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ChemDraw User`s Manual

1. 28 Printing Background Color 28 Macintosh Print Preferences 28 Optimize Pictures for High Resolution Non PostScript Printing 29 Include PostScript 29 Include ChemDraw Laser Prep 29 Scripts Macintosh 30 Closing ChemDraw 30 Chapter 2 Tutorials Tutorial 1 Reaction Schemes 31 Tutorial 2 Drawing an Intermediate 38 Tutorial 3 Using Rings 41 CambridgeSoft Administrator Tutorial 4 Fischer Projections 44 Tutorial 5 Perspective Drawings 49 Tutorial 6 Newman Projections 53 Tutorial 7 Showing Stereochemistry 56 Chapter 3 Drawing Chemical Structures Drawing Settings 59 Configuring Settings for Documents 61 Configuring Settings for Objects 62 Drawing Bonds 62 Multiple Bonds
2. 69 Changing Bond Types 69 Changing Double Bonds 69 Changing Orientation of Wedged and Dative Bonds 69 Changing Alignment of Double Bonds 70 Moving Atoms 70 Changing Bond Crossings 71 Changing the Bond Order 71 Automatic Warnings 71 Chapter 4 Struct lt gt Name Struct Name 73 Auto Update 74 Name Struct 74 Converting Names to Structures 75 Insert Structure 75 Paste Special 75 Converting Captions to Structures 75 Types of Structures Supported by Struct Name 76 Chapter 5 Drawing Captions and Atom Labels Creating a New Line and Closing Text Boxes 79 Formatting Text 80 Setting Font parameters 80 Setting the Baseline Style
3. 23 Setting the Default Document Location 23 Creating a Document 23 Creating a New Document 23 Creating a Document Using a Style Sheet or Sta tionery Pad 23 Opening a Document 24 Setting the Default Open File Format 24 Saving Changes Automatically 24 Reversing and Repeating Actions 25 Undoing Actions 25 Redoing Actions 25 Repeating Actions 25 Discarding Recent Changes to a Document 25 Saving Documents 26 Setting the Default Save File Format 26 Saving a Document with a Different Name or Location 26 Saving a Document in a Different File Format 27 Closing a Document 27 Accessing Documents Quickly 27 The ChemDraw Items Folder 27 The Open Special Submenu 28 The Window Menu 28 Printing
4. 215 Resizing Structures With a Macro 215 Using ChemDraw Excel Functions 215 Using ChemProp Functions 217 ChemProp Properties 217 Inserting Functions 218 Appendices Appendix A Accessing the CambridgeSoft Web Site Registering Online 221 Accessing the Online ChemDraw User s Guide 222 Accessing CambridgeSoft Technical Support 222 Finding Information on ChemFinder com 222 Finding Chemical Suppliers on ACX com 223 Finding ACX Structures and Numbers 223 ACX Structures 223 ACX Numbers 224 Browsing SciStore com 224 Browsing CambridgeSoft com 225 Using the ChemOffice SDK 225 Appendix B Technical Support Serial Numbers 227 Troubleshooting 228 Performance 228 System Crashes 228 Appendix C The Chemistry of ChemDraw Da
5. 80 Specifying Line Spacing 81 Aligning Text 81 Captions 81 Atom Labels 82 Automatic Alignment 82 Changing the Default Caption or Atom Label Text Format 83 Specifying Document Settings for New Text 83 Setting an Individual Text Format Before Typ ing 83 Changing the Spacing of Individual Text Ob jects 83 Fractional Character Widths Macintosh 84 Coloring Text 84 Creating Captions 84 Changing the Caption Width 85 Editing a Caption 85 Adding Analysis Data to a Caption 85 Labeling Atoms with the Text Tool 86 Specifying the Margin Width 86 Editing Atom Labels 87 Deleting an Atom Label 87 Label
6. 62 Double Bonds 63 Double Either Bonds 63 Triple Bonds 63 Quadruple Bonds 63 Drawing Constrained Bonds 64 Drawing with Fixed Lengths 64 Drawing with Fixed Angles 64 Toggling Fixed Lengths and Fixed Angles 64 Dative Bonds and Wedged Bonds 64 Adding a Bond by Clicking 65 Adding Bonds by Dragging 65 Changing the Highlight Box Size 65 Drawing Rings 66 Drawing a Ring 66 Drawing a Ring by Clicking 66 Drawing Cyclohexane Chair Rings 67 Drawing Resonance Delocalized Rings 67 Drawing Cyclopentadiene and Benzene Rings 67 Drawing Acyclic Chains 68 Drawing Chains 68 Adding Chains 68 Changing Chain Direction 68 Editing Bonds
7. 245 Molar Refractivity 246 ClogP and CMR 246 Topological Polar Surface Area 246 Other Properties 246 Appendix F Shortcuts and Hotkeys ChemDraw Hotkeys 252 Appendix G Document Settings ChemDraw Style Sheets or Stationery Pads 256 Appendix H Chemistry File Formats Connection Table File Format 267 ChemDraw 9 Introduction 9 What s New in ChemDraw 9 0 Introduction About ChemDraw ChemDraw is a tool to enable professional scientists science students and scientific authors to communicate chemical structures It is designed to work according to conventions we found most intuitive for such users Our goal has been to make ChemDraw as easy to use as possible while providing superior drawing quality What s New in ChemDraw 9 0 ChemDraw 9 0 is enhanced by the following features Improved Struct Name Significant improvements to the add on that generates systematic names for chemical structures Now with auto update See Struct Name on page 73 Improved Proton NMR predictions Improved display and accuracy See NMR Shift Information ChemNMR on page 147 Improved TLC
8. 144 Expand Generic Structures 145 Spectrum Structure Assignments 146 Assigning Structures to Spectra 146 Viewing Spectral Assignments 146 Removing Spectral Assignments 147 NMR Shift Information ChemNMR 147 ChemDraw 9 Chapter 10 Drawing Query Structures Atom Properties 149 Viewing Atom Property Values 150 Removing Atom Properties 151 Atom Property Options 151 Substituents 151 Implicit Hydrogens 152 Ring Bond Count 152 Unsaturation 153 Reaction Change 153 Reaction Stereo 153 Translation 154 Isotopic Abundance 154 Abnormal Valence 155 Bond Properties 155 Viewing Bond Property Values 156 Remov
9. 95 d orbitals 95 dz2 orbitals 96 The Chemical Symbols Tools Palette 96 H dot and H dash 96 Lone Pair 97 Radical 97 Radical Cation and Radical Anion 97 Charge Symbols 98 Attachment Points 98 Rotating a Symbol 98 The Arrow Tools Palette 99 Drawing an Arrow 99 Editing an Arrow 99 The Drawing Elements Tools Palette 99 Drawing Boxes 100 Drawing Circles and Ovals 100 Resizing or Rotating Drawing Elements 100 Distorting Circle and Ovals 100 Drawing Lines 101 The Brackets Tools Palette 101 Drawing Single Brackets
10. 114 Flatten Command 114 Reflecting Objects Through Planes 115 Flipping Objects 115 Creating Mirror Images 115 Resizing Objects 115 The Resize Handle 116 Scaling Objects 116 Distorting a Selection 117 Joining Objects 117 Grouping Objects 118 Ungrouping Objects 118 Creating Integral Groups 118 Chapter 8 Advanced Drawing Techniques Using Nicknames 121 Applying Nicknames 121 Defining Nicknames 122 Troubleshooting Nicknames 123 Viewing Nicknames 124 Deleting Nicknames 124 Contracting Labels 124 Expanding Labels 125
11. 134 Fusing a Template With an Existing Structure 134 Drawing with the Same Template 134 Creating Templates and Template Documents 134 Creating Templates 135 Orientation of Templates 135 Resizing Template Panes 136 Template Panels 136 Saving Template Documents 136 Chapter 9 Working With Structures Checking Chemistry 137 Check Structure 137 Check Structure when Copying to Clipboard or Exporting 138 Viewing Analysis Information 138 Showing Stereochemistry 139 Stereochemistry Indicators 140 Hiding Indicators 140 Removing Indicators 140 Positioning Indicators 140 Converting Structures to 3D 141 Viewing Chemical Properties 141 Viewing the Chemical Properties Window 141 Mass Fragmentation Tool 143 Drawing Reactions
12. 108 Chapter 7 Manipulating Drawings Using a Selection Tool 109 Selecting Objects with the Lasso Tool 109 Selecting Objects with the Marquee Tool 109 Toggling Between Selection Tools 110 Toggling Between Other Tools 110 Selecting Objects by Clicking 110 Setting the Highlight Box Tolerance 110 Selecting Entire Structures 111 Making Multiple Selections 111 Removing Objects from the Selection 111 Selecting All Objects 111 Deselecting All Objects 111 Deleting Objects 111 Moving Objects 111 Using the Clipboard 112 Cutting 112 CambridgeSoft Administrator Pasting 112 Moving Atoms 112 Duplicating Objects 113 Rotating Objects 113 Structure Perspective
13. Plugin supports Mozilla 1 0 x to 1 2 x and Netscape 7 0 Screen resolution must be 800 x 600 or higher Site License Network Installation Instructions If you have purchased a site license please see the following web site for network installation instructions http www cambridgesoft com services sl Software Developer s kit http sdk cambridgesoft c om ActiveX control http sdk cambridgesoft c om Purchasing CambridgeSoft products and chemicals http chemstore cambridg esoft com For information about Access 12 Introduction CambridgeSoft Installation and System Requirements Administrator ChemDraw 9 ChemDraw Basics 13 The ChemDraw Graphical User Interface Chapter 1 ChemDraw Basics Overview The information required to begin using ChemDraw includes how to do the following Identify the parts of the ChemDraw interface Customize parts of the user environment Create open and save documents Set printing preferences The ChemDraw Graph ical User Interface Although the Macintosh and Windows versions of the ChemDraw graphical user interface GUI differ slightly the essential GUI consists of the same elements The Windows version of Chem Draw is shown below Title bar Menu bar Main tool palette General toolbar Text style toolbar Minimize button Maximize button Close button Object toolbar Magnificat
14. Right click select the property you want and then click the appropriate option From the Structure menu choose Atom Properties The Atom Properties dialog box appears Pro Pro 150 Drawing Query Structures CambridgeSoft Atom Properties Administrator Press the Hotkey The Atom Properties dialog box appears In the Atom Properties dialog box select the properties to associate with the selected atom s Click OK Query indicators appear next to atoms that have associated atom properties The character that appears depends on which query properties have been assigned If more than one property is assigned more than one character appears adjacent to the atom For more information see Query Indicators on page 160 The atom property indicators are shown in the following table Viewing Atom Property Values Except for the three Substituents query properties the characters indicate that a given property is applied but not the value of that property To find the value of a query property setting 1 Select the atom 2 Do one of the following Right click point to an atom and then point to the appropriate property Indicator Query Property Substituents Free Sites followed by the number of free sites T C S R 2HS X3 U Substituents Up to followed by the maximum number of substituents X Substituents Exactly followed by the number of
15. Working with Color With the color capabilities of ChemDraw you can create full color presentations of your chemical drawings to appear on your monitor print on a color printer or create 35mm slides using a film printer Most computers can display any of 16 million colors but the number of colors that can appear at any one time may be limited by the particular monitor and display card installed in your computer In ChemDraw you can choose from a palette consisting of a Background Color a Foreground Color and up to twenty additional colors for any given drawing A palette is stored in every document and Style Sheet or Stationery Pad You can use Style Sheets or Stationery Pads to create a series of documents with the same color scheme Using color you can Color atoms and bonds in a mostly black on white drawing to highlight areas of interest Before After Cl HO O Cl OH O 130 Advanced Drawing Techniques CambridgeSoft Working with Color Administrator Color parts of a structure in a reaction scheme to indicate where starting materials end up in the products of a complicated mechanism Use colored boxes and circles to highlight atoms or molecules Create slides that are easier to view by using light objects on a dark background Coloring Objects Any object that you can select with a selection tool can be colored You can color individual bonds part or all of a chemical s
16. png PNG Portable Network Graphics format is an alternative to the GIF format for adding graphics to web pages You can save but not open files in PNG format The PNG format is fairly new and was designed to address many of the shortcomings of the GIF format In particular the PNG file format offers true color images is less prone to transmission errors and offers a full alpha channel for specifying background or transparency options For additional information about PNG visit http www boutell com boutell png SMD smd Standard Molecular Data SMD file format version 4 3 is an ASCII text file commonly used by programs that search Chemical Abstracts Data bases such as STN Express You can save your ChemDraw document in SMD format and use the file for searching in a Chemical Abstracts database SPC spc Import Only The SPC file format was developed by Galactic Industries as part of the GRAMS software which reads spectral data from every type of spectrometer and converts them to SPC format SPC is a well defined proprietary but open standard format for spectral data ChemDraw imports most one dimensional spectral spc formats When you import an SPC file it appears in the window with a spectrum of a stan dard size that can be re sized by dragging You can export spectral data as part of a cdx file only Template Style Sheet cts The Template Style Sheet file format is used for saving document
17. 101 Drawing Paired Brackets 101 Drawing Daggers 101 Framing Objects 101 The Arc Tools Palette 102 Drawing Arcs 102 Editing Arcs 102 The Pen Tool 102 Drawing B zier Curves by Dragging 103 Drawing Segments by Clicking 103 Editing a Curve 104 Changing the Shape of a Curve 104 Adding a Segment 104 Deleting a Segment 105 Applying a Style to a Shape 105 Filled and Closed Styles 105 Shaded Style 105 Plain Style 105 The TLC Tool 105 Rf Display 107 Resizing Spots 108 Custom Spots
18. CHMS and the creator should be CHMD ChemDraw 9 ChemDraw Excel 207 Setting Up ChemDraw Excel Chapter 13 ChemDraw Excel The ChemDraw Excel add in is an extension of Microsoft Excel for Windows Chem Draw Excel enables you to Add chemical structures and other data from ChemDraw or a ChemFinder database to an Excel spreadsheet Search using the same search features as ChemFinder Perform calculations on chemical structures See the ChemOffice manual for information on other CambridgeSoft add ins for Excel NOTE Any commands you use operate on the cells not the pictures in the cells Setting Up ChemDraw Excel When you install ChemFinder ChemDraw Excel is automatically installed Before you use Chem Draw Excel for the first time do the following 1 From the Tools menu select Add Ins The Add Ins dialog box appears 2 In the Add Ins dialog box check the ChemDraw for Excel checkbox and click OK A ChemOffice menu is added to the Excel menu bar and a ChemOffice tool bar appears 3 From the Tools menu point to Macro and select Security The Macro Security dialog box appears 4 In the Macro Security dialog box click the Security Level tab and set the security level to Medium NOTE ChemDraw Excel no longer requires this step You must set security to Medium only if you will be using ChemDraw Excel worksheets from version 8 or earlier without conversion 5 Click OK to sa
19. ChemDraw 9 Manipulating Drawings 109 Using a Selection Tool Chapter 7 Manipulating Drawings Overview The Lasso or Marquee tools enable you to select objects to edit You can select objects individually or as groups You can then duplicate move resize rotate or delete the selected objects Using a Selection Tool You can use the Lasso or the Marquee selection tool to select all objects You use the Lasso to select objects freehand and the Marquee to select rectangular regions You can set ChemDraw so that the last object drawn to selected when you click the Lasso tool To set this option 1 From the File menu choose Preferences 2 On the General tab select Automatically Select Recent Objects When Choosing Lasso When you click the Lasso tool a selection rectangle appears around the last object drawn Selecting Objects with the Lasso Tool Use the Lasso tool to make freehand selection of irregular areas To select objects using the Lasso tool 1 Select the Lasso tool 2 Press the mouse button while the pointer is not over any object 3 Drag around a portion of a chemical structure or other object As you drag a line appears which defines the Selection area Bonds structures or other objects are selected only if they are entirely within this area The end points of the Lasso are automatically connected when you release the mouse button Selecting Objects with the Marquee Tool Use t
20. ChemFinder moves to the front 2 Open a database and perform a search 3 Return to Excel and from the ChemOffice menu select Get ChemFinder List or click Form has no database or hitlist has no records Load a database and perform your search Then return to Excel and redo the operation 1 Click OK ChemFinder moves to the front 2 Open a database and perform a search 3 Return to Excel and from the ChemOffice menu select Get ChemFinder List or click Exporting Tables ChemDraw Excel allows you to export tables to MDL SDFiles Selected cells are exported to a specified file If no cells are selected the entire spreadsheet is exported The first column of the area to export must have the word Structure in its top cell Structures out side the first column will be discarded To export data 1 Select the information to export 2 From the ChemOffice menu select Export Table or click The Save Table To dialog box appears 3 Type the file name and click Save The table is saved to the specified file Adding Structures You can add chemical structures from any file for mat supported by ChemDraw to a spreadsheet The names of added structures are retained If the struc ture does not have a name ChemDraw assigns the name Structure lt n gt where n is a number unique to the worksheet If you want to export Then a specified area of your spreadsheet Select the area to export the en
21. Documents are the ChemDraw workspace where you create and manipulate structures You can create a new document or open an existing docu ment and edit it Setting the Default Docu ment Location You can set what file location is shown in the Open dialog box by using the Preferences dialog box To set the default location 1 From the File menu choose Preferences The Preferences dialog box appears 2 Click the Directories tab 3 Click the checkbox next to Use Documents Location and type in or browse to the location to use If Use Documents Location is not selected the first time you use the Open dialog box your My Docu ments folder is shown Subsequent uses show the last directory used Creating a Document You can create a new blank document using the ChemDraw default settings or use a Style Sheet or Stationery Pad with customized settings Creating a New Document To create a document From the File menu click New Document Creating a Document Using a Style Sheet or Stationery Pad To create a new document using a different Style Sheet or Stationery Pad 1 From the File menu click Open Special 2 Choose a Style Sheet or Stationery Pad from the list A new document is created with the settings and objects stored in the Style Sheet or Statio nery Pad If you want to apply the settings to the Then click selected object only No selected object and any new objects you draw
22. Front to Back Ordering on page 185 Another way to layer bonds is to use the Hotkey f NOTE You can magnify your view to make changing the bond layering easier For more information see Changing Perspectives on page 181 Changing the Bond Order You can reduce or increase the order of bonds in a structure by using the Bond Properties dialog box or with the shortcut menus as follows To reduce the bond order 1 Point to the bond to change and Right click or Control click 2 Choose the appropriate bond type from the shortcut menu that appears To use the eraser tool to reduce the bond order 1 Click the Eraser tool 2 Click a single double or triple bond The bond order is reduced by one To change the bond order using Hotkeys 1 Click a selection tool 2 Point to a bond 3 Type a number from 1 to 4 to change the order Automatic Warnings ChemDraw automatically checks for correct chemical syntax as you draw If ChemDraw finds a potential problem a wavy red box is displayed around the questionable object The red box is displayed on screen only and does not print 72 Drawing Chemical Structures CambridgeSoft Automatic Warnings Administrator To enable the automatic display of chemical warnings On the View menu choose Show Chemical Warnings This setting applies to all documents To view a description of the problem do one of the following Point at the warning
23. Narrow Abnormal Valence Not Allowed X X X Allowed X X X Bond Properties Bond Type Single X X X Dashed X X X Hashed d d d Exported Query Properties ISIS Mol Rxn 174 Drawing Query Structures CambridgeSoft Export Compatibility Administrator Wedged Hashed X X X Bold X e e Wedged X X X Wavy X X X Hollow Wedged e e e Dative f f f Double Xg Xg Xg Double Either X X X Double Bold h h h Aromatic X X X Tautomeric i i i Triple X X X Quadruple l l l Any X X X S D X X X D A X X X Exported Query Properties ISIS Mol Rxn S A X X X Topology Unspecified X X X Ring X X X Chain X X X Reaction Center Unspecified X X Center X X Make Break X X Change X X Make amp Change X X Not Center X X Other Query Attributes Generic Nicknames Xj Xj Xj Element Lists Xko Xko Xko Element Not Lists Xk Xk Xk Exported Query Properties ISIS Mol Rxn ChemDraw 9 Drawing Query Structures 175 Export Compatibility a Converted to the appropriate number of exact substituents b Free Sites counts of zero translated to Substitution as drawn all other Free Sites values written as substitution counts equal to the total current valence plus the free sites value c Substituent counts of greater than 5 are translated to 6 or more d
24. Pro Pro ChemDraw 9 Sharing Information 201 Importing and Exporting For single step single or multi line reactions Chem Draw uses the point of the reaction arrow as the dividing line to determine which molecules in a reaction are reactants and which are products NOTE You cannot save a reaction with an intermediate step accurately in the RXN file format Molecules whose centers are behind or above the tip of the arrow are considered reactants and all remaining molecules are products The reaction arrow can be at any orientation it does not have to be parallel to the x axis If a reaction contains multiple arrows then the largest arrow is used as the reaction arrow Reaction mapping and reaction center information is stored in the rxn output file JDX jdx dx Import Only The Joint Commission on Atomic and Molecular Properties JCAMP developed the JDX file format for spectral data JDX is a public but not well defined format that has numerous variations ChemDraw supports many of the more common spectral variations with uniform x axis spacing ChemDraw also supports Bruker NMR JCAMP data which is saved with a dx file extension When you import JDX files they appear in the window with a spectrum of a standard size that can be re sized by dragging You can export spectral data as part of a cdx file only JPEG jpg jpeg Import Only ChemDraw supports import of digital images compressed with th
25. The program handles the following elements H D He Li Be B C N O F Ne Na Mg Al Si P S Cl Ar K Ca Sc Ti V Cr Mn Fe Co Ni Cu Zn Ga Ge As Se Br Kr Rb Sr Y Zr Nb Mo Tc Ru Rh Pd Ag Cd In Sn Sb Te I Xe Cs Ba La Ce Pr Nd Pm Sm Eu Gd Tb Dy Ho Er Tm Yb Lu Hf Ta W Re Os Ir Pt Au Hg Tl Pb Bi Po At Rn Fr Ra Ac Th Pa U Nep Pu Am Cm Bk Cf Es Fm Md No Lr Functional groups are expanded automatically In case of 1H NMR it estimates shifts of about 90 of all CHx groups with a standard deviation of 0 2 0 3 ppm The use of polar solvents may strongly increase these deviations It does not estimate shifts of hydrogen atoms bonded to heteroatoms because they are significantly affected by solvents concentration impurities and steric effects In case of 13C NMR it estimates over 95 of the shifts with a mean deviation of 0 29 ppm and standard deviation of 2 8 ppm For more information see F rst A Pretsch E Anal Chim Acta 1990 229 17 Pretsch E F rst A Badertscher M B rgin R Munk M E J Chem Inf Comp Sci 1992 32 291 295 Ultra Ultra 244 How ChemNMR Works CambridgeSoft ChemNMR Limitations Administrator B rgin Schaller R Pretsch E Anal Chim Acta 1994 290 295 B rgin Schaller R Arnold C Pretsch E Anal Chim Acta 1995 312 95 105 B rgin Schaller R Munk M E Pretsch E
26. To display a tools palette do one of the following From the View menu select Other Toolbars then select one of the palettes Click the tool s icon and drag to the palette s title bar Release the mouse button over the title bar The selected palette is displayed and can be dragged anywhere on the screen 94 Drawing Orbitals Symbols Arrows Arcs and Other Shapes CambridgeSoft The Orbital Tools Palette Administrator The Orbital Tools Palette Use the Orbital tools to add orbitals to your chemical structures You draw orbitals so that the node appears first Depending on the orbital type available fill patterns are Background color Shaded Solid color You can modify the fill colors with the Color menu Display the Info window to view the orbital s length and angle relative to the X axis while you draw it You can constrain the length and angle of an orbital by selecting Fixed Lengths and Fixed Angles on the Object menu NOTE Orbitals are not normally part of the structure they are drawn near and are not selected when you double click a bond atom or atom label with a selection tool To group the orbitals with the structure use the Group command from the Object menu For more information see Grouping Objects on page 118 s orbitals The s orbital tools are shown below To draw an s orbital 1 Hold down the mouse button over the Orbital tool and drag to sele
27. To move in a larger increment Press Alt or Option plus an arrow key The selected objects move 10 points in the direction of the arrow For more information about aligning objects see Chapter 11 Working With Page Layout Using the Clipboard Use the Clipboard to remove the objects contained in the Selection rectangle for later use You can paste the copy from the Clipboard to another position in the same document to another ChemDraw document or to a different type of document Cutting To use the clipboard 1 Select the object with a Selection tool 2 From the Edit menu choose Cut The object is transferred to the Clipboard and deleted from a document window Pasting To paste a copy of the contents of the Clipboard into a document window 1 Click a Selection tool 2 From the Edit menu choose Paste For information about transferring ChemDraw pictures to other types of documents see Autoscaling on page 193 Moving Atoms You can move the atoms within a chemical structure using a selection tool To move a single atom 1 Point to an atom using a selection tool 2 Drag the atom The bonds connected to the atom stretch To move multiple atoms Select only the bonds that have atoms on both ends that you want to move ChemDraw 9 Manipulating Drawings 113 Rotating Objects The unselected bonds that are attached to the selected atoms are stretched NOTE You can also
28. To scale objects by a percentage 1 Click Scale by 2 Type the percentage in the box to the right of the button 3 Click Scale This is the only available option when the selection does not contain any atoms or bonds Distorting a Selection In most cases when you resize an object the aspect ratio of the object the ratio of the height to width does not change However it is possible to change the aspect ratio distort of certain objects including chemical structures circles boxes and ovals To distort an object in the horizontal or vertical direction 1 Select the object and Shift drag the Resize handle Shift modifies the resize operation so that you can distort objects along the X axis or Y axis 2 Drag the Resize handle in the desired direction Joining Objects Use the Join command in the Object menu to fuse two chemical structures together Once structures are joined they can be easily selected by double clicking To join chemical structures along the length of a bond 1 Select a bond or atom in one of the molecules 2 Shift click to select the corresponding bond or atom on the second molecule that you wish to fuse 3 From the Object menu choose Join The structures are joined To join chemical structures at one atom to create a spiro linkage 1 Position the two chemical structures so that the atoms you wish to fuse are more or less opposite each other NOTE While you no longer ha
29. Yes SetDefaults 150 dpi Default document location 24 ChemDraw Basics CambridgeSoft Using Documents Administrator ChemDraw provides pre defined Style Sheets or Stationery Pads located in the ChemDraw Items folder For example the ACS Document 1996 is configured to create documents that are set with the bond lengths bond width spacing and fonts used in the 2 column format of all American Chemical Society journals For a list of the settings stored in these documents see Appendix G Document Settings NOTE Predefined Style Sheets or Stationery Pads may restrict your options in unexpected ways For example not all Save As format options are available in all Style Sheets or Stationery Pads For general use you should stay with the default Style Sheet or Stationery Pad Opening a Document To open a document From the File menu do one of the following Choose Open and in the Open dialog box select the name and location of the file and then click Open or OK Choose the document from the list of previ ously opened documents at the bottom of the menu Setting the Default Open File Format You can set what file format is selected by default in the Open dialog box To set the default file format 1 From the File menu choose Preferences The Preferences dialog box appears 2 Click Open Save 3 In the Opening Files section click Use Default File Format and choose the format
30. 2 From the File menu choose Save As 3 Type tut6 cdx in the appropriate text box 4 Select a folder in which to save the file 5 Click Save Create the first bond 1 Click the Solid Bond tool 2 Point in the document window and drag downward to create the first bond 3 Continue pointing at the lower atom and click again to add a second bond 54 Tutorials CambridgeSoft Tutorial 6 Newman Projections Administrator 4 Continue pointing at the same atom and click again to add a third bond 5 Click the Lasso tool The last structure you drew is automatically selected 6 Point within the Selection rectangle and hold the Ctrl or Option key 7 Hold the mouse button and drag a copy of the structure diagonally upward to the right of the original 8 Release the mouse button and depressed key when the copy is positioned Add a bond between the duplicated structures 1 Click the Solid Bond tool 2 Point to the central atom of the lower fragment NOTE When connecting existing atoms the Fixed Length and Fixed Angles commands are ignored 3 Click and drag to the central atom of the upper fragment 4 Release the mouse button when the highlight box over the central atom appears In this step you will use the Orbital tool to draw the hollow circle that is particular to Newman Projections rather than an orbital 1 Click the Orbital tool 2 Click the unfilled s orbital 3 Poi
31. 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 CS 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 loss in 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 CS 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 with 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 A
32. Administrator If the cell contains a valid SMILES string it is replaced by a structure The cell will display a text string starting with Structure and followed by a number To display the structure click the Show Picture icon If the cell did not contain a valid SMILES string the string remains Adding Structures by Name You can type or paste the names of chemicals into cells and convert them into structures as follows 1 Enter the names into cells 2 Select the range of cells to convert NOTE If you want to keep the original text copy it and paste it elsewhere Note that this command can also convert names generated from Excel formulas 3 From the ChemOffice menu select Convert Name To Molecule or click If the cell contains a name supported by ChemDraw Name Struct the structure corresponding to that name is added to the cell with the given name as the name of the cell To show the structure select the cell and choose Show Picture from the ChemOffice menu For more information about Name Struct see the ChemDraw User s Guide Saving Structures You can save a chemical structure to a separate file 1 In the spreadsheet select the cell containing the structure 2 From the ChemOffice menu select Save Molecule or click The Save to File dialog box appears 3 Select an existing file or enter a new file name and click Save The structure is saved with the name and in the location you sele
33. Administrator infinite number of substituents Generic nicknames have meaning only in the context of the search system you are using The generic nicknames recognized as chemically meaningful to ChemDraw are listed in Generic Nicknames file in the ChemDraw Items folder For definitions of the nicknames see Nickname Definitions in the Help file To edit the generic nickname files Open the Generic Nicknames file in a text editor and make your changes See the provided Generic Nicknames file for examples of the correct format To label an atomic position with a generic nickname use the same procedures as labeling an atom 1 Do one of the following Open a text box on an atom position by clicking with the Text tool Double click on an atom position with a Bond tool 2 Type the generic nickname 3 Press Return or click outside the text box NOTE If you perform Check Structure on a structure with a generic nickname a message is displayed because the structure contains variable substituents If you ignore this message the generic nicknames are ignored and ChemDraw reports the chemical formula mass and so on as if the atom label containing the generic nickname were not selected Element Lists You can define your search query more concisely with the element list By labeling an atom position as a list of elements you specify that one of these elements must match in the structure for which you ar
34. Atom labels and captions do not flip along with the object To reflect an object through a plane perpendicular to the Y axis 1 Select the objects to reflect 2 From the Object menu choose Flip Vertical Creating Mirror Images You can create mirror images from structures with defined stereochemistry by duplicating the structure and then rotating it To create a mirror image 1 Draw a structure with defined stereochemistry for example wedged bonds 2 Select the structure and make a copy with Ctrl Drag or Option drag 3 While the copy of the structure is still selected choose Flip Horizontal or Flip Vertical from the Object menu You can also preserve the absolute stereochemistry while flipping by using the Rotate 180 commands on the Object menu Resizing Objects You can resize objects by dragging the resize handle of a selected object or by scaling If all objects in the document window are part of the selection after H3C OH CH3 HO H3C OH H3C OH CH3 HO H3C OH Rotate 180 Horizontal Rotate 180 Vertical 116 Manipulating Drawings CambridgeSoft Resizing Objects Administrator you resize a message appears asking whether you want to change the document settings for that document If you do so all subsequent bonds atom labels and captions are drawn using the new settings The Resize Handle To resize an object or collection of objects 1 Select the o
35. CMYK Planar Uses printing press style of color encoding Groups each color type sequentially This provides better compression For example CCCCCC MMMMMMYYYYYYKKKKK rather than CMYKCMYKCMYKCMYK This option produces far better compression than using the PackBits compression method However many desktop publishing packages do not support CMYK Planar files CMYK Contiguous Uses printing press 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 black and white 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 Compression You can select from the following compression options PackBits Used to reduce files size by encoding repeating bytes of information as output when using the CMYK Planar color option Below is a highly simplified representa tion of this compression scheme For a line of color information such as CCCCC MMMMMYYYYYKKKKK the compression yields a smaller file by representing the infor mation as C46M5Y5K CCITT Group 3 Used for fax transmissions of images CCITT Group 4 Used for fax transmissions of images Deflate Similar to LZW compression Works well with all Color and Re
36. ChemDraw does not install its own fonts If a ChemDraw document contains fonts that are not available on a particular computer they are substi tuted with available fonts Creating a New Line and Closing Text Boxes The default way to create a new line in a caption text box is with the Enter or Return key The default way to create a new line in an atom label is with Alt Enter or Option Return To close the text box click outside the text box or select another tool phenol OH Caption Text phenol OH Atom Label Text 80 Drawing Captions and Atom Labels CambridgeSoft Formatting Text Administrator To change the default do the following 1 From the File menu choose Preferences NOTE In Mac OS X the Preferences dialog box is found on the ChemDraw menu 2 On the General tab choose the appropriate option 3 Click OK Formatting Text Text settings affect how captions and atom labels for the current document are drawn and formatted Formatting options include Font font type Size font size Style font and baseline style Line spacing Alignment These options are described in the following sections Setting Font parameters Changing text formats in the Document Settings dialog box affects the current document only You can also change settings for individual objects by using the Object Settings dialog box the Text menu or the Style toolbar To edit the d
37. J Chem Inf Comput Sci 1996 36 239 243 ChemDraw 9 How ChemProp Works 245 LogP Appendix E How ChemProp Works ChemProp Values ChemProp enables you to calculate predicted values of selected physical and thermodynamic properties for structures of up to 100 atoms The following topics describe how ChemProp obtains its values LogP LogP partition coefficient for n octanol water three fragmentation methods are used to predict the logP values Method one is based on 94 atomic contributions evaluated from 830 molecules by least squares analysis This method works with a standard deviation of 0 47 logP units and can handle molecules containing hydrogen oxygen nitrogen sulfur and halogens 1 Method two is an extension of method one that is based on 120 atomic contributions evaluated from 893 molecules by least squares analysis In addition to the atoms introduced for method one it can handle molecules that contain phosphorus and selenium atoms This method works with a standard deviation of 0 50 logP units 2 Method three is based on 222 atomic contributions calculated from 1868 molecules by least squares analysis This method allows a calculation of logP with a standard deviation of 0 43 logP units and can handle molecules containing hydrogen oxygen nitrogen sulfur halogens and phosphorus atoms If this method is applied to molecules with internal hydrogen bonds the standard deviation is 0 83 logP u
38. Polypeptide builder with residue recognition ChemProp Basic property predictions with Connolly volumes amp surface areas MM2 minimization amp molecular dynamics extended H ckel MO calculations Supports PDB MDL Molfile Beilstein ROSDAL Tripos SYBYL MOL EPS PICT GIF 3DMF TIFF PNG amp more MOPAC Chem3D Advanced Semi Empirical Computation Calculate Hf solvation energy dipoles charges UHF amp RHF spin densities MEP charge densities amp more Optimize transition state geometries AM1 PM3 MNDO amp MINDO 3 methods CAMEO ChemDraw Synthetic Reaction Prediction Expert system predicts and displays products ChemDraw creates starting materials when you choose reaction conditions sold separately Chem3D Plugin Advanced WWW Model Client Works with Microsoft Internet Explorer Visualize 3D molecules on ChemFinder Com SYSTEMS amp LANGUAGES Windows amp Macintosh English amp 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 Chem3D Ultra Ultimate Modeling Visualization amp Analysis Adds MOPAC CLogP Tinker ChemProp ChemSAR amp Chem3D Plugin to Chem3D Pro Includes GAMESS amp Gaussian client interfaces ChemSAR Excel builds SAR tables S O F T WA R E EMAIL info cambridgesoft com WWW www cambridgesoft com TEL 1 800 315 7300 INT L 1 617 588 9300
39. Shift that object is deselected 3 From the Object menu choose Group NOTE You can select individual objects within a group by clicking them Use the Text tool to create a caption containing the name and amount of reactant and then center the caption under the structure 1 Click the Text tool 2 Point below the first structure 3 Click to create a text box The default cursor is flush left 4 From the Text menu choose Centered The cursor moves to the center of the text box Type the caption 1 Type 2 propanone OH O O OH O O OH OH O O O 2 propanone O ChemDraw 9 Tutorials 37 Tutorial 1 Reaction Schemes 2 Press the Enter or Return key to insert a new line 3 Type 2 moles Create an aligned caption for the other structure 1 Press the Tab key to create another Text box that is aligned adjacent to the first NOTE You can use the Tab key in the caption mode of the text tool to create multiple aligned captions with the same font font size style and justification as the previous caption 2 Type 4 hydroxy 4 methyl 2 pentanone press the Enter or Return key and then type 1 mole If your captions are not aligned properly beneath the structures you can move them using a selection tool 1 Click a Selection tool Lasso or Marquee The text box is automatically selected because it is the last object drawn NOTE The object that is automatically sele
40. This is part of the autoscale feature For more information see Autoscaling on page 193 Saving Color Palette Settings You can save the Color Palette in a Style Sheet or Stationery Pad The Color Palette is saved in addition to other document settings such as Page Setup settings Text settings and Drawing settings Drawing With Templates Template documents are collections of structures organized by structural type or functionality A structure in a Template document is named a template Use an existing template instead of drawing the structure to shorten the time required to create documents The Template documents distributed with ChemDraw are stored in the ChemDraw Items folder in the same folder as the ChemDraw application NOTE In ChemDraw Pro you can define your own commonly used structures as templates Any Template documents in the ChemDraw Folder are listed in the Windows menu Macintosh or Open Special on the File menu Windows The Templates Tool The Templates tool contains a palette from which you can select different types of structures or objects The Templates tool has two levels The first level displays the available Template documents The second level displays the templates within each Template document NOTE In ChemDraw Pro the pop up menu is segmented if any Template documents are open for editing The upper segment contains Template documents that are currently open for ed
41. This option scales all objects and text in the document window by the percentage specified This is not a change in magnification The size of objects is changed relative to the paper size margins and orientation you have specified The enlarge or reduce option is useful for changing the size of the available drawing area while keeping the images on the screen at the normal size when you are drawing If your document is set so that the drawing fills the page on one printer and you use another printer that requires larger margins the drawing my disappear off the edge of the document window You can reduce the size of the drawing with the reduce option so that it fits in the document window Paper Type Dimensions US Letter 8 5 x 11 inches US Legal 8 5 x 14 inches A4 Letter 21 x 29 7 cm B5 Letter 17 6 x 25 cm Tabloid 11 x 17 inches International 8 5 x 12 inches Computer 14 x 11 inches ChemDraw 9 Working With Page Layout 181 35mm Slide Boundary Guides Saving Page Setup Settings You can save Page Setup settings in a Style Sheet or Stationery Pad Whenever you open a Style Sheet or Stationery Pad these settings are automatically used The Page Setup settings are saved in addition to the Text settings Drawing Settings and the Color Palette 35mm Slide Boundary Guides If you make 35mm slides from a hard copy of a ChemDraw document or from a screen shot you can display boundary lines that appear on y
42. To change the ordering of the attachment points do one of the following Click the attachment points with the Attachment Point tool Select an attachment point with a selection tool and from the Object menu choose Bring to Front or Send To Back The attachment point numbers are highest in the front Lists You can use an R Group table to construct a list of molecules Anonymous Alternative Groups An anonymous alternative group is a cross between an element list and an alternative group Element lists are restricted to single elements but anonymous alternative groups can contain any structure that can be represented by text Nicknames and generic nicknames are allowed in anonymous alternative groups Anonymous alternative groups are shortcut notation for regular alternative groups eliminating the need to specify a name such as R1 You can define your search query more concisely with the anonymous alternative group By labeling an atom position as a list of substructures you specify that one of these substructures must match in the structure for which you are searching Commas must separate the items in the anonymous alternative group A space after each comma and the brackets are optional Examples of anonymous alternative groups follow To create anonymous alternative groups 1 Open an atom label text box 2 Type an open bracket followed by a list of elements fragments nicknames or generi
43. and click OK 28 ChemDraw Basics CambridgeSoft Printing Administrator A new path is added to the list 4 To rearrange the search order use the Move Up and Move Down buttons 5 To delete a path click the Remove button To delete all added paths click the Default Paths button The Open Special Submenu To select documents from the ChemDraw Items folder On the File menu point to Open Special and select the file to open The Open Special submenu listing documents stored in the ChemDraw Items folder appears The Window Menu The Window menu lists all open ChemDraw and Template documents The document you choose from the Window menu becomes the active window Printing ChemDraw uses the standard system commands to print ChemDraw documents The options that you have available to you depend on the printer that you are using Refer to your printer s documentation for more information In general to print a ChemDraw document 1 From the File menu choose Page Setup 2 Make all appropriate selections for the printer you are using and click OK 3 From the File menu choose Print 4 Make your selections in the Print dialog box and click OK To print a document from the Explorer or from the Finder 1 Select the document you want to print 2 From the File menu choose Print The ChemDraw application is opened and the Print dialog box appears 3 Make your selections in the Print dial
44. b Select the Object Type c Click OK insert an existing graphic a Click Create from File b Type the path or browse to the object to insert c Click OK InsertObject 155 dpi ChemDraw 9 Sharing Information 205 Transferring ChemDraw Documents Across Platforms Transferring ChemDraw Documents Across Plat forms Use the following procedures to transfer Chem Draw documents across platforms From the following table determine the versions of the ChemDraw software between which you want to transfer documents and then follow the appropriate instructions When you transfer ChemDraw files across plat forms fonts are not transferred If a font in the transferred document is not available ChemDraw substitutes fonts for those that are available on the new platform Transferring from Macintosh to Windows To be able to open a ChemDraw file created on the Macintosh in Windows follow the instructions for the appropriate versions shown in the table below Transferring from Windows to Macintosh To be able to open a ChemDraw file created in Windows on the Macintosh follow the instructions for the appropriate versions shown in the table below Transferring Files to ChemDraw Plus 3 1 for the Macintosh Use the following procedure to transfer a Chem Draw for Windows file to ChemDraw Plus 3 1 for the Macintosh A file translator such as PC Exchange or Apple File Exchange must be running on your Macintosh
45. by offset hori zontal and vertical at specified coordinates absolute hori zontal and vertical 92 Drawing Captions and Atom Labels CambridgeSoft Using Bitmap Fonts When Available Macintosh Administrator Press Ctrl Alt Tab or Command Option Tab The text box is automatically selected when you switch to the lasso tool To switch from the Lasso tool to the Text tool when a caption or atom label is selected Press Ctrl Alt Tab or Command Option Tab The Text tool is selected and the text box is opened for editing NOTE Ctrl Alt Tab and Command Option Tab will always toggle between the Lasso and last tool used Using Bitmap Fonts When Available Macin tosh When text appears in a document on the screen it can appear using either a bitmap or a TrueType font To use bitmap fonts if they are available 1 From the File menu choose Preferences 2 Select Use Bitmap Fonts When Available Text drawn using Bitmap fonts looks better and appears more quickly than text drawn using True Type fonts However the size and position of text drawn using Bitmap fonts change somewhat when printed For accurate correspondence between what you see on the screen and what is printed Deselect Use Bitmap Fonts When Available This change affects all documents ChemDraw 9 Drawing Orbitals Symbols Arrows Arcs and Other Shapes 93 Chapter 6 Drawing Orbitals Symbols Arrows Arcs and Other S
46. choose Expand Label Your structure is redrawn in its expanded form Multi Attached Labels Multi attached atom labels enable you to draw chemical structures more efficiently by allowing you to attach bonds anywhere along an atom label Adding Bonds to an Atom Label To add bonds to an atom labels 1 Draw the structure and attach any necessary atom label 2 Select a Bond tool 3 Position the cursor where you want to attach additional bonds The selected part of the atom label is highlighted Pro Pro Ph CH2CH2CHCH3 CH3 Contracted Form Expanded Form H2 C CH2 NH CH3 O CH2CH2NHCH2CH3 O Expanded structure Compact structure with multi attached atom labels Ph CH2CH2CH2CH3 126 Advanced Drawing Techniques CambridgeSoft Using Multi Center Bonds Administrator 4 Click and drag from the atom label to draw your bonds You can determine the orientation of the resulting bond by dragging If you click to add a bond there are several preferential orientations for the resulting bond as outlined below Adding from the end of an atom label creates bonds that are preferentially horizontal Adding from the middle of an atom label creates bonds that are preferentially vertical Adding from the start of an atom label creates bonds that try to attain the chain angle setting in the Drawing Settings dialog box If that angle cannot be attained the next best angle is use
47. expert synthetic chemists designing novel syntheses Entries in ChemSynth are further refined to those with over 50 yield and at least two literature references ChemRXN is a refined selection of over 29 000 fully atom mapped reactions Including carefully selected reactions from InfoChem s ChemSelect database and ISI s ChemPrep database ChemRXN is a terrific combination of utility Patents World Drug Alerts WDA from Derwent is a current awareness application providing information on patents new biologically 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 Database 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 ChemMSDX provides over 7 000 material safety datasheets Extensive collection of chemical reference information in fully searchable database format Includes information on commercial availability properties biological activity organic reactions material safety data sheets and patent or development status Developed by CambridgeSoft in partnership with the leading chemical database publishers EMAIL info cambridgesoft com WWW www cambridgesoft com TEL 1 800 315 7300 INT L 1 617 588 9300 FAX 1 61
48. protein chemistry and other situations ChemDraw has four standard attachment point drawing tools that allow you to indicate a point of attachment while maintaining chemical meaning The bead tool is specifically intended to indicate attachment to a resin but the tools are interchangeable Any if these tools may be used for variable attachments in queries see Using Variable Attachment Positions on page 127 but only the diamond tool will show rank numbers That is if you add more than one diamond to a structure the points will automatically number sequentially Rotating a Symbol With the exception of the charge and the radical symbols you can rotate the symbols by selecting and dragging the Rotation handle on the Selection Rectangle All symbols are rotated around the same end from which they were originally drawn For example the radical cation symbol is rotated and resized from the charge The Info window shows the angle that one of the ends of a symbol makes with the X axis as you rotate symbols To rotate a chemical symbol 1 Select the chemical symbol with a selection tool 2 Drag the Rotation handle on the chemical symbol For more information about rotating and resizing see Rotating Objects on page 113 H2N H O OH NH3 H3N H O OH NH3 1 ChemDraw 9 Drawing Orbitals Symbols Arrows Arcs and Other Shapes 99 The Arrow Tools Palette The Arrow Tools Pal
49. query with the parent structure The parent structure can have attachment points to a list of alternative groups that you can define Alternative groups sometimes called R Groups or G Groups Generic Groups are shown below Defining an Alternative Group In ChemDraw Pro you can create alternative group definitions R G etc that represent a set of substituents any one of which will match the query To define an alternative group 1 Click the Alternative Group query tool 2 Click and drag to create an area large enough to draw the alternative groups The Alternative Group Title box appears 3 Type a title such as R1 in the Alternative Group Title box 4 Draw the substructure fragments in the Alternative Group box H N H N flip H N H N H N H N H N N H H N N H F NH2 OH F NH2 OH 1 1 G G 1 1 168 Drawing Query Structures CambridgeSoft Alternative Groups Administrator Defining Attachment Points Specify where the fragments should bond to the parent structure at the alternative group label 1 Click the diamond shaped Attachment Point tool on the Chemical Symbols palette 2 Do one of the following Click a substructure fragment where you want to place the attachment point Point to a substructure fragment where you want to place th
50. s ChemPrep ChemMSDX Safety Data Searching amp Information Provides full Material Safety Data Sheets for over 7 000 pure compounds ChemFinder Com WWW Reference Searching amp Info WWW links for over 100 000 compounds Enter text queries or use ChemDraw Plugin for structure amp substructure searching Works with Netscape amp 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 EMAIL info cambridgesoft com WWW www cambridgesoft com TEL 1 800 315 7300 INT L 1 617 588 9300 FAX 1 617 588 9390 MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge MA 02140 USA ChemOffice ChemDraw Chem3D ChemFinder amp ChemInfo are trademarks of CambridgeSoft 2002 All other trademarks are the property of their respective holders All specifications subject to change without notice E N T E R P R I S E ChemOffice WebServer ChemOffice WebServer Enterprise Solutions Applications and Databases Enterprise Solutions Applications and Databases ChemOffice WebServer ChemOffice WebServer is the leading solution platform for enterprise corporate intranet and Internet scientif ic information applications Compatible with major databases including Oracle SQL Server and Microsoft Access ChemOffice WebServer is the development and deployment platform for custom applications a
51. the destination document the objects are automatically scaled to match the docu ment settings of the destination document Auto matic scaling assures that the objects being transferred match the settings of the current docu ment Bonds All bonds drawn in the source document using the values specified in the Drawing Settings dialog box can be changed to use the Drawing Settings in the destination document Any resized bond in the source document is scaled in the destination document The scale factor is based on the ratio of the bond s length after resizing source to the Fixed Length in the Drawing Settings dialog box source This scaling process maintains the source document proportions in the destination document All values in the Drawing Settings dialog box are scaled using this method For example the Fixed Length is set to 1 0 cm in a source document A benzene ring is resized in to 200 The bond length is then 2 0 cm a ratio of 2 0 cm 1 0 cm or a scale factor of 2 In the destination document the Fixed Length set to 1 7 cm When the benzene ring is pasted into the destination document the bonds are scaled by a factor of 2 to a final bond length of 3 4 cm Atom Labels Atom labels are scaled the same way as bonds For example in the source document the atom label font size is set to 16 points One or two atom labels in the source document are resized to 8 points a ratio of 8 16 or a scale factor of 0 5
52. understood and will be bound by this license agreement Database Product License 1 Copyright Notice The materials contained in CambridgeSoft Database Products including but not limited to ChemACX ChemIndex and The Merck 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 Database 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 The Merck 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 art work photographs computer software audio and visual elements is owned or controlled separately by the Me
53. you want from the list If Use Default File Format is not selected the first time you use the Open dialog box the ChemDraw format is shown Subsequent uses show the last format used Saving Changes Automati cally You can configure ChemDraw to save changes to a document automatically at the time interval you set To set the frequency at which ChemDraw automat ically saves your changes 1 From the File menu choose Preferences The Preferences dialog box appears 2 Click Open Save Use Default File Format ChemDraw 9 ChemDraw Basics 25 Using Documents 3 Click the checkbox next to Autosave Every and type or select the minutes to use The time starts counting down after the first change is made Reversing and Repeating Actions ChemDraw keeps track of the actions you perform You can reverse actions one at a time by choosing the Undo command The number of actions that can be undone or redone is limited only by the amount of memory RAM and virtual memory available for use by ChemDraw When you save your document the Undo queue is reset and starts over Undoing Actions To undo the last action performed From the Edit menu choose Undo The last action performed is reversed The Redo command changes to reflect the undone action The Undo command changes to reflect the next action you can undo For example if you draw cyclohexane create an atom label text box type a label and select an
54. 0 8667 0 0000 0 0000 C Line 5 0 8667 1 0000 0 0000 C Line 6 0 0000 1 5000 0 0000 C Line 7 0 8667 1 0000 0 0000 C Line 8 0 8667 0 0000 0 0000 C Line 9 0 0000 1 5000 0 0000 O Line 10 1 2 1 1 Line 11 2 3 1 1 Line 12 3 4 1 1 Line 13 4 5 1 1 Line 14 5 6 1 1 Line 15 1 6 1 1 Line 16 6 7 1 1 268 Chemistry File Formats CambridgeSoft Connection Table File Format Administrator Line 2 contains two fields the first field is the number of atom labels and the second field is the number of bonds These fields must be separated by at least one space Lines 3 9 each contain 4 fields describing information about the individual atoms the first field is the X Cartesian coordinate 0 8667 the second field is the Y Cartesian coordinate 0 0000 the third field is the Z Cartesian coordinate 0 0000 and the fourth field is the atom label C The spacing of these fields is very important Any data outside the following columns especially data overlapping the ranges may render a file unreadable Field 1 Columns 0 9 Field 2 Columns 10 19 Field 3 Columns 20 29 Field 4 Columns 31 end Lines 10 16 each contain four fields describing information about the individual bonds between the atoms the first two fields represent the serial numbers of the atoms that are connected by this bond atom 1 and atom 6 the third field is the bond ord
