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PQSMol Manual - Parallel Quantum Solutions

1. Hydrogen Hide Shows or hides hydrogen atoms 1 i Info Window Toggles on off the info window see Section 2 32 Build tools toolbar The bottom toolbar groups complex tools Use these tools to interact with the objects in the Build window Figure 2 4 Build tools bottom toolbar The tools from left to right are gt Default tool The primary action of the default tool is rotation of the molecule Usage Drag the mouse vertically and horizontally to rotate the structure along the X and Y axes respectively Press the lt SHIFT gt key while dragging to rotate around the Z axis i e out of the plane of the Build window To speed up the building process for advanced users the Default tool is overloaded with additional actions 1 Add Attach Connect Use the right mouse button to perform the same actions as described in the Add Attach Connect tool 2 Zoom Drag vertically using the center mouse button 3 Select Press the lt SHIFT gt key while clicking the center mouse button to perform actions described in the Select tool 4 Move Press the lt CONTROL gt key while clicking the center mouse button to perform actions described in the Move tool Parallel Quantum Solutions 9 2 1 Build window Note Each of the overloaded actions is available through its own dedicated tool button The Default tool is the only tool that uses buttons other than the left The remainder of the PQSMoL tools use only the left mouse
2. Figure 4 15 Job Submission confirmation At this point PQSMOL begins to monitor the output of the PQS calculation As soon as output is produced it is displayed in the PQS Output window shown in Figure 4 16 90 PQSMol Manual Output File Hder will be calculated in 1 pass Constructing Hder matrices 1 time for 12 atoms Haster CPU time For de part of hessian 0 01 Elapsed 0 01 mir The CPHF Solver threshold for Lst order density 1 0000E O58 Using delta density in CPHF screeningi OH Using I particle density type screening number of symmetry Unique atoms 12 cphf will be solved only once Solving the CPHF equations 1 time for 12 atoms CPHF Res x Fes Res z chu elapsed oscillating iter HEPI Htry Htrz3 Loose integral threshold 1 0000E 08 1 O 6213E O1 O 8044E 01 04 1474E 00 0 06 O06 F O 2910E O1 O 2077E O1 O 1957E Oo1 2 O 2154E O1 O 3417E O1 0 7456E 01 O08 0 06 F O 1215E O1 O 9690E G2 0 1851E 01 3 O 1026E O1 O 1416E O1 0 2069E 01 0 05 0 05 F O 1651E O2 O 17S8E 02 0 47 0SE 02 4 O 2593E O2 O 4447E G2 0 6643E 02 0 05 O 05 F O 6645E6 O3 O S978E O4 O 6270E 03 5 O f202E O3 0 1154E 02 0 23 4E 02 0 05 0 05 F O 4203E O4 0 1 B1E 03 Oo 3318E 03 Sharp integral threshold 1 0000E 0 O 4667E O3 0 5812E 03 oO S5435E 03 0 06 0 06 F O 44406E O4 O 26583E 04 0 6708E 04 cphf converged For 1 unique atoms Final integral threshold 1 0000E 10 7 O 1162E 03 0 1249E 03 9 1007E 03 1 06 O E F O 1700E 04 O 1220E 04 0 4158
3. Figure 2 9 Rotation about a bond 14 PQSMol Manual Build mode Note The axis of rotation bond divides the molecule into two groups By default the active group is composed of atoms in the group which contains the smaller number of atoms To force the selection of the larger group of atoms right click on the Rotate About a Bond button and select Larger Secion O Larger Sec Rota aie Attac i d a Bond Break tool Breaks a bond Usage Click on a bond to break it To preserve the correct atomic valency the broken bond is replaced by two bonds one on each atom each capped with a dummy atom Dummy atoms are represented by semitransparent green spheres Figure 2 10 Bond break Bond Fuse tool The fuse bond tool allows two bonds in separate segments to be fused into a single bond fusing the two segments together into a united whole After fusion the second of the formerly separate segments is selected and the fuse bond is set as the rotation bond allowing the angle between the two sections to be adjusted Note Not all bonds are fusible A fusible bond has e exactly one closed bond on at least one end e if an end has a closed bond that end also has at least one open bond An open bond is a bond that is connected to an atom with a valency of one i e no other bonds are connected to the atom A closed bond is one which is connected to atoms with valencies higher than one at both ends Usa
4. Sybylo Force Field Band Configuration sf se feeble fafa lili Ee a rola all rishi Cel Eri Ndi Pi Smi Eul Cdi TEJ Tuj Hol Eri Tmj by Lu Toa u elu enol efoeleslenll i Figure 4 3 Segment window with tetrahedral carbon building block selected Step 2 Insert the first tetrahedral carbon building block In the Segment window Figure 4 3 press the carbon button in the periodic table of elements The current element is displayed in large font above the periodic table Also all of the available building blocks for the current element are enabled in the Bond Configuration frame directly above the periodic table The tetrahedral building block is the default building block for carbon and should already be selected It is activated by the last available button in the second row in the Bond Configuration frame Figure 4 3 When selected the building block will appear in the Segment buffer above the Bond Configuration frame At this point your Segment window should look like the one in Figure 4 3 Parallel Quantum Solutions 83 4 1 Example 1 Lactic Acid To insert the block into the build area select the Add Attach Connect tool in the lower toolbar and click the left mouse button anywhere inside the build area At this point your Build window should contain a single building block shown in Figure 4 4 Figure 4 4 Build window with the tetrahedral carbon building block inserted Step 3 Attach the second
5. BOHMD ATOMS ORDER LEHGTH 3 08 C4 1 1 230 794 Angle Cc 8 6 97 9501 E Cc C3 C4 1 1 505364 Torsion C 8 6 7 65 1042 T C3 C 1 1 549739 OP Bend C E 6 7 26 2291 Figure 2 32 Info window atom info top image bond info bottom image The Info window displays information gathered by the info tool The info tool can collect information about atoms Figure 2 32 top image or bonds Figure 2 32 bottom image If a single atom is selected by the info tool the atom s number atom s symbol Sybyl5 2 and Universal atom types and coordinates are displayed When a second atom is selected the distance in Angstroms between the two atoms is displayed Selection of a third atom shows the angle between the three atoms and selection of a fourth gives the torsion and out of plane bend If the info tool is used to select bonds a single bond gives information about the bond number the atoms it connects bond type and bond length Selection of a second bond gives the angle between the two bonds and selection of a third shows the torsion and the out of plane bend Parallel Quantum Solutions 33 2 2 Segment window 2 1 3 Statusbar Pointer Coordinates Torsion Mode Selection Mode Force Field Xx 1296511 Y 4 2035 z 0 0000 Auto Torsion ON Auto selection ON Force Field sybylo 2 DEFAULT LMBJ Rotate LMB SHIFT 2 Rotate RMB Insertt ttach CMB 2oom CME SHIFT 5elect 2 Current Tool Tool Description a
6. Figure 2 53 Job Parameters window density functional After selecting the basis set the density functional can be selected from a list of commonly available functionals Figure 2 53 The default is O3LYP Whichever functional is finally selected will appear in the DFT Method box and also in the input file on the right Parallel Quantum Solutions 49 2 6 PQS Calculation l ZHEH 5 Job specifications TEXT Test Job GEOM Pos tl h o 407421 O 298720 o 552090 Title Test Job Memory in Oo 270075 0 093703 0 920224 c oO 367478 1 121867 052592 a T 1 595360 1 013542 951924 Molecule Characteristics o 2 389140 0 92816 0 849092 c 906822 0 984464 0 953780 limito h 1 215465 231304 4 641264 Charge 0 Symmetry 0 000071 Multiplicity 1 o EEEN 41583719 846167 h 2 5646858 1 823201 2 335932 h 1 5 4127 1 043448 0 319458 Calculation Type hi 0 360849 2 115796 0 397087 h 0 9141296 0 013525 1 472488 E h 0 947723 1 787119 1 7068985 single Point Energy Select type PEEEEEEELLL STEP A PEELbiiitiieds ae La OPTImize Geometry Optimization semiempirical SEMI PH3 JUHP Basis set Method Basis Set DFT method ME semiemp method PRS Properties 241 Vibrational Freg MNOO MIND Electric Field Granen ME A A ae COSMO Chargelspin Density Figure 2 54 Job Parameters window semiempirical If Semiempirical had been selected instead of DFT Figure 2 54 then no
7. Parallel Quantum Solutions 27 2 1 Build window The Build menu File Edit Petit Optimize Symmetry Display Calculation Window Mode i m Restricted Center All O Unrestricted Center selection Face Front Hydrogen Fill Ctl H ry show Angle Presets show Plane Shit ra Auto Selection a ry Auto Torsion Torsion Options e Mode gt restricted sets the restricted building mode Section 2 3 3 e Mode unrestricted sets the unrestricted building mode Section 2 3 3 e Center All centers the contents of the Build window e Center Selection centers the selection in the Build window e Face Front rotate the structure in the Build window so that XY plane is parallel with the screen e Hydrogen Fill replaces all single bond dummy atoms with Hydrogen e Show Angle Presets toggles the Angle Presets window Figure 2 28 When enabled the presets window will automatically appear whenever a rotation bond is selected or a second bond is selected with the bond angle tool Activating any of the preset angles listed will set the torsion about the rotation bond or the bond angle to the selected preset 28 PQSMol Manual Build mode Presets deg Presets deq Figure 2 28 Angle Presets window left image torsion presets right image angle presets e Plane Shift toggles the Plane Shift window Figure 2 15 When enabled the Plane Shift window will automat
8. i ad T c 0 237721 1 033742 0 547019 Title Lactic Acid vibrational frequencie 1 033917 1 408609 1 510835 h 1 333917 1 392117 0 547030 A h 0 437429 1 406609 1 403619 Molecule Characteristics h 0 443531 1 382760 0 321992 C 0 940903 0 365998 O 555302 e h 1 437375 0 721860 1 426808 Charge 0 Symmetry 0 00001 Multiplicity 1 1 746601 0 925765 1 698534 o O 412123 0 873876 0 554740 l o 0 997615 1 057056 0 502510 Calculation Type o 1 055644 1 097101 1 698534 o 1 664027 O 866087 660148 Sella IIIIIIIIII STEP 2 II IIILLLI single Point Energy select type T BASIS 3 21g ee OPT Imize Geometry Optimization Hartree Fock x SCF FORCe JUMP HESS Basis set Methad FREQ Basis set 3 21 A DFT method ales te f semiermp method PAs 7 Properties jv Vibrational Frequencies NMR Chemical Shifts Electric Field Gradient YCD Chargespin Density COSMO Population Analysis Figure 4 14 Input generation window finished input Press the Done button at the bottom of the window to save the input file The input file is saved under the same name as the build file with a inp extension 03C3H6 inp in our example 4 1 3 Submitting the PQS job Submit the job With a completed input file we are ready to submit the job Use the Calculation Submit Job menu item to run the calculation The job is submitted and you should see a confirmation dialog in Figure 4 15 Pals job homespawel TESTs CaHBOs inp submitted
9. 2 and 9 methoxy derivatives Because the ranges were set to the same on all four spectra they can be directly compared Parallel Quantum Solutions 137 4 3 Example 3 Methoxy Substitution in Perfluoroanthracene MMA Spectrum F Atoms Selected value 45 01 7 1 60 00 l t l y 11 0 00 MMA Spectrum F Atoms Selected w 160 00 a O t E 11000 MMA Spectrum F Atoms Selected value 42 430 160 00 tto NN 110 00 MMA Spectrum F Atoms Selected value 39 491 160 00 E y 110 00 Figure 4 79 F NMR spectra from the top perfluoroanthracene 1 methoxy perfluoroanthracene 2 methoxy perfluoroanthracene and 9 methoxy perfluoroanthracene atom no 9 selected In all three derivative spectra the three main signals observed in the parent are split due of course to the loss of symmetry and are shifted downfield The spectra of the three isomers are sufficiently different that in e g a reaction between perfluoroanthracene and methoxide ion in methanol provided one isomer was dominant in the reaction mix it should be possible to determine the actual substitution site whether at positions 1 2 or 9 by comparing the experimentally observed 19 F NMR spectrum with the theoretically simulated spectra 138 PQSMol Manual List of Figures al POS MOLT GCHOM ez wince te oe eo BERR OSS S MERE A E EE EE BG SS Ode 1 2 POSMol executine in bulla mode s e s a AA EE EE hk eee RE ee EE ww 5 22 OS BULA WINCC eto AA A AA E e OS
10. DET Basis SetMethod Basis set B 311g dp sr DFT method BaL F y semiemp method PRs T Properties x Vibrational Frequencies ivf MMR Chemical Shifts Electric Field Gradient Y WED Charge spin Density COSMO Population Analysis Figure 4 33 Job parameters window complete input file The left frame of the job parameters window contains the user interface objects to create the input file The left frame shows the actual source of the input file generated It is updated in real time as options are selected in the left frame Fill in the options as follows In the Job Specification frame enter the optional title CHFC1Br opt freq nmr vcd In the Calculation Type frame select the Geometry Optimization radio button and the DFT item in the dropdown menu In the Basis Set Method frame select the 6 311g dp basis set and B3LYP for the DFT method In the Properties frame check the Vibrational Frequencies NMR Chemical Shifts and VCD checkboxes The resulting input file source is shown in the right frame in Figure 4 33 Press the Done button at the bottom of the window to save the input file Note The input file is saved under the same filename as the build file but with the extension inp Note f you attempt to start the input generator with an untitled build file the Save dialog will be automatically open The input generator will not execute until a valid filename is assigned to the build file 4 2 3 Submittin
11. Fragments Clipboard sybyls 2 Force Field Bond Configuration ta E oor le ale 211 1404 x 0 57695 w 0 91744 z 4 40406 aaa re Torsion ON poe Auto Selection ON STR Re Force Field Syb z DEFAULT LMB Rotate LMB SHIFT Z Rotate RMB Insert Attach CMB Zoom CME SHIFT Select CMB CNTRL Move Figure 4 51 Build Window hydrogen replaced with fluorine E The structure can be optimized by clicking on the Optimize button Ey and the symmetry found by clicking on the Check Symmetry button 26 The resulting point group should be d2h Figure 4 52 Point Group d2h Degrees of Freedom 12 Figure 4 52 Symmetry dialog The entire procedure up to this point could have been considerably simplified as the POLYCYCLIC fragment library already contains an Anthracene fragment which could have been selected directly instead of fusing the naphthalene and benzene rings But where s the fun in that 4 3 2 Creating a PQS input file Step 6 Preparing the input file 118 PQSMol Manual Tutorials Once perfluoroanthracene has been successfully built the PQS input file can be prepared We are going to optimize the geometry using DFT and then compute vibrational frequencies to characterize the nature of the stationary point i e to ensure that it is a minimum and NMR chemical shifts Select the Calculation Job Input menu item to start the input generator Since our build file has
12. NMR Chemical Shifts Electric Field Gradient CIRCO Charge Spin Density COSMO Population Analysis Done Figure 4 13 Input generation window The left frame of the window contains the input fields which are used to generate the input file In the right frame the input file itself is displayed Initially the source of the pqs input file contains only the geometry of the molecule we just created As values are entered on the left the input file is updated in real time This way you can see how the specific options appear in the input file Enter the title Lactic Acid vibrational frequencies into the Title field This option is used only as a descriptive title In the Memory field enter a value of 20 This option controls the amount of memory the program will request from the operating system to execute the job Lactic acid is a neutral closed shell system and we have already determined the point group symmetry C1 so none of the molecular characteristics need to be changed Select the Geometry Optimization radio button in the Calculation Type and choose Hartree Fock from the dropdown menu Choose the 3 21g basis set in the Basis Set dropdown menu In the Properties frame activate the Vibrational Frequencies checkbox Figure 4 14 shows the final input file Parallel Quantum Solutions 89 4 1 Example 1 Lactic Acid HEM 20 Job specifications TEXT Lactic Acid vibrational frequencies GEOHM FaS Ha
13. 132 4 72 Build window 1 methoxy perfluoroanthracene 1 2 133 4 73 View window 1 methoxy perfluoroanthracene fluorine atom no 9 selected 0 134 4 74 NMR window 1 methoxy perfluoroanthracene F NMR spectrum 0 0 00000035 134 4 75 View window 2 methoxy perfluoroanthracene atom no 9 selected 2 2 ee 135 4 76 NMR window 2 methoxy perfluoroanthracene 7F NMR spectrum oaoa 136 4 77 View window 9 methoxy perfluoroanthracene fluorine atom no 9 selected 2 136 4 78 NMR window 9 methoxy perfluoroanthracene F NMR spectrum 0 00 00000034 137 4 79 19 F NMR spectra from the top perfluoroanthracene 1 methoxy perfluoroanthracene 2 methoxy perfluoroanthracene and 9 methoxy perfluoroanthracene atom no 9 selected a a a a 138 Parallel Quantum Solutions 145 Index Area Build 6 11 12 26 29 35 37 39 84 85 98 100 112 117 128 Segment Buffer 6 8 10 11 34 35 37 83 84 86 98 100 117 127 128 View 64 atom labels 9 31 45 Building Modes Auto Selection 11 17 18 29 38 39 Auto Torsion 29 38 39 restricted 2 28 38 39 41 129 unrestricted 2 21 22 28 38 41 44 coordinate axes 9 17 31 drawing plane 8 18 20 29 dynamics trajectory 1 57 61 79 electron density 1 57 61 66 68 70 electrostatic potential 1 57 61 69 70 force field Sybyl5 2 10 25 30 33 35 36 39 43 82 101 133 U
14. 3 4 NMR window Range End 114 570 Range Start 157 00 Zoom Out Halfwidth 0 10 Reference shift 0 0 User Auto By selection Figure 3 20 NMR window O9 selected In the main visualize window atom O9 will be highlighted in green 76 PQSMol Manual View Mode File Options Display Window Help aba el leji elo el LMEJ Rotate CMB Z lt 00m LMB SHIFT lt Rotate LMEJ elect double click deselect Figure 3 21 View window O9 selected The Reference Shift value is set to O by default This value indicates no shift from the computed values There are three modes for setting the value of the reference shift selected by the three radio buttons at the bottom of the NMR window labeled User Auto and By Selection In User mode you may type in the desired value directly into the Reference Shift entry In Auto mode the reference shift value is set so as to make the smallest calculated shift equal to 0 the starting value on the right side of the graph is 0 Finally By Selection mode adjusts the reference shift value so that the currently selected peak is at the point 0 The NMR window in all three modes is shown in Figures 3 22 3 23 and 3 24 for the simulated C NMR spectrum Parallel Quantum Solutions TT 3 4 NMR window MMR Spectrum C Atoms Selected
15. Again for Chlorine only one building block is available Using the Add Attach Connect tool attach the Chlorine building block to the right most dummy atom as shown in Figure 4 29 Calculation Window Help a i Building Blocks Fragments Clipboard o vbylo Force Field Bond Configuration A h EE r IEAA A ee Pes ce aes Ce Prey Ndi Pin Sm Euf Gd TEJ Dy Haj Eri Tmj YE Lu Te i s s tr ZERB EARE EEEE EE x 4 18329 Y 6 04703 Z 0 0000 Auto Torsion ON Auto Selection ON Force Field Syby15 2 SSS DEFAULT LMB Rotate LMB SHIFT Z Rotate RMB InsertAttach CMB Zoom CMB SHIFT 5elect CMB CNTRL Mowe RESTRICTED Figure 4 29 Build and segment windows attaching the Chlorine building block Step 5 Connect the Bromine building block Select Bromine in the periodic table Again for Bromine only one building block is available Using the Add Attach Connect tool attach the Bromine building block to the left front dummy atom Step 6 Fill dummy atoms with hydrogen Press the Hydrogen Fill button H to replace all remaining single bond dummy atoms with hydrogen In our case we only have one such dummy atom Step r Preoptimize PQSMOL has the capability to perform an initial geometry optimization using one of two built in force fields The default force field is Sybyl5 2 this can be seen in the status bar at the bottom of the Build window in Figure 4 30 which i
16. Select All Ctl A select None Ctt Inverse selection Ctl Inverse seg selection e Undo undoes the effects of the last operation the last change made to the current structure in the build area i Note Multiple undo and redo operations are supported e Redo re does the last undone operation i e undoes the undo e Cut removes the current selection Y Oo Tip Structures cut or copied from the Build window are placed in the clipboard and may be reused e Copy copies the current selection into the clipboard e Paste pastes the contents of the clipboard into the Build window e Select All selects all atoms and bonds e Select None deselects all atoms and bonds e Inverse Selection toggles the selection state of all atoms and bonds All selected atoms before the operation become deselected after the operation and vice versa as shown in Figure 2 26 26 PQSMol Manual Build mode gt t L at ag f fef Figure 2 26 Inverse Selection example before left image after right image e Inverse Seg Selection toggles the selection state of all atoms and bonds within segments which have some atoms or bonds selected All selected atoms within a given segment before the operation become deselected after the operation and vice versa as shown in Figure 2 27 p ti 9 999 DUTP Bend 90 000 af g f pe i Figure 2 27 Inverse Segment Selection example before left image after right image
17. The electrostatic potential overlaid and color coded on the density surface is shown in Figure 3 13 Once the electron density has been displayed the Electrostatic Potential checkbox in the lower left corner of the Orbitals window becomes sensitive this was formerly greyed out compare Figure 3 7 and Figure 3 10 Parallel Quantum Solutions 69 3 3 Vibrational Frequencies window File Options Display Window Help 0 0778 BOOBS LMIB Rotate CMB o00m LMB SHIFT 2 Rotate LMB select double click deselect Figure 3 13 View window electrostatic potential The electrostatic potential in Figure 3 13 is overlaid on the electron density surface by activating the Display Potential checkbox The electrostatic potential is calculated over a grid and smoothly interpolated onto the density surface In the default view the highest potential computed is colored red and the lowest blue with a graduation in color for all values in between If the Linear Scale checkbox is activated then the potential is colored with respect to an absolute scale and there will likely be less graduation of color between high and low relative regions of the potential 3 3 Vibrational Frequencies window The Vibrational Frequencies window shows a simulation of the IR Raman or VCD spectra and allows animation and display of individual vibrational modes 70 PQSMol Manual View Mode h ee AAAA N Infrared Raman ED Zoom Out Halfwidth IDO eee
