Wall clock time and date at job start Tue Mar 31 2020 06:01:30 AMSOL-version 7.1 by G. D. Hawkins, D. J. Giesen, G. C. Lynch, C. C. Chambers, I. Rossi, J. W. Storer, J. Li, J. D. Thompson, P. Winget, B. J. Lynch, D. Rinaldi, D. A. Liotard, C. J. Cramer, and D. G. Truhlar Copyright 2004 by Regents of the University of Minnesota. All rights reserved. Notice: recipients of this code are asked to comply with the user agreement in Section 1 of the documentation file. ******************************************************************************* * 1SCF - SCF CALCULATION WITHOUT GEOMETRY OPTIMIZATION * - USE EF ROUTINE FOR MINIMUM SEARCH (DEFAULT) * GEO-OK - OVERRIDE INTERATOMIC DISTANCE CHECK * TLIMIT= - A TIME OF 15. SECONDS REQUESTED * CHARGE - CHARGE ON SYSTEM= -1 * AM1 - THE AM1 HAMILTONIAN TO BE USED * SM5.42R - SM5.42R CALCULATIONS WILL BE PERFORMED * - CHARGE MODEL 2 WILL BE USED (CM2A) * - THE SOLVENT IS WATER ******************************************************************************* Atom NO. Chemical Bond length Bond angle Dihedral angle number (k) symbol (angstroms) (degrees) (degrees) (I) NA:I NB:NA:I NC:NB:NA:I NA NB NC 1 1 N 2 2 C 1.31626 * 1 3 3 Si 1.86796 * 120.00006 * 2 1 4 4 H 1.48508 * 109.47275 * 180.27685 * 3 2 1 5 5 H 1.48503 * 109.47179 * 300.27509 * 3 2 1 6 6 H 1.48500 * 109.47133 * 60.27826 * 3 2 1 7 7 C 1.38805 * 120.00187 * 180.27590 * 2 1 3 8 8 H 1.07994 * 120.00639 * 179.72152 * 7 2 1 9 9 S 1.76209 * 119.99703 * 359.72503 * 7 2 1 10 10 C 1.81000 * 99.99796 * 179.97438 * 9 7 2 11 11 C 1.50695 * 109.47114 * 180.02562 * 10 9 7 12 12 O 1.21287 * 120.00111 * 359.97438 * 11 10 9 13 13 N 1.34774 * 120.00192 * 180.02562 * 11 10 9 14 14 C 1.46504 * 119.99982 * 179.97438 * 13 11 10 15 15 H 1.08993 * 108.45052 * 32.69280 * 14 13 11 16 16 C 1.52572 * 108.51057 * 150.23317 * 14 13 11 17 17 C 1.50881 * 109.35682 * 206.26742 * 16 14 13 18 18 C 1.53950 * 110.09258 * 268.11195 * 17 16 14 19 19 N 1.47610 * 112.14225 * 40.56622 * 18 17 16 20 20 C 1.34781 * 118.64160 * 222.15223 * 19 18 17 21 21 O 1.21348 * 120.00008 * 353.98067 * 20 19 18 22 22 C 1.49451 * 119.99629 * 173.98276 * 20 19 18 23 23 N 1.34776 * 119.99519 * 174.07039 * 22 20 19 24 24 O 1.21342 * 119.99978 * 354.06116 * 22 20 19 25 25 C 1.44581 * 122.71235 * 42.13314 * 19 18 17 26 26 C 1.47090 * 108.51123 * 274.99631 * 14 13 11 27 27 H 0.96994 * 120.00026 * 359.72173 * 1 2 3 28 28 H 1.08999 * 109.47056 * 299.99920 * 10 9 7 29 29 H 1.08995 * 109.47262 * 59.99927 * 10 9 7 30 30 H 0.97004 * 120.00279 * 359.97438 * 13 11 10 31 31 H 1.08999 * 109.48762 * 326.22879 * 16 14 13 32 32 H 1.08992 * 109.49212 * 86.29999 * 16 14 13 33 33 H 1.09001 * 109.37048 * 147.92653 * 17 16 14 34 34 H 1.08996 * 109.26492 * 28.23653 * 17 16 14 35 35 H 1.08996 * 108.95068 * 279.88057 * 18 