From chemistry-request@ccl.net Tue Aug 18 08:08:35 1992 Date: Mon, 17 Aug 92 10:45:39-1795 From: Dr. James Stewart To: chemistry@ccl.net Status: R A subroutine which might be useful in converting internal coordinates into catesian coordinates is GMETRY in MOPAC. Anyone who wishes to use GMETRY from any MOPAC, please feel free to do so. James J. P. Stewart --- Administrivia: This message is automatically appended by the mail exploder. CHEMISTRY@ccl.net --- everybody; CHEMISTRY-REQUEST@ccl.net --- coordinator only OSCPOST@ccl.net : send something from chemistry; FTP: www.ccl.net --- From chemistry-request@ccl.net Tue Aug 18 08:49:23 1992 Date: Mon, 17 Aug 92 10:45:16-1795 From: Dr. James Stewart To: chemistry@ccl.net Status: R DIPOLES IN SEMIEMPIRICAL METHODS As far as I know, there have not been any comprehensive surveys of how well semiempirical methods reproduce dipole moments. However, the following data might prove useful: DIPOLE MOMENTS Type of Compound ERROR PM3 MNDO AM1 Unsigned signed Unsigned Signed Unsigned Signed HN 1 0.080 0.080 0.280 0.280 0.380 0.380 HO 1 0.110 -0.110 0.070 -0.070 0.010 0.010 CH 10 0.147 -0.073 0.240 -0.178 0.150 -0.066 CO 1 0.080 0.080 0.090 0.090 0.050 -0.050 CHO 19 0.213 -0.144 0.226 -0.151 0.149 -0.027 CHN 17 0.390 -0.106 0.498 -0.401 0.430 -0.266 CHNO 2 0.515 -0.515 1 0.670 -0.670 1 0.270 -0.270 CS 1 0.740 0.740 0.230 -0.230 1.560 1.560 CHS 6 0.432 0.432 0.070 0.027 0.193 0.130 CSO 1 0.330 -0.330 0.320 -0.320 0.030 -0.030 CHSO 1 0.520 0.520 0.680 0.680 0.000 0.000 CHNS 1 0.610 -0.610 1.020 -1.020 1.360 -1.360 CHF 11 0.210 -0.017 0.410 0.375 0.185 0.063 CHOF 2 0.385 0.055 0.280 0.280 0.480 0.070 CNF 2 0.740 -0.740 1.090 -1.090 1.095 -1.095 COF 2 0.085 0.035 0.210 -0.210 0.180 0.180 CHCl 1 0.300 -0.300 0.340 0.340 0.170 -0.170 CHBr 8 0.223 -0.148 0.258 -0.150 0.290 -0.148 CHOBr 1 0.520 0.520 0.020 0.020 0.160 0.160 CFBr 2 0.185 0.065 0.350 0.350 0.215 0.155 CHI 5 0.374 -0.374 0 0.000 0.000 0 0.000 0.000 CFI 1 0.210 -0.210 0 0.000 0.000 0 0.000 0.000 CBeH 1 0.240 -0.240 1 0.070 -0.070 0 0.000 0.000 CHSi 4 0.323 -0.323 0.438 -0.438 0.245 -0.245 CHSiS 1 0.610 0.610 1.090 1.090 0.660 0.660 CHSiN 1 0.200 -0.200 0.200 -0.200 0.010 0.010 CGeH 4 0.335 -0.105 0.613 -0.207 0.473 -0.348 CGeHO 3 0.250 0.097 0.577 -0.577 0.450 -0.183 CGeHN 1 0.300 -0.300 1.800 -1.800 0.860 -0.860 CGeHF 1 0.950 -0.950 0.680 -0.680 0.820 -0.820 CGeHCl 3 0.083 0.083 0.763 0.763 0.213 -0.213 CGeHBr 2 1.020 1.020 1.135 1.135 0.275 0.005 CSnH 3 0.183 -0.183 0.227 -0.227 0.367 -0.367 CSnHCl 2 0.480 0.040 0.260 -0.220 0.595 -0.595 CSnHBr 1 1.690 1.690 0.300 -0.300 0.440 -0.440 CSnHI 1 1.290 1.290 0 0.000 0.000 0 0.000 0.000 CPbHCl 1 0.030 0.030 0 0.000 