18. Usage Click on three adjacent bonds to select the torsion angle for adjustment The selected bonds are highlighted and the torsion angle between them is displayed in degrees All atoms connected to the open end of the third selected bond are added to the active group and are surrounded by a gray translucent surface Only the atoms and bonds in the active group are affected by the torsion angle adjustment Drag vertically to change the torsion angle Double click to set the torsion angle Figure 2 8 Bond torsion angle adjustment Tip Press the lt SHIFT gt key while dragging the mouse for more accuracy in setting the torsion 3 Rotate About a Bond tool Adjusts the torsion of three automatically selected bonds The bond selection is based on the rotation bond you select The active group in Rotate About a Bond tool includes all atoms and bonds on one side of the rotation bond as shown in Figure 2 9 In essence this tool twists one part of the molecule with respect to the other around the rotation bond Usage Click on a bond to select the axis for rotation The selected bond is highlighted An adjacent bond is automatically selected on each side of the selected bond The torsion and out of plane bend are displayed in degrees All atoms connected to one end of the axis of rotation bond are added to the active group and are surrounded by a gray translucent surface Drag vertically to change the torsion angle Double click to set the angle
19. angle Double click to set 16 PQSMol Manual Build mode Figure 2 12 Bond fuse example 2 Center on Atom tool Centers the structure with respect to a specific atom Usage Click on an atom All atoms and bonds are shifted so that the selected atom is at the origin of the coordinate system 2 Reorient Selection tool Repositions the current selection with respect to a selected reorient atom It is useful for reorienting molecules relative to one another This tool s behavior depends on the state of the Auto Selection mode With Auto Selection mode enabled the entire segment containing the selected reorient atom is automatically selected for reorientation With Auto Selection mode disabled you must first manually select atoms and bonds to reorient and then use the Reorient Selection tool to select the reorient atom and reorient the selection Although an extra step is necessary with the Auto Selection mode disabled this method allows segments or individual unconnected atoms to be repositioned about any given reorient atom not necessarily contained in the segment itself Usage Select an atom to be the reference point for reorientation The atom is highlighted with a green translucent sphere In the Auto Selection mode all atoms and bonds in the selected atom s segment are added to the active group Drag the mouse vertically and horizontally to reposition the atoms and bonds in the active group Drag the mouse while p
20. e e i 4 19942 Y S20671 z 0 0000 Auto Torsion ON Auto Selection ON Force Field Sybyl5 2 DEFAULT LMEJ Rotate LMB SHIFT 2 Rotate RMBJ Insert Attach CMB Zoom CMB SHIFT Select RESTRICTED Figure 2 2 The Build window 6 PQSMol Manual Build mode 2 1 1 Toolbars The majority of actions available in PQSMOt are accessible through the two toolbars in the main window Each toolbar button has an icon and a tooltip to identify its action The top toolbar contains buttons for simple tools that require no interaction with the Build window The bottom toolbar groups more complex tools that often require multiple clicks in the Build window to complete their function Information for each of these tools is displayed in the statusbar at the bottom of the Build window Buttons with a dark triangle in the lower right corner have options available through a drop down menu To access the menu right click on the button Tip To show any button s tooltip move the mouse pointer over the button Simple action toolbar Simple single click tools in PQSMOL are grouped in the top toolbar Figure 2 3 Simple action top toolbar Buttons from left to right are H Hydrogen Fill Fills all free single valencies vacant single bonds capped with green translucent dummy atoms with hydrogen atoms El Optimize Performs a geometry optimization on the current structure using the currently sel
21. gt gt Files F anthracene OMe F anthracene OMel F anthracene lOMe1 F anthracene lhMe F anthracene Obie F anthracene Ohe F anthracene OMe Tutorials basis basisd Control F anthracene OMe1 F anthracene OMe1 F anthracene OMe inp log Anos Out SYI coord deriv hess ie F anthracene OMe F anthracene Olde e basis F anthracene Oldee basis Documents F anthraceane kde control nul selection rhomerpawekl TESTS TUTORIALS nmr_capturel jpgl Figure 4 62 Save dialog naming the NMR spectrum image This completes the first part of this tutorial At this point we have obtained and saved as a JPEG image the simulated 19 F NMR spectrum of perfluoroanthracene We will now build the various methoxy substituted derivatives and obtain their NMR spectra 4 3 5 Building 1 Methoxy Perfluoroanthracene Step 9 Import the prebuilt perfluoroanthracene Start the builder by typing pqsmol at the the command prompt As we have already constructed and optimized the geometry of perfluoroanthracene we can start with that Select the File Import menu item Figure 4 63 Parallel Quantum Solutions 125 4 3 Example 3 Methoxy Substitution in Perfluoroanthracene wis Edit Build Optimize Symmetry Display Calculation Window Help CA EEE ae eji Open Existing Ctl O ingot Dave Ctl S Save As uit Building Blocks Fragments Clipboard Sybylo Force Field Bond Configuration
22. 10 Vectors Reverse Animate 11 F Figure 3 14 Vibrational Frequencies window The default view shown in Figure 3 14 is the simulated IR spectrum with peak height obtained from the computed IR intensities The peaks are fit using a Lorentzian function with half width controlled via the sliding bar bottom right The lowest and highest frequencies have their wavenumbers displayed in green at either end of the wavenumber axis Individual vibrational modes can be displayed and or animated either by selecting a specific frequency from the list to the right or clicking on the actual signal line in the simulated spectrum The most intense signal in the spectrum selected in this way is shown below Figure 3 15 The mode being displayed is highlighted in red or indicated by a small red arrow in the frequency window if the mode has a relatively low intensity au I i Mh Ih d Y Yu a e Infrared Raman YC Zoom Out Halfwidth 10 00 dz jv vectors Reverse Animate 44 Figure 3 15 Vibrational Frequencies window mode 39 selected The Vectors checkbox turns on the displacement vectors which are displayed in yellow in the View window Figure 3 17 The entire structure including the vectors can be rotated as usual by dragging the mouse in the View window The direction of the arrows can be reversed by selecting the Reverse checkbox in the vibrational spectra visualization window and the vibration can be animated by selecting
23. 2 2 Creating a PQS input file 4 23 Submitting a PQS job 4 2 4 Visualizing the PQS job output PQSMol Manual CONTENTS 4 3 Example 3 Methoxy Substitution in Perfluoroanthracene aa eee 111 4 3 1 Building Perfluoroanthracene e a oaoa a de A 112 Az Creatine a POS mpat files r p 4 444 a sedalets dh e a aip aa eee ES oe Oe SE a SS SS 118 ads Submit a POS JOR si see oe ee A Oe ee AAA E A ee Ee a 120 4 3 4 Visualizing the PQS job output 24206500 dec eee aco eo bes amp a ts BRS Be ES 121 4 3 5 Building 1 Methoxy Perfluoroanthracene a 125 AO Nistanzine the POS TODGUBDUL goa serea aa e da a a a ds a aTa A 133 4 3 7 Building 2 and 9 Methoxy Perfluoroanthracene and Visualizing the PQS job outputs 135 4 3 8 Comparing the NMR Spectra of perfluoroanthracene 1 2 and 9 methoxy perfluoroanthracene 137 List of Figures 139 Index 146 Parallel Quantum Solutions 111 Introduction PQSMOL is the graphical user interface that can be used in conjunction with the PQS ab initio program It contains a model builder with two built in molecular mechanics force fields together with options for job input preparation job submission serial or parallel and post job visualization and display The latter includes visualization of molecular orbitals canonical localized and natural electron densities and electrostatic potentials optimization history energy geometry at each cycle of a geometry optimization dyn
24. 22 View window vibrational mode 1 displacement vectors aoa oo e a e a a 96 4 23 Vibrational Frequencies window IR spectrum mode 24 selected 0 0 a 0 97 4 24 View window highest intensity vibrational mode 24 displacement vectors 0 8 4 97 ADS WE UII La eo odo Ge See es a Een Hh em Saeed e Se cere a ok GA a te a Ue Ee onto E Be see ek wet Gee 1 98 4 26 Build and segment windows inserting the tetrahedral carbon building block 99 4 27 Segment window fluorine building block selected 2 0 0 0 2 ee e 100 4 28 Build area attaching the fluorine building block 0 0 0 a 0 00000 2 eee ee 100 4 29 Build and segment windows attaching the Chlorine building block ooo a a a a a 101 4 30 Geometry optimization results e Ll ed de e woe Se Be ee Sree EC aca a BAe eed EES SG 102 4 31 Symmetry results dialog de be e ee Ae Ge ke oe Seg BM oe ca We ee ee Se BE SS 102 AL OVE IO weenie we or eee a OS ae EA oo we te Ge A oo SAS 103 4 33 Job parameters window complete input file 00 0 ce 104 4 34 Job submission confirmation dialog vcd eo Pa eee eS Re Ee ARN URE ee a GS 105 Ao ao AP BD ie Ew ee pete a eee ee le ee EE ee es 105 A530 View window Ibal display waneci ase ea aa RE OS Ee ee AG ae ee Se SEES 106 4 37 Orbitals window electron density selected 107 4 38 View window electron density displayed 108 4 39 Vibrational Frequencies wind
25. Acacia Cel Pry Hdi Pin Smi Euj Gdi Tb Dy Hal Er Tm Yo Lu ee ee ea We eli x Cente THE Er a a rae Torsion ON Auto Selection ON Iza Field DIA DEFAULT LMB Rotate LMB SHIFT Z Rotate RME Inser Attach CMB Zoom CMB SHIFT 5elect CMB CNTRL Move RESTRICTED Figure 4 63 Build window importing an existing structure into PQSMoL The Import Geometry dialog Figure 4 64 will open allowing various file types to be imported We are going to import the final converged geometry of perfluoroanthracene which is available in the coord file F anthracene coord In the File Filter dropdown list select coord coordinates and select the file F anthracene coord from those shown in the Files list Note As all jobs for this tutorial have been run in advance the coord files for all structures are already available normally of course only the coord file for perfluoroanthracene the job run in the first part of this tutorial would be present 126 PQSMol Manual Tutorials Create Dir Delete File Rename File homelpawelfTESTS TUTORIALS _ Directories h Files i F anthracene OMe1 coord we F anthracene OMde coord Home F anthracene OhMe9 coard A F anthracene coord Desktop G Documents File Filter coord coordinates Ki l inp PGS input selection homer pab PGSMol builder pas PGS input coord coordinates 1390 PGs T
26. Auto Selection building mode is active PQSMOLt automatically selects the entire affected segment during the move and reorient operations Figure 2 40 right image Figure 2 40 Move operation with Auto Selection off left and on right The move operation will only modify atoms which are currently selected If the Auto Selection mode is inactive and no selection is made move will have no effect on the structure in the Build window However in this mode it is possible to make custom selections which do not involve all atoms in a given segment This is illustrated in the left image of Figure 2 40 where only the center Carbon atom is selected and moved Note The Auto Selection option affects the move and reorient selection operations only 2 3 3 Restricted Unrestricted There are two restriction modes available in PQSMOL restricted and unrestricted The two modes control the amount of freedom you have when constructing molecules The restricted mode is the default mode of operation In this mode molecules can be constructed using only the well defined building blocks that are recognized by either the Sybyl5 2 or the UFF force field see Figure 2 41 left image This ensures that any molecule that is built can in fact be optimized using one or the other of these force fields Parallel Quantum Solutions 39 2 3 Building Modes You can select the restriction mode through the Build Mode menu A quicker way of changing the current
27. Force Field Bond Configuration Universal Force Field Bond Configuration Cel Pr Mdi Pri Smi Eul Gdi TEI Dy Hol Eri Tmi by Lu Th Pa U Ne Puf Am cn P Ce ES Fn a No ir Figure 2 34 Segment window with the Sybyl5 2 force Figure 2 35 Segment window with the Universal force field selected field selected If the current force field is changed the bond configuration list changes to contain all the building blocks for the current atom in the current force field Also the periodic table changes activating only the buttons for the elements defined in the current force field Note the difference between Figures 2 35 Sybyl5 2 and 2 35 Universal As the Universal force field Parallel Quantum Solutions 35 2 2 Segment window covers essentially the entire periodic table there are many more atom types a total of 126 than for the Sybyl force field Note that although all elements are covered in UFF many metals must have a well defined coordination usually octahedral or they will either not be properly recognized or distort significantly if a geometry optimization is attempted In particular UFF simply does not recognize a trigonal bipyramidal configuration around a central atom On the other hand although the Sybyl force field has far fewer atom types there are default values for most parameters and it can be used even for atoms for which it was not originally defined In these cases equilibrium bond lengths and
28. Optimize mmetry Display Calculation window Building Blocks Clipboard Sybyl5 2 Force Field Bopd Configuration es 5 g He c lope a sla eal s ce iy Y Cr Mn Fel Coli Cul zni Ga Ge As Ree BR kr leer v zl rel la a car nl 6 Ive C3 Ba La HF Tal Re 05 tr Pe Aul Hal Ti Pb Bi PAA Ra Ee Ra Ac RF nb Sal Bh He He Cel Pri Nd Pm Smi Eul Gd Tb Dy Hol Eri Tmi byL Th Pal Ne Pul nf cf k cr Es Fn Hc No tr building blocks fragments clipboard build toolbar statusbar build area build window segment windo Figure 2 1 PQSMol executing in build mode The main window is divided into two vertical frames One frame contains the Build window labeled in red and the other the Segment window labeled in green The Build window contains a menubar purple simple action toolbar olive the Parallel Quantum Solutions 2 1 Build window build area yellow the build toolbar brown and the statusbar blue The Segment window provides access to a set of basic building blocks a library of fragments and a clipboard The Building Blocks tab the Fragments tab and the Clipboard tab are labeled in black The Segment buffer which displays segments to be inserted into the build area is labeled in orange 2 1 Build window File Edit Build Optimize Symmetry Display Calculation Window Help a
29. PVM can be deleted by clicking the Reset PVM button Old scratch files for the current named job can be removed on all nodes in the cluster by clicking the Tidy Job button see the PQS Manual for more details To prevent accidental interruption of an executing job several checks are performed before stopping PVM daemons Figure 2 60 shows the dialog window displayed when the Reset PVM button is clicked while PQS jobs are executing on any of the nodes in the cluster The dialog window in Figure 2 61 is displayed when the Tidy button is clicked while PQS jobs are executing 54 PQSMol Manual Build mode There are POS jobs which use PYM currently There are executing POS jobs Tidying executing Resetting PVM kill these jobs the job may interfere with these jobs Are you sure Are you sure Cancel YES Cancel Yes Figure 2 60 PVM reset warning dialog Figure 2 61 Tidy job warning dialog Removing a node from the PVM by clicking on the Toggle button of an active PVM node while a PQS job is running produces the dialog window shown in Figure 2 62 Also if a PQS job is scheduled to run in the queue and the nodes are removed from the PVM either by resetting the PVM with the Reset PVM button or by stopping a PVM daemon with a Toggle button the dialog window in Figure 2 63 is displayed There are jobs in the SGE queue A PYM Pals job is currently executing stopping PYM will interfere with ary stopping PYM will Kill the job queu
30. and to locate atoms that are symmetry equivalent within the given threshold The higher the threshold the more likely that symmetry will be found however setting the threshold too high may find symmetry that is really not present Setting the threshold to a value greater than 1 0 is not recommended 2 6 PQS Calculation The procedure for running a PQS calculation involves the following steps building a molecule creating a PQS input file submitting the PQS job e displaying calculation results 2 6 1 PQS input file The PQS input file contains the geometrical structure and a series of commands instructing the program to perform calculations on the given structure PQS input files use a set of specific keywords and a strict syntax PQSMOt assists in creating PQS input files through the Job Parameters window The Calculation Job Input menu item opens the Job Parameters window Figure 2 51 Note If the structure in the Build window the system you are about to do the calculation on has not previously been saved as a pqb file you will be prompted to save it as such with a default filename corresponding to the empirical formula 46 PQSMol Manual HEH 5 Build mode Job specifications TEXT Test Job GEOH Pos tn h o 407424 O 2398720 o 5520390 Title Test Job Memory 4 in Oo 270075 0 093703 o 020224 c Oo 367478 1 121867 0 052592 a T 1 595360 1 013542 0 954924 Molecule Characteristics o 2 389140 0 092516
31. atom of selected element type All bonds to that atom will remain as they were both with respect to distance and angles x Add Valence tool Adds a free valence to an atom allowing another bond to be formed to that atom The new bond will be automatically positioned as far away geometrically from any existing bonds up to three as possible Once four or more bonds are already present the new bond will be placed in the same location every time and will have to be moved into an appropriate position When the free valence is in place other building blocks can be added to it using the Add Attach Connect tool Usage Click on an atom to add a valence A new bond capped with a dummy atom is added to the selected atom Drag the mouse horizontally and or vertically to rotate the new bond along the X and Y axes respectively Press the lt SHIFT gt key while dragging the mouse to rotate the bond about the Z axis i e out of the plane of the Build window Figure 2 20 Add Valence example Note This tool is only available in unrestricted mode Remove Valence tool Removes monovalent atoms and their valencies Usage Click on any monovalent atom to delete it from the current molecule Note This tool is on ly available in unrestricted mode Bond Type tool Changes the bond type for a bond Parallel Quantum Solutions 21 2 1 Build window Usage Click on a bond to change its type Each click will advance the
32. basis set selection is required and the desired semiempirical method can be selected from the corresponding pulldown menu Note that the Properties that can be selected depend on the calculation type and unavailable properties are grayed out For semiempirical wavefunctions most of the properties can no longer be selected The window containing what will become the input file can be edited by hand Simply move the mouse pointer to the desired location in the window click and start typing Note that anything typed in may be deleted if further selections are made in the left hand window so you should only edit the input file when you have made all the major job selections 2 6 2 Job submission Once the input file has been prepared the Calculation Submit Job menu item will submit the job This will be serial only and will run in the background If so configured PQSMOt may also submit parallel jobs to run in the background or to a queuing system such as SGE DQS or PBS see following subsection 50 PQSMol Manual ai ri F co coco JL etr Loe 12 h 1 433292 O 733391 13 h 1 446642 0 512032 Point Group Cl Energy is O 1612265555 gradient converged in Hessian Updated using BFGS Update 6 cycles Humber of degrees of freedom 33 33 Hessian modes will be used to form the next step Hessian Eigenvaluest Oo oo 950 O01 962 0 002555 o c45614 oO 202285 oO 905 711 0158137 0 159592 0 160151 0 182416 0 196357 0 245254
33. bond type to the next element in the following list Single Double Triple Amide Aromatic O single Double O Triple O Amide o Aromatic 2 1 2 Menu At the top of the PQSMoL main window is the menubar Figure 2 21 Almost all of the functions of PQSMOL are available by activating the appropriate menu item The functions have been grouped according to their type File Edit Build Optimize Symmetry Display Calculation Window Figure 2 21 The PQSMol Menubar in build mode The File menu The file operations have been grouped into the File menu eile Edit Build Optimize Symmetry Display Calculation Window Build Mew Qpen Existing Cil O impor Dave Ctl s Dave As IT e Build New starts a new build project If the currently edited structure has been modified since the last save operation you are presented with the Save Changes dialog Figure 2 22 The Save button in the dialog saves the 22 PQSMol Manual Build mode current molecule If the project is untitled the Save As dialog is displayed The Ignore button in the dialog causes the last changes in the edited molecule to be lost The Cancel dialog button cancels the operation Do you want to save changes to untitled Save Ignore Cancel Figure 2 22 Save Changes dialog e Open Existing opens an existing build file The File Open dialog Figure 2 23 lets you browse directories for a specific file The file list is filtered so that only t
34. frequencies of the molecule 30 in this example Select the first frequency A small red arrow appears under the corresponding frequency in Parallel Quantum Solutions 95 4 1 Example 1 Lactic Acid the vibrational spectrum and details for that mode appear in green font at the top of the window mode number symmetry frequency and intensity This mode is primarily a twisting about the C O bond and has a low intensity that does not show up in the simulated IR spectrum Now activate the Vectors checkbox in the bottom left corner of the window as shown in Figure 4 21 This will show the atomic displacements in the vibrational mode 1 as yellow vectors at each atom of the structure in the View window Figure 4 22 Activate the Animate checkbox to animate the structure by showing the motion in the vibrational mode 1 File Options Display Window Help 1 MB Rotate CMB Zoom LMME SHIFT Z Rotate M Lal Select double Click deselect Figure 4 22 View window vibrational mode 1 displacement vectors Other vibrational modes can be selected from the list at the right side of the Vibrational Frequencies window or by directly selecting the peak in the simulated spectrum 96 PQSMol Manual Tutorials 20 A MA In Al tae y L ath Hl z Infrared Raman YOO