17 16 36 36 H 1.09001 * 108.88037 * 161.20248 * 18 17 16 37 37 H 0.96998 * 120.00363 * 359.97438 * 23 22 20 38 38 H 0.97007 * 119.99337 * 180.02562 * 23 22 20 39 39 H 1.08992 * 109.44741 * 149.23141 * 25 19 18 40 40 H 1.09002 * 109.44731 * 29.30871 * 25 19 18 41 41 H 1.08997 * 109.33103 * 296.20497 * 26 14 13 42 42 H 1.08998 * 109.32713 * 55.86141 * 26 14 13 Note: An asterisk (*) indicates this parameter was or will be optimized. Cartesian coordinates (angstroms) NO. Atom X Y Z 1 7 0.0000 0.0000 0.0000 2 6 1.3163 0.0000 0.0000 3 14 2.2502 1.6177 0.0000 4 1 3.7103 1.3464 -0.0068 5 1 1.8865 2.3993 -1.2091 6 1 1.8966 2.3935 1.2159 7 6 2.0103 -1.2020 -0.0058 8 1 3.0903 -1.2021 -0.0103 9 16 1.1293 -2.7281 -0.0058 10 6 2.5158 -3.8914 -0.0152 11 6 1.9874 -5.3027 -0.0171 12 8 0.7911 -5.5023 -0.0122 13 7 2.8441 -6.3431 -0.0234 14 6 2.3303 -7.7151 -0.0247 15 1 1.3922 -7.7316 -0.5793 16 6 3.3336 -8.6073 -0.7495 17 6 2.6141 -9.7994 -1.3306 18 6 2.6330 -10.9684 -0.3290 19 7 2.4082 -10.5163 1.0581 20 6 3.1581 -11.0519 2.0416 21 8 3.9196 -11.9641 1.7957 22 6 3.0517 -10.5222 3.4351 23 7 3.7097 -11.1331 4.4402 24 8 2.3730 -9.5421 3.6614 25 6 1.4172 -9.5224 1.4050 26 6 2.0586 -8.1133 1.3649 27 1 -0.4850 0.8400 0.0041 28 1 3.1204 -3.7290 -0.9075 29 1 3.1285 -3.7337 0.8724 30 1 3.8009 -6.1835 -0.0270 31 1 3.8090 -8.0429 -1.5517 32 1 4.0923 -8.9482 -0.0451 33 1 3.1081 -10.1056 -2.2527 34 1 1.5815 -9.5258 -1.5473 35 1 3.6001 -11.4679 -0.3861 36 1 1.8518 -11.6784 -0.6008 37 1 4.2520 -11.9167 4.2593 38 1 3.6403 -10.7895 5.3447 39 1 1.0397 -9.7211 2.4080 40 1 0.5937 -9.5668 0.6923 41 1 2.9931 -8.1263 1.9259 42 1 1.3752 -7.3957 1.8188 RHF calculation, no. of doubly occupied orbitals= 59 REFERENCES FOR PARAMETERS IN GAS-PHASE HAMILTONIAN: H: (AM1): M.J.S. DEWAR ET AL, J. AM. CHEM. SOC. 107 3902-3909 (1985) C: (AM1): M.J.S. DEWAR ET AL, J. AM. CHEM. SOC. 107 3902-3909 (1985) N: (AM1): M.J.S. DEWAR ET AL, J. AM. CHEM. SOC. 107 3902-3909 (1985) O: (AM1): M.J.S. DEWAR ET AL, J. AM. CHEM. SOC. 107 3902-3909 (1985) Si: (AM1): M.J.S.DEWAR, C. JIE, ORGANOMETALLICS, 6, 1486-1490 (1987). S: (AM1): M.J.S. DEWAR, Y.-C. YUAN, INORGANIC CHEM., 29, 589 (1990) REFERENCE FOR CHARGE MODEL 2: J. Li, J. Xing, C. J. Cramer, and D. G. Truhlar, J. Chem. Phys. 111 (1999) 885. REFERENCE FOR THE PARAMETERIZATION OF THE SM5.42R SOLVATION MODEL: J. Li, T. Zhu, G. D. Hawkins, P. Winget, D. A. Liotard, C. J. Cramer, and D. G. Truhlar, Theor. Chem. Acc. 103 (1999) 9-63 P. Winget, J. D. Thompson C. J. Cramer,and D. G. Truhlar, J. Phys. Chem. B. submitted. CHARGE=-1 AM1 1SCF TLIMIT=15 GEO-OK SM5.42R & SOLVNT=WATER ZINC001065876403.mol2 42 1SCF WAS SPECIFIED, SO GEOMETRY OPTIMIZATION WAS NOT USED SCF FIELD WAS ACHIEVED Wall clock time and date at job start Tue Mar 31 2020 06:01:30 Heat of