Wall clock time and date at job start Wed Apr 1 2020 04:44:01
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 1.31514 * 1
3 3 Si 1.86803 * 120.00112 * 2 1
4 4 H 1.48495 * 109.47349 * 239.99899 * 3 2 1
5 5 H 1.48505 * 109.47077 * 0.02562 * 3 2 1
6 6 H 1.48500 * 109.47093 * 119.99820 * 3 2 1
7 7 C 1.37875 * 120.00041 * 180.02562 * 2 1 3
8 8 H 1.07999 * 119.99970 * 180.02562 * 7 2 1
9 9 C 1.50701 * 120.00038 * 359.97438 * 7 2 1
10 10 C 1.53004 * 109.46957 * 179.97438 * 9 7 2
11 11 N 1.46507 * 109.46770 * 180.02562 * 10 9 7
12 12 C 1.34774 * 119.99765 * 180.02562 * 11 10 9
13 13 O 1.21588 * 119.99889 * 0.02562 * 12 11 10
14 14 N 1.34777 * 119.99902 * 179.97438 * 12 11 10
15 15 C 1.46496 * 119.99867 * 179.97438 * 14 12 11
16 16 C 1.53002 * 109.47030 * 180.02562 * 15 14 12
17 17 N 1.46506 * 109.47035 * 180.02562 * 16 15 14
18 18 S 1.65596 * 119.99677 * 165.00247 * 17 16 15
19 19 O 1.42106 * 106.40283 * 178.54151 * 18 17 16
20 20 O 1.42105 * 106.40421 * 311.45913 * 18 17 16
21 21 C 1.76198 * 107.22309 * 65.00118 * 18 17 16
22 22 C 1.33386 * 125.20236 * 89.99215 * 21 18 17
23 23 C 1.38427 * 114.92036 * 179.97438 * 22 21 18
24 24 C 1.33386 * 114.92159 * 0.02562 * 23 22 21
25 25 S 1.75879 * 125.20398 * 269.69841 * 21 18 17
26 26 H 0.97000 * 119.99712 * 359.97438 * 1 2 3
27 27 H 1.09000 * 109.46531 * 60.00524 * 9 7 2
28 28 H 1.08988 * 109.47359 * 300.00263 * 9 7 2
29 29 H 1.09000 * 109.46944 * 60.00934 * 10 9 7
30 30 H 1.08997 * 109.47281 * 300.00102 * 10 9 7
31 31 H 0.96999 * 120.00184 * 359.97438 * 11 10 9
32 32 H 0.96999 * 120.00047 * 0.02562 * 14 12 11
33 33 H 1.09004 * 109.47074 * 60.00441 * 15 14 12
34 34 H 1.09004 * 109.47714 * 300.00350 * 15 14 12
35 35 H 1.09004 * 109.46930 * 60.00232 * 16 15 14
36 36 H 1.09000 * 109.47312 * 300.00176 * 16 15 14
37 37 H 0.96996 * 120.00063 * 345.00668 * 17 16 15
38 38 H 1.07999 * 122.54429 * 359.97036 * 22 21 18
39 39 H 1.08003 * 122.54021 * 180.02562 * 23 22 21
40 40 H 1.08001 * 125.20201 * 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 7 0.0000 0.0000 0.0000
2 6 1.3151 0.0000 0.0000
3 14 2.2492 1.6177 0.0000
4 1 3.1029 1.6964 -1.2124
5 1 1.2842 2.7465 0.0006
6 1 3.1029 1.6964 1.2125
7 6 2.0045 -1.1940 -0.0005
8 1 3.0845 -1.1940 -0.0001
9 6 1.2510 -2.4991 -0.0005
10 6 2.2454 -3.6621 -0.0018
11 7 1.5128 -4.9308 -0.0024
12 6 2.1867 -6.0980 -0.0031
13 8 3.4026 -6.0979 -0.0027
14 7 1.5128 -7.2652 -0.0031
15 6 2.2453 -8.5339 -0.0044
16 6 1.2511 -9.6968 -0.0048
17 7 1.9836 -10.9656 -0.0054
18 16 1.1980 -12.3754 0.3651
19 8 2.1599 -13.4145 0.2447
20 8 0.4683 -12.1264 1.5588