35. geometry changes are displayed Note that redisplaying the geometry does take some time especially for large systems and too small a value will cause a noticeable slowdown in the apparent speed of the optimization 2 4 3 Force Field Symbols Geometry optimization is performed based on the force field atom type assigned to each atom The Sybyl5 2 force field has 33 atom types defined for the following elements Carbon Nitrogen Oxygen Sulfur Phosphorus Hydrogen Bromine Chlorine Fluorine Iodine Sodium Lithium Potassium Calcium Aluminum and Silicon Depending on the number of bonds and its environment an atom of one type may be represented by multiple force field symbols For example available Carbon Sybyl force field types are C 1 C 2 C 3 C ar The basic building blocks and the fragment library in PQSMoL contain molecule segments with correct force field types defined for both Universal and Sybyl5 2 force field However when building molecules from fragments imported from foreign file formats PQSMoL will attempt to guess the force field types for the atoms in the imported geometries You can manually change the assigned force field symbol of each atom in the molecule by selecting Optimize Check Atom Types in the main menu Parallel Quantum Solutions 43 2 4 Optimization Force Field Symbols Atom Type syaylae HI H hydrogen Ne ALS nitrogen spa Ca Ey carbon spo C4 C carbon spe Oo O 2 ox
36. implies is for building a new molecule or modifying an existing one View mode is for visualization of already computed quantities Structures read into PQSMoL in view mode cannot be modified Parallel Quantum Solutions 1 1 1 Starting PQSMol In view mode there is one main View window and several additional windows for displaying various properties In build mode there are two the main Build window and the Segment window The latter provides access to the various fragments and building blocks from which new molecular structures can be constructed As well as using predefined fragments you can build your own fragments and store them for future use Within build mode you can choose either restricted mode the default or unrestricted mode In restricted mode molecules can be constructed only using well defined building blocks that are recognized by either of the two available force fields this ensures that any molecule that is built can be optimized using one or the other of these force fields In unrestricted mode all generic structural motifs are accessible for any atom in the periodic table Additionally one can add and delete valency bonding to any atom increasing or decreasing the number of bonds that can be made to other atoms The nature of a bond single double aromatic etc can also be changed In other words you can build just about anything However the downside is that once you have switched to unrestricted
37. line representing the energy level of the 24 orbital is highlighted in red see Figure 4 18 92 PQSMol Manual Molecular Localized Matural e Alpha Alpha Matural Beta Beta Energy Levels Closed Shell Orbial424 Energy 0 43 Isosurface level Cross sections Electrostatic Potential Default View Full Wiew hic a GFF Elect dd da oe 3 30 eg c EJ 6 eo Ll 24H ed ce e 0 13 16 14 0 050000 1 000 1 000 1 000 Display Potential Linear scale Figure 4 18 Orbitals window HOMO selected Tutorials The corresponding view window displaying the HOMO is shown in Figure 4 19 Move the Isosurface level slider to change the isosurface displayed in the View window Also experiment with the Cross Sections sliders to produce various display results Parallel Quantum Solutions 93 4 1 Example 1 Lactic Acid File Options Display Window Help LMIB Rotate CMB oo0m LMB SHIFT 2 Rotate LMB select double click deselect Figure 4 19 View window HOMO displayed Select other molecular orbitals in the list to see their display in the View window Try changing the default settings in the Display Orbital submenu in the menu at the top of the View window including changing the grid resolution under Display Orbital Grid Resolution Step 13 Save a screen shot from the View window Once you have produced a publication quality image in the View wi
38. mode there is no guarantee you will be able to optimize the geometry of your system as many atom types may no longer be recognizable by the force fields The basic idea then is to build your system using a combination of well defined atom types or building blocks and predefined structural fragments optimize the structure using either of the two available forcefields possibly symmetrize the resulting geometry and then prepare the input for and submit a PQS job The job can be submitted either in serial or parallel in the background or to a job queue depending on what options are available on the particular machine When the job has finished various results can be visualized If you are already familiar with existing model builders such as SPARTAN PCModel or MAESTRO then you should have no difficulty in using PQSMOL which is fairly intuitive Build commands are accessed via drop down menus and toolbars you need a three button mouse right left and center mouse buttons are all potentially active The plan from here on is to describe all of the build visualize tools available in PQSMot and how to use them The vast majority are accessed through various buttons in either the upper or lower toolbar in the main Build View window The icons have some pictorial relationship to the actual function they represent and simply positioning the mouse pointer over a button will display a tooltip with a brief description of its function
39. oom Out Halfwidth 10 00 Vectors Reverse Animate Ii Figure 4 23 Vibrational Frequencies window IR spectrum mode 24 selected File Options Display Window Help LMB Rotate CME Zoom LMB SHIFT Z Rotate LME Select double click deselect Figure 4 24 View window highest intensity vibrational mode 24 displacement vectors Figure 4 24 shows the displacement in the most intense IR mode 24 and Figure 4 23 shows the corresponding Vibrational Parallel Quantum Solutions 97 4 2 Example 2 CHFCIBr Frequencies window with the peak highlighted in red 4 2 Example 2 CHFCIBr Our next example is simple to build The molecule is CHFCIBr Figure 4 25 Figure 4 25 CHFCIBr This system is chiral and we are going to calculate and examine its VCD spectrum This involves both an NMR and a standard Hessian computation enabling both the IR and NMR spectra to be simulated as well 4 2 1 Building CHFCIBr Step 1 Start the builder by typing pgsmol at the command prompt As shown in Figure 4 25 the whole molecule consists of 4 atoms with the tetrahedral carbon in the center We will start with this carbon Step 2 Insert the tetrahedral carbon building block When PQSMozL is first started the default current element is carbon The current element is displayed in large font above the periodic table in the Segment window and the current element s button is highlighted with a green background There m
40. or Beta spin canonical orbitals Alpha or Beta spin localized orbitals or Natural orbitals The default is alpha spin canonical orbitals In the example shown in Figures 3 7 and 3 8 the system aspirin is closed shell and so there is only one possibility and the other orbital types are greyed out The actual orbital to be visualized can be chosen either by selecting the orbital number in the list probably the easiest or by clicking on the desired energy level in the graph Due to the fact that in the default energy scale many orbitals are close together it is often difficult to select an orbital for display from the energy level graph There is a zoom option that expands the energy scale in a selected region allowing individual orbitals to be separated and selected 66 PQSMol Manual View Mode For example selecting the HOMO for display produces the image in Figure 3 9 in the View window File Options Display Window Help sepa elrjajil Wulo Jul _ILMB Rotate CMB Zoom LMBI SHIFT Z Rotate LMB Select double click deselect Figure 3 9 View window HOMO orbital displayed The size of the orbital lobes can be changed using the sosurface level slider bar in the Orbitals window Using the Cross Sections slider bars in the X Y and Z directions in that order cuts off the o
41. selecting the Reorient Selection tool 2 and clicking on any atom in the benzene fragment the atom will be highlighted with a green translucent sphere and the fragment can be reoriented by dragging the mouse vertically The result is shown in Figure 4 48 114 PQSMol Manual Tutorials File Edit Build Optimize Symmetry Display Calculation Window Help al ei i a E el F K i it a i ES J pe pi M 1 8054 Y 101371 z 7 9964 Auto Torsion ON Torsion EI Selection ON Force Field ield SybyI5 2 RECRIENT SELECTION LMB to select the rotation origin LMB s8 Rotate LMB SHIFT 4 Rotate RESTRICTED Figure 4 48 Build window reorienting the benzene fragment Step 4 Fuse the naphthalene and benzene fragments Select the Bond Fuse tool Click on the approximately vertical ring bond in the naphthalene fragment closest to the benzene Click on the corresponding bond in the benzene fragment The two rings will be fused at the selected bonds When the segments are fused the newly fused bond is automatically defined as a rotation bond and designed with a white torus Figure 4 49 Parallel Quantum Solutions 115 4 3 Example 3 Methoxy Substitution in Perfluoroanthracene File Edit Build Optimize Symmetry Display Calculation Window Help i ge p 25 641 OUTF Bend 1 6 198 x 0 07809 Y 4 60401 z 5 73193 aaa Torsion ON Auto Selection ON DE Fie
42. tetrahedral carbon building block Confirm that the tetrahedral carbon building block in the Bond Configuration frame is still selected Attach the building block to the structure in the build area by moving the mouse over the lower right dummy atom of the structure The a atom will be highlighted with a circle surrounding it and the cursor will change to A indicating that this atom is a valid attachment point Figure 4 5 left image Press the left mouse button over the the atom to attach the building block Figure 4 5 right image Figure 4 5 Build window attaching the second tetrahedral carbon building block Step 4 Attach the Carboxyl functional group Click on the Fragments tab in the Segment window and then on the FUNCTIONAL GROUPS tab Select the carboxyl fragment in the list on the left side of the window The carboxyl functional group appears in the Segment buffer Click on the left most hydrogen atom in the group to set it as the attachment point for the fragment The Segment window should now look like the one in Figure 4 6 84 PQSMol Manual Tutorials Building Blocks Fragments Clipboard AMINGO ACIDS alkene alkoxy BIC YCLIC alkyne amide amino FUNCTIONAL GROUPS anhydride cis anhydride trans carbonyl LIGANDS Carbo cyano MONOCYCLIC hydrazone hydroxyl NUCLEOTIDES CHAINS nitra FOLYCYCLIC ome sulfone SOLYENTS sulfonic sulfoxide SUGARS ORGANOMETALLICS Ts USER
43. the Animate checkbox Parallel Quantum Solutions 71 3 3 Vibrational Frequencies window Infrared Raman VCD Zoom Gut Halfwidth 10 00 42 Vectors Reverse animate 44 Figure 3 16 Vibrational Frequencies window zoom around the selected mode 19 To zoom in on a specific frequency region position the mouse pointer ins the graph of the vibrational spectrum and drag the mouse the center mouse button over the region Dragging the mouse horizontally changes the frequency range and vertically changes the intensity scale An expansion about the group of low intensity signals in the left part of the IR spectrum is shown above Figure 3 16 To return to the full frequency and intensity ranges spectrum press the Zoom Out button To change the currently displayed spectrum select one of the three radio buttons labeled Infrared Raman and VCD in the bottom left corner of the Vibrational Frequencies window Note that if polarizability derivatives have not been computed i e there are no Raman intensities available then all Raman active modes are given the same intensity in the simulated Raman spectrum 72 PQSMol Manual View Mode File Options Display Window Help spa etel amall LMEJ Rotate CMB Z lt 00m LMEJ SHIFT 2 Rotate LMEJ elect double click deselect Figure 3 17
44. the PQS job output When the job is finished PQSMOL is automatically started in View mode with the job s output file as an argument Figure 4 36 Note You can also start the job visualization via Calculation Visualize Output menu item in the Build window menubar File Options Display Window Help elba ali Wi ES Aaa olas LME Rotate CMEj Zoom LMB SHIFT Z Rotate LME Select double click deselect Figure 4 36 View window initial display Step 10 Examine the electron density Press the Orbitals button Ll in the toolbar at the bottom of the view window to open the Orbitals window Figure 4 37 The graph on the left side of the window shows the the energy levels for the individual orbitals The orbital list on the right contains the calculated orbitals By default the list and the graph are limited to displaying orbitals from an energy level of 2 5Ev and no more than the first 10 virtual orbitals To display all calculated orbitals press the Full View 106 PQSMol Manual Tutorials button The Default View button toggles back the default orbital range In the list on the right select Elect ron density item as shown in Figure 4 37 Molecular Localized Matural e Alpha Alpha Matural Default View Beta Beta Full jas Energy Levels Moe Closed Shell OFF 44 43 de 4 40 ag db ae 36 du L dd H dd de a1 30 J eb m Isosurface level 0 050000 Cr
45. transition states they should not be optimized in the builder as neither force field is capable of handling transition structures 36 PQSMol Manual Build mode Building Blocks Fragments Clipboard Building Blocks Fragments Clipboard g al IS g g _A AAAA AMINO ACIDS Import Geometry From al ae ASN asp CHAINS B ALA FUNCTIONAL GROUPS C SH CYSSC HETEROCYCLIC GABA LIGANDS GLN GLU MONOCYCLIC GLY HIS MUCLECTIDES Save Fragment As EU PIC YENE phenollpat Add To Lib LYS SOLVENTS MET ME SUGARS PHE ORGANOMETALLICS PRO S H PRO TS SERIF USER LIB Figure 2 36 Segment buffer with the Fragments tab Figure 2 37 Segment buffer with the Clipboard tab se selected lected The actual fragments available under each category are accessible in a list on the left side of the window Fragments selected from the list appear in the Segment buffer As shown in Figure 2 36 when the Fragments tab is first selected the first available AMINO ACID alanine is displayed Note the circle around one of the atoms nominally a hydrogen atom This is the attachment point for the fragment It indicates where the new bond will form if the fragment is attached to an existing structure in the build area The attachment point can be changed by clicking on another open atom in the current fragment 2 2 3 Clipboard The Clipboard tab allows you to manipulate segments copied or cut from the Build window When a copy o
46. tzvp_ahl OPTImize SCF DFTPF E3LYP FORCE JUMP HHF HESS FRELI anthracene O 005 O Oooo D y oO O Ogio oO Ogg OO O Oooo oO ogg OO O Oooo O ADO O O D p OO O Oooo OOO ADO O Oooo D y oO O Ogg D p OO OPT FREQ 2 4323335 3 643256 3 643256 2 433335 1 216418 1 216415 LALALA ALA LALALA 2461604 2461604 2 461604 4 195495 4 195495 2 461604 0 000000 A 4 795495 4 195495 36432506 36432506 2433335 1 216415 1 216418 2433335 EP d HIIIILIIITLII richs HHR 1 394623 O 697640 O 697640 1 294623 O Poon a2 O 7OO592 1 393336 1 393336 2 roogi 2 725457 2 rendir 1 362835 1 462535 2 7 25457 2 20062 2 2o06 1 362835 1 362835 O 697640 0 697640 1 494623 OD OOO 1 394623 Figure 4 54 Input generation window finished input Press the Done button to save the changes to the input file 4 3 3 Submitting a PQS job Step 7 Submit the PQS job Once the input has been prepared select the Calculation Submit Parallel Job menu item Figure 4 55 Note The Calculation gt Submit Parallel Job menu item is only active in parallel installations of the PQS ab initio package If you do not have a QuantumCube or other parallel system this option will be greyed out and the job will have to be submitted in serial mode however all the jobs in this example have been run in advance and all output files should be avail
47. will be prepared ready for job submission However all the output files have been included on the PQSMoL CD so there is no need to actually run the jobs Before starting the tutorial you should create a test directory and copy all the files in the directory TUTORIALS EXAMPLE3 on the CD into this directory Change directory into this test directory before starting the tutorial 4 3 1 Building Perfluoroanthracene Step 1 Start the builder by typing pgsmol at the command prompt First we are going to construct the parent compound perfluoroanthracene This comprises three fused aromatic rings and we are going to build this from two existing fragments benzene in the MONOCYCLIC fragment library and naphthalene in the BICYCLIC fragment library Step 2 Insert the naphthalene fragment In the Segment window select the Fragments tab then select BICYCLIC Scroll down to select naphthalene Insert the Naphthalene fragment into the build area either by using the Default tool and right clicking or by using the Add Attach Connect tool At this point the Build window is shown in Figure 4 46 112 PQSMol Manual Tutorials File Edit Build Optimize Symmetry Display Calculation Window Help Building Blocks Fragments Clipboard AMINO ACIDS azulene pof bicyclo 2 1 0 pentane paf BIC CLIC BICyclo 2 2 D hexane pot IE e i ai bicyclo 2 2 1 heptane pot SRAI hicyclo 2 22 octane pqt FUNCTIONAL_GROUPS bicyclo 3 1 0 hexane p
48. window finished input a a a a a a a e a a 120 Parallel Job Duoni somde de ata ee ee des A dadas eo 121 View window perfluoroanthracene job visualization e e a e a e 122 NMR window Initial F NMR spectrum of perfluoroanthracene o 123 NMR window F NMR spectrum with zero halfwidth 123 NMR window F NMR spectrum using CF3Cl as referente 123 NMR window F NMR spectrum with modified range 124 NMR window Capturing an image of the F NMR spectrum 124 Save dialog naming the NMR spectrum image 125 Build window importing an existing structure into PQ MOL 2 000048 126 Import dialog importing a coord file into PQSMOL 0 0 0 00000000040 12 Import info dialog geometry imported with an existing pqb file 2 127 Import info dialog geometry imported without an existing pqb file 2 00 4 128 Build window perfluoroanthracene imported into the Segment buffer 128 PQSMol Manual LIST OF FIGURES 4 68 Build window perfluoroanthracene inserted 2 a a a a e a a e a a 129 4 69 Build window bent oxygen building block selected o 0002 eee ee 130 4 70 Build window perfluoroanthracene with the oxygen building block attached at position 131 4 71 Build window attaching the tetrahedral carbon building block 0 0 0
49. 0 3359505 O 436047 0 439659 0 5 5651 Oo 5795 72 Oo 9 A Minimum Search Taking Simple RFO Step Searching For Lambda that Minimizes Along All modes Build mode Value Taken Lambda O O0Q00004 Step Taken Stepsize is 0 001694 Hax imum Gradient ALA OLS Fo Displacement OOOO Energy change C OA Transforming Internal Coordinate Hessian to Cartesian Coordinates Hessian Transformation does not Include Derivative of B matrix Optimize memory status memory needed 115582 high water Hemory status request number high water Total master CPU time Termination on Thu Hay 18 11111142 20065 2 memory marks Charges O Hultiplicity 1 davePFunctioni Semiemp pm Basis sett pm Energy ist O 161226559 au dipolerD 0 01 Elapsed Total master CPU time Termination on Thu Hay 18 11111142 2006 115661 total available memory 0 01 Elapsed 0 35 7549 O 946359 0 460 44 total Output File Ha NI 0 306672 1 190710 0024525 0 046 799 Oo 042564 0 O56262 0 962637 O la4653 O 160497 O 166734 0 173745 0 234550 0 341597 0 335031 0 45 7385 O 421016 0 445950 Tolerance Chvgd E Og YES KI Gg HO Ad YES 115661 total available memory 500000 od GoL min Log File h 1 111630 Figure 2 55 Job Output window Following job submission the Job Output window Figure 2 55 will automatically open displaying both the output file upper window and the summary log file lower window Both o
50. 0 849092 c 906822 0 984464 0 953780 e ity ge h 4 215465 0 231304 1 641264 Charge oymmetry 0 00001 Multiplicity 1 o 1 seeE26 11983719 1 846167 h 2 564658 1 823204 2 3389732 h 1 804127 1 043448 0 319455 Calculation Type hi 0 360849 2 115796 0 337087 h 911296 013535 1 472485 E z h 0 947723 1 787119 1 706885 single Point Energy select type PIEEEELLLLL STEP A ILILILILIL ae BASIS 3 219 Geometry Optimization DFT Y OPTI mize SCF DFTP 03L P Select type FORCES Basis SetimMethod semiempirical JUMP Basis Set 321g Dartree Fock DFT method O3L YP MP2 semiemp method PRs of Properties Vibrational Frequencies Electric Field Gradient Population Analysis NMR Chemical Shifts COSMO ChargerSpin Density Figure 2 51 Job Parameters window calculation type Initially just the current geometry will be displayed in the input file in the text area on the right Filling in various options in the window on the left will add lines and keywords into the input file for example whatever is typed in the Title box will appear just above the geometry in the input file on the right The entries in Job Specifications and Molecule Characteristics require data to be typed in to make changes those in Calculation Type and Basis Set Method involve pulldown menus and those in Properties are simple check boxes Parallel Quantum Solutions 47 2 6 PQS Calculation Job specifications Title T
51. 06 112 113 Dynamics Trajectory 61 64 79 PQSMol Manual INDEX Info 9 10 33 NMR 61 62 64 73 79 123 Optimization History 61 62 64 80 Optimization Options 30 Orbitals 61 62 64 66 69 95 106 108 Segment 2 5 6 8 33 36 40 83 84 86 98 99 112 117 128 129 Building Blocks 6 21 34 36 39 43 86 117 Clipboard 6 8 37 Fragments 6 34 36 37 84 112 129 Symmetry Options 30 Vibrational Frequencies 62 64 70 72 95 97 108 110 View 2 60 62 65 67 71 73 75 77 80 92 96 106 109 111 122 Parallel Quantum Solutions 147
52. 28 4 1 4 2 4 3 4 4 4 5 4 6 4 7 4 8 4 9 4 10 4 11 142 View window electron density 220 E A a ia Ss 69 View window electrostatic potential a e a a a 70 Vibrational Frequencies window 24 240 000 e e A a Eee aa 71 Vibrational Frequencies window mode 39 selected a a a a a 71 Vibrational Frequencies window zoom around the selected mode 19 0048 12 View window motion in the most IR active mode of aspirin ooo oe a a ee 13 NNR window C1 Selected sea A E e Oe ee E A T4 View window C1 selected y 4 4 44 u ados da ee mo oe tee od A OS SR AME EM 15 NMR window O9 selected dd ri ad BY aa a le al lo e a a A me 76 View window 09 Selected 40d rana A a a a e e AR AA id 77 13C NMR Spectrum by selection reference shift o 18 25 NMR Spectrum auto reference shift die de Sno a BR awe Bed be SEES oe OSES ES 78 13C NMR Spectrum user selected 100 reference shift 2 2 o o 78 O NVI SPCCEEUMT ZOOUl4 amp amp Adee ak chee eh eh Pare rl a adds ae 79 179 NMR Spectrum user defined range ooo 19 Dy amics Era jeCbOry WANGOWE s s g A OA secure te Gane eae acct et eee Oe Ee A GS ee a es 80 Optimization History window 42 2444 6444 hboe ee eG GEG RRAD AE PAAA GS OSHS RRB e ela 80 Lactic acid tructure diagramari bee eS Eee ES SSG RK A oe RA EOE EES 82 Lache acid tech arcada ae aaa aaa ds ed a he das te e 82 Segment window with tetr
