spin Density and UHF Spin Density ChemOffice 2005 Chem3D UHF Spin Density The UHF Spin Density removes the closed shell restriction In doing so separate wave functions for alpha and beta spin electrons are computed For more information see the MOPAC online manual page 152 The following table contains the keywords automatically sent to MOPAC and those you can use to affect this property Keyword Description UHF Automatically sent to MOPAC if you choose Open Shell Unrestricted wave functions to specify the use of the Unrestricted Hartree Fock methods GEO OK Automaticall
493. tion is 2 73 kcal mole which is in agreement with literature values To further illustrate points about minimization e Delete the value from the Optimal column for the dihedral angle and click the MM2 icon on the Calculation toolbar After the minimization is complete you are still at 0 degrees This is an important consideration for working with the MM2 minimizer It uses first derivatives of energy to determine the next logical MM2 and MM3 Computations 155 Minimize Energy move to lower the energy However for saddle points transition states the region is fairly flat and the minimizer is satisfied that a minimum is reached If you suspect your starting point is not a minimum try setting the dihedral angle off by about 2 degrees and minimize again Comparing Two Stable Conformations of Cyclohexane In the following example you compare the cyclohexane twist boat conformation and the chair global minimum To build a model of cyclohexane 1 From the File menu choose New An empty model window appears 2 Select the Text Building tool 3 Click in the model window A text box appears 4 Type CH2 CH2 5 and press the Enter key CAUTION W hile there are other perhaps easier methods of creating a cyclohexane model you should use the method described to follow this example Before minimizing it is wise to use the Clean Up Structure command to refine the model This generally improves the ability of
494. tion 105 106 Partition coefficient 207 Paste command 127 Paste special 15 Performing a molecular dynamics compu tation 158 Perspective rendering 60 Pi atoms table 280 Pi bonds and atoms with pi bonds 141 Pi bonds table 271 281 PI keyword 172 Pi orbital SCF computation 291 Pi system SCF equations 141 PIATOMS TBL see Pi atoms table PIBONDS TBL see Pi bonds table Planarity 107 PM3 150 169 200 PNG file format 121 Polarizability 188 Pop up information 105 Positioning by bond angles 103 Positioning by dihedral angle 104 Positioning example 103 PostScript files background color 60 Potential energy function choosing 148 167 Potential energy surfaces PES 130 133 Potential functions parameters 293 PRECISE keyword 171 172 183 Pre defined substructures 38 Previous Users help for 11 Principal Moments of Inertia ChemProp Std 206 Chem3D 9 0 1 Print command 118 Printing 118 background color 60 Properties selecting 215 sorting 215 tab GAMESS 212 tab Gaussian 202 tab MM2 161 Properties tab 201 Property calculation definition 130 Property filters 215 Pro R 102 Pro S 102 Protein Data Bank File FORTRAN format 260 Protein Data Bank file 259 Protein Data Bank file format 126 Protein Data Bank Files 259 Proteins highlighting binding sites 94 Publishing formats 119 Q Quality field 273 Quantum mechanical methods applications summary 131 Quantum mechanics theory in Brief 143 Quartic stretching term 291 Que
495. tion of a model 1 From the MOPAC Interface submenu of the Calculations menu choose Compute Properties The Compute Properties dialog box appears 2 On the Theory tab choose a potential energy function to use for performing the calculation NOTE For more information about the potential energy functions available in MOPAC see Computation Concepts CambridgeSoft Computing Properties 3 On the Properties tab select the properties to calculate Job Type Theory Properties General Properties ME Gradient Norm Dipole Charges Cosmo Solvation in Water Electrostatic Potential Molecular Surfaces Spin Density Hyperfine Coupling Constants Y Charges Mulliken X 4 On the Properties tab set the charges 5 On the General tab type any additional keywords if necessary 6 Click Run MOPAC Properties The following section describes the properties that you can calculate for a given conformation of your model either as a single point energy computation using the Compute Properties command or after a minimization using either the Minimize Energy or Optimize to Transition State commands Heat of Formation AH This energy value represents the heat of formation for a model s current conformation It is useful for comparing the stability of conformations of the same model NOTE The heat of formation values include the zero point energies To obtain the zero point energy for
496. to be performed as a closed shell A CI calculation is automatically invoked to correct errors in energy values inherent to the 1 2 electron approximation For more information see Configuration Interaction on page 167 With the addition of the 1 2 electron approximation RHF methods can be run on any starting configuration UHF The UHF method treats alpha spin up and beta spin down electrons separately allowing them to occupy different molecular orbitals and thus have different orbital energies For many open and closed shell systems this treatment of electrons CambridgeSoft MOPAC Semi empirical Methods results in better estimates of the energy in systems where energy levels ate closely spaced and whete bond breaking is occurring UHF can be run on both open and closed shell systems The major caveat to this method is the time involved Since alpha and beta electrons are treated separately twice as many integrals need to be solved As your models get large the time for the computation may make it a less satisfactory method Configuration Interaction The effects of electron electron repulsion ate underestimated by SCF RHF methods which results in the overestimation of energies SCF RHF calculations use a single determinant that includes only the electron configuration that describes the occupied orbitals for most molecules in their ground state Further each electron is assumed to exist in the average field