55. 121 Using Nicknames Chapter 8 Advanced Drawing Techniques Overview ChemDraw provides advanced drawing features that allow you to Label functional groups with Nicknames Contract and expand sections of structures Add bonds to specific characters in atom labels Create bonds whose attachment is not explicitly defined Color objects Draw with Templates Clean up structures Using Nicknames Nicknames allow you to create short names for functional groups to use as an atom label or part of a label When an atom is labeled with a Nickname the chemical significance of the expanded structure is retained Commonly used Nicknames such as Me Et and Ph are provided with ChemDraw in the ChemDraw Nicknames file located in your ChemDraw Items folder You can edit this list using tools in ChemDraw You should not attempt to edit this file directly You can assign HotKeys to Nicknames For example in the Nicknames and HotKeys provided with ChemDraw the Hotkey 4 labels an atom with Ph which is a Nickname representing a phenyl group For more information see Labeling Atoms with HotKeys on page 87 You can use Generic Nicknames when drawing query structures For more information see Generic Nicknames on page 161 Applying Nicknames To use a Nickname to label an atom 1 Create a structure 2 Double click an atom with a bond tool or click an ato
56. 617 588 9300 FAX 1 617 588 9390 MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge MA 02140 USA ChemOffice ChemDraw Chem3D ChemFinder amp ChemInfo are trademarks of CambridgeSoft 2002 All other trademarks are the property of their respective holders All specifications subject to change without notice R E S E A R C H amp Registration System Registration System Chemical and Biological Registration Chemical and Biological Registration Registration System Registration System includes a robust data model for pure compounds batches salt management automatic duplicate checking and unique ID assignments Compounds may be entered individually or with SD files The data model resides entirely in Oracle and uses Oracle s security and transaction framework For companies intending to modify or construct their own registration system ChemOffice WebServer includes a powerful Software Developer s Kit SDK to add custom functionality Instead of inventing a proprietary language ChemOffice WebServer SDK extends the Microsoft and Oracle 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 ChemDraw interface makes ChemOffice WebServer the best choice for your corporate scientific information User Friendly Chemical Registration New c
57. Addins describes tasks that must be performed in conjuction with Microsoft Excel If you are not familiar with this product please consult the relevant User s Manual for more detailed information The chapters in this guide are organized by task They are intended to help you familiarize yourself with the ChemDraw applications and start using them as quickly and efficiently as possible New users should read the Basics chapter to get an overview of the product and how it works Chapter 2 Tutorials demonstrates most of the features of the application Perform the tutorials in the order 10 Introduction CambridgeSoft Conventions Administrator they are presented Experienced users can skip to Chapter 3 and the subsequent chapters which provide more detailed information Conventions The following notations are used throughout this user s guide The Ultra symbol indicates that a feature is available in the Ultra version only The Pro symbol indicates that a feature is available in both the Pro and Ultra versions Features that are available in the Standard version are not indicated by a symbol NOTE Notes such as this are used to highlight information supplemental to the main text When a shortcut key sequence is given the Windows OS sequence is listed first with the Macintosh OS sequence following for example Use the command Shift Control G or Shift Command G to ungroup objects For a list of keyboard
58. Bond Tool icon 62 Hashed Wedge Bond tool icon 62 H Dash Symbol drawing 96 H Dot and H Dash specification 235 H Dot Symbol drawing 96 Headers creating 178 Heat of Formation definition 142 Help Windows 10 Henry s Law 245 Henry s Law definition 142 Hide Crosshair command 184 Hide Rulers command 183 Hiding Atom Numbering 90 palettes 17 High resolution non PS printing 29 printing 29 Highlight box selecting 110 size 65 Hollow Wedge Tool icon 62 Home page CambridgeSoft 225 Hotkeys atom hotkeys 252 bond alignment 70 bond editing hotkeys 71 253 bond layering 71 Creating 88 File 88 Hard coded 89 labeling by pointing 87 labeling multiple atoms 88 labeling the last atom drawn 87 labeling with a selection tool 88 overview 87 table of 252 How to use this guide 9 Hydrogens implicit 152 Hyphens Font submenu 81 I Implicit Hydrogens 152 Imported objects selecting 110 Imported Picture 198 Importing spectral data 201 202 using file formats 196 Include ChemDraw LaserPrep 195 Indicators Atom Numbering 90 query 160 query editing 160 query positioning 160 stereochemical stereochemistry 140 237 stereochemistry positioning 140 Indicators stereochemical 161 Info window 19 Insert Name as Structure 74 Inserting files 204 name as structure 74 objects 204 ChemDraw 9 xi Inserting continued rows in tables 190 Integral Groups Creating 118 Interface 13 Internet CambridgeSoft web site 225 IR spectra se
59. Check Structure command identifies valence and label errors in your structure Check Structure You can check the chemistry of a selected structure part of a structure or caption in Formula style with the Check Structure command The structure is checked using normal valences and elements and defined Nicknames To check the valences of all selected atoms in a structure 1 Select a structure part of a structure or caption with a selection tool 2 From the Structure menu choose Check Structure Each label in the structure is checked sequentially When a label is incorrect a message window appears To continue checking the structure when a message appears Click Ignore To ignore all subsequent errors in a structure Click Ignore All To stop checking a structure when a message appears Click Stop 138 Working With Structures CambridgeSoft Viewing Analysis Information Administrator The check ends and the atom that is causing the problem is selected Check Structure when Copying to Clipboard or Exporting To have ChemDraw perform a check structure analysis on any structure copied to the Clipboard 1 From the File menu choose Preferences 2 Click the Check Structure When Copying to Clipboard or Exporting check box This change affects all documents Viewing Analysis Information The Analysis window displays the chemical formula exact mass molecular weight m z and element
60. Converted to Wedged Hashed e Converted to Wedged f Converted to a Single with a positive charge applied to that atom at the base of the dative bond and a negative charge applied to the atom at the point of the dative bond g Interpreted by ISIS as unspecified cis trans stereochemistry hConverted to Double i Converted to S D j Only M X Q A others written as aliases k Truncated to the first 5 elements l Converted to single m An RGFile will be created automatically n Converted to non anonymous alternative groups o Lists of greater than 5 elements converted to alternative groups p The low end of the repeat range is always treated as 1 Alternative Groups X Xm Anonymous Alternative Groups n n Link Nodes p p p Bracket properties X X X Atom Atom mapping X X Variable Attachment Positions 3D query properties Exported Query Properties ISIS Mol Rxn 176 Drawing Query Structures CambridgeSoft Export Compatibility Administrator ChemDraw 9 Working With Page Layout 177 Controlling the Drawing Area Chapter 11 Working With Page Layout Overview The presentation quality of your ChemDraw document is determined by how well the chemical structures and other objects are placed on the page layout Effective layout of a drawing includes proper alignment of chemical structures and other objects appropriate page size and page orientation The pa
61. Ctrl drag or Option Drag the spot If you want to then ChemDraw 9 Drawing Orbitals Symbols Arrows Arcs and Other Shapes 107 The TLC Tool Rf Display When you select Show Rf a text label appears near the spot showing the spot s retention factor value By default the tag will show the Rf to two decimal places You can change the tag as follows Select the tag with the Lasso or Marquee tool and drag it to a new location or Right click or Control click on the tag and choose Position Select the tag with the Text tool and edit the Rf value If you change the Rf the spot will move to the new position indicated If you edit the Rf to have different precision that precision will be preserved Delete a spot Click on the spot with the Eraser tool NOTE If you erase all spots in a lane the lane will be deleted Display or set the Rf for a spot add a custom spot 1 Right click or Control click on a spot 2 Point to TLC Spots and take the appropriate action NOTE To display Rf for all spots Right click or Control click in the plate and select Show Rf from the TLC Spots submenu Change the style or color of a spot 1 Right click or Control click on a spot 2 Choose the style or color NOTE To change the style for all spots Right click or Control click in the plate and choose the style from the TLC Spots submenu If you want to then TLCEnlarge or sm
62. Multi Attached Labels 125 Adding Bonds to an Atom Label 125 Using Multi Center Bonds 126 Creating a Multi Center Bond 126 Viewing Attachment Points 127 Using Variable Attachment Positions 127 Using Structure CleanUp 128 Working with Color 129 Coloring Objects 130 Displaying the Color Palette 130 Customizing the Color Palette 131 Windows Color Settings 131 Adding or Customizing Windows Colors 132 Macintosh Color Settings 132 Adding or Customizing Macintosh Colors 132 Removing Colors 133 Templates and Color 133 Saving Color Palette Settings 133 Drawing With Templates 133 The Templates Tool 133 Choosing a Template 134 Using Templates 134 Drawing a Template
63. Relative flag indicates the exact stereoisomer as drawn or its enantiomer The Racemic flag indicates a mixture of the exact stereoisomer as drawn and its enantiomer COOH NH2 Abs COOH NH2 COOH NH2 Rel COOH NH2 COOH NH2 OR COOH NH2 COOH NH2 COOH NH2 AND Rac ChemDraw 9 The Chemistry of ChemDraw 239 Chemical Conventions Critical messages that may affect the final analysis Message Description There are too many bonds to this unlabeled Carbon Displayed for every unlabeled atom with more than 4 filled valences Filled valences include sum of bond orders charge radicals and free sites Aromatic bonds count 1 5 each rounded down unless it is the only bond to the atom Charge is signed and includes charge implied by dative bonds The Substituents query property treats Free Sites Up to and Exactly the same way an atom with 2 explicit bonds and Substituents Up To 3 or Substituents Exactly 3 or Substituents Free Sites 1 has three filled valences An atom in this label has an invalid valence Displayed in a variety of cases where ChemDraw cannot find a place to put a bond or cannot find a bond to put on an atom Valid valences for each element are listed in the Isotopes Table file ChemDraw can t interpret this label Displayed when ChemDraw finds text that it cannot identify as an element nickname generic
64. USA ChemOffice ChemDraw Chem3D ChemFinder amp ChemInfo are trademarks of CambridgeSoft 2002 All other trademarks are the property of their respective holders All specifications subject to change without notice BioAssay HTS BioAssay HTS Biological Assay and High Throughput Screening 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 tify 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 The database does the rest Users can set up unlimited levels of drill down This allows users for example to click an IC50 and see a graph of percent inhibition ve
65. Width 2 pt Line Width 0 6 pt Margin Width 1 6 pt Hash Spacing 2 5 pt Chain Angle degrees 120 Bond Spacing of length 18 Atom Label Font Win Mac Arial Helvetica Atom Label Size 10 pt Caption Font Win Mac Arial Helvetica Caption Size 10 pt Drawing Area Width x Height 540 pt x 720 pt Page Size US Letter Reduction 100 N HO H O ACS 1996 Morphine ChemDraw 9 Document Settings 257 ChemDraw Style Sheets or Stationery Pads Fixed Length 17 pt Bold Width 2 pt Line Width 1 pt Margin Width 1 6 pt Hash Spacing 2 5 pt Chain Angle degrees 120 Bond Spacing of length 18 Atom Label Font Win Mac Arial Helvetica Atom Label Size 10 pt Caption Font Win Mac Times New Roman Times Caption Size 12 pt Drawing Area Width x Height 540 pt x 720 pt Page Size US Letter Reduction 100 Drawing Atom Label and Caption Text Settings in Journal Style Sheets or Stationery Pads Adv Synth Catal N H HO O HO Morphine 258 Document Settings CambridgeSoft ChemDraw Style Sheets or Stationery Pads Administrator Fixed Length 17 pt Bold Width 2 9 pt Line Width 0 54 pt Margin Width 2 pt Hash Spacing 2 pt Chain Angle degrees 120 Bond Spa
66. a sophisticated spelling checker for chemical compounds For example if you re investigating organic acids a compound with the structural formula CH3COO would probably represent acetic acid Present the same formula in a paper on transition metal chemistry and you might be describing a novel methylated cobalt oxide If you had asked ChemDraw to interpret it beforehand you would have received a message reporting a valence error and you might have been prompted either to add a negative charge or to change the capitalization ChemDraw can offer only suggestions If you and your audience understand what you are trying to depict then you can ignore these suggestions In many cases you can teach ChemDraw to understand the notation you re using For more information see Applying Nicknames on page 121 Database Conventions Most databases require not only that you draw a structure in a way that makes sense but that you draw it in the way that the database expects it Consider ferrocene which is represented in at least four different ways in major databases Fe Fe Fe Fe Merck Index and 3 other isomers Beilstein 232 The Chemistry of ChemDraw CambridgeSoft Chemical Conventions Administrator A successful search in one database might not produce any hits in another When in doubt consult the documentation for your database and see if it offers any clues to the conventions used Chemical Conventio
67. after each comma and brackets are optional The word NOT must be in all caps and must be followed by a space Alternatively the word NOT may be replaced with a minus sign For example NOT F Cl Br I NOT C O N NOTE An element not list may contain only atomic elements plus D deuterium and T tritium To create an element not list 1 Open an atom label text box 2 Type an open bracket the word NOT and a space NOT followed by a list of elements separated by commas Cl Br I followed by a close bracket Link Nodes You can specify a variable length chain or ring by indicating that one of the atoms can be repeated some number of times using link nodes Link nodes must have exactly two connecting bonds The atom label must conform to the following conditions No more than a single element symbol or a generic nickname The last part of the label in the form number hyphen number with the number and hyphen subscripted Parentheses or braces may be used instead of brackets Brackets can be omitted if not needed for clarity for example with O1 3 To create a link node 1 Open an atom label text box 2 Type in the following format Representing Polymers and Other Repeating Units Brackets parentheses and braces enclose structures or structural fragments that are to be repeated a number of times The bracket properties in ChemDraw allow you to specify
68. alone if an order of zero is specified Multiple Group the Repeat Count must be a positive integer SRU n the SRU label can be any text You can also edit the text for these Bracket Usage types directly in the document using the Text tool You cannot edit the text displayed for the other Bracket Usage types Bracket Usage Representations of polymers are either structure based or source based The type of bracket you use depends on which type of representation you need For references see Polymer Representations on page 238 Structure based Polymer Representations Structure based polymer representations enclose only a portion or a structure within brackets One or more bonds cross each of the enclosing brackets The crossing bonds match up making the polymer structure more explicit You create a structure based polymer representation by enclosing a portion of a structure in brackets with a bracket type of SRU n The subscript n is recommended by IUPAC to notate structure based representations of unknown size but you can edit the text using the text tool ChemDraw 9 Drawing Query Structures 165 Representing Polymers and Other Repeating Units A structure based representation of poly vinyl chloride is shown below You can also use the Bracket Usage types Crosslink xl Graft grf and Modification mod to represent specific types of repeating units in a s
69. and hold down the mouse button The name of the new Template document appears in the menu Orientation of Templates To make the templates that you create as easy to draw with as possible it is recommended that you orient your structures so that the bond that establishes the position of the template for Drawing Area Resize Handle Template Panel Pane Templates2 250 dpi 136 Advanced Drawing Techniques CambridgeSoft Drawing With Templates Administrator example the bond used for fusing is left and vertical The most vertical left bond is drawn first For examples see Using Templates on page 134 Resizing Template Panes To resize the Template panes in the Template panel Drag the Resize handle on the lower right corner of the Template panel The percentage the block of Template panes is enlarged or reduced appears in the Info window Template Panels To increase the size of the Template panel Drag the Template dividing line To add a row of panes to the Template panel 1 Select a Template pane 2 From the Edit menu choose Add Row Before or Add Row After The new row is added before or after the Template pane you selected To add a column to the Template panel 1 Select a Template pane 2 From the Edit menu choose Add Column Before or Add Column After The new column is added to the right or left of the Template pane you selected To delete a row of Template panes
70. because the representation used for printing when Include PostScript is not selected is the same as that used for drawing to the screen better correspon dence between the screen and printed output may be observed For more information see Transferring PostScript Macintosh on page 195 Include ChemDraw Laser Prep Selecting the include ChemDraw Laser Prep allows you to print to a printer that cannot be initialized using ChemDraw If you create drawings with this option off they will not print on PostScript printers without the use of ChemDraw To Include ChemDraw Laser Prep 1 From the File menu choose Preferences 2 Click Include ChemDraw Laser Prep 3 Click OK NOTE When you select Include ChemDraw Laser Prep you should also select Include PostScript 30 ChemDraw Basics CambridgeSoft Scripts Macintosh Administrator For more information see Transferring PostScript Macintosh on page 195 Scripts Macintosh The Scripts menu contains scripts that you can use to perform tasks within ChemDraw or between ChemDraw and another scriptable application Scripts found in the Scripts menu are created using Apple s Script Editor application With the proper script extensions in conjunction with Apple s Script Editor application you can create scripts using the AppleScript scripting language and add scripts to the Scripts menu by placing them in the ChemDraw Folder NOTE Scripts no
71. below to delete the bonds The resulting structure is shown below Add double bonds to the structure 1 Click the Solid Bond tool 2 Point to the atom indicated below 3 Drag upward to draw a double bond Add another double bond 1 Point to the bond shown below 2 Right click point to Double and then choose Plain Realign the double bond so it is centered 1 Point to the center of the upper double bond 2 Right click point to Bond position and then choose Centered 44 Tutorials CambridgeSoft Tutorial 4 Fischer Projections Administrator Add a carbon atom label 1 Point to the atom shown below 2 Press the c key on your keyboard c is a Hotkey assigned to the atom label C The CH atom label appears with the correct number of hydrogen atoms Add an oxygen atom label to complete the structure 1 Point to the atom shown below 2 Press the o key on your keyboard o is a Hotkey assigned to the atom label O Save and close the document 1 From the File menu choose Save 2 From the File menu choose Close Tutorial 4 Fischer Projections This tutorial demonstrates creating a Fischer projection of glucose shown below by drawing a linear series of bonds You can also create the same drawing using a template Create a document from a template by opening the appropriate document template 1 From File menu point to Open Special and then choose ACS Document 19
72. by the Structure CleanUp command For more information see Drawing with Fixed Lengths on page 64 and Using Structure CleanUp on page 128 Adjust this If you want to 10 14 18 Bold Width Set the width of the line used when bold and wedge bonds are drawn The Bold Width setting must be greater than the Line Width setting The end of a wedge is 1 5 times the bold width Line Width Set the width of all bonds lines and arrowheads in the drawing Margin Width Change the amount of space surrounding all atom labels that will erase portions of the bonds to which they are attached The margin width also determines the amount of white space surrounding the front bonds in a bond crossing For more information see Editing Atom Labels on page 87 and Changing Bond Crossings on page 71 Adjust this If you want to 2 Point 4 Point 8 Point 1 Point 1 5 Point 0 5 Point ChemDraw 9 Drawing Chemical Structures 61 Drawing Settings Configuring Settings for Documents To configure the drawing settings for an entire document 1 From the File menu choose Document Settings The Document settings dialog box appears 2 Click the Drawing tab and configure the settings 3 Click OK when you are finished The settings you chose are applied to the entire document Hash Spacing Set the spacing between the hashed lines used when wedged hashed bonds hashed bonds
73. delete a curve segment The cursor appears as the Eraser tool before you click You can also delete entire curves using a selection tool or the Eraser tool Applying a Style to a Shape All curves are drawn with the last curve style chosen until you change the selections Certain styles are mutually exclusive For example if you choose Closed you cannot also choose Arrow at Start You can use the Doubled style to represent cell membranes The lines are separated by twice the Bold Width setting for the drawing Doubled lines cannot be dashed or include arrows To apply a style to a curve 1 Select a curve using either the Pen tool or a selection tool 2 From the Curves menu choose a style Filled and Closed Styles The illustration below shows a shape with the Plain style applied The following illustration shows the shape above with the Filled and Closed styles applied Shaded Style You can apply shading to any curve however the shaded style works best with convex or slightly concave shapes Shading may not appear as desired in extremely concaved shapes The illustration below shows shapes with the Plain style applied The following illustration shows the above shapes with the Shaded style applied Plain Style To remove all styles from a curve With a curve selected choose Plain from the Curves menu The TLC Tool The TLC Tool is a drawing tool that allows you to easily depict Thin Layer Chroma
74. deployed by large pharmaceutical companies with Oracle 8i and 9i Adds chemical data types to Oracle linking chemical applications to enterprise software systems without special programming Confers Oracle s security and scalability simplifying large systems architectural considerations Makes legacy chemical data such as MDL ISIS accessible to ChemOffice WebServer applications S O L U T I O N S EMAIL info cambridgesoft com WWW www cambridgesoft com TEL 1 800 315 7300 INT L 1 617 588 9300 FAX 1 617 588 9390 MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge MA 02140 USA ChemOffice ChemDraw Chem3D ChemFinder amp ChemInfo are trademarks of CambridgeSoft 2002 All other trademarks are the property of their respective holders All specifications subject to change without notice K N O W L E D G E E Notebook Enterprise E Notebook Enterprise Desktop to Enterprise Knowledge Management Desktop to Enterprise Knowledge Management E Notebook E Notebook 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 Microsoft Word documents spectra and other types of data and then search this data by text sub structure or meta data You can organize your electronic pages by projects experiments or any other classifi cation that c
75. each of which is printed on a single piece of paper Posters A single large document composed of as many pieces of paper as necessary 178 Working With Page Layout CambridgeSoft Setting up Pages Administrator Paged Document Setup To create a document with one or more page 1 From the File menu choose Document Settings The Document Settings dialog box appears 2 On the Layout tab ensure Pages is selected 3 Specify the number of pages in the Document Size section The size of the pages is determined by the Page Setup settings For more information see Page Setup on page 179 4 Type the Margin settings The units of the margins are set in the Preferences dialog box The paper size minus the margins determines the drawing area 5 Create Headers and Footers as described in Creating Headers and Footers on page 178 6 Click OK A document is created using your settings Poster Documents Setup You can create a poster by creating a single large drawing area which will be printed on as many separate pages as necessary When you set the document size and how much each page overlaps ChemDraw calculates the number of pages needed and the margin sizes You can set registration marks which mark the overlap setting on each page to use as a guide when assembling the poster from the separate pages To create a poster document 1 From the File menu choose Document Settings 2 On the Lay
76. for a sin gle element is different from that of the whole structure The following table outlines the ChemDraw Excel functions Only CHEM COMPOSITION and CHEM NUM ATOMS take an optional second argument The others only take the reference cell argument Function Action ISSTRUCTURE Returns TRUE if cell referred to is any ChemDraw Excel chemistry object including reactions otherwise it returns FALSE ISREACCTION Returns TRUE if cell reference is any ChemDraw Excel chemistry object and reaction otherwise it returns FALSE CHEM FORMULA Returns formula for structure in cell reference it returns N A error if cell doesn t contain a ChemDraw structure CHEM MOLWEIGHT Returns molecular weight for structure in cell reference Returns N A error if cell doesn t contain ChemDraw structure CHEM NUM HBACCEPTORS Returns number of hydrogen bond acceptors based on topology Returns N A error if cell doesn t contain ChemDraw structure CHEM NUM HBDONORS Returns number of hydrogen bond donors based on topology Returns N A error if cell doesn t contain a structure CHEM SMILES Returns SMILES string for structure Returns N A error if cell doesn t contain ChemDraw structure Function Action ChemDraw 9 ChemDraw Excel 217 Using ChemDraw Excel Functions Using ChemProp Functions If you are using ChemDraw Pro or Ultra with the ChemProp add on installed you can calculate phys ica
77. from one end of the bond to the other in a document window 4 Move the end of the bond to other angles The Info Window shows that the bond angle is constrained to 15 degree increments Toggling Fixed Lengths and Fixed Angles If Fixed Lengths or Fixed Angles are selected you can temporarily deselect them To toggle Fixed Lengths and Fixed Angles Press the Alt or Option key and drag from one end of a bond to the other end in the document window Dative Bonds and Wedged Bonds Dative bonds and wedged bonds are drawn with a fixed orientation in a document window To draw a dative bond 1 Click the Dative Bond tool 2 Drag from the positive to the negative end arrow head of the dative bond ChemDraw 9 Drawing Chemical Structures 65 Drawing Bonds To draw a wedged bond 1 Click one of the wedged bond tools 2 Drag from the narrow end of the wedged bond to the wide end of the wedged bond To change the orientation of the dative or wedged bond Click the center of the dative or wedge bond using the appropriate tool The orientation of the bond is inverted Adding a Bond by Clicking To add a fixed length bond 1 Select a bond tool 2 Click an atom A new bond is drawn and joined to the atom you clicked Bonds drawn by this method are always drawn using the Fixed Length specified in the Drawing Settings dialog box The angle that the deposited bond makes with its nearest nei
78. in the parent compound By numbering your attachment points you have unambiguously specified that the methyl group must be adjacent to the amine group The conformations that are not of interest are excluded Showing Attachment Rank Indicators You can hide the attachment rank indicators if required For example sometimes particularly in publication quality drawings the numbering of attachment points is implicit and the numbered attachment rank indicators are superfluous To hide the attachment rank indicators and remove the numbers from the attachment points 1 From the File menu choose Preferences 2 In the Preferences dialog box click Display 3 Deselect Show Attachment Rank Indicators The following illustration shows an alternative group definition and a parent structure with the attachment rank indicators hidden This change affects all documents Attachment Point Numbering Numbered attachment points allow you to specify precisely how the structure fragments are connected to your parent structure The numbering of the attachment points is related to the front to back order of the attachment points NH2 O NH2 R1 NH2 R1 O 1 2 1 2 R1 NH2 R1 O 170 Drawing Query Structures CambridgeSoft Anonymous Alternative Groups Administrator To set the order of the attachment points Click the ends of the bonds in order The last point clicked has the highest number
79. include Registration System for managing proprietary compound informa tion Inventory Manager for reagent tracking needs and chemical databases for complete management of chem ical inventories Formulations amp Mixtures and CombiChem Enterprise also provide tailored approaches to man aging chemical data Applied BioInformatics BioAssay HTS and BioSAR Browser applications process biological assay data to pinpoint the structural deter minants of biological activity BioAssay HTS 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 The Merck Index and ChemACX Database provide reference information property estimations and searchable compilations of commercially available chemicals Development and deployment platform for workgroup and enterprise chemical information applications Webserver and browser components facilitate application deployment to desktops with minimal impact and training Enterprise Solution applications address areas of Knowledge Management Research amp Discovery Applied BioInformatics and Chemical Databases EMAIL info cambridgesoft com WWW www cambridgesoft com TEL 1 800 315 7300 INT L 1 617 588 9300 FAX 1 617 588 9390 MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge MA 02140 USA ChemOffice ChemDraw Chem3D ChemFinder amp ChemInfo are tra
80. 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 ChemOffice Enterprise ChemOffice Enterprise includes licenses for ChemDraw ActiveX and licenses for Chem3D ActiveX The ActiveX software products may be installed on computers other than that one on which ChemOffice Enterprise is installed However 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 Agreement 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
81. linked by registry number CAS number or Catalog driven data mining and analysis operation Both form and table views available within simple web interface ChemDraw for Spotfire Role based security specifies operations allowed for administrators publishers and browsers EMAIL info cambridgesoft com WWW www cambridgesoft com TEL 1 800 315 7300 INT L 1 617 588 9300 FAX 1 617 588 9390 MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge MA 02140 USA ChemOffice ChemDraw Chem3D ChemFinder amp ChemInfo are trademarks of CambridgeSoft 2002 All other trademarks are the property of their respective holders All specifications subject to change without notice C H E M I C A L ChemACX Database ChemACX Database AAvailable Chemicals and Screening Compounds vailable Chemicals and Screening Compounds ChemACX on CD ROM ChemACX on the Web ChemACX Database Sifting through chemical catalogs is a poor use of time for any researcher The Available Chemicals Xchange database ChemACX Database provides a complete tool for research chemical sourcing and purchasing The database can be accessed from both desktop and enterprise environments and boasts an impressive list of major suppliers from Alfa Aesar and Aldrich to TCI and Zeneca with hundreds in between The enterprise pro curement solution for ChemACX saves time by streamlining the entire purchasing process Use ChemACX to build an internal requisiti
82. move atoms using the bond tool that was used to draw the atom For more information see Moving Atoms on page 70 Duplicating Objects To duplicate objects with a selection tool 1 Click a selection tool 2 Select the objects 3 Ctrl drag or Option drag to create a copy and position it A copy of the selected objects is moved to the new position To duplicate the selected objects and constrain the positioning of the copy to the same position as the original objects 1 Select a selection tool 2 Select the objects 3 Ctrl Shift drag or Option Shift drag to create a copy and position it To place a copy of an object on the Clipboard 1 Select the objects using a selection tool 2 From the Edit menu choose Copy A copy of the object is placed on the Clipboard You can transfer the copy on the Clipboard by the pasting it to the current document another ChemDraw document or a different document type For information about transferring ChemDraw pictures to other types of documents see Autoscaling on page 193 Rotating Objects To rotate objects 1 Select the objects to rotate using a selection tool The Rotation handle is located on the upper right corner of the selection rectangle 2 Drag the Rotation handle clockwise or counterclockwise The screen and Info window indicate the magnitude of the rotation around the center of the Selection rectangle By default atom labels do not r
83. nickname or alternative group name Parentheses don t match Displayed when parentheses cannot be matched into nested open close pairs This label has conflicting or unassignable charges Displayed when a plus and minus charge have been assigned to the same element charges have been assigned in more than one way or a charge has been assigned to a nickname generic nickname or Alternative Group name Formula cannot be computed for queries Displayed for every label that contains a generic nickname an element list or an alternative group This is a status message only analysis continues as if the problematic label were not selected Text not in Formula style won t be interpreted Displayed for the first caption that is not an atom label or Alternative Group name and which contains any text not in Formula Subscript or Superscript style This is a status message only and appears only once regardless of how many captions are in the selection This named alternative group contains no attachment point Displayed for any structure within an Alternative Group Box where the structure lacks an attachment point This is a status message only Message Description 240 The Chemistry of ChemDraw CambridgeSoft Chemical Conventions Administrator This named alternative group contains fragments with inconsistent valences Displayed for any Alternative Group Box whose contained structure
84. of the following Move the Crosshair axes and align it with the object Select an object and drag it until it is aligned with either axis of the Crosshair or a grid line In either case if a bond or side of the object is parallel to one of the axis it disappears when it is exactly positioned over a Crosshair axis To align another object on the Crosshair 1 Select a second object 2 Drag the second object to the Crosshair axis or grid line and align it to the first You can also move selected objects in small increments to align them with the Crosshair using the Arrow keys available on some keyboards To move 1 point in the direction of an Arrow key NOTE 1 point equals 1 72 inch or 0 035 cm Select the objects and then press an Arrow key To move 10 points using the Arrow key for example to the right Press Alt Right Arrow or Option Right Arrow Hiding the Crosshair To hide the Crosshair From the View menu choose Show Crosshair The check mark next to the Show Crosshair command disappears Centering on a Page To center an object or group of objects at the center of the page 1 Select the object you want to center using a selection tool 2 From the Object menu choose Center on Page The selected objects move so that the center of the Selection rectangle is positioned at the center of the page ChemDraw 9 Working With Page Layout 185 Arranging Objects Al
85. on the printer you have chosen For the Macintosh the version of the printer driver for that printer is installed in your System Folder To set the paper size orientation and margins 1 From the File menu choose Page Setup The Page Setup dialog box appears The dialog box appears slightly different depending on the printer and platform you have To include the Type file name amp f page number amp p date printed amp d time printed amp t To align the text Type centered amp c right amp r left default amp l 180 Working With Page Layout CambridgeSoft Page Setup Administrator A Windows dialog box for a typical postscript printer is shown below The Macintosh Page Setup dialog box with common settings for a LaserWriter is shown below 2 Select a paper size from the drop down list The available page sizes vary depending on the type of printer Listed below are common sizes available The page orientation you choose determines which of the measurements is height and which is width Page Orientation To choose the orientation of the page Click the vertical portrait or horizontal landscape orientation button The orientation of a document window changes to the orientation you have chosen This is evident when the rulers are visible Reduce or Enlarge Some printers include an option to reduce or enlarge your drawings by a variable percentage 25 400
86. settings and row and column characteristics for creating ChemDraw Template documents Windows Metafile wmf The Windows Metafile file format saves the Graphic Device Interface GDI representation of a ChemDraw drawing Using the WMF file format you can transfer ChemDraw drawings to other applications such as Microsoft Word that support that WMF file format on the same or Pro Pro Pro Pro Pro Pro ChemDraw 9 Sharing Information 203 Importing and Exporting different computers rather than using the Clip board The WMF file format contains ChemDraw structural information TIFF file tif TIFF format Tagged Image File Format is a high resolution format commonly used for saving graphics for importing into desktop publishing applications on the same or on different computer platforms TIFF images can be saved using a variety of resolution color and compression options As TIFF images can get rather large choosing appro priate options is important The TIFF format is for export only Resolution Available resolutions range from 72 computer monitor to 1440 dpi high resolution output When choosing a resolution keep in mind that the size of the file increases as the square of the resolu tion Color You can select from the following color options Monochrome Forces all objects to black and white RGB Indexed Stores colors using computer monitor style of color encoding
87. 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 For more information on using the ChemACX website see the ChemOffice Enterprise Workgroup amp Databases Manual Finding ACX Structures and Numbers ChemOffice searches ACX and returns information about related structures and numbers You can place the returned information in your document ACX Structures There are two ways to find ACX structures by ACX number or by name 224 Accessing the CambridgeSoft Web Site CambridgeSoft Browsing SciStore com Administrator 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 2 Type the ACX registry 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 2 Type in a name As with ChemFinder com you can use a chemical name or a trade name 3 Click OK The Structure appears in your document 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 F
88. substituents H Implicit Hydrogens R Ring Bond Count S Unsaturation C Reaction Change T Reaction Stereo L Translation I Isotopic Abundance none Abnormal Valence Indicator Query Property ChemDraw 9 Drawing Query Structures 151 Atom Property Options From the Structure menu choose Properties and view the settings on the Atom Properties tab Removing Atom Properties To remove all atom properties from an atom 1 Select the atom 2 From the Structure menu choose Properties 3 Click Use Defaults The atom properties are removed and the characters no longer appear To remove specific atom properties 1 Select the atom 2 Do one of the following Right click point to an atom point to the property you want and then choose the appropriate option 3 From the Structure menu choose Properties and then click the atom property to remove Atom Property Options The following topics describe the atom properties you can associate with an atom Substituents The three Substituents properties specify the number of substituents that may be bonded to the selected atoms In ChemDraw a substituent is defined as a non hydrogen atom connected by a bond of any order For example in the figure below the carbonyl carbon indicated by the arrow in propanal has a substituent count of two the alpha carbon and the aldehyde oxygen The double bond to the aldehyde oxygen cou
89. 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 ChemDraw Plugin Create precise database queries by specifying atom and bond properties and include stereochemistry Display spectra structures and annotations on the same page Use the Online Menu to query ChemACX Com by structure identify available vendors and order online Stereochemistry Structure to Spectrum NMR Correlation S O F T WA R E ChemDraw Pro Premier Drawing amp Information Query Query databases precisely by specifying atom amp bond properties reaction centers substituent counts R groups amp substructure Read ISIS files with Macintosh Windows cross platform compatibility Structure Clean Up improves poor drawings Display spectra from SPC and JCAMP files Chemical intelligence includes valence bonding amp atom numbering Right button menus speed access to features ChemDraw Std Publication Quality Structure Drawing Draw and print structures amp reactions in color and save as PostScript EPS GIF SMILES amp more Collections of pre defined structure templates
90. the Info window CHO OH H H HO OH H OH H CH2OH C6H12O6 Exact Mass 180 06 Mol Wt 180 16 m e 180 06 100 0 181 07 7 1 182 07 1 4 C 40 00 H 6 71 O 53 29 O OH OH OH CH2OH OH 50 Tutorials CambridgeSoft Tutorial 5 Perspective Drawings Administrator Even though Fixed Angles is on the angle is not constrained The Fixed Angles feature constrains angles only when they are being drawn For example if you created this ring by dragging instead of clicking the angle would be constrained when Fixed Angles is on Change cyclohexane to tetrahydropyran 1 Click outside the structure to deselect it 2 Point to the atom indicated below 3 Type o Add vertical bonds 1 Click the Solid Bond tool 2 Point to the atom shown below 3 Drag upward to create a bond 4 Point to C1 again 5 Drag downward to create another bond 6 Repeat for the atoms indicated by the arrows below The result appears as shown below Draw one bond upward at C5 1 Point to the atom shown below O O O O O O O ChemDraw 9 Tutorials 51 Tutorial 5 Perspective Drawings 2 Hold the mouse button and drag upward For the downward bond for C5 you must turn Fixed Lengths off or the bond will be joined to the upward bond of C3 You can temporarily disable Fixed Lengths using a modifier key 1 Point to the atom shown below 2 Hold d
91. the first point is rather than being between them Geometry and constraint objects update dynamically when you change the structure they cannot be moved independently They may be used with cdx mol skc and tgf files full read write compatibility they are not compatible with other formats They can however be saved in print only formats such as TIFF Query Tools Palette ChemDraw provides Query tools to enable you to draw query structures Option Search Result Angle Defines an angle constraint between three points in order Indicated as a range Dihedral Defines a dihedral torsional angle constraint among four points in order between two lines or two planes Indicated as a range Distance Defines a distance constraint between two points a point and a line or a point and a plane Indicated as a range in Angstroms Line Defines the best fit line for the selected points Plane Defines the best fit plane for the selected points or for a point and a line Exclusion Sphere Defines an exclusion sphere around a point If more than one point is selected the exclusion sphere is around the first selected point and the subsequent points are allowed within the exclusion sphere when the query is evaluated Indicated as a range in beginning at 0 Normal Defines the normal from a defined plane in the direction of a point Point Defines a point positioned at a specified distance from a
92. the property of their respective holders CambridgeSoft End User License Agreement for Software Products Important This CambridgeSoft Software License Agreement Agreement is a legal agreement between you the end user either an individual or an entity and CambridgeSoft 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 CambridgeSoft 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 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 is in 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
93. to an unselected bond which defines a bond from sulfur as the connection point for the group This allows you to define a Nickname You must leave a bond unselected for each connection point You cannot define more than two connection points or one attachment point on a single atom in a nickname The definition in the figure below was used for the amino acid Ala The unselected bond at each end of the structure indicates the connection points Nitrogen on the left and Carbon on the right You can draw a peptide chain by Stringing Nicknames together Stringing Nicknames together in an atom label as long as there is a bond attached Am Amyl Americium Np para Nitrophenyl Neptunium Pr Propyl Praeseodymium incorrect definitions correct definitions H Gly Ala OH H GlyAlaOH 124 Advanced Drawing Techniques CambridgeSoft Contracting Labels Administrator Stringing Nicknames together and not including bonds Viewing Nicknames To view the list of defined Nicknames From the File menu choose List Nicknames The List Nickname dialog box appears To insert a nickname into your document 1 Select the nickname 2 Click Insert The nickname appears in your document Deleting Nicknames To delete a Nickname 1 From the File menu choose list Nicknames 2 Select the Nickname that you want to delete from the list 3 Click Delete The Nickname is removed from the
94. two rows and two columns Click in the document window type the numbers of rows and columns in the Insert Table dialog box and then click OK ChemDraw 9 Working With Page Layout 187 Creating Tables The table appears in the document window To resize the rows or columns 1 Place your pointer on the border to resize The pointer changes to a double headed arrow 2 Drag the border to the desired size To customize the borders of the table 1 With the Table tool selected point to a border and right click or option click The Table Borders dialog box appears 2 In the Setting section click the borders to which you want to apply the settings 3 In the Style section select the style color and width of the border to apply 4 In the table diagram click the borders to customize 5 Click OK To make a cell fit around its contents such as in the table shown below 1 Point to a border and right click 2 Choose Size To Fit Contents O OH O OH 188 Working With Page Layout CambridgeSoft Creating Tables Administrator The cells resize to fit around the contents To add rows or columns to the table 1 Point to the border where you want to add the rows or columns The arrow appears as shown below 2 Right click or Option click and from the menu that appears choose the appropriate option To align all of the objects in the table Point to a border right click p
95. where you want the import to start The upper left corner of the import is at this cell Data is filled down and to the right 2 From the ChemOffice menu select Import Table or click The Import Table dialog box appears 3 Type or select the file name to import and click Open All records are added to your spreadsheet Converting and Upgrading Instead of copying and pasting information from a non ChemDraw Excel worksheet you can convert the existing worksheet into a ChemDraw Excel worksheet To convert a worksheet Select Convert Worksheet from the ChemOffice menu The work sheet is converted to a ChemDraw Excel worksheet Upgrading Workbooks ChemDraw Excel 9 0 improvements have made workbooks created with older versions incompati ble You can open and maintain old workbook for ChemDraw 9 ChemDraw Excel 209 Importing Hit Lists mats but you may get error messages depending on your Excel security settings and will be asked if you want to upgrade each time you open them To upgrade a workbook 1 From the Tools menu point to Macro and select Security 2 Click the Trusted Sources tab and make sure that CambridgeSoft Corporation is listed as a trusted source Make sure the Trust access to Visual Basic Project checkbox is selected 3 Select Upgrade Workbook from the ChemOffice menu 4 To maintain tight security go back to the Macro Security dialog box and uncheck the Trust access to Vi
96. with the appropriate wedged hashed or plain bond sometimes it is useful to indicate the relative stereochemistry of a molecule as a whole considering the relationship between all stereocenters Stereochemical flags apply to the Stereocenter Indicator Double bond Z if the highest ranking ligand of each pair are on the same side of the bond otherwise E 1 R S Cahn C K Ingold and V Prelog Speci fication of Molecular Chirality Angew Chem Int Ed Engl 1966 5 385 414 errata 1966 5 511 Angew Chem 1966 78 413 447 V Prelog and G Helmchen Basic Principals of the CIP System and Proposals for a Revision Angew Chem 1982 94 614 631 Angew Chem Int Ed Engl 1982 21 567 583 P Mata A M Lobo C Marshall and A P Johnson The CIP Sequence Rules Analysis and Proposal for a Revision Tetrahedron Asymme try 1993 4 657 668 Tetrahedral atom When the lowest ranking ligand is located behind the central atom R when remaining 3 ligands are arranged clockwise in descending order S when remaining 3 ligands are arranged counterclockwise in descending order r or s is used for pseudoasymmetric atoms Stereocenter Indicator 238 The Chemistry of ChemDraw CambridgeSoft Chemical Conventions Administrator nearest structure if no structure is within the distance specified by the Fixed Length value the stereochemical flag is not assigned to any structure P
97. with the mouse to display a tool tip that describes the error Right click on the warning and choose Explain This Warning Select the structure and choose Check Structure from the Structure menu For more information see Checking Chemistry on page 137 To select which types of chemical warnings to display 1 From the File menu choose Preferences 2 Click Display The Display tab appears 3 In the Chemical Warnings section click the types of warnings you want to display To disable the automatic error checking on a specific object Right click the object and deselect Display Warnings When Display Warnings is deselected for an object Red boxes are not displayed for questionable objects Problems are reported by the Check Structure command For more information on the Check Structure commands see Check Structure on page 137 ChemDraw 9 Struct lt gt Name 73 Struct Name Chapter 4 Struct lt gt Name Struct lt gt Name is CambridgeSoft s package of structure to name and name to structure algorithms included with ChemDraw Ultra Together they give you unprecedented power and convenience in creating and naming structures Struct Name generates systematic names for chemical structures with support for the Cahn Ingold Prelog rules for stereochemistry It is under continuing development to improve the range of compounds covered Name Struct is a comprehens
98. 1 Select the object that you want to send to the back in this example the two upper orbitals 2 From the Object menu choose Send to Back The selected object appears behind all other objects in the same layer Bring to Front To place one object in front of another within a layer 1 Select the object that you want to move forward 2 From the Object menu choose Bring to Front The selected object now appears in front of all other objects NOTE When bonds have 3D coordinates those coordinates always determine the visible bond crossings Bring To Front and Send To Back have no visible effect in this case Creating Tables You can create tables of ChemDraw objects with the Table tool or tables of text with the Text tool Creating Tables with the Table Tool Tables created with the Table tool are containers for drawings and data To place a structure in a table you can draw it directly in the table or copy or drag it into the table The Table tool enables you to do the following Create and modify tables Customize the borders Add or delete rows and columns Resize the table and its cells manually Fit a cell around its contents automatically Align cell contents To create a table with the Table tool 1 On the Main Tools palette click the Table tool 2 Do one of the following Click and drag in the document window to create the table The default table has
99. 1 elemental analysis 139 exact mass 139 formula 139 Molecular Weight 139 Calculations see ChemProp lt amp nopage gt 245 CambridgeSoft accessing the website 221 225 CambridgeSoft com 225 Can J Chem Document 256 Caption text boxes closing 79 creating new line 79 Captions Analysis information 139 autoscaling 194 coloring 84 converting to structures 75 creating 84 creating tables 188 editing 85 formula 80 inserting from structure 73 inserting rows in tables 190 justification 81 setting Font Size and Styles 83 subscript 80 superscript 80 Table column spacing 189 iv CambridgeSoft Administrator Captions continued text overview 84 width 85 Carbon 13 shifts see 13C 1H shifts estimating Cation drawing 97 CCITT Group 3 and 4 203 CD Template 198 cds format 199 cdx file format 198 saving as 26 cdxml format 198 Center on Page command 184 Centering objects 184 Chain Angle description 59 Changing aspect ratio 117 Bond orientation 70 bond type 69 default settings 21 perspective 181 settings when transferring 194 tolerance 110 Character Map 20 Charges specifications 234 symbols drawing 98 Check Structure overview 137 when copying 138 Checking Chemistry 137 Chem3D 141 Chem3D objects caution when sharing files 198 ChemBioNews Com 224 ChemClub com 221 ChemDraw 2 x file format 198 199 3 5 file format 199 cdx format 198 closing 30 ctp ctr file formats 198 ChemDraw continued customizing 20 Hot
100. 1 show stereochemistry 139 Structure searching in ChemDraw Excel 212 Structures 3D 141 Aligning 34 Style Sheet file format 199 Page Setup settings 181 saving document settings 21 Style sheet Document settings 21 Style Sheets color palette 133 creating 255 default 21 provided 255 Style caption 80 Subscript command 80 Substituents 151 Substructure searching in ChemDraw Excel 212 Superatom ISIS 200 Superscript command 80 Suppliers finding online 223 Suppress chemical warnings 31 72 Syntax Checking 137 Synthesis Synlett Document 256 ChemDraw 9 xix System requirements 11 T Table tool 186 Tables column spacing 189 creating 188 creating with Table tool 186 inserting rows 190 moving in 189 TCL spots crescent 107 Technical support 227 228 serial numbers 227 system crashes 228 troubleshooting 228 Template Panels 136 Template Tool description 16 using 133 Templates Autoscaling 134 coloring 133 creating 134 135 drawing with 134 file format 202 fusing 134 fusing with existing structure 134 orientation 134 135 overview 133 panel 136 resizing 136 resizing template panes 136 reusing 134 saving template documents 136 spiro linkage 134 Text atom label format 82 Atom label textbox 86 atom label editing 87 atom labels automatic justification 82 Text continued caption editing 85 caption creating tables 188 coloring 84 creating 79 formatting 80 types 79 Text Box closing 79 creating new line 7
101. 13C NMR Shifts ChemNMR redraws the molecule with the estimated shifts and displays the information and line spectrum in a new window as shown below Ultra Ultra H H 7 02 7 02 7 18 7 01 3 22 6 58 6 39 ChemNMR H 1 Estimation Estimation Quality blue good magenta medium red rough Protocol of the H 1 NMR Prediction Node Shift Base Inc Comment ppm rel to TMS CH 7 02 7 26 1 benzene 0 12 1 C C 0 12 1 C CH 7 02 7 26 1 benzene 0 05 1 C C 0 19 1 C CH 7 18 7 26 1 benzene 0 04 1 C C 0 12 1 C CH 7 01 7 26 1 benzene 0 05 1 C C 0 20 1 C CH2 3 22 1 37 methylene 1 22 1 alpha 1 C C C C C C 1 0 63 1 alpha C C H 6 58 5 25 1 ethylene 1 65 1 1 C C R C C C C 1 gem 0 32 1 C 1 C C C C C C 1 trans H 6 39 5 25 1 ethylene 0 09 1 1 C C R C C C C 1 trans 1 05 1 C 1 C C C C C C 1 gem 0 1 2 3 4 5 6 7 PPM 148 Working With Structures CambridgeSoft NMR Shift Information ChemNMR Administrator ChemDraw 9 Drawing Query Structures 149 Atom Properties Chapter 10 Drawing Query Structures What Are Query Structures Using a query structure to specify properties for atoms and bonds provides an efficient way to search chemical databases such as ChemFinder DARC RS3 or ISIS Base You can use a query structure to narrow or broaden your search For example creating a query structure indicating a bond as either double or single might broaden your search Indica
102. 22 deleting 124 generic 161 ChemDraw 9 xiii Nicknames continued overview 121 troubleshooting 123 Nicknames generic description 161 editing 162 nicknames dat 121 NMR see ChemNMR Spectra Non PostScript printing high resolution 29 Macintosh 196 Normal view 181 Numbering atoms 89 O Object Add Frame 101 Align 34 Distribute 185 Group 118 Join 117 Ungroup 118 Objects aligning 184 centering 184 deleting 111 Distributing 185 distributing 185 grouping 118 joining 117 moving 111 ordering 185 reflecting 115 selecting all 111 ungrouping 118 using crosshair with 183 using rulers with 182 Objects embedding 204 OLE 194 Online Help see Help Online Menu browse SciStore com 224 CambridgeSoft homepage 225 ChemOffice SDK 225 CS technical support 222 lookup suppliers on SciStore com 223 register online 221 Online menu ACX numbers 224 ACX structures 223 Open command 24 Open Special command 23 Opening ChemDraw Excel 207 Orbital Tool description 15 fill patterns 94 Fixed Angle 94 overview 94 Orbitals drawing 94 grouping 94 type 94 Ordering objects 185 Orientation Benzene Ring Tool 67 Cyclohexane Chairs 67 Cyclopentadiene Ring Tool 67 double Bond 70 of page 180 rings 66 templates 134 user defined templates 135 Original view 181 Overlap multipaged documents 178 P Packbits compression 203 Page border 177 layout 177 xiv CambridgeSoft Administrator Page continued orientation 180 over
103. 3D Molecular Modeling and Analysis Molecular Modeling and Analysis Chem3D Ultra includes MOPAC Tinker and set up control interfaces for optional use of GAMESS 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 Excel to explore structure activity relationships and use add on Conformer for conformational searching Publish and view models on the web using the Chem3D Plugin Chem3D Pro brings workstation quality molecular visualization and display to your desktop Convert ChemDraw and ISIS Draw sketches into 3D models View molecular surfaces orbitals electrostatic potentials charge densities and spin densities Use built in extended H ckel to compute partial atomic charges Use MM2 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 Large Molecular Visualization Molecular Modeling amp Analysis D E S K T O P Chem3D Pro Premier Modeling Visualization amp Analysis Create 3D models from ChemDraw or ISIS Draw accepts output from other modeling packages Model types space filling CPK ball amp stick stick ribbons VDW dot surfaces amp wire frame Compute amp visualize partial charges 3D surface properties amp orbital mapping
104. 4990 EMAIL info cambridgesoft com MAIL 100 CambridgePark Drive Cambridge MA 02140 USA MAE 04980 0408