53. 30 pdb Protein Database mop MOFFAT Cancel Car mat 4 matris hin Out PoS output log PGS log page PGS mol viewer compressed eye AY 4 format Figure 4 64 Import dialog importing a coord file into PQSMoL As the structure is imported into the Segment buffer the dialog in Figure 4 65 should appear When an existing and compatible pqb file is found with the same name as the file being imported PQSMoL will extract forcefield data atom types and connectivity from this file Equivalent pgb file found Bonding and force field symbols read from ihomepawel TESTS TUTORIALS F anthracene pab Figure 4 65 Import info dialog geometry imported with an existing pqb file Parallel Quantum Solutions 127 4 3 Example 3 Methoxy Substitution in Perfluoroanthracene e a corresponding is not found in the same directory as the file to be imported i e Note f ding pqb i found in th di he file to b d you are importing raw structural data then PQSMoL will attempt to derive forcefield data using an internal algorithm The import info dialog in this case would look like the one in Figure 4 66 Connectivity 26 bonds autodetected fusing sybylo 2 FF ovbylo Force Field symbols 4 autodetected Universal Force Field symbols 24 autodetected Figure 4 66 Import info dialog geometry imported without an existing pqb file Press the OK button to import the structure The result is g
54. 9E 04 cphf converged for 7 unique atoms a O c256E O4 O 2399E 04 O 3006E 04 1 05 0 05 F O 5201E 0858 0 2i45E 95 o 4296E 05 cphf converged for 12 unique atoms 3 last iteration with full densi O 0 O 06 F Log File a Ak Pas ibe rey cdot E ea ae ee davefFunctioni RHF Basis sett 3 219 Humber of contracted basis Function 1 Ge Energy ist 33 9 790866654 au dipolerD 1 524451 0 423950 1 508361 total 2 5 96562 Total master CPU time 3 65 Elapsed 34 09 min Termination on Fri Oct 20 d2142156 2006 Figure 4 16 PQS Output window Tutorials Two files produced by PQS are monitored In the top frame the contents of the out file in our example C3H603 out and in the bottom frame the 1og file in our example C3H603 1l0g are displayed 4 1 4 Visualizing the PQS job output Step 11 Visualize the output As soon as the job finishes PQSMoL is launched in View mode in a separate window with the current job output file as an argument producing the window in Figure 4 17 Parallel Quantum Solutions 91 4 1 Example 1 Lactic Acid lle Options Display Window Help LMB Rotate CMB Zoom LMB SHIFT Z Rotate LMB Select double click deselect Figure 4 17 View window initial display Step 12 Examine the calculated molecular orbitals Press the Orbitals button 0 the toolbar at the bottom of the View window Select the HOMO 24 in the list on the right side of the window A
55. Figure 4 56 Parallel Quantum Solutions 121 4 3 Example 3 Methoxy Substitution in Perfluoroanthracene lle Options Display Window Help LMB Rotate CMB Zoom LMB Figure 4 56 View window perfluoroanthracene job visualization We are going to visualize and capture an image of the NMR spectrum Press the NMR button wy in the toolbar at the bottom of the View window This will initially display the C NMR spectrum carbon being the first atom listed To display the F NMR spectrum you can either select a fluorine atom e g F9 from the NMR spectrum window or click on one of the fluorine atoms of perfluoroanthracene in the View window The resulting NMR spectrum is shown in Figure 4 57 Note the red arrow below the peak corresponding to the selected fluorine atom F9 122 PQSMol Manual Tutorials AMA Spectrum F Atoms Selected value s24 4357 Ted OFF C1 C Ca C4 Co C C7 C Range End 337 905 Range Start 297 978 Zoom Out Halfwidth 0 10 Ea F10 Edil Reference Shift 0 User Auto By selection Figure 4 57 NMR window Initial F NMR spectrum of perfluoroanthracene The halfwidth of the peaks can be controlled using the slider bar sliding this all the way to the left reduces the half width to zero and simply displays a vertical line 4 58 NMA Spectrum F Atoms Selected value 324 4357 Tred Range End 337 905 Range Start 297 378 Zo
56. LIB Figure 4 6 Segment window Carboxyl functional group selected Attach the Carboxyl group to the right most upper dummy atom in the build area by positioning the cursor over the atom until it is highlighted and clicking The operation is shown in Figure 4 7 Figure 4 7 Build window attaching the Carboxyl group Step 5 Attach the bent oxygen building block Parallel Quantum Solutions 85 4 1 Example 1 Lactic Acid In the Segment window select Building Blocks tab and then select oxygen in the periodic table The list of available bond configurations changes The default bent configuration for oxygen is automatically selected and the corresponding building block appears in the Segment buffer We will use this block for the remaining O H group needed In the Build window attach the building block at the dummy atom on the center carbon closest to the double bonded oxygen as shown in Figure 4 8 Figure 4 8 Build window attaching the bent oxygen building block Step 6 Fill with hydrogens H The Hydrogen Fill tool is activated by the first button in the upper toolbar Hj It replaces all the green semi transparent dummy atoms with real hydrogen atoms right image in Figure Figure 4 9 Build window after Hydrogen Fill Step F Preoptimize Finally we finish building Lactic Acid by performing an initial energy The second button in the top toolbar El executes the optimization The result of the optimization i
57. NMR and Optimization History windows e Graph Plot displays a color chooser dialog for the graph foreground color see Figure 2 30 The color selected in this window will be used as the plot color in the Orbitals Vibrational Frequencies NMR and Optimization History windows e Graphics opens the Graphics Options window Figure 3 3 Animation Options Animation speed 0 100 opin Speed a axis 0 010 opin Speed Y axis 0 010 opin Speed z axis 0 010 Graphics Options sphere Ciuality 26 00 Cylinder Quality 13 00 Rotation Guality 13 Perspective Angle 45 Adaptive Label Calors wf Antialiasing Figure 3 3 Graphics options window The Animation Speed slider adjusts the speed of the vibrational frequencies animation The Spin Speed X axis Spin Speed Y axis and Spin Speed Z axis control the rotation speed of the displayed structure providing the spin is enabled in the Popup menu see Figure 3 5 62 PQSMol Manual View Mode The Sphere Quality and the Cylinder Quality sliders control the number of polygons used to draw atoms spheres and bonds cylinders Rotation Quality controls the number of polygons used to draw atoms during a rotation Perspective Angle adjusts the angle of view Changes to this value produce a similar effect as changing a lens in a photographic camera i e setting this value to the maximum of 100 will produce a fish eye effect The Adaptive Label Colors checkbox when selected causes all atom label
58. Output Visualize Output 32 PQSMol Manual Build mode The Calculation menu provides an interface to the PQS program It controls various aspects of job input preparation job submission job progress monitoring and post job visualization and display See Section 2 6 for a detailed discussion on running a PQS calculation e Job Input prepares a PQS input file containing the geometrical structure from the Build window See Section 2 6 1 e Submit Job runs a serial PQS calculation see Section 2 6 2 e Submit Parallel Job submits a parallel PQS calculation in the background or into a queue see Section 2 6 2 e Job Output monitors the PQS output and log files e Visualize Output launches PQSMOL in view mode with the output file from the PQS calculation as an argument see Chapter 3 The Window menu File Edit Build Optimize Symmetry Display Calculation TAN e Segment toggles on off or repositions the Segment window frame Selecting the appropriate option will either position the Segment window frame to the right of the Build window position it to the left of the Build window or hide it entirely e Info toggles on off the info window Figure 2 32 ATOM TYPE SYEYL UFF ras Y Z 5 j O 2 O_z 2 080 1 113 0 900 Distance 5 2 2 245 2 H H 3 H_3 Oo 061 1 112 1 329 Angle amp Z 6 275 1501 6 C C 3 C_3 1 216 O 222 0 605 Torsion 5S 2 6 106 180 63 3 10 H H H_ 2 114 0 157 O 029 OP Bend S amp S 2 6 10 1 1619
59. PQSMOL User s Manual c Parallel Quantum Solutions 2006 www pqs chem com Conventions used in this manual Filenames commands typed in at the command prompt are written in typewriter font pqsview aspirin out The term mouse click refers to the left mouse button being pressed The term mouse drag refers to holding down the left mouse button while moving the mouse The term icon refers to an object in the graphical user interface which is a small image usually on top of a button The term button refers to an object in the graphical user interface which triggers an action when activated The term radio button refers to an object in the graphical user interface which is usually grouped with a set of other objects of the same type These objects are mutually exclusive i e only one of the objects can be active at a time The term slider bar refers to an object in the graphical user interface which has an associated range of values and can be adjusted within this range The term entry refers to an object in the graphical user interface which accepts text input Contents 1 Introduction 1 LIL Strune POMOL 2 ina ardor Be Gs Ge Dk EA Bok Oo es dE a er MA ES ES SE we ee 2 2 Build mode Dil Bald wnd NW AA ei eine Sie AA RR RA a a a te GE Ee E 6 ZA SPOOMAtSiy E EEE A eee AA Soe AA eh ee BG A a 7 DNS OO RN O ed ae Ge SGA ER ees a ets eee eee as Be BAe Oe ek eee 22 Dlr taunt Aena CAA A eG eal A Re oe O A A AAC ee 8 E A 34 214 Vs
60. R Spectrum zoom Press the Zoom Out button to return to the default NMR spectrum view The default values displayed in the Range End and Range Start entries in the NMR window are taken directly from the PQS job output and represent the largest and smallest isotropic shieldings for that atom reported in the output file The starting and ending ranges can be adjusted by explicitly setting values in the Range End and Range Start boxes These should be greater than the highest value currently shown and smaller than the lowest if you want to ensure that the whole spectrum is displayed Adjusting the range from 150 to 200 ppm normally 140 57 to 157 for the simulated 70 NMR spectrum is shown below Figure 3 26 This has the effect of slightly compressing the spectrum Range End 150 Range start 200 Zoom Out Halfwidth 0 10 Reference shift 0 0 User Auto By selection Figure 3 26 170 NMR Spectrum user defined range The point of doing this is that spectra of related compounds e g isomers can be individually simulated and adjusted so they are on the same scale i e the starting and ending ranges for all spectra are identical This allows a much clearer comparison between different simulated spectra in reports or publications Tip Right mouse clicking with the mouse pointer in a given window e g the NMR window enables a JPEG image of the graph to be captured 3 5 Dynamics Trajectory window The Dynamics Tra
61. RS Oe G 21 The PQSMol Menubar in build modes seua e aa Re ee Ee Ee oe ai Ye 22 ve lt e OS pac a a Se we Sy OR A Se ee ee eo oe e 23 File Open dilo reas pe ee bag Geee ara ES OEE Oo ee Eee EER OI 23 limpOrtcOMelty dialo 24664 oe ea ee ae ee SS RG Oe ee 6 eee eA REE EE GC 24 Mile Save As dialoe va eee oo ee ee VEG ae Pewee eee Ad 25 Inverse Selection example before left image after right image 2 004 27 Inverse Segment Selection example before left image after right image 27 Angle Presets window left image torsion presets right image angle presets 29 Torsion OPLOS WINdOW e de be os oe ee eee Ee A a LAA es eo a a ae eee eee 29 Backeround Color WIdOW s s seranti aoea g ua EECA RABBLE EEA MERE RA Ye ER 32 Graphics Options Window en 2 0 S00 ae eee de he wee Ee ee A bee EER UA EERE OS 32 Info window atom info top image bond info bottom image 0 0000 eee eee 33 Statu Par PUE modernos sme be eee hol me ee Bee Bee ge as a ee 34 Segment window with the Sybyl5 2 force field selected 2 e 35 Segment window with the Universal force field selected a 35 Segment buffer with the Fragments tab selected a a a a 37 Segment buffer with the Clipboard tab selected a a aa 37 Addition to User Library confirmation dialog ura aca aa A a ee ed he 38 Statusbar with the Building Modes highlighted 000 ee 38 Move operation wit
62. S et ee 8 a E AAA 6 23 pimple Action Op toolbar Riba A YES eh A SO oS EA 7 24 Build tools bottom toolbars senes i peaa eS Siw te daa Doh ee hE FO Se EEE ata 9 2s DCEO ds ee Scns nr ee eee a E eh ae oe ee ee E AE ee 12 2 6 Bond length adjustment The active group is surrounded by a gray translucent surface 13 21 Bond angele adjustments aorta He he Ge A ad ei te te A al AE ER ee eee 13 2 8 Bond torsi n angle adjustment aca sei deo MRR OLR ER AAA 14 2 9 Rotation a DOM a DOU arrasada eGR oe AA eae REE A VA ee RS 14 DA Bone Break wu we GE AB EER ERE ROGER AG Eee ee eS AEE AA 15 2IL Bond tiserexamplesel 22466264 XO EEM AAA ARA RAID 16 2212 Bond fuse example F 2 aa LA eee A E AAA 17 2213 Recornentiexample speed na dera baaa Ed A A AAA 18 ZN OMA A saca oes es te Gh als e e AAA AAA A AAA 18 o AAA E wee YE eo oe eee 19 2 16 Snap to Plane example starting configuration coito a aa alada Bd Re we 19 2 17 Snap to Plane example first atom selected a a a a 20 2 18 Snap to Plane example second atom selected a a a a 20 2 19 Snap to Plane example third atom selected 2 2 2 ee 20 Parallel Quantum Solutions 139 LIST OF FIGURES 2 20 2 21 222 2 20 2 24 2 29 2 26 221 2 28 2 29 2 30 2 31 2 32 2 33 2 34 2 39 2 36 2 31 2 38 2 39 2 40 2 41 2 42 2 43 2 44 2 45 2 46 2 47 140 Add Valence cxamiple 4464 53 6526 6 O 2S eee OSS 8 A O
63. Section 2 4 for a detailed discussion of the optimization process e Force Field Sybyl5 2 sets Sybyl5 2 as the current force field e Force Field gt UFF sets UFF as the current force field e Force Field Options shows the Force Field options window see Section 2 4 1 e Check Atom Type checks or modifies the Force Field atom types see Section 2 4 3 e Options shows the Optimization options window see Section 2 4 2 e Optimize executes the optimizer see Section 2 4 The Symmetry menu File Edit Build Optimize fis Display Calculation Window Check symmetry Options See Section 2 5 for a detailed discussion of the symmetry operation e Check Symmetry executes the symmetrizer see Section 2 5 e Options shows the Symmetry options window see Section 2 5 1 30 PQSMol Manual Build mode The Display menu File Edit Build Optimize Symmetry PRISE Calculation Window View Moge GO Ball O CPK O Ball amp Stick a Ball amp Stickl o Ball amp Stickll O Tube O Tubell O Stick Labels Coordinates Hydrogen Hide Options O Skeleton File Edit Build Optimize Symmetry Display Calculation Window View Mode Labels Coordinates Hydrogen Hide Options Background laraphics View Mode offers nine viewing modes which differ from each other primarily in the radii of the spheres representing atoms and the radii of the cylinders representing bonds The Skeleto
64. View window motion in the most IR active mode of aspirin 3 4 NMR window The NMR window Figure 3 18 allows visualization of the simulated NMR spectrum for each active nucleus Parallel Quantum Solutions 73 3 4 NMR window ah Range End 176 314 Range Stat 33 6650 Zoom Out Halfwidth 0 10 ag C 1L Reference shift 0 0 User Auto By selection c11 F Figure 3 18 NMR window C1 selected The default is to display the NMR spectrum for all atoms of the same atom type as the first listed atom in the input geometry in this case carbon This particular atom is highlighted in the list to the right C1 and is also highlighted in red in the simulated spectrum The atom is also highlighted in blue in the View window as shown in Figure 3 19 74 PQSMol Manual View Mode File Options Display Window Help ba etali uj I 21 LMEJ Rotate CMB Z lt 00m LMEJ SHIFT 2 Rotate LMEJ elect double click deselect Figure 3 19 View window C1 selected The selected atom can be changed by clicking either on the desired atom in the View window or by selecting the atom in the list in the NMR window For example clicking on atom O9 in the list will display the 170 NMR spectrum with the peak for atom O9 highlighted in red in the spectrum Figure 3 20 Parallel Quantum Solutions 75
65. able to you in the TUTORIAL EXAMPLE3 directory on the PQSMot CD so there is no need to actually run the job 120 PQSMol Manual Tutorials Background Job SGE Job Name F anthracene Processes Al H F anthracene a H cwd pe pwm 4 5 binrbash source etec profile de pym sh source retorprofile drpos sh ed homepawel TESTS pas F anthracene 4 GE Tidy Job submit Job show QUEUE Figure 4 55 Parallel Job Submission dialog The Job Submission window will appear Figure 4 55 The job is being submitted to the parallel SGE job queue The job submission script appears in the large window and requires two user supplied entries the job name F anthracene and the number of processors in this case 4 Pressing the Submit Job button will send the script to the job queue At this point you can exit PQSMot unless you actually want to run this job We will use the files copied from the TUTORIAL EXAMPLES directory on the PQSMoL CD at the beginning of this example Click on Done in the Job Submission window and then select the File Quit menu item 4 3 4 Visualizing the PQS job output Step 8 Capture the F NMR spectrum of perfluoroanthracene Note Make sure you are in the directory where the files from the TUTORIAL EXAMPLE3 directory were copied To view the output of the perfluoroanthracene job start PQSMOt in View mode by typing pqsview F anthracene out at the command prompt
66. ahedral carbon building block selected 0 83 Build window with the tetrahedral carbon building block inserted 84 Build window attaching the second tetrahedral carbon building block 84 Segment window Carboxyl functional group selected a a a aa 85 Build window attaching the Carboxyl group aooo e a 85 Build window attaching the bent oxygen building block oaoa a a a a a 8 86 Build window after Hydrogen Fil asar we eRe CRA AREER AME RELA Ye O 86 Build window OptimilZation Tesults es dc al a Be Gok tds am hee EE BS Rw a 87 Smells oy oe He Hk ees hae as ce et es ee ee ee See cee E N 87 PQSMol Manual LIST OF FIGURES Ale OVC III AN 88 AL Input senerati n WINKOW asis d dekh a E Ae eth A he ee a ae ee ES aua 89 4 14 Input generation window finished input 2 2 a e a a a a 90 A lo JOO SUD mission COn Matias RO as hw a a me RR wh AA em AAA 90 AAO OSO MUNI ota Gee SE os Sede oe lt a we BE We a Se Be es a a 91 AA View WandOwe AMUIOICCIS LAY vel e oh ott oh mech Bod ee eter Qk Be ete Beet a Bp ae awe ek A 92 4 18 Orbitals window HOMO selected 93 4 19 View window HOMO displaved s hz amp amp oh 2 664 hele A a Bede e a A A ee t 94 MOV DAVE lima re QUalO ao a o e A a ee eG EE ee de de en 95 4 21 Vibrational Frequencies window IR spectrum mode 1 selected 0 0 0 00 0 95 4
67. al Section 3 2 E IR Raman VCD Spectra Activates the vibrational spectrum window This allows a simulation of the IR Raman or VCD spectra and animation and display of individual vibrational modes Section 3 3 rr E NMR Spectra Activates the NMR window This shows a simulation of the NMR spectrum for each active nucleus Section 3 4 pl Dynamics Trajectory Activates the Dynamics Trajectory window This provides an interface for displaying a complete or partial dynamics trajectory displaying the geometry at each cycle Section 3 5 Optimization History Activates the Optimization History window shown below This window provides an energy vs cycle number plot Section View Modes Change the molecule drawing scheme Options are Ball CPK Ball amp Stick Ball amp StickII Ball amp StickIII Tube Tubell Stick and Skeleton 3 1 2 Menu The File menu MIES Options Display Window Open Ctl o Guit Cta e Open opens a new file e Quit exits PQSMoL Parallel Quantum Solutions 61 3 1 View window The Options menu File pois Display Window Background Graph Background Graph Flot Graphics e Background displays a color chooser dialog for the View window background see Figure 2 30 e Graph Background displays a color chooser dialog for the graph background color see Figure 2 30 The color selected in this window will be used as a background color in the Orbitals Vibrational Frequencies
68. ality Following a description of all the build visualize tools several tutorials will be presented covering all aspects of PQSMOL including building a molecule input preparation job submission and displaying the final results 1 1 Starting PQSMol To start PQSMOL in build mode from the command line prompt type the following command and press lt Enter gt pqsmol To start PQSMOL in view mode type pqsview and press lt Enter gt You may also start PQSMOL with a specific file name passed as a command line argument pqsmol filename This command will launch PQSMoL in build mode and open the file filename The only valid file extension in build mode is pqb In view mode there are several input file types available 2 PQSMol Manual Introduction pqsview filename where the filename extension may be one of inp standard PQS job input file coord PQS coordinate file out PQS job output file log PQS job log file mop MOPAC input file car Biosym CAR file zmat Z Matrix input file hin Hyperchem input file XYZ XYZ coordinate file Please report any problems with PQSMoL by email to tech pqs chem com Parallel Quantum Solutions 3 Build mode When PQSMoL is started without command line arguments the application runs in build mode In Figure 2 1 individual components of the interface are labeled and surrounded with colored rectangles simple action toolbar menu segment buffer rile Edit Build
69. alue of 0 will turn off optimization animation If both the GTOL and ETOL convergence criteria are satisfied or the maximum number of optimization cycles Steps has been exceeded the optimization will stop In line with similar criteria in the PQS program GTOL and ETOL are measured in atomic units 42 PQSMol Manual Build mode Checking the Calculate Hessian box will compute by central difference on the gradient and invert the Hessian matrix before starting the optimization This is rarely needed and is unlikely to speed up the optimization it might be useful in cases where there appear to be convergence problems Normally the optimization will proceed silently i e with no print out Setting the Print Flag to a small integer value the bigger the value the more print out will write intermediate quantities such as the energy RMS gradient and RMS displacement at each optimization cycle to filename debug in the current working directory As the filename implies this might help debug any apparent convergence problems Finally the Optimization Animation update gives the number of optimization cycles between each update of the geometry in the Build window The default is to redisplay the geometry every 40 cycles The final converged geometry is always displayed in addition to intermediate geometries depending on the number of cycles the optimization actually takes Setting this to a smaller value increases the rate at which
70. ame File fhome pawel TESTS y Directories S E F10C14 pqb wf FIOCTSHs pqb Home COMPLEXESs ME3H3 pgh JONS OVENGCe4 H42 pq TPY contractecd OG AHE pagk TPY segmented aspirin pgb iotest azt pgb Desktop hig pagk a brech pgb br cha pab G brelfenh pgb bri nchd pqb m hd Documents File Filter pop PGtsrmol build file M selection homerparwelfTESTS C3H603 pqh Figure 4 12 Save As dialog You may keep this name or overwrite it with another In either case as soon as the file name is accepted and the file is saved by pressing the OK button the input generator window appears Figure 4 13 88 PQSMol Manual Tutorials GEOM Pas cdob specifications c Oo 937721 1 0223742 Oo 547019 h 1 933917 1 406609 1 510835 iHa h 1 933917 1 392117 0 547030 Tite Memory Siaarae3 alaoeos 403619 h 0 443531 1 382760 0 321992 o O 340903 Oo 365998 o 558902 Molecule Characteristics h 1 437375 O 721960 1 426808 h 1 746601 0 929769 1 699534 l raie 412123 0 873876 0 554740 Charge o Symmetry 0 00001 Multiplicity i 0 9936109 1 657056 0 502510 a 1 055644 1 037101 1 698534 a 4 664027 O 866067 0 660148 Calculation Type IIIIIIIIII STEP 2 IIIIIIDIIILI Single Point Energy Select type ha O Geometry Optimization Selecttype ha Basis SetMvethad Basis set DFT method semiermp method Vibrational Frequencies
