Wall clock time and date at job start Tue Mar 31 2020 03:21:41
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 C
2 2 C 1.53000 * 1
3 3 H 1.09007 * 109.46721 * 2 1
4 4 C 1.50694 * 109.47355 * 239.99710 * 2 1 3
5 5 H 1.08000 * 120.00563 * 239.99848 * 4 2 1
6 6 C 1.37885 * 119.99902 * 60.00012 * 4 2 1
7 7 N 1.31516 * 119.99913 * 359.97438 * 6 4 2
8 8 Si 1.86798 * 119.99766 * 179.97438 * 6 4 2
9 9 H 1.48506 * 109.46985 * 179.97438 * 8 6 4
10 10 H 1.48494 * 109.47276 * 299.99832 * 8 6 4
11 11 H 1.48498 * 109.47150 * 60.00043 * 8 6 4
12 12 N 1.46497 * 109.47021 * 119.99638 * 2 1 3
13 13 C 1.46497 * 120.00073 * 60.00310 * 12 2 1
14 14 S 1.65606 * 120.00188 * 240.00233 * 12 2 1
15 15 O 1.42096 * 106.40395 * 203.54186 * 14 12 2
16 16 O 1.42108 * 106.39975 * 336.45918 * 14 12 2
17 17 N 1.65593 * 107.21842 * 89.99816 * 14 12 2
18 18 C 1.46500 * 119.99925 * 65.00539 * 17 14 12
19 19 C 1.50700 * 109.47412 * 164.99847 * 18 17 14
20 20 C 1.38647 * 120.79035 * 269.71836 * 19 18 17
21 21 C 1.38208 * 119.16211 * 179.79766 * 20 19 18
22 22 N 1.31864 * 120.76254 * 0.48648 * 21 20 19
23 23 C 1.31867 * 121.73081 * 359.74411 * 22 21 20
24 24 C 1.38204 * 120.76231 * 0.02562 * 23 22 21
25 25 H 1.08995 * 109.47131 * 60.00355 * 1 2 3
26 26 H 1.09002 * 109.47106 * 180.02562 * 1 2 3
27 27 H 1.08998 * 109.47089 * 300.00187 * 1 2 3
28 28 H 0.97001 * 119.99646 * 179.97438 * 7 6 4
29 29 H 1.09001 * 109.46905 * 89.99959 * 13 12 2
30 30 H 1.09005 * 109.47144 * 209.99900 * 13 12 2
31 31 H 1.08993 * 109.47302 * 330.00087 * 13 12 2
32 32 H 0.97005 * 120.00537 * 244.99777 * 17 14 12
33 33 H 1.09006 * 109.47312 * 284.99498 * 18 17 14
34 34 H 1.09004 * 109.47167 * 44.99686 * 18 17 14
35 35 H 1.08000 * 120.41972 * 0.02562 * 20 19 18
36 36 H 1.07996 * 119.61465 * 180.20552 * 21 20 19
37 37 H 1.08002 * 119.62086 * 179.97438 * 23 22 21
38 38 H 1.08003 * 120.42280 * 180.02562 * 24 23 22
Note: An asterisk (*) indicates this parameter was or will be optimized.