105. 6 Saving a copy of a document 27 changes automatically 24 defaults 21 document 26 in different file formats 27 structures in ChemDraw Excel 212 template documents 136 with different name or location 26 ChemDraw 9 xvii Saving customized settings 21 Scale command 116 dialog box 116 Scaling by a percentage 117 fixed length 116 objects 116 when Transferring information 193 SciStore com 224 Scrap files 193 Scripts menu 30 SDK Online accessing 225 Searching ChemDraw Excel 212 databases 149 export compatibility 172 for chemical information online 222 query properties supported 149 Select All command 111 Selecting all 111 bonds 110 Lasso 109 Marquee 109 Pen tool shapes 104 several objects 111 structures 111 Selection Rectangle Resize handle 116 Rotation handle 113 Selection Tool definition 15 deleting with Delete key 111 deselecting objects 111 distorting objects 117 highlight box 110 joining 117 Lasso 15 Marquee 15 selecting all 111 Selection Tool continued selecting several objects 111 using 109 Selection adding to 111 Send to Back command 186 Set Color Button 131 Setting margin width 86 preferences 20 Settings document 21 highlight box 65 tolerance 65 Shaded style shapes 105 Shapes closed 105 filled 105 plain 105 shaded style 105 Sharing Information 191 Shift key deselecting objects 111 Shortcuts see Keyboard shortcuts Shortcuts table of 247 249 Show Crosshair 183 Show Page 182 Show R
106. 62 Topological Polar Surface Area 246 Topology 157 TPL style sheet 202 Trackball tool 114 Transferring information across platforms 205 keeping in scale 193 Translation query property 154 Triple bond drawing 63 Troubleshooting online 222 Tutorial 31 Types of bonds 232 U Undo 25 command 25 lost on save 25 Ungroup command 118 Ungrouping Objects 118 Unsaturation 153 Unspecified atom properties in queries 151 Up to in queries 152 Use Bitmap Fonts When Available 92 Use Defaults atom properties 151 ChemDraw 9 xxi Use Defaults continued bond properties 156 Bracket properties 164 Preferences 21 User guide online 222 User Defined Templates 134 Using the clipboard 112 V Variable attachment command 127 View menu 17 Viewing analysis information 138 atom properties 150 bond properties 156 chemical properties 141 Spectrum structure assignments 146 W Warnings chemical 71 Web site CambridgeSoft accessing 225 Wedge Bond drawing 64 What s New 9 White space adjusting in atom labels 86 Window analysis 138 chemical properties 141 Window menu overview 28 stationery documents 23 Windows Help 10 Windows Metafile 202 WMF format 202 Z Zooming see Changing Perspectives Desktop Software Enterprise Solutions Research amp Discovery Applied BioInformatics Knowledge Management Chemical Databases C A M B R I D G E S O F T Document Manager E Notebook Enterprise Desktop Enterprise Disc
107. 7 588 9390 MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge MA 02140 USA ChemOffice ChemDraw Chem3D ChemFinder amp ChemInfo are trademarks of CambridgeSoft 2002 All other trademarks are the property of their respective holders All specifications subject to change without notice C O N S U L T I N G amp Consulting amp Services Consulting amp Services Development Installation amp T Development Installation amp Training Services raining 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 CambridgeSoft now offers the following professional services to assist businesses in fully utilizing the power of technology Decision Making CambridgeSoft believes that successful technology utilization begins with the assessment and decision making process Our 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 proces
108. 9 GIF Image gif 200 ISIS SKC and ISIS TGF 200 ISIS Reactions rxn 200 JDX jdx dx Import Only 201 JPEG jpg jpeg Import Only 201 MDL MolFile mol 201 Molecular Simulations MolFile msm 201 PICT Macintosh 202 PICT scaled 4X Macintosh 202 PNG file png 202 SMD smd 202 SPC spc Import Only 202 Template Style Sheet cts 202 Windows Metafile wmf 202 TIFF file tif 203 Inserting Objects from Other Applications 204 Transferring ChemDraw Documents Across Platforms 205 Transferring from Macintosh to Windows 205 Transferring from Windows to Macintosh 205 Transferring Files to ChemDraw Plus 3 1 for the Macintosh 205 Chapter 13 ChemDraw Excel Setting Up ChemDraw Excel 207 Importing Tables 208 Converting
109. 9 Text Settings captions font size and style 83 changing defaults 21 Text Tool atom labels 86 labeling atoms 86 toggling with lasso tool 89 Text tool 15 TGF file format 200 TIFF options 200 203 resolution 200 203 TIFF format 203 Tilting an object 117 TLC spots custom about 108 custom adding 107 display or set Rf 107 enlarged 107 resizing 108 Rf about 107 tails 107 wide 107 TLC tool 105 Toggling between tools 110 fixed length fixed angle 64 text tool with lasso tool 91 Tolerance effect on highlight box 110 setting 65 xx CambridgeSoft Administrator Tool Alternative Group 167 Arrow 99 Reaction Atom To Atom Mapping 170 Templates 133 Text 79 Toolbars and Menus 17 Tools Acyclic Chain 68 acyclic chain 15 Arc 102 arc 15 arrow 15 attachment point 168 benzene ring 66 bold bond 62 bold wedge bond 62 Bond 15 62 Bracket 101 brackets 15 Chemical Symbol 96 chemical symbols 15 cyclohexane chair 66 cyclohexane ring 66 cyclooctane ring 66 cyclopentadiene ring 66 cyclopentane ring 66 cyclopropane ring 66 dashed bond 62 dative bond 62 Drawing Elements 99 drawing elements 15 eraser 15 hashed bond 62 hashed wedge bond 62 hollow wedge bond 62 Lasso 109 lasso 15 Marquee 109 marquee 15 mass fragmentation 143 Tools continued multiple bond 63 Multiple bonds 15 Orbital 94 orbital 15 Pen 102 pen 15 Query 159 ring 16 Structure perspective 15 Table 186 template 16 Text 15 Trackball 114 wavy bond
110. 96 The new document created is based on a Style Sheet or Stationery Pad NOTE These special documents allow you to have pre configured settings for different tasks In this example the ACS template provides the required settings for structures to be published in all ACS journals One column layout Page Setting Bonds with a Fixed length of 0 2 inches Drawing Setting Atom Labels in 10 point Arial or Helvetica font Text Setting 2 From the File menu choose Save As 3 Type tut4 cdx in the appropriate text box CH CH O Fischer Glucose 70 CHO CH2OH OH H H HO OH H OH H ChemDraw 9 Tutorials 45 Tutorial 4 Fischer Projections 4 Select a folder in which to save the file 5 Click Save Draw the first bond 1 Click the Solid Bond tool 2 Point in the document window Drag downward vertically to draw the first bond Add a second bond 1 Point to the lower atom 2 Drag downward to draw the second bond 3 Repeat step 1and step 2 three times to draw a total of five bonds NOTE When you drag the pointer along the length of the bonds the pointer alternates between an arrow and a cross The arrow indicates you are pointing over the center of a bond and the cross indicates you are pointing to an atom Add horizontal bonds to the second atom in the string of bonds you created Point to C2 and click the atom to add a perpendicular bond 46 Tuto
111. Any For ChemFinder the same as default Included for compatibility with other systems where the default may be different Natural Indicates an isotopically unmodified nuclide Enriched Indicates a mixture of isotopically substituted and isotopically unmodified nuclides Deficient Indicates a depleted label that is the nuclide is present in less than the natural ratio Nonnatural Indicates an isotopically substituted nuclide that is essentially all the molecules of the compound have only the indicated nuclide ChemDraw 9 Drawing Query Structures 155 Bond Properties Abnormal Valence The Abnormal Valence property specifies whether selected atoms can have a valence other than normal Normal valences for each element are defined in the Isotopes Table file in the ChemDraw Items folder NOTE The Abnormal Valence atom property does not provide a visual indicator The Abnormal Valence options are described in the following table NOTE If Abnormal Valence is Allowed any Invalid Valence messages for those atoms are ignored automatically by the Check Structure command Bond Properties To define bond properties of selected bonds in a structure 1 Do one of the following Select a bond using a selection tool Shift click to select multiple bonds 2 Then do one of the following Right click point to Bond point to the property you want and then choose the appropriate opti
112. ChemDraw Chemical Structure Drawing Standard ChemOf ce Com ChemDraw Chemical Structure Drawing Standard CS ChemDraw 9 0 for Windows and Macintosh ChemDraw is a standalone application within ChemOf ce an integrated suite including Chem3D for molecular modeling and analysis BioAssay for biological data retrieval and visualization Inventory for managing and searching reagents E Notebook for electronic journal and information ChemFinder for searching and information integration and ChemInfo for chemical and reference databases User s Guide Revision 9 0 1 12 22 04 License Information ChemOf ce ChemDraw Chem3D ChemFinder and ChemInfo programs all resources in the ChemOf ce ChemDraw Chem3D ChemFinder and ChemInfo application les and this manual are Copyright 1986 2004 by CambridgeSoft Corporation CS with all rights reserved worldwide MOPAC 2000 and MOPAC 2002 are Copyright 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 on the part of CS Both these materials and the right to use them are owned exclusively by CS Use 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 ChemOf ce ChemDraw Chem3D CS MOPAC ChemFinder Inventory E Notebook BioAssay and ChemInfo are not supplied wi
113. Click the atom to add a bond Change a single bond into a double bond 1 Point to the atom shown below and hold the mouse button down 2 Drag as shown below over the existing single bond Release the mouse button Add labels to the structure 1 Point to the atom shown below ChemDraw 9 Tutorials 33 Tutorial 1 Reaction Schemes 2 Double click the atom 3 Type an uppercase O in the text box that appears 4 Close the text box by doing one of the following Click in an empty area of the window Click another tool Next you duplicate a structure and then create another structure from the duplicate Duplicate the structure 1 Click the Lasso tool The last structure drawn is automatically selected 2 Point over the Selection Rectangle 3 Press and hold Ctrl or Option The hand pointer with a plus sign indicates that you are in the duplication mode of a selection tool 4 Drag the Selection Rectangle to the right A copy of the structure appears as you begin drag The original structure remains in its position Release the mouse button when the copy is clear of the original NOTE When you create a copy as shown above you can drag it anywhere in the document window If you want the copy to remain aligned with the original hold Shift while dragging Modify the duplicated structure 1 Click the Solid Bond tool 2 Point in the copied structure to the atom shown b
114. Command E toggle fixed angles Command G group selected objects Shift Command G ungroup objects Shift Command H flip horizontal Option Shift Command H rotate 180 horizontal Command J join selected objects Command K scale ChemDraw 9 Shortcuts and Hotkeys 251 Structure Commands Text Commands Drawing Commands Command L toggle fixed lengths Command R rotate Shift Command V flip vertical Option Shift Command V rotate 180 vertical Command bring to front Command send to back Shift Click select multiple objects Enter to execute Command Shift Command K clean up structure Shift Command N convert name to structure Option Command N convert structure to name Enter to execute Command Shift Command C centered Shift Command J justified Enter to execute Command Shift Command L flush left Shift Command M automatic justification Shift Command R flush left Shift Option 8 in a label insert symbol Enter to execute Command Shift click with saturated double bond ring tools change orientation of double bonds Command click with ring tools except chairs create resonance delocalized ring Option Shift click with the pen tool remove a curve segment Shift drag with resize handle distort limit resize to X or Y axis Command drag copy a selected object Command drag with alkane chain tool change directio
115. Creating Headers and Footers 178 Page Setup 179 Page Orientation 180 Reduce or Enlarge 180 Saving Page Setup Settings 181 35mm Slide Boundary Guides 181 Changing Perspectives 181 Magnifying with the View Menu 181 Magnify 181 Actual Size 181 Reduce 182 Fit to Window 182 Using the Magnification Control 182 Arranging Objects 182 Using Rulers 182 Showing Rulers 182 Hiding Rulers 183 Using the Crosshair 183 Displaying the Crosshair 183 Moving the Crosshair 184 Aligning Objects using the Crosshair 184 Cam
116. Critical Pressure CHEMPROP CRITICAL PRESSURE Critical Volume CHEMPROP CRITICAL VOLUME Heat of Formation CHEMPROP HOF 218 ChemDraw Excel CambridgeSoft Using ChemDraw Excel Functions Administrator NOTE Using ChemProp requires that you have a version of ChemDraw that includes ChemProp installed Inserting Functions To insert a ChemDraw Excel function into your worksheet 1 Select an empty cell 2 From the Insert menu select Function The Paste Functions dialog box appears 3 Select ChemDraw Functions 4 Select the function to insert from the list and click OK A dialog box appears 5 Enter the structure cell reference for which you want to calculate properties in the Structure box 6 If the function takes a second argument enter it in the Element type box Element type arguments are optional 7 Click OK Each property is calculated using the best avail able method For more information about calcula tion methods see the ChemDraw manual If the cell reference argument does not point to a valid struc ture cell N A appears in the cell Gibbs Free Energy CHEMPROP GIBBS Ideal Gas Thermal Capacity CHEMPROP IDEAL GAS tPSA CHEMPROP TPSA Property Function ChemDraw 9 Appendices 219 Appendices This section contains the Appendices for each of the sections Section I General Appendix A Accessing the CambridgeSoft Web Site Appendix B Technical Suppo
117. Draw 9 Drawing Query Structures 157 Bond Properties The Bond Type options are described in the following table NOTE Not all bond types are supported in all file formats When an unsupported bond type is saved to a given file format it is converted to the closest equivalent that is supported Topology The Topology property specifies the ring environment of the selected bonds The Topology options are described in the following table Option Search Result Single all and Dative Finds compounds with the bond type you select for the selected bonds Double or Double Bold Finds compounds whose selected bonds are double Double Either Finds compounds whose selected bonds are double bonds and have either cis trans stereochemical configuration Aromatic Finds compounds whose selected bonds are aromatic Tautomeric Finds compounds whose selected bonds are tautomeric Triple Finds compounds whose selected bonds are triple Quadruple Finds compounds whose selected bonds are quadruple Any Finds compounds regardless of the bond type of the selected bonds S D Finds compounds whose selected bonds are single or double D A Finds compounds whose selected bonds are double or aromatic S A Finds compounds whose selected bonds are single or aromatic Option Search Result Unspecified Default Finds compounds regardless of environment Ring Finds compounds where the selected bonds are
118. Draw structures using ChemDraw Excel for Windows Find reagents with ChemFinder and design experiments ChemDraw Excel Search Chemical Databases D E S K T O P ChemFinder Pro Premier Searching amp Information Advanced search and structure query features Stores structures and reactions along with calculated data and associated information Search by substructure including stereochemistry using ChemDraw Import export MDL SD and RD files 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 Adds chemical calculations to Excel functions Useful for graphing and analyzing chemical data Purchase Excel High Throughput Purchasing Finds vendor and price information from ChemACX Database or ChemACX Com Search for suppliers and purchase online Maintains lists of compounds CombiChem Excel Combinatorial Chemistry in Excel Generate combinatorial libraries Choose starting materials and reaction schemes View structures and track plate well assignments SYSTEMS amp LANGUAGES English amp Japanese Windows 95 98 Me NT 2000 XP This software is Windows only All specifications subject to change without not
119. Drawing elements are not a part of the structure they are drawn near If you double click on a bond atom or atom label with a drawing tool they are not selected To group drawing elements with a structure use the Group command in the Object menu For more information see Grouping Objects on page 118 Some drawing element types are available with fill patterns hollow no fill pattern gray and black You can change the type of box circle or oval using the Curves menu Arrows 94 dpi 100 Drawing Orbitals Symbols Arrows Arcs and Other Shapes CambridgeSoft The Drawing Elements Tools Palette Administrator The Info window indicates the length and angle relative to the X axis while you use any of the drawing element types Drawing Boxes To draw a box 1 Select one of the box tools 2 Point where you want a corner of the box to be located 3 Drag from one corner of the box diagonally to the opposite corner Drawing Circles and Ovals To draw a circle or oval 1 Select one of the circle or oval tools 2 Point where you want the center of the circle to be located 3 Drag outward from the center Resizing or Rotating Drawing Elements A drawing element is resized or rotated from the same point that it was originally drawn For example a shadowed box is resized from the corner where the plain edges meet You cannot rotate Boxes Brackets or Daggers When a box or closed bracket is rotate
120. FAX 1 617 588 9390 MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge MA 02140 USA ChemOffice ChemDraw Chem3D ChemFinder amp ChemInfo are trademarks of CambridgeSoft 2002 All other trademarks are the property of their respective holders All specifications subject to change without notice CS ChemFinder CS ChemFinder Searching and Information Integration Searching and Information Integration ChemFinder Pro is a fast chemically intelligent relational database search engine for personal group or enterprise use Extended integration with Microsoft Excel and Word adds chemical searching and database capability to spreadsheets and documents An ever increasing number of chemical databases are available in ChemFinder format Compatibility with MDL ISIS databases is provided by SDfile and RDfile import export ChemFinder provides network server workgroup functionality when used with ChemOffice WebServer ChemFinder Word is an extension of Microsoft Excel and Word for Windows Create structure search able spreadsheets and index documents with embedded ChemDraw structures ChemDraw Excel adds chemical intelligence to Microsoft Excel for Windows Show structures in spread sheet cells tabulate chemical calculations and analyze data with Excel functions and graphs Purchase Excel uses ChemDraw Excel to manage reagent lists and track purchasing information CombiChem Excel builds combinatorial libraries with embedded Chem
121. Font Win Mac Times New Roman Times Atom Label Size 10 pt Caption Font Win Mac Times New Roman Times Caption Size 10 pt Drawing Area Width x Height 8 5 cm x 25 4 cm 1 column 17 cm x 25 4 cm 2 column Page Size US Letter Reduction 100 Drawing Atom Label and Caption Text Settings in Journal Style Sheets or Stationery Pads N HO O H J Mol Med Morphine ChemDraw 9 Document Settings 261 ChemDraw Style Sheets or Stationery Pads Fixed Length 30 pt Bold Width 2 pt Line Width 1 pt Margin Width 2 pt Hash Spacing 2 7 pt Chain Angle degrees 120 Bond Spacing of length 12 Atom Label Font Win Mac Arial Helvetica Atom Label Size 10 pt Caption Font Win Mac Times New Roman Times Caption Size 12 pt Drawing Area Width x Height 7 5 in x 10 in Page Size US Letter Reduction 100 Drawing Atom Label and Caption Text Settings in Journal Style Sheets or Stationery Pads N H OH O OH New Document Morphine 262 Document Settings CambridgeSoft ChemDraw Style Sheets or Stationery Pads Administrator Fixed Length 30 pt Bold Width 4 pt Line Width 1 6 pt Margin Width 2 pt Hash Spacing 2 7 pt Chain Angle degrees 120 Bond Spacing of length 15 Atom Label Font W
122. ILES string is a way to describe a chemical structure in a line of text Several software packages use SMILES strings as a way to enter and store chemical structure information A SMIRKS string is a way to describe chemical reactions in text If you select a reaction and use the Copy As SMILES command a SMIRKS string is copied to the clipboard If you use the Paste Special SMILES command when a SMIRKS string is on the clipboard a reaction is pasted into your docu ment Creating SMILES Strings To create the SMILES string for the following structure 1 Select the structure using a selection tool 2 From the Edit menu point to Copy As and then choose SMILES The SMILES string corresponding to the trans 2 amino cyclohexanol molecule is trans ferred to the Clipboard To display the SMILES string Paste the string in a document window NH2 OH N C H 1 C H O CCCC1 192 Sharing Information CambridgeSoft Using Drag and Drop Administrator When the SMILES string is on the Clipboard you can transfer it to another application that can inter pret and manipulate SMILES strings If you select more than one structure in Chem Draw and choose Copy SMILES from the Edit menu the SMILES string for each structure is copied to the Clipboard and separated from the previous SMILES string by a period SMILES supports an alternate notation for aromatic structures using lowercase letters Chem Draw generates this ty
123. Keys File 88 Nicknames 121 ChemDraw Items folder description 27 Hotkeys 87 isotope table 155 nicknames 121 Open Special 28 overview 27 scripts 22 style sheets and stationery pads 24 templates 133 window menu 27 ChemDraw Laser Prep 29 ChemDraw Excel adding structure files 211 adding structures 210 adding structures as SMILES 211 adding structures by name 212 adding structures with ChemDraw 211 aligning structures 215 Get ChemDraw List command 209 naming molecules 214 overview 207 searching 212 starting 207 ChemFinder com 223 Chemical name structure from 74 Chemical properties calculating 141 ChemProp 141 Chemical Properties window 18 141 Chemical Symbols palette 96 rotating 98 tool 15 96 Chemical syntax checking 71 Chemical Warnings overview 71 ChemDraw 9 v Chemical Warnings continued suppressing 31 72 Chemically significant text 233 Chemicals purchasing online 224 Chemistry checking 137 of ChemDraw 231 ChemNMR description 243 using 147 ChemOffice SDK accessing 225 ChemProp boiling point 246 calculations 245 ClogP 246 CMR 246 critical pressure 246 Critical temperature 246 critical volume 246 description 245 Freezing point 246 Gibbs Free Energy 246 Heat of Formation 246 Henry s Law 245 Ideal Gas Thermal Capacity 246 logP 245 molar refractivity 246 Thermal Capacity 246 TPSA 246 using 141 ChemProp using with ChemDraw Excel 217 ChemStore com lt Italic gt see SciStore com chm files 198 CI
124. LE objects that can be copied and pasted into other OLE client applications When a drawing is transferred from ChemDraw into another document type that supports OLE you can open the drawing and edit it from within the client application For example to edit a ChemDraw drawing inserted into Microsoft Word for Windows version 6 0 or later do one of the following Select a ChemDraw drawing in a Word docu ment and from the Edit menu point to CS ChemDraw Drawing Object and then choose Edit Double click a ChemDraw drawing in a Word document The ChemDraw tools and menus replace those of Word Use the ChemDraw tools to edit the drawing When you have finished making changes Click in another area of the document The Word tools and menus are restored Edit Graphic Object Macintosh ChemDraw supports the Edit Graphic Object EGO protocol for editing ChemDraw structures pasted into other types of documents When you drag an object from ChemDraw into another type of document that supports the EGO protocol or copy it with the clipboard you can double click on the object and it appears in a ChemDraw document window When you close the ChemDraw docu ment window any changes you made are reflected in the other document NOTE As of this writing versions of Microsoft Word after 5 0 do not support EGO Transferring PostScript Macintosh To obtain the highest quality drawings possible on a PostScript prin
125. Large choice of bonds arrows brackets orbitals reaction symbols amp LabArt Style templates for most chemical journals Compatible with Chem3D ChemFinder ChemInfo E Notebook amp Microsoft Office ChemDraw Plugin Advanced WWW Structure Client Embed live ChemDraw documents in WWW pages Works with Netscape amp Internet Explorer Included with ChemDraw Ultra amp Pro SYSTEMS amp LANGUAGES Windows amp Macintosh English Japanese French German 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 ChemDraw Ultra Ultimate Drawing Query amp Analysis Adds ChemDraw Excel ChemNMR Name Struct AutoNom amp ChemFinder Word to ChemDraw Pro Name Struct AutoNom creates structures from names amp vice versa ChemNMR predicts 1H amp 13C NMR line spectra with peak to structure correlation Polymer notation based on IUPAC standards ChemDraw Excel brings chemistry to Excel EMAIL info cambridgesoft com WWW www cambridgesoft com TEL 1 800 315 7300 INT L 1 617 588 9300 FAX 1 617 588 9390 MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge MA 02140 USA ChemOffice ChemDraw Chem3D ChemFinder amp ChemInfo are trademarks of CambridgeSoft 2002 All other trademarks are the property of their respective holders All specifications subject to change without notice CS Chem3D CS Chem
126. MD 202 SPC 202 style sheet 199 Template 198 TGF 200 TIF 202 TIFF 203 TPL Style sheet 202 WMF 202 File formats CML 199 JPEG 201 File formats table 197 Files inserting 204 Fill patterns orbital tool 94 Filled style shapes 105 Filtering tables 212 Fit to Window 182 Fixed Angles bonds 64 orbitals 94 toggling on off 64 Fixed Lengths bonds 64 description 60 Fixed Lengths continued drawing with 64 scaling 116 toggling on off 64 Flags stereochemical See Indicators Flatten command 114 Flip Horizontal command 115 Flip type 166 Flip Vertical command 115 Flush Left justification 81 Flush Right justification 81 Font imaging speed 92 new captions 83 substitution 79 Footers creating 178 Format atom labels 82 text 80 Formula command description 138 using 80 Free Energy definition 142 Free Energy calculation 246 Free Sites drawing 161 in queries 152 Freezing Point calculation 246 Front to Back ordering 185 Fusing templates 134 G G Groups 167 Galactic Industries file format 202 Generic Groups 167 Generic Nicknames description 161 editing file 162 Get ChemDraw Excel List 209 Getting Started Tutorial 31 x CambridgeSoft Administrator Gibbs Free Energy definition 142 GIF format 200 GRAMS software 202 Graphical User Interface 13 Grouping orbitals 94 using 118 Grouping Objects 118 Groups Integral 118 GUI see Graphical User Interface H Hard Coded HotKeys 89 Hash Spacing description 61 Hashed
127. P Rules 236 Clearing mapping 172 spectrum structure assignments 147 stereochemical markers 139 Click to select objects 110 Clipboard 191 Check Structure 138 Clipboard 191 continued copy 113 cutting 112 moving objects 112 pasting 112 Clipping files 193 CLogP 142 ClogP 246 Closed Brackets rotating 100 Closed style shapes 105 Closing caption text box 79 ChemDraw 30 documents 27 CML file format 199 CMR 142 CMYK Planar and Contiguous 200 203 Color autoscaling 194 menu 130 overview 129 saving settings 133 Color dialog box 131 132 Color Palette 131 Coloring captions 84 objects 130 Colors maximum number of 129 131 194 Column spacing 189 Compression 203 Connection Table example file 267 file format 199 267 Contract label 124 Conventions 10 Convert name to structure limitations 74 Convert structure to name automatic captions 73 Converting name to structure 75 to 3D 141 Converting Names to Structures 75 vi CambridgeSoft Administrator Copy and Check Structure 138 As SLN command 192 As SMILES command 191 duplicating objects 113 objects 113 with Clipboard 191 with drag and drop 192 Creating atom labels 86 HotKeys 88 mirror images 115 new document 23 SLN strings 192 tables 188 templates 135 text 79 Critical Pressure definition 142 Critical pressure calculation 246 Critical Temperature definition 142 Critical temperature calculation 246 Critical Volume definition 142 Critical volume calcul
128. Page Layout 177 Chapter 12 Sharing Information 191 Chapter 13 ChemDraw Excel 207 Appendices 219 Appendix A Accessing the CambridgeSoft Web Site 221 Appendix B Technical Support 227 Appendix C The Chemistry of ChemDraw 231 Appendix D How ChemNMR Works 243 Appendix E How ChemProp Works 245 Appendix F Shortcuts and Hotkeys 247 Appendix G Document Settings 255 Appendix H Chemistry File Formats 267 ChemDraw 9 Contents Introduction What s New in ChemDraw 9 0 9 Conventions 10 Additional Information 10 Quick Reference Card 10 Help System 10 CambridgeSoft Web Pages 10 Installation and System Requirements 11 Microsoft Windows Requirements 11 Macintosh Requirements 11 Site License Network Installation Instructions 11 Chapter 1 ChemDraw Basics The ChemDr
129. Park Drive Cambridge MA 02140 USA ChemOffice ChemDraw Chem3D ChemFinder amp ChemInfo are trademarks of CambridgeSoft 2002 All other trademarks are the property of their respective holders All specifications subject to change without notice C H E M I C A L The Merck Index The Merck Index Chemistry s Constant Companion Chemistry s Constant Companion Industry Standard Among printed chemical reference works one that stands out for its integrity detail and longevity is The Merck Index This encyclopedia of chemicals drugs and biologicals has 10 250 monographs 446 named reactions and 23 additional tables Merck amp Co Inc the publisher of The Merck Index has chosen CambridgeSoft to pro duce the complete contents of the 13th edition in a fully searchable ChemOffice format Detailed Monographs The 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 Merck Index so valuable is its extensive coverage The information provided includes chemical common and generic names trademarks CAS 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 ChemDraw structure as well as substructure Moving this information to th
130. Plate tool Includes support for crescent shaped spots custom spots and transparent backgrounds See The TLC Tool on page 105 Fragmentation tools The Mass Fragmentation tool is quicker and smoother New Dissociation and Retrosynthesis tools See Mass Fragmentation Tool on page 143 and Drawing Reactions on page 144 Support for more file formats Import JPEG import and export GIF TIFF PNG and BMP Import and export Chemical Markup Language CML Expand generic structures Generate collections of up to 500 molecules with the expansion tool See Expand Generic Structures on page 145 Smarter chemical warnings Support for linear atoms and hydrogen bonds Easier to use warnings now appear on tooltips tPSA Calculation An algorithm to calculate Topological Polar Surface Areas for the prediction of pharmaceutical transport properties has been added to ChemProp See Topological Polar Surface Area on page 246 Multiple ChemDraw Items folders See About This User s Guide This User s Manual contains information for the ChemDraw application for Windows and Macintosh It assumes that you are familiar with the basics of your Windows operating system If you are not please refer to your system manual before using the applications Some of the material describes tasks that must be performed in conjuction with other integrated CambridgeSoft products The material on the
131. Ruler guides that bracket the object With this bracketing you can quickly establish the height and width of the selected objects Hiding Rulers To Hide the rulers From the View menu choose Show Rulers The check mark disappears Using the Crosshair Use the Crosshair to align objects relative to each other and to space objects a consistent distance apart The axes of the Crosshair can be moved within a document window Displaying the Crosshair To show the Crosshair From the View menu choose Show Crosshair A check mark appears next to the Show Crosshair command and the Crosshair appear within a document window To assist you in aligning objects the Crosshair includes grid lines that extend from the major division marks on each axis You can also show the Rulers while the Crosshair are displayed so that you can see the unit measurement associated with each of the divisions on the Crosshair axes Ruler Guides Ruler Guides 184 Working With Page Layout CambridgeSoft Arranging Objects Administrator Moving the Crosshair To move the Crosshair 1 Position the pointer where the Crosshair axes intersect When the pointer is near to the center of the Crosshair it changes to an arrow 2 Drag the Crosshair To constrain the movement of the Crosshair to the X or Y direction Shift drag the crosshair Aligning Objects using the Crosshair To use the Crosshair to align objects do one
132. S 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 The 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 Massachusetts 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 CambridgeSoft Database Products Important This CambridgeSoft End User License Agreement is a legal agreement between you either an individ ual or a single entity and CambridgeSoft Corporation for the CambridgeSoft 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
133. The destination document has an atom label font size is set to 14 points When the atom label is pasted into the destination document the font size is scaled by a factor of 0 5 to give a final atom label font size of 7 points 194 Sharing Information CambridgeSoft Embedding Objects Windows Administrator Captions ChemDraw autoscales captions are autoscaled using the ratio of the fixed length in the destination document to the fixed length in the source docu ment times the caption font size The font size of the caption can be any size and is not related to the setting in the Settings dialog box This assures that captions are always in proportion to the bonds with which they are pasted For example If the source document has a fixed length of 1 0 cm and the destination document has a fixed length of 2 0 cm and the caption you are pasting is 12 points then the resulting caption size after autoscaling is 2 0 cm 1 0 cm x 12 points 24 points Non bond Objects and Color All objects that are not affected by settings in the Document Settings dialog boxes such as arrows and boxes are scaled to maintain the same propor tions to bonds that were present in the source docu ment With the exception of the foreground and back ground color the other colors present in the selec tion to be pasted are added to the destination document s Color Palette if they are not already present up to a maximum of 20 total colors Th
134. To transfer from Windows to ChemDraw Plus 3 1 for the Macintosh 1 In ChemDraw for Windows save the file in the ChemDraw chm format 2 Insert the disk with the ChemDraw for Windows files into the Mac floppy drive 3 If you are using PC Exchange double click the floppy disk icon to display the files From Mac Version To Window s Version Instructions 4 0 4 0 Save as ChemDraw and add cdx to the file name 4 0 3 x Save as ChemDraw 3 x and add chm to the file name 3 5 x 3 x Save as ChemDraw and add chm to the file name From Windows Version To Mac Version Instructions 4 0 4 0 Save as the default ChemDraw cdx 3 5 x 4 0 Save as ChemDraw 3 x chm 3 5x 3 x Save as ChemDraw 3 x chm and follow the instruc tions in Transfer ring files to Chem Draw Plus 3 1 for the Macintosh below 206 Sharing Information CambridgeSoft Transferring ChemDraw Documents Across Platforms Administrator 4 From the Control Panels select PC Exchange 5 Select Add 6 Change the DOS suffix to chm 7 In the application selection find CSC Chem Draw on your Mac and click once to highlight the selection 8 Change the document type to CHMS If you are using a translator other than PC Exchange you need to use an editor such as ResEdit or Disktop to change the type and creator of the files being transferred The type should be
135. Ultra Win Chem3D Pro Win Chem3D Std Win Chem3D Plugin Pro Win E Notebook Ultra Win ChemFinder Pro Win ChemFinder Std Win Software CS ChemOffice CS ChemOffice Software Suites E Notebook Ultra Desktop to Enterprise Solutions Desktop to Enterprise Solutions ChemOffice WebServer Enterprise Solutions amp Databases Oracle Cartridge amp Database Webserver Knowledge Management E Notebook Enterprise Document Mgr Discovery LIMS amp 21CFR11 Compliance Research amp Discovery Registration System Formulations amp Mixtures Inventory Manager amp CombiChem Enterprise Applied BioInformatics BioAssay HTS amp BioSAR Browser Chemical Databases The Merck Index ChemACX amp ChemSAR Properties ChemOffice Ultra Ultimate Drawing Modeling amp Information Adds The Merck Index E Notebook CombiChem MOPAC BioAssay amp ChemACX to Office Pro ChemOffice Pro Premier Drawing Modeling amp Information Includes ChemDraw Ultra Chem3D Pro ChemSAR Excel ChemFinder Pro ChemINDEX amp ChemRXN databases Also Available Separately ChemDraw Ultra Ultimate Drawing Query amp Analysis Adds ChemDraw Excel ChemNMR Name Struct AutoNom amp ChemFinder Word to ChemDraw Pro ChemNMR Stereochemistry Polymers amp BioArt ChemDraw Pro Premier Drawing amp Database Query Define complex database queries ISIS Draw amp Base compatible via copy paste Structu
136. Unspecified Default Finds compounds regardless of whether the selected bonds are affected by the reaction Center Finds compounds where the selected bonds are affected by a reaction but the type of change is unspecified Make Break Finds compounds where the selected bonds are either broken or created in a reaction Change Finds compounds where the bond order of the selected bonds changes in a reaction Make amp Change Finds compounds where the selected bonds are formed broken or undergo a change in bond order Option Search Result Not Center Finds compounds where the selected bonds are not part of the reaction center Not Modified Finds compounds where the selected bond s orders do not change but which may or may not be part of the reaction center Unmapped Finds all compounds Option Search Result ChemDraw 9 Drawing Query Structures 159 Query Tools Palette In the table below points are may be atoms centroids or points Lines may be lines or Normals All constraint values can be edited with the text tool Only exclusion spheres show the change visually When you create a point a dialog box is displayed Specify the distance from the first selected point to the calculated point The distance may be specified as an absolute value in or as a percentage of the distance between the selected points Negative values indicate that the calculated point is further from the second point than
137. actual size F6 fit to window F7 magnify F8 reduce F11 toggle rulers Ctrl H toggle crosshair Enter to execute Command F2 bring to front F3 send to back Ctrl E toggle fixed angles Ctrl G group selected objects Shift Ctrl G ungroup objects Shift Ctrl H flip horizontal Alt Shift H rotate 180 horizontal Ctrl J join selected objects Ctrl K scale selected object Ctrl L toggle fixed lengths Ctrl R rotate Shift Ctrl V flip vertical Alt Shift V rotate 180 vertical Shift Click with Lasso Marquee or Structure Perspective tools select multiple objects Enter to execute Command Shift Ctrl K clean up structure Shift Ctrl N convert name to structure Alt Shift Ctrl N convert structure to name Enter to execute Command F9 in a label subscript the selected character or the next character typed Enter to execute Command ChemDraw 9 Shortcuts and Hotkeys 249 Help Commands Drawing Commands ChemDraw Mac Shortcuts See also ChemDraw Hotkeys on page 252 File Commands F10 in a label superscript the selected character or the next character typed Shift Ctrl C centered Shift Ctrl J justified Shift Ctrl L flush left Shift Ctrl M automatic justification Shift Ctrl R flush right Enter to execute Command F1 Help contents Shift F1 context sensitive Help Enter to execute Command Sh
138. ad that file becomes the default To view the default Style Sheet or Stationery Pad Click the File menu The New menu item displays the name of the Style Sheet or Stationery Pad Saving Customized Settings as Style Sheets or Stationery Pads Every new document created with ChemDraw uses a Style Sheet or Stationery Pad to obtain its docu ment settings Style Sheets or Stationery Pads can also contain predefined objects When you create a new document you actually create an untitled copy of the Style Sheet or Stationery Pad Any changes you make to the copy of the Style Sheet or Statio nery Pad do not affect the Style Sheet or Stationery Pad itself You can create a Style Sheet or Stationery Pad with your own customized setting by saving it as a cds file If you store the cds file in the ChemDraw Items folder it appears in the Open Special menu so you can access it from the File menu To save a document s setting as a Style Sheet or Stationery Pad 1 Choose Save As from the File menu Preferences Gen 150dpi 22 ChemDraw Basics CambridgeSoft Customizing ChemDraw Administrator The Save As dialog box appears 2 Name the file and change the type in OS X format to CD Style Sheet cds or ChemDraw Stationery 3 To save the file in the ChemDraw items folder click the Go To ChemDraw Items button 4 Click Save Applying Document Settings From Other Documents To apply document settings to the ac
139. age appear on the screen Using the Magnification Control When you use the Magnification control you can display magnifications from 10 to 999 of the normal size of your page The magnification control allows you to select a specific value To use the Magnification controls Windows Select a value from the drop down list or type a value Macintosh Do one of the following Select a value from the drop down list Select Other from the drop down list In the dialog box that appears type a value and click OK Arranging Objects This section describes methods for positioning aligning and layering objects in a document window Using Rulers You can use the rulers to position objects a measured distance away from some reference point or create objects of an approximate size The units used for the ruler are set in the Preferences dialog box where you have the choice of inches centimeters or points Showing Rulers To display the rulers From the View menu choose Show Rulers Macintosh Windows ChemDraw 9 Working With Page Layout 183 Arranging Objects A check mark appears next to the Show Rulers command and the rulers appear along the top and left edges of a document window As you move the pointer Ruler Guides appear on each ruler indicating the position of the pointer Ruler guides also appear when you drag selected objects In this case however there are two
140. al analysis for the entire document a structure part of a structure or a caption in Formula style To view analysis information From the View menu choose Show Analysis Window The Analysis window appears Values for selected objects in the document window are shown If nothing is selected in your document values for the entire document are shown You can have this window open as you draw in the document It shows the current values as you draw The Decimals setting applies to Exact Mass Molecular Weight and m z only The following table describes the analysis properties AnalysisToolbar 150 dpi Property Description Formula The molecular formula showing the exact number of atoms of each element in the molecule and charges radicals and isotopes Exact Mass The exact molecular mass of the structure where atomic masses of each atom are based on the most common isotope for the element Molecular Weight The average molecular mass of the structure where atomic masses are based on the natural abundance of all isotopes of the element ChemDraw 9 Working With Structures 139 Showing Stereochemistry To paste information about a structure as a caption 1 Click the check boxes for the information that you want to paste 2 Click Paste The information appears as a multiline caption below the structure You can edit this information with the text tool The information in the label updates a
141. al 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 Notebook Enterprise and Document Manager are at the leading edge of the integration of corporate knowledge management with 21CFR11 Compliance These products are designed so that as your organization reviews its internal processes for 21CFR11 Compliance the software can be configured to support these internal processes Major requirements of 21CFR11 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 Notebook Enterprise and Document Manager can be integrated with existing critical data systems Document and Record Management E Notebook Data Capture M A N A G E M E N T 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 individu
142. als 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 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 With CambridgeSoft 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 E Notebook Enterprise and Document Manager integrate corporate knowledge with regulatory compliance Consulting teams analyze and adapt existing procedures to comply with new regulations Systems include authentication and digital signatures and adapt to changing regulations and demands EMAIL info cambridgesoft com WWW www cambridgesoft com TEL 1 800 315 7300 INT L 1
143. alysis Window The Analysis window appears You can drag the window to any position CHO CH2OH CHO CH2OH H CHO CH2OH H H H H Fischer Glucose 70 C H O C H 2O H O H H H H O O H H O H H ChemDraw 9 Tutorials 49 Tutorial 5 Perspective Drawings 3 Click Paste to paste the information as a caption below the structure Save and close the document 1 From the File menu choose Save 2 From the File menu choose Close Tutorial 5 Perspective Drawings In this tutorial you will learn how to create a perspective drawing by drawing the following D glucose as a Haworth projection Create a new document using the ChemDraw default style 1 From File menu point to Open Special and then choose New Document 2 From the File menu choose Save As 3 Type tut5 cdx in the appropriate text box 4 Select a folder in which to save the file 5 Click Save Draw a ring 1 Click the Cyclohexane Ring tool 2 Point in an empty area of a document window 3 Click to add a ring Rotate the ring 1 From the Edit menu choose Select All 2 Point to the upper right corner of the Selection Rectangle the Rotation handle NOTE The cursor changes to a curved double sided arrow to indicate the rotation mode of a selection tool is activated 3 Drag the Rotation handle to the right about 30 degrees The amount of rotation is displayed on the screen and in
144. an they were created for ChemDraw Template ctp ctr Use the ChemDraw Template file format to save template documents that appear in the template pop up menu ChemDraw cdx The ChemDraw file format is the native format for ChemDraw version 4 0 and later This is a public tagged file format that stores information about a ChemDraw structure in a series of data blocks This format is designed to be easily generated and inter preted by other programs This format accurately stores anything that can be drawn in ChemDraw NOTE Imported drawings saved within a ChemDraw file created using ChemDraw for Macintosh are lost when the file is opened using ChemDraw for Windows The same applies for objects saved in ChemDraw for Windows and opened on a Macintosh However all ChemDraw specific information is preserved Imported drawings include any graphics pasted into a ChemDraw document from another Macintosh application They also include Chem3D drawings imported using the Insert Object dialog box or the Get 3D Model Edit menu command in ChemDraw for Windows ChemDraw XML xml The cdxml file format is an interpreted version of cdx that conforms to the XML specification unlike binary cdx format cdxml is text based but contains some data For information about XML in general see www xml org ChemDraw 3 5 chm ChemDraw 3 5 file formats are used for saving or opening ChemDraw documents using the version 3 5 x of Che
145. and Upgrading 208 Upgrading Workbooks 208 Importing Hit Lists 209 Importing a Hitlist 209 Error Messages 209 Exporting Tables 210 Adding Structures 210 Adding Structures with ChemDraw 211 Adding a Structure From a File 211 Adding a Structure with a SMILES String 211 Adding Structures by Name 212 Saving Structures 212 ChemDraw 9 Searching 212 Filter Tables 212 Similarity Searches 213 Working with Structures 214 Naming Structures 214 Using the Clipboard 214 Viewing Structures 214 Showing and Hiding Structures 214 Aligning Structures 215 Resizing Structures
146. 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 Data are owned by CS or its suppliers You may not copy distribute or otherwise make the Included Data publicly available Licensed users of ChemOffice Enterprise and Workgroup and the accompanying Plugin software products may access search and view the Included Data and may transmit the results of any search of the Included Data to other users of the licensed ChemOffice 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 distribute 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 Data All rights not specifically granted under this Agreement are reserved by CS 5 Separation of Components The Software
147. ard system commands for transferring information within and between ChemDraw documents and between ChemDraw and documents created using other applications You can transfer information using the Clipboard drag and drop file formats When you drag and drop ChemDraw information or use the clipboard the object you are copying can be edited Using the Clipboard You can use the clipboard to transfer part or all of the information within an active document window between applications on the same computer or a networked computer Use the standard Copy and Paste or Cut and Paste tools to transfer infor mation to any application that supports these tools The information is transferred as a ChemDraw drawing object Double clicking on it will open ChemDraw and allow you to edit the object See Embedding Objects Windows on page 194 and Edit Graphic Object Macintosh on page 195 for more information on editing ChemDraw objects embedded in other documents If the Clipboard contains ChemDraw structures and you are pasting into another ChemDraw docu ment the pasted information is scaled to the settings in the current document For more infor mation see Autoscaling on page 193 If you are pasting the ChemDraw drawing into a document from which you are planning to print to a PostScript printer see Transferring PostScript Macintosh on page 195 SMILES and SMIRKS Strings A SM
148. argin Width adjusting 60 description 60 effect on Bond crossings 60 specifying 86 Margin width specifying 86 Marquee tool 109 Mass Fragmentation Tool 143 Mass spectra importing as JDX 201 importing as SPC 202 mass charge displaying 139 Maximize objects 181 MDL MolFile 201 MDL RGFile 201 Melting Point definition 142 Menus view 17 Menus and toolbars 17 Message Area display of fixed angles 64 Messages analysis 238 status 238 Mirror images creating 115 mol 201 mol file format 201 Molar refractivity 246 Molecular Design Limited see MDL Molecular mass definition 138 Molecular Simulations MolFile 201 Molecular Weight caption 139 definition 138 display in status bar 18 how calculated 139 Monochrome 200 203 Moving atoms bond tool 70 atoms Selection Tool 112 crosshair 184 in tables 189 objects 111 MS see spectra MSI MolFile format 201 Multi attached atom labels command 125 Multi Center Attachments command 126 overview 236 Multiple Attachment Points 168 Multiple Bond tool 63 Multiple bonds tool 15 Multiple Undo 25 Multiple paged documents setup 178 N Name inserting as structure 74 of structure inserting 73 Name to structure seeName Struct Name automatic structure from 74 Name Struct 74 converting 75 limitations 74 paste special 75 with German names 74 NameStruct 73 Native file format 26 New Color Button 131 New Command 23 New document 23 New Slide 256 New Template creating 134 Nicknames defining 1
149. ark Drive Cambridge MA 02140 USA ChemOffice ChemDraw Chem3D ChemFinder amp ChemInfo are trademarks of CambridgeSoft 2002 All other trademarks are the property of their respective holders All specifications subject to change without notice Document Manager Document Manager Desktop to Enterprise Document Searching Desktop to Enterprise Document Searching Document Manager Everyone produces reports electronically but searching information located in these reports has always been difficult Thousands of Microsoft 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 Manager solves this problem and requires no change in how you write and distribute reports Easy to Use Document Manager manages a repository of new documents These can be Microsoft Word Excel PowerPoint or many other document types When a new document is added Document Manager 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 ChemDraw and ISIS Draw Finding infor mation in reports is now as simple as entering a query through your web browser Unattended Data Indexing As new documents are added they are automatically indexed an
150. aterials 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 SIIA 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 ChemDraw ChemOffice Manuals Includes Databases Desktop Applications Software Tips Enterprise Solutions A Guide to CambridgeSoft Manuals Enterprise Solutions ChemOffice Chem3D ChemFinder And Databases amp E Notebook Chemical Structure Drawing Standard ChemDraw Chem3D ChemFinder E Notebook Desktop Inventory Desktop B
151. ation 246 Crosshair displaying 183 moving 184 using to align objects 184 CT file format 199 CTP file format 198 CTR file format 198 CTS file format 202 Curves autoscaling 194 for creating arrows 105 segment deleting 105 Custom templates 134 Customized settings saving 21 Customizing ChemDraw 20 saving document settings 21 using Scripts 30 Cut objects 112 Cycloalkane rings converting to delocalized rings 67 Cyclohexane Chair Ring Tool description 66 orientation 67 Cyclohexane Ring Tool 66 Cyclooctane Ring Tool 66 Cyclopentadiene Ring Tool 66 Cyclopentadiene Ring changing orientation 67 Cyclopentadiene rings drawing 67 Cyclopentane Ring Tool 66 Cyclopropane Ring Tool 66 D Daggers 101 Dashed Bond Tool icon 62 Databases support for query structures 149 supported 149 Dative Bond drawing 64 Tool icon 62 Default atom properties resetting 151 bond properties resetting 156 changing 21 document location 23 file format 24 save file format 26 Stationery pad 21 Style Sheet 21 Defined Nickname 122 Deflate compression 203 Delete Column from template 136 Delete Row from template 136 ChemDraw 9 vii Deleting atom labels 87 Backspace key 111 curve segment 105 Delete key 111 Nicknames 124 objects 111 Pen tool shapes 105 Delocalized rings drawing 67 Deselecting objects 111 Detecting errors Automatic error checking 71 Check Structure command 137 Disable chemical warnings 31 72 Discarding changes 25 Displ
152. ation about these options see Chapter 12 Sharing Information 5 Click Save or OK If you type a name that already exists in the same directory the existing document is replaced If you do not want to replace the original ChemDraw document use a different name For information about other file formats see Chapter 12 Sharing Information Closing a Document To close a ChemDraw document From the File menu choose Close If the document contains unsaved information you are prompted to save the file Accessing Documents Quickly You can access ChemDraw documents quickly by placing them in the ChemDraw Items folder and then selecting them from the Open Special menu You can access open documents quickly by using the Window menu The ChemDraw Items Folder The ChemDraw Items Folder is located by default in the same folder as your ChemDraw application It contains the ChemDraw preferences hotkeys nicknames and isotopes files scripts and the generic nicknames file It also contains template documents and template Stationery Pads You can have multiple ChemDraw Items folders This is useful in corporate installations for maintaining personal files such as nicknames as well as standard templates To add a path to a ChemDraw Items folder 1 From the File menu choose Preferences The Preferences dialog box appears 2 Click the Directories tab 3 Click the Add New button browse to a loca tion
153. aving the file For more information see Drawing Boxes on page 100 and Using Multi Center Bonds on page 126 These options only affect embedded images Objects created in ChemDraw always output at maximum resolution and in full color To include correct PostScript font names in Windows EPS files you must have Adobe Type Manager ATM installed Only ATM fonts are saved in the EPS file Pro Pro Pro Pro 200 Sharing Information CambridgeSoft Importing and Exporting Administrator Resolution Available resolutions range from 72 computer monitor to 1440 dpi high resolution output When choosing a resolution keep in mind that the size of the file increases as the square of the resolu tion Color You can select from the following color options Monochrome Forces all objects to black and white Grayscale Translates colors to shades of gray 24 bit RGB Stores colors using computer monitor style of color encoding 32 bit CMYK Uses printing press style of color encoding Groups each color type sequentially This provides better compression GIF Image gif Graphics interface format GIF is useful for working with the hypertext markup language HTML used in displaying information on the World Wide Web A GIF image can be displayed directly on a Web page rather than having to down load the drawing for viewing in a Helper applica tion The default GIF format con
154. aw Graphical User Interface 13 The Main Tools Palette 14 Setting the Default Tool 16 Tearing Off Palettes 17 Optional Toolbars 17 Showing and Hiding Toolbars 17 Docking and Undocking Toolbars 17 The Status Bar or Message Area Windows 18 The Analysis Window 18 The Chemical Properties Window 18 The Info Window 19 Periodic Table 19 Character Map 20 Customizing ChemDraw 20 Setting Preferences 20 Document and Object Settings 21 Default Style Sheet or Stationery Pad 21 Saving Customized Settings as Style Sheets or Stationery Pads 21 Applying Document Settings From Other Doc uments 22 Applying Object Settings from Other Docu ments 22 Using Documents
155. aying atom mapping 171 cross hairs 183 entire page 182 reaction mapping 171 rulers 182 Distorting objects 117 Distributing Objects 185 Distributing objects 185 Document location default 23 multi paged 177 posters 178 reverting to last saved 25 saving 26 settings 256 Stationery pad settings 256 style sheet settings 256 Document Settings overview 21 Document Setup multiple paged documents 178 Posters 178 Document window drawing area 177 enlarging 177 orientation 180 Document window continued reducing 177 Documentation web page 222 Double bond changing type 69 drawing 63 orientation 70 Double either bonds drawing 63 Drag and drop 192 Drawing acyclic chains 68 Arcs 102 bonds by clicking 65 boxes 100 charge symbols 98 cyclopentadiene rings 67 double bonds 63 double either bonds 63 dz2 orbitals 96 fixed length bonds 64 free sites 161 H Dash Symbol 96 H Dot Symbol 96 mirror images 115 orbitals 94 quadruple bonds 63 radicals 97 resonance delocalized rings 67 rings 66 rings with fixed length 66 sigma orbitals 94 single bonds 62 s orbitals 94 stereochemical symbols 161 structure automatically from name 74 triple bonds 63 with templates 134 Drawing area 177 Drawing daggers 101 Drawing Elements autoscaling 194 viii CambridgeSoft Administrator Drawing Elements continued color 99 distorting 100 fill patterns 99 resizing 100 rotating 100 Drawing Elements Tool 15 Drawing settings changing default
156. ays grouped If you group part of a structure with other objects the resulting group contains the entire structure If you add atoms or bonds to a grouped structure the new atoms and bonds are part of the group To group several objects 1 Select the objects to group using a selection tool 2 From the Object menu choose Group To select an individual object within a group Move the selection tool over an object until it is highlighted and click once The object is selected not the group To select grouped objects Move the selection tool over an object until it is highlighted and double click The entire group is selected Ungrouping Objects To ungroup objects that are grouped 1 Select a group as above 2 From the Object menu choose Ungroup All the objects previously grouped become individual objects Creating Integral Groups To create a group in which individual objects cannot be accessed 1 Select the objects to group using a selection tool 2 From the Object menu choose Group ChemDraw 9 Manipulating Drawings 119 Grouping Objects 3 With the group selected right click point to Group and then click Integral To restore an Integral group to a regular group 1 Select the Integral group 2 Right click point to Group and then deselect Integral 120 Manipulating Drawings CambridgeSoft Grouping Objects Administrator ChemDraw 9 Advanced Drawing Techniques
157. bel that is parsed from right to left A bond attached to the open parenthesis of a repeating group is treated as if bonded to the first of those groups CH2COOC OPh 3 CH2CCH3 O H3CCH2C O CH2 4OH CH2 CH2 3OH A bond attached to the close parenthesis or repeat count of a repeating group is treated as if bonded to the last of those groups Implicitly using standard valence rules Explicitly using a space period unsuperscripted or unsubscripted bullet or combination An unsuperscripted unsubscripted integer at the start of a fragment is recognized as a stoichiometric multiplier and is treated as if the appropriate number of fragments were drawn explicitly CH2 4 CH2 CH2 2CH2 COO Na COO Na COO Na COO Na COO Na COO 3 3Na COO 3 Na Na Na 234 The Chemistry of ChemDraw CambridgeSoft Chemical Conventions Administrator is not recognized by ChemDraw and generates an error message if you try to analyze it Generally empirical formulas C2H6 and H2SO4 are not recognized but structural formulas CH3CH3 and HOSO2OH are Molecular weight and elemental analyses of empirical structures is possible but the Expand Label command does not work with them Empirical structures are discarded when they are transferred to other applications that require unambiguous structures Chemically significant text must be entirely in Formula or for isotopes and c