0.000 0 0.000 0.000 CHP 3 0.080 -0.040 0.610 0.610 0.603 0.603 CHPF 1 0.060 -0.060 0.740 0.740 0.060 -0.060 CAsH 1 0.390 -0.390 0 0.000 0.000 0 0.000 0.000 CAsHCl 2 0.330 0.330 0 0.000 0.000 0 0.000 0.000 CZnH 4 0.150 -0.050 0.220 0.025 0.180 -0.020 CHgHN 1 0.620 -0.620 0 0.000 0.000 0 0.000 0.000 CHgHCl 2 0.155 0.045 0 0.000 0.000 0 0.000 0.000 CHgHBr 2 0.445 0.445 0 0.000 0.000 0 0.000 0.000 CHgHI 2 0.845 0.605 0 0.000 0.000 0 0.000 0.000 CSeH 3 0.627 0.627 0 0.000 0.000 0 0.000 0.000 CSeS 1 1.260 1.260 0 0.000 0.000 0 0.000 0.000 O 1 1.180 1.180 0.650 0.650 0.670 0.670 HNO 3 0.177 0.077 0.390 0.390 0.290 0.290 NO 1 0.090 0.090 0.590 0.590 0.470 0.470 HS 1 0.800 0.800 0.510 0.510 0.890 0.890 SO 1 2.060 2.060 2.150 2.150 2.720 2.720 HF 1 0.430 -0.430 0.160 0.160 0.090 -0.090 HOF 1 0.550 -0.550 0.420 -0.420 0.630 -0.630 NOF 2 0.985 -0.565 0.745 -0.555 0.890 -0.540 OF 1 0.080 0.080 0.020 0.020 0.190 -0.190 NF 2 0.245 0.245 0.090 -0.090 0.350 0.150 HCl 1 0.260 0.260 0.360 0.360 0.260 0.260 OCl 1 2.440 2.440 0.090 0.090 0.640 0.640 FCl 1 0.540 0.540 0.590 0.590 0.030 0.030 SCl 1 0.230 0.230 0.620 0.620 0.330 -0.330 HBr 1 0.430 0.430 0.230 0.230 0.550 0.550 OBr 1 1.710 1.710 0.380 0.380 0.750 0.750 FBr 1 0.830 0.830 0.680 0.680 0.040 0.040 ClBr 1 0.460 -0.460 0.230 0.230 0.070 -0.070 HI 1 0.530 0.530 0 0.000 0.000 0 0.000 0.000 BrI 1 0.200 -0.200 0 0.000 0.000 0 0.000 0.000 AlF 1 1.760 1.760 1.220 -1.220 0.530 -0.530 GaF 1 1.350 1.350 0 0.000 0.000 0 0.000 0.000 InF 1 1.320 -1.320 0 0.000 0.000 0 0.000 0.000 InCl 1 0.120 0.120 0 0.000 0.000 0 0.000 0.000 TlCl 1 0.330 0.330 0 0.000 0.000 0 0.000 0.000 TlBr 1 0.410 0.410 0 0.000 0.000 0 0.000 0.000 TlI 1 0.300 0.300 0 0.000 0.000 0 0.000 0.000 HSiF 2 0.190 0.060 1.110 1.110 0.160 0.160 HSiCl 2 1.520 1.520 2.075 2.075 0.570 0.570 HSiBr 1 1.660 1.660 1.900 1.900 0.380 0.380 GeO 1 0.210 -0.210 0.240 0.240 0.660 -0.660 GeHN 1 0.030 -0.030 0.740 -0.740 0.710 -0.710 GeS 1 1.520 -1.520 3.480 3.480 2.250 2.250 GeHF 1 0.320 -0.320 0.720 -0.720 0.400 -0.400 GeF 1 0.900 -0.900 1.970 1.970 0.540 0.540 GeHCl 1 0.190 0.190 1.490 1.490 0.380 0.380 GeHBr 1 1.220 1.220 1.940 1.940 0.610 0.610 GeHI 1 0.780 0.780 0 0.000 0.000 0 0.000 0.000 SnO 1 1.380 -1.380 1.370 -1.370 0.040 0.040 SnS 1 0.430 -0.430 0.090 -0.090 2.540 2.540 PbO 1 0.870 -0.870 0 0.000 0.000 0 0.000 0.000 PbS 1 0.650 -0.650 0 0.000 0.000 0 0.000 0.000 HP 2 0.935 0.935 0.845 -0.075 1.295 0.415 PF 1 1.220 1.220 1.410 1.410 0.630 0.630 POF 1 0.270 0.270 0.560 -0.560 0.880 0.880 AsH 1 0.540 0.540 0 0.000 0.000 0 0.000 0.000 AsCl 1 0.270 -0.270 0 0.000 0.000 0 0.000 0.000 AsBr 1 0.240 0.240 0 0.000 0.000 0 0.000 0.000 AsI 1 0.080 -0.080 0 0.000 0.000 0 0.000 0.000 