Cartesian coordinates (angstroms)
NO. Atom X Y Z
1 6 0.0000 0.0000 0.0000
2 6 1.5300 0.0000 0.0000
3 1 1.8933 1.0278 0.0000
4 6 2.0324 -0.7104 -1.2304
5 1 2.6533 -1.5885 -1.1313
6 6 1.6993 -0.2394 -2.4827
7 7 0.9427 0.8296 -2.6034
8 14 2.3226 -1.1197 -4.0078
9 1 1.8270 -0.4201 -5.2204
10 1 3.8076 -1.1190 -4.0076
11 1 1.8282 -2.5199 -4.0080
12 7 2.0183 -0.6905 1.1962
13 6 1.6644 -2.0931 1.4281
14 16 2.9703 0.1143 2.2863
15 8 3.7118 -0.8787 2.9816
16 8 3.5794 1.1831 1.5748
17 7 1.9606 0.8092 3.3997
18 6 1.1509 -0.0350 4.2817
19 6 0.6167 0.7951 5.4204
20 6 1.3314 0.9233 6.6015
21 6 0.8118 1.6964 7.6225
22 7 -0.3528 2.2996 7.4861
23 6 -1.0619 2.1962 6.3792
24 6 -0.6040 1.4440 5.3140
25 1 -0.3633 0.5138 -0.8900
26 1 -0.3633 -1.0277 0.0005
27 1 -0.3633 0.5139 0.8899
28 1 0.7088 1.1611 -3.4845
29 1 2.4158 -2.7376 0.9718
30 1 1.6238 -2.2851 2.5003
31 1 0.6905 -2.3002 0.9847
32 1 1.9053 1.7753 3.4681
33 1 0.3187 -0.4565 3.7178
34 1 1.7669 -0.8422 4.6782
35 1 2.2839 0.4284 6.7208
36 1 1.3640 1.8040 8.5444
37 1 -2.0119 2.7044 6.3044
38 1 -1.1891 1.3634 4.4098
RHF calculation, no. of doubly occupied orbitals= 53
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
ZINC000283037644.mol2 38
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 03:21:41
Heat of formation + Delta-G solvation = -62.735292 kcal
Electronic energy + Delta-G solvation = -22553.262099 eV
Core-core repulsion = 19135.686157 eV
Total energy + Delta-G solvation = -3417.575943 eV
No. of doubly occupied orbitals = 53
Molecular weight
(most abundant/longest-lived isotopes) = 299.109 amu
Computer time = 0.45 seconds
Orbital eigenvalues (eV)
-41.10204 -38.35193 -37.89620 -36.90414 -36.80257 -34.51509 -32.99540 -32.12026
-30.89542 -27.38837 -27.25659 -26.92796 -24.38410 -23.01095 -22.57689 -20.35026
-18.92577 -18.57913 -18.40287 -17.63769 -17.36038 -17.05430 -16.61847 -16.38952
-15.87203 -15.15981 -14.92302 -14.85205 -14.66146 -14.54422 -14.21822 -13.88554
-13.73000 -13.39340 -13.18327 -13.13284 -13.00554 -12.87889 -12.76975 -12.57832
-12.51166 -12.22420 -12.13209 -11.87114 -11.13692 -10.73298 -10.61337 -10.48761
-10.42110 -10.07122 -9.66185 -8.10686 -6.23853 -0.41414 0.21586 0.26316
1.43720 1.45705 1.52408 2.05993 2.44204 2.62429 2.90756 3.17865
3.36162 3.55375 3.63590 3.82763 4.05480 4.16107 4.23295 4.37496
4.51068 4.69329 4.73916 4.74784 4.86018 4.92922 5.00974 5.03938
5.07524 5.17619 5.22601 5.37990 5.63287 5.70900 5.77555 5.89607
5.99988 6.18537 6.32591 6.83609 7.02502 7.45091 8.93010
Molecular weight = 299.11amu
Principal moments of inertia in cm(-1)
A = 0.026567 B = 0.004027 C = 0.003761
Principal moments of inertia in units of 10**(-40)*gram-cm**2
A = 1053.703052 B = 6951.556188 C = 7442.353895