497. to create a model of ethane 3 Point to an atom using the Move Objects Tool 4 Drag the atom to a new location g 6 Manipulating Models 95 Moving Atoms or Models Dragging moves atoms parallel to the X Y plane changing only their X and Y coordinates If Automatically Rectify is on then the unselected rectification atoms that are adjacent to selected atoms move with the selected atoms To move a model 1 With the Move Objects tool drag across the model select it 2 Drag the model to the new location Note that the View axis has moved relative to the model coordinates 96 Manipulating Models Moving Models with the Translate Tool Use the Translate tool Y to move a model in the view window When you use the Translate tool you move both the focus view and the model coordinates along with the model Thus the model s position does not change relative to the origin Rotating Models Chem3D allows you to freely rotate the model around axes When you select the Trackball tool four pop up rotation bars are displayed on the periphery of the model window You can use these rotation bars to view your model from different angles by rotating around different axes You can also open the Rotate dialog box where you can use the rotate dial or type the number of degrees to rotate To display the Rotation bars e Select the Trackball tool from the Building
498. to find out whether there are commercial suppliers of the substance T he structures could also be used as input to Chem3D to obtain three dimension al models and to perform electronic structure and physical property calculations Information can also be brought into any ChemOffice desktop or enterprise solution including ChemD raw E xcel ChemFinder Word E N otebook and Registration System ChemOffice Formats The M erck Index is available in two ChemOffice compatible formats T he desktop edition isa CD ROM ina ChenF inder database format for use by an individual researcher The enterprise edition designed for workgroups and larger user communities is served by ChenOfficeWebServer to connected users The M eck Index thus adds to the growing set of reference databases served by Chemo ffice WebServer Just as ChemO ffice integrates the desktop edition of TheM eck Index with the scientist s everyday activities the enterprise edition becomes an inte gral part of the applications deployed on ChemOffice WebServer Web Versions The complete contents of The M erck Index are also available online through your favorite web browser To meet your specific needs single user subscriptions corporate extranet subscriptions and intranet webservers are all available EMAIL info cambridgesoftcom WWW _ www cambridgesoftcom a e EN TEL 1 800 315 7300 INTL 1 617 588 9300 FAX 1 617 588 9390 o e MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambri
499. toluene 193 Calculation toolbar 22 Cambridge Crystal Data Bank files 246 CambridgeSoft accessing the website 223 227 CambridgeSoft com 227 Cart Coords 1 see Cartesian coordinate file format Cart Coords 2 see Cartesian coordinate file format Cartesian coordinate 28 121 displaying 109 file format 121 243 FORTRAN file format 246 pop up information 105 positioning 100 e iii CC1 see Cartesian coordinate file format CC2 see Cartesian coordinate file format CCD see Cambridge Crystal Data Bank file format CCITT Group 3 and 4 120 Centering a selection 100 Changing atom to another atom type 83 atom to another element 82 bond order 83 elements 77 orientation 99 stereochemistry 88 Z matrix 101 Charge field 275 Charge property 186 Charge adding formal 77 Charge Charge contribution 140 Charge Charge energy MM2 209 Charge Dipole energy MM2 209 Charge Dipole interaction term 291 Charges 186 Charges adding 80 Charges from an electrostatic potential 186 Charges pop up information 105 Chem3D changes to Allinger s force field 290 property broker 205 synchronizing with ChemDraw 74 ChemBioNews Com 226 ChemClub com 223 ChemDraw panel 22 synchronizing with Chem3D 74 transferring models to 127 ChemDraw panel 74 ChemFinder com 225 Chemicals purchasing online 226 ive CambridgeSoft ChemOffice SDK accessing 227 ChemProp Pro critical pressure 207 critical temperature 207 critical volume 207 free e
500. tom that describes adjacent atoms by their positions in the file not contain a connection table Missing Printing and Exporting Models 121 Exporting Models Using Different File Formats If you want the file to Then click Include Serial Numbers contain serial numbers Include Atom Type contain atom type numbers Text Numbers contain internal coordinates Save All Frames for each view of the model Connection Table Chem3D uses the atom symbols and bond orders of connection table files to guess the atom symbols and bond orders of the atom types There are two connection table file formats CT and CON The CON format is supported only for import When you save a file as a Connection Table an Options button appears in the Save As dialog box To specify the save options 1 Click Options The Connection Table Options dialog box appears Connection Table Opti EJEA Start with 1 Blank Line 2 Blank Lines 3 Blank Lines 2 Select the appropriate options If you want to add Then click a blank line to the top of 1 Blank Line the file 122 Printing and Exporting Models If you want to add Then click two blank lines to the top 2 Blank Lines of the file three blank lines to the top 3 Blank Lines of the file Gaussian Input Use the Gaussian Input GJC GJF file format to interface with models submitted for Gaussian calculations Either file for
