Wall clock time and date at job start Tue Mar 31 2020 18:33:00 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 1.31631 * 1 3 3 Si 1.86796 * 120.00394 * 2 1 4 4 H 1.48498 * 109.47488 * 179.97438 * 3 2 1 5 5 H 1.48507 * 109.46888 * 299.99842 * 3 2 1 6 6 H 1.48506 * 109.47086 * 59.99313 * 3 2 1 7 7 C 1.38800 * 119.99818 * 179.97438 * 2 1 3 8 8 H 1.07998 * 120.00343 * 180.02562 * 7 2 1 9 9 S 1.76209 * 120.00035 * 359.97438 * 7 2 1 10 10 C 1.80999 * 99.99748 * 180.02562 * 9 7 2 11 11 C 1.50697 * 109.46863 * 180.02562 * 10 9 7 12 12 O 1.21283 * 120.00399 * 0.02562 * 11 10 9 13 13 N 1.34774 * 120.00140 * 180.02562 * 11 10 9 14 14 C 1.46510 * 120.00274 * 180.02562 * 13 11 10 15 15 C 1.52991 * 109.47091 * 179.97438 * 14 13 11 16 16 N 1.46907 * 109.47194 * 180.02562 * 15 14 13 17 17 C 1.46903 * 111.00077 * 180.02562 * 16 15 14 18 18 C 1.52996 * 109.46721 * 179.97438 * 17 16 15 19 19 C 1.50701 * 109.46977 * 179.97438 * 18 17 16 20 20 C 1.32569 * 119.99865 * 127.27868 * 19 18 17 21 21 C 1.47813 * 119.99838 * 8.22628 * 20 19 18 22 22 C 1.39542 * 120.13988 * 216.02460 * 21 20 19 23 23 C 1.37972 * 119.85389 * 180.02562 * 22 21 20 24 24 C 1.38339 * 120.14633 * 0.02562 * 23 22 21 25 25 C 1.38344 * 120.28213 * 0.02562 * 24 23 22 26 26 C 1.37974 * 120.14717 * 359.97438 * 25 24 23 27 27 H 0.96999 * 119.99886 * 0.02562 * 1 2 3 28 28 H 1.08994 * 109.47146 * 60.00403 * 10 9 7 29 29 H 1.08997 * 109.47269 * 300.00276 * 10 9 7 30 30 H 0.97000 * 120.00118 * 0.02562 * 13 11 10 31 31 H 1.09007 * 109.46714 * 59.99691 * 14 13 11 32 32 H 1.08995 * 109.46895 * 300.00278 * 14 13 11 33 33 H 1.08998 * 109.47652 * 60.00431 * 15 14 13 34 34 H 1.09007 * 109.47639 * 299.99566 * 15 14 13 35 35 H 1.00898 * 110.99793 * 56.04429 * 16 15 14 36 36 H 1.08994 * 109.47349 * 60.00033 * 17 16 15 37 37 H 1.08997 * 109.47102 * 299.99883 * 17 16 15 38 38 H 1.09003 * 109.47325 * 60.00047 * 18 17 16 39 39 H 1.08997 * 109.47291 * 299.99834 * 18 17 16 40 40 H 1.08001 * 120.00282 * 307.28297 * 19 18 17 41 41 H 1.08003 * 120.00354 * 188.22293 * 20 19 18 42 42 H 1.08003 * 120.06751 * 0.04482 * 22 21 20 43 43 H 1.08000 * 119.92345 * 179.72676 * 23 22 21 44 44 H 1.08002 * 119.85908 * 180.02562 * 24 23 22 45 45 H 1.08006 * 119.92472 * 180.02562 * 25 24 23 46 46 H 1.07993 * 120.07195 * 180.02562 * 26 25 24 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 2.2504 1.6176 0.0000 4 1 3.7104 1.3463 0.0006 5 1 1.8917 2.3963 -1.2126 6 1 1.8916 2.3965 1.2125 7 6 2.0103 -1.2021 0.0005 8 1 3.0903 -1.2022 0.0010 9 16 1.1292 -2.7281 0.0019 10 6 2.5157 -3.8915 0.0029 11 6 1.9872 -5.3027 0.0036 12 8 0.7910 -5.5023 0.0029 13 7 2.8439 -6.3431 0.0049 14 6 2.3302 -7.7152 0.0050 15 6 3.5021 -8.6986 0.0060 16 7 2.9870 -10.0744 0.0054 17 6 4.0867 -11.0483 0.0069 18 6 3.5121 -12.4663 0.0069 19 6 4.6402 -13.4655 0.0079 20 6 4.6748 -14.4253 0.9217 21 6 