71. amics trajectories animation of vibrational modes and simulation of IR Raman VCD and NMR spectra File Edit Build Optimize Symmetry Display Calculation Window Help Molecular Localized Natural e Alpha Alpha Natural Default View Beta Beta Full View MO S OFF Elect 26 25 24 23 22 21 20 19 16 TL 16H 15 14 Presets deg Done in 21 Cycles Energy 0 002572 8 Unchanged 0 30 45 60 90 Building Blocks Fragments Clipboard File Options Display Window 13 12 11 OrbialH 4 Energy 0 375 Ev 10 n Isosurface level 0 050000 Cross Sections n 1 000 1 000 1 000 Range End 299 43 Range Start 301 43 Zoom Out Halfw Electrostatic Potential Reference Shift 0 0 e User Auto By Selection Display Potential Linear Scale Hemory reques high wa Total Termin X 1 61019 Y 3 8027 Z 0 6096 Point Group c2 Degrees of Freedom 6 The existing Master proces 2 slaves wol Slave on pin Slave ont pin GEOM POS OK e Infrared Raman YCD Zoom Out Halfwidth 10 00 Vectors Reverse Animate 4 seba e ejil follo pu alalrj lalo LMB Rotate CMB Zoom LMB SHIFT Z Rotate LMB Select double click deselect Figure 1 1 PQSMol in action There are two modes of operation for PQSMoL build mode and view mode Build mode as the name
72. among the computing processes and gathers the results It is necessary to schedule this additional job in PVM This means that a two process parallel PQS job is in fact a three process PVM job The number entered in the Processes entry box in the job submission window refers to the number of computing slave processes only Background Job SGE Parallel Environment Mode CPUs Processes PYM Job Available Allocated status otatus ni 4 J Ti Toggle ne 4 E aff Toggle n3 4 D 4 Toggle nd 4 D 4 Toggle Tidy Job Reset PYM Processes A 1 Launch Job Figure 2 59 Parallel Job Submission window background job nodes ready Figure 2 59 shows the status of a cluster with all nodes up connected and ready to run a parallel job You may select a number of computing processes in the 4 Processes entry box The processes will be allocated to the nodes according to the order in which the nodes were added to the PVM round robin In our example we have a total of five PVM processes with node n1 added first and n2 added second to the PVM So the first PVM process p1 PQS master process is assigned to node n1 the second to n2 and so on resulting in three processes on n1 pl p3 p5 and two processes on n2 p2 p4 In our example cluster we have a 16 CPU system comprising four dual processor dual core nodes with four CPUs from nodes ni and n2 in the PVM The Launch Job button will submit a 4 processor parallel job The existing
73. angles involving unknown atom types will be assumed to have values as derived from the original geometry If you are building an organometallic system and have the geometry around the metal atom more or less correct then you might be better off using the Sybyl force field to optimize the structure rather than UFF even though the metal is recognized in UFF but not in Sybyl Taking idealized geometrical parameters directly from the input geometry has a couple of side effects that the user needs to be aware of 1 slightly different starting structures for the same system will optimize to different final geometries and 2 if optimized structures are reoptimized they will again change For more details about the Sybyl 5 2 and Universal force fields see the User s Guide to PQS 2 2 2 Fragments In addition to the building blocks a large library of preconstructed molecular fragments can be accessed via the Fragments tab in the Segment window The available fragments are the same for both the Sybyl5 2 and Universal force fields Currently these are grouped under e AMINO ACIDS e NUCLEOTIDES e BICYCLIC e POLYCYCLIC e CHAINS e SOLVENTS e FUNCTIONAL GROUPS e SUGARS e HETROCYLCIC e ORGANOMETALLICS e LIGANDS e TS Transition States e MONOCYCLIC All fragments except those in the last two categories have been preoptimized using the Sybyl force field Fragments in the TS group are basically templates for common organic reaction
74. are shown in Figures 4 75 4 78 File Options Display Window Help lt a esjejil epujo LMBJ Rotate CMB Zoom LMB SHIFTZ Rotate LMB Select double click deselect Figure 4 75 View window 2 methoxy perfluoroanthracene atom no 9 selected Parallel Quantum Solutions 135 4 3 Example 3 Methoxy Substitution in Perfluoroanthracene ren OFF Range End 160 Range start 110 Zoom Cut Halfwidth 0 00 0 Reference Shift 179 42 8 User Auto By selection Figure 4 76 NMR window 2 methoxy perfluoroanthracene 7F NMR spectrum File Options Display Window Help LME Rotate CMEB Zoom LMB SHIFT Z Rotate LME Select double click deselect Figure 4 77 View window 9 methoxy perfluoroanthracene fluorine atom no 9 selected 136 PQSMol Manual Tutorials req 4 OFF C1 Ce La C4 Loa CE LA Co Range End 160 Range Start 110 Zoom Out Halfwidth 0 00 F 10 F11 F Reference Shit 179 42 6 User Auto By selection Figure 4 78 NMR window 9 methoxy perfluoroanthracene F NMR spectrum 4 3 8 Comparing the NMR Spectra of perfluoroanthracene 1 2 and 9 methoxy perflu oroanthracene All four 9F NMR spectra are shown together in Figure 4 79 The parent perfluoroanthracene is at the top followed by the 1
75. ate RMBEInsertAttach CMB Zoom CME SHIFT Select CMB CNTRL Mowe Figure 4 68 Build window perfluoroanthracene inserted Step 10 Attach the oxygen building block Select the Building Blocks tab in the Segment window and select oxygen in the periodic table The result is shown in Figure 4 69 There are only two possible building blocks for oxygen in restricted mode either a double bond or a bent configuration with two single bonds with the latter which is the one we want as the default Parallel Quantum Solutions 129 4 3 Example 3 Methoxy Substitution in Perfluoroanthracene File Edit Build Optimize Symmetry Display Calculation Window Help A By Se B 9l e are i delle h mass 2 gt apar Cej Pre Hdi Pr Sm Euj Gd TEJ Dy Ha Erd Tmj YB Lu lh t de ME SE DT me F hast E Sa A See Pul Aml Cm Ek ICE ES ml Hd Noll x 0 97541 Y 34065 Z 3 7516 Can Torsion ON Auto Selection ON Auto Selection ON T Force Field Sybyl5 2 E 0 E E Pl DEFAULT LMB Rotate LMB SHIFT 2 Rotate RMB InsertAttach CMB Zoom CMB SHIFT Select CMB CNTRL Move RESTRICTED Figure 4 69 Build window bent oxygen building block selected Using either the Add Attach Connect tool or the overloaded right click in the Default tool attach the oxygen building block to the to top fluorine in the right most benzene ring This is the 1 position The result is shown in Fi
76. ay be multiple building blocks available for a given element These are listed in the Bond Configuration frame The default building block for carbon is the tetrahedral block The current building block is displayed in the Segment buffer At this point we should have the correct building block ready to insert into the Build window The Segment window should look like the one in Figure 4 26 To insert the building block first select the Add Attach Connect tool from the toolbar at the bottom of the window and click anywhere inside the build area 98 PQSMol Manual Tutorials File Edit Build Optimize Symmetry Display Calculation Window Help Hejas aaae aerea etal BE eater de eae ale E Bal a HE Ta u Ref tr Pe Aul Hal 1 Pb Bi Pol Ae f 2 a Qs ES NATA af E Cel Fri Hdi Emi Sm Eul Gd To Dy Hal Er Tm 176 Lu y EdE L b E A Pulliam cm Bk ice Es F L eff _ Y a TEE z 0 0000 E A Torsen ON Torsion Le Selection TEE Field Sabz Ee e EEEE IL DEFAULT RESTRICTED Figure 4 26 Build and segment windows inserting the tetrahedral carbon building block Tip You may also insert into the Build window using the Default tool by right clicking in the Build window Note If for some reason the building block in your Segment window is different than the one in Figure 4 26 you can select the tetrahedral carbon building block by clicking on the carbon button in the per
77. button aj Zoom tool Moves the viewpoint directly over the center of the selected area of interest and zooms in to show the atoms within Usage Drag the mouse over the area of interest to zoom in Double click to return to full view Note In the full view zoom out the origin of rotation is the center of the coordinate system point 0 0 0 0 0 0 The zoom operation effectively changes the origin of rotation for the molecule to be the center of the selected area of interest l Info tool Displays information about atoms bonds distances angles torsions and out of plane bends For each atom the information includes atom type atom position in the input geometry assigned symbols for Sybyl5 2 and Universal force fields and the Cartesian coordinates This information is displayed in the info window at the bottom of the Build window The info window is automatically opened when the Info tool is selected It is not however automatically closed when a different tool is selected Use the Info Window button in the simple action toolbar to close the info window Usage Click on any atom to get its coordinates click on two atoms to get the distance between them click on three for the 1 2 3 angle and click on four to get the 1 2 3 4 torsion and out of plane bend To clear the current info selection double click over empty space in the window Tip This tool also works with bonds Click on any bond to get its length any two adjace
78. e a molecule whose geometry is not exactly symmetrical and to determine the point group symmetry of the structure File Edit Build Optimize Mia Display Calculation Window Check Symmetry Options Figure 2 48 Symmetry menu The Symmetry Check Symmetry will execute the symmetrizer This is equivalent to clicking the 34 button in the upper toolbar Point Group dad Degrees of Freedom 3 Figure 2 49 Symmetry output If any symmetry is found the geometry will be symmetrized so that the structure does indeed conform fully to the particular point group If it seems as if the system should have symmetry but check symmetry fails to find any i e the point group is C1 even with a large threshold then manipulating the structure by hand e g ensuring that groups of atoms are in the same plane or reoptimizing with tighter optimization thresholds may help to locate the desired symmetry 2 5 1 Symmetry Options Symmetry options are available in the menubar under Symmetry Options see Figure 2 50 symmetry Options Threshold 0 05 Close Figure 2 50 Symmetry Options window The only symmetry option is the symmetry Threshold The code used to determine the point group symmetry is essentially a copy of the same code that is in the PQS program This attempts to recognize symmetry planes and axes of symmetry Parallel Quantum Solutions 45 2 6 PQS Calculation relative to the center of mass of the system
79. ected force field See Section 2 4 Check Symmetry Determines the molecular point group symmetry See Section 2 5 Select All Selects everything all atoms and bonds in the Build window Subsequent build operations such as Cut Paste are applied to the complete structure Deselects all atoms and bonds that are currently selected Ei Center All Positions the current structure in the center of the Build window Parallel Quantum Solutions T 2 1 Build window bal Face Front Rotates the current structure so that the XY plane is parallel with the screen aj Copy Copies that part of the structure that is currently selected into the clipboard and displays it in the Segment buffer xj Copies that part of the molecule that is currently selected into the clipboard displays it in the Segment buffer and removes it from the Build window amp Paste Pastes the contents of the clipboard into the Build window a Undoes the effects of the last operation i e the last change made to the current structure in the Build window el Redo Re does the effect of the last operation before the undo i e undoes the undo Drawing Plane Toggles on off the drawing plane QO PQSMol Manual Build mode e Atom Labels Toggles on off atom labels E Coordinate Axes Toggles on off the coordinate axes Note The spacing between the tic marks on each coordinate axis is one Angstrom
80. ed jobs which use PYM Are you sure Are you sure Cancel Was Cancel Yes Figure 2 63 Removing nodes from PVM while jobs are Figure 2 62 Removing nodes from PVM warning dialog scheduled in the queue Parallel Quantum Solutions 55 2 6 PQS Calculation Background Job SGE Job Name aspirin H aspirin a cud E pe pum 5 bin bash v PATH POS_ROOT PYH_ROOT PYM_ARCH POS_SCRDOIF POS_BASDIR cd t rusrrlocalrsharerPUSrpdgqs_prem x np 5 aspirin Tidy Job iv Show Queue Processes 4 2 1 Submit Job queer ame aqtype used tot loadavg arch states a all qe ni EIF era Oo De lx24 am064 1389 0 55500 cadion_BIG malagoli r Grid 2006 10133105 z all q n EIF eee 0 32 lx24 amc6 4 1389 0 55500 cadion_BIG malagoli ir Grid 2006 10133105 2 all qEna EIF ara O 4 lx24 am064 1388 0 55000 anmulene_B malagoli 5 gerig gob 1033 05 all q n BIP eve 0 54 lx24 amc6 4 13082 0 5505000 annulene_E malagoli ir O64 2008 1033105 ALL LL LL LL LE LE LE LL LL LL LE LE LE LE LE LE LE EL EE LL EE LE LE LE LE LE LE LE LL EL A LE AE RE LE LE LE Lk Ek EL Ek EE Uk Ok Lk LE LE Rk RL Rk 2 LE LE Lk 2 EE EL Lk Ek Lk LE Lk LE LE EL EL AL AL LE LE LE LE LL Y Done Figure 2 64 Parallel Job Submission window queue The SGE tab allows jobs to be submitted into the SGE job queue Figure 2 64 In this example a job with the name aspirin is being set up for submission on four CPUs Normally the only infor
81. election area in the statusbar or use the Build Auto Selection item in the main menu bar ik Select tool The Select tool works in two ways It either selects individual atoms and or bonds or can be used to create rectangular selection areas selecting any objects they encompass The selected atoms and bonds are surrounded by a translucent gray surface Selection operations are cumulative Usage Form a rectangular box selection area which selects all atoms in the box for a subsequent action e g Cut Move by clicking anywhere in the build area close to the atoms to be selected and dragging the mouse horizontally and vertically to define the box dimensions Releasing the mouse will complete the box definition The selected atoms and bonds are surrounded by a translucent gray surface To toggle the selection of an individual atom or bond click on the atom or on the bond Parallel Quantum Solutions 11 2 1 Build window Figure 2 5 Selection Selections can be cleared with the Select None button in the simple action toolbar 4 Hide Nonessential Deemphasizes atoms which are not part of the area of interest Usage Drag the mouse over the area of interest The atoms inside the selected area are unchanged Outside of this area all Hydrogen atoms become hidden and only the bond structure for the remainder of atoms is shown 1 Bond Length tool Adjusts the length of a bond Usage Click on a bond to select
82. em Shore 025 he a e AA de ODE eed ee ES AS 34 as IIA 34 Dei BUNNS Blocks i and go oh ek is e o a Dl tae atte ta AA Ap ek a we Ge ie E EA 35 Kaa Paene A E ee SCR A A ah ee ee ua eae Ge SS SO E a 36 Der E MO Od Gh nuke eee coe eae A ap erent a eG ee Se ce aa nk Ga E A 37 ZO Ae UNIO Modest tr Ie he ets es Be Causa ae Oe id Be de De ee i 38 Dog AE LORO aaa Ds ARS Se ee we ee AD AAA 39 2 5 2 SI AAA 39 23 3 Restricted Unrestricted ge t 40 44444 ac u eT a dd ew ale rs eB eee 39 2A O aO e ergo woe he Ge ees ee e ES Se Ges Dh ee ote ee amp A a eee Bo ae Bem es 41 2AT Force Field OPON sas amp E A A ee ek hee A 42 Das PB On ON LORS Ea o o E A IS EA A 42 24 3 Foree Field Symbols s a a I DE A a Be Ee a 43 Parallel Quantum Solutions i CONTENT 2 0 2 6 S Ss ate ce He kG e a os a GS eee OG 2 5 1 Symmetry Options PQS Calculation 2 6 1 PQS input file 2 6 2 Job submission 2 6 3 Job Results 3 View Mode 11 3 1 3 2 3 3 3 4 3 9 3 6 View WINdON ia Gos ce dt ee A ee hoe i Ace Ee eg 3 1 1 Toolbar A te ee eS 3 1 3 Statusbar Orbitals window Vibrational Frequencies window NMR window aaa a WS Dynamics Trajectory window Optimization History window Tutorials 4 1 Example 1 Lactic Acid 4 2 4 1 1 Building the Lactic Acid molecule 4 1 2 Creating a PQS input file 4 1 3 Submitting the PQS job 4 1 4 Visualizing the PQS job output Example 2 CHFCIBr 4 2 1 Building CHFCIBr 4
83. enter shifts the structure so that it is centered in the View window The Window menu File Options Display ras Info Oirhitals Vib Frequencies NMR Dynamics Trajectory Optimization Hist Figure 3 4 Addition to User Library confirmation dialog e Info toggles the Info window e Orbitals toggles the Orbitals window Section 3 2 e Vib Frequencies toggles the Vibrational Frequencies window Section 3 3 e NMR toggles the NMR window Section 3 4 e Dynamics Trajectory toggles the Dynamics Trajectory window Section 3 5 e Optimization Hist toggles the Optimization History window Section 3 6 The Popup menu The popup menu is activated by pressing the right mouse button inside the view area 64 PQSMol Manual View Mode Figure 3 5 View window popup menu activated via the right mouse button e Capture saves the current image in the View window as a JPEG file A file save dialog similar to Figure 2 25 is displayed to specify a file name e Spin animates the rotation of the molecule around the X Y and or Z axes See Figure 3 3 for rotation speed controls 3 1 3 Statusbar LMIB Rotate CMB o0m LMB SHIFT 24 Rotate LMB select double click deselect Figure 3 6 Statusbar in view mode The statusbar displays help information about mouse function The acronyms LMB RMB and CMB denote Left Mouse Button Right Mouse Button and Center Mouse Button respectively Parallel Quantum Solutio
84. eoe2 40339 932 45952 117751365 A O 79531 Oo 25414 O 46596 Y 0 16353 0 88101 O Z 0 55365 O 27615 O 6361 Rotational Symmetry Humber is 1 The Molecule is an Asymmetric Top Translational Enthalput 0 559 kcalrimol Rotational Enthalput 0 559 kcalrmol Vibrational Enthalput 14 029 kcalrimol gas constant RT gt 1 0 593 kcalrimol Translational Entropyt 40 874 cal mol K Rotational Entroput 27230 calrmol K Vibrational Entropyt 6 01 calrmol K Total Enthalput 16 399 kcalrimol Total Entropyt 3 124 calrmol K Hemory status t request number 12 memory marks high water 343248 total available memory Sooogooo Total master CPU time 29 62 Elapsed 20 37 mir Termination on Tue Sep 19 173351 3 2006 PHRASE Sd ES LS TAIL LIS 4 LLZ sx Cycle 1 Energy 3172 940455466 RHSG 001150 xe Cycle 2 Energy 73172 9426607375 RHSG A al sx Cycle 3 Energy 412 94 2939600 RHSG 0 00143 sx Cycle 4 Energy 3172 942972992 RHSG G 00047 HH Cycle B Energy 3172 742976940 RMSG 0 00008 sx Cycle 6 Energy 3172942977023 RHSG 0 00002 Close Figure 4 35 Job output window Two files are monitored in the job output window the out file in the text area at the top of the window and the log file in the bottom As output is produced it is added to the end of the file and the display scrolls down Use the scrollbars on the left side of the windows to scroll up and down through the file Parallel Quantum Solutions 105 4 2 Example 2 CHFCIBr 4 2 4 Visualizing
85. est Job Molecule Characteristics Charge 0 Symmetry Calculation Type 0 00001 Memory Multiplicity 1 J HEH 5 TEST Test Job GEOH PLI5 O 407421 0 3 00 75 O 367478 1 595360 2 259140 0 906522 1 215465 1 762526 2 564658 1 504127 O 360849 0 595 720 O 093708 1 121867 1 012542 9 092516 0 984464 9 231304 1 983719 1 5823201 11049445 2 115796 0 552090 Oo 280224 0 082592 0 951921 9 349092 O 954750 1 641264 1 846167 2 338932 0 319455 Oo 397087 S3I3575307300003 gt 3 0 911296 0 013535 O 947725 1 797119 STEP 4 IIIIIIIIIII 1 4 2455 cingle Point Energy 1 706885 BASIS 3 219 OPT Imize SCF DFTP 03L P FORCe JLIMP Geometry Optimization Basis Set Method Basis set d 21q Y DFT method al sto 1 sta 51 sto 5 0 sto b semiemp method Properties Vibrational Freg Electric Field Gr Charge Spin De d 21 9 d 21 q d 4 214 4 21g d 4 22q56 4 31 9 31 6 31 6 31 9 0 b 9139 dp 6 319 3df3pd 6 31 g 0 6 31 9 dp B 31 0 6 31 0 0 B 314 q dp B 3114q 6 311 9 0 6 3119 df b 3119 dp 6 311 g 2 df pd 6 3119 3df3pd 6 311 9 dp B 311 q 6 311 9 dp 6 311 9 2d p 6 311 9 2 df2pa 6 311 9 3d3p 6 311 9 3dfapa ano_rasaames AUG CC AC Oz aug cc pewdz AaUG CC povgz aud cc poyvt Figure 2 52 Job Parameters window basis set 48 PQSMol Manual Build mode As shown above
86. evels to be zoomed and dragging the mouse with the center mouse button vertically A zoom about the HOMO energy level is shown in Figure 3 11 Pressing the Full View button displays all orbital energy levels in the energy level graph and allows access to all orbitals via the list Because of the extended energy scale from deep core to the highest virtuals the energy levels are compressed and the zoom feature would definitely be required to select orbitals for display from the energy level graph The expanded full range energy level graph and orbital list are shown in the Orbitals window in Figure 3 8 Note the difference in the starting and ending energy levels in the graph and the top orbital number as compared to Figure 3 7 In Figure 3 8 the electron density has been selected which forms and displays the density from all the occupied orbitals The corresponding View window displaying the electron density isosurface is shown in Figure 3 12 68 PQSMol Manual View Mode File Options Display Window Help Xp e jejil 1 ulul jo LMIB Rotate Ch4B lt o00m LMB SHIFT 2 Rotate LMB select double click deselecti Figure 3 12 View window electron density As in the case of the orbitals the density surface can be expanded and or contracted via the Isosurface level slide bar in the Orbitals window
87. f these windows will be updated in real time When the job completes successfully the Visualize Output window automatically opens allowing post job visualization Parallel Job submission This feature allows a job to be submitted in parallel to the background or to the SGE job queue assuming it is configured and is available on your system using the Parallel Virtual Machine PVM software A window similar to the one in Figure 2 56 appears the exact details are system dependent Parallel Quantum Solutions 91 2 6 PQS Calculation Background Job SGE Parallel Environment Mode CPUs Processes PYM Job Available Allocated Status otatus n 4 D Check nz 4 0 Check n3 4 D Check ne 4 0 Check Tidy Job Reset PVM Processes Z 1 Launch Job Figure 2 56 Parallel Job Submission window background job initial view All configured nodes are listed in the Background Job tab Figure 2 56 Each row in the list contains the node name the number of available CPUs on the node an entry containing the number of processes allocated to your job you can allocate more processes than there are CPUs but this is not advisable an icon representing the state of the PVM an icon representing the state of the current job and a status button Initially the PVM status of each node is represented with a question mark icon and the status button is labeled Check This indicates that the state of each node is unknown To check the status of a gi