501. tom type number in the Angle Type field For example the record for bond angle type 1 2 1 is before the record for bond angle type 1 3 1 2 For multiple records where the second atom type number is the same the records are sorted by the first atom type number in the Angle Type field For example the record for bond angle type 1 3 2 is listed before the record for bond angle type 2 3 2 3 For multiple records where the first two atom type numbers are the same the records are sorted by the thitd atom type number in the Angle Type field For example the record for bond angle type 1 1 1 is listed before the record for bond angle type 1 1 2 280 Parameter Tables Pi Atoms The Pi Atoms table Conjugated Pisystem Atoms xml contains the parameters which are used to correct bond lengths and angles for pi atoms in your model In Chem3D additional information is used to compute the pi system portions of the MM2 force field for the pi atoms in your model The records in the Pi Atoms table are comprised of six fields Atom Type Electron Ionization Repulsion Quality and Reference Atom Type The Atom type number field contains the atom type number to which the rest of the Conjugated Pisystem Atoms record applies Electron The Electron field contains the number of electrons that a particular pi atom contributes to the pi system For example an alkene carbon atom type number 2 contributes 1 electron to the pi system w
502. tom types because atom types are required to complete these tasks To assign atom types as you build e Inthe Chem3D Model Settings dialog box select the Model Build tab then check the Correct Atom Types checkbox ChemOffice 2005 Chem3D To assign atom types after building Select the atom s and use the Rectify command on the Structure menu Atom type information is stored in the Atom Types table To view the Atom Types table From the View menu select Parameter Tables then select atom types xml Rectification Rectification is the process of filling open valences of the atoms in your model typically by adding hydrogen atoms To rectify automatically as you build do the following In the Chem3D Model Settings dialog box select the Model Build tab and then check the Rectify checkbox If you activate automatic rectification in the Model Settings dialog box you have the option of showing ot hiding hydrogens If you turn off automatic rectification the Show Hs and Lps command on the Model Display submenu of the View menu is deactivated and you will not have the option of displaying hydrogens Bond Lengths and Bond Angles You can apply standard measurements bond lengths and bond angles automatically as you build or apply them later Standard measurements are determined using the atom types for pairs of bonded atoms or sets of three adjacent atoms and are found in the external tables Bond Stretchin
503. traints 29 atom types table 272 283 bond orders 141 compute properties command 161 constants table 272 282 display every iteration control 152 199 xii CambridgeSoft 203 editing parameters 289 guessing parameters 153 minimize energy dialog 152 minimum RMS gradient 152 parameters 289 properties tab 161 property server 208 references 289 restrict movement of select atoms 153 159 server 208 tutorial example 41 MM2 force field in Chem3D 290 MNDO 149 168 200 MNDO d 150 170 Model see also es see also Internal coordinates Cartesian coordinates Z Matrix 28 data 105 display 25 display control panel 58 display toolbar 15 20 settings control panels 55 56 settings changing 55 56 settings dialog box 25 types 55 56 Model area 14 Model building basics 24 Model building controls setting 73 Model Explorer 27 Model Explorer stacking windows 40 Model information panel see also Model Explorer Measurements table Cartesian Coordinates table Z Matrix table see also 23 Model window 13 Models building 73 docking 46 editing 73 Molar Refractivity ChemProp Pro 207 Molecular Design Limited MolFile mol 124 Molecular Dynamics 143 example 160 job type tab 159 overview 158 settings 158 simulation 142 Molecular electrostatic potential 70 Molecular electrostatic potential surface calculation types required 65 definition 70 dialog 70 Molecular Formula ChemProp Std 206 Molecular mechanics applications
504. traints the additional term and force constant is E A TOi stance Molecular Dynamics Simulation In its broadest sense molecular dynamics is concerned with simulating molecular motion Motion is inherent to all chemical processes Simple vibrations like bond stretching and angle bending give rise to IR spectra Chemical reactions hormone receptor binding and other complex processes are associated with many kinds of intramolecular and intermolecular motions The MM2 method of molecular dynamics simulation uses Newton s equations of motion to simulate the movement of atoms Conformational transitions and local vibrations are the usual subjects of molecular dynamics studies Molecular dynamics alters the values of the intramolecular degrees of freedom in a stepwise fashion The steps in a molecular dynamics simulation represent the changes in atom position over time for a given amount of kinetic energy The driving force for chemical processes is described by thermodynamics The mechanism by which chemical processes occur is described by kinetics Thermodynamics describes the energetic relationships between different chemical states whereas the sequence ot rate of events that occut as molecules transform between their various possible states is described by kinetics CambridgeSoft Molecular Mechanics Theory in Brief The Molecular Dynamics MM2 command in the Calculations menu can be used to compute a molecular dynamics