3.5214 -14.6291 1.8234 22 6 3.7277 -15.0101 3.1498 23 6 2.6468 -15.1992 3.9862 24 6 1.3607 -15.0124 3.5123 25 6 1.1493 -14.6357 2.1980 26 6 2.2216 -14.4434 1.3513 27 1 -0.4850 0.8400 -0.0004 28 1 3.1243 -3.7307 0.8928 29 1 3.1244 -3.7322 -0.8871 30 1 3.8007 -6.1836 0.0059 31 1 1.7224 -7.8756 -0.8857 32 1 1.7206 -7.8748 0.8943 33 1 4.1102 -8.5384 0.8963 34 1 4.1114 -8.5389 -0.8837 35 1 2.3682 -10.2284 -0.7765 36 1 4.6982 -10.9045 0.8977 37 1 4.7006 -10.9047 -0.8822 38 1 2.9003 -12.6104 -0.8836 39 1 2.8985 -12.6097 0.8963 40 1 5.4206 -13.3996 -0.7358 41 1 5.5456 -15.0584 1.0073 42 1 4.7314 -15.1563 3.5209 43 1 2.8051 -15.4984 5.0118 44 1 0.5179 -15.1613 4.1711 45 1 0.1427 -14.4911 1.8342 46 1 2.0552 -14.1489 0.3257 RHF calculation, no. of doubly occupied orbitals= 60 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 ZINC001123792035.mol2 46 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 18:33:00 Heat of formation + Delta-G solvation = -22.851208 kcal Electronic energy + Delta-G solvation = -23690.671800 eV Core-core repulsion = 20091.405945 eV Total energy + Delta-G solvation = -3599.265855 eV No. of doubly occupied orbitals = 60 Molecular weight (most abundant/longest-lived isotopes) = 334.146 amu Computer time = 0.75 seconds Orbital eigenvalues (eV) -40.63264 -40.28926 -38.12297 -36.43856 -35.12439 -34.58157 -32.35950 -31.78191 -31.01300 -29.60417 -27.81682 -27.39903 -24.22056 -23.41410 -23.14484 -22.50558 -21.76440 -20.09552 -19.82987 -17.89571 -17.47331 -17.28689 -17.18834 -16.87797 -16.67518 -16.39456 -16.05945 -15.83518 -15.44809 -15.20807 -15.06190 -14.72316 -14.63096 -14.36393 -14.23960 -13.94670 -13.61491 -13.45523 -13.15839 -12.99089 -12.90355 -12.73736 -12.60406 -12.51914 -12.31698 -12.08770 -11.82285 -11.70210 -11.54692 -11.15635 -11.00407 -10.62634 -10.27049 -10.14786 -9.75997 -9.43909 -9.07438 -8.66809 -8.34585 -6.12841 0.14091 0.53213 1.26777 1.41950 1.46626 1.50160 1.58585 1.60232 2.20131 2.27885 2.97275 2.99755 3.23646 3.37821 3.84126 3.88039 4.01583 4.03474 4.06775 4.13431 4.21636 4.25122 4.30742 4.31090 4.34919 4.48280 4.51234 4.61032 4.63463 4.69775 4.77384 4.91350 4.92216 5.05939 5.12477 5.15003 5.24015 5.39801 5.42541 5.49647 5.54324 5.66148 5.73761 5.91891 5.99030 6.14847 6.20372 6.39005 6.49343 7.06841 7.23484 8.74986 Molecular weight = 334.15amu Principal moments of inertia in cm(-1) A = 0.024919 B = 0.001391 C = 0.001357 Principal moments of inertia in units of 10**(-40)*gram-cm**2 A = 1123.377673 B =20126.339153 C =20635.959818 Net atomic charges, atomic populations, and dipole contributions calculated with CM2 Atom NO. Type Charge No. of electrons 1 N -0.912 5.912 2 C 0.013 3.987 3 Si 1.000 3.000 4 H -0.256 1.256 5 H -0.274 1.274 6 H -0.274 1.274 7 C -0.546 4.546 8 H 0.084 0.916 9 S -0.154 6.154 10 C -0.129 4.129 11 C 0.533 3.467 12 O -0.567 