21 6 0.0030 -12.6546 -0.8993
22 6 0.2192 -13.3380 -2.0242
23 6 -0.8718 -13.4270 -2.8714
24 6 -1.9739 -12.8155 -2.4348
25 16 -1.6593 -12.0811 -0.8679
26 1 -0.4850 0.8401 0.0004
27 1 0.6241 -2.5566 -0.8904
28 1 0.6247 -2.5571 0.8895
29 1 2.8726 -3.6047 0.8878
30 1 2.8713 -3.6039 -0.8922
31 1 0.5428 -4.9308 -0.0016
32 1 0.5428 -7.2652 -0.0031
33 1 2.8727 -8.5921 0.8851
34 1 2.8714 -8.5912 -0.8949
35 1 0.6241 -9.6384 -0.8945
36 1 0.6248 -9.6398 0.8855
37 1 2.9288 -10.9798 -0.2228
38 1 1.1732 -13.7878 -2.2565
39 1 -0.8337 -13.9519 -3.8146
40 1 -2.9166 -12.7809 -2.9606
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
ZINC000273594740.mol2 40
1SCF WAS SPECIFIED, SO GEOMETRY OPTIMIZATION WAS NOT USED
SCF FIELD WAS ACHIEVED
Wall clock time and date at job start Wed Apr 1 2020 04:44:01
Heat of formation + Delta-G solvation = -106.541312 kcal
Electronic energy + Delta-G solvation = -24422.735348 eV
Core-core repulsion = 20489.966129 eV
Total energy + Delta-G solvation = -3932.769219 eV
No. of doubly occupied orbitals = 59
Molecular weight
(most abundant/longest-lived isotopes) = 347.081 amu
Computer time = 0.61 seconds
Orbital eigenvalues (eV)
-40.97906 -38.86630 -38.36128 -37.59738 -37.09111 -36.48057 -35.02377 -34.68573
-31.58407 -30.90259 -29.19616 -26.55047 -25.44569 -23.91999 -22.85655 -22.03462
-21.45869 -20.25824 -19.68040 -19.53137 -18.57908 -18.40446 -17.29065 -17.10524
-16.97428 -16.75574 -16.47179 -16.08370 -15.86738 -15.52125 -15.30633 -15.02694
-14.86004 -14.26646 -14.23474 -13.90115 -13.55952 -13.50918 -13.35566 -13.26045
-13.19955 -13.18594 -12.88470 -12.70179 -12.55009 -12.51071 -12.18943 -11.85195
-11.67082 -11.49094 -11.21806 -10.71566 -10.57865 -10.36679 -10.33054 -9.70581
-9.58973 -8.21829 -6.31668 -0.83316 -0.48386 0.39734 0.81524 1.43383
1.45849 1.46263 1.53531 1.65164 2.10035 2.18633 2.43494 2.59883
3.13056 3.33647 3.46200 3.62661 4.02351 4.05308 4.29916 4.36663
4.39657 4.45167 4.51723 4.56036 4.84408 4.85238 4.89979 4.95245
5.03819 5.29730 5.34100 5.45890 5.54419 5.63257 5.81682 5.92453
6.06393 6.19989 6.81527 7.15220 7.37440 7.61570 8.89731
Molecular weight = 347.08amu
Principal moments of inertia in cm(-1)
A = 0.020449 B = 0.001701 C = 0.001623
Principal moments of inertia in units of 10**(-40)*gram-cm**2
A = 1368.962599 B =16458.323009 C =17251.354571
Net atomic charges, atomic populations, and dipole contributions
calculated with CM2
Atom NO. Type Charge No. of electrons
1 N -0.926 5.926
2 C 0.007 3.993
3 Si 0.964 3.036
4 H -0.268 1.268
5 H -0.281 1.281
6 H -0.269 1.269
7 C -0.546 4.546