158. bjects to resize The resize handle is located in the lower right corner of the selection rectangle 2 Point to the Resize handle The cursor becomes a double headed arrow 3 Drag the resize handle until the object is the size you want The screen and Info window indicate the percentage enlarged or reduced Scaling Objects To resize objects with the Scale command 1 Select the objects to scale 2 Do one of the following From the Object menu choose Scale Double click the Resize handle The Scale Objects dialog box appears Use the first two options in the Scale Objects dialog box to scale all selected objects so that the median selected bond has a specified length based on the following scale factor To scale bonds so that the Fixed Length becomes the new median bond length 1 Select the top option The fixed length presently in the Drawing Settings dialog is shown in parentheses at the end of the line for this button 2 Click Scale To scale the bonds to a new fixed length that you specify 1 Select the middle option 2 Type the new median bond length in the box to the right of the button Resize handle 50 scale factor new median bond length current median bond length ChemDraw 9 Manipulating Drawings 117 Joining Objects 3 The current median bond length for the selection is shown in the highlighted text box when the dialog box initially appears 4 Click Scale
159. bridgeSoft Administrator Hiding the Crosshair 184 Centering on a Page 184 Aligning Objects 185 Distributing Objects 185 Front to Back Ordering 185 Send to Back 186 Bring to Front 186 Creating Tables 186 Creating Tables with the Table Tool 186 Creating Tables with the Text Tool 188 Creating the First Row column headings 188 Creating a New Row 189 Adjusting Row or Column Spacing 189 Moving Around In Tables 189 Inserting a New Row 190 Chapter 12 Sharing Information Using the Clipboard 191 SMILES and SMIRKS Strings 191 Creating SMILES Strings 191 Pasting SMILES from Clipboard 192 Creating SLN Strings 192 Using Drag and Drop 192 Transferring Between ChemDraw Documents 193 Autoscalin
160. button You can tear off these toolbars and place them anywhere in the ChemDraw screen You cannot dock torn off toolbars To tear off a toolbar Click the arrow on the lower right of the tool Holding the mouse button down point to the title bar and release the mouse button You can drag the toolbar by its title bar to repo sition it You can also show or hide a toolbar by selecting it from the Other Toolbars submenu on the View menu Optional Toolbars ChemDraw provides a number of optional toolbars and information windows to facilitate production of ChemDraw documents These toolbars are accessed from the View menu They are divided into three basic groups Standard Toolbars and Show Windows Tool Palettes Templates Showing and Hiding Tool bars To show or hide a toolbar From the View menu select a toolbar A check mark appears next to the item when the toolbar is displayed Docking and Undocking Toolbars The standard toolbars can be docked or undocked Docked toolbars can attach to any edge of the DefaultTool 150 dpi standard toolbars templates tool palettes information windows 18 ChemDraw Basics CambridgeSoft Optional Toolbars Administrator ChemDraw window Undocked toolbars can float anywhere in the ChemDraw screen To dock a toolbar Drag the toolbar to the edge of the ChemDraw screen where you want it to dock D
161. c nicknames separated by commas followed by a close bracket Atom to Atom Mapping You can create correspondences between atoms in different structures for use in creating queries for searching a reaction database The reactions mapped can be single or multi step You can assign atom to atom mapping for creating records for a reaction database and for creating queries for searching a reaction database You can assign atom mapping in two ways Automatic mapping using the Map Reaction Atoms command from the Structure menu Manual mapping using the Reaction Atom Atom Map tool on the main tools palette During either type of mapping process the mapping algorithm perceives and assigns a reaction center for the reactants and products When a reaction map is established you can point to an atom in one structure with the Reaction Atom Atom Map tool selected to highlight the mapped atom in the other structure OMe OPh OCH3 OH X S Se M B C ChemDraw 9 Drawing Query Structures 171 Atom to Atom Mapping Always Display and Print Atom Mapping To make the symbols always appear and print on the atoms when reaction mapping has been performed 1 From the File menu choose Preferences 2 In the Preferences dialog box click Display 3 Select Always Display and Print Reaction Mapping 4 Click OK Deselect Always Display and Print Atom Mapping to show the symbols only when you se
162. c references for over 10 000 chemicals drugs and biologicals ChemINDEX includes 100 000 chemicals public NCI compounds and others World Drug Index WDI from Derwent contains over 58 000 compounds with known biological activity WDI 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 ChemACX SC is a library of screening compounds Derwent Patents ISI Reactions D ATA B A S E S Reactions Organic Syntheses is the electronic version of the annual and collective volumes of trusted peer reviewed syn thesis procedures published since 1921 by Organic 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 Updated daily CCR is an excellent way to stay on top of recent developments ChemReact and ChemSynth from InfoChem are carefully selected from a database of over 2 5 million reac tions through an automated process of reaction classification With over 390 000 reaction types ChemReact is for
163. can customize the Color menu Colors can be added or existing colors can be changed Changing a color for example Other 2 changes all objects that are using the color NOTE If you select an individual or grouped object that contains multiple colors there is a check mark next to each of the colors in the Color menu The purpose of the check marks is to alert you that a change would affect more than one color ChemDraw 9 Advanced Drawing Techniques 131 Working with Color Customizing the Color Palette You can add remove or change the default foreground and background color and specify the other colors available for coloring objects Changes made to the color palette affect the current document only You can save Color Palette settings foreground background and up to 20 other colors in a Style Sheet or Stationery Pad For more information see Saving Customized Settings as Style Sheets or Stationery Pads on page 21 A summary of each of the options is described in the following table Windows Color Settings To change the palette of colors used in the current document 1 From the File menu choose Document Settings The Document Settings dialog box appears 2 Click the Colors tab 3 Double click the color to change The Color dialog box appears Option Description New Color Add a new color box and set its color using the Color Picker or Color Wheel dialog box Remove Color Delete a colo
164. ce Desktop to WebServer Registration System Formulations amp Mixtures Inventory Manager KNOWLEDGE MANAGEMENT RESEARCH amp DISCOVERY ChemOffice E Notebook ChemDraw Chem3D ChemFinder ChemInfo ChemACX Database ChemSAR Properties The Merck Index Chemical Databases BioAssay HTS BioSAR Browser S O L U T I O N S The Merck Index CombiChem Enterprise ChemACX Database ChemSAR Properties RESEARCH amp DISCOVERY APPLIED BIOINFORMATICS CHEMICAL DATABASES CONSULTING amp SERVICES 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 Registration System Formulations amp Mixtures Inventory Manager CombiChem Enterprise 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 Managing the huge 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 Sys
165. cheme 1 Click the Arrow tool to display the Arrow palette NOTE The triangle in the lower right corner of the Arrow icon indicates it contains a palette 2 Holding the mouse button down move the mouse to the palette title bar then release the mouse button The palette becomes a floating tool bar Drag the palette to the location you want O O O O OH O O OH ChemDraw 9 Tutorials 35 Tutorial 1 Reaction Schemes 3 Click the third arrow from the left in the top row 4 After the arrow is selected release the mouse button NOTE The arrow you choose from the palette becomes the default arrow type To change the arrow type display the arrow palette and select the arrow type you want Draw the arrow you selected 1 Point after the first structure and hold down the mouse button 2 Drag the Arrow to the length you want Release the mouse button NOTE If you need to change the length or the angle relative to the X axis of the arrow 1 Hold Shift and point to the arrowhead a highlight box appears when you are pointing correctly 2 Drag the arrowhead to the length and angle you want Use the Text tool to add line formula or other captions for representing reagents and reactions Insert text in the drawing 1 Click the Text tool 2 Point above the arrow A text insertion point appears as shown below 3 Click to create a text box 4 Type OH NOTE If you want t
166. cing of length 14 Atom Label Font Win Mac Arial Helvetica Atom Label Size 10 pt Caption Font Win Mac Arial Helvetica Caption Size 12 pt Drawing Area Width x Height 368 x 720 pts Page Size US Letter Reduction 100 Drawing Atom Label and Caption Text Settings in Journal Style Sheets or Stationery Pads Helvetica Chimica Acta N HO O H HO Morphine ChemDraw 9 Document Settings 259 ChemDraw Style Sheets or Stationery Pads Fixed Length 18 pt Bold Width 2 5 pt Line Width 1 pt Margin Width 2 pt Hash Spacing 2 5 pt Chain Angle degrees 120 Bond Spacing of length 20 Atom Label Font Win Mac Arial Helvetica Atom Label Size 12 pt Caption Font Win Mac Arial Helvetica Caption Size 12 pt Drawing Area Width x Height 693 pt x 918 pt Page Size US Letter Reduction 80 Drawing Atom Label and Caption Text Settings in Journal Style Sheets or Stationery Pads N H HO O HO J Chin Chem Soc Morphine 260 Document Settings CambridgeSoft ChemDraw Style Sheets or Stationery Pads Administrator Fixed Length 14 4 pt Bold Width 2 pt Line Width 0 6 pt Margin Width 1 6 pt Hash Spacing 2 5 pt Chain Angle degrees 120 Bond Spacing of length 18 Atom Label
167. ckball tool 2 Place the cursor inside the marked rectangle and drag in any direction The structure will rotate on the X or Y axis or a combination of X and Y 3 Use Shift drag to limit the rotation to the X or Y axes only You can also select part of a complex molecule and rotate it around a particular bond NOTE Do not try to use the Trackball to rotate objects such as orbitals or boxes It was designed to manipulate chemical structures only Flatten Command Although the Trackball tool is not intended to be a 3D modeling tool it does introduce z coordinate information that is saved in cdx files This pseudo 3D structure can be confusing when opening files that have been saved after perspective manipulation To remove perspective information 1 Select a structure with the Marquee or Lasso Tool 2 On the Object menu click Flatten All z coordinate information is removed from the structure ChemDraw 9 Manipulating Drawings 115 Reflecting Objects Through Planes Reflecting Objects Through Planes You can reflect structures through planes perpendicular to the X axis or Y axis using a selection tool Used with duplicating you can create mirror images of chemical structures for representing racemic mixtures and other stereoisomers Flipping Objects To reflect an object through a plane perpendicular to the X axis 1 Select the objects to reflect 2 From the Object menu choose Flip Horizontal
168. crap files Windows To create a clipping file or a scrap file 1 Select an object in a ChemDraw document 2 Drag the selection out of the ChemDraw docu ment window onto the desktop C1 CC CC C1 c1ccccc1 Pro Pro Pro Pro C 1 CCCCC 1 ChemDraw 9 Sharing Information 193 Transferring Between ChemDraw Documents A clipping file or a scrap file is created on your desktop To view the information within a clipping file or a scrap file Double click the file s icon A window appears showing the ChemDraw drawing Click the close box to close the clip ping file s window To use the contents of a clipping or scrap file in a document Drag the clipping or scrap file into an open window of an application that supports the drag and drop feature The contents of the clipping or scrap file are copied to the open window The clipping or scrap file is unchanged Transferring Between ChemDraw Documents Whether you use the clipboard or drag and drop when you move objects into another ChemDraw document they will behave in a well defined way In particular you should be aware of the behavior of Autoscaling Bonds Atom Labels Captions Non bond Objects and Color Pasting to an Empty Document Window Autoscaling When you transfer ChemDraw objects using the Clipboard or drag and drop from one ChemDraw document the source document to another Chem Draw document
169. ct the s orbital tool from the palette 2 Point to an atom where the orbital will be centered 3 Drag outward Sigma Orbitals The orbital tools are shown below To draw a orbital 1 Hold down the mouse button over the Orbital tool and drag to select the orbital tool from the palette 2 Point where the orbital will be centered 3 Drag outward along the long axis of the orbital Single Lobe Orbitals Single lobe orbitals are commonly used for indicating a lone pair The single lobe orbital tools are shown below ChemDraw 9 Drawing Orbitals Symbols Arrows Arcs and Other Shapes 95 The Orbital Tools Palette To draw a single lobe orbital 1 Hold down the mouse button over the Orbital tool and drag to select the single lobe orbital tool from the palette 2 Point to an atom where the narrow end of the orbital is to be attached 3 Drag from the narrow end of the lobe to its wide end p orbitals The p orbital tools are shown below To draw a p orbital 1 Hold down the mouse button over the Orbital tool and drag to select the p orbital tool from the palette 2 Point to an atom where the node of the orbital is to be attached 3 Drag from the orbital node to the wide end of the filled lobe Hybrid Orbitals The hybrid orbital tools are shown below To draw a hybrid orbital 1 Hold down the mouse button over the Orbital tool and drag to select the hybrid orbital too
170. cted Searching You can perform the same types of searches in ChemDraw Excel as you can in ChemFinder Exact structure searching Substructure searching Similarity searching Filter Tables Filter tables allows you to search for exact struc tures and substructures To perform a structure search 1 Select a cell containing the label Structure 2 From the ChemOffice menu select Filter Table or click The Search Query dialog box appears ChemDraw 9 ChemDraw Excel 213 Searching 3 Select the search options 4 Click Search The hit list is displayed in a column named Match Items matching the search criteria are labeled as TRUE Similarity Searches You can perform similarity searches to find struc tures with features corresponding to your search structure For more information about similarity searching see the ChemFinder User s Guide To search for similarity 1 Select a cell containing the label Structure 2 From the ChemOffice menu select Similarity Table or click The Similarity Query dialog box appears 3 Select the Search Type 4 Select the Similarity Is value 5 Select the Sort order 6 Click Search If you want to Then search for a structure a To load a structure right click and select Read Structure b To edit the structure double click it c Select the Search Type d Select the Filter Type search for a formula a Type the mole
171. cted is set in the Preferences dialog box 2 Press the Left or Right Arrow key to center the caption beneath its structure This method maintains the alignment created by the Tab key To complete the drawing add a shadowed box around the scheme 1 Click the Drawing Elements tool 2 Select the shadowed box from the palette of drawing elements 3 Point to the upper left corner of the reaction scheme Hold the down the mouse button and drag diagonally downward to the right to draw the box 2 propanone O 2 propanone 2 moles O 2 propanone 2 moles O SelectRectangle 150 dpi pentanone 60 O O OH OH 2 propanone 2 moles 4 hydroxy 4 methyl 2 pentanone 1 mole 38 Tutorials CambridgeSoft Tutorial 2 Drawing an Intermediate Administrator Save and close the document 1 From the File menu choose Save Your document is saved 2 From the File menu choose Close Tutorial 2 Drawing an Intermediate In this tutorial you will draw the following intermediate structure starting from a ring and then add arrows with customized shapes using the Pen tool Create a new ChemDraw document 1 From the File menu choose New Document 2 From the File menu choose Save As 3 Type tut2 cdx in the appropriate text box 4 Select a folder in which to save the file 5 Click Save Draw a ring 1 Click the Cyclohexane Ring tool 2 Point in the document window The Cyclohexane cur
172. ctivity analysis program Users may choose among assays registered in the dictionary or search for assays of interest Providing Catalog Capabilities The power of BioSAR Browser 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 Browser 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 Browser 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 Browser provides a forms based interface in addition to a tabular view Researchers have demonstrated that both form and tabular views are essential Forms provide highly detailed information about one compound whereas tabular views make comparisons between Form and Table Views Data Dictionary Organizes Reports D I S C O V E R Y compounds more feasible There 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 i
173. cular formula or formula query in the And Or Formula Query box b select Clear search for a structure and a formula a To edit the structure double click it b Select the Search Type c Select the Filter Type d Type the molecular formula in the And Or Formula Query box see the R Group Analysis click the Show R Group Analysis box see the previous query click Restore Previous Query If you want to Then 214 ChemDraw Excel CambridgeSoft Working with Structures Administrator The hit list is displayed in a column named Match Items matching the search criteria are labeled as TRUE Working with Structures ChemDraw Excel allows you to rename structures and use the clipboard to cut copy and paste struc tures Naming Structures Excel recognizes certain characters as formulas To prevent the system from interpreting a chemical structure name as an Excel formula you can rename a structure To name a structure 1 Select the structure 2 From the ChemOffice menu select Name Molecule or click The Name Molecule dialog box appears 3 Type the name and click OK Using the Clipboard You can cut copy and paste structures using the clipboard After you cut or copy a structure it is placed on the clipboard You can then paste it into another cell or another application To cut a structure from a cell 1 Select the structure 2 From the ChemOffice menu select Cu
174. curve you want 6 Press the Esc key or click another tool NOTE To place the fewest strategically placed control points for obtaining the smoothest curve work in a magnified view Editing a Curve You can edit a curve by selecting it and manipulating it with the direction lines To select an existing curve 1 Select the Pen tool 2 Point at the curve The cursor will change from a to an arrow when you are positioned correctly 3 Click to select the curve The direction lines appear Changing the Shape of a Curve Use the endpoints of the direction lines to increase or decrease the breadth of the curve or change its direction To change the shape of a curve 1 Select the Pen tool and click the existing curve you want to edit 2 Drag the direction lines to create the shape you want Adding a Segment To extend an existing curve by adding a segment 1 Select the Pen tool and click the existing curve you want to edit 2 Point to the endpoint of a curve until the cursor appears as a hand 3 Alt click or Option click the endpoint The cursor appears as a hand with a sign inside 4 Drag to connect more segments to your curve ChemDraw 9 Drawing Orbitals Symbols Arrows Arcs and Other Shapes 105 The TLC Tool Deleting a Segment To delete a curve segment In the edit mode of the Pen tool Alt Shift click or Option shift click the control point where you want to
175. d Using Multi Center Bonds You can draw with chemical significance polyhapto structures such as ferrocene Cp 2Fe Creating a Multi Center Bond To create a multi center attachment point 1 Select the structure whose center you want defined as a multi center attachment point 2 From the Structure menu choose Add Multi Center Attachment An asterisk is displayed with the fragment to show that it contains a multi center node The asterisk is not visible once a bond is drawn to it You can view the attachment point with a bond or selection tool For more information see Viewing Attachment Points on page 127 To draw a bond to a multi center attachment point 1 Click the Bond tool 2 Point to the asterisk and either click or drag to create a bond To make the bond in ferrocene appear that it is coming from within the ring 1 Double click the wedged bond to make it come forward 2 Select the downward bond Ph CH2CH2CHCH3 Fe Fe ChemDraw 9 Advanced Drawing Techniques 127 Using Variable Attachment Positions 3 Double click on the cyclopentadienyl ring with a selection tool The entire structure including the single bond is selected The Cp ring and the single bond are associated as one structural unit because ChemDraw recognizes the bond between them NOTE For the best looking structure you may need to draw a longer than normal bond You can toggle the Fixed Length command by typ
176. d rotate the structure you will be able to remove the actions as follows 1 Remove the rotation 2 Remove atom label 3 Remove the ring At each step the text of the Undo command indi cates the action being removed Redoing Actions When you undo an action the Redo command becomes active so you can reverse the effect of the Undo command To redo the last action undone From the Edit menu choose Redo The last action undone is reinstated The Undo command changes to reflect that action The Redo command changes to reflect the next action that can be redone Repeating Actions If an action is repeatable the name of the action appears next to the Repeat command on the Edit Menu To repeat an action From the Edit menu choose Repeat The last action performed is repeated Discarding Recent Changes to a Document To retrieve the last saved version of a file From the File menu choose Revert Autosave 26 ChemDraw Basics CambridgeSoft Using Documents Administrator All changes made to the file since it was saved last are discarded and the previous version of the file appears NOTE You can use the Undo command in the Edit menu to remove each individual action since the last save Saving Documents To save a ChemDraw document in the default ChemDraw cdx file format 1 From the File menu choose Save The Save dialog box appears The appearance of the dialog box depends on
177. d along with objects within its borders the area of the box or closed bracket increases to accommodate the rotation of the contained objects To resize or rotate a drawing element 1 Select the Drawing Element tool 2 Hold down the Shift key and point to an end or edge of a drawing element A highlight box appears 3 Drag the object to the new size or orientation The Info window shows the percentage enlarged or reduced when you drag the Resize handle and the number of degrees the object rotates when you drag the Rotation handle To scale atom labels when resizing Hold the Control or Command key while dragging to resize Distorting Circle and Ovals You can distort circles and ovals Shift dragging the Resize handle to convert them into an equivalent closed curve You can distort gray shaded circles and ovals to convert these objects to solid filled curves with fill the same color as the curve You can also distort boxes and closed brackets The remaining Drawing Element types cannot be distorted For more information see Rotating Objects on page 113 and Resizing Objects on page 115 ChemDraw 9 Drawing Orbitals Symbols Arrows Arcs and Other Shapes 101 The Brackets Tools Palette Drawing Lines Lines drawn with the line tool differ in two significant ways from bonds drawn with the bond tools They are not included in chemical interpretation of the drawing Lines that cross ap
178. d by selecting it with the Lasso or Marquee tool By default captions are considered to be chemically significant if possible For example if you create a label like CH3OH you will be able to attach bonds to it and it will be modified appropriately even though you intended it to be a label not a molecule Moreover it s values are included in the Analysis Window which could be confusing If you try to label structures A B and C the B and C labels will be marked with a red box because they have incorrect valences To fix this do the following 1 Select the label with the Lasso or Marquee tool 2 Right click or Control click in the selection 3 Deselect the Interpret Chemically command Alternately you can change the default by unchecking the Interpret Chemically When Possible option on the Captions tab of the Docu ment Settings dialog box Changing the Caption Width To change the width of a caption 1 Select a caption using the Text tool The Caption text box appears around the caption The right side of the text box contains a Resize handle 2 Drag the Resize handle The point at which the text wraps is adjusted as you drag the Resize handle Editing a Caption To open a caption for editing 1 Click the Text tool 2 Point at a caption and click to open the text box The caption text is highlighted To change all of the highlighted text within an ope
179. d chemical information is extracted Similarly if a document is modified it is re indexed No administration of the server is necessary other than routine back up Search Documents by Structure Unattended Data Repository Indexing K N O W L E D G E 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 functional groups and many others Queries 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 ChemFinder Word the desktop version searches Word documents Excel spreadsheets ChemDraw files ChemFinder 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 h
180. d information while Inventory Manager works with chemical databases for complete management of chemical inventories Applied BioInformatics 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 include the ChemACX Database of commercial ly available chemicals The Merck Index 13th 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 CS E Notebook CS E Notebook Electronic J Electronic Journal and Information ournal 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 Notebook 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 ChemDraw documents Excel spreadsheets Word documents and spectral data E Notebook automatically performs stoichiometry calculations on ChemDraw reaction pages Search by struc ture keyword dates and other types of data Maintain required hardcopy archives by printing out pages Information cannot be accide
181. dashed bonds dashed arrows or dashed curves are drawn Color Change the color in of selected objects For more information see Customizing the Color Palette on page 131 Units Set the units used in the Object Settings dialog box to centimeters inches points or picas Atom and Bond Indicators Set which indicators you want to display in your drawings For more information about using indicators see Atom Numbering on page 89 and Showing Stereochemistry on page 139 Adjust this If you want to 2 Point 4 Point 8 Point 62 Drawing Chemical Structures CambridgeSoft Drawing Bonds Administrator Configuring Settings for Objects To configure the drawing settings for a selected object 1 Select the object 2 From the Object menu choose Object Settings The Object Settings dialog box appears with the Drawing tab displayed 3 Configure the settings and click OK The settings you chose are applied to the selected object only Drawing Bonds The Main Tools palette contains the bond tools shown below Multiple Bonds The Multiple Bond tool on the Main toolbar includes the following palette Solid Bond Dashed Bond Hashed Wedged Bond Bold Wedged Bond Hashed Bond Bold Bond Hollow Wedged Bond Wavy Bond Multiple Bonds ChemDraw 9 Drawing Chemical Structures 63 Drawing Bonds You can use the tools on the Multiple Bond palette to create the foll
182. demarks of CambridgeSoft 2002 All other trademarks are the property of their respective holders All specifications subject to change without notice Oracle Oracle Cartridge Cartridge Enterprise Infrastructure for Database Security Enterprise Infrastructure for Database 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 Oracle s 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 Oracle s native SQL language Tools like PowerBuilder Visual Basic and Visual C readily lend themselves as database clients With the addition of the ChemDraw 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 CDX it supports CDXML MolFile Rxn and SMILES formats Moreover there are built in e
183. e background color in the destination document is unchanged and all objects colored using the fore ground color are changed to match the foreground color in the destination document Pasting to an Empty Docu ment Window If you paste a ChemDraw drawing into an empty ChemDraw document and the settings between the documents are different the Change Settings dialog box appears To change the settings in the destination document to match the settings in the source document Click Change Settings All of the settings in the destination document are changed to match those of the source docu ment All of the colors in the Color Palette of the destination document are changed to those specified in the source document To scale the objects from the source document to the settings in the destination document Click Don t Change Settings The settings from the source document are scaled to those in the destination document using the ratios given above NOTE If the source document was created in a ChemDraw version earlier than 3 0 the name of the document appears as Unknown in the dialog box Embedding Objects Windows ChemDraw supports the Object Linking and Embedding OLE protocol on Windows This allows you to edit ChemDraw structures that are ChemDraw 9 Sharing Information 195 Edit Graphic Object Macintosh pasted in other types of documents ChemDraw is an OLE server which means it can create O
184. e 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 Licensee s site At CambridgeSoft s request Licensee will provide a knowl edgeable employee to assist in said audit 2 Ownership The Software is and at all times shall remain the sole property of CS This ownership is protected by the copyright laws of the United States and by international treaty provisions Upon expiration or termination of this agreement you shall promptly return all 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
185. e attachment point and press the Hotkey An attachment point symbol appears 3 Repeat step 2 for all fragments When you create a parent compound that contains an alternative group you defined an attachment point symbol appears next to the label The attachment point number matches that found in the definition The number displayed in the attachment point symbol is the attachment rank order See the example in Multiple Attachment Points on page 168 Multiple Attachment Points If you have well defined multiple attachment points on your structure fragments you can perform searches for specific materials This type of search is especially useful for searching for conformationally similar structures For example you want to find the two compounds below Attachment point symbol R1 NH2 OH F 1 1 1 R1 1 NH2 O NH2 ChemDraw 9 Drawing Query Structures 169 Alternative Groups However you are not interested in the two compounds below By specifying the attachment points order you can exclude the unwanted compounds The parent structure below satisfies the necessary requirements To specify the attachment points order 1 Draw the parent structure shown below 2 Create an Alternative Group Box labeled R1 3 Draw the structure fragments and label them with attachment points When the alternative group definition is complete the attachment point symbols appear
186. e based Polymer Representations 165 Repeat Pattern 166 Flip Type 166 Alternative Groups 167 Defining an Alternative Group 167 Defining Attachment Points 168 Multiple Attachment Points 168 Showing Attachment Rank Indicators 169 Attachment Point Numbering 169 Lists 170 Anonymous Alternative Groups 170 Atom to Atom Mapping 170 Always Display and Print Atom Mapping 171 Automatic Mapping 171 Manual Mapping 171 Clearing Reaction Mapping 172 Exporting Reaction Mapping 172 Export Compatibility 172 Chapter 11 Working With Page Layout Controlling the Drawing Area 177 Setting up Pages 177 Paged Document Setup 178 Poster Documents Setup 178
187. e bond to another 1 Click the Bold Dashed or Solid Bond tool 2 Point to one of the bonds in the double bond 3 Click the bond The double bond changes to the new bond type One of the bonds in the double bond is always a solid or dashed bond NOTE If you click a tautomeric bond solid dashed a second time with the dashed bond tool you create an aromatic double bond dashed dashed Changing Orientation of Wedged and Dative Bonds When you draw or change a bond to a wedged or dative bond the orientation of the bond is chosen appropriately To change the orientation Click the dative or wedged bond with the tool used to create it CO2H HO H CH3 70 Drawing Chemical Structures CambridgeSoft Editing Bonds Administrator The dative or wedged bond is changed to the opposite orientation Changing Alignment of Double Bonds The bonds in a double bond can have any one of three alignments relative to other bonds Above Below Centered To change the alignment of a double bond 1 Click the bond tool used to create the existing double bond 2 Do one of the following Click the center of the double bond The alignment changes Click the center of the double bond again to change to the next alignment Right click or Control click point to Bond Position and then choose the alignment You may also use Hotkeys to change the alignment 1 Click a bond or
188. e 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 Merck 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 Massachusetts United States of America Q IS IT OK TO COPY MY COLLEAGUE S 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 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 earnings 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 protectio
189. e caption 2 Choose Convert Name to Structure from the Structure menu The molecular structure and name appear in the drawing area Br OH O 2 bromobenzoic acid 76 Struct lt gt Name CambridgeSoft Name Struct Administrator Types of Structures Supported by Struct Name Struct Name can name compounds in the following classes of structures category ChemDraw 8 supports ChemDraw 9 adds principal groups in both rings and chains Acid Halides Amide derivatives of acids Alcohols and chalcogen analogs Anhydrides Aldehydes and chalcogen analogs Carbonic acids Amides Imides Amines and Imines Nitric acids Carboxylic Acids Peroxy acids Carboxylic Esters Salts Heteroatomic acid halides Sulfides and chalcogen analogs Heteroatomic acids P B As Sulfoxides and chalcogen analogs Heteroatomic esters Hydrazides Hydrazines Hydroperoxides Ketones and chalcogen analogs Nitriles ChemDraw 9 Struct lt gt Name 77 Name Struct Peroxides S Se and Te Amides S Se and Te Acid Halides S Se and Te Acids S Se and Te Esters Ringed structures Carbomonocyclic structures Bridged monocyclic structures Heteromonocyclic structures Fused polycyclic trivially named structures Ring fusions of only two rings Ring fusions of two multiple ring systems Other compounds Phosphorous and Arsenic compounds Si Ge Sn and Pb compounds Boron compounds Organome
190. e click using a bond or ring tool The highlighted atom label text appears within the Atom Label text box 2 Type the new atom label text over the high lighted text If all the text is not highlighted and you want to select all of the atom label From the Edit menu choose Select All To edit part of the atom label 1 Drag the insertion point over part of the atom label 2 Type the new characters 3 Close the Atom Label text box Deleting an Atom Label To delete an atom label leaving the underlying bonds unchanged do one of the following Click the Eraser tool and then click the atom label With the atom label selected press the spacebar Backspace or Delete Key Labeling Atoms with HotKeys Use HotKeys for rapid labeling of atoms and applying atom and bond properties The file CS ChemDraw Hotkeys in the ChemDraw Items folder contains the Hotkeys provided with ChemDraw You can change most Hotkeys or add new ones by editing the file in a text editor A few are hard coded See Hard Coded HotKeys on page 89 For a list of standard Hotkeys see Shortcuts and Hotkeys on page 247 TIP You can access Hotkey Help directly from the Help menu Use the following methods to label an atom with a Hotkey Method 1 Labeling the last atom drawn 1 Draw a bond by dragging the bond tool in the direction you want the bond oriented 2 Type a Hotkey The last atom drawn is labe
191. e fully searchable ChemOffice 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 Organic Name Reactions Query Search Form D ATA B A S E S Integrated Information Having The Merck Index in ChemOffice format confers another valuable benefit integration with other infor mation sources For example after locating a substance in The Merck Index it is a simple matter to copy the name structure or other data elements to search ChemACX Database to find out whether there are commercial suppliers of the substance The 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 ChemDraw Excel ChemFinder Word E Notebook and Registration System ChemOffice Formats The Merck Index is available in two ChemOffice compatible formats The desktop edition is a CD ROM in a ChemFinder database format for use by an individual researcher The enterprise edition designed for workgroups and larger user communities is served by ChemOffice WebServer to connected users The Merck Index thus adds to the growing set of reference databases served by ChemOffice WebServer Just as ChemOffice integrates the desktop edition of The Merck Ind
192. e most reliable methods for calculation for the given structure Log P and MR values based on literature values rather than a calculation are included in the report file Viewing the Chemical Properties Window To view predicted properties for a selected structure 1 Select the structure to analyze 2 From the View menu choose Show Chemical Properties Window The Chemical Properties window appears To Position Type a value for the position by from the atom or bond center to indicator center angle in degrees or clock in clock time from the atom or bond center to bottom left of indicator baseline offset horizontal and vertical at specified coordinates absolute horizontal and vertical Pro Pro ChemProperties 150 dpi 142 Working With Structures CambridgeSoft Viewing Chemical Properties Administrator The following basic values are displayed NOTE The CLogP and CMR algorithms incorporated in ChemDraw are licensed from BioByte Corp and have been extensively tested and peer reviewed as providing highly accurate results The values produced by these algorithms in ChemDraw should be exactly the same as values produced by the standalone CLogP and CMR applications from BioByte For further information about CLogP and CMR please refer to the BioByte web site at http www biobyte com and to the manuals for ClogP and CMR at http clogp pomona edu medchem chem papers 14 clogp html and
193. e or install any additional soft ware ChemDraw users can either use the ChemDraw Plugin to draw chemical structures directly in the brows er s search page or alternatively submit queries to the database server directly from ChemDraw ChemFinder users can access their own copy of the database right from their local hard drive Electronic Requisitions Traditional sourcing databases were conceived merely 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 This 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 Fully structure searchable database of 500 000 products from 300 chemical catalogs separate ChemACX SC database contains screening compounds Search by name synonym partial name formula and other criteria as well as structure and substructure Shopping cart system works with requisition forms and purchasing systems such as SAP Ariba and Commerce1 to streamline chemical purchasing EMAIL info cambridgesoft com WWW www cambridgesoft com TEL 1 800 315 7300 INT L 1 617 588 9300 FAX 1 617 588 9390 MAIL CambridgeSoft Corporation 100 Cambridge
194. e 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 I 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 I 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 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 th
195. e right applying standard rules of valence to determine which atoms are bound to which The exception is with an atom label in Automatic alignment on the left side of a compound This sort of atom label is displayed backwards H3CO instead OCH3 and is therefore parsed from right to left Standard valences for each atom are defined in the Isotopes Table By definition a simple atom label has all bonds attached to the first or last character A multi attached atom label has bonds connected to more than one character or has all of its bonds attached to a specific character in the middle of the atom label Multi attached atom labels are always parsed from beginning to end but again the beginning might be on the right if the atom label was in Automatic style and on the left side of the original structure Multiple fragments within a single label can be specified in the following ways Chemically Significant Text Often it is simpler to write a chemical formula like MeOH or H2O than it is to draw out an entire atoms and bonds structure ChemDraw correctly interprets any unambiguous structural formula For example CH3COCH2CH3 is recognized as methyl ethyl ketone and MeOH is recognized as methanol On the other hand C6H6 might mean benzene or it might mean one of over 200 other isomers C6H6 A series of any combination of the above A multi attached label that is parsed from left to right A multi attached la
196. e searching The elements in the element list must be separated by commas A space after each comma and brackets are optional An example of an element list is shown below NOTE An element list may contain only atomic symbols plus D deuterium and T tritium To create an element list 1 Open an atom label text box 2 Type an open bracket followed by a list of elements separated by commas Cl Br I followed by a close bracket 3 Close the text box The following example shows a query structure created to find compounds matching the following criteria a Non oxygen chalcogenide bonded to another atom X S Se Te Br I Cl Br I Cl ChemDraw 9 Drawing Query Structures 163 Element Not Lists b Not necessarily carbon a generic nickname c The bond type between the chalcogenide and the other atom to be a single or double bond The A label indicates that the atom may match any atom except hydrogen The mark near the bond indicates that the bond has special properties The bond type specified in the Bond Properties dialog box must be single or double S D The S Se Te specifies that one of these elements must match in the target structures Element Not Lists The element not list specifies that the elements in the list match must not match in the structure for which you are searching Commas must separate the elements in the element not list A space
197. e sequence To edit the atom number style Select the atom number indicator with the Text tool and use the Text menu or Text formatting toolbar Positioning Atom Number Indicators Atom number indicators are positioned automati cally and move appropriately if a structure is modi fied You can reposition them by dragging them to the desired position or with the Position Indicators dialog box To reposition an indicator numerically 1 Right click the indicator to move and choose Position The Position Indicators dialog box appears 2 Click the appropriate Position option and type a value Typing Non Roman Text Use the Character Map for entering non Roman text see Character Map on page 20 Any font available on the computer can be entered into a label using Character Map NOTE Two byte fonts such as Chinese may not work reliably with the Character Map Using the Text Tool with the Lasso Tool The Text tool used in conjunction with a selection tool enables you to perform additional edits such as simultaneously changing several captions or atom labels For more information about selection tools see Chapter 7 Manipulating Drawings You can toggle between the Text tool and the Lasso tool as follows To position Type a value for Position from the atom or bond center to the indicator center by angle or by clock from the atom or bond center to bottom left of indicator baseline
198. e spectra ISIS Reactions 200 SKC file format 200 TGF file format 200 Isotopes specifications 235 Isotopes Table file 155 Isotopes text file 155 Isotopic Abundance 154 J J Mol Mod 1 Column 256 2 Column 256 JCAMP file format 201 JDX file format 201 Joback s Fragmentation Method 246 Joining structures 117 Joining Objects 117 JPEG file format 201 Justification atom labels 82 captions 81 K Kekule structures 67 Keyboard shortcuts edit commands 250 drawing commands 249 251 edit commands 247 file commands 247 249 help commands 249 object commands 248 250 Keyboard shortcuts continued structure commands 248 251 text commands 248 251 view commands 248 250 L Lab supplies purchasing online 224 Labels auto update 74 contracting 124 expanding 125 Landscape page orientation 180 Lasso tool selecting objects 109 toggling with Text Tool 89 Layering atom labels 86 objects 185 Layout page 177 Lewis dot symbol see Lone Pair Symbol Ligand defined 237 Limitations name to structure 74 Line Width 60 Lines drawing 101 Link nodes 163 List Nicknames command 124 LogP 245 Lone Pair Symbol 97 M m z displaying 139 Magnifying with Magnification control 182 with View menu 181 Make Spectrum Structure Assignment 146 Manual Mapping clearing 172 overview 171 Mapping atom 170 automatic 171 xii CambridgeSoft Administrator Mapping continued clearing 172 exporting 172 manual 171 reaction 170 M
199. e widely used JPEG Joint Photographic Experts Group algorithm JPEG images are imported as objects and can be scaled after importing MDL MolFile mol MDL Information Systems Inc MolFile MDL MolFile file format is used by several other Windows Macintosh and UNIX chemical data bases and drawing applications such as ISIS Draw ISIS Base MACCS and REACCS ChemDraw Pro provides two MDL MolFile formats MDL MolFile Text MDL MolFile Mac for Macintosh only This file type is saved with an mMol file type and can be saved and opened with ISIS MDL MolFile files are ASCII text files that can be created or edited in common word processing applications or text editors Atom and bond prop erty information is stored in the MolFile MDL RGFile rgf file format is used by several other chemical databases and drawing applications The MDL File RGFile supports alternate groups whereas an MDL Molfile cannot When you save a ChemDraw file that contains alternate groups as an MDL MolFile it is automatically saved as an MDL RGFile Molecular Simulations MolFile msm Molecular Simulations MolFile format is an ASCII text file used by applications such as ChemNote You can save a ChemDraw Pro document in Molecular Simulations MolFile format for export to one of these applications NOTE ChemDraw uses the file extension msm for Molecular Simulations MolFiles rather than the standard mo
200. ear a spot Shift drag the spot When you position the cursor on a spot and press Shift the cursor assumes one of three shapes depending on how it is positioned 1 Cross arrows used to enlarge a spot 2 Horizontal arrow used to widen a spot 3 Vertical arrow used to elongate a spot or create a crescent NOTE You may want to zoom in to make positioning easier If you want to then 108 Drawing Orbitals Symbols Arrows Arcs and Other Shapes CambridgeSoft The TLC Tool Administrator Resizing Spots You can resize spots by holding down the Shift key while pointing at an edge of the spot Dragging the left or right sides of the spot will adjust the spot s width only Dragging from the top will adjust its height only Dragging from the bottom will adjust the tail only Dragging from any of the other four corners will scale all three values By using combinations of these dragging motions you can reproduce any sized or shape spot you want Custom Spots The TLC tool can create the most common spot shapes Other types of spots such as smears can be reproduced as custom spots The Add Custom Spot command allows you to insert a graphic file for a spot Typically these files would be produced by scanning a TLC plate and saving the spots in a library of spot shapes Solvent front Crescent shaped spot Default spot Enlarged spot Elongated spot Widened spot Origin Lanes
201. eb www cambridgesoft com services mail SYSTEM CONFIGURATION Please cut here or photocopy page US 1 617 588 9300 FAX 1 617 588 9390 WWW www cambridgesoft com EU 00 800 875 20000 FAX 44 1223 464990 EMAIL info cambridgesoft com MAIL 100 CambridgePark Drive Cambridge MA 02140 USA 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 The Merck Index ChemACX Database 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 knowledge 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 CS ChemOf ce Desktop to Enterprise Solutions US 1 617 588 9300 FAX 1 617 588 9390 WWW www cambridgesoft com EU 00 800 875 20000 FAX 44 1223 46
202. ect the structure 2 Right click point to Atom and then deselect Show Atom Number To hide an individual atom number do one of the following 1 Point to or select the atom right click and then deselect the Show Atom Number 2 Point to or select the atom number right click and then select Hide Indicator To remove an atom number indicator Click the indicator with the Eraser tool Editing Atom Numbers You can edit the text and style of atom number indi cators If you want to Then show previously assigned atom numbers Right click point to Atom and then click Show Atom Number Any previously assigned numbers remain unchanged assign new atom numbers Type the Hotkey apostrophe The atoms in the struc ture are numbered sequentially 1 2 3 4 5 6 If you want to Then show a previously assigned atom number Right click and choose Show Atom Number A previously assigned number is displayed assign an atom number Type the Hotkey apostrophe The atoms are numbered in the sequence you choose ChemDraw 9 Drawing Captions and Atom Labels 91 Using the Text Tool with the Lasso Tool To edit atom number text 1 Click the Text tool 2 Do one of the following Select the atom number indicator and type the changes Double click the atom number indicator to change to the next character in th
203. ed to the structure Creating HotKeys To add or edit ChemDraw HotKeys Use a text editor Notepad etc to open the CS ChemDraw Hotkeys file in the ChemDraw Items folder You can use any uppercase or lowercase alphanu meric key as a Hotkey with the exception of the hard coded HotKeys listed previously If a capital and lowercase Hotkey do not exist the Hotkey is assigned to both If a key is used more than once in the file the one closer to the end of the file takes precedence To add a Hotkey 1 Add a new line and type the key you want to use 2 Type a space 3 Type the letters to associate with the Hotkey HotKeys defined for single elements always result in the adding of the appropriate number of hydrogen atoms 4 Save and close the HotKeys file To create a new HotKeys file 1 Create a text file named CS ChemDraw Hotkeys 2 Save the file in the ChemDraw Items folder 3 Click OK or Save H3C C H2 H3C C H2 ChemDraw 9 Drawing Captions and Atom Labels 89 Labeling Atoms With a Bond or Ring Tool Hard Coded HotKeys You cannot edit hard coded HotKeys The following table contains a list of hard coded HotKeys NOTE In earlier versions of ChemDraw quite a few more keys were hard coded In ChemDraw 9 0 all keys not listed above can be customized Labeling Atoms With a Bond or Ring Tool To avoid switching back and forth between tools you can label atoms with a bond or ring too
204. elow and click isobutene w textbox 100 O 34 Tutorials CambridgeSoft Tutorial 1 Reaction Schemes Administrator Add several bonds to a single atom 1 Point to the atom shown below 2 Click the atom three times allowing a pause between each click NOTE If you click too fast the click is interpreted either as a double click which opens a text box or a triple click which duplicates your last atom label Create an atom label using HotKeys HotKeys are keys on your keyboard that are linked to specific atom labels For more information about HotKeys see Labeling Atoms with HotKeys on page 87 1 Point to the atom shown below 2 Type O or o When you use HotKeys that represent a single element the correct number of hydrogen atoms is added to the label Align the structures 1 Select the structures 2 On the Object menu point to Align and then choose T B centers You structures should appear as shown below In the following steps you use a different method for selecting structures and then separate the structures to make room for an arrow 1 Click the Marquee tool NOTE Alternatively you can select the Lasso tool and hold Alt or Option to use the Marquee tool The last object drawn is selected Drag the selection to make room for an arrow Press Shift to maintain the alignment of the structure and drag the Selection Rectangle to the right Add arrows to the reaction s
205. enance 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 Accessed through your favorite web browser the system uses Oracle with robust data model to manage chemical products and their properties Checks for uniqueness during registration and optionally registers duplicates as batches of existing substance User administration and data entry are done through simple easy to learn web forms highly configurable system avoids tedious and expensive customization EMAIL info cambridgesoft com WWW www cambridgesoft com TEL 1 800 315 7300 INT L 1 617 588 9300 FAX 1 617 588 9390 MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge MA 02140 USA ChemOffice ChemDraw Chem3D ChemFinder amp ChemInfo are trademarks of CambridgeSoft 2002 All other trademarks are the property of their respective holders All specifications subject to change without notice Inventory Manager Inventory Manager Chemical and Biological Inventory Integration Chemical and Biological Inventory Integration Database Technology Inventory Manager is a ChemOffice WebServer based application designed to manage the rea
206. er 1 and the fourth field is the bond type 1 The bond types for the Connection Table format are as follows value bond type 1 Single 2 Dashed 3 Hashed 4 Wedged hash with first atom at narrow end 5 Wedged hash with second atom at narrow end 6 Bold 7 Wedged with first atom at narrow end 8 Wedged with second atom at narrow end 9 Wavy 10 Hollow wedge with narrow end towards 1st atom 11 Hollow wedge with narrow end towards 2nd atom 12 Dative bond with arrow towards 2nd atom 13 Dative bond with arrow towards 1st atom 14 Any bond property 15 Single Double bond property 16 Double Aromatic bond property 17 Single Aromatic bond property value bond type ChemDraw 9 Chemistry File Formats 269 Connection Table File Format Double bonds are bit encoded using a bitmask The default value 0 indicates a normal two solid lines double bond with the second line on the right looking from the first atom to the second Other values are as follows So for example a bitmask value of 13 1 4 8 means a double bond with one dashed and one solid line 4 where the user specifically wants 8 the second line to be on the left 1 NOTE This connection table format is obsolete and is documented here for historical purposes only This format should never be used for critical work where chemical information is important value bond type posi
207. er property in the Atom Properties dialog box Option Search Result Any Default Finds all compounds regardless of the stereochemistry at the selected atoms Inversion Finds compounds in which the selected atoms have an inverted stereo configuration after a reaction 154 Drawing Query Structures CambridgeSoft Atom Property Options Administrator Translation The Translation property specifies what is required to match in the structure query and possible database hits in a Markush DARC query The translation options are described in the following table For more information refer to the Markush DARC User Manual Isotopic Abundance The Isotopic Abundance property gives you the ability to distinguish between different isotopic compounds for example between mono and hexa deuterobenzene by specifying a nuclide at any location The isotopic abundance options are described in the following table Retention Finds compounds whose selected atoms have an unchanged stereo configuration after a reaction Option Definition Equal Default Matches specific to specific or generic to generic terms Broad Translates specific query atoms to corresponding superatoms in the database Narrow Translates query superatoms to corresponding specific atoms or groups in the database Any Translates generic or specific terms to any term Option Search Result Option Search results Unspecified Default
208. es Inventory Manager E Notebook 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 Notebook From here you navigate to the desired compound and include it in your stoichiometry calcula tions The enterprise edition of E Notebook integrates with procurement and inventory management systems Not 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 Notebook 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 Custom organization of notebook pages at personal or enterprise levels with links to chemical registration Notebook pages include ChemDraw reaction schemes Microsoft Word and Excel documents and spectral data using the Galactic Spectral Control Oracle Cartridge provides detailed security and data integrity SQL Server also available EMAIL info cambridgesoft com WWW www cambridgesoft com TEL 1 800 315 7300 INT L 1 617 588 9300 FAX 1 617 588 9390 MAIL CambridgeSoft Corporation 100 CambridgeP
209. ette Use the Arrow tools to add arrows to show the conversion of reactants to products and to indicate electron flow NOTE Use the Pen tool to make customized arrows For more information see The Pen Tool on page 102 Drawing an Arrow To draw an arrow 1 Click the Arrow tool 2 Point in the document where you want the beginning of the arrow to appear 3 Drag to where you want the arrowhead to be Editing an Arrow To lengthen shorten or rotate an arrow 1 Click the Arrow tool 2 Hold down the Shift key and point to the head of the arrow A highlight box appears over the head of the arrow 3 Drag the arrowhead The arrow is resized and rotated relative to its end The Info window shows the change in length and the angle the arrowhead makes with the X axis as you drag You can resize and rotate an arrow using a selection tool by dragging the Resize or Rotation handle on the Selection rectangle see Rotating Objects on page 113 and Resizing Objects on page 115 The resize or rotation occurs around the center of the Selection rectangle The Info window indicates the percentage enlargement or reduction when you drag the Resize handle and the number of degrees rotated when you drag the Rotation handle You cannot change the aspect ratio ratio of height to width of arrows The Drawing Elements Tools Palette The Drawing Elements tools provides shapes you can add to your drawing
210. ews 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 2 Select the Register tab Register tab 222 Accessing the CambridgeSoft Web Site CambridgeSoft Accessing the Online ChemDraw User s Guide Administrator 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 Accessing CambridgeSoft Technical Support The Online menu link Browse CS 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 men
211. ex 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 Merck 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 Encyclopedic reference for over 10 000 chemicals drugs and biologicals Fully searchable by ChemDraw structure substructure names partial names synonyms and other data fields Available in desktop enterprise and online formats EMAIL info cambridgesoft com WWW www cambridgesoft com TEL 1 800 315 7300 INT L 1 617 588 9300 FAX 1 617 588 9390 MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge MA 02140 USA ChemOffice ChemDraw Chem3D ChemFinder amp ChemInfo are trademarks of CambridgeSoft 2002 All other trademarks are the property of their respective holders All specifications subject to change without notice C H E M I C A L Chemical Databases Chemical Databases Reference Chemicals Reactions P Reference Chemicals Reactions Patents and MSDS atents and MSDS Databases ChemOffice WebServer provides a full range of compound and reaction databases essential for research Databases are available at ChemFinder Com or over corporate intranets Reference The Merck Index contains encyclopedi