505. trophenoxide ion is formed Perform minimization as in the last step Phenoxide p Nitro m Nitro o Nitro C1 0 39572 C1 0 41546 C1 0 38077 C1 0 45789 C2 0 46113 C2 0 44929 C2 0 36594 C2 0 75764 C3 0 09388 C3 0 00519 C3 0 33658 C3 0 00316 C4 0 44560 C4 0 71261 C4 0 35950 C4 0 41505 C5 0 09385 C5 0 00521 C5 0 10939 C5 0 09544 C6 0 46109 C6 0 44926 C6 0 41451 C6 0 38967 O7 0 57746 O7 0 49291 07 0 54186 07 0 48265 H8 0 16946 H8 0 18718 H8 0 21051 N8 1 38805 H9 0 12069 H9 0 17553 N9 1 31296 H9 0 16911 H10 0 15700 N10 1 38043 H10 0 19979 H10 0 17281 H11 0 12067 H11 0 17561 H11 0 14096 H11 0 13932 H12 0 16946 H12 0 18715 H12 0 17948 H12 0 18090 013 0 70347 013 0 65265 013 0 71656 014 0 70345 014 0 64406 014 0 65424 192 MOPAC Computations CambridgeSoft Computing Properties Example 4 Calculating the Dipole Moment of meta Nitrotoluene Create a model of w nitrotoluene 1 From the File menu choose New Model 2 Click the Text Building tool 3 Click in the model window A text box appears 4 Type PhCH3 and press the Enter key A model of toluene appears Reorient the model using the Trackball tool until it is oriented like the model shown in step 8 5 From the Edit menu choose Select All 6 Select Show Serial Numbers from the Model Display submenu of the View menu NOTE Show Serial Numbers i
506. tructure Qe i e Ta l 1 1 p U If you set the bond angle C 1 C 2 C 3 to 108 degrees C 3 becomes the end moving atom C 1 and C 2 remain stationary H 11 and H 12 move because they ate not part of the ring but are bonded to the moving atom If the Automatically Rectify check box is selected H 10 may move because it is a rectification atom and is positioned relative to C 3 Setting Constraints You can override the standard measurements which Chem3D uses to position atoms by setting constraints Constraints can be used to set an optimal value for a particular bond length bond angle dihedral angle or non bonded distance which is then applied instead of the standard measurement when you use Clean Up Structure or perform a Docking Overlay or MM2 computation To set constraints ChemOffice 2005 Chem3D e Enter a new value for the constraint in the Optimal field of the Measutements table In the case of dihedral angles and non bonded distances a constraint will have the effect of keeping that measurement constant or nearly so while the remainder of the model is changed by the computation The constraint doesn t remove the atoms from a computation Setting Charges Atoms are assigned a formal charge based on the atom type parameter for that atom and its bonding You can display the charge by pointing to the atom To set the formal charge of an atom 1 Click the Text tool 2 Sele
507. type If there is no rectification type for an atom it is never rectified For example if the rectification type of O Carboxyl is H Carboxyl the bound to type of H Carboxyl should be either O Carboxyl or empty Otherwise when assigning atom types hydrogen atoms bound to O Carboxyl atoms are not assigned H Carboxyl Parameter Tables 275 Atom Types Geometry The geometry for an atom type describes both the number of bonds that extend from this type of atom and the angles formed by those bonds Possible geometries ate e 0 Ligand e 1 Ligand e 5 Ligands e Bent e Linear e Octahedral e Square planar e Tetrahedral e Trigonal bipyramidal Trigonal planar e Trigonal pyramidal NOTE Standard bond angle parameters are used only when the central atom has a tetrahedral trigonal or bent geometry Number of Double Bonds Triple Bonds and Delocalized Bonds The number of double bonds number of triple bonds and number of delocalized bonds ate integers ranging from zero to the number of ligands as specified by the geometry Chem3D uses this information both to assign atom types based on the bond orders and to assign bond orders based on atom types Bound to Order Specifies the order of the bond acceptable between this atom type and the atom type specified in the bound to type 276 Parameter Tables For example for C Carbonyl only double bonds can be formed to bound to type O Carboxylate If there is no b
508. type represented by the second atom type number For example the 1 1 bond type has a bond dipole of zero since both alkane carbons in the bond are of the same electronegativity The 1 6 bond type has a bond dipole of 0 440 since an ether or alcohol oxygen is more electronegative than an alkane car bon 278 Parameter Tables Finally the 1 19 bond type has a bond dipole of 0 600 since a silane silicon is less electronegative than an alkane carbon NOTE The 1 5 bond type has a dipole of zero despite the fact that the carbon and hydrogen atoms on this bond have unequal electronegativity This approximation drastically reduces the number of dipoles to be computed and has been found to produce acceptable results Record Order The order of the records in the Bond Stretching table window is as follows 1 Records are sorted by the first atom type number in the Bond Type field For example the record for bond type 1 3 is before the record for bond type 2 3 2 For records where the first atom type number is the same the records are sorted by the second atom type number in the Bond Type field For example bond type 1 1 is before the record for bond type 1 2 Angle Bending 4 Membered Ring Angle Bending 3 Membered Ring Angle Bending The Angle Bending table Angle Bending Parameters xml contains information about bond angles between atoms of various atom type In addition to standard bond angles are information u
509. uch as these which have distinctly non spherical electron distributions For atom types such as O Carbonyl which have more nearly spherical electron distributions no explicit lone pairs are necessary NOTE Lone pairs are added automatically to atoms which require them at the beginning of an MM2 computation Torsional Parameters The Torsional Parameters table Torsional Parameters xml contains parameters used to compute the portions of the MM2 force field for the torsional angles in your model The 4 CambridgeSoft Torsional Parameters Membered Ring Torsional Parameters 4 membered Ring Torsionals xml contains torsional parameters for atoms in 4 membered rings Each of the records in the Torsional Parameters table and the 4 Membered Ring Torsional Parameters table consists of six fields Dihedral Type V1 V2 V3 Quality and Reference Dihedral Type The Dihedral Type field contains the atom type numbers of the four atom types which describe the dihedral angle For example angle type 1 2 2 1 is a dihedral angle formed by an alkane carbon bonded to an alkene catbon which is first bonded to a second alkene carbon which is bonded to another alkane carbon In other words angle type 1 2 2 1 is the dihedral angle between the two methyl groups of 2 butene The two alkene carbons are the central atoms of the dihedral angle Vi The V1 or 360 Periodicity Torsional constant field contains the first of three