88. frequency number will be highlighted in the Frequencies list on the right 4 3 Example 3 Methoxy Substitution in Perfluoroanthracene In this example we look at nucleophilic substitution in aromatic perfluorocarbons specifically methoxy OCH3 substitution in perfluoroanthracene Perfluoroanthracene is shown schematically in Figure 4 42 and its structure in Figure 4 43 The ring carbon substitution sites are labeled in red and there are effectively three different single substitution sites 1 2 and 9 Other sites are equivalent by symmetry Figure 4 42 Perfluoroanthracene showing substitution sites Figure 4 43 Perfluoroanthracene Figures 4 44 and 4 45 show methoxy substitution at site 1 Experimentally the actual substitution site is often determined primarily by 7F NMR and we are going to calculate and compare the F NMR spectra for methoxy substitution at all three sites Such a study has already been published M Muir and J Baker J Fluorine Chem 126 2005 727 and this example duplicates part of this work showing how PQS and PQSMoL can be used in a real research topic Parallel Quantum Solutions 111 4 3 Example 3 Methoxy Substitution in Perfluoroanthracene Figure 4 44 1 methoxy perfluoroanthracene substitu tion at site 1 Figure 4 45 1 methoxy perfluoroanthracene Note During this tutorial perfluoroanthracene and various methoxy substituted derivatives will be constructed and input files
89. g PGs log pogz PGsmal viewer compressed eye CANS format Cancel Figure 2 24 Import geometry dialog Note Imported structures are placed in the clipboard The type of file to be imported is selected via the File Type pulldown menu and the actual file is selected in the Files list e Save saves the current structure in the Build window If the project is untitled then the Save As dialog is displayed e Save As saves the current structure in the Build window under an alternative name The default file type is the PQSMoL build file pqb Additionally coord and inp formats are available 24 PQSMol Manual Build mode Create Dir Delete File Rename File fhomevpawel TE STS Home Files big coord hig coord cl coord ci hiz coord cen coord E COMPLEXES TPY contracted TPY segmented intest cCcend coord censo coord c4hd coord cahi coord chi coord ch4 2 coord cl c coord pab PGismol build file coord PGs coordinate file inp PGS input file CALL files Selection Pome pave E Figure 2 25 File Save As dialog e Quit exits PQSMot If the currently edited molecule has been modified since the last save operation you are presented with the Save Changes dialog Figure 2 22 Parallel Quantum Solutions 25 2 1 Build window The Edit menu File Build Optimize Symmetry Display Calculation Window Undo Cth 2 Redo Ctl Cut Ctl Copy Cte Faste Ct
90. g a PQS job Step 9 Submit the PQS job We are now ready to run the PQS calculation Use the Calculation Submit Job menu item to submit the job You should now see the confirmation dialog in Figure 4 34 104 PQSMol Manual Pals job fhome pawel TESTS BrclFCH inp submitted Figure 4 34 Job submission confirmation dialog Tutorials Press the OK button to close the Job Submission confirmation dialog As soon as any output is generated by PQS job it is displayed and updated in real time in the output window Figure 4 35 a f cl bre hi STANDARD THERHODYHAHIC QUANTITIES AT This Molecule has gero point vibrational energyi O oo O 008 9 o12 O 009 O or O 009 TAGI O 000 0 005 0 531 0 135 9 531 om l pal l 0 0LF 0 01E o 004 0 003 LOA CL 9 290 O Fa2 GQ Imaginary Frequencies 2 0 045 Oey O 003 Oo OL t 196 2398 18 E AND 13 073 kcal mol 0 000 OOOO Dy OG O 477 Output 0 030 0 000 OOGG 0 000 0 352 1 00 ATH RMSD RMSD RHSD RMSD RMSD RHSD Log 0 05196 0 01549 000456 0 00216 oO 00031 o o0007 File a 0 000 0 000 0 000 o 801 File HH HH HH HH HH HH Atom i Element c Has Hass 12 01115 Atom 2 Element f Has Hass 18 99840 Atom 3 Element cl Has Hass 35 452 70 Atom 4 Element br Has Hass CA Bodo Atom 5 Element h Has Hass 1 00794 Molecular Hass 147 274193 amu Principal axes and moments of inertia in atomic units 1 3 Eigenvalues
91. ge Move the mouse pointer over a bond If the bond is fusible it will be highlighted with a yellow translucent surface The surrounding open and closed bonds will be highlighted with a green translucent surface Click on the bond to select it as the fuse bond Move the pointer over a matching fuse bond in a separate segment Parallel Quantum Solutions 15 2 1 Build window Note A matching fuse bond has e the same number of open and closed bonds as the fuse bond at both corresponding ends If the bond is a matching fuse bond it will be highlighted with a yellow translucent surface and the surrounding open and closed bonds will be highlighted with a gray translucent surface Click to fuse the two bonds fuse bond matching fuse bond l i Figure 2 11 Bond fuse example 1 Note Bond fusion involves moving one of the two segments so as to fuse onto the other segment at the position of the fuse bond During this procedure the segment containing the initially selected fuse bond will remain stationary while the second segment will move Bear this in mind if there are other segments in the Build window whose position relative to one or other of the segments to be fused you wish to remain unchanged When the segments are fused the newly fused bond is automatically selected as the axis of rotation and all atoms and bonds in the matching fuse bond segment are added to the active group Drag the mouse vertically to adjust the dihedral
92. ground job nodes checked 53 2 59 Parallel Job Submission window background job nodes ready e 54 200 PVN eset warnine Talog erca ie We a Bode ae oh ah tae is hae a I a eh eG a a a T ad 55 20L Gdy ob aio IAEA 55 2 62 Removing nodes from PVM warning dialog 55 2 63 Removing nodes from PVM while jobs are scheduled in the queue 02500 55 2 64 Parallel Job Submission window queue oaoa a a a a a 56 3 1 PQSMOL running in view mode de gob ded hot ea ee a a eS le ERS Dds Oe Oe SA 59 ovo Toolbar I view mode do e a Adidas a BR as ee Bee AAA 60 99 Graphics Options WiMdOW errado o EEE eed ic eee e ES ES oe 62 3 4 Addition to User Library confirmation dialog 4 5 lt lt e A a See de OK bd o 64 3 5 View window popup menu activated via the right mouse button e 65 0 OAS Dr EW View Ode 4 cae unde AD A A A Re SAA Ok GS Se 65 dl Orbivals window Initial adisplad sarsa ae a a de ee ee ES ee da eee aS 66 3 8 Orbitals window electron density selected full view e so 66 3 9 View window HOMO orbital displayed 67 3 10 Orbitals window HOMO orbital selected 200008 ara jaa ee a E A E o A A AAA 68 3 11 Orbitals window HOMO orbital zoom 68 Parallel Quantum Solutions 141 LIST OF FIGURES 3 12 3 13 3 14 3 15 3 16 10 lg 3 18 3 19 3 20 3 21 3 22 3 23 3 24 3 20 3 26 321 3
93. gure 4 70 130 PQSMol Manual Tutorials File Edit Build Optimize Symmetry Display Calculation Window Help mese 6 C2 92 a ox 0 90585 w EI E 3 6870 Put Ti Torsion ON f Auto Selection ON IED DEFAULT LMB J Rotate LMB SHIFT Z Rotate RMB InsertAttach CMB Zoom CMB SHIFT Select RESTRICTED Figure 4 70 Build window perfluoroanthracene with the oxygen building block attached at position 1 Step 11 Attach the tetrahedral carbon building block In the periodic table select carbon This will show the five building blocks available for carbon with the 4 bond sp3 hybridized carbon again the one we want the default Position the mouse pointer over the free valence the green dummy atom on the oxygen atom and right click to attach the carbon atom The result is shown in Figure 4 71 Parallel Quantum Solutions 131 4 3 Example 3 Methoxy Substitution in Perfluoroanthracene File Edit Build Optimize Symmetry Display Calculation Window Help ERRE aeter Building Blocks Clipboard Sybylb Force Field Bond Configuration sa k ca aale EE eid fl el alr el Ba aH Tall Re e tr Pe Au a Ta Pb i Po Atl ea Ac RF nb So Br He He Ce Pr Ad Pm Smi Euj Gd Tb Dy Hal Er Tmi YE Lu rial wel Plane slo el ED 7 Al E 3 7941 7941 au Auto Torsion ON EENE Auto Selection ON Selection ON T Force Field ET E DEFAULT LMEB Rotate KAE SHIFT Z Ro
94. h Auto Selection off left and on right oaa aaa 02 02 2004 39 Segment window in restricted mode left and in unrestricted mode right a 40 Lower toolbar in restricted mode top and in unrestricted mode bottom Note the last four buttons in DORIC Cs aiii e e ae Oona ee ee as e oe Eo eee aa eee 41 Statusbar with the current forcefield highlighted 0 0 eee 41 CoG i Ze CU oes AO e a de de Se 2 acid A E a io 41 Force Held COPLAS WwindOwW i nur a eee a AA eS E 42 obi Za CIO OPUS dede amp 4 5 dle do ve me E dd e er o do e a a e a O a o 42 Force held Sy Mile obio ys A A a BEE ee e RA E 44 PQSMol Manual LIST OF FIGURES 2AS Dy im TACO a sw ee ww ee Re Ee we et a ee en es eG EG a 45 DAD Symmetry OUD 6 ae woe oY ee ee ow EERE Sa eo ee ERG Se SAE oe Pee A 45 2 90 Symmetry Options Window arora 2026044 e888 See eee OU ee eee GAS SEE 6S SEARS A5 2 51 Job Parameters window calculation type a a 47 2 52 Job Parameters window basis set dd A AA AA A A AAA 48 2 53 Job Parameters window density functional a ra dd te eh E ee ee Pe ey ee Ee 49 2 54 Job Parameters window semiempirical a a a a a a a 50 200 JOP OULPUWINGOW pea cpa 6 2 i eai eae a n a e a SS a a a 51 2 56 Parallel Job Submission window background job initial view 00000 eee 52 25 Backerotina Job icon legend e sne as ee Be oe PO eh we EG Be ee Ow ED ee we SHS 52 2 58 Parallel Job Submission window back
95. he pqsmol build files with the pqb extension are displayed You can change the current browse directory by selecting entries in the Directories list on the left and a specific file can be selected from the Files list on the right side Create Dir Delete File Rename File fhomefpawelTESTs Directories Files tu big pob af ciz pak Home COMPLEXES ci hi pgb TF contracted ci4hiz pgb TF segmented che pgb iotest c h pab c4h1 O pqb Desktop c4hb pob c4ho pob coh E pq Z cBh12 ngb ch 2 pgb oka nah Documents 4 b File Type pgb PFOSmol builder file Selection homepawely TES Ts Figure 2 23 File Open dialog e Import allows a range of different file types other than pqb files to be imported The Import Geometry dialog is shown in Figure 2 24 Parallel Quantum Solutions 23 2 1 Build window Create Dir Delete File Rename File home paweVTESTS r Directories z Files b ig inp ae big inp COMPLEXES ci inp TF Y contracted cl hi2 inp TPY segmented cl4h12 inp lotestr c he irip c h4 inp Desktop c h4 ing a c ho irp c4h inp cahe inp ons z Documents x se MN File Type inp POIS input ba inp Fas input Selection homer arre pgb PGSMol builder pqs PGS input coord coordinates 4390 PGS T90 pdb Protein Database mop MOP AC Car mal 2 matris hin Out PGS output lo
96. ically appear whenever a drawing plane is activated It is used to shift the drawing plane by a specific distance in Angstroms To set the plane shift back to 0 Angstroms press the Reset button e Auto Selection toggles the building mode Section 2 3 2 e Auto Torsion toggles the torsion building mode Section 2 3 1 e Torsion Options shows the Torsion Options window Figure 2 29 If the Auto Torsion building mode is active PQSMOL attempts to find the minimal energy configuration during an attach operation When a new segment is attached to the existing structure inside the build area it is rotated around the attachment bond starting at a torsion of 0 degrees The torsion angle is repeatedly incremented by Degree Step degrees until a full rotation is completed At each point in the rotation the van der Waals energy is calculated using the van der Waals Cutoff given in Angstroms The segment is attached at the torsion angle with the lowest van der Waals energy The Animate Optimization check box toggles the animation of the torsion optimization process Torsion Optimization Options Degree step 15 0000 van der Waals Cutoff 10 0000 Y Animate Optimization Close Figure 2 29 Torsion Options window Parallel Quantum Solutions 29 2 1 Build window The Optimize menu File Edit Build agit Symmetry Display Calculation Window Force Field A A A E Check Atom Types o Universal Ciptions Options Optimize Refer to
97. imization cycles Selecting the Loop checkbox will repeatedly loop through the entire history i e will play continuously This can be stopped by either deselecting the Loop checkbox or by closing the entire Optimization Mistory window 80 PQSMol Manual Tutorials 4 1 Example 1 Lactic Acid To get you started using PQSMOLt and PQS we will begin the tutorials with a simple example molecule Lactic Acid Lactic acid also known as milk acid or 2 hydroxypropanoic acid is used in several biochemical processes in the human body Its chemical formula is C3HgQ3 It is schematically shown in Figures 4 1 and 4 2 OH Figure 4 1 Lactic acid structure diagram Figure 4 2 Lactic acid structure In this example we will e build the molecule e perform an initial optimization using the Sybyl5 2 force field e create a PQS input file e run a PQS calculation e examine the molecular orbitals and display the vibrational frequencies 4 1 1 Building the Lactic Acid molecule Step 1 Start the builder by typing pgsmol at the command prompt 82 PQSMol Manual Tutorials We will begin constructing the molecule by first connecting two tetrahedral carbon building blocks Then we will attach the carboxyl functional group from the fragment library The bent oxygen building block for the remaining O H group will be attached next and we will finish by filling all dummy atoms with hydrogens Building Blocks Fragments Clipboard
98. in Figure 2 52 a Geometry Optimization has been chosen and DFT has been selected from among the available calculation methods The basis set can be selected from a pulldown menu There are a large number of choices which cover all of the basis sets stored in the PQS basis library in the PQS ROOT BASDIR directory The selected basis set will appear in the Basis Set box and will also be added to the input file on the right MEM 5 Job specifications TEXT Test Job GEOM Pas Aia h 0 407421 0 898720 0 552090 Title Test Job Memory jo h 0 370075 0 093703 0 980224 c 0 367478 1 121867 082592 7 c 1 595360 1 013542 951921 Molecule Characteristics o 2 359140 0 092816 0 549092 C 0 906622 0 984464 0 953780 l i alir h 1 215465 0 231304 1 641264 Charge 0 oymmetry 0 00001 Multiplicity 1 EEEN 4583745 1 846167 h 2 564668 1 823201 2 338932 l h 1 804127 1 049448 6 319458 Calculation Type h O 360849 2 115796 0 397087 h 0 911296 013525 1 472488 a z h 0 947723 1 787119 1 706885 single Point Energy select type MILELULELE STEP A LIIIIIIITILII oe BASIS 3 21g Geometry Optimization OFT hi OPTImize SCF DFTP 03LYP FORCE Basis Set Method n Basis set d e1q DFT method OLYF semiemp method OL YP Properties OPW wh Vibrational Freg OWNS Electric Field Gry BaL F BLYP Chargesapin De BSP wy BPW 91 BY Pog Bi Ty BV WS mo A TS A E HFS HFB B97 B37 1 Boy 2 EFAG OPEB HTH Pid PBE
99. iodic table Figure 4 26 shows the Build window with the tetrahedral carbon inserted Step 3 Connect the fluorine building block In the Segment window press the fluorine button in the periodic table There is only one building block available for fluorine Your Segment window should now be identical to the one in Figure 4 27 Parallel Quantum Solutions 99 4 2 Example 2 CHFCIBr Building Blocks Clipboard ovbwlo d Force Field Bond Configuration al lla Esti y crfimfrefcofmi cu zn lll Se 1 2 m6 Ho Te Ru Al Pa As Ca Th Sn Sb Te Bal La He Tal Re os TFt aula 71 Pb Bi Pol Atl Ra Ac RF Db Sa Bh Hs He Cel Pe od Fmi Sm Eul Gd Tb Duj Hol Er Tmi voy Lu leal re a en x Cl Figure 4 27 Segment window fluorine building block selected Using the same Add Attach Connect tool move the mouse over the top most dummy atom in the build area The dummy atom will be highlighted with a circle around it The mouse pointer will change to a plus sign with a letter A as shown in the left image of Figure 4 28 This indicates that the dummy atom is a valid attachment point for the segment in the Segment buffer Figure 4 28 Build area attaching the fluorine building block 100 PQSMol Manual Tutorials Click the mouse button over the atom The result is shown in the right image of Figure 4 28 Step 4 Connect the Chlorine building block Select Chlorine in the periodic table
100. irections of the arrows To show an animation of the vibrational mode in the View window activate the Animate checkbox in the Vibrational Frequencies window To view other modes either select another peak in the simulated spectrum or select another mode number in the Frequencies list Parallel Quantum Solutions 109 4 2 Example 2 CHFCIBr lle Options Display Window Help Seibel etali lun Ll ala a gt LME Rotate CME Z00m LMEB SHIFT 4 Rotate LMB select double click deselect Figure 4 40 View window displacements in the most intense IR mode in CHFCIBr Step 12 Examine the Vibrational Circular Dichroism Spectrum Select the VCD radio button at the bottom of the Vibrational Frequencies window This will display the simulated VCD spectrum Figure 4 41 110 PQSMol Manual Tutorials O Infrared Raman CD Zoom Out Halfwidth 10 00 Ea wi Vectors Reverse Animate Figure 4 41 Vibrational Frequencies window VCD spectrum Frequency no 5 selected The corresponding vibrational modes can be displayed and or animated in exactly the same way as for the simulated IR spectrum Selecting the peak with positive rotational strength signal pointing up with the Vectors checkbox activated will show the corresponding atomic displacements in the View window Figure 4 40 At the same time the
101. it for length adjustment The selected bond is highlighted and its length is displayed in Angstroms The selected bond partitions the atoms in the system into two groups stationary and active The active group is surrounded by a gray translucent surface The stationary group is unaffected by the bond length adjustment All atoms in the active group will move when the bond length is adjusted Dragging the mouse up down will increase decrease the bond length Double click to set the length Double click while pressing the lt SHIFT gt key to set the default length for that bond 12 PQSMol Manual Build mode lt Bond Angle tool Adjusts the angle between two bonds Usage Click on two adjacent bonds to select the angle for adjustment The selected bonds are highlighted and the angle between them is displayed in degrees All atoms connected to the open end of the second selected bond are added to the active group and are surrounded by a gray translucent surface Only the atoms and bonds in the active group are affected by the bond angle adjustment Drag vertically to change the angle Double click to set the angle Figure 2 7 Bond angle adjustment 3 Bond Torsion tool Adjusts the torsion of three selected bonds The active group in the Bond Torsion tool includes all atoms and bonds connected to the third selected bond not including the rotation bond as shown in Figure 2 8 Parallel Quantum Solutions 13 2 1 Build window
102. iven in Figure 4 67 which shows perfluoroanthracene imported into the Segment buffer Because of the symmetry of this molecule and the orientation of the coordinate axes in the Segment buffer the structure is shown on edge Drag the mouse pointer in the Segment window to reorient the structure File Edit Build Optimize Symmetry Display Calculation Window Help 3 e al a i Building Blocks Fragments Clipboard Import Geometry From homespawel TESTS TUTORIALS Browse save Fragment As x 0 86816 Y 5 31743 Z 3 2032 T Aulo To Torsion ON Auto Selection ON T Force Field Sybyl5 2 DEFAULT LMB Rotate LMB SHIFT Z Rotate RMB Insertf ttach CMB Zoom CMB SHIFT Select CMB CMTRL Mowe RESTRICTED Figure 4 67 Build window perfluoroanthracene imported into the Segment buffer Using either the Add Attach Connect tool or the overloaded right click in the Default tool insert the perfluoroan thracene segment into the build area Figure 4 68 128 PQSMol Manual Tutorials File Edit Build AS symmetry Display Calculation Window Help HEY i az ms aje 8 i Building Blocks Fragments Clipboard Import Geometry From TUTORIALS F anthracene coard Browse Save Fragment As Add To Lib D eer Y 4 32707 Fl E 8739 Auto Torsion DN Auto selection ON Force Field sybyl5 2 DEFAULT LMB Rotate LMB SHIFT 2 Rot
103. jectory window Figure 3 27 provides an interface to visualize a dynamics trajectory Parallel Quantum Solutions 79 3 6 Optimization History window Prev Play Met Loop Dynamics Step 1 Figure 3 27 Dynamics Trajectory window When first invoked the trajectory is loaded starting at the initial geometry step 1 This geometry is displayed in the View window Selecting the Play button will run through the entire trajectory displaying each geometry sequentially in the View window Selecting the Loop checkbox will play the trajectory repeatedly The trajectory can also be played in either direction forward on back via the slider bar and stepped forward or back via the Next and Prev buttons respectively 3 6 Optimization History window The Optimization History window Figure 3 28 provides an energy with cycle number plot Geometry Optimization Histogram Prev Play ect Loop Figure 3 28 Optimization History window As can be seen in Figure 3 28 the starting and final energies are given as well as the total number of optimization cycles 15 in this case Clicking on any of the points cycles in the graph will display the geometry on that optimization cycle in the View window Clicking on Prev or Next button will display the previous or next geometry relative to the currently selected point respectively Pressing the Play button will run through the complete optimization history displaying all geometries at all opt
104. lace Add Valence Remove Valence and Bond Type Figure 2 42 2 4 Optimization The optimizer in PQSMoL is a bare bones minimizer based on a direct BFGS update of the approximate inverse Hessian matrix with a preliminary energy only line search if the starting structure has large residual forces It cannot be used to optimize transition structures Geometry optimization is performed using the current force field Available force fields are Sybyl5 2 and UFF The current force field is displayed in the upper left corner of the statusbar Figure 2 43 You can select the current force field via Optimize Force Field in the menubar Figure 2 1 2 2 87664 Y 5 10961 2 0 0000 Force Field syhyls e Figure 2 43 Statusbar with the current forcefield highlighted Tip You can also change the current force field by clicking on the force field name in the statusbar File Edit Build Pais Symmetry Display Calculation Window Force Field sybylod Check Atom Types Universal Options Options Optimize Figure 2 44 Optimize menu The Optimize menu enables you to set the current force field set the force field options check and change the force field atom types and set the optimization options Optimize Optimize will start the optimization This is equivalent to clicking the El button in the upper toolbar Parallel Quantum Solutions 41 2 4 Optimization 2 4 1 Force Field Options Force field o
105. ld BTA FUSE BONDS LMB over first bond LMB over en hond RESTRICTED Figure 4 49 Build window fusing the naphthalene and benzene fragments attachment Drag the mouse to rotate about the rotation bond or select the dihedral angle 180 from the rotation preset window that automatically appears The final result should be as shown in Figure 4 50 116 PQSMol Manual Tutorials File Edit Build Optimize Symmetry Display Calculation Window Help ae ali X 0 13778 13778 Y 1 84151 2 4 29360 Tato Torsion ON Auto Torsion ON CEE Auto Selection ON T 7 Force Field Sybyl5 2 FUSE BONDS LME over first bond LMB over matching bond RESTRICTED Figure 4 50 Build window fusing the naphthalene and benzene fragments rotation Double click inside the build area to clear the selection and set the angle Step 5 Add the fluorine atoms Select Building Blocks tab in the Segment window and select fluorine from the periodic table In the default Sybyl 5 2 force field there is only one fluorine building block which will be shown in the Segment buffer Select the Add Attach Connect tool and replace every ring hydrogen atom by fluorine You have now built perfluoroanthracene Figure 4 51 Parallel Quantum Solutions 117 4 3 Example 3 Methoxy Substitution in Perfluoroanthracene File Edit Build Optimize Symmetry Display Calculation Window Help EPIA o ale 8 i Building Blocks