6.567 13 N -0.711 5.711 14 C 0.125 3.875 15 C 0.063 3.937 16 N -0.698 5.698 17 C 0.070 3.930 18 C -0.106 4.106 19 C -0.134 4.134 20 C -0.134 4.134 21 C -0.071 4.071 22 C -0.124 4.124 23 C -0.132 4.132 24 C -0.133 4.133 25 C -0.135 4.135 26 C -0.118 4.118 27 H 0.271 0.729 28 H 0.111 0.889 29 H 0.112 0.888 30 H 0.417 0.583 31 H 0.058 0.942 32 H 0.056 0.944 33 H 0.084 0.916 34 H 0.053 0.947 35 H 0.348 0.652 36 H 0.067 0.933 37 H 0.042 0.958 38 H 0.080 0.920 39 H 0.080 0.920 40 H 0.133 0.867 41 H 0.133 0.867 42 H 0.135 0.865 43 H 0.137 0.863 44 H 0.135 0.865 45 H 0.133 0.867 46 H 0.134 0.866 For the charges calculated by CM2: Dipole moment (debyes) X Y Z Total from point charges 14.106 -33.180 1.854 36.101 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 0.822 3.178 4 H -0.180 1.180 5 H -0.199 1.199 6 H -0.200 1.200 7 C -0.694 4.694 8 H 0.102 0.898 9 S 0.073 5.927 10 C -0.280 4.280 11 C 0.319 3.681 12 O -0.445 6.445 13 N -0.366 5.366 14 C 0.000 4.000 15 C -0.066 4.066 16 N -0.331 5.331 17 C -0.058 4.058 18 C -0.143 4.143 19 C -0.152 4.152 20 C -0.152 4.152 21 C -0.071 4.071 22 C -0.142 4.142 23 C -0.150 4.150 24 C -0.151 4.151 25 C -0.153 4.153 26 C -0.136 4.136 27 H 0.080 0.920 28 H 0.129 0.871 29 H 0.130 0.870 30 H 0.254 0.746 31 H 0.076 0.924 32 H 0.075 0.925 33 H 0.102 0.898 34 H 0.071 0.929 35 H 0.167 0.833 36 H 0.085 0.915 37 H 0.061 0.939 38 H 0.098 0.902 39 H 0.098 0.902 40 H 0.151 0.849 41 H 0.151 0.849 42 H 0.153 0.847 43 H 0.155 0.845 44 H 0.152 0.848 45 H 0.151 0.849 46 H 0.151 0.849 Dipole moment (debyes) X Y Z Total from point charges 11.903 -33.470 2.538 35.614 hybrid contribution 2.004 1.376 -0.810 2.562 sum 13.906 -32.094 1.728 35.020 Atomic orbital electron populations 1.70194 1.08007 1.28556 1.48061 1.26140 0.95966 1.03352 0.93721 0.84888 0.78611 0.76265 0.78058 1.17977 1.19923 1.19975 1.23251 0.95391 0.91949 1.58799 0.89809 1.85610 1.10674 0.99340 1.97059 1.23364 1.03526 0.94152 1.06948 1.20086 0.86199 0.86736 0.75101 1.90698 1.17523 1.86126 1.50146 1.45609 1.10400 1.05006 1.75603 1.21204 0.97050 0.79860 1.01836 1.21933 0.94961 0.87414 1.02305 1.60251 1.19917 1.01924 1.50974 1.21854 0.92311 0.90707 1.00967 1.21117 0.97292 0.92382 1.03502 1.23334 0.99424 0.94890 0.97584 1.21821 0.97052 1.00366 0.95977 1.19313 0.93662 0.99856 0.94260 1.21531 0.99830 0.99661 0.93196 1.21382 0.92709 1.00223 1.00658 1.21508 0.97817 0.99558 0.96169 1.21387 0.99675 0.99826 0.94365 1.21621 0.91994 0.99302 1.00706 0.91993 0.87089 0.87001 0.74555 0.92388 0.92507 0.89755 0.92890 0.83312 0.91475 0.93945 0.90203 0.90157 0.84926 0.84895 0.84745 0.84466 0.84755 0.84863 0.84862 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 -56.21 13.22 21.65 0.29 -55.92 16 2 C 0.01 0.73 5.49 84.86 0.47 1.20 16 3 Si 1.00 43.58 29.55 68.60 2.03 45.61 16 4 H -0.26 -10.39 7.11 99.48 0.71 -9.68 16 5 H -0.27 -11.57 7.11 99.48 0.71 -10.87 16 6 H -0.27 -11.62 7.11 99.48 0.71 -10.91 16 7 C -0.55 -31.23 9.50 67.95 0.65 -30.59 16 8 H 0.08 4.43 7.80 -2.91 -0.02 4.41 16 9 S -0.15 -8.60 20.57 -56.49 -1.16 -9.76 16 10 C -0.13 -5.07 6.16 71.23 0.44 -4.63 16 11 C 0.53 19.78 7.85 87.66 0.69 20.46 16 12 O -0.57 -26.76 15.86 -3.04 -0.05 -26.81 16 13 N -0.71 -17.66 5.56 -463.06 -2.57 -20.23 16 14 C 0.12 2.79 5.93 86.37 0.51 3.30 16 15 C 0.06 0.94 5.80 86.30 0.50 1.44 16 16 N -0.70 -10.19 6.50 -513.89 -3.34 -13.53 16 17 C 0.07 0.83 5.67 86.30 0.49 1.32 16 18 C -0.11 -1.19 4.18 29.85 0.12 -1.06 16 19 C -0.13 -1.31 9.46 24.53 0.23 -1.08 16 20 C -0.13 -1.52 9.80 23.65 0.23 -1.29 16 21 C -0.07 -1.03 5.21 -20.12 -0.10 -1.14 16 22 C -0.12 -1.73 9.79 22.52 0.22 -1.51 16 23 C -0.13 -1.78 10.03 22.23 0.22 -1.55 16 24 C -0.13 -1.85 10.04 22.32 0.22 -1.62 16 25 C -0.13 -1.96 10.03 22.23 0.22 -1.74 16 26 C -0.12 -1.74 7.30 22.52 0.16 -1.58 16 27 H 0.27 15.45 8.31 -92.71 -0.77 14.68 16 28 H 0.11 3.92 8.14 -2.40 -0.02 3.90 16 29 H 0.11 3.91 8.14 -2.40 -0.02 3.89 16 30 H 0.42 7.17 8.47 -92.71 -0.79 6.38 16 31 H 0.06 1.40 8.14 -2.38 -0.02 1.38 16 32 H 0.06 1.52 8.14 -2.39 -0.02 1.50 16 33 H 0.08 1.19 8.14 -2.39 -0.02 1.17 16 34 H 0.05 0.64 8.14 -2.38 -0.02 0.62 16 35 H 0.35 4.56 8.73 -89.70 -0.78 3.77 16 36 H 0.07 0.89 8.14 -2.39 -0.02 0.87 16 37 H 0.04 0.41 8.14 -2.39 -0.02 0.39 16 38 H 0.08 0.76 7.95 -2.39 -0.02 0.74 16 39 H 0.08 1.19 4.73 -2.39 -0.01 1.18 16 40 H 0.13 0.85 8.06 -2.91 -0.02 0.83 16 41 H 0.13 1.09 8.06 -2.91 -0.02 1.07 16 42 H 0.13 1.38 8.06 -2.91 -0.02 1.36 16 43 H 0.14 1.27 8.06 -2.91 -0.02 1.25 16 44 H 0.13 1.37 8.06 -2.91 -0.02 1.35 16 45 H 0.13 1.53 8.06 -2.91 -0.02 1.51 16 46 H 0.13 1.67 6.13 -2.91 -0.02 1.65 16 Total: -1.00 -78.13 400.45 -0.12 -78.24 By element: Atomic # 1 Polarization: 23.05 SS G_CDS: -0.59 Total: 22.46 kcal Atomic # 6 Polarization: -25.34 SS G_CDS: 5.28 Total: -20.06 kcal Atomic # 7 Polarization: -84.05 SS G_CDS: -5.63 Total: -89.68 kcal Atomic # 8 Polarization: -26.76 SS G_CDS: -0.05 Total: -26.81 kcal Atomic # 14 Polarization: 43.58 SS G_CDS: 2.03 Total: 45.61 kcal Atomic # 16 Polarization: -8.60 SS G_CDS: -1.16 Total: -9.76 kcal Total: -78.13 -0.12 -78.24 kcal The number of atoms in the molecule is 46 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. ZINC001123792035.mol2 46 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 55.391 kcal (2) G-P(sol) polarization free energy of solvation -78.125 kcal (3) G-ENP(sol) elect.-nuc.-pol. free energy of system -22.734 kcal (4) G-CDS(sol) cavity-dispersion-solvent structure free energy -0.117 kcal (5) G-P-CDS(sol) = G-P(sol) + G-CDS(sol) = (2) + (4) -78.242 kcal (6) G-S(sol) free energy of system = (1) + (5) -22.851 kcal 1SCF WAS SPECIFIED, SO GEOMETRY OPTIMIZATION WAS NOT USED Total computer time = 0.76 seconds