212. ey 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 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 SIIA also offers a number of other m
213. first point in the direction of a second point in order or in the direction of the normal Centroid Defines a point positioned at the average position of all other points selected Option Search Result 160 Drawing Query Structures CambridgeSoft Query Indicators Administrator To display the Query tools select Show Query Tools from the Other Tools entry on the View menu or click the Query Tools icon on the Main Tool Palette Click The Query tools palette appears Query Indicators You can display small characters to indicate query properties you assign to atoms and bonds Viewing Query Indicators To display query indicators for a structure Select a structure to which query indicators are assigned right click point to Atom or Bond and then click Show Query Indicator To display query indicators for individual atoms or bonds Select the atom or bond right click and choose Show Query Indicator Hiding Query Indicators To hide an individual indicator 1 Select the indicator to hide 2 Right click and select Hide Indicator Removing Query Indicators To delete a query indicator 1 Click the indictor 2 Click the eraser tool and then click the indicator Positioning Query Indicators Query indicators are positioned automatically and move appropriately if a structure is modified You can reposition them by dragging them to the desired position or with the Indicato
214. fixed length If Fixed Angles is on the angle the first bond in the ring makes with the X axis is restricted to 15 degree increments For more information see Drawing Constrained Bonds on page 64 To draw a ring 1 Click a ring tool 2 Position the pointer in a document window The cyclohexane tool is shown below 3 Drag from the beginning to the end of the first bond When you point in a document window the pointer changes to a ring tool pointer The highlight box on the ring tool pointer indicates the atom that is drawn first The bond directly below the highlight box is the bond that is drawn first Drawing a Ring by Clicking To quickly draw a ring Click a ring tool and then click in a document window A ring appears in a document window centered around the pointer The ring is drawn using the Fixed Length specified in the Drawing Settings dialog box The ring is deposited in the orientation shown on the ring tool icon If you click an atom the ring is fused to that atom If you click a bond the ring is fused to that bond Cyclopropane Cyclobutane Cyclopentane Cyclohexane Cycloheptane Cyclooctane Cyclohexane Chair 1 Cyclohexane Chair 2 Cyclopentadiene Benzene First atom drawn First bond drawn ChemDraw 9 Drawing Chemical Structures 67 Drawing Rings If you click an atom in a ring a spiro linkage is formed Drawing Cyclohexane Chair Rings You can draw Cyclohe
215. forms to the GIF 89a specifications with transparent backgrounds You can change this from the options menu ISIS SKC and ISIS TGF You can save a ChemDraw document in an ISIS file format for export to an ISIS application or import a file created by an ISIS application into Chem Draw ChemDraw Pro provides two ISIS file formats ISIS Sketch skc For saving files as a binary sketch file for transfer to another ISIS application running on the same operating system this format is used on the Clipboard ISIS TGF tgf For saving as an ASCII text file a Transportable Graphics File for transfer to ISIS applications on different plat forms NOTE When transferring between ChemDraw and ISIS Draw if information in a file or on the Clipboard contains only non bond unsupported objects the information is imported as a WMF metafile or PICT graphic However if a supported object such as a bond is also in the file or on the Clipboard then only the supported object appears NOTE Object types in ISIS not supported in ChemDraw such as polymers are not transferred Object types in ChemDraw not supported in ISIS are not transferred However in some cases such as different arrow types the arrow is converted to the most similar form ISIS Reactions rxn The ISIS Reactions format is an MDL developed format for storing chemical reaction information used by the ISIS family of products and others Pro Pro
216. from the Template panel 1 Select a Template pane in the row you want to delete 2 From the Edit menu choose Delete Row To delete a column of Template panes from the Template panel 1 Select a Template pane in the column you want to delete 2 From the Edit menu choose Delete Column The column is removed and all other columns are moved to the left Saving Template Documents To save a Template document and have it available in the Template pop up menu and the Window menu 1 From the File menu choose Save As The Save As dialog box appears Saving a Template document in the ChemDraw Items folder makes it accessible in the Open Special submenu and in the Templates tools palette 2 Type a name for the Template document and click OK or Save ChemDraw 9 Working With Structures 137 Checking Chemistry Chapter 9 Working With Structures Overview You can perform the following functions on the structures you create Check a structure to identify valence and label errors View analysis information about a structure Assign Atom to Atom mapping Show Stereochemistry In ChemDraw Pro display the chemical properties for a structure In ChemDraw Pro break existing structures across one or more bonds to mimic the fragmentation in a mass spectrometer In ChemDraw Ultra assign structures to spectra and calculate NMR shift information Checking Chemistry The
217. from the Multiple Bonds tool palette Text Create atom labels and captions Pen Draw freehand shapes such as custom arrows and orbitals Arrows toolbar Draw arrows Arrows of different types can be selected from the Arrows toolbar Orbitals toolbar Draw orbitals Orbitals of different types can be selected from the Orbitals toolbar Drawing Elements toolbar Draw annotations that lack chemical significance such as boxes and lines Drawing Elements of different types can be selected from the Drawing Elements toolbar Includes the Arc tools Brackets toolbar Draw brackets parentheses and braces Brackets of different types can be selected from the Brackets tool palette Chemical Symbols toolbar Draw chemically significant symbols such as charges radicals and lone pairs Symbols of different types can be selected from the Symbols tool palette Arcs toolbar Draw arcs Arcs of different degrees can be selected from the Arcs tool palette NOTE The Arcs tool is a separate tool only on ChemDraw Standard Acyclic Chain Draw chains of any length Tool Use to Pro Pro 16 ChemDraw Basics CambridgeSoft The Main Tools Palette Administrator Setting the Default Tool Use the Preferences dialog box to set which tool is automatically selected when you open documents To set the default tool 1 From the File menu choose Preferences The Preferences dialog box appears 2 Click t
218. fy deployment readiness or logistical issues that must be addressed prior to a large scale deployment When early release programs are employed 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 Develop customized training materials for users system administrators and help desk personnel If you choose to outsource training management CambridgeSoft can schedule and conduct training for all users and stakeholders SOFTWARE Application Name Version Number Serial Number SYSTEM Windows version MacOs version Web Browser s version CS Software Problem Report Name Title Firm Street City State Zip Country Tel Fax Email USER INFORMATION Please Print Legibly DETAILS OF THE PROBLEM Submit this form via WWW www cambridgesoft com services mail EMAIL support cambridgesoft com FAX 1 617 588 9360 MAIL CambridgeSoft 100 CambridgePark Dr Cambridge MA 02140 USA For faster response and accuracy use the W
219. g 193 Bonds 193 Atom Labels 193 Captions 194 Non bond Objects and Color 194 Pasting to an Empty Document Window 194 Embedding Objects Windows 194 Edit Graphic Object Macintosh 195 Transferring PostScript Macintosh 195 Importing and Exporting 196 Graphics export border preference 197 File Formats 197 Bitmap bmp 198 ChemDraw Template ctp ctr 198 ChemDraw cdx 198 ChemDraw XML xml 198 ChemDraw 3 5 chm 198 ChemDraw 2 0 and ChemDraw 2 1 chm Im port Only 199 ChemDraw Stationery Style Sheet cds 199 Connection Table ct 199 Chemical Markup Language cml 199 Encapsulated PostScript Macintosh PostScript eps Windows 19
220. ge layout tools include setup of the page and the use of the ruler and the grouping layering aligning and distributing commands You can also organize information on the page using tables Controlling the Drawing Area The size of a document window is not necessarily the same as the size of the drawing area of the page A document window in most cases actually covers only a portion of the drawing area The following options allow you to set the drawing area displayed on your screen Document Settings and Page Setup from the File menu allow you to set the size and orientation of the page margins headers footers and the document type and size View menu options Actual Size Fit to Window Magnify and Reduce Magnification Controls enlarge and reduce Dragging to enlarge the drawing area Windows Point to a border or corner of a document window and drag to resize Macintosh Drag the Size box in the lower right corner of the document window The size of drawing area displayed depends on the size and resolution of your monitor In some cases you can see the entire document If you magnify a document the drawing area size and drawing objects become bigger If you increase the magnification so that the page size becomes bigger than the screen scroll bars become available Setting up Pages You can create two types of documents Pages A single document containing one or more sheets
221. gent tracking needs of chemical and pharmaceutical research centers The system manages data associated with both commercially and internally produced chemical substances Although Inventory Manager is a stand alone application it can be tightly integrated with CambridgeSoft s Registration System and chemical procurement ChemACX Database Inventory Manager 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 Manager has a fully cascading location model This 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 chemicals 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 Substructure Search Form Viewing Information by Container R E S E A R C H amp Discovery Reagents amp Stockroom Inventory Manager integrates fully with CambridgeSoft s ChemACX Database of available chemicals and Registration System It als
222. ghbor is equal to the Chain Angle set in the Drawing Settings dialog box If this angle cannot be established a smaller angle is used Adding Bonds by Dragging To control the orientation of bonds that you draw you can add bonds by dragging By using this dragging method for drawing the bond you can control the orientation of the other end of the bond To add a bond by dragging 1 Click a bond tool 2 Point to an atom A highlight box appears over the atom indicating where the bond will be joined 3 Drag from the atom at which you are pointing to the end of the new bond A new bond is drawn and joined to the atom where the highlight box appeared Changing the Highlight Box Size The size of highlight box is controlled by the Tolerance value in the Preferences dialog box With the default Tolerance setting of 5 pixels the highlight box appears on atoms if the pointer is located in a square region 10 pixels on a side or 5 pixels from the atom To change the Tolerance 1 From the File menu choose Preferences 2 On the General tab select or type the tolerance and then click OK 66 Drawing Chemical Structures CambridgeSoft Drawing Rings Administrator Drawing Rings The Main Tools palette contains the following ring tools that enable you to draw ring sizes and types Drawing a Ring If Fixed Lengths is on when you draw a ring the length of each bond in the ring is automatically set to the
223. gle and the cursor changes to a hand NOTE If the bond or other object is part of a group you can select it as an individual object For more information see Grouping Objects on page 118 Setting the Highlight Box Tolerance You determine the size of the highlight box and how close you must get to activate an object by setting the Tolerance The standard setting for the Tolerance is 5 pixels At this setting the highlight box appears on bonds if the pointer is located 5 pixels or less from any point on the bond To set the Tolerance 1 From the File menu choose Preferences 2 Select or type the tolerance This change affects all documents ChemDraw 9 Manipulating Drawings 111 Using a Selection Tool Selecting Entire Structures To select an entire chemical structure Using a selection tool double click a bond or atom within the structure The entire chemical structure is selected If the chemical structure or other object is part of a group the entire group is selected For more information see Grouping Objects on page 118 Making Multiple Selections To make multiple selections or add more objects to the selection Press Shift and select the other objects You can add objects to the Selection by clicking double clicking or by using the selection tools Removing Objects from the Selection To remove an object from the selection Press Shift and select an object conta
224. gned for small expansions and is limited to a maximum of 500 generated structures For large combinatorial expansions use CambridgeSoft s CombiChem for Excel Four kinds of abbreviated combinatorial definitions may be used Definitions are expanded into multiple complete molecules If more than one site is present in the selection the expansion will include all permutations of substitutions Expansions are generated into a new document To generate a combinatorial library 1 Select at least one combinatorial substitution definition NOTE For alternative group R tables both the alternative group label and the table must be selected If the label is selected but not the table the label will not be modified by the expansion and will appear as a label in all generated structures 2 Choose Expand Generic Structure from the Structure menu definition example Alternative Groups and R tables Anonymous Alternative Groups Element Lists Pro Pro R1 1 R1 F 1 Cl 1 Br 1 NH2 1 OMe OH NH2 I Br Cl F Variable Attachment definition example 1 CH3 146 Working With Structures CambridgeSoft Spectrum Structure Assignments Administrator The structures are generated to a new document Spectrum Structure Assignments ChemDraw Ultra enables you to assign structures to spectra You can then display the structure associated with a specific peak by placing the pointer on t
225. gned to any atom A floating charge placed within a delocalized system is recognized by the Analyze Structure function but is discarded when saved to formats that require all charges to be associated with specific atoms NH3 N H3 NH3 N H3 CO2 CO O NH3 Fe Fe 2 Fe2 NH3 N H3 ChemDraw 9 The Chemistry of ChemDraw 235 Chemical Conventions Isotopes and Elements By default ChemDraw correctly recognizes all isotopes in the full Table of the Elements This data is provided by CRC Press Inc Isotopes are defined in the Isotopes Table file You can edit this file to add new isotopes in any text editor Radicals Radicals are indicated with the appropriate symbol from the Chemical Symbols Palette As with charges they are assigned to the nearest atom Radicals always occupy one free valence in addition to any charge effects H Dot H Dash H Dot and H Dash symbols from the Chemical Symbols Palette indicate the stereochemistry of a single hydrogen atom These symbols are most commonly used in fused systems Complexes Compounds with electron pairs can act as Lewis bases bonding with Lewis acids that are electron deficient Similar behavior can be seen between lone pairs and metals The best representation of these types of interaction is with a dative bond from the electron pair donor to the acceptor With a plain bond instead of the dative bond ChemDraw would re
226. h contains the three tokens N and C and H3 If you label C3 the tokens are placed from left to right because there are bonds to the left of the atom If you label C5 the tokens are placed from right to left because there are bonds to the right of the atom In ChemDraw Pro you can force an entire multi atom label to be a token by defining it as a Nickname This prevents the label from flipping when applied to the left side of a structure For example if you define the Nickname CH3 and label C5 with the combined label and nickname NCH3 the final orientation is CH3N instead of H3CN In this case the Nickname CH3 is a token For more examples see Using Nicknames on page 121 If you label C1 the second and third tokens are placed above the first token since there are bonds below the atom Stacked Above Centered Flush Left Flush Right OMe CH2 N RNH N CH2 OMe N CH2 OMe NCH3 H3CN Pro Pro CH3 N ChemDraw 9 Drawing Captions and Atom Labels 83 Formatting Text If you label C4 the second and third tokens are placed below the first token Changing the Default Caption or Atom Label Text Format Each new caption or atom label uses default docu ment settings for the font size and style of captions and atom labels You can change the format by Changing the document settings for subse quent drawings in the current document Choosing a new format for an individual ca
227. hapes Overview ChemDraw provides the following tools and tool palettes that enable you to add chemical symbols and shapes to your documents A tool palette is indicated by a in the lower right corner of the tool Orbital tools palette to draw orbitals Chemical Symbols tools palette to draw charges radicals and other symbols Arrow tools palette to draw arrows Drawing Elements tools palette to draw boxes circles and lines Brackets tools palette to draw brackets braces parentheses and daggers Arc tools palette to draw arcs Pen tool to draw freehand shapes TLC tool to reproduce TLC experiments You can use the tool palettes as extensions of the Main Tool Palette or you can tear them off and place them anywhere on your screen Selecting Tools From a Palette Some tools have a palette containing different types of that tool When you choose a tool type from the palette it becomes the default tool To use a different tool type select it To select a tool and use its default tool type Click the tool s icon to select it To choose a different tool type from the palette 1 Click the tool s icon and hold down the mouse button The palette appears 2 Drag to select a tool type from the palette 3 Release the mouse button over the tool you want to select The selected tool is now displayed on the Main Tools Palette
228. harges Superscript style ChemDraw does not recognize a chemical formula embedded within a larger block of text Charges Charges may be created as part of a textual atom label or with the appropriate symbol from the Chemical Symbols Palette Charges are always assigned to a specific element in the atom label whose acceptable valences become those of the similar isoelectronic neutral element If you draw a bond add an atom label and then delete the bond you have a chemically meaningful text block whose font size and style match other atom labels If you create a caption with the text tool and set it to Formula style you have a chemically meaningful text block whose font size and style match other captions A charge following an element is assigned to that element NH4 H2O O A charge that does not follow an element is assigned to the next element Charges that follow a monovalent element with a repeat count are assigned to the element before that element Charges that follow other repeating units are distributed among those units Charges may be superscripted Multiple charges are recognized appropriately Charges may have repeat counts as long as both the charge and the repeat count are superscripted A floating charge placed with the Chemical Symbols Tool is assigned to the nearest atom If no atom is within the distance set as the Fixed Length the charge is ignored and not assi
229. hat peak Assigning Structures to Spectra To assign structures to a spectrum 1 Open a spectral file 2 Draw the structure or structures you want to assign to the spectrum 3 Select specific atoms and bonds in the structure 4 Shift click the peak or peaks to which you want the structure assigned The selection rectangle surrounds the selected objects 5 From the Structure menu choose Make Spectrum Structure Assignment The selected atoms and bonds in the structure are associated with the selected spectral peaks Viewing Spectral Assignments To view the spectral assignments 1 Click the Lasso or Marquee tool 2 Place the pointer over a peak 1 CH3 1 CH3 1 CH3 Ultra Ultra 0 2 4 6 8 10 PPM O ChemDraw 9 Working With Structures 147 NMR Shift Information ChemNMR The assigned atoms or bonds are highlighted Removing Spectral Assignments To remove spectrum to structure assignments 1 Click the Lasso or Marquee tool 2 Select the objects from which to remove the assignment 3 From the Structure menu choose Clear Spectrum Structure Assignment NMR Shift Information ChemNMR ChemNMR is a feature of ChemDraw Ultra only ChemNMR estimates and displays proton and carbon 13 chemical shifts in ppm for a selected molecule To view 1H or 13C NMR information 1 Select the target chemical structure 2 From the Structure menu choose 1H NMR Shifts or
230. he Marquee tool to select objects and structures within a rectangular area To select objects using the Marquee tool 1 Select the Marquee tool The pointer becomes a Marquee 110 Manipulating Drawings CambridgeSoft Using a Selection Tool Administrator 2 Drag diagonally across the chemical structures or other objects As you drag a rectangle appears which defines the Selection area Bonds and other objects are selected only if they are entirely within the rectangle You can use the Marquee to select several objects at once if they can be surrounded by a rectangle Toggling Between Selection Tools You can set one selection tool to behave like the other as follows Click the Lasso or Marquee tool and press the Alt or Option key Toggling Between Other Tools To toggle a selection tool and the last drawing tool used Press Ctrl Alt Tab or Command Option Tab This command will toggle the last selection tool you have used with the last drawing tool you have used If you haven t used either selection tool it defaults to the Lasso tool Selecting Objects by Clicking To select an object by clicking 1 Select the Lasso or the Marquee tool 2 Point to an object in a document window A highlight box appears over the selected object If you point at a bond the highlight box appears over the length of the bond 3 Click the object The selected objects appear within the Selection Rectan
231. he Open Save tab Query Tools toolbar Draw stereochemical flags indicate free sites alternative groups and correspondences between atoms in query structures Various options can be selected from the Query tool palette Templates toolbars Draw structures with templates stored in template documents Templates can be selected from the Templates toolbars Rings Draw common structural compo nents Table Draw tables with multiple rows and columns TLC Plate Draw TLC plates with multiple lanes and adjustable solvent front and spots Tool Use to Pro Pro Benzene Ring Cyclopentadiene Ring Cyclohexane chair 2 Cyclooctane Ring Cyclohexane Ring Cyclobutane Ring Templates Query tools Chemical Symbols Brackets Drawing Elements Orbitals Cyclohexane chair 1 Cycloheptane Ring Cyclopentane Ring Cyclopropane Ring Acyclic Chain Table Wavy bond Hollow Wedged Bond Bold Wedged Bond Bold Bond Hashed Wedged Bond Hashed Bond Dashed Bond Multiple Bonds Solid Bond TLC plate Structure Perspective Lasso Arrows Pen Text Eraser Marquee Fragmentation tools ChemDraw 9 ChemDraw Basics 17 Optional Toolbars 3 In the Opening Files section click the Default Tool to be automatically selected when you open a document Tearing Off Palettes Some tools have toolbars extending from them indicated by an arrow at the bottom right of the tool
232. he Pen tool 2 Point to where you want the beginning of the curve to appear and click An anchor point appears and the cursor changes from a to a hand 3 Move the cursor to another position and click A line connects the two points 4 Position the cursor on one of the points the in the hand will disappear when you are correctly positioned and drag to create an arc A direction line appears tangentially to the curve Use the direction line to control the curviness of the segment The slope of the direction line determines the slope of the curve The length of the direction line determines the height of the curve Direction points appear at the ends of the direction line Use the direction points to adjust the curve by dragging a point You can further adjust the shape by dragging an endpoint of the curve Drawing Segments by Clicking You can draw shapes with corners by clicking repeatedly in an outline of the shape you want To draw segments 1 Select the Pen tool 2 Point to where you want the beginning of the curve to appear Customized orbitals Unique arrows Geometric shapes Curves and axes Anchor Point Direction Line Direction Point 104 Drawing Orbitals Symbols Arrows Arcs and Other Shapes CambridgeSoft The Pen Tool Administrator 3 Click to deposit an anchor point 4 Move the cursor and click again to add a second point 5 Continue until you have the
233. he Reaction Atom Atom Map tool 2 Point to the atom in the reactant whose mapping you want to establish For example in the following drawing you would point to the acyclic carbon adjacent to the ether oxygen Ph OSiMe3 O Ph O O Ph Rxn OSiMe3 Rxn Rxn O Ph O Rxn Rxn Rxn Rxn O 1 2 3 4 5 6 O 7 Rxn 1 2 3 4 5 6 OH 7 Rxn 172 Drawing Query Structures CambridgeSoft Export Compatibility Administrator 3 Drag from the reactant atom to the corresponding product atom The remaining atoms are automatically mapped based on the manual mapping you performed You can continue to set or change the mapping for other atoms in the reaction if necessary until you get exactly the mapping you want For this example additional manual mapping is not necessary Clearing Reaction Mapping To clear all reaction mapping 1 Select the structures whose mapping you want to remove 2 From the Structure menu choose Clear Reaction Map Exporting Reaction Mapping Reaction mapping and reaction center perception information are stored in the native ChemDraw file format cdx for reopening in ChemDraw and the ISIS Reaction file format for transfer to other applications that read atom mapping such as ChemFinder and ISIS Base You can also copy mapped reactions to these same applications using the Clipboard Export Compatibility Because quer
234. he center of the ring select just the ring not the entire molecule 3 From the Structure menu choose Add Variable Attachment An asterisk appears in the center of your fragment You can treat this attachment node as you would treat the end of a normal bond 1 Click a Bond tool 2 Point to the asterisk and drag to draw a bond NOTE In the example above Fixed Lengths was disabled using Ctrl L or Command L so a bond could be drawn extending further from the ring After you draw a bond from the attachment node the asterisk disappears To verify that the node is present do one of the following Click a Selection tool and place the pointer on the attachment point The attachment node is highlighted Click a Bond tool and place the pointer on the attachment point The attachment node and the atoms it represents are highlighted For more information about viewing the attachment points see Viewing Attachment Points on page 127 Using Structure CleanUp The Structure CleanUp command is used to neaten the appearance of molecules by regularizing bond lengths and angles Graphic objects such as arrows and aromatic circles are not affected Use Structure CleanUp to redraw structures that you may have drawn freehand or to neaten structures that you may have imported from another application Structure CleanUp may not create the best structure Most structures have many clean forms a problem that
235. he file 5 Click Save 6 From the View menu choose Show General Toolbar 7 From the View menu choose Show Info Window The Info window appears and displays drawing parameters as you draw 2 propanone Rx 60 O O OH OH 2 propanone 2 moles 4 hydroxy 4 methyl 2 pentanone 1 mole 32 Tutorials CambridgeSoft Tutorial 1 Reaction Schemes Administrator 8 Click the Object menu and make sure there is a check mark next to the Fixed Lengths and Fixed Angles commands If either command is not checked select it NOTE Applying fixed lengths and fixed angles enables you to create structures with consistent bond lengths and angles The fixed length dimension is set in the Drawing Settings dialog box The fixed angle dimension increments angles by 15 degrees Create a bond 1 Click the Solid Bond tool 2 Position the pointer anywhere in the document window and click The bond is extended to its fixed length at a 30 degree angle Add a second bond 1 Point to the right atom of the bond 2 Click the atom to add a bond A second bond is drawn forming a 120 degree angle between the bonds NOTE The angle used when clicking to add bonds is controlled by the Chain Angle setting in the Drawing Settings dialog box in the File menu If this bond angle cannot be established the next smaller and logical bond angle is used Add a third bond 1 Continue pointing to the atom shown below 2
236. he left and a broad arrow pointing to the reactants as is customary in retrosynthetic analyses In most cases you will have to clean up the reaction by adding or deleting atoms or bonds The following example cuts two bonds and gives the results shown The result is a reasonable approximation of the Beyer Method for quinolines and can quickly be cleaned up to the correct reaction These tools are found in the Fragmentation tools section of the Main tools palette operation behavior drag Breaks bond s The action does not take place until you release the mouse button so you can test alternatives drag holding down the Alt or Option key Draws a freehand line If you release the mouse button before releasing the Alt or Option key the dashed line display remains drag across a bond then press the Alt or Option key Allows you to change direction and draw a polyline If you release the mouse button before releasing the Alt or Option key the dashed line display remains Pro Pro NH2 R N R NH2 R N R Reaction created with the Retrosynthesis tool Reaction created with the Dissociation tool cut these bonds NH2 R O H N R ChemDraw 9 Working With Structures 145 Expand Generic Structures Expand Generic Structures You can generate multiple structures from an abbreviated combinatorial structure with ChemDraw s Expand Labels tool The tool is desi
237. he mouse button over the Chemical Symbols tool and drag to select the radical from the palette 2 Point to the atom where you want the radical symbol to appear 3 Click to draw the symbol Radical Cation and Radical Anion Use the charge radical symbols to represent radicals that are charged To draw a radical cation or radical anion symbol 1 Hold down the mouse button over the Chemical Symbols tool and drag to select the symbol from the palette 2 Point to the atom where you want the symbol to appear O O O O O O H dot symbol OH 98 Drawing Orbitals Symbols Arrows Arcs and Other Shapes CambridgeSoft The Chemical Symbols Tools Palette Administrator 3 Drag from the charge portion of the symbol to the radical portion of the symbol To quickly deposit a radical cation or radical anion symbol in a horizontal orientation Click to deposit the symbol Charge Symbols Use the charge symbols to represent charges on structures To draw a charge and associate it with a structure 1 Hold down the mouse button over the Chemical Symbols tool and drag to select the charge symbol from the palette 2 Click to the atom to which you want the charge to correspond The number of hydrogen atoms increases or decreases as appropriate for the addition of the charge Attachment Points The ability to indicate an attachment point is useful in polymer bound combinatorial synthesis
238. hierarchical list it first identifies key substructures of a molecule A substructure provides the base value for the estimated shift For example benzene would be identified as the key substructure of trinitrotoluene When a substructure happens to be a ring system not available in the data ChemNMR approximates its base shift using embedded rings and if necessary it will even disassemble the ring into acyclic substructures ChemNMR views remaining parts of the molecule as substituents of a substructure Each substituent adds to or subtracts from the base shift of the substructure to which it is attached Additivity rules determine the increment of each contribution If an increment for a substituent cannot be determined ChemNMR uses embedded substituents smaller structural units with the same neighboring atoms Or it will use increments of identical or embedded substituents of a corresponding substructure by assuming that the effects of the substituents are of the same magnitude ChemNMR provides a detailed protocol of the estimation process applied It gives substructures as names compound classes in most cases substituents in form of a linear code respectively The data set for the 1H NMR Shift tool currently contains 700 base values and about 2000 increments The 13C NMR Shift tool is based on 4000 parameters It also implements models for ethylenes cis trans and cyclohexanes equatorial axial ChemNMR Limitations
239. hin the cell regard less of its position it is not affected by the Align All Pictures To align structures From the ChemOffice menu select Align Pictures or click The cells adjust to display their entire contents Resizing Structures To resize pictures use the Resize Picture command NOTE When pictures are resized larger than their cells use Align Pictures to enlarge the cells Align Pictures does not make cells smaller To resize pictures 1 Select the chemistry cells whose pictures you want to resize It is not necessary to only select chemistry cells Non chemical cells or chemical cells without pictures will be ignored 2 From the ChemOffice menu select Resize Picture or click Resize handles appear on the selected structures 3 Click drag the resize handles to resize a picture Any changes you make to a picture is proportionately reflected in the other pictures 4 To end resizing click a cell and the pictures are deselected Resizing Structures With a Macro To resize a large number of structures simulta neously create the following macro CFXL xla CFxlDoSelectPicture and assign it to an Excel button or menu item Then do the following 1 Select the cells to be resized 2 Run the macro 3 Resize one structure All of the selected structures resize by the same amount 4 Select the Structure column and align see Aligning Structures on page 215 For more infor
240. 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 The 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 written 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 softwar
241. http clogp pomona edu medchem chem papers 13 cmr html To paste the basic properties into your document Click Paste Property Description Boiling Point The boiling point for the structure Reported in Kelvin at 1 atm Melting Point The melting point for the structure Reported in Kelvin at 1 atm Critical Temperature The temperature above which the gas form of the structure cannot be liquefied no matter the applied pressure Tc Reported in Kelvin Critical Pressure The minimum pressure that must be applied to liquefy the structure at the critical temperature Pc Reported in bars Critical Volume The volume occupied at the compound s critical temperature and pressure Vc Reported in cm3 mol Gibbs Energy The Gibbs free energy G for the structure Reported in kJ mol at 1 atm and 298 15K Henry s Law The inverse of the logarithm of Henry s law constant log H no units Heat of Formation The heat of formation Hf for the structure Reported in kJ mol at 1 atm and 298 15K tPSA Calculation of polar surface area based on fragment contributions CLogP The calculated n octanol water partition coefficient log Pow CMR The calculated Molar Refractivity Property Description Ultra Ultra Ultra Ultra ChemDraw 9 Working With Structures 143 Mass Fragmentation Tool To create a report and view results for other fragmentation methods including the B
242. ica Caption Size 9 pt Drawing Area Width x Height 8 9 cm x 25 4 cm 1 column 19 cm x 27 7 cm Page Size US Letter Reduction 100 Drawing Atom Label and Caption Text Settings in Journal Style Sheets or Stationery Pads RSC 1 and 2 column N H HO O Morphine ChemDraw 9 Document Settings 265 ChemDraw Style Sheets or Stationery Pads Fixed Length 17 pt Bold Width 2 pt Line Width 0 8 pt Margin Width 1 3 pt Hash Spacing 2 5 pt Chain Angle degrees 120 Bond Spacing of length 18 Atom Label Font Win Mac Arial Helvetica Atom Label Size 10 pt Caption Font Win Mac Arial Helvetica Caption Size 10 pt Drawing Area Width x Height 12 cm x 26 7 cm Page Size A4 Reduction 100 Drawing Atom Label and Caption Text Settings in Journal Style Sheets or Stationery Pads SYNTHESIS SYNLETT Na H HO O Morphine 266 Document Settings CambridgeSoft ChemDraw Style Sheets or Stationery Pads Administrator ChemDraw 9 Chemistry File Formats 267 Connection Table File Format Appendix H Chemistry File Formats Overview File formats other than ChemDraw may not preserve all of your data ChemDraw can create many types of items particularly graphical objects such as boxes and curves that cannot be saved into chemical file formats Other file fo
243. icates the percentage enlarged or reduced When you drag the Rotation handle the Info window indicates the degree rotated For more information see Rotating Objects on page 113 and Resizing Objects on page 115 The Pen Tool Use the Pen tool to draw shapes that are not provided in the Arrow Orbital or Drawing Elements palettes For example you can draw irregularly shaped arrows curves depicting graphs or reaction coordinate diagrams and other irregularly shaped solids The Pen tool has two modes Drawing Used to create shapes The hand cursor appears with a sign inside Edit Used to edit shapes The hand cursor appears without a sign inside NOTE To enter edit mode directly from drawing mode press the Esc key Arcs 94 dpi ChemDraw 9 Drawing Orbitals Symbols Arrows Arcs and Other Shapes 103 The Pen Tool Some examples of shapes that you can draw using the Pen tool are shown below To toggle between a selection tool and the Pen tool do one of the following Press Ctrl Alt Tab or Command Option Tab Click a selection tool The last drawn curve and a selection tool are selected Drawing B zier Curves by Dragging A B zier curve is a curve that is calculated to connect separate points into a smooth line You can draw B zier curves with the Pen tool by clicking and dragging repeatedly to create curved segments To draw a Bezier Curve 1 Select t
244. icates that the property is applied but not the value of the property To find the value of a query bond property setting 1 Select the bond 2 Do one of the following Right click point to the bond and then point to the appropriate property From the Structure menu choose Bond Properties and view the settings of the drop down list boxes Removing Bond Properties To remove all bond properties from selected bonds 1 Select the bonds 2 From the Structure menu choose Properties 3 Click Use Defaults The bond properties are removed and the indicators are no longer adjacent to the selected bonds To remove specific bond properties 1 Select the bond 2 Do one of the following Right click point to the appropriate property and then click the property to remove From the Structure menu choose Properties and then click the bond property to remove Bond Property Options The following are the atom properties that you can associate with an atom Bond Type This property specifies the bond type of the selected bonds The default bond type corresponds to the current type of the bond single double etc as drawn Indicator Bond Query Property Any Bond Type Any S D Bond Type Single Double D A Bond Type Double Aromatic S A Bond Type Single Aromatic Rng Topology Ring Chn Topology Chain R C Topology Ring or Chain Rxn Reaction Center Chem
245. ication and Line Spacing There are four available justifications Flush Left creates left justified caption text Centered creates centered caption text Flush Right creates right justified caption text Justified creates right left justified caption text 82 Drawing Captions and Atom Labels CambridgeSoft Formatting Text Administrator Atom Labels Use the Centered Flush Left Flush Right Stacked Above or Automatic justifications to create labels that identify atoms and functional groups in your chemical structure without obscuring any bonds or other atom labels NOTE When using Stacked Above justification enter the tokens from top to bottom using Alt Enter or Option Return to go to a new line For instance in the example below enter OMe Alt Enter Option Return CH2 Alt Enter Option Return N If you change the justification after the label is entered it will in most cases generate a warning Examples of the atom label justifications are shown below Automatic Alignment When you justify Atom labels automatically Chem Draw breaks the label into tokens A token consists of an uppercase letter followed by any numbers or lowercase letters The first token is attached to the atom and the rest of the label appears without obscuring other parts of the chemical structure For example to create N methylpiperidine label an atom in cyclohexane with the atom label NCH3 whic
246. ice ChemFinder Word Search structures in documents amp folders ChemDraw Excel Add chemical intelligence to spreadsheets Purchase Excel Organize chemical purchasing information S O F T WA R E EMAIL info cambridgesoft com WWW www cambridgesoft com TEL 1 800 315 7300 INT L 1 617 588 9300 FAX 1 617 588 9390 MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge MA 02140 USA ChemOffice ChemDraw Chem3D ChemFinder amp ChemInfo are trademarks of CambridgeSoft 2002 All other trademarks are the property of their respective holders All specifications subject to change without notice D E S K T O P CS ChemInfo CS ChemInfo Reference and Chemical Databases Reference and Chemical Databases 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 NCI compounds and more ChemRXN is a col
247. icular object as follows For the entire document use the Document Settings dialog box For an object use the Object Settings dialog box Changes made to the drawing settings affect the active document window only Drawing settings can be saved in Style Sheets or Stationery Pads To apply settings from other documents to your document select Apply Document Settings from from the File menu The drawing settings are described in the following table Adjust this If you want to Chain Angle Set the angle from 1 to 179 degrees between bonds created by the Acyclic chain tool or modified by the Structure CleanUp command For more information see Drawing Acyclic Chains on page 68 and Using Structure CleanUp on page 128 60 Drawing Chemical Structures CambridgeSoft Drawing Settings Administrator Bond Spacing Set the distance between the lines in double or triple bonds The distance is set either as The percent of the length of the bond between 1 and 100 This allows for proportional spacing to be used if different bond lengths are used in the drawing An absolute value you choose in the units specified for your document Fixed Length Constrain the length of the bonds drawn to the length you specify when the Fixed Lengths command in the Object menu is selected a check mark is next to it This also adjusts the preferred bond length for structures modified
248. ification 2 From the View menu choose Magnify The magnification occurs around the center of the selected object The magnification percentage appears in the Magnification drop down list You can continue to magnify your view to a maximum of 400 Actual Size To return to the actual size from any other magnification From the View menu choose Actual Size The view is returned to the original size Windows Macintosh 182 Working With Page Layout CambridgeSoft Arranging Objects Administrator Reduce To reduce the magnification 1 Select an object around which you want to reduce the magnification NOTE If you do not select an object the last object drawn is the center point of the magnification 2 From the View menu choose Reduce The reduction in magnification appears in the Magnification drop down list You can reduce the magnification until the entire page fits on the screen In the reduced view you can continue to use all of the drawing tools In particular you can use a selection tool to rearrange the drawing in order to take better advantage of the space available Fit to Window Fit to Window reduces the magnification until the entire page is visible in the document window To view the entire drawing area in a document window at once From the View menu choose Fit to Window The Magnification control shows the reduction in magnification that was required to have the entire p
249. ift click with saturated double bond ring tools change orientation of double bonds Enter to execute Command Ctrl click with ring tools except chairs create resonance delocalized ring Alt Shift click with pen tool remove a curve segment Shift drag with resize handle distort limit resize to X or Y axis Ctrl drag copy a selected object Ctrl drag with alkane chain tool change direction of a chain Shift Ctrl drag copy a selected object constrained to X and Y axes Ctrl Alt Tab toggles the Lasso and the previous drawing tool Enter to execute Command Command M minimize the ChemDraw window Command N new document Enter to execute Command 250 Shortcuts and Hotkeys CambridgeSoft Administrator Edit Commands View Commands Object Commands Command O open document Command P print Shift Command P page set up Command Q quit Command S save document Shift Command S save as Command W close document Enter to execute Command Command A select all Command C copy Command V paste Command X cut Command Y repeat last command Command Z undo Del clear Enter to execute Command Enter to execute Command Command H toggle crosshair Command actual size Command fit to window Command gt magnify Command lt reduce Command toggle rulers Enter to execute Command
250. igning Objects Use the Align commands to align objects relative to each other Examples of the types of alignments are shown on the menu To align two or more objects 1 Select the objects with a selection tool 2 From the Align submenu choose one of the Align commands If you select only part of a structure or group with a selection tool only that part is used for the alignment operation but the entire structure or group is moved Distributing Objects Use the distribute commands to distribute objects horizontally or vertically and at an equal distance apart For reactants and products with different shapes select the parts of the objects to distribute To distribute 3 or more objects 1 Select the 3 or more objects to distribute 2 On the Object menu point to Distribute and then choose Vertically or Horizontally The space between the objects is equalized The upper lower right and left positions of objects in your selection remain unchanged Front to Back Ordering The front to back ordering is a useful method for changing the orientation of one object relative to another object within the same picture layer For additional information specific to the layering of bonds see Changing Bond Crossings on page 71 H CH2Br OH H CH2Br OH 186 Working With Page Layout CambridgeSoft Creating Tables Administrator Send to Back To place one object behind another within a layer
251. ile Format and choose the format you want from the list If Use Default File Format is not selected the first time you use the Save dialog box the ChemDraw format is shown Saving a Document with a Different Name or Location You can save a copy of your document under a different name location or file format Saving a copy under a different name or location is useful for keeping earlier revisions of your document Saving SaveFileFormats 150 dpi ChemDraw 9 ChemDraw Basics 27 Accessing Documents Quickly a file as a different format is useful for creating Style Sheet or Stationery Pad and for exporting informa tion to other applications To save a copy of a ChemDraw document under a different name or in a different location 1 From the File menu choose Save As The Save As dialog box appears 2 Choose a new location in which to save the document 3 Type a new file name 4 Click Save or OK Saving a Document in a Different File Format To save a ChemDraw document in another file format 1 From the File menu choose Save As The Save As dialog box appears 2 Select a folder in which to save the document 3 Type a file name in the in the File name or Save As box 4 Select a file format from the File Format or Save as Format list NOTE When you select some formats the Options button becomes active Click it to open a dialog box for setting options specific to these formats For more inform
252. iments The software models real world workflow as much as possible Starting Out To start the user simply draws a generic reaction step in a ChemDraw 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 R E S E A R C H amp Finding Reagents Flexibility is the key when dealing with databases of chemical compounds CombiChem Enterprise can use reagent lists from a variety of different sources SD files ChemFinder databases ChemFinder hit lists ChemOffice WebServer hit lists ChemACX Database or directly from the user via ChemDraw Regardless of the source CombiChem 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 resu
253. in Mac Arial Helvetica Atom Label Size 12 pt Caption Font Win Mac Times New Roman Times Caption Size 16 pt Drawing Area Width x Height 7 5 in x 10 in Page Size US Letter Reduction 100 Drawing Atom Label and Caption Text Settings in Journal Style Sheets or Stationery Pads ChemDraw 9 Document Settings 263 ChemDraw Style Sheets or Stationery Pads Fixed Length 20 pt Bold Width 1 33 pt Line Width 1pt Margin Width 1 25 pt Hash Spacing 3 pt Chain Angle degrees 120 Bond Spacing of length 8 Atom Label Font Win Mac Arial Helvetica Atom Label Size 12 pt Caption Font Win Mac Arial Helvetica Caption Size 12 pt Drawing Area Width x Height 540 pt x 720 pt Page Size US Letter Reduction 100 Drawing Atom Label and Caption Text Settings in Journal Style Sheets or Stationery Pads N H HO O Morphine Phytomedicine 264 Document Settings CambridgeSoft ChemDraw Style Sheets or Stationery Pads Administrator Fixed Length 0 43 cm Bold Width 0 056 cm Line Width 0 016 cm Margin Width 0 044 cm Hash Spacing 0 062 cm Chain Angle degrees 120 Bond Spacing of length 20 Atom Label Font Win Mac Arial Helvetica Atom Label Size 9 pt Caption Font Win Mac Arial Helvet
254. ined within the Selection rectangle by clicking double clicking or with a selection tool The object is removed from the selection NOTE Objects may appear within the borders of the Selection rectangle but not be selected Only objects that are shimmering are selected Selecting All Objects To select all objects within a document window From the Edit menu choose Select All Deselecting All Objects To deselect all selected objects do one of the following Click in any empty area in a document window that is outside the Selection rectangle Press Esc Select a different tool Select another object without holding down Shift The selected objects are deselected Deleting Objects To delete selected objects do one of the following Press Delete Press Backspace From the Edit menu choose Clear Moving Objects To move an object 1 Select the object using a selection tool 2 Point within the border of the Selection rectangle 3 Click and drag the object 112 Manipulating Drawings CambridgeSoft Using a Selection Tool Administrator To constrain the movement to the horizontal or vertical direction Shift drag the selected objects Small incremental movements are often useful for aligning objects To move an object a small distance 1 Select the object 2 Press an arrow key The selected object moves 1 point in the direction of the arrow
255. ing Atoms with HotKeys 87 Method 1 Labeling the last atom drawn 87 ChemDraw 9 Method 2 Labeling an atom by pointing 87 Method 3 Labeling an Atom with a Selection Tool 88 Method 4 Labeling multiple atoms 88 Creating HotKeys 88 Hard Coded HotKeys 89 Labeling Atoms With a Bond or Ring Tool 89 Repeating an Atom Label 89 Atom Numbering 89 Showing and Hiding Atom Numbers 90 Editing Atom Numbers 90 Positioning Atom Number Indicators 91 Using the Text Tool with the Lasso Tool 91 Using Bitmap Fonts When Available Macintosh 92 Chapter 6 Drawing Orbitals Symbols Arrows Arcs and Other Shapes Selecting Tools From a Palette 93 The Orbital Tools Palette 94 s orbitals 94 Sigma Orbitals 94 Single Lobe Orbitals 94 p orbitals 95 Hybrid Orbitals
256. ing Bond Properties 156 Bond Property Options 156 Bond Type 156 Topology 157 Reaction Center 158 3D Properties 158 Query Tools Palette 159 Query Indicators 160 Viewing Query Indicators 160 Hiding Query Indicators 160 Removing Query Indicators 160 Positioning Query Indicators 160 Drawing Stereochemical Symbols 161 Drawing Free Sites 161 Generic Nicknames 161 Element Lists 162 Element Not Lists 163 Link Nodes 163 Representing Polymers and Other Repeating Units 163 Setting Bracket Properties 164 Bracket Usage 164 Structure based Polymer Representations 164 Sourc
257. ing Ctrl L or Command L Viewing Attachment Points After you draw a bond from the multi center attachment point the asterisk disappears You can verify the node is present with a bond or a selection tool This provides a way to check the definition of a pre existing multi center attachment point To view a node with a selection tool Select the selection tool and position the cursor over to attachment point The attachment node is highlighted To view a node with a bond tool Select the bond tool and position the cursor over the attachment point The attachment node and all the atoms it represents are highlighted Using Variable Attachment Positions You can use the Add Variable Attachment command to draw different positional isomers of a compound using an abbreviated notation that retains chemical significance For example you can explicitly draw the three isomers of dibromobenzene shown below Alternately you can express all three isomers as a single parent structure by using a variable attachment Fe Pro Pro Br Br Br Br Br Br o Dibromobenzene m Dibromobenzene p Dibromobenzene Br Br 128 Advanced Drawing Techniques CambridgeSoft Using Structure CleanUp Administrator To use variable attachment 1 Draw the structural fragment to which you want to assign a variable attachment node 2 Select the fragment using a selection tool TIP To get the attachment in t
258. ing us If you can reproduce the problem please record the exact steps that you took to do so Record the exact wording of any error messages that appear Record anything that you have tried to correct the problem You can deliver your CS Software Problem Report Form to Technical Support by the following methods Internet http www cambridgesoft com 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 Macintosh With ChemDraw launched choose About CS ChemDraw from the Apple menu The serial number appears at the bottom left Windows 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 228 Technical Support CambridgeSoft Troubleshooting Administrator Troubleshooting This section describes
259. ioAssay Desktop ChemDraw Excel ChemFinder Office CombiChem Excel ChemSAR Excel MOPAC MM2 CS Gaussian GAMESS Interface ChemOffice WebServer Oracle Cartridge E Notebook Workgroup Enterprise Document Manager Registration Enterprise Formulations amp Mixtures Inventory Workgroup Enterprise Discovery LIMS BioAssay Workgroup Enterprise BioSAR Enterprise ChemDraw Spotfire The Merck Index ChemACX ChemSCX ChemMSDX ChemINDEX NCI amp AIDS ChemRXN Ashgate Drugs Structure Drawing Tips Searching Tips Importing SD Files ChemDraw 9 Contents by Chapter Introduction 9 Chapter 1 ChemDraw Basics 13 Chapter 2 Tutorials 31 Chapter 3 Drawing Chemical Structures 59 Chapter 4 Struct lt gt Name 73 Chapter 5 Drawing Captions and Atom Labels 79 Chapter 6 Drawing Orbitals Symbols Arrows Arcs and Other Shapes 93 Chapter 7 Manipulating Drawings 109 Chapter 8 Advanced Drawing Techniques 121 Chapter 9 Working With Structures 137 Chapter 10 Drawing Query Structures 149 Chapter 11 Working With
260. ion control Scroll bars Status bar Resize 14 ChemDraw Basics CambridgeSoft The Main Tools Palette Administrator The Mac GUI is shown below The Main Tools Palette Use the main tools palette to create and manipulate drawings The appearance of the toolbar is slightly different for the different versions of ChemDraw The toolbar for ChemDraw Ultra is shown below Main tool palette Title bar Menu bar General toolbar Magnification control Scroll bar Resize Object toolbar ChemDraw 9 ChemDraw Basics 15 The Main Tools Palette The table below describes the functions of the tools for all versions Some of the tools have multiple options that can be selected from a tool palette Tool Use to Selection Lasso Select objects by dragging around them Marquee Select objects by dragging diagonally across them Selected objects can be further manipulated using menu commands Structure Perspective Rotate a selected object in three dimensions Frag mentation toolbar Fragmentation tool Splits mole cules across specific bonds Dissociation tool Breaks bonds and draws a reaction Retrosynthesis tool Breaks bonds and draws a reaction Bond Draw bonds and set bond properties Eraser Delete objects Click on an object to delete drag to delete multiple objects Multiple Bond toolbar Draw multiple bonds and set bond properties Bonds of different types can be selected
261. is particularly noticeable with straight chain alkanes Br Br Br Br Br Pro Pro ChemDraw 9 Advanced Drawing Techniques 129 Working with Color If you select only part of a structure when you choose Structure CleanUp the other atoms and bonds are not be affected NOTE For some compounds the Structure CleanUp command produces a structure that extends beyond the bounds of the page To view the entire structure scale the structure or increase the size of the printed page For more information see Resizing Objects on page 115 and Setting up Pages on page 177 General Rules for Structure CleanUp are The Fixed Length setting in the Drawing Settings dialog determines optimum bond lengths A given ring is redrawn only if all of its bonds are selected Multi attached atom labels and variable attachment points cannot be cleaned Multi center bonds cannot be cleaned Structures are rotated so that as many bonds as possible are directed at a multiple of 15 degrees Structure CleanUp preserves stereochemical meaning rather than the precise identity of any wedged or hashed bonds as shown below Using Structure CleanUp 1 Select the structure or part of the structure you want to clean up with a selection tool 2 From the Structure menu choose Structure CleanUp NOTE Structure CleanUp does not position molecules relative to other objects Overlap may occur
262. it list you can browse search refine or export it to any destination Indexes chemical structure information in documents and compiles a structure searchable database Monitors designated folders or drives and automatically indexes new documents as they appear Documents are searchable by structure and free text M A N A G E M E N T EMAIL info cambridgesoft com WWW www cambridgesoft com TEL 1 800 315 7300 INT L 1 617 588 9300 FAX 1 617 588 9390 MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge MA 02140 USA ChemOffice ChemDraw Chem3D ChemFinder amp ChemInfo are trademarks of CambridgeSoft 2002 All other trademarks are the property of their respective holders All specifications subject to change without notice K N O W L E D G E 21CFR11 Compliance 21CFR11 Compliance Electronic Records and Signatures Regulations 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 pharmaceuticals 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 21CFR11 Although 21CFR11 has been in the draft stage for almost a decade fin
263. ites 1 On the Query tools palette click the Free Site tool 2 Position the pointer over the atom to which you want to apply free sites 3 Click to add the symbol 4 Continue to click the atom to increment the free site number To decrement the number of free sites Hold the Alt or Option key while clicking the atom You can also change the free sites by using the Atom Properties dialog box or the shortcut menu For more information see Atom Properties on page 149 Generic Nicknames Generic nicknames represent a class of elements or structural moieties For example M can be a generic nickname for all metals X can represent halides Ary can represent an aromatic substructure If you are using a query system that recognizes generic nicknames you can use these nicknames in your ChemDraw query structure You can assign Generic nicknames like other nicknames to HotKeys For information on assigning a Hotkey to a nickname see Chapter 9 Working With Structures You cannot define the meaning of a generic nickname in ChemDraw because generic nicknames represent multiple and perhaps an from the atom or bond center to bottom left of indicator baseline offset horizontal and vertical at specified coordinates absolute horizontal and vertical To Position Type a value for Free Site tool 162 Drawing Query Structures CambridgeSoft Element Lists
