From hyper!burton@autodesk.com Mon May 3 20:06:26 1993 From: hyper!burton@autodesk.com (Ian Burton) Subject: Reaction Dynamics Scripts To: autodesk!hyperchem@netcom.com Date: Mon, 3 May 93 16:49:57 EDT Cc: burton@autodesk.com (Ian Burton) Status: RO To all those HyperChem users interested in Reaction Dynamics: Included is a set of scripts and .HIN files which simulate several organic reactions using molecular dynamics and semi-empirical computations in HyperChem. There is one example of an SN2 reaction, two examples of elimination reactions, and one example of an aromatic substitution reaction. There are four scripts which will run the dynamics and save the coordinate data in snapshot files. These snapshots can then be played back by running another script. Here is a summary of the files that are included in this message: elim_1.hin Elimination reaction showing the attack of 2-chlorobutane by OH- at the 1 position to form 1-butene. elim_2.hin Elimination reaction showing the attack of 2-chlorobutane by OH- at the 3 position to form 2-butene. sn2_d.hin Simple SN2 reaction showing one chlorine in chloromethane displaced by an incoming chloride ion. subst_1.hin Example of acid cataalysed nitration of toluene at the para position. This example picks up the reaction at the point where the nitronium ion is attacking the ring at the para position. Then the HSO4- ion comes along and picks up the acidic hydrogen to yield p-nitrotoluene and and sulphuric acid. elim_1.scr elim_2.scr sn2_d.scr subst_1.scr Four script files that generate the snapshot files using the above .hin files. runreact.scr Script file which will playback the four snapshots in succession with explanatory message boxes between each reaction. The scripts as supplied will run with no changes from release 3 or release 2 for SGI. When using release 2 for Windows the last two lines in the script files elim_1.scr, elim_2.scr, sn2_d.scr and subst_1.scr should be commented out and the snapshot files saved and the dynamics calculation run from HyperChem interactively. These scripts and hin files are offered without any type of warranty against errors. However if anyone does have any comments or suggestions or require assistance feel free to contact me over the net. Ian. -- Ian Burton Hypercube, Inc. Internet: burton@hyper.com #7-419 Phillip St. Telephone: (519) 725-4040 Waterloo, Ontario Facsimile: (519) 725-5193 Canada N2L 3X2 -----------------------------ELIM_1.HIN--------------------------------- forcefield mm+ sys 0 view 40 0.06440141 55 15 -0.5515213 -0.8215088 -0.1447328 0.678472 -0.3408409 -0.6507712 0.4852835 -0.4571114 0.7453518 4.457105 1.044241 -56.21931 mol 1 atom 1 - C C4 - -0.2222362 4.200977 -1.502765 0.008260466 4 2 s 6 s 7 s 8 s vel 1 0 0 0 atom 2 - C C4 - -0.05177784 2.847558 -2.152133 -0.3355071 4 1 s 3 s 4 s 9 s vel 2 0 0 0 atom 3 - Cl CL - -0.1376214 1.540617 -1.133653 0.2579613 1 2 s vel 3 0 0 0 atom 4 - C C4 - -0.1654983 2.725286 -2.306082 -1.862906 4 2 s 5 s 10 s 11 s vel 4 0 0 0 atom 5 - C C4 - -0.2151637 1.371867 -2.95545 -2.206674 4 4 s 12 s 13 s 14 s vel 5 0 0 0 atom 6 - H H - 0.0821138 5.01039 -2.133528 -0.3592854 2 1 s 15 s vel 6 0 0 0 atom 7 - H H - 0.08949077 4.262961 -0.5213667 -0.4619691 1 1 s vel 7 0 0 0 atom 8 - H H - 0.09084296 4.287522 -1.393783 1.08934 1 1 s vel 8 0 0 0 atom 9 - H H - 0.1092852 2.785573 -3.133538 0.1347077 1 2 s vel 9 0 0 0 atom 10 - H H - 0.09687686 2.787258 -1.324673 -2.333112 1 4 s vel 10 0 0 0 atom 11 - H H - 0.08647501 3.534704 -2.936834 -2.230462 1 4 s vel 11 0 0 0 atom 12 - H H - 0.07678127 1.285325 -3.064415 -3.287755 1 5 s vel 12 0 0 0 atom 13 - H H - 0.07268304 1.309896 -3.93686 -1.736468 1 5 s vel 13 0 0 0 atom 14 - H H - 0.08774829 0.5624495 -2.3247 -1.839118 1 5 s vel 14 0 0 0 atom 15 - O ** - -0.9918413 8.044895 -6.366479 -2.1822 2 16 s 6 s vel 15 -16.56889 22.95872 9.918124 atom 16 - H HO - -0.008158922 8.824766 -6.971682 -2.540016 1 15 s vel 16 -16.56889 22.95872 9.918124 endmol 1 selection LINE 2 selectrestraint 1 0.000000 0.000000 0.000000 0.000000 0.000000 selectatom 15 molecule 1 selectatom 2 molecule 1 endselection LINE selection POINT 1 selectrestraint 1 0.000000 0.000000 0.000000 0.000000 0.000000 selectatom 6 molecule 1 endselection POINT ---------------------------ELIM_2.HIN--------------------------------- forcefield mm+ sys 0 view 40 0.06440141 55 15 -0.5515213 -0.8215088 -0.1447328 0.678472 -0.3408409 -0.6507712 0.4852835 -0.4571114 0.7453518 4.457105 1.044241 -56.21931 mol 1 atom 1 - O ** - -0.9918413 8.044895 -6.366479 -2.1822 2 2 s 13 s vel 1 -22.22686 20.09618 1.452715 atom 2 - H HO - -0.008158922 8.824766 -6.971682 -2.540016 1 1 s vel 2 -22.22686 20.09618 1.452715 atom 3 - C C4 - -0.2222362 3.967429 -1.117312 0.2994517 4 4 s 8 s 9 s 10 s vel 3 0 0 0 atom 4 - C C4 - -0.05177784 2.848788 -2.03304 -0.2312871 4 3 s 5 s 6 s 11 s vel 4 0 0 0 atom 5 - Cl CL - -0.1376214 1.28469 -1.286412 0.07489049 1 4 s vel 5 0 0 0 atom 6 - C C4 - -0.1654983 3.030782 -2.240532 -1.746352 4 4 s 7 s 12 s 13 s vel 6 0 0 0 atom 7 - C C4 - -0.2151637 1.912142 -3.15626 -2.277092 4 6 s 14 s 15 s 16 s vel 7 0 0 0 atom 8 - H H - 0.0821138 4.936105 -1.579711 0.1098304 1 3 s vel 8 0 0 0 atom 9 - H H - 0.08949077 3.919338 -0.1536462 -0.2076349 1 3 s vel 9 0 0 0 atom 10 - H H - 0.09084296 3.838613 -0.9704317 1.371802 1 3 s vel 10 0 0 0 atom 11 - H H - 0.1092852 2.896881 -2.996712 0.2757851 1 4 s vel 11 0 0 0 atom 12 - H H - 0.09687686 2.982674 -1.276858 -2.253418 1 6 s vel 12 0 0 0 atom 13 - H H - 0.08647501 3.999462 -2.70292 -1.935983 2 6 s 1 s vel 13 0 0 0 atom 14 - H H - 0.07678127 2.040957 -3.303123 -3.349443 1 7 s vel 14 0 0 0 atom 15 - H H - 0.07268304 1.960251 -4.119936 -1.770025 1 7 s vel 15 0 0 0 atom 16 - H H - 0.08774829 0.9434631 -2.693873 -2.08746 1 7 s vel 16 0 0 0 endmol 1 selection LINE 2 selectrestraint 1 0.000000 0.000000 0.000000 0.000000 0.000000 selectatom 1 molecule 1 selectatom 4 molecule 1 endselection LINE selection POINT 1 selectrestraint 1 0.000000 0.000000 0.000000 0.000000 0.000000 selectatom 13 molecule 1 endselection POINT ------------------------SN2_D.HIN-------------------------------------- forcefield mm+ sys 0 view 40 0.1723351 65.17224 25.17224 -0.964171 0.0306737 -0.2635024 0.2014884 0.7307889 -0.6521886 0.1725596 -0.681914 -0.7107859 7.660254 -0.07485066 -62.92634 mol 1 atom 1 - C C4 - -0.1726346 2.68752 0.1347401 -0.04416489 5 2 s 3 s 4 s 5 s 6 s vel 1 0 0 0 atom 2 - H H - 0.1525642 3.041492 1.178935 0.06508911 3 1 s 6 s 4 s vel 2 0 0 0 atom 3 - H H - 0.1554894 3.002945 -0.3117366 -1.007925 3 1 s 6 s 4 s vel 3 0 0 0 atom 4 - Cl H - -0.2927232 0.9185067 0.192497 -0.06451225 4 1 s 2 s 3 s 5 s vel 4 0 0 0 atom 5 - H H - 0.1573043 2.974346 -0.4945997 0.8214973 3 1 s 6 s 4 s vel 5 0 0 0 atom 6 - Cl ** - -0.9996357 15 0 0 4 3 s 5 s 2 s 1 s vel 6 -49.99669 0.5471326 -0.1793382 endmol 1 selection LINE 2 selectrestraint 1 0.000000 0.000000 0.000000 0.000000 0.000000 selectatom 6 molecule 1 selectatom 4 molecule 1 endselection LINE selection POINT 1 selectrestraint 1 0.000000 0.000000 0.000000 0.000000 0.000000 selectatom 1 molecule 1 endselection POINT --------------------------------SUBST_1.HIN--------------------------------- forcefield mm+ sys 0 view 40 0.1889285 57.34164 17.34164 0.1229032 -0.6898811 -0.7134136 -0.9844207 0.006332894 -0.1757148 0.1257403 0.7238951 -0.6783549 -4.345691 1.626282 -58.033 mol 1 atom 1 - C CA - -0.1054187 0.6101148 -4.494684 -2.278157 3 2 a 6 a 7 s vel 1 0 0 0 atom 2 - C CA - -0.07457018 1.962808 -4.406279 -1.940986 3 1 a 3 a 8 s vel 2 0 0 0 atom 3 - C CA - -0.1029944 2.325336 -4.117157 -0.6251996 3 2 a 4 a 9 s vel 3 0 0 0 atom 4 - C CA - -0.09792852 1.345255 -3.914144 0.3405768 3 3 a 5 a 10 s vel 4 0 0 0 atom 5 - C CA - -0.1090126 0 -4 0 3 4 a 6 a 11 s vel 5 0 0 0 atom 6 - C CA - -0.09708786 -0.3658912 -4.292037 -1.31053 3 1 a 5 a 12 s vel 6 0 0 0 atom 7 - H H - 0.1045893 0.3237152 -4.724368 -3.310284 1 1 s vel 7 0 0 0 atom 8 - C C4 - -0.06470251 2.997479 -4.615946 -2.985979 4 2 s 13 s 14 s 15 s vel 8 0 0 0 atom 9 - H H - 0.1052414 3.384267 -4.050003 -0.3519894 1 3 s vel 9 0 0 0 atom 10 - H H - 0.1015483 1.635211 -3.686576 1.371624 1 4 s vel 10 0 0 0 atom 11 - H H - 0.1024286 -0.7703741 -3.837461 0.7606188 1 5 s vel 11 0 0 0 atom 12 - H H - 0.1015794 -1.425073 -4.362169 -1.579561 1 6 s vel 12 0 0 0 atom 13 - H H - 0.04341817 4.016219 -4.566209 -2.579687 1 8 s vel 13 0 0 0 atom 14 - H H - 0.04629755 2.878335 -5.596979 -3.464869 1 8 s vel 14 0 0 0 atom 15 - H H - 0.0466122 2.915871 -3.852413 -3.771316 1 8 s vel 15 0 0 0 endmol 1 mol 2 atom 1 - N N1 - 1.360451 0 0 -3.637979e-012 2 2 d 3 d vel 1 -0.0006130118 -50 -0.0005701142 atom 2 - O O1 - -0.180223 -0.7995496 0.1679358 0.7901073 1 1 d vel 2 -0.0006130118 -50 -0.0005701142 atom 3 - O O1 - -0.1802278 0.7996906 -0.1679103 -0.7899762 1 1 d vel 3 -0.0006130118 -50 -0.0005701142 endmol 2 mol 3 atom 1 - S S4 - 2.394036 0.1219539 -9.457726 0.1646854 4 2 d 3 d 4 d 5 s vel 1 -8.266968 48.46902 9.078073 atom 2 - O O1 - -0.9443636 -0.05904962 -8.007938 -0.02049657 1 1 d vel 2 -8.266968 48.46902 9.078073 atom 3 - O O1 - -0.9781342 0.04910327 -10.28738 -1.063424 1 1 d vel 3 -8.266968 48.46902 9.078073 atom 4 - O O1 - -0.9780579 1.200749 -9.866434 1.09766 1 1 d vel 4 -8.266968 48.46902 9.078073 atom 5 - O O2 - -0.694375 -1.303323 -9.903411 1.010443 2 1 s 6 s vel 5 -8.266968 48.46902 9.078073 atom 6 - H HO - 0.200895 -1.361683 -10.82317 1.217571 1 5 s vel 6 -8.266968 48.46902 9.078073 endmol 3 selection POINT 1 selectrestraint 1 0.000000 0.000000 0.000000 0.000000 0.000000 selectatom 11 molecule 1 endselection POINT selection LINE 2 selectrestraint 1 0.000000 0.000000 0.000000 0.000000 0.000000 selectatom 2 molecule 3 selectatom 11 molecule 1 endselection LINE -------------------------------ELIM_1.SCR----------------------------------- ; ; ELIM_1.SCR ; Author: Ian Burton ; Date: 23/04/1993 ; ; This script file shows a simple elimination reaction: ; OH- + CH3CHClC2H5 -> CH2=CHC2H5 + H2O + Cl- ; ; The reactants are found in the .hin file elim_1.hin ; with the correct velocities set for the reactants. ; file-format hin open-file elim_1.hin ; ; The following window colors need not be used, I just like ; looking at black carbons. ; window-color white color-element 1 white color-element 6 black color-element 8 red color-element 17 green ; ; render-method spheres show-hydrogens yes ; ; Set up the computation for PM3, RHF ; In release 2 the semi-empirical method ; must be AM1. To run PM3, the PM3 parameter ; files must be copied to the AM1 files. ; calculation-method semi-empirical semi-empirical-method pm3 ; ; Set SCF convergence fairly moderate, and ; lots of iterations. ; scf-convergence 0.01 max-iterations 500 accelerate-scf-convergence yes quantum-total-charge -1 multiplicity 1 uhf no excited-state no ; ; Dynamics stuff ; Just need to set a run time and temp - no ; annealing here. ; The run will be saved in a snapshot file to ; avoid having to run this script every time. ; To play it back, just read in the HIN file ; and set playback in the dynamics dialog box, ; then proceed. ; screen-refresh-period 1 dynamics-heat-time 0 ; ; This simulation collects a lot of points. ; When the snapshot file is played back, not ; all of the points need to be displayed. ; dynamics-run-time 0.5 dynamics-cool-time 0 dynamics-time-step 0.001 dynamics-starting-temp 0 dynamics-simulation-temp 300 dynamics-final-temp 0 dynamics-restart yes dynamics-playback record dynamics-constant-temp no dynamics-collection-period 1 dynamics-snapshot-period 1 ; ; Dynamics snapshots are saved in the file associated ; with HIN file arom_1.hin. This snapshot file can be ; using the script file runreact.scr. Original HIN file ; is not touched. This next statement does not work ; in HyperChem release 2. In order to run this using ; release 2, delete the next two lines and save the ; snapshot data from the menu, and run the dynamics ; simulation from the dynamics dialog box. (Except for ; SGI version) ; dynamics-snapshot-filename elim_1.hin do-molecular-dynamics ---------------------------------ELIM_2.SCR---------------------------------- ; ELIM_2.SCR ; Author: Ian Burton ; Date: 23/04/1993 ; ; ; This script file shows a simple elimination reaction: ; OH- + CH3CHClC2H5 -> CH2=CHC2H5 + H2O + Cl- ; ; The reactants are found in the .hin file elim_1.hin ; with the correct velocities set for the reactants. ; file-format hin open-file elim_2.hin ; ; The following window colors need not be used, I just like ; looking at black carbons. ; window-color white color-element 1 white color-element 6 black color-element 8 red color-element 17 green ; ; render-method spheres show-hydrogens yes ; ; Set up the computation for PM3, RHF ; In release 2 the semi-empirical method ; must be AM1. To run PM3, the PM3 parameter ; files must be copied to the AM1 files. ; calculation-method semi-empirical semi-empirical-method pm3 ; ; Set SCF convergence fairly moderate, and ; lots of iterations. ; scf-convergence 0.01 max-iterations 500 