8 H 0.059 0.941
9 C 0.024 3.976
10 C 0.160 3.840
11 N -0.732 5.732
12 C 0.699 3.301
13 O -0.639 6.639
14 N -0.731 5.731
15 C 0.134 3.866
16 C 0.107 3.893
17 N -1.103 6.103
18 S 2.742 3.258
19 O -0.977 6.977
20 O -0.980 6.980
21 C -0.816 4.816
22 C 0.011 3.989
23 C -0.174 4.174
24 C -0.158 4.158
25 S 0.194 5.806
26 H 0.265 0.735
27 H 0.010 0.990
28 H 0.009 0.991
29 H 0.043 0.957
30 H 0.044 0.956
31 H 0.408 0.592
32 H 0.415 0.585
33 H 0.065 0.935
34 H 0.074 0.926
35 H 0.097 0.903
36 H 0.094 0.906
37 H 0.431 0.569
38 H 0.167 0.833
39 H 0.176 0.824
40 H 0.202 0.798
For the charges calculated by CM2:
Dipole moment (debyes) X Y Z Total
from point charges -6.128 -31.140 -6.574 32.411
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 -0.566 5.566
2 C -0.192 4.192
3 Si 0.789 3.211
4 H -0.193 1.193
5 H -0.207 1.207
6 H -0.195 1.195
7 C -0.585 4.585
8 H 0.077 0.923
9 C -0.014 4.014
10 C 0.036 3.964
11 N -0.387 5.387
12 C 0.399 3.601
13 O -0.521 6.521
14 N -0.390 5.390
15 C 0.008 3.992
16 C -0.020 4.020
17 N -0.866 5.866
18 S 2.830 3.170
19 O -0.967 6.967
20 O -0.970 6.970
21 C -1.019 5.019
22 C -0.025 4.025
23 C -0.204 4.204
24 C -0.296 4.296
25 S 0.459 5.541
26 H 0.074 0.926
27 H 0.028 0.972
28 H 0.027 0.973
29 H 0.061 0.939
30 H 0.063 0.937
31 H 0.244 0.756
32 H 0.252 0.748
33 H 0.084 0.916
34 H 0.093 0.907
35 H 0.115 0.885
36 H 0.112 0.888
37 H 0.269 0.731
38 H 0.185 0.815
39 H 0.193 0.807
40 H 0.219 0.781
Dipole moment (debyes) X Y Z Total
from point charges -6.113 -30.693 -4.761 31.656
hybrid contribution 0.328 0.316 -1.611 1.674
sum -5.786 -30.376 -6.372 31.572
Atomic orbital electron populations
1.70047 1.07469 1.28002 1.51033 1.25858 0.95810 1.03032 0.94510
0.85516 0.78303 0.78230 0.79097 1.19336 1.20672 1.19450 1.21449
0.93620 0.91955 1.51465 0.92298 1.19126 0.94247 0.91588 0.96424
1.21073 0.94613 0.81124 0.99632 1.45194 1.10482 1.04364 1.78666
1.16097 0.85088 0.81225 0.77726 1.90875 1.13776 1.87314 1.60133
1.44685 1.10531 1.03427 1.80316 1.21243 0.94313 0.80464 1.03150
1.21493 0.94328 0.81515 1.04665 1.55110 1.22408 1.20580 1.88539
1.00243 0.72304 0.71835 0.72660 1.93577 1.60629 1.55324 1.87173
1.93584 1.74142 1.85303 1.43957 1.35611 1.18020 1.24582 1.23706
1.20429 1.01509 0.91033 0.89538 1.20770 0.91901 1.04329 1.03365
1.26705 1.04443 1.00344 0.98129 1.84462 1.00845 1.51755 1.17043
0.92580 0.97164 0.97268 0.93899 0.93742 0.75607 0.74828 0.91616
0.90731 0.88463 0.88821 0.73100 0.81531 0.80653 0.78060
Number of geometries 1
Number of calculations of the screened coulomb radii 1
The total number of SCF iterations 16.