264. ith reductions to about 20 of original size File Formats ChemDraw supports both import and export except as noted below of the following file formats To export a ChemDraw file to one of these formats use the Save As option when saving For additional information on importing files see Inserting Objects from Other Applica tions on page 204 Format Import Export Bitmap bmp YES YES ChemDraw Template ctp ctr YES YES ChemDraw cdx YES YES ChemDraw XML xml YES YES ChemDraw 3 5 chm YES YES ChemDraw 2 0 and Chem Draw 2 1 chm YES NO ChemDraw Stationery Style Sheet cds YES YES Connection Table ct YES YES Chemical Markup Language cml YES YES Encapsulated PostScript Macintosh PostScript eps Windows YES YES Graphic Image Format gif YES YES ISIS skc tgf rxn YES YESa JCAMP jdx dx YES NO JPEG jpg jpeg YES NO MDL MolFile mol YES YES Format Import Export 198 Sharing Information CambridgeSoft Importing and Exporting Administrator Bitmap bmp Bitmap bmp files store raster graphics in an array of individual bits Bitmap images are the most common format for continuous tone images Because they represent a fixed number of pixels bitmaps are resolution dependent and may appear jagged and lose detail if they are scaled on screen or printed on a higher resolution printer th
265. iting Pro TemplateExample 150 dpi Pro 134 Advanced Drawing Techniques CambridgeSoft Drawing With Templates Administrator Choosing a Template To choose a template from the Template palette 1 Hold down the mouse button over the Templates tool A menu listing the Template documents appears 2 Point to a Template document name A palette containing the available templates appears 3 Choose a template from the palette When you display the Template palette that was last used a blinking box appears around the currently selected template until you drag to another template Using Templates When you draw with templates the first bond drawn determines the position of the template in a document window All remaining bonds are drawn counterclockwise The most nearly vertical bond on the far left atom is drawn first from top to bottom If there are two equivalent bonds the atoms that are at a lower position are used to draw the first bond Drawing direction of template structures Templates are automatically scaled to the document settings of the current document in the active window For more information see Autoscaling on page 193 After a template is drawn in a document window the structures or objects can be manipulated by standard drawing and editing methods Drawing a Template To draw a template Click in a document window The template is drawn centered around the pointer in the o
266. itten consent of CambridgeSoft 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 The 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 CambridgeSoft 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 The recipi ent must agree to the terms of this Agreement in full and register this transfer in writing with CambridgeSoft 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 c
267. ive algorithm for converting English chemical names into chemical structure diagrams It is designed to interpret chemical names as they are actually used by chemists In other words it recognizes the shorthand and slang of everyday usage in addition to recognizing most of the official IUPAC IUBMB and CAS rules and recommendations In addition it has an extensive algorithm for the identification of common typos typing errors such as mehtyl to increase the odds of generating structures for the names it is given Struct Name You can insert the name of a selected structure as a caption using the Convert Structure to Name command from the Structure menu The Struct Name algorithm in use since ChemDraw 8 0 is a new proprietary naming algorithm developed by CambridgeSoft It replaces Beilstein s AutoNom algorithm used in earlier versions of ChemDraw In ChemDraw 9 0 an auto update feature has been added that renames the structure as you modify it The conversion of a structure to a name is limited by many factors Specifically Struct Name makes little or no attempt to name the following Bridged ring systems with more than one bridge for example tricycles Radicals Compounds with non standard valence states Spiro ring systems Isotopically modified compounds Polymers Biochemicals including specialized nomenclature for amino acids carbohydrates and steroids Fo
268. ividual mixture elements An example is shown below Bracket type Mixture ordered f is primarily used to describe manufacturing processes where the ordering of components is a critical part of the Cl n Cl mon HO O O OH HO OH mer mer co COOH O COOH O O O COOH COOH c1 c3 c2 c4 mix 166 Drawing Query Structures CambridgeSoft Representing Polymers and Other Repeating Units Administrator process and where a different ordering might produce a different final product As with Unordered Mixtures individual elements of an ordered mixture should be surrounded by brackets with a bracket usage of Component c Unlike with Unordered Mixtures however components of Ordered Mixtures must represent their ordering You can do this by editing the c label with the text tool to include a number c1 c2 and so on You use the bracket type Multiple Group to indicate that the enclosed items are repeated a specific known number of times Multiple Group brackets may enclose entire structures or may enclose a portion of the structures only You can edit the numeric repeat count with the text tool Examples follow Because Multiple Group brackets represent a specific repeat count unlike the unknown repeat count of the other bracket types it is possible to calculate accurate molecular weights and related data for s
269. ject completion to make sure that 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 These 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 CambridgeSoft 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 Make certain that all tech nical and logistical installation processes are managed Deployment amp Training Develop a comprehensive road map for deployment of technology solutions across the enterprise Our experts help you plan and deploy your solutions by Application Deployment Document define and execute all of the actions required to support end user acceptance Manage the deployment process to assure a smooth roll out to the end users Beta and Pre Release Programs Beta and pre release programs involve a limited deployment to a small set of users in order to identi
270. l To label an atom using a bond or ring tool 1 Click the Bond or Ring tool 2 Point to an atom and double click An atom text label appears over the atom 3 Type the text Repeating an Atom Label You can repeat an atom label using the text bond or ring tools To label several atoms with the same text using the Text tool 1 Click the Text tool 2 Label a single atom 3 Double click another atom to repeat the previous label To label several atoms with the same text using a bond ring or Acyclic Chain tool 1 Click the tool 2 Triple click an atom to repeat the previous label Atom Numbering You can add sequential numbering indicators to the atoms in a structure ChemDraw recognizes the following types of indicators Numbers 1 2 3 and so on Text ending with a number atom1 Greek letters in the Symbol font Letters a b c and so on The default indicator is numbers Hotkey Function Enter or Return Opens the atom label text box space Removes an atom label Delete or Backspace Deletes objects 90 Drawing Captions and Atom Labels CambridgeSoft Atom Numbering Administrator Showing and Hiding Atom Numbers To add Atom Numbering to an entire structure 1 Select the structure 2 Do one of the following To number individual atoms 1 Select the atom 2 Do one of the following To hide Atom Numbering in a structure 1 Sel
271. l used by Molecular Simulation Inc ChemDraw recognizes files with the mol file extension as MDL MolFiles In addition the extension msi used in earlier Pro Pro Pro Pro Pro Pro 202 Sharing Information CambridgeSoft Importing and Exporting Administrator versions of ChemDraw is no longer recognized in ChemDraw To open Molecular Simulations MolFiles that have a mol or msi extension you must first change the extension to msm PICT Macintosh PICT files contain a QuickDraw representation of a ChemDraw drawing that can be used by various drawing applications You can save a ChemDraw document in the PICT format so it can be opened by one of these other applications The PICT file format contains ChemDraw structural information PICT files created by earlier versions of ChemDraw can be reopened and edited by ChemDraw version 8 0 However the pictures contained in PICT files created by versions of CS ChemDraw earlier than version 3 5 or by other applications are treated as a single non editable imported picture All colors are saved in the PICT file except for the Background color PICT scaled 4X Macintosh PICT scaled 4X files are the same as PICT files except that the drawing is four times larger When these larger files are placed into certain other appli cations and shrunk back down to 1 4 size they may provide higher quality output than regular PICT files PNG file
272. l and thermodynamic properties in Chem Draw Excel For detailed information on the properties calculated and how ChemProp calculates them see Viewing Chemical Properties on page 141 and Appendix E How ChemProp Works ChemProp Properties In ChemDraw Excel you can use the ChemProp functions to calculate the following properties CHEM COMPOSITION Returns elemental percent by weight for all elements in structure unless optional second argument specifies a single element symbol as a string In this case the elemental percent is expressed as a decimal number between 0 and 1 75 1 would be 0 751 Returns N A error if the cell referenced in first argument doesn t contain a ChemDraw structure or if second argument is not a valid element symbol CHEM NUM ATOMS Returns total number of atoms in the structure unless optional second argument specifies a single element symbol as a string In this case it returns the number of atoms of that element only Returns N A error if the cell referenced in first argument doesn t contain a ChemDraw structure or if second argument is not a valid element symbol Function Action Property Function LogP Ultra only CHEMPROP LOGP Molar Refractivity Ultra only CHEMPROP MR Henry s Law Constant CHEMPROP HENRY LAW CONSTANT Boiling Point CHEMPROP BOILING Freezing Temperature CHEMPROP FREEZING Critical Temperature CHEMPROP CRITICAL TEMP
273. l from the palette 2 Point to an atom where the node of the orbital is to be attached 3 Drag from the orbital node to the wide end of the major lobe of the orbital d orbitals The d orbital tools are shown below To draw a d orbital 1 Hold down the mouse button over the Orbital tool and drag to select the d orbital tool from the palette 2 Point to an atom where the node of the orbital is to be attached 96 Drawing Orbitals Symbols Arrows Arcs and Other Shapes CambridgeSoft The Chemical Symbols Tools Palette Administrator 3 Drag from the center of the orbital to the wide end of a filled lobe dz2 orbitals The dz2 orbital tools are shown below To draw a dz2 orbital 1 Hold down the mouse button over the Orbital tool and drag to select the dz 2 orbital tool from the palette 2 Point to an atom where the node of the orbital will be attached 3 Drag from the center of the orbital to the wide end of a lobe The Chemical Symbols Tools Palette Use the Chemical Symbols tools to add chemical symbols to your structure When you click the Chemical Symbols tool the following palette appears When you attach a symbol other than H dot or H dash to an atom it remains at a fixed distance from the central character of the atom label If you drag the symbol it will maintain that fixed distance as it moves around the atom You can however use a symbol without attaching it to an atom p
274. lace or move it anywhere and resize it H dot and H dash To represent a hydrogen atom that is coming out of the plane toward you along the Z axis use the H dot symbol To represent a hydrogen atom that is directed backwards into the plane away from you along the Z axis use the H dash symbol You can draw H dots and H dashes only by clicking atoms Symbols 94 dpi ChemDraw 9 Drawing Orbitals Symbols Arrows Arcs and Other Shapes 97 The Chemical Symbols Tools Palette To draw an H dot or an H dash 1 Hold down the mouse button over the Chemical Symbols tool and drag to select the symbol from the palette 2 Point to the atom 3 Click the atom Lone Pair Use the lone pair symbol to indicate a lone pair of electrons common in Lewis structure representations To draw a lone pair 1 Hold down the mouse button over the Chemical Symbols tool and drag to select the lone pair from the palette 2 Point to the atom where you want the lone pair located and drag in the appropriate direction to position it 3 Release the mouse button The lone pair is offset from the atom at a fixed position To deposit a lone pair symbol in a horizontal orientation Click in a document window To change the orientation Click and drag the symbol to the desired orientation Radical Use the radical symbol to indicate a single non bonded electron To draw a radical symbol 1 Hold down t
275. lap 178 setup 179 Page Definition Language PostScript 28 QuickDraw 28 Page Setup page layout 179 saving settings 181 Paged documents 178 Paired brackets 101 Palette Arcs 102 Brackets 101 Chemical Symbols 96 color 131 Multiple bonds 62 orbital tools 94 Query tools 159 single bonds 62 Palettes showing 17 tearing off 17 Paper Size 180 Parentheses 101 Paste Duplicating objects 113 objects 112 Paste Special name as structure 75 SMILES 192 Pen Tool 15 Pen tool shapes deleting segments 105 selecting 104 Periodic Table 19 Perspectives changing 181 PICT file format 202 PICT scaled 4x file format 202 Picture Layers atom labels 86 Plain style shapes 105 PNG file format 202 Polymers flip type 166 repeat pattern 166 source based 164 structure based 164 Portrait page orientation 180 Positioning atom number indicators 91 crosshair 183 objects 111 query indicators 160 rulers 182 stereochemistry indicators 140 using the Clipboard 112 Posters setup 178 PostScript commands 195 EPS TEXT 199 print quality 28 printing 29 Preferences Check Structure 138 drawing see Drawing Settings 21 highlight box 65 Include ChemDraw LaserPrep 195 Include PostScript 195 Initialize PostScript Printer 195 overview 20 print 28 require CTRL ENTER 79 require Option Return 79 text see Text Settings 21 Use Bitmap Fonts When Available 92 Print Quality 28 Printing atom mapping 171 background color 28 ChemDraw 9 xv Printing c
276. late panel Top half of the window consists of individual panes where newly created templates appear Drawing area Bottom half of the window where you can draw new templates The templates you define are not limited to atoms and bonds Templates can contain any ChemDraw objects such as captions boxes arcs orbitals arrows reaction mechanism symbols and curves The ChemDraw objects in Template documents can be colored However the colors do not appear in the Templates tool palette You can paste pictures from other applications into a Template pane Pasted objects are scaled to the current Template document settings For more information see Autoscaling on page 193 Creating Templates To create a new template 1 Select a Template pane by clicking it 2 Draw a structure or object in the drawing area of the Template window The structure appears in the Template pane as you draw The tools in the Tools palette are used to draw a template in the drawing area of the Template window exactly as they are used to draw structures in the drawing area of a document window To select a different Template pane Click another Template pane When you select a Template pane the contents of the pane appear in the drawing area As you define templates they become available for use in your document without having to save the Template document To view the newly defined Template Point at the Templates tool
277. lationships 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 ChemOffice product line provide additional ways to analyze structural and biological data and perform structure searches Both ChemFinder and ChemOffice WebServer make it easy to create customized forms for viewing data Users can export data to Excel or Spotfire for further analysis and reporting Effectively manages data from complex biological assays involved with lead optimization Adapts quickly and flexibly to different assays and biological models Closely integrated with Microsoft Excel ChemOffice and ChemDraw D I S C O V E R Y EMAIL info cambridgesoft com WWW www cambridgesoft com TEL 1 800 315 7300 INT L 1 617 588 9300 FAX 1 617 588 9390 MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge MA 02140 USA ChemOffice ChemDraw Chem3D ChemFinder amp ChemInfo are trademarks of CambridgeSoft 2002 All other trademarks are the property of their respective holders All specifications subject to change without notice R E S E A R C H amp BioSAR Browser BioSAR Browser Biological and Chemical Meta Data Catalog Biological and Chemical Meta Data Catalog BioSAR Browser BioSAR Browser a strategic must for any discovery organization interested in serious data mining is a data dic tionary driven structure a
278. lect the Reaction Atom Atom Map tool When this option is deselected atom mapping symbols do not print even though a reaction map has been created Automatic Mapping To automatically create a reaction map 1 Draw the reaction you want to map For example 2 Select the reactants and products in the reaction 3 From the Structure menu choose Map Reaction Atoms The symbol Rxn appears next to the bonds in the reactant and product that are perceived by the algorithm as being modified by the reaction These symbols are bond properties that are automatically applied For more information about the Reaction Center bond property see Bond Properties on page 155 Manual Mapping In situations that require manual mapping of atoms you can use the Reaction Atom Atom Map tool This might be necessary when the automatic mapping is applied to complicated reactions In these cases you can manually readjust the reaction mapping The following figure shows how to amend the initial mapping by using the Reaction Atom Atom Map tool When you perform manual mapping with the Reaction Atom Atom Map tool you can suppress automatic re mapping of atoms other than your target atom To suppress automatic re mapping 1 From the File menu choose Preferences 2 On the General tab select Automatic Reaction Mapping 3 Click OK To use the Reaction Atom Atom Map tool to supplement the automatic mapping 1 Click t
279. lection of 30 000 fully atom mapped reactions selected and refined from the chemical literature It includes reactions from InfoChem s ChemSelect database and ISI 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 the ChemDraw Plugin for structure and substructure searches View live ChemDraw files on Windows and Macintosh clients ChemRXN database on CD ROM ChemINDEX database on ChemFinder Com S O F T WA R E The Merck Index Encyclopedic chemical reference ChemACX Pro Chemical searching amp buying The Merck Index Chemistry s Constant Companion Over 10 000 monographs of chemicals drugs amp biologicals ChemACX Pro Chemical Searching amp Buying Database of commercially available chemicals 300 catalogs with 500 000 chemical products ChemACX SC database with 500 000 structures from leading screening compound suppliers ChemACX Com WWW Chemical Searching amp Buying 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 amp anti cancer assay data ChemRXN Reaction Searching amp Information Includes ChemSelect with reactions from InfoChem GmbH amp ISI
280. led Each time you draw a bond the last atom drawn is the Hotkey atom NOTE When you are pointing rather than drawing the last atom highlighted is the atom labeled Thus if you click to create a bond and linger with the cursor over the origin you will highlight the origin and it will be labeled rather than the last atom drawn Method 2 Labeling an atom by pointing 1 Using a bond tool or the Text tool position the pointer over an atom A highlight box appears over the atom 88 Drawing Captions and Atom Labels CambridgeSoft Labeling Atoms with HotKeys Administrator 2 Type a Hotkey for example c The label is added to the atom highlighted If the label is a single element such as C then the appropriate number of hydrogen atoms are added to the label Repeatedly typing the hotkey will cycle the number of hydrogens NOTE The last atom highlighted is always the atom labeled even if you are no longer pointing to it that is even if it is no longer highlighted This is true even if you switch documents Method 3 Labeling an Atom with a Selection Tool 1 Using a selection tool position the pointer over an atom A highlight box appears over the atom 2 Type a Hotkey for example c Method 4 Labeling multiple atoms 1 Select several atoms using a selection tool 2 Type a Hotkey for example c The selected atoms are labeled The element or label associated with the Hotkey is add
281. leshooting see Defining Nicknames on page 122 Character Map The floating Character Map window displays the 256 ASCII characters in any font The default font is Symbol Use it to add symbols or styled fonts to labels The character map is active only when a text box is open for editing It will appear grayed out at all other Times New Roman With a text box open mouse over the character map to view a larger version of the characters in the top right corner of the window Click any character in the table to enter that character in the text box The selected font shown in the character map window is applied to that character only It does not change the active font in the text box NOTE You can cancel a selection by dragging to some other character before releasing The 8 most recently used characters are displayed at the top of the window These characters remember their font and are not affected by changes to the window A single character may appear more than once in this section if the versions use different fonts Click the button to toggle between the 8 most recently used characters and the entire character map Customizing ChemDraw You can customize ChemDraw by configuring Preferences and Document Settings Preferences allow you to change the default behavior of certain options that apply to every open document Document Settings allow you to change the default behavior of options that will affect o
282. list Contracting Labels You can compress an area of a structure and replace it with a text label by using the Contract Label command Contracted labels are similar to Nicknames but they are for one time use only in the current document To create a contracted label 1 Select the area of the structure to contract 2 From the Structure menu choose Contract Label The Contract Label dialog box appears 3 Type a label for the contracted structure and click OK The label replaces the selected portion of the structure NOTE If the area of the structure you contract contains errors an error dialog box appears Click Ignore to view any other errors Click Ignore All to ignore all errors or Stop to end the contract process HGlyAlaOH ListNicknames 150 dpi Pro Pro ContractLabel 150 dpi molecule ChemDraw 9 Advanced Drawing Techniques 125 Expanding Labels Expanding Labels If your structures contain defined nicknames long atom labels or contracted labels ChemDraw can restore your structures to the fully expanded form When you expand a label containing a divalent nickname for example HAlaOH the first attachment is to the character left of the nickname H The second attachment is to the character right of the nickname OH To expand atom labels 1 Select a selection tool 2 Select the label to expand or double click the structure to expand all possible labels 3 From the Structure menu
283. llowing Periodic Table The Periodic Table window displays a floating peri odic table It can be used both for reference and to insert elements into structures Click an element symbol to highlight the element and activate the Text tool Drag across the table to highlight each element in turn Click the button to show or hide the detailed information After selecting an element click in the document to add an atom label consisting of that element and the appropriate number of hydrogens Labeling behavior is as follows Field Shows Pointer X Y current mouse coordinates Pointer dX dY change in X and Y coordinates of a moved selection Selection X Y W H position of a selection width height of a selection Angle angle of a bond rotation of a selection Dist length of a bond distance a selection has been moved of original size when resizing a selection click on to an existing unlabeled atom label the atom an existing labeled atom cycle the hydrogen count if it matches the selected element or change the label an empty space create a new atom 20 ChemDraw Basics CambridgeSoft Customizing ChemDraw Administrator Double clicking on an existing atom will open it for editing without changing the label NOTE Some element names conflict with ChemDraw Hotkeys and may not be interpreted correctly by Chemical Warnings or Check Structure For more information and troub
284. lor The Color Picker dialog box appears 4 Use one of the icons on the left to select a method of defining your color then select a color For more information about the Macintosh color options refer to your System documentation 5 Click OK The new color appears in the Colors tab in place of the original color and is added to the color menu Adding or Customizing Macintosh Colors To add a new color to the Color menu 1 On the Color tab click New Color or Set Other Color The Color Picker dialog box appears Color Refiner box Luminosity box ChemDraw 9 Advanced Drawing Techniques 133 Drawing With Templates 2 Click a color in the Color Wheel 3 If necessary adjust the hue saturation brightness and RGB components by typing the values in 4 Click OK The new color is added to the list of Other Colors Removing Colors To remove a color from the Color menu 1 Click the color you want to remove A highlight box appears around the color 2 Click Remove Color The color disappears from the list of other colors Objects that were drawn in the removed color are changed to the Foreground color Templates and Color The background and foreground colors used in a template from the template pop up palette are not used when the template is drawn in a document window However any other colors used in the template are added to the color palette of the current document if they are not already present
285. lt from running the experiment CombiChem Enterprise evaluates the products using several in silico 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 The 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 used in this thin layer chromatography CombiChem Enterprise provides ways to organize the data and navigation is simple When used with E Notebook Enterprise the data for a library of shared compounds and the entire experiment is automatically documented and made available to the entire organization Reagent lists can be drawn from varied sources Reaction based library generation allows for evaluation by product or reagent Data management is simplified and library specifications are available to others on the network D I S C O V E R Y EMAIL info cambridgesoft com WWW www cambridgesoft com TEL 1 800 315 7300 INT L 1 617 588 9300 FAX 1 617 588 9390 MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge MA 02140
286. lue of zero finds a substituent count as drawn You can also use the Free Sites symbol in the Chemical Symbols palette to apply free sites For more information see Chapter 6 Drawing Orbitals Symbols Arrows Arcs and Other Shapes on page 93 Up to Finds compounds in which the selected atoms may contain a range of substituents up to the number specified Exactly Finds compounds in which the selected atoms contain the exact number of substituents as specified up to 15 substituents Option Search Result Option Search Result Allowed Default Finds compounds regardless of whether hydrogen atoms are attached to the selected atoms Not allowed Finds compounds with no additional hydrogen atoms attached to the selected atoms Option Search Result Any Default Finds compounds in which the selected atoms can be a member of any type of ring or a member of no ring at all No ring bonds Finds compounds in which the selected atoms are acyclic As drawn Finds compounds in which the selected atoms reside in the same type and number of rings as drawn ChemDraw 9 Drawing Query Structures 153 Atom Property Options Unsaturation The Unsaturation property specifies whether a multiple bond is attached to the selected atoms The unsaturation options are described in the following table Reaction Change The Reaction Change property specifies whether a change occurs at selected atoms after a reactio
287. m pid 278 http products cambridge soft com ProdInfo cfm pid 279 ChemDraw 9 Introduction 11 Installation and System Requirements Installation and System Requirements Before installation see the ReadMeFirst and any other ReadMe documents on the installation CD ROM Microsoft Windows Requirements Windows 2000 or XP Microsoft Excel add ins require Office 2000 2003 or XP 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 the activation each time you access the page If you visit a site frequently you can add it to the list of trusted sites in IE s security settings Screen resolution must be 800 x 600 or higher Macintosh Requirements Ignore this if it shouldn t be here It s conditional text and disappears when not needed Mac OS X 10 1 x or later
288. m with the Text tool An atom label text box appears Pro Pro NHOH NHOH 122 Advanced Drawing Techniques CambridgeSoft Using Nicknames Administrator 3 Type a Nickname label such as Et To select a Nickname to apply to an atom using a Hotkey 1 Point to an atom 2 Press the Hotkey The Choose Nickname dialog box appears 3 Select a Nickname from the list 4 Click OK NOTE Nicknames are tokens and do not flip orientation when applied to the left side of a structure when using Automatic Justification For example in the absence of a defined Nickname the label OTHP appears as PHTO when applied to the left side of a structure However since the Nickname THP is defined the label appears as THPO For more information see Aligning Text on page 81 Defining Nicknames To define your own Nicknames you must have ChemDraw Pro You can define Nicknames with one or two attachment points The attachment points must be single bonds To define a new Nickname 1 Create a structure containing the functional group you want to define as a Nickname 2 Select the functional group You must indicate the connection point for the functional group by selecting the new fragment without the bond connected to the attachment point NOTE If stereochemistry is indicated in a structure that you are defining as a Nickname the stereochemistry is retained 3 From the Str
289. mDraw These documents can also be MDL RGFile rgf YES YES Molecular Simulations MolFile msm YES YES PICT Macintosh Portable Network Graphics png YES YES Standard Molecular Data smd YES YES Galactic Industries spc YES NO Template Style Sheet cts Windows Metafile emf wmf YES YES TIFF file tif YES YES a May have limitations See the appropriate section in the text Format Import Export ChemDraw 9 Sharing Information 199 Importing and Exporting opened in versions 3 0 3 0 1 3 0 2 and 3 1 of ChemDraw as long as atom properties are not used in the files NOTE When you save a ChemDraw file in one of these formats all features specific to later versions are lost For example multi attached atom labels variable attachment points and multicenter bonds are not be saved ChemDraw 2 0 and ChemDraw 2 1 chm Import Only ChemDraw 2 0 and ChemDraw 2 1 file formats are used for opening ChemDraw documents using the version 2 x file format of ChemDraw for Macin tosh You cannot save files in these formats ChemDraw Stationery Style Sheet cds Use ChemDraw Stationery file format to save document settings and other objects Connection Table ct The Connection Table file format is a simple format that saves a list of atom connectivities in terms of an element serial number X and Y coor dinates bond order and bond type For more informatio
290. mal donor acceptor pairs Another representation of heme N N N N HO O Fe N N N N HO O Fe M Fe Ti Cl Cl Mn OC CO CO ChemDraw 9 The Chemistry of ChemDraw 237 Chemical Conventions CIP rules are designed to order ligands by their priority and determine a descriptor based on the orientation of the ordered ligands in space A ligand is an entity attached to a stereocenter For example a tetrahedral carbon has four ligands corresponding to its four substituents When a tetrahedral carbon is in a ring it still has four ligands the two ligands outside the ring a third consisting of the ring unpeeled clockwise and a fourth consisting of the ring unpeeled counterclockwise Five rules are used to determine the priority of ligands are summarized below in simplified form For more detailed information see the references They are checked sequentially as follows Rule 1 Higher atomic number precedes lower Rule 2 Higher atomic mass precedes lower Rule 3 cis precedes trans Rule 4 Like pairs of descriptors precede unlike pairs Rule 5 R precedes S ChemDraw checks differences up to 15 atoms distant from the stereocenter Stereochemical Indicators After the ligands are ranked an indicator is assigned as shown in the following table 1 Stereochemical Flags While the chirality of a specific stereocenter can be indicated
291. mation on creating and storing mac ros see Excel Help Using ChemDraw Excel Functions ChemDraw Excel supplies nine functions that return information about chemistry objects in a specified cell Seven of these functions take only one argument the cell to which the function refers The remaining two functions may also take a string as an optional second argument The function ISSTRUCTURE is an example of a function that takes only one argument To deter mine whether the content of cell A1 in an Excel spreadsheet is a ChemDraw Excel chemistry object you type ISSTRUCTURE A1 into a second cell The second cell then displays TRUE or FALSE depending on whether A1 contains a chemistry object The function CHEM COMPOSITION is one of the functions that may take an optional second argument It works in one of two ways 216 ChemDraw Excel CambridgeSoft Using ChemDraw Excel Functions Administrator With First Argument Only Without the second argument it displays elemental composition by weight percent of the entire chem ical structure in cell A1 when you type CHEM COMPOSITION A1 into a second cell For benzene it displays C 92 26 H 7 74 With Both Arguments The second argument lets you find the percent composition of a single element in the structure Typing CHEM COMPO SITION A1 C returns the weight percent of car bon in the structure For benzene it would display 0 922582 Notice that the display format
292. mbridgeSoft Showing Stereochemistry Administrator Only tetrahedral and double bond stereochemistry are supported and only non racemic stereochemistry is interpreted Stereochemical indicators for aromatic bonds are not shown ChemDraw calculates and displays the following stereochemical terms R S Standard tetrahedral stereochemistry r s Tetrahedral stereochemistry determined by other stereochemical centers For example cis decalin and myo inositol E Z Standard double bond stereochemistry The atom label settings determine the font style and size of the terms Stereochemistry Indicators To show the stereochemistry of a structure Select a structure right click and then click Show Stereochemistry The stereocenters are marked as shown in the following example If you make changes to the drawing that affect the stereochemistry the stereochemistry is recalculated Hiding Indicators To hide an individual indicator 1 Select the indicator to hide 2 Right click and choose Hide Indicator Removing Indicators To delete an indicator 1 Click the indicator 2 Click the eraser tool and then click the indicator Positioning Indicators Stereochemistry indicators are positioned automatically and move appropriately if a structure is modified You can reposition them by dragging them to the desired position or with the Indicator Position dialog box To reposi
293. ment so you can see arrows or other objects that are in small places choose Magnify from the View menu Save and close the document 1 From the File menu choose Save 2 From the File menu choose Close Tutorial 3 Using Rings In this tutorial you will draw more complex structures by using rings Open a new ChemDraw document 1 From the File menu choose New Document 2 From the File menu choose Save As 3 Type tut3 cdx in the appropriate text box 4 Select a folder in which to save the file 5 Click Save Create a ring 1 Click the Cyclohexane Ring tool 2 Point in an empty area of a document window 3 Click to add a ring Fuse a second ring to the first 1 Point to the center of lower right bond in the ring O OH CH O 42 Tutorials CambridgeSoft Tutorial 3 Using Rings Administrator 2 Click to fuse another ring Fuse a third ring 1 Point to the bond shown below 2 Click to fuse another ring Your document should contain the structure shown below Fuse a fourth ring 1 Point to the bond shown below 2 Click to fuse another ring Remove atoms and their bonds from the ring using the Eraser tool 1 Click the Eraser tool 2 Point to the atom shown below A highlight box appears on the atom to be removed 3 Click to delete the atom and its bonds ChemDraw 9 Tutorials 43 Tutorial 3 Using Rings 4 Click each of the atoms shown
294. n This property is only meaningful when searching a database containing chemical reactions The reaction change options are described in the following table Reaction Stereo The Reaction Stereo property specifies that the selected atoms are stereocenters in a reaction This property is only meaningful when searching a database containing chemical reactions The reaction stereo options are described in the following table Simple ring Finds compounds in which the selected atoms is a member of only one ring the atom has two ring bonds Fusion Finds compounds in which the selected atoms lies at ring fusions the atom has three ring bonds Spiro or higher Finds compounds in which the selected atoms is a member of a spiro or higher linkage the atom has four or more ring bonds Option Search Result Unspecified Default Finds compounds regardless of whether a multiple bond is attached to the selected atoms Must be absent Finds compounds that do not have a multiple bond attached to the selected atoms Must be present Finds compounds that have at least one multiple bond double triple or aromatic attached to the selected atoms Option Search Result Option Search Result May be anything Default Finds all reactions regardless of any change to selected atoms after a reaction Must be as specified Finds all reactions that are changed at the selected atoms exactly as specified by the reaction cent
295. n All boiling points are estimated at a pressure of 1 atm Ultra Ultra 1 Ertl P Rohde B and Selzer P 2000 Fast Calculation of Molecular Polar Surface Area as a Sum of Fragment Based Contributions and Its Application to the Prediction of Drug Transport Properties J Med Chem 43 3714 3717 ChemDraw 9 Shortcuts and Hotkeys 247 Appendix F Shortcuts and Hotkeys Shortcuts are key sequences used by power users to save time The following tables list the ChemDraw shortcuts ChemDraw Hotkeys are used for rapid labeling of atoms and for applying atom and bond properties The tables list the default ChemDraw Hotkeys See Labeling Atoms with HotKeys on page 87 for information on customizing Hotkeys ChemDraw Windows Shortcuts See also ChemDraw Hotkeys on page 252 File Commands Edit Commands Enter to execute Command Ctrl N new document Ctrl O open document Ctrl W close document Alt F4 exit Ctrl S save document Shift Ctrl S save as Shift Ctrl P page set up Ctrl P print Enter to execute Command Ctrl Z undo Ctrl X cut Ctrl C copy Ctrl V paste Shift Ctrl Z redo Del clear Ctrl A select all Ctrl Y repeat last command Enter to execute Command 248 Shortcuts and Hotkeys CambridgeSoft Administrator View Commands Object Commands Structure Commands Text Commands Enter to execute Command F5
296. n see Chemistry File Formats on page 267 Chemical Markup Language cml CML is an extensible chemically aware markup language based on XML ChemDraw supports both import and export of the format More infor mation can be found at http www xml cml org and http cml sourceforge net Encapsulated PostScript Macintosh PostScript eps Windows Encapsulated PostScript EPS files are ASCII text files containing the scalable PostScript representa tion of a ChemDraw drawing that can be opened using other applications and platforms There are two types one containing text only and one containing a graphic representation of the drawing The latter are known as Postscript with Preview or Postscript Mac For text only files programs that do not support the display of raw PostScript can only print not view an image on screen Use EPS files to share ChemDraw drawings with desktop publishing applications such as Adobe PageMaker and QuarkXPress The Options dialog box allows you to select the resolution in dpi and color depth of the saved file The defaults are 300 dpi and Monochrome For Windows EPS with Preview there is also a Preview option default WMF If you select a color option all colors are saved in the EPS file except for the Background color To save an EPS file with a colored background create a large colored rectangular box using the Drawing Elements tool and choose Send to Back before s
297. n text box Type the new caption text over the highlighted text The highlighted text disappears as you type the new caption If not all the text is highlighted and you want to select all of the caption text From the Edit menu choose Select All To change part of the caption text Drag the insertion point over a part of the caption Adding Analysis Data to a Caption You can add any of the properties from The Anal ysis Window to a caption If auto update is on the values will update as you modify your structure Resize handle 86 Drawing Captions and Atom Labels CambridgeSoft Labeling Atoms with the Text Tool Administrator To add values to a Struct Name label 1 Point to the label 2 Right click point to Analysis and choose a property from the list The property appears in the label displaying the current value NOTE You may need to update the window before you can see the new value If you don t see it immediately it will appear with the next modification to the structure Labeling Atoms with the Text Tool The default format options of any new atom labels you create are specified in the Atom Labels tab of the Document Settings dialog box You may edit these options at any time The settings affect the current document only To place an atom label on an atom 1 Click the Text tool 2 Point to an atom The pointer changes when it is positioned correctly over an atom
298. n 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 I 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 purpose 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
299. n of a chain Shift Command drag copy a selected object constrained to X and Y axes Enter to execute Command 252 Shortcuts and Hotkeys CambridgeSoft ChemDraw Hotkeys Administrator ChemDraw Hotkeys Hotkeys are used for rapid labeling of atoms and for applying atom and bond properties The following tables list the default ChemDraw Hotkeys See Labeling Atoms with HotKeys on page 87 for information on customizing Hotkeys See also ChemDraw Windows Shortcuts on page 247 Atom Hotkeys NOTE All Hotkeys can be edited except lt Enter gt or lt Return gt lt Space gt lt Backspace gt and lt Delete gt Command Option Tab toggles the Lasso and the previous drawing tool Hotkey Result a A A or 5 Ac b Br c C C or l lower case L Cl d D e Et Enter to execute Command E COOCH3 f F h H i I k K l Cl m Me n N N Na o O p P P or 4 Ph q Q non hydrogen heteroatom r R s S S Si t TMS Hotkey Result ChemDraw 9 Shortcuts and Hotkeys 253 ChemDraw Hotkeys Bond Editing Hotkeys T OTs x X 1 n Bu 2 s Bu 3 t Bu 4 Ph 5 Ac lt Enter gt Open an atom label text box slash Display the Atom Properties dialog box equals Display the Choose Nickname dialog box period Add an attachment point single quote Add an atom number lt space gt Remo
300. n to an existing atom 1 Click the Acyclic Chain tool 2 Point to the atom to which you want to attach the chain 3 Drag in the direction you want the chain to grow To specify a chain length 1 Click the Acyclic Chain tool 2 Click an existing atom or an empty area in a document window The Add Chain dialog box appears 3 Type the number of bonds in the chain 4 Click Add To add another chain of the same length anywhere in a document window Alt click or Option click an existing atom or click in an empty area within the document window Changing Chain Direction To change the direction of the chain as you draw 5 2 AddChain 150 dpi ChemDraw 9 Drawing Chemical Structures 69 Editing Bonds Press the Ctrl or Command key while drawing chains in the direction you want NOTE If Fixed Lengths is off use Ctrl Alt or Command Option to reverse chain direction Fixed Angles must be on to reverse direction Editing Bonds You can modify the appearance of chemical structures by Changing bond types Changing bond alignment and orientation Moving atoms Layering bonds Changing the bond order Changing Bond Types To change a single bond from one type to another 1 Click a bond tool 2 Point at the center of an existing bond and click The bond that you click changes to the new bond type Changing Double Bonds To change one type of doubl
301. nd other resources for the Application Programming Interfaces APIs NOTE You must activate Javascript in your browser in order to use the ChemOffice SDK page 226 Accessing the CambridgeSoft Web Site CambridgeSoft Using the ChemOffice SDK Administrator ChemDraw Appendix Technical Support 227 Serial Numbers Appendices Appendix B Technical Support Overview CambridgeSoft Corporation CS provides technical support to all registered users of this software through the internet and through our 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 our website please do the following before contacting Technical Support 1 Check the ReadMe file for known limitations or 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 If all your attempts to resolve a problem fail fill out a copy of the CS Software 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 Try to reproduce the problem before contact
302. nd those listed below ChemOffice Browser ChemOffice Browser including ChemDraw Java ActiveX and the ChemDraw and Chem3D Plugins brings the power and chemical intelligence of ChemOffice to Internet and intranet applications User Friendly amp IT Ready User friendly and IT ready ChemOffice 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 Browse Detailed Compound Information Easy Management of Search Results S O L U T I O N S Knowledge Management Knowledge Management applications organize and distribute chemical information E Notebook Enterprise streamlines daily record keeping with rigorous security and efficient archiving and facilitates information retrieval by structure and text searching Document Manager indexes the chemical structure content of docu ments Discovery LIMS tracks laboratory requests and 21CFR11 Compliance implements an organization s reg ulatory compliance processes Research amp Discovery Research and discovery applications
303. ng Appendices 4 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 230 Technical Support CambridgeSoft Troubleshooting Administrator ChemDraw 9 The Chemistry of ChemDraw 231 Database Conventions Appendix C The Chemistry of ChemDraw Overview ChemDraw automatically converts lines characters and other symbols into chemically meaningful figures as you work This work occurs in the background but you can choose to view this chemical data using Check Structure Analyze Structure and Expand Atom Labels ChemDraw also uses this chemical data when exporting to file formats that support only a subset of the notations that ChemDraw does This appendix describes how ChemDraw interprets what you draw and how you can help ChemDraw better interpret what you mean Chemical Intelligence in ChemDraw ChemDraw was designed as a tool to aid in chemical communication Most chemists would understand AcOo C6H4COOH immediately whether or not they recognized it as aspirin Most computer programs however require what is known as a complete connection table in this case a collection of 21 atoms connected by 5 double bonds and 16 single bonds in a specific pattern ChemDraw takes what makes sense to a chemist and converts it into what makes sense to another application This chemical intelligence can be used as
304. nits Henry s Law Henry s Law Constant The air to water partition coefficient that is expressed as ratio of vapor pressure to water solubility or as a unitless distribution coefficient that can be evaluated as a ratio of the concentration in air to the concentration in water Two methods are used to predict Henry s Law constant 1 The first is an approach based on the bond contribution method This method uses 59 bond contribution values and 15 correction factors The contributions were calculated by least squares analysis using a data set of 345 chemicals This method estimates with a mean error of 0 30 units and a standard deviation of 0 45 units and can handle molecules containing carbon hydrogen oxygen nitrogen sulfur phosphorus and halogens 2 In the second method Henry s Law constant is estimated from an equation found using linear regression Multifunctional compounds were omitted from this study This method should not be used for compounds where distant polar interaction is present Pro Pro 246 How ChemProp Works CambridgeSoft Molar Refractivity Administrator Molar Refractivity Molar refractivity Two fragmentation methods are used to estimate the molar refractivity value 1 Method one includes 93 atomic contributions evaluated from 504 molecules by using a constrained least squares technique This method works with a standard deviation 1 27 cm3 mol and can handle molecules containing h
305. nline Menu Overview The ChemOffice Online menu gives you quick access to the CambridgeSoft web site from within ChemOffice With the Online menu you can Register your software Search for compounds by name or ACX number and insert the structure in a worksheet Use ACX numbers or names or structures in the worksheet to search for chemical information Browse the CambridgeSoft website for technical support documentation software updates and more To use the Online menu you must have internet access Registering Online ChemOffice 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 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 registration 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 ChemBioN
306. nly the active document Setting Preferences Preferences affect the way the ChemDraw applica tion works regardless of the document with which you are working To open the Preferences dialog box From the File menu choose Preferences ChemDraw 9 ChemDraw Basics 21 Customizing ChemDraw The Preferences dialog box appears To restore the CambridgeSoft default settings Click the Use Defaults button Document and Object Settings Document and object settings are user definable settings that are applied to the current document Settings include Drawing settings set drawing options such as the fixed length used to draw bonds Caption and label text settings set text options such as the font used for atom labels and captions Color settings set available colors for objects and the document background Print Page Setup set options such as the page size used and text displayed in footers You can apply document settings in the following ways Customize settings for the entire document using the Document Settings dialog box Apply settings to the entire current document from an existing document Apply settings to selected objects in the current document from an existing document Default Style Sheet or Stationery Pad When you open ChemDraw the last Style Sheet or Stationery Pad used opens as the default If you choose another Style Sheet or Stationery P
307. ns The following table describes the chemical conventions understood by ChemDraw A single bond near a closed circle is recognized as aromatic Atom Labels A simple atom label may contain any of the following Bond Description Single bond unspecified stereochemistry Single bond down stereochemistry into the plane of the paper away from the viewer from the first drawn atom to the second drawn atom Single bond up stereochemistry out of the plane of the paper toward the viewer from the first drawn atom to the second drawn atom Single bond mixture of up and down stereochemistries in some unspecified proportion Dative bond Often used to indicate polar bonds such as the N O bond in pyridine N oxide Double bond with cis trans stereochemistry as drawn HC HC CH CH CH HC HC CH CH CH Fe Fe Aldrich MDL ACD Double bond with cis trans stereochemistry unknown Tautomeric bond either single or double according to rules of tautomerism Aromatic bond part of a delocalized resonance system Triple bond Quadruple Bond A single element An element and some number of hydrogen atoms A nickname Repeating units within parentheses Cl O CH3 H N Me Ala C OCH3 3 O CH2 4CH3 ChemDraw 9 The Chemistry of ChemDraw 233 Chemical Conventions When analyzing an atom label ChemDraw starts at the left and continues to th
308. nt to the left center carbon and drag outward ChemDraw 9 Tutorials 55 Tutorial 6 Newman Projections The size of the orbital is constrained just like bonds The constraint is based on a percentage of the Fixed Length setting in the Drawing Settings dialog box NOTE Orbitals are not automatically grouped with the closest structure If you want to group the orbital with the existing structure so you can move them as a unit choose Group from the Object menu Move part of the structure to the front to overlap the orbital 1 Click the Marquee tool 2 Point above the structure and drag around the upper fragment to select the three bonds NOTE Only bonds that are completely within the Lasso area are selected Do not select the bond connecting the two fragments Alternately you can Shift click on each bond separately Rotate the selection 1 Double click the Rotation handle in the upper right of the Selection Rectangle to open the Rotate dialog box 2 Type 180 in the text box select degrees CW and then click Rotate Change the layering of the structure so that the selection is in front From the Object menu choose Bring to Front Orient the front part of the structure to create a Newman projection 1 Point within the Selection Rectangle until the pointer changes to a hand RotateObjectsDB 150 dpi 56 Tutorials CambridgeSoft Tutorial 7 Showing Stereochemistry Administrator 2 Drag
309. ntal Orientation Vertical Orientation 68 Drawing Chemical Structures CambridgeSoft Drawing Acyclic Chains Administrator Drawing Acyclic Chains You can draw long hydrocarbon chains with the Acyclic Chain tool The behavior of the Acyclic Chain tool is affected by the Fixed Lengths and Fixed Angles switches on the Object menu and by the Chain Angle setting on the Object Settings dialog box NOTE Modifying the Chain Angle value for an existing object will have no effect on that object but new bonds chains sprouted from it will sprout at the specified angle The effect of Fixed Lengths and Fixed Angles is noted in the specific sections where it applies Drawing Chains To draw an acyclic chain 1 Click the Acyclic Chain tool 2 Drag in the direction you want the chain to grow in a document window A number appears at the end of the chain indicating how many atoms you have drawn When Fixed Lengths is on the pointer on the acyclic chain can be dragged to make any angle relative to the X axis At a constant chain length the positions of the first bond and all subsequent odd numbered atoms depend on the direction you drag Before releasing the mouse button this position can be changed by dragging in the opposite direction When Fixed Angles is on the angle the acyclic chain makes relative to the X axis is constrained to 15 degree increments Adding Chains To add an acyclic chai
310. ntally modified Spectral controls from Thermo Galactic are available CombiChem Excel builds combinatorial libraries with embedded ChemDraw structures using ChemDraw 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 Scanned Images in Notebook Pages Automatic Stoichiometric Calculations D E S K T O P E Notebook Ultra Ultimate Journaling amp Information Advanced search and structure query features Stores structures and models for easy retrieval Stores physical and calculated data Search by substructure including stereochemistry using ChemDraw Search and store chemical reaction data CombiChem Excel combinatorial libraries Integration with ChemDraw and Chem3D Import export MDL SD amp RD files CombiChem Excel Combinatorial Chemistry in Excel Generate combinatorial libraries Choose starting materials amp reaction schemes View structures amp track plate well assignments ChemFinder Pro Premier Searching amp Information Advanced search amp structure query features Stores structures amp reactions along with calculated data amp associated information Search by substructure including stereochemistry using ChemDraw Integration with ChemDra
311. nts When you save in these formats ChemDraw automati cally expands all atom labels and saves the file using the expanded form For more information see Expanding Labels on page 125 The following formats do not support nicknames or structural fragments Connection Table MSI MolFile SMD Some formats can be saved with different options If a format has no save options the Options button is grayed out The following text based formats can use the Text Options ChemDraw XML CML Connection Table ISIS TGF ISIS Reactions MDL MolFile Molecular Simulations MolFile ChemDraw 9 Sharing Information 197 Importing and Exporting SMD Other format options are noted in format descrip tions Graphics export border preference An explicit preference option allows the user to specify the size of the border when exporting pictures This preference affects the output of all graphical formats including but not necessarily limited to wmf pict eps tiff gif bmp and png It applies to both the clipboard and saved files The default value is 2 points 0 278 in 0 071 cm The value can be zero meaning that the exported image is exactly snug against the objects in the graphic However this is not recommended because a bug in Windows causes clipping at the edges of metafiles when they are reduced in size The default value should prevent clipping w
312. nts as only one substituent and hydrogen atoms never count as substituents The substituent count atom property allows you to specify the number of bonds to an atom in the target structure This includes bonds already drawn in the query structure The substituent options are described in the following table Option Search Result Unspecified Default Search is determined by the target database Some databases including ISIS find compounds with any substitution at this atom and some databases including DARC find only compounds with substitution exactly as drawn H O 152 Drawing Query Structures CambridgeSoft Atom Property Options Administrator Implicit Hydrogens The Implicit Hydrogens property specifies whether additional implicit hydrogen atoms may be attached to the selected atoms If implicit hydrogen atoms are not allowed all valences to that atom must be filled by bonds to non hydrogen atoms The implicit hydrogen options are described in the following table Ring Bond Count The Ring Bond Count specifies the number of bonds attached to an atom that are part of rings of any size For simple cases this also specifies the maximum number of rings in which an atom can reside The ring bond count options are described in the following table Free Sites Finds compounds in which the selected atoms may contain a range of substituents up to the number specified plus the number of bonds as drawn A va
313. o functions completely as a stand alone application Through this architecture CambridgeSoft s enterprise solutions are truly plug and play There are no added system integration costs and the applications can live on different servers in different parts of the world Flexibility The flexibility of the location model allows Inventory Manager 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 empty 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 Manager 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 Manager 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 Once a product is ordered its chemical information is stored and it is given an on order status reducing duplicate ordering of popular reagents Integrated with Registration System and ChemACX for procu