510. ufficient to handle abnormally long bonds A quartic stretch term is used to correct problems caused by these very long bonds With the addition of the cubic and quartic stretch term the equation for bond stretching becomes Both the cubic and quartic stretch constants are defined in the MM2 Constants table To precisely reproduce the energies obtained with Allinger s force field set the cubic and quartic stretching constant to 0 in the MM2 Constants tables Angle Bending Energy TED LRD Arn l es The bending energy equation is also based on Hooke law The Ky parameter controls the stiffness of the spring s bending angular force Computation Concepts 137 Molecular Mechanics Theory in Brief constant while Oy defines the equilibrium angle This equation estimates the energy associated with deformation about the equilibrium bond angle The constant 0 02191418 is a conversion factor to obtain the final units as kcal mole Unique parameters for angle bending are assigned to each bonded triplet of atoms based on their atom types C C C C O C C C H For each triplet of atoms the equilibrium angle differs depending on what other atoms the central atom is bonded to For each angle there are three possibilities XR2 XRH or XH2 For example the XH2 parameter would be used for a C C C angle in propane because the other atoms the central atom is bonded to are both hydrogens For isobutane the XRH parameter w
511. uing minimizations 153 QuickTime file format 121 R R field 284 RECALC keyword 171 183 Record order 278 280 281 287 288 Recording minimization 153 molecular dynamics 160 Rectification 27 Rectification when deselecting 92 Rectifying atoms 90 Red blue anaglyphs 59 Reduct field 284 Reference description field 277 Reference field 273 Reference number field 277 References table 272 277 References MM2 289 References MOPAC 293 Refining a model 90 Reflecting a model through a plane 89 Refractivity ChemProp Pro 207 Registration online 223 Removing bonds and atoms 76 measurements from a table 108 selected properties 215 Rendering types 55 Repeating a GAMESS Job 214 Repeating a Gaussian Job 204 Repeating an MM2 Computation 163 Repeating MOPAC Jobs 178 Replacing atoms 37 atoms with substructures 81 Replaying molecular dynamics 160 Repulsion field 280 Requirements Windows 11 Reserializing a model 88 Resetting defaults 115 Resizing models 100 Resizing models 235 Resolve density matrix 172 Restrict movement of select atoms MM2 159 xvio CambridgeSoft Restrictions on the wave function 145 RGB indexed color 120 RHF 145 147 166 RHF spin density 189 RHF spin density example 197 Ribbons display 57 RMAX keyword 171 RMIN keyword 171 Roothaan Hall matrix equation 146 ROSDAL 262 ROSDAL file format 126 Rotating around a bond 98 around a specific axis 98 dihedral angles 97 98 fragments 97 models 96 two dihed
512. ulsion are underestimated by SCF RHF methods which results in the overestimation of energies SCF RHF calculations use a single determinant that includes only the electron configuration that describes the occupied orbitals for most molecules in their ground state Further each electron is assumed to exist in the average field created by all other electrons in the system which tends to overestimate the repulsion between electrons Repulsive interactions can be minimized by allowing the electrons to exist in more places i e more orbitals specifically termed virtual orbitals The multi electron configuration interaction MECI method in MOPAC addresses this problem by allowing multiple sets of electron assignments i e configurations to be used in constructing the molecular wave functions Computation Concepts 147 Quantum Mechanics Theory in Brief Molecular wave functions representing different configurations are combined in a manner analogous to the LCAO approach For a particular molecule configuration interaction uses these occupied orbitals as a reference electron configuration and then promotes the electrons to unoccupied virtual orbitals These new states Slater determinants or microstates in MOPAC ate then linearly combined with the ground state configuration The linear combination of microstates yields an improved electronic configuration and hence a better representation of the molecule Approximate Hamilton
513. ure is checked for novelty If a duplicate already exists in the data base the user can elect to register the information as a new batch of the existing compound or assign it a unique registry number Oracle Cartridge Registration System is the only true n tiered application of its kind that is designed around thin clients and thin servers T his translates into ultimate flexibility on both the client and server side O racle is supported as a host both with native security on a variety of platforms and operating systems T he chemical information is direct ly stored in the O racle tables Web Based User Interface W hile the business logic of Registration System is complex its user interface is clean and simple Web browser support for Netscape Navigator and Internet Explorer plus a choice of ChenD raw Plugin ActiveX or Java client tools are provided T his significantly reduces training time and cost of client maintenance Advanced Chemistry Features Duplicate checking is stereochemically aware Batch data is maintained separately from compound data Registration numbers support multiple sequences including one for synthesized and one for procured Compounds can be tracked by project and notebook reference and registered in batches from SD files or other sources of molecular information EMAIL info cambridgesoftcom WWW _ www cambridgesoftcom A D o TEL 1 800 315 7300 INTL 1617 588 9300 FAX 1617 588 9390 o e MAIL CambridgeSoft Corpo