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 -0.93 -53.70 13.29 21.45 0.28 -53.42 16
2 C 0.01 0.37 5.46 84.65 0.46 0.83 16
3 Si 0.96 43.28 29.54 68.60 2.03 45.31 16
4 H -0.27 -11.66 7.11 99.48 0.71 -10.96 16
5 H -0.28 -12.28 7.11 99.48 0.71 -11.58 16
6 H -0.27 -11.76 7.11 99.48 0.71 -11.06 16
7 C -0.55 -30.22 9.11 25.60 0.23 -29.98 16
8 H 0.06 3.18 7.74 -2.91 -0.02 3.16 16
9 C 0.02 1.17 5.09 29.85 0.15 1.32 16
10 C 0.16 6.79 5.61 86.38 0.48 7.27 16
11 N -0.73 -24.41 5.56 -478.52 -2.66 -27.07 16
12 C 0.70 22.66 8.57 179.06 1.53 24.20 16
13 O -0.64 -26.48 16.34 -3.99 -0.07 -26.55 16
14 N -0.73 -15.19 5.56 -478.53 -2.66 -17.85 16
15 C 0.13 2.32 5.82 86.38 0.50 2.82 16
16 C 0.11 1.23 6.34 86.38 0.55 1.77 16
17 N -1.10 -12.95 6.00 -187.47 -1.12 -14.07 16
18 S 2.74 45.13 5.88 -56.49 -0.33 44.80 16
19 O -0.98 -20.82 17.80 -128.00 -2.28 -23.09 16
20 O -0.98 -22.16 17.38 -128.00 -2.22 -24.38 16
21 C -0.82 -10.97 6.55 66.72 0.44 -10.53 16
22 C 0.01 0.12 9.84 21.22 0.21 0.33 16
23 C -0.17 -1.26 10.18 21.22 0.22 -1.05 16
24 C -0.16 -1.10 11.23 66.72 0.75 -0.35 16
25 S 0.19 2.24 23.21 -56.49 -1.31 0.93 16
26 H 0.27 14.51 8.31 -92.71 -0.77 13.74 16
27 H 0.01 0.52 8.14 -2.39 -0.02 0.50 16
28 H 0.01 0.47 8.14 -2.39 -0.02 0.45 16
29 H 0.04 1.91 8.14 -2.39 -0.02 1.90 16
30 H 0.04 1.97 8.14 -2.39 -0.02 1.95 16
31 H 0.41 11.22 8.49 -92.71 -0.79 10.43 16
32 H 0.41 5.70 8.49 -92.71 -0.79 4.92 16
33 H 0.07 1.30 8.14 -2.38 -0.02 1.28 16
34 H 0.07 1.31 8.14 -2.39 -0.02 1.29 16
35 H 0.10 0.71 8.14 -2.38 -0.02 0.69 16
36 H 0.09 1.06 7.75 -2.39 -0.02 1.04 16
37 H 0.43 3.75 8.65 -96.75 -0.84 2.91 16
38 H 0.17 1.26 8.05 -2.91 -0.02 1.23 16
39 H 0.18 0.35 8.06 -2.91 -0.02 0.33 16
40 H 0.20 0.18 8.06 -2.91 -0.02 0.16 16
Total: -1.00 -80.27 376.25 -6.13 -86.39
By element:
Atomic # 1 Polarization: 13.69 SS G_CDS: -1.31 Total: 12.38 kcal
Atomic # 6 Polarization: -8.90 SS G_CDS: 5.53 Total: -3.37 kcal
Atomic # 7 Polarization: -106.25 SS G_CDS: -6.16 Total: -112.41 kcal
Atomic # 8 Polarization: -69.46 SS G_CDS: -4.57 Total: -74.02 kcal
Atomic # 14 Polarization: 43.28 SS G_CDS: 2.03 Total: 45.31 kcal
Atomic # 16 Polarization: 47.37 SS G_CDS: -1.64 Total: 45.73 kcal
Total: -80.27 -6.13 -86.39 kcal
The number of atoms in the molecule is 40
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.
ZINC000273594740.mol2 40
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 -20.148 kcal
(2) G-P(sol) polarization free energy of solvation -80.266 kcal
(3) G-ENP(sol) elect.-nuc.-pol. free energy of system -100.414 kcal
(4) G-CDS(sol) cavity-dispersion-solvent structure free energy -6.127 kcal
(5) G-P-CDS(sol) = G-P(sol) + G-CDS(sol) = (2) + (4) -86.394 kcal
(6) G-S(sol) free energy of system = (1) + (5) -106.541 kcal
1SCF WAS SPECIFIED, SO GEOMETRY OPTIMIZATION WAS NOT USED
Total computer time = 0.61 seconds