314. o realign the caption select a selection tool and drag the caption Add a charge symbol using the specialized symbols available in the Chemical Symbols tool palette 1 Click the Chemical Symbol tool NOTE A red box appears around the OH label indicating an error i e that you haven t added the charge yet 2 Holding the mouse button down select the circled negative charge symbol shown below then release the mouse button SelectArrow 150 dpi O O OH O O OH O O OH O O OH O O OH SelectMinus 36 Tutorials CambridgeSoft Tutorial 1 Reaction Schemes Administrator 3 Point to the center of the OH label Moving the cursor slightly right or left will cause either the O or the H to be selected 4 With the H selected drag the charge symbol around the atom to the desired position Objects added from the Chemical Symbols palette are automatically associated with the structure they are closest to Some objects such as arrows are not associated automatically You can manually group objects using the Group command You can then select the grouped objects to manipulate or move them together To group objects 1 Click a Selection tool the Lasso or Marquee tool 2 Hold Shift and click the arrow the OH caption and the charge symbol The Shift key allows you to add objects to a selection without deselecting other objects NOTE If you click a selected object while holding
315. ocument text settings for captions and atom labels 1 From the File menu choose Document Settings 2 In the Document Settings dialog box click Captions or Atom Labels The Windows Captions tab containing the text settings is shown below 3 Change the settings if desired The options are described in the following sections 4 Click OK The formatting is applied to the current docu ment Setting the Baseline Style You can specify the following baseline styles Normal Use this for standard text Superscript Reduces the text size by about 25 percent and raises its baseline To change the default for Select Atom Label text Require Alt Enter or Option Return to Create New Line in Atom Labels Caption text Require Alt Enter or Option Return to Create New Line in Captions ChemDraw 9 Drawing Captions and Atom Labels 81 Formatting Text Subscript Reduces the text by about 25 percent and lowers the baseline Formula Formats in a way that is appro priate for most chemical formulas that is numbers are automatically subscripted You must however captitalize manually You can apply several styles to the same selected caption You can also apply multiple styles to different portions of a single caption If the captions you select have more than one style when you select the text with the Lasso or Marquee tool and select Style from the Text menu a hyphen appears ne
316. 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 Databases 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 The User shall cooperate in the defense of any claim brought against CambridgeSoft Merck and or other Database Suppliers In no event shall CS Merck 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 softwar
317. og box and click OK Printing Background Color Print Background Color controls whether the Background Color contained in your ChemDraw document is printed To change whether the Background color is printed 1 From the File menu choose Preferences 2 Click Print Background Color 3 Click OK Macintosh Print Preferences When you print a document ChemDraw creates both a QuickDraw representation and a PostScript representation of the document s contents ChemDraw 9 ChemDraw Basics 29 Printing QuickDraw is the graphical format that is supported by the Macintosh Operating System Every printer that supports the MacOS can convert QuickDraw representations into printed output However QuickDraw does not support some features for example high resolution printing that are available only on some printers If you are transferring information to another appli cation from which you print ChemDraw pictures you should consider including PostScript commands and the ChemDraw LaserPrep File with the pictures For information about special situa tions to consider see Transferring PostScript Macintosh on page 195 Optimize Pictures for High Resolution Non PostScript Printing The Macintosh High Resolution Clipboard supports high resolution printers Most applica tions support the High Resolution Clipboard Because this was not always the case in the past this preference continues to be available for user
318. ognized Cyclohexane ChemDraw 9 Struct lt gt Name 75 Name Struct Converting Names to Structures There are two ways to insert a name into the document window as a structure Insert Structure dialog box Paste Special command Insert Structure Insert Structure is designed for typed in entries For example to insert 2 bromobenzoic acid 1 Choose Convert Name to Structure from the Structure menu The Insert Structure dialog box appears 2 Type 2 bromobenzoic acid NOTE You can also copy a name to the clipboard and then type Crtl V or Command V to paste the name into the dialog box 3 Click OK The molecular structure and name if Paste name below structure is selected appear in the drawing area If you should happen to type the name incorrectly Insert Structure will try to correct the error Click OK to accept the suggested spelling or click Cancel and start again to make a manual correction Paste Special The Paste Special command allows you to paste a name copied to the clipboard from another application as a structure in ChemDraw To paste a name from the clipboard 1 Click in the document window 2 From the Edit menu point to Paste Special and then choose Name as Structure The structure appears in your document Converting Captions to Structures If a caption is already present in the drawing area you can convert it to a structure as follows 1 Select th
319. oint to Align and then choose the alignment you want The cell contents shift and stay in a fixed position relative to the cell The default alignment is unaligned Creating Tables with the Text Tool ChemDraw allows you to create tables of text using the Tab key with the Text tool Creating the First Row column headings To create the first row and establish the columns of a table Click the Text tool 3 Click in a document window where you want the table to start 4 Type a caption 5 Press Tab A second caption box appears 6 Type a second caption The second column is placed 20 points 20 72 inch 0 71 cm to the right of the first If you want to Then choose add an empty row above the indicated row Add Row Before add an empty row below the indicated row Add Row After add an empty column to the left of the indicated column Add Column Before O OH O OH add an empty column to the right of the indicated column Add Column After delete the indicated row and its contents Delete Row delete the indicated column and its contents Delete Column If you want to Then choose ChemDraw 9 Working With Page Layout 189 Creating Tables 7 Press Tab again to create a third column and so on NOTE The style font and size that you set in each column are maintained in all the rows that follow The following illustration shows the creation of new c
320. olumns using the Tab key Compound M W LogP LD50 tab tab tab To change the spacing between columns one point at a time while editing a caption Select the caption 8 Move the caption with the arrow keys For more information on moving objects see Moving Objects on page 111 To create another column with this same spacing as the previous Press Tab A third caption text box appears Creating a New Row To start a new row that is exactly aligned with the first Press Tab twice at the end of a row A caption text box appears exactly aligned under the first caption positioned exactly 20 points below the first caption in the first row The following diagram illustrates the creation of a new row To change the spacing between rows as you create the table Select the captions in a row 9 Move the captions using the arrow keys For more information on moving objects see Moving Objects on page 111 To continue and fill in the row with captions Press Tab to create another caption in the row and then press Tab twice to begin a new row The spacing between the newest row and the row directly before it have the same spacing that you specified between the previous two rows Adjusting Row or Column Spacing To use a selection tool to adjust the spacing in a table Select all of the captions with a selection tool 10 Shift drag the caption The movement is constrained to the X axi
321. olymer Representations Brackets are used to enclose repeated structures or structural fragments ChemDraw provides bracket properties to specify the orientation and context of the repeating units An explanation of the bracket properties is given in Representing Polymers and Other Repeating Units on page 163 References Graphic Representations Chemical Formulae of Macromolecules Recommendations 1994 Pure Appl Chem 66 2469 2482 1994 Source Based Nomenclature for Copolymers Recommendations 1985 Pure Appl Chem 57 1427 1440 1985 Also available at http www iupac org publications books pbook PurpleBook C7 pdf Basic Definitions of Terms Relating to Polymers 1974 Pure Appl Chem 40 479 491 1974 Also available at http www iupac org reports 1996 6812jenkins index html Also see the Guide for the authors of papers and reports in polymer science and technology from IUPAC Query Properties By their nature query properties do not represent actual chemical features but describe broad classes or groups of features For information on using query properties see Chapter 10 Drawing Query Structures Analysis Messages When ChemDraw is unable to analyze your structure fully two general types of messages are displayed Status messages that report a problem that may not affect the final analysis The Absolute flag indicates the exact stereoisomer as drawn The
322. ompounds 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 Display amp Format Results D I S C O V E R Y Duplicate Checking with Override When compounds are registered the structure 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 This translates into ultimate flexibility on both the client and server side Oracle is supported as a host both with native security on a variety of platforms and operating systems The chemical information is direct ly stored in the Oracle tables Web Based User Interface While 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 ChemDraw Plugin ActiveX or Java client tools are provided This significantly reduces training time and cost of client maint
323. on From the Structure menu choose Properties On the Bond Properties tab select the bond properties to associate with the selected bonds from the drop down lists Click OK Point to an bond and press the Hotkey The Bond Properties dialog box appears In the Bond Properties dialog box select the properties to associate with the selected atoms Click OK Query indicators appear next to bonds that have associated bond properties Option Search Result Not allowed Default Finds compounds where the selected atoms only have valences that are normal for that element If necessary hydrogen atoms are automatically added to or removed from the atom before transferring it to the chemical database If the Check Structure When Copying to Clipboard or Exporting preference is turned on an error message warns of abnormal valences Allowed Finds compounds with the specific valence drawn one bond many bonds S D Rxn Rng Any D A S A R C 156 Drawing Query Structures CambridgeSoft Bond Properties Administrator The characters that appears depends on which query properties have been assigned If more than one property is assigned more than one descriptor appears adjacent to the atoms For more information see Query Indicators on page 160 The indicators are described in the following table Viewing Bond Property Values The descriptor for the Reaction Center query property ind
324. on atom labels 82 Mapping 171 Autosave 24 Autoscale bonds 193 empty document window 194 template color 133 when transferring 193 B Background color printing 28 Baseline style captions 80 Benzene Ring changing orientation 67 drawing 67 Benzene Ring Tool 66 Bezier curves 103 BitMap file format 198 Bitmapped Fonts 92 printing quality 29 bmp files 198 Boiling Point definition 142 Boiling point calculation 246 Bold Bond Tool icon 62 Bold Wedge Bond Tool icon 62 Bold Width 60 Bond crossings changing 71 white space 60 Bond order changing 71 ChemDraw 9 iii Bond Properties defining 155 descriptors 156 reaction center 158 removing 156 topology 157 types 156 viewing 156 Bond query indicators 156 Bond Spacing description 60 Bond tool description 15 icons 62 repeating a label 89 Bonds adding 125 autoscaling 193 changing bond type 69 changing type 69 double either 157 drawing 64 drawing by clicking 65 editing 69 Fixed Length 64 layering 71 margin width 60 multi center attachment 126 orientation changing 70 orientation dative bond 64 orientation wedge bond 64 quadruple 63 selecting 110 types 232 Border of page 177 Boxes drawing 100 rotating 100 Braces 101 Bracket usage 164 Brackets description 15 drawing 101 paired 101 setting properties 163 single 101 tool 101 using to represent polymers 163 Bring to Front command 186 Bruker JCAMP file format 201 C Calculating chemical properties 14
325. on print the form on your company template fill it out and submit it to purchasing ChemACX SC ChemACX SC is an additional fully structure searchable database containing the catalogs of leading screening compound suppliers including ChemBridge Maybridge Sigma Aldrich s Rare Chemical Library and others Data Quality Over 500 000 products from 300 research chemical and biological catalogs have been selected to have their product catalogs prepared for electronic delivery The 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 D ATA B A S E S Data Currency A premium is placed on the accuracy and currency of the ChemACX Database Many 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 won t 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 ChemACX Com enterprise users can access their private ChemACX Database via a standard web browser There is no need to configur
326. onforms to your workflow Desktop to Enterprise E Notebook allows organization of notebook pages at either the personal or enterprise level Enterprise groups can organize and store notebook pages in a central data repository allowing colleagues to take advantage of each other s work All access to data is subject to granular security E Notebook works with Oracle Cartridge and SQL Server for departments or entire enterprises and Microsoft Access for individuals or small groups ChemDraw amp Stoichiometry Calculations While not quantum theory stoichiometric calculations remain long and tedious E Notebook tackles this trou blesome problem First draw your reaction directly in the page Then simply enter the mass volume and den Automatic Stoichiometric Calculations Scanned Images in Notebook Pages M A N A G E M E N T sity volume and molarity and other factors of the limiting reagent and specify the number of equivalents of the other reactants The 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 Notebook manages all the other kinds of data chemists store in their notebooks For free form data you can include Microsoft Word or Excel documents For spectral data you can take advantage of the Galactic Spectral Control embedded in the notebook that allows for analysis and storage of hundreds of kinds of spectra fil
327. ontinued ChemDraw Laser Prep 29 drawing elements fill 99 effect of PostScript commands 195 high resolution non PostScript 29 include PostScript 29 orientation of page 180 overview 28 page setup 179 paper size 180 PostScript atom labels 29 preferences 28 reaction mapping 171 Properties atom in searching 149 atom abnormal valence 155 atom description 151 atom implicit hydrogens 152 atom query 150 atom reaction changes 153 atom reaction stereo 153 atom resetting defaults 151 atom ring bond count 152 atom substituents 151 atom unsaturation 153 atom viewing values 150 bond 155 bond descriptors 156 bond types 156 bond reaction center 158 bond removing 156 bond topology 157 bond viewing 156 brackets 163 calculating 141 Proton shifts see 13C 1H shifts estimating Q Quadruple bonds 63 Queries multiple rings 163 Queries see searching Query indicators editing 160 overview 160 Query Properties 3D 158 Query properties exported 172 overview 238 Query Structures description 149 exporting 172 Query Tools palette 159 Quick Reference Card description 10 QuickDraw bitmapped image 29 print quality 28 Quitting 30 R R Groups 167 Racemic flag drawing 161 Radicals drawing 97 specification 235 Reaction Atom Atom Map Tool 170 Reaction Atom To Atom Mapping 170 Reaction center 158 Reaction Changes 153 Reaction mapping always display and print 171 automatic 171 clearing 172 exporting 172 manual 171 over
328. otate with the structure To rotate an atom label with a structure Press Ctrl or Command while dragging the structure Rotation handle 114 Manipulating Drawings CambridgeSoft Structure Perspective Administrator If a single atom is unselected when a structure is rotated the structure rotates around the unselected atom NOTE Captions and atom labels that contain multiple colors change to the foreground color when rotated However all colors contained in the captions are printed To rotate the selected objects a specified number of degrees 1 Do one of the following From the Object menu choose Rotate Double click the rotation handle The Rotate Objects dialog box appears 2 Type a number and click degrees CW for a clockwise rotation or degrees CCW for counterclockwise rotation 3 If you want to rotate the atom label text click Rotate Atom Labels 4 Click Rotate Objects are rotated around the center of the Selection rectangle To repeat the same rotation on any object in the document window 1 Immediately after performing a rotation select the other objects to rotate 2 From the Edit menu choose Repeat Rotate Structure Perspective You can rotate molecules or portions of molecules through three dimensions with the Trackball tool The Trackball behaves similarly to the Marquee tool To rotate a structure 1 Select the structure by dragging over it with the Tra
329. ouble click the toolbar background This will dock the toolbar in the default position All toolbars default to the top of the ChemDraw window except for the Tools toolbar which defaults to the left side To undock a toolbar Drag the toolbar into the position you want The Status Bar or Message Area Windows The status bar or message area displays information about the menu or toolbar you are using The Analysis Window The Analysis window displays the chemical analysis of the selected structure If nothing is selected the values shown are for the entire document See Viewing Analysis Information on page 138 for information on the Analysis window The Paste button inserts all selected items into the document The button shrinks the window to just the title bar The Chemical Proper ties Window The Chemical Properties window displays proper ties of the selected structure When no structure is selected properties will be displayed only if there is one and only one structure in the document The Paste button inserts all selected items into the document The button shrinks the window to just the title bar while leaving it active NOTE CLogP and CMR values are displayed only in ChemDraw Ultra Pro Pro ChemDraw 9 ChemDraw Basics 19 Optional Toolbars The Info Window The Information window shows size positioning information about what s going on in ChemDraw The fields show the fo
330. our screen positioned at 7 inches and 10 5 inches to match the 2 3 ratio for the 35 mm slide format These guides help you keep your drawing within this region to maintain the proper ratio but are not printed The drawing area of the page must be at least 7 x 10 5 inches for these boundary lines to be visible To display the 35mm slide boundary lines 1 From the File menu choose Preferences 2 Select the Show 35mm Slide Boundary Guides check box 3 Click the OK button Two 35mm Slide Boundary Guides appear in the same orientation you have chosen in the Page Setup dialog box These guides appear in every document This preference affects all documents Changing Perspectives You can use a close up view of objects in your reaction scheme to make sure they are properly positioned At times you may want to reduce your view so that you can move groups of objects around the page You can change the magnification to perform these functions by using the Magnify and Reduce commands in the View menu the Zoom tool or the magnification controls Magnifying with the View Menu When you use the View menu to magnify or reduce the magnification is set to the next higher or lower value You can magnify up to 400 or reduce to 25 Magnify To magnify using the View menu 1 Select the object around which you want to magnify your view NOTE If you do not select an object the last object drawn is the center point of the magn
331. out tab click Poster 3 Type the Height Width and Page Overlap The number of pages and the margin dimensions are calculated 4 Select whether to Print Registration Marks 5 Create Headers and Footers as described in Creating Headers and Footers on page 178 6 Click OK An example of a 19 inch by 14 inch poster consisting of six 8 5 inch by 11 inch pieces of paper with a 1 inch overlap is shown below Creating Headers and Footers You create headers and footers in the Document Settings dialog box In poster documents only one header and footer appear for the entire document 1 1 8 5 11 19 X 14 Poster 1 ChemDraw 9 Working With Page Layout 179 Page Setup To create headers and footers 1 From the File menu choose Document Settings 2 Click the Footer tab 3 Type the value of the position from the edge of the page that you want the header or footer to appear 4 Type the text to appear in the header or footer 5 Type additional information in the Text box from the following table 6 Position the text horizontally by typing the characters in the table below Any text following these characters is appropriately aligned Page Setup The Page Setup parameters that affect the size of the drawing area are Page size Orientation These parameters are specified in the Page Setup dialog box The Page Setup dialog box and the options available vary depending
332. overy LIMS 21CFR11 Compliance DESKTOP SOFTWARE ENTERPRISE SOLUTIONS KNOWLEDGE MANAGEMENT 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 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 information retrieval integrate smoothly with ChemOffice and Microsoft Office to speed day to day research tasks 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 ChemOffice WebServer Oracle Cartridge E Notebook Enterprise Document Manager Discovery LIMS 21CFR11 Compliance ChemOffice Desktop to ChemOffi
333. owing multiple bonds NOTE You can also draw multiple bonds by right clicking over a bond and selecting the bond type from the shortcut menu or by using the bond properties dialog box For more information see Bond Properties on page 155 Double Bonds There are three ways to draw a double bond Use the Double bond tool Using the Solid Dashed or Bold bond tool a click an existing single bond b drag over the length of an existing single bond Double Either Bonds To draw a double either bond select the double either bond tool from the Multiple Bonds palette or 1 Draw a bond using the Wavy Bond tool 2 Point to the center of the bond and click to create a double bond 3 Click again to create a double either bond Triple Bonds You can draw a triple bond by drawing another single bond on top of a double bond All bonds in a triple bond are solid bonds To draw a triple bond select the triple bond tool from the Multiple Bonds palette or 1 Click any bond tool 2 Drag from one end of an existing double bond to the other Quadruple Bonds To draw a quadruple bond select the quadruple bond tool from the Multiple Bonds palette or 1 Click any bond tool 2 Drag from one end of an existing triple bond to the other The triple bond changes to a quadruple bond To change a quadruple bond into a single bond 1 Click any bond tool 2 Drag from one end of an existing quadru
334. own below and then type O in the text box that appears 3 With the Text tool click the atom shown below and then type OH in the text box that appears Display the stereochemical markers 1 Select the entire structure with the Lasso or Marquee 2 From the Object menu choose Show Stereochemistry The S marker appears 3 Select the structure and from the Object menu choose Flip Horizontal The R marker appears 4 With the structure selected do the following Click the Object menu While holding the mouse button press the Alt or Shift Option key and choose Rotate 180 Vertical The Wedged bond becomes hashed and the R stereochemistry is preserved Save and close the document 1 From the File menu choose Save 2 From the File menu choose Close NH2 O NH2 S OH O NH2 R HO O NH2 R HO O NH2 58 Tutorials CambridgeSoft Tutorial 7 Showing Stereochemistry Administrator ChemDraw 9 Drawing Chemical Structures 59 Drawing Settings Chapter 3 Drawing Chemical Structures Overview ChemDraw provides the following tools for drawing chemical structures Bond tools Ring tools Text tools An acyclic chain tool Automatic error checking Drawing Settings Drawing settings are document settings that affect how bonds and other objects are drawn You can configure the drawing settings for an entire document or for a part
335. own the mouse button press the Alt or Option key and drag downward from C5 Stop dragging about half the distance to the upward bond on C3 Distort the structure to change its aspect ratio to give the perspective of viewing the structure along the Z axis 1 Click the Lasso tool 2 Point to the Resize handle lower right corner and press the Shift key NOTE The cursor changes to a cross with arrows at each end indicating the distortion function of a selection tool 3 Drag upwards until you have distorted the structure to about 50 as shown on the screen or in the Info window Next you create OH labels Because this label is repeatedly used you will learn how to repeat a label Only labels created by opening a text box are repeatable 1 Select the Solid Bond tool point to the atom shown below and double click to open a text box O O O Resize handle O 52 Tutorials CambridgeSoft Tutorial 5 Perspective Drawings Administrator 2 Type OH move the pointer to the next atom as shown and triple click to repeat the atom label 3 Triple click the remaining atoms as shown below to repeat the OH label NOTE If you find it difficult to place the labels because of the size of the drawing choose Magnify from the View menu Add the CH2OH label 1 Triple click the upper atom of C5 2 Press the Enter or Return key to open the atom label text box and type CH2 before the OH NOTE The Ente
336. ows 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 savers and virus protection If you do need to contact us be sure to determine what type and version of drivers you are using 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 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 3 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 ChemDraw Appendix Technical Support 229 Troubleshooti
337. part of a ring Chain Finds compounds where the selected bonds are part of a chain and are specifically not part of a ring Option Search Result 158 Drawing Query Structures CambridgeSoft 3D Properties Administrator Reaction Center The Reaction Center property specifies how the selected bonds are affected in a reaction This property is only meaningful when searching a database containing chemical reactions The Reaction Center options are described in the following table 3D Properties 3D queries are particularly useful in pharmacophore searching where the user is looking for a particular 3D relationship among atoms and bonds for example in a series of potential receptor ligands To create a 3D query you add geometries lines planes etc and constraints specified as ranges to a query structure For example you might specify that two atoms must be between 4 and 5 apart or that two planes must be separated by 80 100 degrees To assign 3D properties to a structure select the structure or sub structure and then select one of the following options from the Add 3D Property entry on the Structure menu NOTE Because some 3D properties specify an order you should use Shift Click to select them in the proper order rather than using the Marquee or Lasso tool to select them all at once Ring or Chain Finds compounds where the selected bonds are part of either a ring or a chain Option Search Result
338. pe of SMILES string for any structure drawn with explicit aromatic bonds either by using the Aromatic bond type in the Atom Prop erties dialog box or by placing a circle within any ring structure Pasting SMILES from Clipboard If you have a SMILES string then you can auto matically convert that text string into a ChemDraw structure To paste a SMILES string as a ChemDraw structure 1 Select the SMILES string using the Text tool 2 From the Edit menu choose Copy 3 From the Edit menu point to Paste Special and then choose SMILES The SMILES string is drawn as a structure NOTE Pasting SMILES uses the same routines as the Structure CleanUp command For more information see Using Variable Attachment Positions on page 127 Creating SLN Strings You can copy a ChemDraw structure to the Clip board as an SLN string for export to a Tripos appli cation To copy a ChemDraw structure as an SLN string 1 Select a structure 2 From the Edit menu point to Copy As and then choose SLN The Structure is copied to the clipboard as an SLN String Using Drag and Drop You can use the drag and drop feature to copy objects to place in other documents To use this feature in other applications they must support drag and drop As when using the clipboard the information is transferred as a ChemDraw object and can be edited You can also use the drag and drop feature to create clipping files Macintosh or s
339. pear solid To draw using a line tool 1 Select a line tool 2 Point where you want the line to start 3 Drag from one end of the line to the other end The Brackets Tools Palette Brackets includes braces brackets and parentheses Drawing Single Brackets A single bracket can be drawn in any orientation To draw a single bracket 1 Select a single bracket tool 2 Point where you want the bracket to start 3 Drag from one end of the bracket to the other end Drawing Paired Brackets Paired brackets can only be placed in a vertical orientation A rectangle or box defines their position To draw a paired brackets 1 Select a paired bracket tool 2 Point where you want a corner of the bracket to be located 3 Drag from one corner of the box diagonally to the opposite corner Drawing Daggers To draw a dagger 1 Select a dagger tool 2 Point where you want the symbol to be located 3 Click to deposit the dagger NOTE The size of the dagger symbol is proportional to the Atom Label font size specified in the Text Settings dialog box Framing Objects You can enclose your drawings or group structures with a rectangle brackets parentheses or braces To enclose your object 1 Select the drawing to enclose 2 On the Object menu point to Add Frame and then choose the type of frame to add 102 Drawing Orbitals Symbols Arrows Arcs and Other Shapes CambridgeSof
340. ple bond to the other Double Bold Double Tautomeric Aromatic Double Either Dative Triple Quadruple 64 Drawing Chemical Structures CambridgeSoft Drawing Bonds Administrator The quadruple bond changes into a single bond corresponding to the tool used to draw over the bond NOTE You can also use the Eraser tool to reduce the bond order For more information see Changing the Bond Order on page 71 Drawing Constrained Bonds You can draw any bond length and create any angle relative to the X axis The Info Window displays the bond length and angle as you drag the bond However you can draw bonds that are constrained to A fixed length A fixed angle relative to the X axis Drawing with Fixed Lengths To draw bonds that are constrained to a fixed length 1 From the Object menu choose Fixed Lengths A check mark appears next to the Fixed Lengths command indicating that it is selected All the bonds drawn are constrained to the fixed length specified in the Drawing Settings dialog box 2 Click a bond tool 3 Drag from one end of the bond to the other The Info Window displays the bond length Drawing with Fixed Angles To draw bonds with constrained angles that are multiples of 15 degrees relative to the X axis 1 From the Object menu choose Fixed Angles A check mark appears next to the Fixed Angles command indicating that it is on 2 Click a bond tool 3 Drag
341. port a valence error The dative bond more accurately represents the electron donation Complexes may also be represented with explicit lone pairs and without any bonds If you use a plain bond to indicate a complex you may want to set Abnormal Valence to Allowed in the Atom Properties dialog A superscripted number before the element symbol indicates isotope numbers Isotopes can be included anywhere that regular elements can Deuterium and Tritium can be indicated by their one letter symbols 35Cl CH2 13COOH D3C OD T O T Ph C Ph Ph C O Boron trifluoride ammonia complex Boron trifluoride acetic acid complex H H NH3 F3B HO O F B F F 236 The Chemistry of ChemDraw CambridgeSoft Chemical Conventions Administrator Multi center Attachments Multi center attachments are meaningful only when created using Add Multi Center Attachment from the Structure Menu This command creates a pseudo atom that is disregarded during chemical calculations but still allows you to create diagrams that look meaningful to an experienced chemist 3 or Allyl complex Ferrocene a Aryl complex Cp2TiCl2 another Aryl complex C5H5Mn CO 3 Stereochemistry Absolute stereochemistry is calculated for tetrahedral atoms and double bonds according to the Cahn Ingold Prelog CIP priority rules The Heme a compound with two formal covalent bonds and two for
342. ption or label from the Text menu or toolbar before you type Selecting text and applying a new format to an individual label after you type Specifying Document Settings for New Text To specify the text settings for new captions and atom labels in the current document 1 From the File menu choose Document Settings 2 In the Document Settings dialog box click Captions or Atom Labels 3 Click the appropriate options 4 Click OK These settings affect all new captions or atom labels in the current document To use these settings in new documents save them in a Style Sheet or Statio nery Pad For more information see Saving Customized Settings as Style Sheets or Stationery Pads on page 21 Setting an Individual Text Format Before Typing You can set the text format for an individual caption or atom label before you type The format change is applied to the current text only To set the text format before you type 1 Click the Text tool and then click in the docu ment window A text box appears 2 Set the text format in one of the following ways From the Text menu choose the format options From the Style toolbar choose the format options 3 Type the text in the text box The format is applied to the typed text Any subsequent text you type is formatted according to the default document settings for the current document Changing the Spacing of Individual Text Objects Yo
343. r Position dialog box To reposition an indicator numerically 1 With a selection tool click the indicator to move 2 Right click and choose Position The Position Indicator dialog box appears 3 Click the appropriate Position option and type a value Alternative Reaction Relative Racemic Stereochemistry Free Site Stereochemistry Absolute Stereochemistry Atom Atom Group Map To Position Type a value for from the atom or bond center to indicator center angle degrees or clock o clock ChemDraw 9 Drawing Query Structures 161 Drawing Stereochemical Symbols Drawing Stereochemical Symbols ChemDraw provides three types of stereochemical flags that indicate that the molecule with which they are associated represents one of the following Racemic A racemic mixture Absolute A pure enantiomer of known configuration Relative A pure enantiomer of unknown configuration The font and size for stereochemical flags is determined by the default Atom Label size for the document To draw a stereochemical flag 1 On the Query tools palette click the tool for the flag you want to use 2 Position the pointer next to the structure to which you want to assign the flag 3 Click to deposit the symbol Drawing Free Sites Use the Free Sites tool to increment or decrement the number of free sites in a query structure To increment the number of Free S
344. r a caption or atom label 1 Select the Text tool 2 Click in the position where you want to place the text 3 From the Color menu choose a color 4 Type the caption or atom label To color individual characters 1 Select part of an existing caption or atom label using the Text tool 2 From the Color menu choose a color NOTE Macintosh Captions that contain multiple colors change to the foreground color when rotated However all colors contained in the caption are printed To color several captions or atom labels at once 1 Select the captions or labels using a selection tool 2 From the Color menu choose a color Creating Captions The default format options of any new captions you create are specified in the Captions tab of the Docu ment Settings dialog box You may edit these options at any time The settings affect the current document only To create a caption 1 Click the Text tool 2 Point in an empty space in a document window A caption text box with a flashing insertion point appears 3 Type a caption The text box widens as you type to accommo date the caption 4 To create a new line press the Enter or Return key ChemDraw 9 Drawing Captions and Atom Labels 85 Creating Captions 5 To close the text box click outside the text box or select another tool NOTE You can verify the chemical significance of a caption or atom label using the Check Structure comman
345. r box that you have selected in the left side of the dialog box Any objects using the removed color are changed to the Foreground color Set Color Change the color associated with a color box that you have selected in the left side of the dialog box Any objects using the old color are changed to the new color ColorPalette 150 dpi 132 Advanced Drawing Techniques CambridgeSoft Working with Color Administrator 4 Click a color box in the Basic Colors or the Custom Colors section A highlighted border appears around the color you select 5 Click OK The color is changed to the new color and added to the Color menu Adding or Customizing Windows Colors To add colors or create customized colors 1 In the Color dialog box click Define Custom Colors The Color dialog box appears 2 Click a color in the Color Refiner box to set the hue and saturation The pointer turns into a Crosshair when you click You can drag to a different region to change the hue and saturation 3 Click in the Luminosity box to set the brightness of the color 4 If necessary change the hue saturation luminosity and RGB components by typing the values in the text boxes 5 Click Add to Custom Colors Macintosh Color Settings To change the palette of colors used in the current document 1 From the File menu choose Document Settings The Document Settings dialog box appears 2 Click the Colors tab 3 Click New Co
346. r or Return Hotkey opens a text box for the last atom labeled The definition for this particular Hotkey cannot be changed Change the type of the front bonds 1 Click the Bold Bond tool 2 Point to the center of the bond shown below The cursor changes to a bold arrow as you point at the bond 3 Click to change to the new bond type 4 Click the Bold Wedge bond tool 5 Point to each of the bonds shown below 6 For each bond point slightly off center in the direction that you want the wide end of the wedge to be oriented and click NOTE If you move the pointer too far the highlight box disappears Choose Magnify from the View menu if you find it difficult to place the pointer The resulting structure is shown below NOTE If the wedge is pointed in the wrong direction click the bond again to flip its orientation O OH O OH OH OH OH O OH OH OH CH2OH OH O OH OH OH CH2OH OH O OH OH OH CH2OH OH O OH OH OH CH2OH OH O OH OH OH CH2OH OH ChemDraw 9 Tutorials 53 Tutorial 6 Newman Projections Save and close the document 1 From the File menu choose Save 2 From the File menu choose Close Tutorial 6 Newman Projections This tutorial demonstrates how to draw a Newman projection You can also create the same drawing using a template Create a ChemDraw document 1 From the File menu choose New Document
347. r such compounds only the fully systematic organic name is produced Nomenclature types added in ChemDraw 9 0 include Most of the most common fused ring systems both those with trivial names naphthalene indole and those with systematic names benzo e 1 4 diazepine thieno 3 2 b thiophene Most salts Structures with a net charge Simple mixtures and multicomponent systems Heterochains Multiplicative nomenclature Ring assemblies Bicyclics Basic inorganics Struct Name generates names with proper CIP stereochemistry descriptors It has no theoretical limits to the size of the structures that can be named Ultra Ultra 74 Struct lt gt Name CambridgeSoft Name Struct Administrator To insert the name of a structure into your drawing 1 Select the drawing for which you want to insert a name 2 From the Structure menu choose Convert Structure to Name The name of the structure appears as a caption under your drawing Auto Update ChemDraw 9 0 captions include an auto update feature Data including the chemical name and analysis can be included in a caption and will update automatically when you modify the structure For more information on adding data to captions see Adding Analysis Data to a Caption on page 85 To toggle the auto update feature 1 Point to the label 2 Right click and select Auto update A check mark appea
348. r the fragments on either side of the bond are displayed as if the bond were homolytically broken That is a single bond turns into a monoradical on each fragment a double bonds turns into a pair of diradicals If more than one bond is crossed all fragments on each side of the line are considered together If the only bond crossed is a ring bond a single formula mass pair is displayed NOTE It is possible to draw lines that tie themselves in knots Use this tool with caution to avoid unrealistic fragmentation Pro Pro Chemical Formula C6H12 Exact Mass 84 09 Chemical Formula C3H7 Exact Mass 43 05 Chemical Formula C3H7 Exact Mass 43 05 Chemical Formula C3H7 Exact Mass 43 05 Chemical Formula C3H7 Exact Mass 43 05 Chemical Formula C4H9 Exact Mass 57 07 Chemical Formula C2H5 Exact Mass 29 04 144 Working With Structures CambridgeSoft Drawing Reactions Administrator You can reposition the formula and mass displays they are text objects or delete them altogether Mass Fragmentation tool procedures Drawing Reactions Two new tools speed the drawing of synthesis reactions Both tools are used in a similar manner to the Mass Fragmentation tool they are used to cut a bond or bonds in a product The Dissociation tool draws the resulting fragments as a standard reaction The Retrosynthesis tool draws the reaction with the product on t
349. rck 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 Merck 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 Database producer are prohibited 3 Grant of License CD DVD Databases CambridgeSoft Software Products are licensed not sold CambridgeSoft 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 is in use or installed on only one computer at a time If the Software is permanently installed on your computer other than a network server you may also use the Software on a portable or home com puter 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 wr
350. re CleanUp and Chemical Intelligence Chem3D Ultra Ultimate Modeling Visualization amp Analysis Adds MOPAC CLogP Tinker ChemProp ChemSAR amp Chem3D Plugin to Chem3D Pro Advanced modeling amp molecular analysis tool E Notebook Ultra Ultimate Journaling amp Information E Notebook ChemDraw Std Chem3D Std ChemDraw Excel amp CombiChem Excel Includes ChemFinder ChemFinder Word ChemINDEX amp ChemRXN databases Some features are Windows only All specifications subject to change without notice ChemOffice Ultra includes it all providing ChemDraw Ultra Chem3D Ultra E Notebook Ultra ChemFinder CombiChem BioAssay and The Merck Index for a seamlessly integrated suite for chemists Use ChemDraw Excel and ChemFinder Word for Microsoft Office integration Predict spectra use Name Struct and visualize 3D molecular surfaces and orbitals with MOPAC Use the ChemDraw 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 ChemDraw web based interface and Oracle Cartridge security Knowledge Management with E Notebook Enterprise streamlines daily record keeping with rigorous security and efficient archiving Document Manager indexes chemical structure content of documents and folders Research amp Discovery efforts are improved with Registration System by organizing new compoun
351. re is a valence and charge error somewhere in this aromatic system Displayed for any odd membered ring drawn as a delocalized system with a circle in the middle where there is no corresponding associated charge For example a delocalized representation of cyclopentadiene must include either a negative charge or a multicenter attachment The stereocenter has conflicting or ambiguous stereobonds specified Displayed for any stereocenter tetrahedral atom asymmetric double bond etc where the absolute stereochemistry cannot be determined from the structure as drawn For example this message would be shown for a carbon atom attached by bold bonds to four different ligands This message is displayed only when Show Stereochemistry is also turned on Message Description ChemDraw 9 The Chemistry of ChemDraw 241 Chemical Conventions This label has an unrecognized isotopic mass Displayed for every label that has a numeric superscript immediately preceding an atomic symbol where the superscripted number does not correspond to a recognized isotope For example 24CH3 Message Description 242 The Chemistry of ChemDraw CambridgeSoft Chemical Conventions Administrator ChemDraw 9 How ChemNMR Works 243 ChemNMR Limitations Appendix D How ChemNMR Works Overview ChemNMR estimates chemical shifts for all hydrogen or carbon atoms for which additivity rules are available Following a
352. rement and life cycle chemical tracking Cascading location model allows different labs to track reagents at different levels stockroom refrigerators Designed for tracking reagents high throughput discovery libraries and true HTS plate management at multiple levels D I S C O V E R Y EMAIL info cambridgesoft com WWW www cambridgesoft com TEL 1 800 315 7300 INT L 1 617 588 9300 FAX 1 617 588 9390 MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge MA 02140 USA ChemOffice ChemDraw Chem3D ChemFinder amp ChemInfo are trademarks of CambridgeSoft 2002 All other trademarks are the property of their respective holders All specifications subject to change without notice CombiChem Enterprise CombiChem Enterprise Desktop to Enterprise Combinatorial Chemistry Desktop to Enterprise Combinatorial Chemistry Benefits of Combinatorial Chemistry Combinatorial chemistry in particular the technique of parallel synthesis has become an essential element of the drug discovery process This 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 5 and 100 This increase in productivity creates data management challenges CombiChem Enterprise has been developed to provide the software tools required by the combinatorial chemist to manage and document parallel synthesis exper
353. rials CambridgeSoft Tutorial 4 Fischer Projections Administrator Add a horizontal bond in the opposite direction Continue pointing to C2 and click the atom to add a perpendicular bond in the opposite direction Add bonds to the next three carbon atoms 1 Point to C3 and click the atom to add a perpendicular bond 2 Continue pointing to C3 and click the atom to add a perpendicular bond in the opposite direction 3 Repeat step 1 and step 2 for the fourth C4 and fifth C5 atoms ChemDraw 9 Tutorials 47 Tutorial 4 Fischer Projections Add labels to C1 and C6 1 Point to C1 2 Double click C1 to create a text box then type CHO 3 Point to C6 4 Double click C6 to create a text box then type CH2OH 5 Type Esc to deselect the label 6 Add the H and OH labels CHO 48 Tutorials CambridgeSoft Tutorial 4 Fischer Projections Administrator 1 Point to the atom shown below 2 Type h to label the atom using the Hotkey label for hydrogen 3 Repeat step 2 for the remaining hydrogen atoms shown below 4 Label the remaining atoms by typing o to label them with OH The result should appear as shown below View the basic properties of the structure you drew and paste the information into your document 1 Click a selection tool to automatically select the last structure drawn If the structure is not selected double click the structure 2 From the View menu choose An
354. rientation that it appears in the Templates palette Fusing a Template With an Existing Structure To draw a template and fuse it with an existing structure Click an existing bond in a document window To deposit a template and create a spiro linkage with an existing structure Click an existing atom in a document window To draw a template in a document window and control the size and orientation Drag from the beginning of the first bond in the template to the end of the first bond When you drag upwards the bulk of the template is drawn to the left and when you drag downwards the bulk of the template is drawn to the right Templates must contain at least one bond in order to be drawn by the dragging method Drawing with the Same Template To draw another template of the same type 1 Click the Templates tool 2 Draw the template in a document window Creating Templates and Template Documents In ChemDraw Pro you can create new templates and add them to existing Template documents or create new Template documents To create a new Template document On the File menu point to Open Special and then choose New Templates Pro Pro ChemDraw 9 Advanced Drawing Techniques 135 Drawing With Templates A new and untitled Template window appears The Template window is similar to a document window The Template window is divided into two halves by a moveable horizontal line Temp
355. riminal 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 User 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 The 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 amp Company Incorporated Whitehouse Station New Jersey USA and is registered in the United States Patent and Trademark Office CambridgeSoft and ChemACX are trademarks of CambridgeSoft Corporation Cambridge Massachusetts USA and are registered in the United States Patent and Trademark Office the European Union CTM and Japan Any use
356. rmats sometimes contain data that cannot be interpreted by ChemDraw ChemDraw always tries to interpret other file formats so that as much chemically relevant data is preserved as possible even if that causes the actual appearance of the file to change when it is saved and reopened Most file formats supported by ChemDraw are proprietary or extremely complex and are documented more thoroughly elsewhere For example you can find more information about CambridgeSoft s CDX file format at sdk cambridgesoft com Connection Table File Format The connection table format file described in this section is generated for the cyclohexanol structure shown below All references to atom serial numbers are based on the Atom Numbering shown The following is a sample Connection Table file produced for cyclohexanol using ChemDraw The line numbers are added for purposes of discussion only Each line represents a data record containing one or more fields of information about the structure Individual fields are delimited by space s or a tab The fields in the Connection Table format file used by ChemDraw are discussed below The field value for Carbon 6 from the example file is included in parentheses for reference Line 1 is the molecule name The molecule name is the file name when the file was created using ChemDraw 6 5 4 3 2 1 OH 7 Line 1 Cyclohexanol Line 2 7 7 Line 3 0 0000 0 5000 0 0000 C Line 4
357. rom the Online menu choose Find ACX Numbers from Structure The ACX number appears in the Find ACX Numbers from Structure dialog box Browsing SciStore com Browse ChemStore com opens the SciStore formerly ChemStore page of the CambridgeSoft web site http scistore cambridgesoft com To access Browse SciStore com From the Online menu choose Browse ChemStore com The SciStore Com page opens in your browser ChemDraw Appendix Accessing the CambridgeSoft Web Site 225 Browsing CambridgeSoft com Appendices You can search SciStore Com for 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 From the Online menu choose Browse CambridgeSoft com The CambridgeSoft web site in your browser Check the CambridgeSoft web site for new product information You can also get to SciStore Com ChemBioNews Com and other pages through CambridgeSoft Com Using the ChemOffice SDK The ChemOffice Software Developer s Kit SDK enables you to customize your applications To browse the ChemOffice SDK From the Online menu choose Browse ChemOffice SDK The CS ChemOffice SDK page opens in your browser The ChemOffice SDK page contains documentation sample code a
358. roto Crippen Viswanadhan Joback and Joback Stein methods Click Report When you create a report a detailed list of information used for performing the calculation is shown in a text file The list includes additional properties and literature references used to perform the calculation Mass Fragmentation Tool The Mass Fragmentation tool allows you to break existing structures across one or more bonds This mimics the molecular fragmentation in a mass spectrometer but does not have any predictive qualities you must specify what bonds are to be broken To fragment a structure Drag the mouse across one or more bonds A line is drawn across the bonds that disappears when you release the mouse button The operation is not final until the mouse is released This means you can drag the line around holding the mouse button down to see different possibilities and still back out without breaking any bonds When the mouse button is released any bonds crossed by the line are broken If you want the line to remain on display hold down the Alt or Option key after drawing the line NOTE The order in which you release the mouse button and the Alt or Option key determines whether the line remains displayed or not Releasing the mouse button first leaves the line displayed The Alt or Option key also allows you to turn corners and cut more than one bond When the line crosses a bond the formula and exact mass fo
359. rred with each drawing The transferred drawings can be printed inde pendently of ChemDraw If you do not check the Include PostScript check box when printing to a PostScript printer ChemDraw sends QuickDraw commands to the printer For more informa tion see Printing Background Color on page 28 To print to a non PostScript printer Deselect both Include PostScript and Include ChemDraw Laser Prep on the General tab of the Preferences dialog box Importing and Exporting Many applications can use the information contained within a ChemDraw document and saved to another file format Similarly ChemDraw can import and work with information in a number of file formats Not all formats are supported for both import and export See the individual format descriptions for details File formats are available in a pop up menu at the bottom of the Open and Save As dialog boxes To export a file 1 From the File menu choose Save As 2 In the Save As dialog box do the following a Type a name for the file and choose a location in which to save it Use the Go To ChemDraw Items button to quickly locate the ChemDraw Items folder b Select a file format from the bottom of the dialog box c Click OK or Save A copy of the current document is saved in the format you specified The current document remains unchanged Some file formats do not support atom labels that contain nicknames or structural fragme
360. rs next to the command when it is selected Successive clicks toggle the command on and off When auto update is on default the label updates each time you modify the structure NOTE For large complex structures it may take the new label a few seconds to appear on the screen depending on the speed of your processor You do not have to wait for the new label to appear before continuing to modify your structure Name Struct You can draw a structure automatically from a chemical name using Name Struct Name Struct recognizes most organic nomenclature Inorganic chemistry is also usually recognized especially when the rules closely match those for organic chemistry The following are not supported Coordination complexes Polyboranes Polymers Some highly bridged ring systems including fullerenes and porphyrins porphines Some stereochemistry designators D L DL endo exo syn anti r t c Although some trade names are supported Name Struct is not intended to interpret trade or common names A chemical database such as chemfinder com is more appropriate for obtaining structures for trade or common names See Finding Information on ChemFinder com on page 222 for more information NOTE Because the syntax of German is very similar to that of English Name Struct can also interpret many German names Chemical names in other languages however will generally not be rec
361. rsus concentration Click again and the software displays the original triplicate results with outliers marked The software even supports complex in vivo models Flexible Assay Definition Tools Automated Curve Fitting amp Data Analysis R E S E A R C H amp 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 as it is gathered BioAssay HTS contains a complete plate inventory system that tracks plates and compound groups across plates It easily manages 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 IC50 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 Re
362. rt Contact information and hints on what you should know to effectively report problems Includes a troubleshooting section Section II ChemDraw Appendix C The Chemistry of ChemDraw Describes how ChemDraw interprets what you draw and how you can help ChemDraw better interpret what you mean Appendix D How ChemNMR Works Describes how ChemNMR estimates chemical shifts for hydrogen or carbon atoms and it s limitations Appendix E How ChemProp Works Describes how ChemProp enables you to calculate predicted values of selected physical and thermodynamic properties Appendix F Shortcuts and Hotkeys Contains tables listing ChemDraw shortcuts and hotkeys for both Windows and Mac versions Appendix G Document Settings Drawing settings and a sample structure for each of the Style Sheets or Stationery Pads provided with ChemDraw Appendix H Chemistry File Formats Most file formats supported by ChemDraw are proprietary or extremely complex and are documented more thoroughly elsewhere This Appendix describes the connection table format in detail Note however that the format is obsolete and is documented here for historical purposes only 220 Appendices CambridgeSoft Administrator ChemDraw Appendix Accessing the CambridgeSoft Web Site 221 Registering Online Appendices Appendix A Accessing the CambridgeSoft Web Site O
363. s 21 Fixed Angles 64 margin width effect on atom labels 86 margin width effect on bond crossing 60 Duplicating labels 89 objects 113 dx file format 201 dz2 orbitals drawing 96 E Editing atom labels 87 atom numbers 90 bond orientation 70 bond type 69 bonds 69 captions 85 embedded objects 194 generic nickname file 162 query indicators 160 Element list 162 not list 163 recognized 235 Elemental Analysis caption 139 description 139 Embedded objects 204 Embedding objects 194 Encapsulated PostScript see EPS file format Enclosing objects 101 Enlarge document window 177 page size 180 EPS file format overview 199 Text 199 Eraser Tool 15 Eraser Tool changing bond order with 71 Error checking 71 Error Messages 238 Exact Mass caption 139 definition 138 Excel add in see ChemDraw Excel 207 Exiting 30 Expanding labels 125 Exporting checking structure 138 compatibility 172 mapping 172 PNG 202 query properties 172 query structures 172 TIFF 203 using file formats 196 F FAQ online accessing 222 File Format Stationery pad 199 File format Bitmap 198 cdx 26 cdxml 198 ChemDraw 198 ChemDraw 3 5 199 ChemDraw Stationery 199 Connection Table 199 connection table 267 CT 199 CTP 198 ChemDraw 9 ix File format continued CTR 198 cts 202 EPS TEXT 199 GIF 200 ISIS 200 ISIS Reactions 200 JDX 201 MDL MolFile 201 MDL RGFile 201 MSI MolFile 201 native 26 PICT 202 PICT scaled 4x 202 PNG 202 rxn 200 S
364. s 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 Most 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 of a data catalog driven mining program ChemDraw for Spotfire ChemDraw 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 ChemDraw for Spotfire adds chemistry to DecisionSite providing structure visualization and searching servic es Highlight a spot in Spotfire s DecisionSite 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 The 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