accelerate-scf-convergence yes quantum-total-charge -1 multiplicity 1 uhf no excited-state no ; ; Dynamics stuff ; Just need to set a run time and temp - no ; annealing here. ; The run will be saved in a snapshot file to ; avoid having to run this script every time. ; To play it back, just read in the HIN file ; and set playback in the dynamics dialog box, ; then proceed. ; screen-refresh-period 1 dynamics-heat-time 0 ; ; This simulation collects a lot of points. ; When the snapshot file is played back, not ; all of the points need to be displayed. ; dynamics-run-time 0.5 dynamics-cool-time 0 dynamics-time-step 0.001 dynamics-starting-temp 0 dynamics-simulation-temp 300 dynamics-final-temp 0 dynamics-restart yes dynamics-playback record dynamics-constant-temp no dynamics-collection-period 1 dynamics-snapshot-period 1 ; ; Dynamics snapshots are saved in the file associated ; with HIN file arom_1.hin. These snapshots can be ; replayed using the script runreact.scr. Original HIN file ; is not touched. This next statement does not work ; in HyperChem release 2. In order to run this using ; release 2, delete the next two lines and save the ; snapshot data from the menu, and run the dynamics ; simulation from the dynamics dialog box. (Except for ; SGI version) ; dynamics-snapshot-filename elim_2.hin do-molecular-dynamics -------------------------------SN2_D.SCR----------------------------------- ; SN2_D.SCR ; Author: Ian Burton ; Date: 23/04/1993 ; ; ; This script file shows a simple SN2 reaction: ; Cl- + CH3Cl -> ClCH3 + Cl- ; ; The reactants are found in the .hin file sn2_d.hin ; with the correct velocities set for the reactants. ; file-format hin open-file sn2_d.hin ; ; The following window colors need not be used, I just like ; looking at black carbons. ; window-color white color-element 1 white color-element 6 black color-element 8 red color-element 17 green ; ; render-method spheres show-hydrogens yes ; ; Set up the computation for PM3, RHF ; In release 2 the semi-empirical method ; must be AM1. To run PM3, the PM3 parameter ; files must be copied to the AM1 files. ; calculation-method semi-empirical semi-empirical-method pm3 ; ; Set SCF convergence fairly moderate, and ; lots of iterations. ; scf-convergence 0.01 max-iterations 500 accelerate-scf-convergence yes quantum-total-charge -1 multiplicity 1 uhf no excited-state no ; ; Dynamics stuff ; Just need to set a run time and temp - no ; annealing here. ; The run will be saved in a snapshot file to ; avoid having to run this script every time. ; To play it back, just read in the HIN file ; and set playback in the dynamics dialog box, ; then proceed. ; screen-refresh-period 1 dynamics-heat-time 0 ; ; This simulation collects a lot of points. ; When the snapshot file is played back, not ; all of the points need to be displayed. ; dynamics-run-time 0.7 dynamics-cool-time 0 dynamics-time-step 0.001 dynamics-starting-temp 0 dynamics-simulation-temp 300 dynamics-final-temp 0 dynamics-restart yes dynamics-playback record dynamics-constant-temp no dynamics-collection-period 1 dynamics-snapshot-period 1 ; ; Dynamics snapshots are saved in the file associated ; with HIN file arom_1.hin. This snapshot can be ; replayed using the script runreact.scr. Original HIN file ; is not touched. This next statement does not work ; in HyperChem release 2. In order to run this using ; release 2, delete the next two lines and save the ; snapshot data from the menu, and run the dynamics ; simulation from the dynamics dialog box. (Except for ; SGI version) ; dynamics-snapshot-filename sn2_d.hin do-molecular-dynamics ---------------------------------SUBST_1.SCR---------------------------------- ; SUBST_1.SCR ; Author: Ian Burton ; Date: 23/04/1993 ; ; ; This script file runs a dynamics simulation which ; shows the acid catalysed nitration of toluene. ; The simulation starts with a nitronium ion attacking ; the aromatic carbons of the toluene and as the nitronium ; attaches itself to the ring, the HSO4- ion abstracts the ; hydrogen ion to yield the nitrated product. ; This simulation should be run using the PM3 parameter ; set, as AM1 yields the sulfonated product. ; ; The reactants are found in the ,hin file subst_1.hin ; with the correct velocities set for the reactants. ; file-format hin open-file subst_1.hin ; ; The following window colors need not be used, I just like ; looking at black carbons. ; window-color white color-element 1 white color-element 6 black color-element 7 blue color-element 8 red color-element 16 yellow color-element 17 green ; ; The simulation looks best when rendered in spheres. ; To eliminate artifacts in the rendering, and to give ; the correct overlap in spheres rendering in the ; products, bonds can be drawn between the nitrogen and the ; para-carbon, and between the oxygen on the HSO4- group and ; the para-hydrogen. ; render-method spheres show-hydrogens yes ; ; Set up the computation for PM3, RHF ; In release 2 the semi-empirical method ; must be AM1. To run PM3, the PM3 parameter ; files must be copied to the AM1 files. ; calculation-method semi-empirical semi-empirical-method pm3 ; ; Set SCF convergence fairly moderate, and ; lots of iterations. ; scf-convergence 0.01 max-iterations 500 accelerate-scf-convergence yes quantum-total-charge 0 multiplicity 1 uhf no excited-state no ; ; Dynamics stuff ; Just need to set a run time and temp - no ; annealing here. ; The run will be saved in a snapshot file to ; avoid having to run this script every time. ; To play it back, just read in the HIN file ; and set playback in the dynamics dialog box, ; then proceed. ; screen-refresh-period 1 dynamics-heat-time 0 ; ; This simulation dynamics-run-time 0.5 dynamics-cool-time 0 dynamics-time-step 0.001 dynamics-starting-temp 0 dynamics-simulation-temp 300 dynamics-final-temp 0 dynamics-restart yes dynamics-playback record dynamics-constant-temp no dynamics-collection-period 1 dynamics-snapshot-period 1 ; ; Dynamics snapshots are saved in the file associated ; with HIN file arom_1.hin. This snapshot file can be ; replayed using the script runreact.scr. Original HIN file ; is not touched. This next statement does not work ; in HyperChem release 2. In order to run this using ; release 2, delete the next two lines and save the ; snapshot data from the menu, and run the dynamics ; simulation from the dynamics dialog box. (Except for ; SGI version) ; dynamics-snapshot-filename subst_1.hin do-molecular-dynamics ----------------------------------RUNREACT.SCR--------------------------------- ; RUNREACT.SCR ; Author: Ian Burton ; Date: 23/04/1993 ; ignore-script-errors yes errors-are-omsgs omsgs-to-file react.err render-method spheres dynamics-time-step 0.001 color-element 1 white color-element 6 black color-element 7 blue color-element 8 red color element 15 yellow color-element 17 green file-format hin open-file sn2_d.hin quantum-total-charge -1 multiplicity 1 zoom 0.7 omsgs-not-to-file message "Example of SN2 reaction. Chloride displacing chloride in CH3Cl." append-omsgs-to-file react.err pause-for 2 dynamics-restart yes dynamics-playback playback screen-refresh-period 2 dynamics-collection-period 2 dynamics-run-time 0.5 do-molecular-dynamics pause-for 2 open-file elim_1.hin zoom 0.7 omsgs-not-to-file message "Example 1 of elimination reaction." message "Dehydrohalogenation of 2-chlorobutane with OH- attacking at 1 position." append-omsgs-to-file react.err pause-for 2 dynamics-restart yes dynamics-playback playback screen-refresh-period 2 dynamics-collection-period 2 dynamics-run-time 0.5 do-molecular-dynamics omsgs-not-to-file message "Minor product 1-butene. (20%)" append-omsgs-to-file react.err pause-for 2 open-file elim_2.hin zoom 0.7 omsgs-not-to-file message "Example 2 of elimination reaction." message "Dehydrohalogenation of 2-chlorobutane with OH- attacking at 3 position." append-omsgs-to-file react.err pause-for 2 dynamics-restart yes dynamics-playback playback screen-refresh-period 2 dynamics-collection-period 2 dynamics-run-time 0.5 do-molecular-dynamics omsgs-not-to-file message "Major product 2-butene. (80%)" append-omsgs-to-file react.err pause-for 2 open-file \molecule\hin\react\subst_1.hin quantum-total-charge 0 multiplicity 1 zoom 0.7 omsgs-not-to-file message "Example of aromatic substitution reaction." message "Acid catalyzed nitration of toluene at the para position." message "Nitronium ion attacks the para aromatic carbon and HSO4- removes the acidic hydrogen." append-omsgs-to-file react.err pause-for 2 dynamics-restart yes dynamics-playback playback screen-refresh-period 2 dynamics-collection-period 2 dynamics-run-time 0.5 do-molecular-dynamics select-name toluene zoom 1.0 omsgs-not-to-file message "Products: p-Nitrotoluene and sulphuric acid." append-omsgs-to-file react.err ________________________________________________________________________ From hobbes.chem.uh.edu!madura@netcom.com Wed May 5 23:53:57 1993 Date: Wed, 5 May 93 21:44:46 -0500 From: madura@hobbes.chem.uh.edu (Jeffry Madura) To: hyperchem@autodesk.com Status: RO Can someone help me locate the following information? I remember seeing a description (perhaps a script file) of how to use hyperchem to generate a phi/psi map of a peptide. I can't seem to locate it right now. Does any one have this script which they can e-mail me. Thanks. Regards, jeffry d. madura madura@moe.chem.usouthal.edu Dr. Jeffry D. Madura University of South Alabama Department of Chemistry Chem. Bldg. Room 223 Mobile, AL 36688 e-mail madura@moe.chem.usouthal.edu phone (205) 460-7430 FAX (205) 460-7928 ________________________________________________________________________ From e154jos2.tuwien.ac.@!ujordis@netcom.com Thu May 6 15:35:25 1993 Date: Thu, 6 May 93 17:47:19 +0200 To: madura@hobbes.chem.uh.edu Subject: Hyperchem Phi/Psi From: ujordis@email.tuwien.ac.@ (Univ. Doz. Dr. Ulrich Jordis) Reply-To: ujordis@email.tuwien.ac.@ Cc: hyperchem@autodesk.com Status: RO You will probably get an answer from the hyperchem people; however, I do have an EXCEL Macro that allows the automatic generation of an energy surface for two independably definable torsion angles. Please let me know if you still need this - it should be possible to send you the macro via lectronic mail. Have you written any other intersting applications or macros that students might be interested in? Sincerely U. Jordis -- ----------------------------------------------------------- Univ.Doz.Dr. Ulrich Jordis ujordis@email.tuwien.ac.at Institute E154 Tel: +43 1 58801-5013 Fax: +43 1 5874211 ________________________________________________________________________ From uoft02.utoledo.edu!DSMITH@netcom.com Wed May 12 00:26:04 1993 Date: Tue, 11 May 1993 13:10:58 -0500 (EST) From: "DR. DOUGLAS A. SMITH, UNIVERSITY OF TOLEDO" Subject: use of color in molecular modeling To: chemistry@osc.edu, mmodinfo@uoft02.utoledo.edu, hyperchem@autodesk.com Status: RO In response to my recent question on stereo viewing, I was asked about the use of color in molecular modeling. So.... I have a general question for anyone out there who wishing to open a dialog about the use of color in molecular modeling. Please send responses directly to me and I will summarize for the net. I use color all the time in my modeling - I find that in addition to simple uses such as identifying atoms or residues by type or charge or hydrophobicity, mapping properties onto surfaces is quite useful. Use of color rather than or in addition to grids or translucent surfaces is also advantageous. And color is certainly cheap on today's hardware and software. Would any one else like to comment on why color is or is not important, useful, advantageous, indespensible, etc.? In addition to opinions, I would like to hear success stories where the use of color has enhanced the chemistry or helped to solve a problem which was insoluble without it or would have taken a longer time or would have resulted in a lower quality answer. Doug Douglas A. Smith Assistant Professor of Chemistry The University of Toledo Toledo, OH 43606-3390 voice 419-537-2116 fax 419-537-4033 email dsmith@uoft02.utoledo.edu --- Administrivia: This message is automatically appended by the mail exploder: CHEMISTRY@osc.edu --- everyone CHEMISTRY-REQUEST@osc.edu --- coordinator OSCPOST@osc.edu send help from chemistry Anon. ftp kekule.osc.edu CHEMISTRY-SEARCH@osc.edu --- search the archives, read help.search file first --- ________________________________________________________________________ From ciens.ula.ve!alejo@netcom.com Wed May 12 04:59:54 1993 Date: Tue, 11 May 93 14:25:40-040 From: ALEJANDRO MUJICA To: hyperchem@autodesk.com Subject: Ask for some detailed information Cc: avilan@ciens.ula.ve Status: RO Hello! We are an international ATC (Autodesk Trainning Center) at "Universidad de Los Andes", in Merida, Venezuela, and there is a great interest among both Chemistry and Biology department regard the use of HyperChem Modeller software for both educational and research purposes. At the moment we would like detailed information about some aspects in order to aply this tool in research projects: 1.