Net atomic charges, atomic populations, and dipole contributions
calculated with CM2
Atom NO. Type Charge No. of electrons
1 C -0.135 4.135
2 C 0.272 3.728
3 H 0.025 0.975
4 C -0.540 4.540
5 H 0.056 0.944
6 C 0.019 3.981
7 N -0.913 5.913
8 Si 0.953 3.047
9 H -0.283 1.283
10 H -0.280 1.280
11 H -0.266 1.266
12 N -0.995 5.995
13 C 0.100 3.900
14 S 2.798 3.202
15 O -1.006 7.006
16 O -1.017 7.017
17 N -1.115 6.115
18 C 0.154 3.846
19 C -0.059 4.059
20 C -0.160 4.160
21 C 0.088 3.912
22 N -0.509 5.509
23 C 0.088 3.912
24 C -0.157 4.157
25 H 0.064 0.936
26 H 0.044 0.956
27 H 0.039 0.961
28 H 0.264 0.736
29 H 0.040 0.960
30 H 0.083 0.917
31 H 0.080 0.920
32 H 0.420 0.580
33 H 0.093 0.907
34 H 0.095 0.905
35 H 0.151 0.849
36 H 0.178 0.822
37 H 0.177 0.823
38 H 0.153 0.847
For the charges calculated by CM2:
Dipole moment (debyes) X Y Z Total
from point charges -4.989 -1.607 17.011 17.801
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 C -0.194 4.194
2 C 0.168 3.832
3 H 0.042 0.958
4 C -0.579 4.579
5 H 0.074 0.926
6 C -0.181 4.181
7 N -0.552 5.552
8 Si 0.779 3.221
9 H -0.208 1.208
10 H -0.206 1.206
11 H -0.191 1.191
12 N -0.837 5.837
13 C -0.045 4.045
14 S 2.808 3.192
15 O -0.989 6.989
16 O -1.002 7.002
17 N -0.878 5.878
18 C 0.029 3.971
19 C -0.069 4.069
20 C -0.181 4.181
21 C -0.068 4.068
22 N -0.218 5.218
23 C -0.068 4.068
24 C -0.177 4.177
25 H 0.083 0.917
26 H 0.063 0.937
27 H 0.058 0.942
28 H 0.073 0.927
29 H 0.059 0.941
30 H 0.101 0.899
31 H 0.098 0.902
32 H 0.255 0.745
33 H 0.111 0.889
34 H 0.113 0.887
35 H 0.169 0.831
36 H 0.195 0.805
37 H 0.194 0.806
38 H 0.171 0.829
Dipole moment (debyes) X Y Z Total
from point charges -4.417 -1.176 17.543 18.129
hybrid contribution 0.356 -0.292 -1.814 1.871
sum -4.060 -1.469 15.730 16.312
Atomic orbital electron populations
1.21903 0.96576 1.00331 1.00600 1.18406 0.92422 0.91284 0.81091
0.95765 1.21642 1.31668 1.13057 0.91562 0.92599 1.25607 0.95239
0.95707 1.01570 1.69963 1.37235 1.23633 1.24354 0.85694 0.78410
0.79096 0.78922 1.20786 1.20619 1.19107 1.57549 1.69990 1.21050
1.35110 1.21402 1.01837 0.80253 1.01029 1.01179 0.73514 0.72289
0.72266 1.93518 1.69678 1.61131 1.74573 1.93560 1.75793 1.57550
1.73250 1.55849 1.62124 1.17992 1.51793 1.20368 0.95727 0.91991
0.89003 1.20307 0.94744 0.96887 0.94913 1.22375 1.01688 1.00233
0.93755 1.23171 0.91808 0.92361 0.99493 1.67707 1.07578 1.20778
1.25775 1.23174 0.99828 0.95639 0.88186 1.22372 0.96507 0.97582
1.01267 0.91707 0.93675 0.94218 0.92679 0.94142 0.89866 0.90155
0.74512 0.88864 0.88654 0.83149 0.80514 0.80599 0.82925
Number of geometries 1
Number of calculations of the screened coulomb radii 1
The total number of SCF iterations 18.