365. s 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 Readiness Assessment Strategic Planning Prototype or Proof of Concept Business Case Development Custom Application Development Data Integration Installation amp Customization of Applications Application Development Beta amp Pre Release Programs Controlled Pilots Training DECISION MAKING CUSTOM DEVELOPMENT DEPLOYMENT amp TRAINING MANAGE THE PROCESS S E R V I C E S EMAIL info cambridgesoft com WWW www cambridgesoft com TEL 1 800 315 7300 INT L 1 617 588 9300 FAX 1 617 588 9390 MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge MA 02140 USA ChemOffice ChemDraw Chem3D ChemFinder amp ChemInfo are trademarks of CambridgeSoft 2002 All other trademarks are the property of their respective holders All specifications subject to change without notice Business Case Development Business cases help define a clear and purposeful solution based on well defined and documented business needs Having a business case helps to justify good projects stop bad projects before they are started and provides the basis for ongoing measurements after pro
366. s have varying numbers of attachment points Since all structures within an Alternative Group Box are to be used interchangeably they must have the same number of attachments This is a status message only This named alternative group contains no fragment Displayed for any Alternative Group Box that is empty This is a status message only Part of a molecule is outside of the alternative group definition Displayed for any Alternative Group Box whose border crosses part of a structure This is a status message only This isolated bond is probably not intended to have chemical significance Displayed for unlabeled single bonds unattached to other bonds All bonds are interpreted chemically usually as C2H6 and may cause unexpected results if intended as a graphical line only This is a status message only The atom is very close to another atom or bond Displayed for any atom that is nearly touching another atom or bond but not bound to it If a bond really was intended the analysis of the structure produces incorrect results This is s status message only Message Description The stereocenter has no stereobonds specified Displayed for any asymmetric center without attached wedged hashed dashed or bold bonds This is a status message only and appears only when Show Stereochemistry is tuned on and there is at least one other wedged hashed dashed or bold bond in the structure The
367. s or Y axis so that you can maintain the row or column alignment Moving Around In Tables To move within an existing table Click the Text tool and select a caption 11 Press Ctrl arrow or Command arrow to move to the next caption in the direction of the arrow Alternatively you can use the following key combinations Compound M W LogP LD50 1 Use To move Tab right Shift Tab left Ctrl Enter or Command Return down 190 Working With Page Layout CambridgeSoft Creating Tables Administrator Inserting a New Row To insert a row Select a selection tool and select a row of captions 12 Shift drag the selected row Shift constrains the movement to the Y axis to maintain the column alignment 13 Select the first caption in the row above or below the space you created 14 Ctrl Shift drag or Command Shift drag to create a copy of the caption and position it in the empty space you created The placement of this copied caption sets the position of the inserted row To fill in the inserted row with caption text Click the Text tool and select the first caption in the inserted row 15 Type new text 16 Press Tab to move to the second caption in the inserted row and so on Ctrl Shift Enter or Command Shift Return up Use To move ChemDraw 9 Sharing Information 191 Using the Clipboard Chapter 12 Sharing Information Overview ChemDraw includes many of the stand
368. s to turn off if an application being used does not support the High Resolution Clipboard If you are unsure if the application uses a High Resolution Clipboard try transferring pictures with this check box selected and deselected and see which picture prints with higher quality If you are printing to a non PostScript printer dese lect Include ChemDraw LaserPrep and Include PostScript to reduce the size of each picture Do not deselect this option if the document will ever be printed to a PostScript printer Printers that use the PostScript page definition language use the PostScript representation The PostScript representation describes objects by using mathematical shapes that can be precisely imaged at whatever resolution is used by your printer The PostScript representation created by ChemDraw is composed of two parts the Post Script commands and the ChemDraw Laser Prep The ChemDraw Laser Prep contains specific instructions that enable the printer to interpret the PostScript commands contained in a ChemDraw document Include PostScript To transfer ChemDraw pictures to another document that will be printed on a PostScript printer 1 From the File menu choose Preferences 2 Click Include PostScript 3 Click OK When Include PostScript is deselected no Post Script commands are generated This usually results in lower quality printing particularly of drawings cut and pasted into other applications However
369. scription 167 multiple attachment points 168 Always Display and Print Atom Mapping 171 Analysis information 138 messages 238 Analysis window 18 Anion drawing 97 Anonymous Alternative Groups 170 Apply Settings command 22 Arc Tool description 15 using 102 Arcs drawing 102 resizing 102 arcs 102 Arrow Tool description 15 overview 99 palette 99 Arrows autoscaling 194 created with curves 105 resizing 99 Aspect Ratio changing 117 Assigning atom mapping 170 structures to spectra 146 Atom moving 112 numbering 89 ii CambridgeSoft Administrator Atom continued query properties 150 Atom Label text boxes closing 79 Atom Labels automatic justification 82 creating 86 deleting 87 editing 87 hotkeys 87 justification 82 layering 86 margin width 86 multi attached 125 overview 79 repeating 89 specification 232 text boxes creating new line 79 white space 86 Atom Numbering editing 90 hiding 90 position 91 showing 90 Atom properties abnormal valence 155 description 151 implicit hydrogens 152 in query structures 149 reaction changes 153 reaction stereo 153 resetting defaults 151 ring bond count 152 substituents 151 unsaturation 153 viewing 150 Atom To Atom Mapping 170 Attachment Point defining 168 multiple 168 numbering 169 symbol 168 Attachment point tool 98 Attachment Point Tool 168 Attachment Rank indicators showing 169 Auto Update 74 Automatic drawing of structure 74 error checking 71 justificati
370. selection tool 2 Point to the bond and type Moving Atoms You can use any of the bond tools to move an atom within acyclic or cyclic structures You cannot use a ring tool To move an atom in a chemical structure 1 Click a bond tool 2 Point at the atom to move A highlight box appears over the atom 3 Shift drag the atom You can convert ring types by dragging one atom on top of an adjacent atom For example you can use this method if you want to convert a 6 membered ring into a 5 membered ring Hotkey Result c to center a double bond CO2H HO H CH3 l to position a double bond to the left above r to position a double bond to the right below Hotkey Result ChemDraw 9 Drawing Chemical Structures 71 Automatic Warnings To convert ring types 1 With a bond tool selected point to an atom and Shift Drag 2 Release when one atom is on top of the other The bond between the atoms disappears NOTE You can also move atoms using a selection tool For more information see Moving Objects on page 111 Changing Bond Crossings When one bond crosses another white space is used to indicate which bond is in front of the other To change which bond is in front 1 Click any bond tool 2 Double click the bond to bring it to the front The bond appears in front You can also layer bonds using the Bring to Front and Send to Back commands For more information see
371. shortcuts see Shortcuts and Hotkeys on page 247 A bold font is used to indicate that you are to take a particular action for example From the Help Menu choose Help Contents Additional Information Additional sources of ChemDraw information are The Quick Reference Cards The Help system CambridgeSoft Web Pages http www cambridgesoft com Quick Reference Card The ChemDraw Quick Reference Cards are located in the back of the manual The cards provide summaries of ChemDraw Desktop Application commands and features Because many of the instructions require knowledge of the interface elements use the Quick Reference card as you perform the tutorials in Chapter 2 Tutorials Help System ChemDraw provides the following types of Help ChemDraw Help An HTML reference guide Context sensitive Help Windows Help topics related to user interface objects To access Context sensitive Help type Shift F1 ToolTips Short descriptions of user interface objects displayed by pointing Status Bar The lower left corner of the GUI displays useful information as you work CambridgeSoft Web Pages The following table contains the addresses of ChemDraw related web pages Ultra Ultra Pro Pro For information about Access Technical Support http www cambridgesoft com services ChemDraw Plugin http products cambridge soft com ProdInfo cf
372. solution options Setting TIFF options To set these options 204 Sharing Information CambridgeSoft Importing and Exporting Administrator Click the Options button in the Save dialog box to display the TIFF options dialog box 3 Select the options you want and click OK NOTE In the Macintosh version you may want to increase the memory allocated to ChemDraw if you are saving large TIFF files Inserting Objects from Other Applications You can insert graphics or documents created in other applications into ChemDraw You can edit inserted objects using the ChemDraw Edit menu Inserted objects can be resized or rotated using the resize and rotate handles of a selected object You cannot flip inserted objects To insert a graphic from another application into ChemDraw 1 From the Edit menu chooseInsert File 2 In the Open dialog box select the file type from the drop down menu 3 Select the graphic and click Open The file is embedded into the ChemDraw file NOTE If you select file type All files and choose a file type that ChemDraw does not support such as txt you will get an error message and the file will not be embedded Windows only To insert an object from another application into ChemDraw 1 From the Edit menu choose Insert Object The Insert Object dialog box appears 2 Take the appropriate action If you want to Then create a new object a Click Create New
373. sor appears 3 Click to add a ring Delete an atom and its bonds from the ring 1 Click the Eraser tool 2 Point to the atom shown below 3 Click the atom NOTE You can delete a bond individually by pointing at the center of the bond and clicking You can also drag the eraser to make multiple deletions Add a bond 1 Click the Solid Bond tool 2 Point to the atom shown below 3 Click to add a bond O OH ChemDraw 9 Tutorials 39 Tutorial 2 Drawing an Intermediate Add second and third bonds 1 Point to the atom shown below and click to add another bond 2 Add a third bond by dragging to make sure it has the desired orientation a Continue pointing to C4 b Hold the mouse button and drag diagonally upward toward the right c When the bond is oriented release the mouse button to deposit the bond Create a double bond 1 Point to the atom shown below 2 Drag diagonally downward over the existing bond to create a double bond Change the orientation of the double bond 1 Point to the center of the double bond 2 Click the bond twice to move the second line to the outside The bond moves to the inside on the first click and to the outside on the second click NOTE You can move a double bond by clicking it when a bond tool is selected The cursor corresponding to the bond tool that is selected appears Add an atom label 1 Point to the atom to label sho
374. 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 Performance Below are some ways you can optimize the performance of CambridgeSoft Desktop Applications Macintosh Increase the total amount of memory that the application can use Select the ChemDraw application icon in the Finder when ChemDraw is not running From the Edit menu choose Get Info Increase the memory allocation in the Preferred size text box in the Memory Requirements section of the dialog box Windows In the Performance tab in the System control panel allocate more processor time to the application Install more physical RAM The more you have the less ChemOffice Desktop Applications will have to access your hard disk to use Virtual Memory 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 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 your computer Macintosh or restart Wind
375. sual Basic Project checkbox Importing Hit Lists You can perform a search in ChemFinder and then import the hit list structures with data into Excel using the Get ChemFinder List command To use the Get ChemFinder List command Chem Finder must be open with a hitlist present Importing a Hitlist To import a hitlist 1 From the ChemOffice menu select Get ChemFinder List or click the icon A message box similar to the one below appears appears 2 Click Yes to import the hitlist The records are imported into Excel starting with the currently selected cell and moving down and to the right Error Messages If all conditions required to use the Get Chem Finder List command are not met one of the fol lowing error messages may appear ChemFinder is not running would you like to start it up ChemFinder is not running Do the following 1 Click Yes The message After loading your desired database and performing your search return to Excel and redo the operation appears 2 Click OK ChemFinder opens 3 Open a database and perform a search 4 Return to Excel and from the ChemOffice menu select Get ChemFinder List or click No database loaded in ChemFinder Load a database and perform your search Then return to Excel and redo the operation 210 ChemDraw Excel CambridgeSoft Exporting Tables Administrator ChemFinder is running but no database is loaded Do the following 1 Click OK
376. t Molecule or click The structure is removed from the cell and is placed on the clipboard To copy a structure from a cell 1 Select the structure 2 From the ChemOffice menu select Copy Molecule or click The structure remains in the cell and a copy is placed on the clipboard To paste a structure 1 Select the area into which you want to paste the structure 2 From the ChemOffice menu select Paste Molecule or click The structure is pasted from the clipboard Viewing Structures ChemDraw Excel allows you to select whether or not to display structures in a cell You can also adjust the height and width of cells to display their entire contents Showing and Hiding Structures To show structures 1 Select the cells in which you want to display pictures 2 From the ChemOffice menu select Show Picture or click The structures are displayed in the selected cells To hide structures 1 Select the cells in which you do not want to display pictures 2 From the ChemOffice menu select Hide Picture or click The structures are hidden and the cells resize ChemDraw 9 ChemDraw Excel 215 Using ChemDraw Excel Functions Aligning Structures A structure may fall outside the boundaries of its cell because it is too big or because it is improperly positioned within the cell Use the Align All Pictures command to enlarge the cell or reposition the struc ture If the entire structure is wit
377. t The Arc Tools Palette Administrator The frame you selected is inserted in your drawing The Arc Tools Palette Use the Arc tools to draw solid or dashed arcs of different angles 90 120 180 and 270 Drawing Arcs Where you access the arc tools depends on which version of ChemDraw you are using To draw an arc 1 Do one of the following In ChemDraw Std point to the Arc tool and drag in the palette to select the angle In ChemDraw Pro or Ultra point to the Drawing Elements tool and drag in the tool palette to select the angle 2 Dragging from left to right creates a convex arc from right to left a concave one The Info window shows the length between the ends and the angle the clockwise end makes with the X axis while you draw an arc Editing Arcs To resize or rotate an arc using the Arc tool 1 Select the Arc tool 2 Hold down the Shift key and point to the clockwise end of the arc A highlight box appears 3 Drag the clockwise end of the arc The arc is resized and rotated relative to the end from which it was drawn The Info window indicates the distance between the ends of the arc and the angle the clockwise end makes with the X axis You can resize and rotate an arc by dragging the Resize or Rotation handle on the Selection rectangle The resize or rotation occurs around the center defined by the Selection rectangle When you drag the Resize handle the Info window ind
378. t stored within the ChemDraw Folder are not accessible from the Scripts menu For more information about AppleScript and the Script Editor application see your system manuals Closing ChemDraw To close the ChemDraw application From the File menu choose Exit ChemDraw or Quit ChemDraw If you have unsaved document windows open you are prompted to save them before you can close the application ChemDraw 9 Tutorials 31 Tutorial 1 Reaction Schemes Chapter 2 Tutorials Overview The tutorials are designed to teach you the fundamental drawing techniques available in ChemDraw Before you begin you may want to review Conventions on page 10 to familiarize yourself with the terminology used in the tutorials You may also want to use your Quick Reference Card while you perform the tutorials ChemDraw automatically checks for correct chemical syntax as you draw If ChemDraw finds a potential problem a red box is displayed around the erroneous object The red box is displayed on screen only and does not print To disable the automatic warning on a specific object Right click the object and deselect Display Warnings Tutorial 1 Reaction Schemes In this tutorial you will draw the following simplified reaction scheme Create a ChemDraw Document 1 Start ChemDraw 2 From the File menu choose Save As 3 Type tut1 cdx in the appropriate text box 4 Select a folder in which to save t
379. tabase Conventions 231 Chemical Conventions 232 Atom Labels 232 Chemically Significant Text 233 Charges 234 Isotopes and Elements 235 Radicals 235 H Dot H Dash 235 Complexes 235 Multi center Attachments 236 Stereochemistry 236 Stereochemical Indicators 237 Stereochemical Flags 237 Polymer Representations 238 References 238 Query Properties 238 Analysis Messages 238 Appendix D How ChemNMR Works ChemNMR Limitations 243 Appendix E How ChemProp Works LogP 245 Henry s Law
380. tallic compounds category ChemDraw 8 supports ChemDraw 9 adds 78 Struct lt gt Name CambridgeSoft Name Struct Administrator ChemDraw 9 Drawing Captions and Atom Labels 79 Chapter 5 Drawing Captions and Atom Labels Creating Text ChemDraw enables you to create the following types of text Caption text Create annotations chemical names chemical formulas page titles and information in tables Atom label text Identify atoms and substructures by their chemical symbols and formulas The behavior of atom labels is controlled by the Automatic Atom Labels checkbox on the General tab of the Preferences dialog box This preference controls two aspects of the behavior of atom labels The default preference is to use Automatic Atom Labels When Automatic Atom Labels is selected The alignment of atom labels will adjust according to the positions of any bonds attached to the atom label For example a CH3 atom label entered at the left end of a horizontal bond would reverse itself to H3C Hydrogens will be added to or removed from atom labels as necessary to preserve standard valences when bonds are added or changed You can use HotKeys to quickly label atoms For more information see Labeling Atoms with HotKeys on page 87 You create and edit caption and atom label text with the Text tool You set the text format in the Docu ment Settings or Object Settings dialog box
381. tem and chemical databases for complete management of chemical inventories CombiChem Enterprise and Formulations amp Mixtures are also important parts of research data management Enterprise Solutions Enterprise Solutions Consulting Development Support amp Training CambridgeSoft s scientific staff has the industry experience and chemical and biological knowledge to maximize the effectiveness of your information systems Oracle Cartridge or SQL DB Chemical Databases BioAssay HTS BioSAR Browser APPLIED BIOINFORMATICS CHEMICAL DATABASES ChemDraw Spotfire Win BioAssay Pro Win Purchase Excel Win CombiChem Excel Win ChemFinder Office Win ChemDraw Excel Win Name Struct Win Mac Struct Name Win Mac ChemNMR Win Mac CLogP ChemDraw Win Mac BioArt Win Mac Structure Clean Up Win Mac Polymer Draw Win Mac LabArt Win Mac ChemSAR Excel Win 3D Query Win MOPAC Chem3D Win GAMESS Client Win Gaussian Client Win Tinker Chem3D Win CAMEO ChemDraw Win The Merck Index Win ChemACX Ultra Win ChemSCX Win ChemMSDX Win ChemINDEX Ultra Win ChemRXN Win NCI amp AIDS Win Available Separately ChemOffice Ultra ChemOffice Pro ChemDraw Ultra ChemDraw Pro ChemDraw Std Chem3D Ultra Applications amp Features Databases Includes ChemDraw Ultra Win Mac ChemDraw Pro Win Mac ChemDraw Std Win Mac ChemDraw Plugin Pro Win Mac Chem3D
382. ter ChemDraw creates both a screen representation and a PostScript representa tion of your drawing PostScript is a page definition language used to describe drawings Many printers including most Apple LaserWriter printers use PostScript to create high quality output For best print quality under all circumstances we recommend that you leave the Include PostScript and Include ChemDraw Laser Prep preferences selected default when you copy and paste from ChemDraw to other applications The ChemDraw Laser Prep option adds approximately 11K to 12K to each drawing but these options give you the greatest flexibility if you give your document to someone else or later want to print it on a Post Script printer If you never plan to print to a PostScript printer or never plan to give your document to someone who uses a PostScript printer you can turn the prefer ences off To deselect the PostScript preferences 1 From the File menu choose Preferences 2 Deselect Include PostScript and Include ChemDraw LaserPrep To transfer only a few drawings to another document NOTE You can also transfer drawings to a document in a remote location whose printer cannot be initialized by ChemDraw In the Preferences dialog box select Include PostScript and Include ChemDraw Laser Prep 196 Sharing Information CambridgeSoft Importing and Exporting Administrator The PostScript commands and the ChemDraw Laser Prep are transfe
383. th 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 ChemOf ce ChemDraw 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 Database Products for further details Trademarks ChemOf ce ChemDraw Chem3D ChemFinder ChemInfo and ChemACX are registered trademarks of CambridgeSoft Corporation Cambridge Scienti c Computing Inc The Merck 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 Microsoft Word are registered trademarks of Microsoft Corp Apple Events Macintosh Laserwriter Imagewriter QuickDraw and AppleScript are registered trademarks of Apple Computer Inc Geneva Monaco and TrueType are trademarks of Apple Computer Inc The ChemSelect Reaction Database is copyrighted by InfoChem GmbH 1997 AspTear is copyrighted by Softwing Copyright 1986 2004 CambridgeSoft Corporation Cambridge Scienti c Computing Inc All Rights Reserved Printed in the United States of America All other trademarks are
384. the context and orientation of the repeating units A S Se Te S D b c a NOT F Cl Br NOT C O N CH2 3 7 164 Drawing Query Structures CambridgeSoft Representing Polymers and Other Repeating Units Administrator To enclose structures with brackets 1 Click the Bracket tool and select one of the double bracket tools 2 Click drag across the structure to draw the brackets 3 Right click or Control click and select the appropriate bracket properties from the menu that appears The bracket properties are described in the following sections NOTE This method will give a default value for component order multiple group repeat count or SRU label To change a default value use the Bracket Properties dialog box Setting Bracket Properties You can change the properties of brackets by the context menus or Bracket Properties dialog box To use the Bracket Properties dialog box 1 Select the right bracket with a selection tool 2 From the Structure menu choose Bracket Properties The Bracket Properties dialog box appears The Flip Type option appears only for brackets with exactly two crossing bonds and is disabled in other cases You can customize the text that appears to the bottom right of the bracket for the following bracket types Component c the Component Order must be a non negative integer and is displayed as the letter c followed by that integer or c
385. the platform you are using 2 Choose a folder in which to store the file 3 Type a file name in the File name Windows or Save As Macintosh text box You may type up to 255 characters for a file name including spaces For example my first structure in ChemDraw 4 Click Save or OK to create the file The title of the document window changes to the name of the saved file The file name is added to the bottom of the File menu CAUTION ChemDraw uses the cdx file format to store chemical information accurately with a structure drawing Other file formats may be capable of storing a picture of your drawing but they might lose chemically relevant information about the structure For example if you save a ChemDraw drawing in the eps file format you will store only a picture of the structure without storing the chemical significance of the connections between atoms and bonds To save a document that has previously been saved From the File menu choose Save The contents of the file are updated to reflect the information currently in the window without displaying the Save As dialog box Setting the Default Save File Format You can set what file format is selected by default in the Save As dialog box To set the default file format 1 From the File menu choose Preferences The Preferences dialog box appears 2 Click Open Save 3 In the Saving Files section click the checkbox next to Use Default F
386. the selection until the central atom of the selection is centered within the orbital 3 Release the mouse button and click outside the Selection Rectangle to deselect the structure Save and close the document 1 From the File menu choose Save 2 From the File menu choose Close Tutorial 7 Showing Stereochemistry This tutorial demonstrates using Stereochemistry markers and the flip command Create a new document 1 From the File menu choose New Document 2 From the File menu choose Save As 3 Type tut7 cdx in the appropriate text box 4 Select a folder in which to save the file 5 Click Save Draw the following structure 1 Click the Solid Bond tool 2 Click in the document window and drag downward to create the first bond 3 Continue pointing at the lower atom and click again to add a second bond 4 Continue pointing at the same atom and click again to add a third bond 5 Point to the atom shown below and click 6 Point to the atom shown below and click twice to create two bonds 7 Pointing to the bond shown below right click point to Double and then choose Plain OH O NH2 ChemDraw 9 Tutorials 57 Tutorial 7 Showing Stereochemistry 8 Click the Wedged Bond tool point to the atom below and then click Add atom labels 1 With the Text tool click the atom shown below and then type NH2 in the text box that appears 2 With the Text tool click the atom sh
387. ting atom properties where a particular atom must have a charge of 3 might narrow your search Because ChemDraw is not a chemical database application the interpretation of query structures involves other programs Not all databases support the same query properties If you use a query structure containing properties not understood by a given database one of the following may happen An error message appears The unsupported properties are ignored To use query structures for searching you may do either of the following Paste the query structure into a database search window and initiate a search Save the structure in an appropriate file format and open the file in the database application For more information on query properties see Query Properties on page 238 or consult the documentation for your chemical database NOTE ChemOffice 2005 does not prevent or warn you if you try to assign conflicting or nonsensical properties For example you can require that one of the atoms in benzene is not part of any ring which is inherently impossible The results of such a search depend on the query system used but usually no matches are found Atom Properties To assign properties to selected atoms in a structure 1 Do one of the following Select a single atom by clicking it with a selection tool Select multiple atoms by Shift clicking the atoms 2 Then do one of the following
388. tion 1 The second line is on the left looking from the first atom to the second 2 The two lines are centered 4 A double bond with one dashed and one solid line 8 A modifier to the previous two values indicating that the user specifically set the positioning If this bit is not present ChemDraw calculated the positioning automatically 16 A double bond with one bold and one solid line 32 A crossed bond 64 A double bond with two dashed lines value bond type position 270 Chemistry File Formats CambridgeSoft Connection Table File Format Administrator ChemDraw 9 i Index Numerics 13C 1H shifts estimating 147 35 mm Slide Boundary lines 181 3D models 141 3D Query Properties 158 A Abnormal Valence 155 Abnormally shaped arrows creating 105 Absolute flag drawing 161 ACS Document 1996 256 Actual Size command 181 ACX information finding 223 ACX number search 224 ACX structure search 223 Acyclic Chain Tool description 15 Acyclic chains adding 68 length 68 Add 3D query property 158 chemical names 73 column to template 136 row to template 136 to selection 111 Add Frame 101 Adding structures in ChemDraw Excel 210 Aligning objects Align Submenu 185 overview 185 rulers 182 with crosshair 184 Aligning Structures 34 Alternative Groups attachment point numbering 169 Alternative Groups continued attachment point symbol 168 Attachment Rank indicators 168 defining 167 de
389. tion an indicator numerically 1 With a selection tool click the indicator to move 2 Right click and choose Position The Position Indicator dialog box appears Cholesterol 60 cholesterol S S S R R R S R HO H H H Z PositionIndicators 150 dpi ChemDraw 9 Working With Structures 141 Viewing Chemical Properties 3 Click the appropriate Position option and type a value Converting Structures to 3D You can convert a two dimensional structure drawn in ChemDraw to a three dimensional structure To use this feature you must have CambridgeSoft Chem3D installed on your computer To convert a structure to 3D 1 Select the structure to convert 2 From the Edit menu choose Get 3D Model The 3D structure appears in the document window NOTE 3D Objects inserted in this way cannot be transferred between platforms For more information see File Formats on page 197 To edit the 3D structure 1 Double click the 3D structure Chem3D opens 2 Edit the structure and close Chem3D when you are finished The edited structure appears in the ChemDraw document window Viewing Chemical Properties ChemDraw Ultra using an add on ChemProp calculates predicted values for the physical and thermodynamic properties of a selected structure of up to 100 atoms You can view the values in the Chemical Properties window The properties are calculated using th
390. tire spreadsheet Do not make any selection ChemDraw 9 ChemDraw Excel 211 Adding Structures Adding Structures with ChemDraw The most direct way to insert a new structure into a cell is by using ChemDraw To add a structure with ChemDraw 1 Double click in a cell The ChemDraw Excel dialog box appears 2 Click Yes ChemDraw opens 3 Draw the structure in ChemDraw 4 From the ChemDraw File menu click Close and Return to New Molecule The new structure appears in the cell Adding a Structure From a File To add a structure from a file 1 Select the cell into which you want to add the structure 2 From the ChemOffice menu select Load Molecule or click The Choose Molecule to Load dialog box appears NOTE You can use the sample molecule file SAMPLE cdx contained in the ChemDraw system directory or any cdx file to load 3 Type the file name of the structure to add and click Open The information is stored in the selected cell Adding a Structure with a SMILES String You can insert SMILES strings into cells and con vert them to structures To insert SMILES strings 1 Type or paste SMILES strings into cells 2 Select the range of cells or single cell to convert NOTE If you want to keep the original text copy it and paste it elsewhere 3 From the ChemOffice menu select Convert SMILES To Molecule or click 212 ChemDraw Excel CambridgeSoft Saving Structures
391. tive window that are contained in a different document On the File menu point to Apply Document Settings from and then choose the document from which to apply the settings The settings in the active document window change to those found in the Style Sheet or Stationery Pad that you choose NOTE When you apply settings they apply to the current document only are not saved as the default for the next document Use Open Special from the File menu if you want to change the default document settings To apply the document settings from a document or style sheet not listed in the menu 1 From the Apply Document Settings from submenu choose Other The Select document dialog box appears 2 Open the appropriate folder and select a ChemDraw document or Style Sheet Statio nery Pad 3 Click Open Applying Object Settings from Other Documents You can apply settings from another document to selected objects in the current document You can apply the chosen settings to the selected objects only or to all new objects drawn in the current document To apply object settings 1 Select the object 2 On the Object menu point to Apply Object Settings from and then choose the document from which to apply the settings SaveAs 200 dpi SelectSettings 200 dpi ChemDraw 9 ChemDraw Basics 23 Using Documents A dialog box appears 3 Take the appropriate action The settings are applied Using Documents
392. 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 don t 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 company s 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 it is run Q Can I take a piece 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 th
393. to indicate that you will create an atom label rather than a caption 3 Click the atom An Atom Label text box appears over the atom 4 Type an atom label Numbers are automatically subscripted The justification you choose determines how the letters in an atom label are positioned on a bond Numbers leading open parentheses and trailing closed parentheses are ignored in the positioning of atom labels 5 To close the text box click outside the text box or select another tool NOTE You can use HotKeys to label an atom instead of using the Text tool You can also label atoms using Nicknames that are text representations of substructures For more information see Labeling Atoms with HotKeys on page 87 and Using Nicknames on page 121 Specifying the Margin Width You can adjust the white space surrounding the atom label so that some of the attached bond is hidden To adjust the white space 1 From the File menu choose Document Settings The Document Settings dialog box appears 2 On the Drawing tab type a new Margin Width value 3 Click OK o xylene Chemical Formula C8H10 Molecular Weight 106 16 Cl Cl 0 278 pt 0 6 pt ChemDraw 9 Drawing Captions and Atom Labels 87 Labeling Atoms with HotKeys 4 The margin width is applied to all subsequent drawings in the current document Editing Atom Labels To edit an atom label 1 Click an existing label using the Text tool or doubl
394. tography plates within a ChemDraw document The tool creates a Pro Pro 106 Drawing Orbitals Symbols Arrows Arcs and Other Shapes CambridgeSoft The TLC Tool Administrator rectangular plate with origin line solvent front and one or more lanes The lanes can be populated with spots of different Rf size shape or color To create a TLC plate 1 Select the TLC tool 2 Drag in any direction from the point of origin The number of lanes is a function of the width of the plate you create You can manipulate parts of the plate as follows If you want to then Change the height or width of the plate Drag a border or corner The number of lanes will not change Move the origin or solvent front Drag the origin or solvent front line Show or hide the origin solvent front borders or side ticks 1 Right click or Control click in the plate 2 Select the appropriate action NOTE Use the Transparent option if you want to overlay the TLC plate on a scanned plate Change the order of lanes Drag the origin tick to the new location Add delete or duplicate a lane 1 Position the cursor on the lane you want to delete or duplicate or between lanes to add 2 Right click or Control click in the plate 3 Select the appropriate action NOTE You can also delete lanes with the Eraser tool Move a spot Drag the spot The Rf displays as you drag Duplicate a spot
395. tructure or objects such as boxes curves arrows orbitals and reaction mechanism symbols The border of objects that are shaded or filled such as white filled s orbitals in the Orbitals palette are the same color as the shading or fill The border of objects that are hollow such as circles and hollow boxes in the Drawing Elements palette can be colored but the inside of the object cannot To color an object 1 Select the object in a document window with a selection tool 2 Do one of the following On the Style toolbar click the Color button and select the color from the menu that appears From the Color menu choose a color In the Object Settings dialog box on the Drawing tab click the Color button and select the color from the menu that appears Displaying the Color Palette You can use the color palette to specify the color of objects and text in the document within the active window To view the Color palette 1 From the File menu choose Document Settings 2 Click the Colors tab Use the Color tab to specify the following colors Background Color Fills the background of the current document in the active window Foreground Color Default color used when you draw a new object Other Colors Colors available in the Color Menu for changing the color of individual objects The colors are represented in the same order that they appear in the Color menu You
396. tructure based representation but they are rarely encountered and using them is discouraged Source based Polymer Representations Source based polymer representations enclose an entire discrete chemical substance in brackets The mode of polymerization may be obvious from context or it might be unknown Source based representations are useful when describing processes where the starting materials are known but the exact structure of the reaction product is not You can create a source based representation by enclosing a structure in Monomer mon brackets A source based representation of poly vinyl chloride is shown below You can use Mer mer brackets for components of a copolymer where those individual components are known not to repeat themselves or alternate with the other components An example is shown below Copolymers represent substances with more than one repeating unit In general you can use bracket type Component co You can also use Copolymer alternating alt Copolymer random ran and Copolymer block blk to represent different specific types of copolymers in a source based representation but they are rarely used and their use is discouraged The bracket type Mixture unordered mix is not for polymers but to represent a collection of substances that may all be present but not necessarily in known amounts Bracket type Component c indicates ind
397. u 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 ChemFinder 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 ChemDraw Appendix Accessing the CambridgeSoft Web Site 223 Finding Chemical Suppliers on ACX com Appendices Follow the links to do substructure queries The following illustration shows part of the page for Benzene 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 To use Find Suppliers on ACX Com menu access 1 In ChemOffice select a
398. u can change the text settings for a specific caption or atom The setting change is applied to the selected object only You can also choose whether to have the settings applied to the selected text and to all subsequent text you type To change the text settings for a specific caption or atom label 1 Select the text to change with a selection tool 2 From the Text menu select the appropriate options To change only a part of a single caption you must use the Text tool Select part of the caption with the Text tool N CH3 84 Drawing Captions and Atom Labels CambridgeSoft Creating Captions Administrator To specify a font and size for selected text do one of the following Choose the font and size from the Text menu Right click and choose the font and size from the right click menu From the Style Toolbar select the font and size from the drop down menus Fractional Character Widths Macin tosh On the Macintosh you can choose to have the spacing between characters as close to proportional as possible If you are printing to a PostScript printer this option improves the font appearance To set fractional widths 1 From the File menu choose Document Settings 2 In the Document Settings dialog box click the Footer tab 3 Click Fractional Widths Coloring Text You can color captions and atom labels before or after they are typed and as a whole or in part To colo
399. uch structures That data is displayed in the Analysis window as with any other structure Repeat Pattern For simple linear polymers the repeating units may connect head to tail or head to head or their repeat pattern might be a mixture or unknown You can also assign this property to brackets Because of its prevalence the Head to Tail type is assumed to be the default Repeat Pattern and does not receive any special annotation on the brackets as shown below Flip Type For ladder type polymers those polymers with two connecting bonds on each side there is a potential ambiguity in the order of the connections You can assign the Flip Type property to resolve that ambiguity This property is appropriate only for brackets with exactly two crossing bonds and is disabled in other cases O O O O HO OH O Na Na 2 H O H 3 O O 14 13 14 O O 13 hh eu O O O O O O O O mixture of the above or unknown repeat pattern ChemDraw 9 Drawing Query Structures 167 Alternative Groups Because of its prevalence the No Flip type does not receive any special annotation Alternative Groups You can create a search query that contains variable functional groups or substructures Instead of submitting multiple queries on structures that share a common substructure you can submit a single
400. ucture menu choose Define Nickname The number of connection points is shown by radicals in the Formula You can have only one or two connection points in a nickname 4 Type a short name for the Nickname 5 Click OK The Nickname is defined If you use a Nickname that is the same as an element name a message indicates that the element is replaced with the Nickname For example using Ac for an acetyl group replaces the element Actinium The Check Structure command recognizes the label as an acetyl group rather than Actinium ChemDraw provides the following default Nickname Element conflicts NHOH Et ChooseNickname 150 dpi Pro Pro Symbol Nickname Element Ac Acetyl Actinium DefineNickname 150 dpi ChemDraw 9 Advanced Drawing Techniques 123 Using Nicknames To remove the overriding Nicknames choose List Nicknames from the File menu and delete the overriding Nickname definition For more information see Deleting Nicknames on page 124 Troubleshooting Nicknames If the command Define Nicknames is dimmed check for the following A connection point is not present More than 2 connection points are defined The connection point is not a single bond In the example below the functional group was drawn and the entire group selected Because there is no atom that indicates a connection point you cannot define a Nickname In the example below the sulfonamide group is attached
401. ulers command 182 Show Stereochemistry 139 Showing Atom Numbering 90 palettes 17 sigma orbitals drawing 94 Similarity searching in ChemDraw Excel 213 single bonds drawing 62 Single brackets 101 skc format 200 SLN strings 192 SMD file format 202 SMILES creating 191 overview 191 xviii CambridgeSoft Administrator SMILES continued paste 192 viewing clipboard 191 SMIRKS overview 191 s orbitals drawing 94 SPC file format 202 Spectra assigning structures 146 exporting 201 202 importing 201 202 importing as JDX 201 importing as SPC 202 removing assignments 147 Spectrum structure assignments making 146 removing 147 viewing 146 Spiro linkage templates 134 Squiggly Bond tool see Wavy Bond tool 62 Standard Molecular Data see SMD Starting ChemDraw Excel 207 Stationery Pad saving document settings 21 Stationery pad Default 21 Document settings 21 file format 199 Page Setup settings 181 Stationery Pads creating 255 provided 255 Status bar 18 Status messages 238 Stereochemical Indicators 237 Stereochemical symbols drawing 161 Stereochemistry drawing mirror images 115 how calculated 236 indicators 140 237 indicators repositioning 140 Stereochemistry continued removing markers 140 showing 139 terms supported 140 Struct Name 73 Structure 3D perspective tool 15 automatic error checking 71 checking 137 CleanUp command 128 converting to name 73 Diagram Generation 128 perspective tool 114 selecting 11
402. utomatically as you edit the structure You can show or hide the information as follows 1 Right click in the label It does not matter which tool you are using 2 Point to Analysis and select or deselect the item you want to show hide Showing Stereochemistry When the Show Stereochemistry option is selected ChemDraw calculates the absolute stereochemistry for tetrahedral atoms and double bonds according to the Cahn Ingold Prelog CIP priority rules For more information about the CIP rules see Stereochemistry on page 236 m z Mass charge where charge 1 The weights of the most common isotopes and a graphical representation of the isotopic abundance is shown The molecular weight shown takes the isotopes for each atom and their natural abundance into account Where there is more than one abundant isotope ChemDraw computes multiple molecular weights Low abundance combinations whether because the isotope is in low abundance or because it includes many moderate abundance contributions are not taken into account NOTE You cannot paste the graph in a document Elemental Analysis The percent by weight of each element in the structure Property Description O HO OH HO OH HO Chemical Formula C6H12O6 Exact Mass 180 06 Molecular Weight 180 16 m z 180 06 100 0 181 07 6 9 182 07 1 4 Elemental Analysis C 40 00 H 6 71 O 53 29 glucose 140 Working With Structures Ca
403. ve an atom label Hotkey Result lt Backspace gt or lt Delete gt Remove an atom label or bond Hotkey Result 1 Change to single bond 2 Change to double bond 3 Change to triple bond 4 Change to quadruple bond c Center a double bond l Position a double bond to the left r Position a double bond to the right f Bring a bond to the front Hotkey Result 254 Shortcuts and Hotkeys CambridgeSoft ChemDraw Hotkeys Administrator ChemDraw 9 Document Settings 255 Appendix G Document Settings Creating Style Sheets or Stationery Pads To create your own Style Sheet or Stationery Pad 1 Create a new document 2 Enter the settings in the Page Setup Drawing Text Settings and Color Palette dialog boxes 3 From the File menu choose Save As 4 In the Save As dialog box a Select the CD Style Sheet or Stationery Pad file format b Type a name for the document c Select the ChemDraw Items folder as the location for saving the template 5 Click OK or Save 256 Document Settings CambridgeSoft ChemDraw Style Sheets or Stationery Pads Administrator ChemDraw Style Sheets or Stationery Pads This following table contains drawing settings and a sample structure for each of the Style Sheets or Stationery Pads ChemDraw provides Drawing Atom Label and Caption Text Settings in Journal Style Sheets or Stationery Pads Fixed Length 14 4 pt Bold
404. ve and exit To create a ChemOffice worksheet From the ChemOffice menu select New ChemOffice Worksheet or click A ChemOffice worksheet appears When a ChemOffice worksheet is active ChemDraw Excel appears in the title bar and the ChemDraw tool bar is active New worksheet Import table Export table Import ChemFinder list Name Struct SMILES Struct Structure controls Load Save Cut Copy Paste Name Structure controls Show Hide Resize Align Filter amp Similarity tables 208 ChemDraw Excel CambridgeSoft Importing Tables Administrator Importing Tables ChemDraw Excel allows you to import from the following sources MDL SDFiles Imports all records in the file Each structure is given the name stored in the SDFile ChemDraw databases Imports all fields stored in the main form Molecular weight and formula fields are not imported because ChemDraw Excel calculates them Each structure is named Structure lt n gt where n is a unique number NOTE In order to import cfw files into Excel make sure you save them with the allow CAL OLE Automation access security setting checked See Setting Security Options in Chapter 3 of the ChemFinder manual for details When you import a table structure data are trans formed into structure drawings in the first column and all other fields are imported in separate col umns To import a table 1 Select the cell
405. ve to position the chemical structures exactly attempts to fuse atoms that are not approximately lined up will lead to incorrect results 2 Select the two atoms to be fused selected bonds 118 Manipulating Drawings CambridgeSoft Grouping Objects Administrator 3 From the Object menu choose Join NOTE When you join two differently colored bonds or atom labels the color of the front object becomes the color of the resulting joined object When you join two atoms that are labeled the front atom label becomes the atom label of the resulting atom For more information about front to back ordering of objects see Chapter 11 Working With Page Layout Grouping Objects You can group a number of objects drawn separately Grouping creates an association between objects so they can be easily selected You can select all grouped objects by double clicking with a selection tool Objects within a group can be selected individually and manipulated while still remaining part of the group If you want to group objects so that the individual objects in the group cannot be accessed you can create an Integral group When you select any object in an Integral group the entire group is selected Grouping does not lock the position or orientation of objects Grouped objects maintain their relative positions when they are centered on the page aligned or distributed Atoms and bonds making up a single chemical structure are alw
406. view 170 Reaction Stereo 153 Red boxes on objects 71 Redo 25 Reduce document window 177 xvi CambridgeSoft Administrator Reduce continued object 182 page size 180 Reflection 115 Registration marks 178 Registration online 221 Relative flag drawing 161 Remove colors 133 rulers 183 Remove Color button 131 Repeat command rotations 114 Repeating a Label bond tool 89 Repeating actions 25 Repositioning atom number indicators 91 query indicators 160 stereochemistry indicators 140 Require Ctrl Enter to Create New Line in Atom La bels 80 Ctrl Enter to Create New Line in Captions 80 Requirements Windows 11 Reset defaults atom properties 151 bond properties 156 Resize Handle 116 Resizing arcs 102 arrows 99 drawing elements 100 handle double clicking 116 objects 116 template panes 136 Resolution TIFF 200 203 Resonance Delocalized rings drawing 67 Reversing actions 25 Revert command 25 RGB Indexed color 200 203 RGFile format 201 Ring Bond Count 152 Ring pointer icon appearance 66 Ring Tool 16 Rings drawing 66 drawing with fixed length 66 orientation 66 Rotate chemical symbols 98 command 114 dialog box 114 drawing elements 100 objects 114 Rotating objects 113 Rotation handle 113 of Objects 113 Rotation handle 113 RSC Document 256 Ruler Guides 183 Rulers hiding 183 showing 182 RXN file format 200 S Sample code SDK web site 225 Save As command 26 Save command default file format 26 using 2
407. w amp Chem3D Import export MDL SD amp RD files ChemInfo Std Reference amp Reaction Searching ChemINDEX for small molecule information ChemRXN for reaction databases BioAssay Pro Biological Assay Structure Activity Set up biological models amp visualize information Search data by structure to isolate key structural determinants of biological activity Tabulate amp analyze structure activity relationships with spreadsheet templates Available in ChemOffice Ultra SYSTEMS amp LANGUAGES English amp Japanese Windows 95 98 Me NT 2000 XP This software is Windows only All specifications subject to change without notice S O F T WA R E EMAIL info cambridgesoft com WWW www cambridgesoft com TEL 1 800 315 7300 INT L 1 617 588 9300 FAX 1 617 588 9390 MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge MA 02140 USA ChemOffice ChemDraw Chem3D ChemFinder amp ChemInfo are trademarks of CambridgeSoft 2002 All other trademarks are the property of their respective holders All specifications subject to change without notice D E S K T O P CS ChemDraw CS ChemDraw Chemical Structure Drawing Standard Chemical Structure Drawing Standard ChemDraw Ultra adds ChemDraw Excel ChemNMR Name Struct Beilstein s AutoNom CLogP and ChemFinder Word to ChemDraw Pro With rich polymer notation atom numbering BioArt templates and modern user interface ChemDraw is more powerful
408. wn below 40 Tutorials CambridgeSoft Tutorial 2 Drawing an Intermediate Administrator 2 Double click the atom to open a text box 3 Type O and then type Label an atom with OH 1 Point to the atom shown below 2 Double click the atom to open a text box 3 Type OH Next you will add an arrow that is not included in the arrow palette to indicate electron flow To create a customized arrow using the Pen tool 1 Click the Pen tool 2 From the Curves menu choose Arrow at End 3 Point near the double bond where you want to indicate the start of electron flow 4 Drag downward and to the left Release the mouse button The hand with a cursor indicates that you are in the editing mode of the Pen tool 5 Position the cursor where you want the arrowhead to appear 6 Drag upward to create a curve segment O O O O OH O O O OH O O O OH O O O OH ChemDraw 9 Tutorials 41 Tutorial 3 Using Rings Refine the shape of the arrow 1 Point to the handle pointing away from and to the right of the curve This is a tangent handle that controls the tangent of the curve that it touches 2 Drag the handle upward to the right to make the arrowhead point more inward 3 Press Esc when you are finished 4 Create additional arrows as described above to complete the intermediate as shown below NOTE If you want to magnify the entire docu
409. xane chair rings in two orientations horizontal and vertical When you draw a cyclohexane chair ring by clicking the chair is drawn in a horizontal orientation To orient a cyclohexane chair ring to a vertical orientation 1 Click one of the Cyclohexane Chair Ring tools 2 Drag in the structure to the orientation you want Drawing Resonance Delocalized Rings Any of the ring tools except the cyclohexane chairs can be drawn in a resonance delocalized form To draw a resonance delocalized ring 1 Click a ring tool 2 Press the Ctrl or Command key and drag or click to draw the ring A circle appears inside the ring NOTE The circle is automatically grouped with the ring when drawn For more information on grouping objects see Grouping Objects on page 118 Drawing Cyclopentadiene and Benzene Rings The double bonds in the cyclopentadiene or benzene ring tools can be drawn in either of two forms When you draw a cyclopentadiene or benzene ring a double bond is drawn first The Cyclopentadiene and Benzene Ring tool pointers indicate this orientation To shift the orientation so the first bond drawn is a single bond do one of the following Shift drag from the beginning of the first single bond to the end of the single bond Shift click in a document window to draw the bond with a Fixed Length In the figure below the arrow indicates the direction in which the first bond is drawn Horizo
410. xt to each style other than Plain that is applied to a portion of the selection A check mark appears next to each style that applies to all of the selected text Choosing a style other than Plain adds the new style to all of the selected captions Previously applied styles are not affected that is for example if you select Italic for a section that is Bold it will be Bold Italic Specifying Line Spacing You can specify the three types of line spacing Automatic Consistently spaced lines of text based on the height of the tallest character in the entire caption This is the default line spacing Variable Lines of text with different spacing based on the tallest character and the lowest descender in each line Fixed Consistently spaced lines using a spacing that you specify Aligning Text You can set the alignment of captions and atom labels to justify text to suit your needs The options available depend on whether you are aligning captions or atom labels Settings are made in the Object Settings dialog box To open the object settings dialog box do the following 1 Select a caption or atom label with the Lasso or Marquee tool 2 On the Object menu click Object Settings The Object Settings dialog box appears Captions You specify the caption justification and line spacing on the Captions tab of the Object Settings dialog box All text in a single caption must have the same Justif
411. xtensions to SQL that allow you to extract data in all supported formats Due to the variety of data formats supported Oracle Cartridge is easily deployed even within existing applications Since no manipulation of the data is needed new records are automatically added to the index for searching Simple Client Server Architecture Web Based Architecture E N T E R P R I S E 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 Oracle Cartridge versions including E Notebook Enterprise Document Manager Registration System Inventory Manager and BioAssay HTS By utilizing Oracle Cartridge you can deal with issues such as scalability and security entirely through the database layer simplifying large systems architectural considerations Oracle Cartridge has the side benefit of providing a database level interface to key applications so developers can integrate CambridgeSoft s solution platform with in house IT solutions without tinkering with the business tier Communicating with Oracle 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
412. y properties are only useful in a chemical database you must transfer your structures from ChemDraw into your search system Not all file formats support the same query properties and not all chemical databases support the same file formats Consult the documentation for your database to see which file formats are supported The following table lists the query properties that ChemDraw writes to ISIS SKC TGF and Clipboard file formats All query properties are written to the ChemDraw CDX file format CDX is the preferred format to use to retain all query properties in a drawing 2 3 4 5 6 7 1 O 8 Rxn 2 3 4 5 6 7 1 OH 8 Rxn Exported Query Properties ISIS Mol Rxn Atom Properties Substituents Unspecified X X X Free Sites b b b Up to a a a Exactly Xc Xc Xc Implicit Hydrogens Not allowed X X X ChemDraw 9 Drawing Query Structures 173 Export Compatibility Allowed X X X Ring Bond Count Any X X X No ring bonds X X X As drawn X X X Simple ring X X X Fusion X X X Spiro or higher X X X Unsaturation Unspecified X X X Must be absent Must be present X X X Reaction Change May be anything X X Must be as specified X X Exported Query Properties ISIS Mol Rxn Reaction Stereo Any X X Inversion X X Retention X X Translation Equal Broad Any
413. ydrogen oxygen nitrogen sulfur and halogens 2 The second method is an extension of method one that includes 120 atomic contributions evaluated from 538 molecules by using a constrained least squares analysis technique In addition to the atoms introduced for method one this method can handle molecules with phosphorus and selenium atoms This method works with a standard deviation of 0 77 cm3 mol ClogP and CMR Specific algorithms for calculating LogP and molar refractivity from fragment based methods developed by the Medicinal Chemistry Project and BioByte For more information see biobyte com Topological Polar Surface Area The polar surface area of a molecule measured in square ngstroms is an imporant property that can be used for the prediction of pharmaceutical transport properties in the body Historically this property has been calculated using time consuming 3D techniques but a recent paper1 has provided a remarkably accurate way of predicting it very rapidly ChemDraw implements this algorithm and displays it on the Chemical Properties window Other Properties Heat of Formation Gibbs Free Energy Ideal Gas Thermal Capacity Freezing Point Critical Temperature Critical Pressure and Critical Volume are estimated using Joback s fragmentation method Normal Boiling Point and Melting Point Estimated in K using two methods 1 Joback s fragmentation method 2 The Joback method as modified by Stei

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