- In the modeling of protein 3D structure from its secuence: Which physical property is used by HyperChem? Hydrogen Bonds? Hidrofobic interactions? All of the above? This is particullarly important in proteins which have few or no alpha-helix and beta-secundary structure. 2.- Is it possible to load information from Protein and Gene Banks through HyperChem? At the moment we are waiting for a Grant copy of the software as to begin working! So we only have your HyperChem brouchure and we want some aditional information. Would you please send us this and any other realted information through e-mail or to our mail and cargo addresses in Miami? Thanks a lot Alejandro Mujica Universidad de Los Andes ATC Director ALEJO@ula.ciens.ve USA Mail Address USA Cargo Address --------------------------------------------------- CITEC-ULA, MRD 1728 CITEC-ULA, MRD-1728 POBox 8537 ZOOM Miami Miami, FL 33102-8537 1915N.W.82ND.Ave. Miami, FL 331 --------------------------------------------------- ________________________________________________________________________ From magnus.acs.ohio-state.edu!tgustafs@netcom.com Wed May 12 08:37:30 1993 From: Terry L Gustafson Subject: Animating Vibrational Motions To: hyperchem@autodesk.com Date: Wed, 12 May 93 7:53:06 EDT Status: RO This is a general request to see if anyone has written a routine or knows how to access the routine within HyperChem for animating the vibrational motions without recalculating the vibrations. Using QuantumPrintLevel=9 in the chem.ini file saves all the displacements. Is there a way to reincorporate that into the animation routine? We have done several relatively large molecules and I don't want to wait 24 hours to recalculate the vibrational spectrum everytime I want to look at the animation. I want to be able to use previous calculations in a course, but I can't recalculate easily in that time frame. Thank you in advance for any suggestions. -- ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Terry L. Gustafson + gustafson.5@osu.edu + "Life in the + + Department of Chemistry + + + + The Ohio State University + VOC: 614-292-1832 + Ultrafast + + 120 West 18th Avenue + + + + Columbus, OH 43210-1173 + FAX: 614-292-1685 + Lane" + ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ________________________________________________________________________ From hyper!slee@autodesk.com Wed May 12 11:50:13 1993 From: hyper!slee@autodesk.com (Thomas Slee) Subject: Re: Animating Vibrational Motions To: autodesk!hyperchem@netcom.com (HyperChem e-mail group) Date: Wed, 12 May 93 10:37:28 EDT Status: RO Terry L Gustafson writes... | | This is a general request to see if anyone has written a routine or knows how | to access the routine within HyperChem for animating the vibrational motions | without recalculating the vibrations. Using QuantumPrintLevel=9 in the | chem.ini file saves all the displacements. Is there a way to reincorporate | that into the animation routine? We have done several relatively large | molecules and I don't want to wait 24 hours to recalculate the vibrational | spectrum everytime I want to look at the animation. I want to be able to use | previous calculations in a course, but Ican't recalculate easily in that time | frame. Thank you in advance for any suggestions. Here is a script that should do the job. ; saveir.scr ;=========== ; Save the existing IR spectrum. This script ; produces or writes over the file "\hyper\chem_ir.scr" ; which can be run later to recover the IR data. ; ; When running chem_ir.scr to regenerate the spectrum ; you must first have the appropriate molecule on the screen. query-response-has-tag true omsgs-to-file \hyper\chem_ir.scr status-message "Saving IR spectrum to \hyper\chem_ir.scr" ;Save computational procedure used. calculation-method ? semi-empirical-method ? ;Save semi-empirical options. quantum-total-charge ? multiplicity ? scf-convergence ? max-iterations ? accelerate-scf-convergence ? uhf ? excited-state ? ;Save spectrum ir-band-count ? ir-frequency ? ir-intensity ? ir-intensity-components ? ir-normal-mode ? vibrational-mode ? status-message "Spectrum saved" -- -- Tom Slee Hypercube, Inc., #7-419 Phillip St., Waterloo, Ont. N2L 3X2 Internet: slee@hyper.com Tel. (519) 725-4040 ________________________________________________________________________ From JCVAXA.JCU.EDU!EWING@netcom.com Wed May 12 22:40:47 1993 Date: Wed, 12 May 1993 21:19 EST From: "DAVID W. EWING (216) 397-4742" Subject: 1993 Morley Medal Symposium To: chminf-l@iubvm.bitnet, autodesk!hyperchem@netcom.com Status: RO 1993 Morley Medal Symposium Honoring Professor Gilles Klopman, 1993 Morley Medalist The Morley Medal is given annually by the Cleveland Section ACS to a chemist for outstanding contributions to chemistry while residing in an area within a 250 mile radius of Cleveland. A bronze medal and $1000 are presented at the section's May meeting. This year we are pleased to announce that the awardee is Professor Gilles Klopman of Case Western Reserve University. The following is the program that will be given in his honor at John Carroll University in Cleveland on May 19. Please note that while attendance at the symposium is open to all, reservations for dinner (which includes the social hour) are required. For directions or more information contact Dave Ewing at ewing@jcvaxa.jcu.edu. A sponsor of this event is Technical Software, Inc., which distributes, among other products, HyperChem. Wednesday, May 19, 1993 John Carroll University, Room 256 Science Center 1:25 Welcoming Remarks Prof. David Ewing, Chairman, Cleveland Section ACS Prof. Herbert Rosenkranz, Symposium Chairman, Department of Environmental and Occupational Health, University of Pittsburgh 1:30 "Predicting the Crystal Structure of Organic Molecular Materials" Dr. Anne Chaka, Lubrizol Corporation 2:30 "Proton Affinities of NH3, H2O and HF: A Quest for the Basis Set Limit" Prof. Janet DelBene, Department of Chemistry, Youngstown State University 3:30 BREAK 3:45 "Construction of 3D QSARs for Antitumor DNA Intercalators" Prof. Anton Hopfinger, Department of Pharmacy, University of Illinois at Chicago 4:45 MORLEY MEDAL ADDRESS "Structure and Bioactivity of Chemicals" Prof. Gilles Klopman, 1993 Morley Medalist Department of Chemistry, Case Western Reserve University 6:00 Social Hour, Faculty Lounge, Administration Building Featuring displays by Technical