HgCl 1 1.220 -1.220 0 0.000 0.000 0 0.000 0.000 HgBr 1 0.950 -0.950 0 0.000 0.000 0 0.000 0.000 SbH 1 0.430 0.430 0 0.000 0.000 0 0.000 0.000 SeH 2 0.760 0.760 0 0.000 0.000 0 0.000 0.000 SeO 2 0.590 0.320 0 0.000 0.000 0 0.000 0.000 SeF 1 0.250 -0.250 0 0.000 0.000 0 0.000 0.000 SeOF 1 0.860 0.860 0 0.000 0.000 0 0.000 0.000 GeSe 1 0.020 -0.020 0 0.000 0.000 0 0.000 0.000 PbSe 1 0.310 -0.310 0 0.000 0.000 0 0.000 0.000 GeTe 1 0.060 0.060 0 0.000 0.000 0 0.000 0.000 SnTe 1 0.580 0.580 0 0.000 0.000 0 0.000 0.000 PbTe 1 0.040 -0.040 0 0.000 0.000 0 0.000 0.000 Totals: 217 0.442 165 0.513 164 0.393 AVERAGES BY ELEMENT Element No. PM3 No. MNDO No. AM1 H 161 0.4 ( 0.1) [ 0.5] 134 0.5 ( 0.0) [ 0.7] 133 0.3 (-0.1) [ 0.4] Be 1 0.2 (-0.2) [ 0.2] 1 0.1 (-0.1) [ 0.1] C 145 0.3 ( 0.0) [ 0.5] 122 0.4 (-0.1) [ 0.5] 121 0.3 (-0.1) [ 0.4] N 35 0.4 (-0.2) [ 0.5] 33 0.6 (-0.4) [ 0.8] 33 0.5 (-0.3) [ 0.6] O 52 0.5 ( 0.1) [ 0.7] 47 0.4 (-0.1) [ 0.6] 47 0.3 ( 0.1) [ 0.6] F 42 0.5 ( 0.0) [ 0.6] 37 0.6 ( 0.2) [ 0.7] 37 0.4 ( 0.0) [ 0.5] Al 1 1.8 ( 1.8) [ 1.8] 1 1.2 (-1.2) [ 1.2] 1 0.5 (-0.5) [ 0.5] Si 11 0.7 ( 0.4) [ 0.9] 11 1.0 ( 0.7) [ 1.3] 11 0.3 ( 0.1) [ 0.4] P 8 0.5 ( 0.4) [ 0.7] 8 0.8 ( 0.4) [ 0.8] 8 0.7 ( 0.5) [ 0.9] S 18 0.7 ( 0.3) [ 0.8] 16 0.7 ( 0.4) [ 1.1] 16 0.8 ( 0.6) [ 1.2] Cl 23 0.5 ( 0.3) [ 0.8] 14 0.8 ( 0.7) [ 1.0] 14 0.3 ( 0.0) [ 0.4] Zn 4 0.2 (-0.1) [ 0.2] 4 0.2 ( 0.0) [ 0.3] 4 0.2 ( 0.0) [ 0.2] Ga 1 1.4 ( 1.4) [ 1.4] Ge 24 0.5 ( 0.0) [ 0.6] 21 1.0 ( 0.3) [ 1.3] 21 0.6 (-0.1) [ 0.7] As 7 0.3 ( 0.1) [ 0.3] Se 12 0.6 ( 0.5) [ 0.7] Br 26 0.6 ( 0.3) [ 0.8] 20 0.5 ( 0.3) [ 0.8] 20 0.3 ( 0.1) [ 0.4] In 2 0.7 (-0.6) [ 0.9] Sn 10 0.7 ( 0.1) [ 0.9] 8 0.4 (-0.4) [ 0.5] 8 0.7 ( 0.0) [ 1.0] Sb 1 0.4 ( 0.4) [ 0.4] Te 3 0.2 ( 0.2) [ 0.3] I 14 0.5 ( 0.1) [ 0.7] Hg 9 0.6 (-0.1) [ 0.8] Tl 3 0.3 ( 0.3) [ 0.3] Pb 5 0.4 (-0.4) [ 0.5] Totals: 618 0.4 ( 0.1) [ 0.6] 477 0.5 ( 0.0) [ 0.7] 474 0.4 ( 0.0) [ 0.6] AFTER ELIMINATING DOUBLE COUNTING Totals: 217 0.4 ( 0.1) [ 0.6] 165 0.5 ( 0.1) [ 0.7] 164 0.4 ( 0.0) [ 0.6] (signed average), [root mean square] To read this table, the first part deals with types of molecule, thus the first entry, NH, means `compounds of N and H only', in other words, ammonia. The integers refer to the number of compounds in each class. Where MNDO and AM1 have the same number of compounds as PM3, the integer is dropped. The only parameterization being done nowadays is by Prof Dewar's group, now Prof Holder's group, by Prof Thiel, and by myself. Prof Dewar has developed SAM1, which gives the following statistics: SAM1 AM1 PM3 Hydrocarbons: 11 0.11 0.14 0.14 CHNO molecules 41 0.25 0.27 0.27 Halogen compounds 69 0.46 0.35 0.43 Results are mean unsigned