106. led F anthracene 0OMel out 4 3 6 Visualizing the PQS job output Step 12 Capture the 9 F NMR spectrum of 1 methoxy perfluoroanthracene This is basically a repeat of Step 8 with perfluoroanthracene replaced by 1 methoxy perfluoroanthracene View the output file for the 1 methoxy derivative by typing pqsview F anthracene OMel out at the command prompt Figure 4 73 Parallel Quantum Solutions 133 4 3 Example 3 Methoxy Substitution in Perfluoroanthracene File Options Display Window Help xa etel uu I esana LME Rotate CME Z00m LMBE J SHIFT 4 Rotate LMEJ select double click deselect Figure 4 73 View window 1 methoxy perfluoroanthracene fluorine atom no 9 selected Exactly the same sequence of operations as described in Step 8 should result in the following 19 F NMR spectrum Figure 4 74 ie l y A eee eee Co Range End 160 Range Start 110 Zoom Out Hatfwidth 0 00 60 iii J PERES H 1C Reference Shit 179 42 6 User Auto By selection E11 F Figure 4 74 NMR window 1 methoxy perfluoroanthracene F NMR spectrum 134 PQSMol Manual Tutorials 4 3 7 Building 2 and 9 Methoxy Perfluoroanthracene and Visualizing the PQS job outputs Steps 9 through 12 can be repeated to construct and capture the F NMR spectra of the 2 and 9 methoxy derivatives The output files are available as F anthracene OMe2 out and F anthracene OMe9 out respectively The structures and NMR spectra
107. mation the user needs to supply is the job name this should already be available in the Job Name box corresponding to the name given in the Job Input section above and the number of CPUs to run on selected by clicking the up and down arrows next to the Processes entry box alternatively the number can be typed directly into the box This information will automatically be used in the SGE script shown in the text area at the top of the window The current status of the SGE parallel job queue is displayed in the text area at the bottom of the window The Show Queue checkbox is automatically activated when SGE job submission is invoked so the status of the job queue will be immediately displayed In this example two 4 processor jobs cadion_BIG and annulene B are already running in the queue submitted by user malagoli Tip To hide the queue deselect the Show Queue checkbox Clicking the Submit Job button will submit the SGE script If all CPUs are currently running other jobs the job will be placed in the queue in a wait state until CPUs are freed up 56 PQSMol Manual Build mode Clicking on the Done button will close the Submit window 2 6 3 Job Results The Calculation Job Results menu item invokes the PQS view mode which opens a separate window allowing post job visualization and display Display options include visualization of molecular orbitals canonical localized and natural electron densities and electr
108. mmand did not receive a response from that node Notice that the label on the status button remains unchanged Clicking on the Check button will cause another attempt to ping the node The icon shown for node n3 indicates a problem with PVM on that node This is a result of more than one PVM daemon executing on the node The status button for this node is labeled Repair If clicked it will execute a command which will kill all running PVM daemons on that node and clean the temporary PVM directory The icons for node n4 show that the PVM daemon is not running and that there are scratch files present on that node The status button is labeled Toggle and if clicked will add this node to the PVM Refer to Figure 2 57 for a complete list of icons and their meanings Tip You can move the mouse pointer over the garbage icon to display a list of scratch files as shown in Figure 2 58 for node n4 Since at least one node is now a part of the PVM node n1 the Launch Job button and the Processes entry box become active compare Figures 2 56 and 2 58 All PVM processes in our example three two computation processes the master process are scheduled to run on the only available node in the PVM node n1 Parallel Quantum Solutions 53 2 6 PQS Calculation Note A parallel PQS job is composed of multiple computing processes and one master process The master process performs little or no computation It simply distributes the workload
109. ms are moved accordingly The drawing plane must be defined before the Snap to Plane tool can be used Figure 2 16 Snap to Plane example starting configuration Usage Click on an atom in the structure to be reoriented The selected atom is highlighted with a green translucent sphere All remaining atoms in the segment are added to the active group and the segment moves so that the atom selected is in the drawing plane Parallel Quantum Solutions 19 2 1 Build window Figure 2 17 Snap to Plane example first atom selected Click on the second atom The atom is highlighted with a green translucent sphere and all atoms in the active group are rotated so that the second atom is also positioned in the drawing plane Figure 2 18 Snap to Plane example second atom selected Click on the third atom in the structure This atom is also highlighted with a green translucent sphere and all atoms in the active group are rotated so that all three selected atoms are positioned in the drawing plane Figure 2 19 Snap to Plane example third atom selected Note This tool is only available if the drawing plane is turned on 20 PQSMol Manual Build mode Replace tool Replaces any atom in the current structure in the Build window with any other atom in the periodic table Usage Click on the atom in the periodic table you wish to substitute Click on any atom in your current structure to replace that atom with an
110. n point the mouse pointer changes to Xx Tip At all times a single atom in the structure in the Segment buffer is highlighted This atom is the attachment point for the segment During the attach operation this atom will be replaced with a bond connecting the newly inserted segment with the structure inside the build area You can change the attachment point of the segment by clicking on any atom that has just one bond connecting it to the reset of the segment Move tool Repositions selected atoms and bonds inside the Build window This tool s functionality depends on the state of the Auto Selection mode With Auto Selection mode enabled a selection is automatically applied to the entire segment containing an atom to be moved The whole segment is then moved With Auto Selection mode disabled a manual selection is required before using the Move tool Although an additional step is required this mode offers more control over atom and bond movement Usage Move the mouse pointer over an atom and click If the Auto Selection option is on the segment containing the atom is selected and highlighted with a gray translucent surface Drag the segment to the desired location and release the mouse button If Auto Selection mode is off first select the atoms to move using either the Select or the Select Segment tool Then using the Move tool drag the selection to the desired location Tip To change the Auto Selection click on the Auto S
111. n view mode is the fastest to render It is recommended for large structures i e containing hundreds of atoms and slow graphics cards Labels toggles atom labels e Coordinates toggles the coordinate axes e Hydrogen Hide shows hides hydrogen atoms e Options Background shows the Background Color window Figure 2 30 Parallel Quantum Solutions 31 2 1 Build window Blue ES3 CS e EA a Y OS ae Ol Saturation 0 25 values E 0 40 Red e 0 30 areon Se oao caca Figure 2 30 Background Color window This allows the background color of the Build window to be set via the slide bars The background color can also be selected by positioning the mouse pointer on the small circle inside the large colored circle and dragging the mouse to the desired location as the small circle moves the slide bars will also shift reflecting the new background color e Options Graphics shows the Graphics Options window Graphics Options SAT 2 Figure 2 31 Graphics Options window This window controls the quality of the graphics again using slide bars Moving the slide bars further to the right increases the corresponding value High quality graphics will give crisp clear pictures but will increase the time taken to display or manipulate any graphical image The Calculation menu File Edit Build Optimize Symmetry Display peee Window Job Input Sub MIT Jok Submit Parallel Job Job
112. nd mouse shortcuts Build Mode Figure 2 33 Statusbar in build mode The statusbar displays information about the current status of PQSMoL Figure 2 33 In the top left corner the 3D coordinates of the mouse pointer in Angstr ms are shown During the add operation point 0 0 0 in the segment being inserted will be aligned with the mouse pointer coordinates On the top right side of the statusbar the Torsion Mode and the Selection Mode are shown as well as the current Force Field In the bottom left corner of the statusbar the name of the Current Tool is displayed The area to the right is the Tool Description which displays information on how to use the tool The acronyms LMB RMB and CMB stand for Left Mouse Button Right Mouse Button and Center Mouse Button respectively In the lower right corner the current restriction mode is displayed The torsion mode selection mode force field and the restriction mode can all be toggled via a mouse click in the corresponding entry in the statusbar 2 1 4 Useful Shortcuts e Ctrl O Open File e Ctrl C Copy e Ctrl S Save File e Ctrl V Paste e Ctrl1 Q Quit e Ctrl A Select All e Ctrl Z Undo e Ctrl N Select None e Ctrl Y Redo e Ctrl I Inverse Selection e Ctrl X Cut e Ctrl H Hydrogen Fill 2 2 Segment window The Segment window provides access to the various fragments and building blocks from which new molecular structures can be constructed The top area of the Segment window is the Segme
113. ndow you can save it in JPEG format via the popup menu Right click anywhere within the View window and select the Capture menu item A dialog prompting for a filename appears Figure 4 20 94 PQSMol Manual Tutorials Create Dir Delete File Rename File home pawel TESTS S Directories 2 Files i 1 wf 13 1 3 6up Amm out Home COMPLEXES FIOCT4 inp JONs FIOC14 pb TPY contracted FIOCTSHS inp TPY segqmented FIOCTSHS pqh lotest INSTALL Desktop INSTALL Laszlo log MOSH basis MCHA basis MZ3HS control bhag Ammar Documents 4 gt selection homerparwelfTESTS mol_capturel pol Figure 4 20 Save Image dialog You may save the image under the suggested name mol_capture1 jpg in the current working directory by simply pressing the OK button To turn off the MO display either toggle the state of the Orbitals button in the toolbar or close the Orbitals window Step 14 Examine the Vibrational spectrum Mn To display the simulated IR spectrum click on the Vibrational Frequencies button ub in the toolbar at the bottom of the View window The simulated IR spectrum is shown in Figure 4 21 req OFF Z a El J E T E Infrared Raman YLO Zoom Out Halfwidth 10 00 q 10 Vectors Reverse Animate 11 F Figure 4 21 Vibrational Frequencies window IR spectrum mode 1 selected The list on the right side of the Vibrational Frequencies window allows access to all of the vibrational
114. niversal 10 25 30 33 35 36 39 44 HOMO 66 68 hydrogen hide 9 31 IR spectrum 1 57 61 70 72 LUMO 66 NMR spectrum 1 57 61 73 75 77 79 98 111 119 122 125 133 135 137 138 Operation Modes Build 1 2 5 60 67 View 1 2 60 91 106 121 optimization 7 30 36 41 43 45 82 86 101 133 options 41 42 optimization history 1 57 61 64 80 orbitals 1 57 61 64 66 69 82 92 94 106 Raman spectrum 1 57 61 70 72 symmetry 7 30 45 46 60 64 102 111 118 128 138 146 options 45 Tools Add Valence 21 41 Add Attach Connect 9 10 84 98 100 101 112 117 128 130 Bond Angle 13 Bond Break 15 Bond Fuse 15 115 Bond Length 12 13 Bond Torsion 13 Center All 7 Center on Atom 17 Check Symmetry 7 30 45 87 Copy 8 34 Cut 8 26 34 Default 9 10 84 99 112 128 130 Define Draw Plane 8 18 Face Front 8 Hydrogen Fill 7 28 34 86 Info 10 Move 9 11 Optimize 7 Paste 8 26 34 Redo 8 26 34 Remove Valence 21 Reorient 17 18 Reorient Selection 17 114 Replace 21 41 Rotate About a Bond 14 Select 9 11 13 18 Select All 7 34 Select None 7 34 Select Segment 11 Snap to Plane 19 Undo 8 26 34 Zoom 10 12 VCD spectrum 1 57 61 70 72 98 110 vibrational frequencies 1 61 62 82 95 119 Windows Build 2 5 11 16 17 21 24 26 28 32 35 37 39 42 44 46 84 86 87 98 99 101 1
115. not yet been named the File Save dialog Figure 4 53 will appear prompting you to provide a filename By default the empirical formula will be provided as a filename this can be changed by typing in an alternative name Here the file has been named F anthracene pqb the file extension must be pqb Create Dir Delete File Rename File fhomepawelGulldevelopmentpgsmal 1 2 E r Directories Files E wf datar imagecapi lic Mo scripts Desktop support Documents File Filter pop PGtsrmol build file Y Selection shome pawel Glldevelopmentpgstal 1 2 F anthracene pqbl Figure 4 53 File Save dialog Once the file has been successfully named the input preparation window will appear Figure 4 54 As shown the job has been set up as a BBLYP tzvp_ahlirchs optimization frequency NMR Parallel Quantum Solutions 119 4 3 Example 3 Methoxy Substitution in Perfluoroanthracene Joh specifications Title perflucrcanthracene OPT FREQ Memory Molecule Characteristics Charge 0 Symmetry 0 005 Calculation Type single Point Energy Geometry Optimization OFT Basis SetMethod Basis set fzvp_ahlrichs DFT method BaL F semiemp method PAs Froperties Electric Field Gradient CO Charge spin Density COSMO Population Analysis Sel HEH 4i TEST perfluoro GEOM POS SYHH c o o o z c o f F f f f f f F f f c o o z o o IIIIIIIIIII ST BASIS
116. ns 65 3 2 Orbitals window 3 2 Orbitals window Molecular Localized Matural Mechs Tecate eM Default View Default View we e Alpha Alpha Natural Alpha Alpha Natural Beta Beta Full wiew Beta Beta Full View h ah Energy Lewels MIC Closed Shell OFF 143 132 131 130 124 120 127 126 120 124 123 122 121 120 114 116 117 447 Energy Levels Closed Shell Isosurace level Isosurface level 0 050000 0 050000 A Cross sections Cross sections 1 000 1 000 1 000 1 000 1 000 1 000 Electrostatic Potential Electrostatic Potential Display Potential Linear scale AE Ple Hingar Scala Figure 3 8 Orbitals window electron density selected full view Figure 3 7 Orbitals window initial display When first invoked the Orbitals window presents the default view which shows all valence occupied MOs above an energy of 2 500 En and the first ten virtual unoccupied MOs Orbital energy levels are displayed in a graph on the left and the orbital numbers are given in the list on the right side of of the window The highest occupied orbital HOMO and the lowest unoccupied orbital LUMO are indicated with an H and an L respectively next to the corresponding orbital numbers in the list The energy levels and the energy range are displayed in the large central window The type of orbitals to be displayed can be selected using radio buttons at the top of the window Alpha
117. nt bonds to get the angle between them or any three bonds sharing two atoms to get the torsion and out of plane bend Add Attach Connect tool The tool performs three distinct actions The Add action inserts the current segment in the Segment buffer into the Build window The Attach action attaches the current segment in the Segment buffer to a structure inside the Build window The Connect action is used to connect two atoms which are already inside the Build window Usage 1 Add Move the mouse pointer over empty space in the Build window The mouse pointer changes to t Click to insert the segment displayed in the Segment buffer into the Build window at the location of the mouse pointer 2 Attach Move the mouse pointer over an atom If the atom is a compatible attachment point the mouse pointer changes to A and the atom under the pointer is highlighted Click to attach the segment displayed in the Segment buffer to the molecule in the Build window at the selected attachment atom If the atom under the mouse pointer is not a compatible attachment point the mouse pointer changes to 10 PQSMol Manual Build mode Xx 3 Connect Move the mouse pointer over an atom click and drag the mouse to a second atom If the second atom is a valid connection point the cursor changes to C Release the mouse button to create a bond between the two atoms If the atom under the mouse pointer is not a compatible connectio
118. nt buffer At any time the Segment buffer stores and displays the segment which would be inserted into the Build window if the user executes the insert operation Immediately below the Segment buffer there are three tabs These are labeled Building Blocks Fragments and Clipboard The Segment buffer is used to display structures selected in all three tabs 34 PQSMol Manual Build mode 2 2 1 Building Blocks The Building Blocks tab contains a periodic table of elements and a Bond Configuration frame The availability of individual element buttons in the periodic table as well as buttons in the Bond Configuration frame depend on the current force field Only elements that are defined in the current force field are available in the periodic table and only the bond configurations known to the current force field are available in the Bond Configuration frame The currently selected basic building block appears in the Segment buffer and can be added to the build area as shown the default is an sp3 hybridized carbon The force field type currently selected is shown in the statusbar of the Build window see Figure 2 33 a click on this box will toggle between the Sybyl5 2 and Universal force fields The current atom type is highlighted in the periodic table as a button with a green background it is also displayed in large font above the periodic table Building Blacks Fragments Clipboard Building Blocks Clipboard Sybyla
119. o static potentials optimization history energy geometry at each cycle of a geometry optimization dynamics trajectories animation of vibrational modes and simulation of IR Raman VCD and NMR spectra All of these will be discussed further in Chapter 3 Parallel Quantum Solutions 57 View Mode File Options Display Window Help hb e elji wmo l alml f A Mer Rotate CMB Zoom LMB SHIFT Z Rotate LMB Select double click deselect Figure 3 1 PQSMOL running in view mode Parallel Quantum Solutions 59 3 1 View window Typing pqsview from the command prompt starts PQSMOL in view mode Without command line arguments PQSMoL opens a file browser to choose a file to visualize If pqsview is followed by a PQS job name with the extension out providing the job has completed successfully and all relevant job files are available the job is opened for visualization It is also possible to start job visualization in build mode using the Calculation Job Results menu item Figure 3 1 shows PQSMOL running in view mode visualizing the results of a calculation on aspirin A successful PQS job generates several files with various extensions From among these PQSMOL running in view mode can open files with extensions coord log out and the input file itself inp From the coord log and inp files only the molecular geometry is extracted To dis
120. om Out Halfwidth 0 00 Reference Shift 0 User Auto By selection Figure 4 58 NMR window F NMR spectrum with zero halfwidth The NMR spectra shown in Figures 4 57 and 4 58 display the raw average shielding values as computed by PQS Experi mental chemical shifts are all given with respect to a reference and a common one for F NMR spectra is the F signal in CF3Cl This can be taken to be 179 42 see M Muir and J Baker J Fluorine Chem 126 2005 727 and typing this value into the Reference Shift entry in the bottom left corner of the NMR window results in the spectrum shown in Figure 4 59 AMA Spectrum F Atoms selected value 1 45 01 7 Ted Range End 158 465 Range Start 117 958 Zoom Out Halfwidth 0 00 Reference Shift 117942 8 User Auto By selection Figure 4 59 NMR window F NMR spectrum using CF3Cl as reference Using a non zero reference of course changes the relative chemical shift values and thus the spectrum range In order Parallel Quantum Solutions 123 4 3 Example 3 Methoxy Substitution in Perfluoroanthracene to directly compare different NMR spectra i e in this case the F spectra of perfluoroanthracene with its methoxy substituted derivatives it is helpful if the different spectra cover the same spectral range To facilitate this we are going to change the Range End entry to 160 ppm and the Range Start entry to 110 ppm This changes the starting and ending values on the X axi
121. oss Sections 1 000 1 000 1 000 Electrostatic Potential Display Potential Linear scale Figure 4 37 Orbitals window electron density selected The corresponding View window is shown in Figure 4 38 Parallel Quantum Solutions 107 4 2 Example 2 CHFCIBr File Options Display Window Help Xea ejteji O uju DAA ea LMB SHIFT Z Rotate LMB Select double click deselect Figure 4 38 View window electron density displayed Use the Isosurface level slider in the Orbitals window to change the displayed isosurface Step 11 Examine the IR Spectrum Press the Vibrational Frequencies button MJ in the toolbar at the bottom of the view window The Vibrational Frequencies window appears Figure 4 39 displaying the simulated IR spectrum Select the most intensive signal in the IR spectrum by clicking on highest peak in the graph or select 5 in the Frequencies list on the right After activating the Vectors checkbox the atomic displacements in this mode will be displayed as yellow arrows at each atom in the structure in the View window Figure 4 40 108 PQSMol Manual Tutorials Freq OFF 1 Z a 4 E T ci Infrared Raman YCD Zoom Out Halfwidth 10 00 9 lv Vectors Reverse Animate Figure 4 39 Vibrational Frequencies window most intense IR mode in CHFCLBr The corresponding View window is shown in Figure 4 40 Activating the Reverse checkbox will reverse the d
122. ot bicyclo 3 2 0 heptane paf HETEROCYCLIC bicyclo 4 2 0 octane por 7 z LIGANDS cis decalin paf fluorene pot MONOCYCLIC NUCLEOTIDES trans decalin paf ORGANOMETALLICS POLYCYCLIC SOLVENTS SUGARS pee Po j lo T5 k gt UE ee Dia Ez USER LIB x 044868 Y 0120 ie 14 30824 oe Su nae Soa A POST Sybyl5 2 DEFAULT LME Rotate LMBE SHIFT Z Rotate RMBE Inserf ttach CME Zoom CMB SHIFT Select CMB CMTRL Mowe RESTRICTED Figure 4 46 Build window inserting the naphthalene fragment Step 3 Insert the benzene fragment Now select the MONOCYCLIC fragment library and select benzene Move the mouse pointer into the Buzld window and insert the fragment in the empty space to the right of the naphthalene fragment This should add the benzene fragment into the Build window as shown in Figure 4 47 Parallel Quantum Solutions 113 4 3 Example 3 Methoxy Substitution in Perfluoroanthracene File Edit Build Optimize Symmetry Display Calculation Window Help EY Y cor 4 58852 58852 aaa Torsion ON Auto Selection ON DEE E BTA DEFAULT LMB Rotate LMB SHIFT Z Rotate RMB AES CMB Zoom CMB SHIFT 5elect RESTRICTED Figure 4 47 Build window inserting the benzene fragment As shown the benzene fragment is oriented differently from the naphthalene fragment It can be reoriented into the build a plane by