Software, Inc. 7:00 Dinner, Faculty Dining Room, Student Activities Center ----> For reservations call 397-4241 by noon Mon., May 17 $18.00 (Students $8.00) 8:00 Presentation of the Morley Medal 8:15 "The Belgianization of a Chemistry Department" Prof. Irvin Krieger, Department of Chemistry, Case Western Reserve University ________________________________________________________________________ From ciens.ula.ve!alejo@netcom.com Thu May 13 16:32:26 1993 Date: Thu, 13 May 93 13:33:32-040 From: ALEJANDRO MUJICA To: hyperchem@autodesk.com Subject: Ask for some detailed information Cc: avilan@ciens.ula.ve Status: RO Hello! We are an international ATC (Autodesk Trainning Center) at "Universidad de Los Andes", in Merida, Venezuela, and there is a great interest among both Chemistry and Biology department regard the use of HyperChem Modeller software for both educational and research purposes. At the moment we would like detailed information about some aspects in order to apply this tool in research projects: 1.- In the modelling of protein 3D structure from its secuence: Which physical properties are used by HyperChem? Hydrogen Bonds? Hidrofobic interactions? All of the above? This is particullarly important in proteins which have few or no alpha-helix and beta-secundary structure. 2.- Is it possible to load information from Protein and Gene Banks through HyperChem? At the moment we are waiting for a Grant copy of the software as to begin working! So we only have your HyperChem brouchure and we want some aditional information. Would you please send us this and any other related information through e-mail or to our mail and cargo addresses in Miami? Thanks a lot Alejandro Mujica Universidad de Los Andes ATC Director ALEJO@ula.ciens.ve USA Mail Address USA Cargo Address --------------------------------------------------- CITEC-ULA, MRD 1728 CITEC-ULA, MRD-1728 POBox 8537 ZOOM Miami Miami, FL 33102-8537 1915N.W.82ND.Ave. Miami, FL 331 --------------------------------------------------- ________________________________________________________________________ From uoft02.utoledo.edu!DSMITH@netcom.com Fri May 14 13:27:41 1993 Date: Fri, 14 May 1993 13:00:32 -0500 (EST) From: "DR. DOUGLAS A. SMITH, UNIVERSITY OF TOLEDO" Subject: how to model high spin, d5 Fe complex? To: hyperchem@autodesk.com Status: RO For anyone who can help with transition metal calculations -- I have need of calculating an optimized geometry and atomic charges (MEP, Mulliken, whatever) for iron(III) tris(catecholate) 3- ion. The iron is a high spin, d5 species. I want to use the geometry and charges in subsequent molecular dynamics and/or Monte Carlo studies. What is the recommended method? In particular, how do I treat the d5 system? I have access to G90 and G92, GAMESS, MOPAC and Hyperchem. I can therefore do ab initio with or without ECPs in the basis set, UHF or CI or MCSCF, GVB, or I can do any one of a number of semiempirical calculations including INDO, ZINDO/1 or /2, MNDO, AM1, PM3. I do not have access to DFT or Xalpha programs. Also, can anyone point me in the direction of previous studies of high spin d5 iron complexes, even such as Fe(OH)6 3-? Thanks in advance for any advice. Doug Douglas A. Smith Assistant Professor of Chemistry The University of Toledo Toledo, OH 43606-3390 voice 419-537-2116 fax 419-537-4033 email dsmith@uoft02.utoledo.edu ________________________________________________________________________ From uoft02.utoledo.edu!DSMITH@netcom.com Fri May 14 15:50:53 1993 Date: Fri, 14 May 1993 13:34:54 -0500 (EST) From: "DR. DOUGLAS A. SMITH, UNIVERSITY OF TOLEDO" Subject: hydrogen bonding involving aromatic hydrogens To: chemistry@osc.edu, hyperchem@autodesk.com, mmodinfo@uoft02.utoledo.edu Status: RO Does anybody have any experience, references, or knowledge of systems in which the hydrogen of an aromatic ring (preferably benzene but any aromatic system is really of interest) is involved in a hydrogen bond? I will summarize responses for the net. Doug Douglas A. Smith Assistant Professor of Chemistry The University of Toledo Toledo, OH 43606-3390 voice 419-537-2116 fax 419-537-4033 email dsmith@uoft02.utoledo.edu ________________________________________________________________________ From autodesk!smtpcc.autodesk.com!billgl@netcom.com Fri May 14 16:56:01 1993 Date: Fri, 14 May 93 13:05:54 PST From: billgl@smtpcc.autodesk.com To: hyperchem@autodesk.com, ALEJANDRO MUJICA Cc: avilan@ciens.ula.ve Subject: Proteins and HyperChem Status: RO Dear Alejandro, Thanks for your questions regarding HyperChem's role in biomolecular modeling and visualization. >1.- In the modelling of protein 3D structure from its secuence: >Which physical properties are used by HyperChem? Hydrogen Bonds? >Hidrofobic interactions? All of the above? This is particullarly >important in proteins which have few or no alpha-helix and >beta-secundary structure. HyperChem provides an atomistic description of the interactions within proteins or between solvent and proteins. HyperChem calculates the energy of a particular conformation of a protein through the use of molecular mechanics "force-fields" that come in four flavors: MM+ (based upon MM2/77), AMBER, Bio+ (based upon the public domain version of Charmm) and OPLS. All four algorithms are based upon public-domain, industry-standard techniques that orginally appeared in peer-reviewd journals (in other words, you can publish the results obtained with HyperChem in research journals). The energy is partitioned into various components such as bond stretching, angle bending, torsional twisting, nonbonded van der Waals attractions and repulsions, nonbonded electrostatic interactions, and hydrogen bonding. Hydrophobic interactions have both an enthalpic (energy) and entropic component. The enthalpic component is captured in HyperChem through the van der Waals attractions (also known as London dispersion forces) that appears as an attractive R**-6 term in the force-field expression. Hydrogen bonding is explicitly accounted for in all of the force fields (except MM+) via an attractive R**-10 term. In addition HyperChem visually diplays hydrogen bonds between all donor-acceptor pairs that have qualitatively the correct orientation (distance and angle). Furthermore the backbone may be displayed in ribbon rendering to better see the secondary and tertiary structure. To go beyond a gas-phase description of the protein 3D structure, HyperChem allows you to place a solute (e.g., protein) into a periodic