formation + Delta-G solvation = -125.714825 kcal Electronic energy + Delta-G solvation = -26057.996296 eV Core-core repulsion = 22163.469545 eV Total energy + Delta-G solvation = -3894.526751 eV No. of doubly occupied orbitals = 59 Molecular weight (most abundant/longest-lived isotopes) = 329.124 amu Computer time = 3.35 seconds Orbital eigenvalues (eV) -42.21024 -40.90877 -39.59482 -38.75164 -36.24064 -34.72292 -34.58705 -33.91680 -32.95213 -30.44139 -28.30499 -27.67379 -26.18061 -25.63625 -22.78680 -21.74446 -21.62696 -20.49260 -19.80775 -19.00453 -18.43052 -17.80418 -17.73850 -17.15598 -16.96148 -16.88373 -16.45800 -16.34260 -15.96683 -15.69949 -15.40445 -15.05255 -14.70542 -14.58221 -14.51192 -14.23513 -13.71091 -13.58077 -13.40687 -13.16126 -12.91743 -12.82993 -12.69460 -12.50911 -12.37988 -11.92901 -11.82581 -11.70414 -11.61444 -11.16043 -10.89771 -10.85322 -10.48463 -10.27345 -10.20059 -9.77088 -8.66298 -8.35053 -6.12738 0.31984 1.27250 1.41081 1.41668 1.47128 1.58331 1.64372 2.08724 2.25703 2.30662 2.61326 2.99051 3.32006 3.49222 3.58371 3.81132 3.94057 3.99374 4.08574 4.17823 4.29313 4.32939 4.43333 4.50526 4.55882 4.64746 4.75405 4.89042 4.92986 5.04731 5.15922 5.22144 5.29952 5.38606 5.41794 5.53800 5.65759 5.90365 6.14066 6.19820 6.52667 6.68074 7.03783 7.06345 7.27168 8.74463 Molecular weight = 329.12amu Principal moments of inertia in cm(-1) A = 0.022942 B = 0.002416 C = 0.002306 Principal moments of inertia in units of 10**(-40)*gram-cm**2 A = 1220.152199 B =11584.588049 C =12141.620035 Net atomic charges, atomic populations, and dipole contributions calculated with CM2 Atom NO. Type Charge No. of electrons 1 N -0.911 5.911 2 C 0.012 3.988 3 Si 0.999 3.001 4 H -0.257 1.257 5 H -0.273 1.273 6 H -0.274 1.274 7 C -0.546 4.546 8 H 0.081 0.919 9 S -0.149 6.149 10 C -0.131 4.131 11 C 0.534 3.466 12 O -0.562 6.562 13 N -0.715 5.715 14 C 0.145 3.855 15 H 0.068 0.932 16 C -0.115 4.115 17 C -0.125 4.125 18 C 0.106 3.894 19 N -0.568 5.568 20 C 0.500 3.500 21 O -0.541 6.541 22 C 0.504 3.496 23 N -0.804 5.804 24 O -0.533 6.533 25 C 0.111 3.889 26 C -0.123 4.123 27 H 0.271 0.729 28 H 0.109 0.891 29 H 0.105 0.895 30 H 0.413 0.587 31 H 0.086 0.914 32 H 0.069 0.931 33 H 0.109 0.891 34 H 0.072 0.928 35 H 0.092 0.908 36 H 0.087 0.913 37 H 0.421 0.579 38 H 0.421 0.579 39 H 0.105 0.895 40 H 0.089 0.911 41 H 0.063 0.937 42 H 0.051 0.949 For the charges calculated by CM2: Dipole moment (debyes) X Y Z Total from point charges 11.727 -26.908 2.624 29.470 Note: The Mulliken population analysis charges presented below were not used in the solvation calculation but are provided for completeness. The chosen solvation model uses CM2 partial charges for calculating solvation energies. Net atomic charges, atomic populations, and dipole contributions