514. us this cutoff speeds the computation significantly even for relatively small molecules Pi Orbital SCF Computation Chem3D determines whether the model contains any pi systems and performs a Pariser Parr Pople pi orbital SCF computation for each system A pi system is defined as a sequence of three or more atoms of types which appeat in the Pi Atoms table window PIATOMS xml The method used is that of D H Lo and M A Whitehead Can J Chem 46 2027 1968 with heterocycle parameters according to G D Zeiss and M A Whitehead J Chem Soc A 1727 1971 The SCF computation yields bond orders which are used to scale the bond stretching force constants standard bond lengths and twofold torsional barriers A step wise overview of the process used to do pi system calculations is as follows 5 A matrix called the Fock matrix is initialized to represent the favorability of sharing electrons between pairs of atoms in a pi system MM2 291 Chem3D Changes to Allinger s Force Field 2920 The pi molecular orbitals are computed from the Fock matrix The pi molecular orbitals are used to compute a new Fock matrix then this new Fock matrix is used to compute better pi molecular orbitals step 6 and Step 7 are repeated until the computation of Fock matrix and the pi molecular orbitals converge This method is called the self consistent field technique or a pi SCF calculation A pi bond order is co
515. use simplified Fock operators in which 1 electron matrix elements and some of the two electron integral terms are replaced by empirically determined parameters Both the SCF RHF and UHF methods underestimate the electron electron repulsion and lead to electron correlation errors which tend to overestimate the energy of a model The use of 146 Computation Concepts configuration interaction CI is one method available to correct for this overestimation For more information see Configuration Interaction on page 147 The Semi empirical Methods Semiempirical methods can be divided into two categories one electron types and two electron types One electron semiempirical methods use only a one electron Hamiltonian while two electron methods use a Hamiltonian which includes a two electron repulsion term Authors differ concerning the classification of methods with one electron Hamiltonians some prefer to classify these as empirical The method descriptions that follow represent a very simplified view of the semiempirical methods available in Chem3D and CS MOPAC For mote information see the online MOPAC manual Extended H ckel Method Developed from the qualitative H ckel MO method the Extended Hiickel Method EH represents the earliest one electron semiempirical method to incorporate both o and p valence systems It is still widely used owing to its versatility and success in analyzing and interpreting ground stat
516. whereas a light background is more suitable for print copy To change the default background color of the model window 1 In the Colors and Fonts tab of the Model Settings control panel click Background Color Model Display Model Building Atom Display Colors amp Fonts Movie Stereo amp Depth Color by O Monochrome Element O Partial Charge O Group O Chain O Depth Background Model Colors color jackground HN gt Alpha Helix Highlighted Beta Sheet mm Coi Nucleic Acid E Ld Lal Lal La Atom Label Font Times New Roman das 12 4 ia Versi The Color dialog box appears 2 Select a color and click OK NOTE The background colors are not saved in PostScript files or used when printing except when you use the Ribbons display Coloring Individual Atoms You can matk atoms individually using the Select Color command in the Model Explorer 60 Displaying Models CambridgeSoft Structure Displays To change an atom to a new solid color 1 In the Model Explorer select the atom s to change 2 From the Right click menu choose Select Color The Color dialog box appeats 3 Select a color and Click OK The color of the atom s changes to the new color To remove a custom atom color from the model display 1 In the Model Explorer select the atoms whose colors you want to change 2 Right click point to Apply Atom Color and ch
517. ws can be either Parallel or Reverse direct or cross eyed Some people find it easier to look directly others can cross their eyes and focus on two images creating an enhanced three dimensional effect In either case the effect may be easier to achieve on a printed stereo view of your model than on the screen Keep the images relatively small and adjust the distance from your eyes To set the Stereo Pairs parameters 1 Open the Model Setting dialog box and click the Stereo and Depth tab The stereo views control panel appears Displaying Models 61 Structure Displays Model Settings Model Display Model Building Atom Display Colors amp Fonts Movie Stereo amp Depth General Stereo Settings Disabled O Render Stereo Pairs O Render Red Blue Anaglyphs Eye Separation Stereo Pair Settings Parallel O Reversed Separation 5 J 0 100 Depth and Perspective C Perspective C Depth Fading Field of view gt preview 2 Select Render Stereo Pairs to display two views of the model next to each other The right view is the same as the left view rotated about the Y axis 3 Specify the Eye Separation Stereo Offset with the slider This controls the amount of Y axis rotation 4 Specify the degree of separation by clicking the Separation arrows About 5 of the width is a typical separation for stereo viewing To select whether the views are cross eyed or direct do one of