box of water. To go beyond a zero temperature description, HyperChem allows you to simulate the dynamic behavior of a protein as it cascades from one conformation to another using molecular dynamics. The CPU time scales roughly as A*N**2 where N is the number of atoms in the protein (plus solvent if used) and A is the number of steps in the dynamics simulation. Clearly, a gas-phase calculation on a small protein is a much more tractable calculation. HyperChem allows you to play back an animation of the molecular dynamics trajectory and you can see how the hydrophobic residues are clustered together. The entropic component to the hydrophobic interactions may be qualitatively discerned from the density of conformational states of various types (i.e., nonpolar residues facing inside versus outside). As you know, folding a protein from just the linear sequence is an as yet unsolved problem in computation chemistry/biology. However, starting from a known 3D structure or a reasonable guess (homology?), you can perform substitution mutations with HyperChem and then perform either a geometry optimization or a molecular dynamics run to test the structural consequences of this mutation. Alternatively, small oligopeptides (e.g., met-enkephalin with 5 residues) may be studied with far less prior knowledge built into the calculation. >2.- Is it possible to load information from Protein and Gene >Banks through HyperChem? Yes to the first and no to the second. HyperChem reads and writes the Brookhaven Protein Data Bank file format, which is, I think, a sort of lingua franca amongst formats. Although we do not read directly from a Gene Bank, HyperChem does provide a nucleotide (and amino acid for that matter) fragment library to construct DNA or RNA in single or double stranded form using the A, B or Z conformations for the phosphodiester backbone. You can construct an oligonucleotide with the desired sequence and secondary structure in seconds by simply clicking on the nucleotide buttons. I hope this answers most of your questions about HyperChem. I sense your enthusiasm about using HyperChem, and I trust that you will find it rewarding. Best Regards, Bill Glauser Scientific Modeling Division Autodesk, Inc. voice: (415) 332-2344 (8638) e-mail: billgl@autodesk.com ________________________________________________________________________ From hyper!slee@autodesk.com Mon May 17 14:24:25 1993 From: hyper!slee@autodesk.com (Thomas Slee) Subject: Re: how to model high spin, d5 Fe complex? To: autodesk!hyperchem@netcom.com (HyperChem e-mail group) Date: Mon, 17 May 93 13:38:07 EDT Status: RO DR. DOUGLAS A. SMITH, UNIVERSITY OF TOLEDO writes... | | For anyone who can help with transition metal calculations -- | | I have need of calculating an optimized geometry and atomic charges (MEP, | Mulliken, whatever) for iron(III) tris(catecholate) 3- ion. The iron is | a high spin, d5 species. I want to use the geometry and charges in subsequent | molecular dynamics and/or Monte Carlo studies. What is the recommended | method? In particular, how do I treat the d5 system? | | I have access to G90 and G92, GAMESS, MOPAC and Hyperchem. I can therefore | do ab initio with or without ECPs in the basis set, UHF or CI or MCSCF, GVB, | or I can do any one of a number of semiempirical calculations including INDO, | ZINDO/1 or /2, MNDO, AM1, PM3. I do not have access to DFT or Xalpha | programs. ...and here are a few limited comments. HyperChem is limited to states up to quartet, so you won't be able to do a direct optimization on the system with HyperChem at the moment. My own feeling is that the charges will not vary very much, however, between spin states, so you may well get somewhere with singlet or triplet studies. Here goes with some second (or more) hand impressions. My feeling for other programs is that UHF and CI for molecular geometry are not the best idea: with UHF you will get spin contamination and if configuration mixing is important for geometry then you may be better off using MCSCF. ROHF is the best approach to use if available and if you can't do an MCSCF. Reliable methods that work well for a wide variety of transition metal compounds are still not really there, I think. I would suggest that you may want to build as much experimental information as you have into the structure, and also see if you can find studies on closely related systems. Your task will be easier if the ligands are fairly rigid. | | Also, can anyone point me in the direction of previous studies of high spin | d5 iron complexes, even such as Fe(OH)6 3-? | You may wish to look at S. O. Sommerer et al. Inorg Chem 1992, 31, 563 for a recent application using ZINDO. The complex is [Fe(DAPSC)(H2O)2]2+, and they look at singlet, triplet and quintet states. Tom -- Tom Slee Hypercube, Inc., #7-419 Phillip St., Waterloo, Ont. N2L 3X2 Internet: slee@hyper.com Tel. (519) 725-4040 ________________________________________________________________________ From ciens.ula.ve!root@netcom.com Thu May 20 14:53:01 1993 Date: Thu, 20 May 93 10:58:48-040 From: Operator To: hyperchem@autodesk.com Subject: From Merida-Venezuela Status: RO Hello! We are an international ATC (Autodesk Trainning Center) at "Universidad de Los Andes", in Merida, Venezuela, and there is a great interest among both Chemistry and Biology department regard the use of HyperChem Modeller software for both educational and research purposes. At the moment we would like detailed information about some aspects in order to apply this tool in research projects: 1.- In the modelling of protein 3D structure from its secuence: Which physical properties are used by HyperChem? Hydrogen Bonds? Hidrofobic interactions? All of the above? This is particullarly important in proteins which have few or no alpha-helix and beta-secundary structure. 2.