123. ow most intense IR mode in CHFCLBr 109 Parallel Quantum Solutions 143 LIST OF FIGURES 4 40 4 41 4 42 4 43 4 44 4 45 4 46 4 47 4 48 4 49 4 50 4 51 4 52 4 53 4 54 4 55 4 56 4 57 4 58 4 59 4 60 4 61 4 62 4 63 4 64 4 65 4 66 4 67 144 View window displacements in the most intense IR mode in CHFCIBr 110 Vibrational Frequencies window VCD spectrum Frequency no 5 selected 111 Perfluoroanthracene showing substitution sites oa o e e a a a a 111 Perftoroantatacene aaa uy e a a aaa aE ee ere a we we e E de aa a E 111 1 methoxy perfluoroanthracene substitution at site 1 o ee 112 lsme ethox perhuoro am Aracena sson sos cis bb aa e e ble ee le aA Ee eS A ee we i 112 Build window inserting the naphthalene fragment 2 a a a 113 Build window inserting the benzene fragment a a a a a 114 Build window reorienting the benzene fragment ooa a a k 115 Build window fusing the naphthalene and benzene fragments attachment 116 Build window fusing the naphthalene and benzene fragments rotation 0 0004 117 Build Window hydrogen replaced with fluorine 2 2 a a 118 SVE O Sos a Beas a AI ABE AAA 118 PUSE IO iio e Bs tae O Ge ies ie is ed de de Heras ao ta he Gh om ee es ee de BO E dee gratis Die e d 119 Input generation
124. play the properties calculated in the PQS job PQSMoOoL must open the out file Visualization options are available via the buttons in the toolbar at the bottom of the View window or in the menu at the top 3 1 View window 3 1 1 Toolbar Figure 3 2 Toolbar in view mode The first six icons in Figure 3 2 provide the same functionality that is available in build mode Figure 2 1 1 Check Symmetry Determines the molecular point group symmetry Unlike in build mode Figure 2 5 there is no option for varying the symmetry threshold Point group symmetry is determined using the same default threshold as in the PQS program itself al E Face Front Rotates the molecule so that the X Y plane is parallel with the screen lod Labels Toggles atom labels Coordinates Toggles the coordinate axes Hydrogen Hide Shows hides hydrogen atoms Info Window 60 PQSMol Manual View Mode Toggles the info window The next five icons activate the visualization windows molecular orbitals vibrational frequencies NMR dynamics trajec tory and optimization history If any of these features are unavailable for the current PQS job i e were not calculated the corresponding button will be greyed out and the feature will not be accessible is Molecular Orbitals Activates the Orbitals window PQSMOL can display canonical localized and natural orbitals the electron density and the electrostatic potenti
125. ptions currently just the van der Waals cutoff are available in the menubar under Optimize Force Field Options see Figure 2 45 The force fields in PQSMoL do not have an Ewald summation or equivalent of all pair wise van der Waals interactions instead there is a simple cutoff default 10 Angstroms beyond which the van der Waals terms are simply neglected This value can be changed here Force Field Options van der Waals Cutoff 10 0000 Close Figure 2 45 Force Field Options window 2 4 2 Optimization Options There are several optimization options available Figure 2 46 Optimization Options oteps 300 Print Flag 0 GTOL 0 00030 ETOL 0 000001 Calculate Hessian Oplimization Animation update 40 Close Figure 2 46 Optimization options e Steps sets the number of optimization cycles default 500 e GTOL sets the convergence criterion for the root mean square gradient default 0 0003 e ETOL sets the convergence criterion on the change in energy from the previous cycle default 10 e Print Flag sets the verbose output level for debugging only e Calculate Hessian calculates a starting Hessian matrix for the Sybyl5 2 force field only there is no effect for the Universal force field e Optimization Animation update sets the number of cycles between geometry updates to the Build window Setting this option to a value of 1 will cause a structure geometry update on every optimization cycle A v
126. r cut operation takes place in the Build window the Clipboard tab is automatically selected and the contents of the clipboard are updated and displayed in the Segment buffer Once in the clipboard a segment can be reused and pasted or attached back in the Build window possibly multiple times The clipboard is also used for importing fragments into PQSMOot When a fragment is imported it is first placed in the Parallel Quantum Solutions 37 2 3 Building Modes clipboard This allows you to inspect the fragment and select its attachment point before using it in the Build window Additionally the clipboard is an interface to the USER LIBrary As well as using the predefined fragments you can build your own fragments and store them in the USER LIBrary The fragment can be constructed in the Build window optimized and then selected in its entirety and copied into the clipboard Once in the clipboard Figure 2 37 it can be added to the user s own fragment library The fragment has to be given a filename with a pqf extension in the Save Fragment As text entry The pqf extension is the common extension for all stored fragments The Add To Lib button saves the file in the user s fragment library producing the dialog shown in Figure 3 4 The fragment will now appear in the list under the USER LIB category Fragment ihome pawel pasmol sfragments phenol pot added to User Fragment Lib 2 3 Building Modes There are three building mode
127. rbitals in those directions enabling the internal structure to be more easily seen Just as in build mode the entire structure can be rotated along with the displayed orbital by dragging the mouse inside the View window This allows the current display orbital to be examined from different perspectives Parallel Quantum Solutions 67 3 2 Orbitals window Molecular Localized Matural Molecular Localized WMatural 9 poo Default view Default View Alpha Alpha Natural a Alpha Alpha Matural e E Beta Beta Full Mie Beta Beta Full iew Energy Levels Moe Moe Closed Shell OFF OFF Elect Elect ar oe oF oF oe oe 14 5d da Ed I I a a ol o0 49 43 45 L 40 L Ab Ab 45 45 44 AA At At dz A Orbial d4 Energy 0 271 Ey HOMO 4 4 Am ul Am bul Isosurtace level Isosuiface level 0 050000 0 050000 Cross Sections Cross Sections 1 000 1 000 1 000 1 000 1 000 1 000 Electrostatic Potential Electrostatic Potential Display Potential Linear scale Display Potential Linear scale Figure 3 10 Orbitals window HOMO orbital selected Figure 3 11 Orbitals window HOMO orbital zoom Figure 3 10 shows the corresponding Orbitals window to the View window in Figure 3 9 The displayed orbital is highlighted with a red line in the energy level graph and the orbital number is highlighted in the orbital list An orbital zoom in the energy level graph can be accomplished by positioning the mouse pointer just below or just above the energy l
128. ressing the lt SHIFT gt key to rotate the active group around the Z axis i e out of the plane of the Build window Double click to set Parallel Quantum Solutions 17 2 1 Build window Figure 2 13 Reorient example Note If Auto Selection mode is off then the atoms to be reoriented should be selected first via the Select tool and then the reference atom for the reorientation selected using the Reorient Selection tool E Define Draw Plane tool Defines a drawing plane by selecting three drawing plane atoms Usage Click on three non linear atoms to define a drawing plane Each selected atom will be highlighted with a red translucent sphere When the third atom is selected the drawing plane intersecting the three atoms will be displayed Figure 2 14 drawing plane Simultaneously with the drawing plane the Plane Shift window appears Figure 2 15 This enables the plane to be shifted vertically perpendicular from its original location by a specific distance in Angstroms To set the plane shift back to 0 Angstr ms press the Reset button 18 PQSMol Manual Build mode Figure 2 15 Plane Shift window To toggle the drawing plane use the drawing plane button in the upper toolbar gt Snap to Plane tool Positions structures in the drawing plane as defined by the Define Draw Plane tool Up to three selected atoms can be position in the drawing plane The segment possibly segments containing these ato
129. restriction mode is to click on the area of the statusbar displaying the current restriction mode in the lower right corner see Figure 2 39 Building Blocks Clipboard Unrestricted Bond Configuration ERE ERE is e is en Ms 7 y cr tial Fe co Ni cu zr eRe Sr Y fzr Nolo Tel Rh Pal Aa Cl S Bb Te fi arf oir Ac RF al E Ht Figure 2 41 Segment window in restricted mode left and in unrestricted mode right In unrestricted mode all generic structural motifs are accessible see Figure 2 41 right image and can be used with any atom in the periodic table Thus you can construct a system containing e g an octahedrally coordinated hydrogen atom Additionally you can add and delete valency bonding to any atom increasing or decreasing the number of bonds that can be made to other atoms The nature of a bond single double aromatic etc can also be changed The downside to being able to build almost anything is that once you have switched to unrestricted mode there is no guarantee that you will be able to optimize the geometry of your system as many atom types may no longer be recognizable to the Sybyl5 2 and the UFF force fields 40 PQSMol Manual Build mode Figure 2 42 Lower toolbar in restricted mode top and in unrestricted mode bottom Note the last four buttons in both images The unrestricted mode allows access to four additional tools not available in the restricted mode Rep
130. s Delete File Rename File home pawel TESTS Directories Fi at COMPLEXES ES TPY contracted TPY seqmentec TUTORIALS otest File Filter pop PGtsrmol build file selection shome pawel TE STs BrclFCH pqh Tutorials na al Files CBH14 pqb CaF cpgb FIOC14 pgh FIOCTSHS pqb MCHA pqh 0016N0c224H42 pab OSC SHE 2 pqb OSC SHE pqb OG CAHE pab ONZC3H6 pgb aspirin pgb azt pgb him nabh 4 Figure 4 32 Save dialog The empirical formula is automatically set as the filename with the pqb extension You may change the filename however it has to end with pqb Click the OK button to save the file under the selected name Step 10 Start the input generator Use the Calculation Job Input menu item to start the input generator The job parameters window is shown in Figure 4 33 Parallel Quantum Solutions 103 4 2 Example 2 CHFCIBr TERAT CHFC1Er opt freq time wcd Job Specifications GEDM PUIS e 0 386306 0 361578 0 319963 as f O 387000 O 998339 O 321556 Title CHFCIBr opt freq nmr v cal Memory a i 599049 O SEES92 5 322441 br 1 278049 998339 1 219520 o h O 908245 O 722147 1 219520 Molecule Characteristics IIIIIIIIII STEP 2 IHIIIIIIDI BASIS 6 3119 dp irali OPTImize Charge 0 oymmetry 0 00007 Multiplicity SCE DETP BILYP FORCe JUMP Calculation Type HHR VCH HESS Single Point Energy Select type PER Geometry Optimization
131. s in PQSMoL e Auto Torsion e Auto Selection e Restricted Unrestricted mode The status of each mode is displayed in the statusbar Figure 2 39 A 2 07664 Y 3 10961 4 0 0000 Auto Torsion ON Auto Selection ON Force Field S byls 2 ROTATE ABOUT amp BOND LMB to select a rotation bond DRAG double click to set SHIFT double c Figure 2 39 Statusbar with the Building Modes highlighted All three modes may be toggled by either clicking in the appropriate area in the statusbar or activating the corresponding menu item Build Auto Torsion Build Auto Selection and Build Mode 38 PQSMol Manual Build mode 2 3 1 Auto Torsion When the Auto Torsion mode is active PQSMOoL attempts to find the minimal energy configuration for the resulting structure during the attach and connect operations When a new segment is attached to the existing structure inside the build area it is rotated around the attachment bond starting at a torsion of O degrees The torsion angle is repeatedly incremented by a specified number of degrees see Figure 2 29 until a full rotation is completed At each point in the rotation the van der Waals energy is calculated using a specified van der Waals Cutoff see Figure 2 29 The segment is attached at the torsion angle with the lowest van der Waals energy Note The Auto Torsion option affects the attach and connect operations only 2 3 2 Auto Selection When the
132. s of the NMR spectrum as shown in Figure 4 60 Range End 160 Range Start 110 Zoom Out Halfwidth 0 00 Reference Shit 11342 6 User Auto By selection Figure 4 60 NMR window F NMR spectrum with modified range Changing the range in this way has the effect of slightly compressing the spectrum Finally we are going to capture an image of the NMR spectrum Position the mouse pointer anywhere inside the NMR spectrum graph and press the right mouse button this will produce a popup menu with a single menu item labeled Capture see Figure 4 61 Range End 160 Range Start 110 Zoom Gut Halfwidth 0 00 Reference Shit 11342 6 User Auto By selection Figure 4 61 NMR window Capturing an image of the F NMR spectrum Note The spectrum image captured in this example has a white NMR plot line on a black back ground This color combination may not be the suitable for printed media You can change the background color of the spectrum with the Options Graph Background menu item and the plot color with Options Graph Plot Activating the Capture menu item will cause the Save Image As dialog shown in Figure 4 62 to appear prompting you for a file name to save a JPEG image As shown the default name is nmr_capture1l jpg Change this to e g F anthracene jpg and press the OK button to save the image 124 PQSMol Manual Create Dir 3 hd Home Desktop Hhometparwelr TESTS TUTORIALS
133. s perfectly adequate for this example Parallel Quantum Solutions 101 4 2 Example 2 CHFCIBr To run the optimizer press the Optimize button El in the top toolbar Figure 4 30 shows the result Press the OK button to close the geometry optimization dialog Done in 11 Cycles Energy 0 000004 Figure 4 30 Geometry optimization results Step 8 Check for symmetry The symmetrizer in PQSMoL is initiated via the Check Symmetry button 34 in the top toolbar This operation attempts to find any axes of symmetry in the built structure within a specified threshold If any symmetry is found the atoms are repositioned to conform exactly with the found symmetry Our example molecule has c1 symmetry i e no detected symmetry as shown in Figure 4 31 Point Group ci Degrees of Freedom 3 Figure 4 31 Symmetry results dialog 4 2 2 Creating a PQS input file PQSMOL includes a built in PQS input generator which lets you create PQS input files in a graphical environment using text entries radio buttons checkboxes and dropdown menus The result is a text file containing the proper keywords formating and syntax required by the PQS program Step 9 Save the build file Before proceeding with input file creation we need to name our build file Use the File Save menu item to name our example file You should now see the dialog in Figure 4 32 102 PQSMol Manual Create Dir 3 is Home Desktop Document
134. s shown in Figure 4 10 86 PQSMol Manual Tutorials Done in 33 Cycles Energy 1 904373 Figure 4 10 Build window optimization results Press the OK button to close the Optimization Progress dialog Step 8 Check for symmetry Use the Check Symmetry tool 34 the third button in the top toolbar to check for any point group symmetry There is no symmetry in lactic acid and so the point group is C1 Figure 4 11 Point Group cl Degrees of Freedom 30 Figure 4 11 Symmetry dialog Press the OK button to close the Symmetry dialog 4 1 2 Creating a PQS input file PQS package requires an input file to specify the type of calculations to be carried out Because of the various capabilities and options available in PQS there are a large number of keywords and options available in the input syntax Refer to the PQS manual for a detailed description PQSMOL has a built in PQS input file generator that provides a simple point and click interface for creating input files with the most common options Step 9 Create a PQS input file Select the Calculation Job Input menu item to start the input generator Since we have not named the structure in the Build window before proceeding with input creation a Save As dialog is presented Figure 4 12 The name of the file is automatically set to the empirical formula with a pqb extension Parallel Quantum Solutions 87 4 1 Example 1 Lactic Acid Create Dir Delete File Ren
135. s to be drawn with a color that is clearly visible against the current background color of the View window When this option is turned off the labels are drawn with the same color as the color of their respective atoms The Antialiasing checkbox turns on antialiasing Tip Turn off antialiasing to speed up image rendering The Display menu File Options Display Window Y j E L kal o dl E O Ball Orbital O CPE ziuz O Ball amp Stick ou Ball amp Stickll Symmetry O Ball amp Sticklll Hydrogen Hide Tube Center O Tubell O Stick O Carcass File Options MEE MENA Window View Mode Orbital Mode b ad Interpolation H Coordinates Grid Resolution F Symmetry Hydrogen Hide enter e View Mode chooses one of the nine display schemes e Orbital Mode chooses one of four surface display schemes Wire Points Transparent Solid e Orbital Interpolation chooses one of three grid point interpolation schemes None Logarithmic Linear e Orbital Grid Resolution selects the number of points along one axis of the cubic grid I e a resolution of 10 gives a cubic grid of 10 1000 points a resolution of 30 gives a cubic grid of 30 27000 points e Labels toggles atom labels Parallel Quantum Solutions 63 3 1 View window e Coordinates toggles coordinate axes e Symmetry checks if the structure in the View window has any symmetry e Hydrogen Hide hides hydrogen atoms e C
136. tate RMmMB Insertr ttach CMB 2o00m CMB SHIFT Select CMB CNTRL Move RESTRICTED Figure 4 71 Build window attaching the tetrahedral carbon building block H Finally press the Hydrogen Fill button H in the top toolbar to fill the three free valencies on the newly attached carbon atom with hydrogens This completes the building of 1 methoxy perfluoroanthracene Figure 4 72 132 PQSMol Manual Tutorials File Edit Build Optimize Symmetry Display Calculation Window Help ae ali 817000 Y 0 0769 Z 0 23618 NUI Torsion SEE Selection TIET Field Sybyl5 2 ROTATE ABOUT A BOND LME to select a rotation bond DRAG double click to set SHIFT double c RESTRICTED Figure 4 72 Build window 1 methoxy perfluoroanthracene At this point we could optimize the geometry of 1 methoxy perfluoroanthracene using the Sybyl5 2 force field However as we have imported the already optimized geometry of perfluoroanthracene optimized at our desired level of theory and all we have done is replace a fluorine by a methoxy group then it might be better to start the ab initio optimization using the structure as is without the force field preoptimization The methoxy group can be rotated about the C O bond to any desired position We can now repeat Step 6 above and prepare the input file If desired you can skip this step and go direct to the examination of the output The output file is cal
137. value 0 000 reg OFF Ce Ci Ca C45 CE O7 CE Range End 176 314 Range Stat 33 6650 Zoom Out Halfwidth 0 10 as Reference Shift 60 904 User Auto 8 By selection 31 7 Figure 3 22 13C NMR Spectrum by selection reference shift NMA Spectrum C Atoms Selected value 35 1 20 reg OFF C C3 i C4 C5 gt MOM CE 0 00 OF C Range End 176 314 Range Start 33 6650 Zoom Out Halfwidth 0 10 OS A C IL Reference shift 33 6650 User A uta By selection cq F Figure 3 23 15C NMR Spectrum auto reference shift MMR Spectrum C Atoms Selected value 31 01 5 reg OFF Ce Ci Ca Ci CE O7 CE Range End 176 314 Range Stat 33 8650 Zoom Out Halfwidth 0 10 as C 1C C 11 Reference Shift 100 User Auto By selection Figure 3 24 19C NMR Spectrum user selected 100 reference shift The zoom option works in a similar way to the zoom in the simulated vibrational spectrum Position the mouse pointer in the NMR window just before the region to be expanded and drag the mouse with the center mouse button over the region A zoom around the five right of center signals in the C simulated NMR spectrum is shown below Figure 3 25 78 PQSMol Manual View Mode Range End 126 314 Range Start 16 134 Zoom Out Halfwidth 0 10 Reference shift 30 User Auto By selection Figure 3 25 13C NM
138. ven node click on the Check button in the corresponding row O status unknown oft PQS job executing no connection Fe 2 PQS scratch files present PVM error x PVM off PQS output present Mo y PVM on SE PQS output and scratch files present Figure 2 57 Background Job icon legend 52 PQSMol Manual Build mode Background Job SGE Parallel Environment cane CPUs Processes PYM Job Available Allocated Status otatus n 4 3 af nae Toggle nz 4 0 cy Check n3 4 0 a T Repair fscrfags 1 faspirin 11 na 4 x Di scrips faspirin 2 scrips faspirin d 3 scrips faspirin 14 scrips faspirin d o Tidy Job Reset PVM Processes 2 1 Launch Job Figure 2 58 Parallel Job Submission window background job nodes checked Figure 2 58 shows the status of the cluster after the Check button has been clicked for each node In this example node ni has a check mark icon indicating that a PVM daemon is running on that node The additional icon of a garbage can in the Job Status column indicates that there are scratch files temporary files left over from a previous PQS calculation on that node The label of the status button for node n1 changes to Toggle This means that there is a connection to that node and the state of the PVM on node n1 can be toggled i e switched on and off by clicking on the Toggle button The icon shown for node n2 indicates no connection to that node the ping co
139. ygen spe CA C a carbon spa HY H hydrogen Z OO Od oxygen spa HI H hydrogen H10 H hydrogen lil H11 H hydrogen Hi H hydrogen Y H13 H hydrogen 2 Suto Detect Undefined Auto Detect All Accept Cancel Figure 2 47 Force field symbols The Force field symbol window Figure 2 47 shows a list of all atoms and their assigned force field symbols To manually change the force field symbol for a given atom select a symbol from a drop down list on the right of the atom label The list can include undefined atom types which are acceptable in the Sybyl force field but not in Universal Attempts can be made to automatically assign any atom types that are currently unknown by clicking on Auto Detect Undefined In general this is only likely to occur if the structure was either imported or built in unrestricted mode Clicking on Auto Detect All will force an automatic detection of all atoms in the system whether defined or not Any changes to the existing atom types will only be implemented by pressing the the Accept button The Cancel button restores the original force field atom types and cancels the operation Note Clicking inside the text entry area of any atom will highlight the corresponding atom in the Build window 44 PQSMol Manual Build mode Tip Turn on atom labels with the Labels button in the top menubar to visually identify all atoms 2 5 Symmetry The symmetrizer allows you to symmetriz

PQSMol Manual - Parallel Quantum Solutions

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