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 C -0.13 -5.69 8.95 71.98 0.64 -5.04 16
2 C 0.27 12.88 2.62 44.24 0.12 13.00 16
3 H 0.02 1.32 6.91 -2.38 -0.02 1.31 16
4 C -0.54 -28.66 8.37 25.60 0.21 -28.44 16
5 H 0.06 2.95 7.65 -2.91 -0.02 2.93 16
6 C 0.02 1.00 5.30 84.66 0.45 1.45 16
7 N -0.91 -50.46 11.32 21.45 0.24 -50.21 16
8 Si 0.95 42.76 29.54 68.60 2.03 44.79 16
9 H -0.28 -12.39 7.11 99.48 0.71 -11.68 16
10 H -0.28 -12.69 7.11 99.48 0.71 -11.98 16
11 H -0.27 -11.40 7.11 99.48 0.71 -10.69 16
12 N -0.99 -38.29 3.12 -520.46 -1.62 -39.92 16
13 C 0.10 3.16 9.53 127.77 1.22 4.38 16
14 S 2.80 102.31 6.09 -56.49 -0.34 101.97 16
15 O -1.01 -38.32 16.68 -128.00 -2.14 -40.46 16
16 O -1.02 -46.90 16.70 -128.00 -2.14 -49.04 16
17 N -1.12 -28.97 6.05 -190.78 -1.15 -30.12 16
18 C 0.15 3.08 6.42 85.63 0.55 3.63 16
19 C -0.06 -1.08 5.31 -19.67 -0.10 -1.19 16
20 C -0.16 -2.75 9.82 22.36 0.22 -2.53 16
21 C 0.09 1.52 11.18 84.68 0.95 2.47 16
22 N -0.51 -10.38 10.36 -195.85 -2.03 -12.40 16
23 C 0.09 1.54 11.18 84.68 0.95 2.49 16
24 C -0.16 -2.68 9.82 22.36 0.22 -2.46 16
25 H 0.06 3.14 6.07 -2.39 -0.01 3.13 16
26 H 0.04 1.76 6.66 -2.39 -0.02 1.75 16
27 H 0.04 1.40 8.14 -2.39 -0.02 1.38 16
28 H 0.26 13.95 8.31 -92.71 -0.77 13.18 16
29 H 0.04 1.34 8.14 -2.39 -0.02 1.32 16
30 H 0.08 2.00 7.79 -2.38 -0.02 1.98 16
31 H 0.08 2.40 6.43 -2.39 -0.02 2.39 16
32 H 0.42 10.11 8.64 -96.74 -0.84 9.27 16
33 H 0.09 1.62 8.10 -2.38 -0.02 1.60 16
34 H 0.10 1.79 7.71 -2.38 -0.02 1.77 16
35 H 0.15 2.12 8.06 -2.91 -0.02 2.10 16
36 H 0.18 2.08 8.06 -2.91 -0.02 2.06 16
37 H 0.18 2.17 8.06 -2.91 -0.02 2.15 16
38 H 0.15 2.14 8.06 -2.91 -0.02 2.12 16
Total: -1.00 -70.08 332.48 -1.50 -71.58
By element:
Atomic # 1 Polarization: 15.82 SS G_CDS: 0.24 Total: 16.06 kcal
Atomic # 6 Polarization: -17.66 SS G_CDS: 5.42 Total: -12.24 kcal
Atomic # 7 Polarization: -128.09 SS G_CDS: -4.56 Total: -132.65 kcal
Atomic # 8 Polarization: -85.22 SS G_CDS: -4.27 Total: -89.49 kcal
Atomic # 14 Polarization: 42.76 SS G_CDS: 2.03 Total: 44.79 kcal
Atomic # 16 Polarization: 102.31 SS G_CDS: -0.34 Total: 101.97 kcal
Total: -70.08 -1.50 -71.58 kcal
The number of atoms in the molecule is 38
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.
ZINC000283037644.mol2 38
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 8.842 kcal
(2) G-P(sol) polarization free energy of solvation -70.082 kcal
(3) G-ENP(sol) elect.-nuc.-pol. free energy of system -61.240 kcal
(4) G-CDS(sol) cavity-dispersion-solvent structure free energy -1.495 kcal
(5) G-P-CDS(sol) = G-P(sol) + G-CDS(sol) = (2) + (4) -71.577 kcal
(6) G-S(sol) free energy of system = (1) + (5) -62.735 kcal
1SCF WAS SPECIFIED, SO GEOMETRY OPTIMIZATION WAS NOT USED
Total computer time = 0.45 seconds