- Is it possible to load information from Protein and Gene Banks through HyperChem? At the moment we are waiting for a Grant copy of the software as to begin working! So we only have your HyperChem brouchure and we want some aditional information. Would you please send us this and any other related information through e-mail or to our mail and cargo addresses in Miami? Thanks a lot Alejandro Mujica Universidad de Los Andes ATC Director ALEJO@ula.ciens.ve USA Mail Address USA Cargo Address --------------------------------------------------- CITEC-ULA, MRD 1728 CITEC-ULA, MRD-1728 POBox 8537 ZOOM Miami Miami, FL 33102-8537 1915N.W.82ND.Ave. Miami, FL 331 --------------------------------------------------- ----- End Included Message ----- ________________________________________________________________________ From PEARL.TUFTS.EDU!RSTOLOW@netcom.com Thu May 20 22:46:28 1993 Date: Thu, 20 May 1993 16:56 EDT From: RSTOLOW@PEARL.TUFTS.EDU Subject: Conversion of Cartesian to Internal Coordinates in HyperChem To: hyperchem@autodesk.com Status: RO Hi, Does HyperChem have the capability of converting from Cartesian coordinates to a z-matrix? Bob Stolow rstolow@pearl.tufts.edu ________________________________________________________________________ From hyper!hurst@autodesk.com Fri May 21 10:30:42 1993 Date: Fri, 21 May 93 09:27:42 -0400 From: hyper!hurst@autodesk.com (Graham Hurst) To: RSTOLOW@PEARL.TUFTS.EDU, autodesk!hyperchem@netcom.com Subject: Re: Conversion of Cartesian to Internal Coordinates in HyperChem Status: RO Bob Stolow (rstolow@pearl.tufts.edu) asks: > Hi, > Does HyperChem have the capability of converting from Cartesian > coordinates to a z-matrix? Yes! This was one of the most user-requested features for release 3. Release 3 can read and write MOPAC-style Z-matrix files. A tip for any release 3 users out there is that the Z-matrix filter has a crude (but hopefully reasonable) facility to infer bond orders based on atomic numbers and interatomic distances. Thus if you've got Cartesian coordinates but no connectivity information (needed for molecular mechanics and for display purposes), save it as a Z-matrix and read it back in again! Be forwarned that the time taken for this bond-inference scheme is proportional to the square of the number of atoms, so if you want to do it for a protein be prepared to wait... Hope this helps, Graham ------------ Graham Hurst Hypercube Inc, 7-419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 internet: hurst@hyper.com ________________________________________________________________________ From biochemistry.cwru.edu!anderson@netcom.com Wed May 26 09:34:33 1993 From: "Vernon Anderson" Date: Wed, 26 May 93 08:17:48 EST To: hyperchem@autodesk.com Subject: van dvan der Waal's radii, apparent discrepancies Status: RO Early in May I sent a query about this problem to Hyperchem, as of yet I have not received a reply: The release 2 manual for Hyperchem indicates that spheres are drawn as "CPK models" and that dots are "van der Waal's radii of the atoms". I have found this to not be the case. I fix the bond length of two atoms until the spheres of dot surfaces just touch and then see if the sum of the radii for the two atoms agrees with the sum of the literature values for the van der Waal's radii. Unfortuantely, at least for carbon (r=1.2 in Hyperchem instead of ca. 1.6) and nitrogen (r=1.1 instead of 1.5), two modestly important atoms, the observed values are dramatically smaller than the real values. I believe the manual is wrong. Is there some way I can generate real van der Waal's surfaces? This is a significant problem when one is looking for or trying to demonstrate steric strain, as in 1,3 diaxial interactions. Thanks. -Vernon- 10900 Euclid Avenue Case Western Reserve University Cleveland, OH 44106-4935 216-368-2599, fax 216-368-4544 anderson@biochemistry.cwru.edu ________________________________________________________________________ From biochemistry.cwru.edu!anderson@netcom.com Wed May 26 09:34:36 1993 From: "Vernon Anderson" Date: Wed, 26 May 93 08:17:48 EST To: hyperchem@autodesk.com Subject: van dvan der Waal's radii, apparent discrepancies Status: RO Early in May I sent a query about this problem to Hyperchem, as of yet I have not received a reply: The release 2 manual for Hyperchem indicates that spheres are drawn as "CPK models" and that dots are "van der Waal's radii of the atoms". I have found this to not be the case. I fix the bond length of two atoms until the spheres of dot surfaces just touch and then see if the sum of the radii for the two atoms agrees with the sum of the literature values for the van der Waal's radii. Unfortuantely, at least for carbon (r=1.2 in Hyperchem instead of ca. 1.6) and nitrogen (r=1.1 instead of 1.5), two modestly important atoms, the observed values are dramatically smaller than the real values. I believe the manual is wrong. Is there some way I can generate real van der Waal's surfaces? This is a significant problem when one is looking for or trying to demonstrate steric strain, as in 1,3 diaxial interactions. Thanks. -Vernon- 10900 Euclid Avenue Case Western Reserve University Cleveland, OH 44106-4935 216-368-2599, fax 216-368-4544 anderson@biochemistry.cwru.edu ________________________________________________________________________ From fs.sciences.WLU.EDU!DESJARDI.S@netcom.com Sun May 30 10:33:42 1993 To: hyperchem@autodesk.com From: DESJARDI.S@fs.sciences.WLU.EDU Organization: Washington & Lee University Date: 30 May 93 09:46:40 EDT Subject: Normal Modes for MM Force Fields Status: RO Is it possible using script commands to make Hyperchem perform a normal mode analysis using a molecular mechanics force field such as MM+ ? There is nothing quantum mechanical about normal mode analysis, although I realize the results are better using a Born- Oppenheimer surface. In particular, I would like to perform a normal mode analysis on a small protein (904 atoms) to try and identify the breathing modes. S. Desjardins Department of Chemistry Washington and Lee University Lexington, VA 24450 (703) 463-8873 ________________________________________________________________________ From fs.sciences.WLU.EDU!DESJARDI.S@netcom.com Sun May 30 14:26:14 1993 To: hyperchem@autodesk.com From: DESJARDI.S@fs.sciences.WLU.EDU Organization: Washington & Lee University Date: 30 May 93 13:06:41 EDT Subject: (Forwarded) Normal Modes for MM Force Fields Status: RO Forwarded message: To: hyperchem@autodesk.com From: DESJARDI.S@fs.sciences.WLU.EDU Organization: Washington & Lee University Date: 30 May 93 09:46:40 EDT Subject: Normal Modes for MM Force Fields Priority: normal Is it possible using script commands to make Hyperchem perform a normal mode analysis using a molecular mechanics force field such as MM+ ? There is nothing quantum mechanical about normal mode analysis, although I realize the results are better using a Born- Oppenheimer surface. In particular, I would like to perform a normal mode analysis on a small protein (904 atoms) to try and identify the breathing modes. S. Desjardins Department of Chemistry Washington and Lee University Lexington, VA 24450 (703) 463-8873