using Mulliken population analysis Atom NO. Type Charge No. of electrons 1 N -0.548 5.548 2 C -0.192 4.192 3 Si 0.821 3.179 4 H -0.181 1.181 5 H -0.198 1.198 6 H -0.199 1.199 7 C -0.694 4.694 8 H 0.100 0.900 9 S 0.078 5.922 10 C -0.282 4.282 11 C 0.320 3.680 12 O -0.440 6.440 13 N -0.368 5.368 14 C 0.042 3.958 15 H 0.086 0.914 16 C -0.154 4.154 17 C -0.163 4.163 18 C -0.014 4.014 19 N -0.300 5.300 20 C 0.282 3.718 21 O -0.419 6.419 22 C 0.282 3.718 23 N -0.371 5.371 24 O -0.411 6.411 25 C -0.013 4.013 26 C -0.163 4.163 27 H 0.080 0.920 28 H 0.127 0.873 29 H 0.123 0.877 30 H 0.249 0.751 31 H 0.105 0.895 32 H 0.088 0.912 33 H 0.127 0.873 34 H 0.091 0.909 35 H 0.111 0.889 36 H 0.105 0.895 37 H 0.253 0.747 38 H 0.255 0.745 39 H 0.123 0.877 40 H 0.107 0.893 41 H 0.082 0.918 42 H 0.070 0.930 Dipole moment (debyes) X Y Z Total from point charges 9.510 -27.018 2.422 28.745 hybrid contribution 1.987 1.404 0.521 2.488 sum 11.497 -25.615 2.943 28.230 Atomic orbital electron populations 1.70185 1.07956 1.28554 1.48070 1.26135 0.95987 1.03332 0.93767 0.84899 0.78570 0.76319 0.78105 1.18094 1.19843 1.19931 1.23233 0.95300 0.92068 1.58751 0.90048 1.85549 1.10497 0.99146 1.97023 1.23383 1.03559 0.94700 1.06541 1.20029 0.86367 0.86609 0.74988 1.90681 1.17198 1.86002 1.50101 1.46076 1.10098 1.05143 1.75467 1.20189 0.98596 0.80338 0.96709 0.91356 1.21333 0.97476 0.96305 1.00237 1.21718 1.02215 0.93616 0.98746 1.22191 1.04044 0.97056 0.78120 1.47742 1.35206 1.39465 1.07538 1.20286 0.81349 0.83232 0.86902 1.90739 1.38866 1.28713 1.83591 1.20163 0.80535 0.83864 0.87200 1.43462 1.49759 1.33387 1.10474 1.90845 1.39508 1.26321 1.84402 1.21902 0.90030 0.85655 1.03679 1.21351 1.01545 0.97124 0.96265 0.91979 0.87276 0.87685 0.75105 0.89497 0.91217 0.87297 0.90884 0.88925 0.89476 0.74690 0.74487 0.87738 0.89307 0.91790 0.92995 Number of geometries 1 Number of calculations of the screened coulomb radii 1 The total number of SCF iterations 15. Note: The number of geometries may not correspond to the number of cycles due to rejected geometry changes. In the following table subtotal= G_P + SS G_CDS. Atom Chem. CM2 G_P Area Sigma k SS G_CDS Subtotal M number symbol chg. (kcal) (Ang**2) cal/(Ang**2) (kcal) (kcal) value 1 N -0.91 -56.36 13.22 21.65 0.29 -56.08 16 2 C 0.01 0.72 5.49 84.86 0.47 1.18 16 3 Si 1.00 43.95 29.55 68.60 2.03 45.97 16 4 H -0.26 -10.58 7.11 99.48 0.71 -9.87 16 5 H -0.27 -11.62 7.11 99.48 0.71 -10.91 16 6 H -0.27 -11.69 7.11 99.48 0.71 -10.98 16 7 C -0.55 -31.48 9.50 67.96 0.65 -30.83 16 8 H 0.08 4.38 7.80 -2.91 -0.02 4.36 16 9 S -0.15 -8.38 20.57 -56.49 -1.16 -9.54 16 10 C -0.13 -5.26 6.16 71.23 0.44 -4.82 16 11 C 0.53 19.89 7.69 87.66 0.67 20.56 16 12 O -0.56 -25.92 15.36 -3.05 -0.05 -25.97 16 13 N -0.71 -18.37 4.88 -452.05 -2.21 -20.57 16 14 