error Prof Thiel is developing MNDO-d, which is a very large improvement over PM3. I was working on improving PM3, until hearing about Prof Thiel's work. Work on PMx has now stopped. My gut feeling is that Prof Thiel's work is so good that even if I had developed PM4, the results would still have been far inferior to those of MNDO-d. NONE of the semiempirical methods are good at predicting dipole moments. No one method is much better than the others. Users should chose a method based on the results in the tables. Many people have said that the charges in PM3, particularly on nitrogen, are questionable. To quote a recent report: "The errors were reduced in PM3 only at the expense of more serious problems, in particular incorrect charge distributions." The definition of charge is highly ambiguous, nevertheless the bulk of the evidence is that charges on N in PM3 should not be trusted. J.J.P. Stewart --- Administrivia: This message is automatically appended by the mail exploder. CHEMISTRY@ccl.net --- everybody; CHEMISTRY-REQUEST@ccl.net --- coordinator only OSCPOST@ccl.net : send something from chemistry; FTP: www.ccl.net --- From chemistry-request@ccl.net Tue Aug 18 12:22:28 1992 Date: 18 Aug 92 09:54 LCL From: PA13808%UTKVM1.BITNET@OHSTVMA.ACS.OHIO-STATE.EDU To: CHEMISTRY@ccl.net Subject: BITNET mail follows Status: R POPULATIONAL ANALYSIS IN GAUSSIAN 90 About a couple of weeks ago Mike Frisch suggested on could do an NBO pop analysis by invoking L607. Unforunately when I try this I am told this link is not implemented on IBM machines which is all i Have! where does this leave me? Am I stumped or can I go the non-standard route method? Maybe some kind person would even send me the route as time is precious. (BLOOR AT UTKVM1) JEB --- Administrivia: This message is automatically appended by the mail exploder. CHEMISTRY@ccl.net --- everybody; CHEMISTRY-REQUEST@ccl.net --- coordinator only OSCPOST@ccl.net : send something from chemistry; FTP: www.ccl.net --- From chemistry-request@ccl.net Tue Aug 18 14:17:31 1992 Date: Mon, 17 Aug 1992 14:55 CST From: C1790@slvaxa.umsl.edu Subject: MODELING POLYMERS To: CHEMISTRY@ccl.net Status: R DEAR NETTERS, I AM CURIOUS TO HEAR FROM ANYONE THAT IS FAMILIAR/EXPERIENCED WITH MOLECULAR MODELING OF POLYMERS ENDOWED WITH HIGH DIELECTRIC MOMENT AND HIGH DIELECTRIC STRENGTH. I WOULD APPRECIATE HEARING OF ANY REFERENCES TO THE LITERATURE ON THE SUBJECT. THANKS, BILL WELSH IN ST. LOUIS (C1790@UMSLVAXA ). --- Administrivia: This message is automatically appended by the mail exploder. CHEMISTRY@ccl.net --- everybody; CHEMISTRY-REQUEST@ccl.net --- coordinator only OSCPOST@ccl.net : send something from chemistry; FTP: www.ccl.net ---