518. xplorer is replaced with two Fragment objects labeled Epinephrine and Methamphetamine De pk Se puise use Siem e Qie mie e au a a i qe de PL Labels The two fragments are hopelessly jumbled together at this point so you might want to separate them before you proceed 44 Chem3D Tutorials 1 Click one of the fragment names in the Model Explorer The entire fragment is selected 2 Click the Move Objects tool e 3 Drag the selected fragment away from the other fragment CambridgeSoft Tutorial 6 Overlaying Models A box or oval indicates the position of the fragment while you are moving it TIP You can rotate a fragment separately from the whole model by selecting at least one atom in it and using the Shift key with the trackball tool Try this to re orient the fragments as in the illustration below ras At this point you have to decide which of the fragments will be the target In this simple example with only two compounds it doesn t really matter You might however have cases where you want to overlay a number of compounds on a specific target Chem3D allows multiple overlays The Model Explorer makes it easy to hide compounds you are not actively working with and to display any combination of compounds you want 1 Click the Epinephrine fragment to select it 2 Point to Overlay on the context right click menu and click Set Target Fragment F Reese
519. xt Tool Visibility gt Select Color Apply Atom Color gt Display Mode Atom Serial Number 13 v Inherit Setting Atom Symbol gt Show Atom Serial Number Atom Dots gt Delete Atom New Group NOTE The Model Explorer cannot update its numbering to match the changes you are making on the model when Serial Numbers are displayed Ifyou forget 88 Building and Editing Models this step you will see different numbers on the tree control and the model If this happens simply hide the serial numbers momentarily and redisplay them 2 Click the Text tool 3 Click the atom to reserialize A text box appears 4 Type the serial number 5 Press the Enter key If the serial numbers of any unselected atoms conflict with the new serial numbets then those unselected atoms ate renumbered also To reserialize another atom with the next sequential numbet e Double click the next atom you want to reserialize To teserialize several atoms at once 1 Click the Text tool 2 Hold down Shift and select several atoms 3 Type the starting serial number 4 Press the Enter key Normally the selected atoms are reserialized in the order of their current serial numbers However the first four atoms selected ate teserialized in the order you selected them Changing Stereochemistry You can alter the stereochemistry of your model by inversion or reflection Inversion The Invert command performs an inversion symmetr
520. y kcal mol Charge Charge Energy kcal mol Charge Dipole Energy kcal mol Dipole Moment Debye Dipole Dipole Energy kcal mol Non 1 4 van der Waals Energy kcal mol Stretch Bend Energy kcal mol ChemOffice 2005 Chem3D Description The sum of the angle bending terms of the force field equation The sum of the electrostatic energy representing the pairwise interaction of charged atoms The sum of the electrostatic energy terms resulting from interaction of a dipole and charged species Molecular dipole moment The sum of the electrostatic energy terms resulting from interaction of two dipoles The sum of pairwise van der Waals interaction energy terms for atoms separated by more than 3 chemical bonds The sum of the stretch bend coupling terms of the force field equation Property Description Torsion Energy The sum of the dihedral kcal mol bond rotational energy term of the force field equation Total Energy The sum ofall terms the kcal mol the force field equation van der Waals Energy kcal mol The sum of pairwise van der Waals interaction energy terms for atoms separated by exactly 3 chemical bonds MOPAC Server The MOPAC server calculates property predictions based on semi empirical computational methods For mote information see The Semi empirical Methods on page 146 and Running MOPAC Jobs on page 178 The MOPAC server provides the fo
521. y Chem3D all other records in a Protein Data Bank file are ignored The COMPND record contains the name of the molecule and identifying information The ATOM record contains atomic coordinate records for standard groups and the HETATM record contains atomic coordinate records for non standard groups The CONECT record contains the atomic connectivity records NOTE The COMPND record is created by Chem3D to include the title of a Chem3D model only when you are saving a file using the Protein Data Bank file format This record is not used when opening a file The following is an example of a Protein Data Bank Output File from Chem3D for L Alanine COMPND Alanine pdb HETATM 1 N 0 0 962 1 HETATM 2 C 0 0 049 0 HETATM 3 C 0 6 0 834 1 HETATM 4 C 2 0 834 1 HETATM 5 O 0 3 1 737 1 HETATM 6 O 1 8 0 459 0 HETATM 7 H 0 9 1 398 HETATM 13 H 1 1 737 1 HETATM 8 H 1 0 642 1 HETATM 9 H 2 1 564 0 HETATM 10 H 1 1 41 1 HETATM 11 H 2 0 211 1 HETATM 12 H 2 4 1 06 1 CONECT 1 2 13 CONECT 2 1 3 4 8 CONECT 3 2 5 6 File Formats 259 Protein Data Bank Files CONECT 4 2 9 10 11 CONECT 5 3 CONECT 6 3 12 CONECT 7 1 CONECT 13 1 CONECT 8 2 CONECT 9 4 CONECT 10 4 CONECT 11 4 CONECT 12 6 END The ATOM or HETATM record contains the record name followed by the serial number of the atom being described the element symbol for that atom then the X Y and Z Cartesian coordinates for that atom A CONECT record is
522. y operation about a selected chiral atom CambridgeSoft Setting Serial Numbers To perform an inversion 1 Select the atom 2 From the Structure menu choose Invert The Invert command only repositions side chains extending from an atom For example if you choose Invert for the structure below when C 1 is selected To invert several dihedral angles such as all of the dihedral angles in a ring simultaneously 1 Select the dihedral angles to invert 2 From the Structure menu choose Invert stereochemistry All of the dihedral angles that make up the ring are negated Atoms positioned axial to the ring are repositioned equatorial Atoms positioned equatorial to the ring are repositioned axial Reflection use the Reflect command to perform reflections on your model through any of the specified planes When you choose the Reflect commands certain Cartesian coordinates of each of the atoms are negated When you choose Reflect Through Y Z ChemOffice 2005 Chem3D Plane all of the X coordinates are negated You can choose Reflect Through X Z Plane to negate all of the Y coordinates Likewise you can choose Reflect Through X Y Plane to negate all of the Z coordinates You can choose Invert through Origin to negate all of the Cartesian coordinates of the model If the model contains any chiral centers each of these commands change the model into its enantiomer If this is done all of the Pro R positioned atoms b