C 0.15 3.24 1.96 43.01 0.08 3.33 16 15 H 0.07 1.81 6.65 -2.39 -0.02 1.79 16 16 C -0.12 -1.69 5.00 29.76 0.15 -1.54 16 17 C -0.12 -1.37 5.71 30.23 0.17 -1.20 16 18 C 0.11 1.29 6.07 86.49 0.52 1.81 16 19 N -0.57 -9.30 2.24 -819.72 -1.84 -11.13 16 20 C 0.50 9.07 7.67 87.27 0.67 9.74 16 21 O -0.54 -11.09 15.81 -3.24 -0.05 -11.14 16 22 C 0.50 8.80 7.89 87.27 0.69 9.49 16 23 N -0.80 -8.00 8.87 -174.50 -1.55 -9.54 16 24 O -0.53 -12.36 12.50 -3.22 -0.04 -12.40 16 25 C 0.11 2.13 4.96 87.38 0.43 2.56 16 26 C -0.12 -2.94 4.38 29.40 0.13 -2.81 16 27 H 0.27 15.50 8.31 -92.71 -0.77 14.73 16 28 H 0.11 3.94 8.14 -2.40 -0.02 3.92 16 29 H 0.10 3.88 8.14 -2.40 -0.02 3.86 16 30 H 0.41 7.98 8.61 -92.71 -0.80 7.18 16 31 H 0.09 1.14 8.05 -2.39 -0.02 1.13 16 32 H 0.07 1.04 7.48 -2.39 -0.02 1.02 16 33 H 0.11 0.76 8.14 -2.39 -0.02 0.74 16 34 H 0.07 0.90 7.30 -2.39 -0.02 0.88 16 35 H 0.09 1.18 7.03 -2.39 -0.02 1.16 16 36 H 0.09 0.84 8.14 -2.39 -0.02 0.82 16 37 H 0.42 2.85 8.32 -92.71 -0.77 2.08 16 38 H 0.42 2.76 8.93 -92.70 -0.83 1.94 16 39 H 0.10 2.22 5.47 -2.39 -0.01 2.20 16 40 H 0.09 1.53 8.06 -2.39 -0.02 1.51 16 41 H 0.06 1.56 7.17 -2.39 -0.02 1.54 16 42 H 0.05 1.62 7.95 -2.39 -0.02 1.60 16 Total: -1.00 -81.44 356.50 -0.81 -82.24 By element: Atomic # 1 Polarization: 21.99 SS G_CDS: -1.30 Total: 20.69 kcal Atomic # 6 Polarization: 2.40 SS G_CDS: 5.07 Total: 7.47 kcal Atomic # 7 Polarization: -92.02 SS G_CDS: -5.30 Total: -97.33 kcal Atomic # 8 Polarization: -49.37 SS G_CDS: -0.14 Total: -49.51 kcal Atomic # 14 Polarization: 43.95 SS G_CDS: 2.03 Total: 45.97 kcal Atomic # 16 Polarization: -8.38 SS G_CDS: -1.16 Total: -9.54 kcal Total: -81.44 -0.81 -82.24 kcal The number of atoms in the molecule is 42 The average number of expansion shells was 16.00 The maximum number of expansion shells was 16 The minimum number of expansion shells was 16 **** NOTA BENE **** This is the net solvation energy for this exact molecular structure (nuclear and electronic)! The standard-state solvation energy should be obtained as the difference between the heat of formation plus delta-G solvation for the relaxed solvated system and that for the relaxed gas-phase system. ZINC001065876403.mol2 42 1SCF run This is a breakdown of the solvation energy calculated without geometric relaxation in solution: (1) E-EN(sol) electronic-nuclear energy of solute -43.472 kcal (2) G-P(sol) polarization free energy of solvation -81.437 kcal (3) G-ENP(sol) elect.-nuc.-pol. free energy of system -124.909 kcal (4) G-CDS(sol) cavity-dispersion-solvent structure free energy -0.806 kcal (5) G-P-CDS(sol) = G-P(sol) + G-CDS(sol) = (2) + (4) -82.243 kcal (6) G-S(sol) free energy of system = (1) + (5) -125.715 kcal 1SCF WAS SPECIFIED, SO GEOMETRY OPTIMIZATION WAS NOT USED Total computer time = 3.35 seconds