523. y sent to MOPAC to override checking of the Z matrix MMOK Automatically sent to MOPAC to specify Molecular Mechanics correction for amide bonds Use the additional keyword NOMM to turn this keyword off SPIN You can add this keyword to print the spin density matrix in the out file RHF Spin Density RHF Spin Density uses the 1 2 electron correction and a single configuration interaction calculation to isolate the alpha spin density in a molecule This method is particularly useful when the UHF Spin Density computation becomes too resource intensive for large molecules For more information see the MOPAC online manual page 28 MOPAC Computations 189 Computing Properties The following table contains the keywords automatically sent to MOPAC and those you can use to affect this property Keyword Description ESR Automatically sent to MOPAC to specify RHF spin density calculation GEO OK Automatically sent to MOPAC to ovetride checking of the Z matrix MMOK Automatically sent to MOPAC to specify Molecular Mechanics correction for amide bonds Use the additional keyword NOMM to turn this keyword off Example 1 The Dipole Moment of Formaldehyde To calculate the dipole moment of formaldehyde 1 From the File menu choose New Model 2 Click the Text Building tool 3 Click in the model window A text box appears 4 Type H2CO and press the Enter key 190 MOPAC Computations A model of formaldehyde a
524. ydrogen atom is a carbon XRH The XRH field contains the optimal value of a bond angle where the central atom of that bond angle is also bonded to one hydrogen atom and one non hydrogen atom In the XRH notation X and R are the same as XR2 and H represents a hydrogen atom bonded to X For example the optimal value of the 1 1 3 angle type for 2 chloropropionic acid is the XRH bond angle of 109 9 since the central carbon C 2 has one attached hydrogen atom The optimal value of the 1 8 1 angle type for N N diethylamine is the XRH value of 107 7 because the central N has Parameter Tables 279 Angle Bending 4 Membered Ring Angle Bending 3 Membered Ring Angle Bending one attached hydrogen atom In this case the XR2 and XRH values for the 1 8 1 angle type are identical As in the N N N triethylamine example above the only attached non hydrogen atom is a lone pair XH2 XH2 is the optimal value of a bond angle where the central atom of that bond angle is also bonded to two hydrogen atoms For example the optimal value of the 1 1 3 angle type for propionic acid is the XH2 bond angle of 110 0 since the central carbon C 2 has two attached hydrogen atoms Record Order When sorted by angle type the order of the records in the Angle Bending table the 4 Membered Ring Angles table and the 3 Membered Ring Angles table is as follows 1 Records are sorted by the second a
525. zed systems hundreds of atoms Systems involving electronic transitions ab initio Gaussian Uses quantum physics Mathematically rigorous no empirical parameters Useful for a broad range of systems Does not depend on experimental data Capable of calculating transition states and excited states Computationally intensive Small systems tens of atoms Systems involving electronic transitions Molecules or systems without available experimental data new chemistry Systems requiring rigorous accuracy Potential Energy Surfaces A potential energy surface PES can describe 132 Computation Concepts e A molecule or ensemble of molecules having constant atom composition ethane for example or a system where a chemical reaction occurs CambridgeSoft Computational Methods Overview e Relative energies for conformations eclipsed and staggered forms of ethane Different potential energy surfaces are generated for e Molecules having different atomic composition ethane and chloroethane e Molecules in excited states instead of for the same molecules in their ground states e Molecules with identical atomic composition but with different bonding patterns such as propylene and cyclopropane Potential Energy Surfaces PES The true representation of a model s potential energy surface is a multi dimensional surface whose dimensionality increases with the nu
526. zero The global minimum represents the most stable conformation the local minima less stable conformations and the saddle points represent transition conformations between minima Single Point Energy Calculations Single point energy calculations can be used to calculate properties of the current geometry of a model The values of these properties depend on where the model currently lies on the potential sutface as follows A single point energy calculation at a global minimum provides information about the model in its most stable conformation A single point calculation at a local minimum provides information about the model in one of many stable conformations Computation Concepts 133 Computational Methods Overview e A single point calculation at a saddle point provides information about the transition state of the model e A single point energy calculation at any other point on the potential energy surface provides information about that particular geometry not a stable conformation or transition state Single point energy calculations can be performed before or after performing an optimization NOTE Do not compare values from different methods Different methods rely on different assumptions about a given molecule Geometry Optimization Geometry optimization is used to locate a stable conformation of a model This should be performed before performing additional computations or analyses of a model

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