Wall clock time and date at job start Sat Apr 11 2020 06:28:14
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 1.86806 * 120.00183 * 2 1
4 4 H 1.48497 * 109.46962 * 239.99752 * 3 2 1
5 5 H 1.48496 * 109.46822 * 359.97438 * 3 2 1
6 6 H 1.48497 * 109.47231 * 119.99739 * 3 2 1
7 7 C 1.37878 * 120.00004 * 179.97438 * 2 1 3
8 8 H 1.07999 * 120.00025 * 180.02562 * 7 2 1
9 9 C 1.50703 * 119.99740 * 0.02562 * 7 2 1
10 10 N 1.46506 * 109.46782 * 179.97438 * 9 7 2
11 11 C 1.34970 * 125.97166 * 125.00043 * 10 9 7
12 12 C 1.35241 * 107.85658 * 179.97438 * 11 10 9
13 13 C 1.40409 * 107.87202 * 359.97438 * 12 11 10
14 14 N 1.40155 * 125.97655 * 180.02562 * 13 12 11
15 15 C 1.34778 * 119.99686 * 0.02562 * 14 13 12
16 16 O 1.21289 * 120.00169 * 0.02562 * 15 14 13
17 17 C 1.50701 * 119.99521 * 179.97438 * 15 14 13
18 18 H 1.09002 * 108.88936 * 38.64820 * 17 15 14
19 19 C 1.52792 * 108.91393 * 280.00135 * 17 15 14
20 20 S 1.81984 * 108.33964 * 186.94768 * 19 17 15
21 21 O 1.42106 * 108.82438 * 176.55306 * 20 19 17
22 22 O 1.42097 * 108.83247 * 308.27716 * 20 19 17
23 23 C 1.81768 * 100.34525 * 62.41731 * 20 19 17
24 24 C 1.50078 * 109.25684 * 315.01280 * 23 20 19
25 25 O 1.21285 * 116.82856 * 200.98297 * 24 23 20
26 26 N 1.31828 * 126.34443 * 20.96148 * 24 23 20
27 27 N 1.31227 * 108.04830 * 359.72240 * 13 12 11
28 28 H 0.96998 * 119.99632 * 0.02562 * 1 2 3
29 29 H 1.08999 * 109.47353 * 59.99435 * 9 7 2
30 30 H 1.09000 * 109.47019 * 299.99088 * 9 7 2
31 31 H 1.07993 * 126.07134 * 0.02562 * 11 10 9
32 32 H 1.07997 * 126.06215 * 180.02562 * 12 11 10
33 33 H 0.96997 * 120.00134 * 180.02562 * 14 13 12
34 34 H 1.09000 * 109.68872 * 306.65705 * 19 17 15
35 35 H 1.08999 * 109.68688 * 67.19790 * 19 17 15
36 36 H 1.09001 * 109.51051 * 74.94704 * 23 20 19
37 37 H 1.09002 * 109.50213 * 195.07828 * 23 20 19
38 38 H 0.96998 * 115.27082 * 174.28919 * 26 24 23
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 1.6178 0.0000
4 1 3.1030 1.6963 -1.2125
5 1 1.2842 2.7464 -0.0006
6 1 3.1029 1.6964 1.2125
7 6 2.0045 -1.1941 0.0005
8 1 3.0845 -1.1941 0.0010
9 6 1.2510 -2.4991 0.0005
10 7 2.2030 -3.6127 0.0005
11 6 2.2420 -4.6224 0.8953
12 6 3.2602 -5.4430 0.5505
13 6 3.8679 -4.9156 -0.6002
14 7 4.9629 -5.4670 -1.2793
15 6 5.5268 -6.6076 -0.8346
16 8 5.0864 -7.1569 0.1529
17 6 6.7038 -7.2008 -1.5652
18 1 7.3551 -6.3932 -1.8995
19 6 6.1948 -7.9644 -2.7868
20 16 7.5995 -8.8441 -3.5385
21 8 7.1233 -9.6218 -4.6283
22 8 8.6593 -7.9211 -3.7484
23 6 8.0532 -9.9587 -2.1763
24 6 8.0629 -9.1881 -0.8885
25 8 8.7054 -9.6588 0.0263
26 7 7.4414 -8.0492 -0.6548
27 7 3.2272 -3.8196 -0.9323
28 1 -0.4849 0.8401 -0.0004
29 1 0.6246 -2.5571 -0.8896
30 1 0.6241 -2.5567 0.8904
31 1 1.5775 -4.7525 1.7366
32 1 3.5534 -6.3444 1.0680
33 1 5.3149 -5.0279 -2.0693
34 1 5.4336 -8.6819 -2.4805
35 1 5.7711 -7.2645 -3.5071
36 1 7.3261 -10.7681 -2.1106
37 1 9.0445 -10.3731 -2.3600
38 1 7.4855 -7.7339 0.2614
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
ZINC001361502687.mol2 38
1SCF WAS SPECIFIED, SO GEOMETRY OPTIMIZATION WAS NOT USED
SCF FIELD WAS ACHIEVED
Wall clock time and date at job start Sat Apr 11 2020 06:28:14
Heat of formation + Delta-G solvation = -65.209800 kcal
Electronic energy + Delta-G solvation = -26906.501132 eV
Core-core repulsion = 22685.112930 eV
Total energy + Delta-G solvation = -4221.388202 eV
No. of doubly occupied orbitals = 60
Molecular weight
(most abundant/longest-lived isotopes) = 342.088 amu
Computer time = 0.58 seconds
Orbital eigenvalues (eV)
-42.42623 -41.70820 -40.49946 -38.31331 -37.29819 -37.08134 -36.31934 -35.32283
-33.02863 -31.98386 -31.58122 -30.96203 -28.71120 -26.88384 -24.97195 -23.33439
-22.17549 -21.55518 -21.11634 -19.86693 -19.22969 -18.83646 -18.67788 -18.29647
-18.08793 -17.34495 -17.13354 -16.86617 -16.59684 -16.43271 -16.33332 -16.03477
-15.58540 -15.36035 -15.00735 -14.51777 -14.27830 -14.03976 -13.94102 -13.84083
-13.66605 -13.48871 -13.29009 -13.21964 -12.95317 -12.73059 -12.57479 -12.28921
-12.18600 -12.08437 -11.64193 -11.42671 -11.32642 -11.16185 -10.72019 -10.50688
-9.79252 -9.17244 -8.33270 -6.47209 -1.31800 0.76136 1.01277 1.21438
1.37458 1.39793 1.40926 1.42997 1.50071 1.74040 2.12496 2.22936
2.37615 2.45843 2.68836 2.76124 2.99285 3.22011 3.45542 3.67477
3.86189 3.96039 4.11327 4.26221 4.36043 4.52965 4.69935 4.87205
4.92009 5.01602 5.10036 5.30072 5.56323 5.79083 5.87657 5.91108
6.14572 6.26016 6.63727 6.70581 6.82823 7.04480 7.23041 8.74258
Molecular weight = 342.09amu
Principal moments of inertia in cm(-1)
A = 0.020788 B = 0.002263 C = 0.002192
Principal moments of inertia in units of 10**(-40)*gram-cm**2
A = 1346.583587 B =12368.969319 C =12773.530506
Net atomic charges, atomic populations, and dipole contributions
calculated with CM2
Atom NO. Type Charge No. of electrons
1 N -0.921 5.921
2 C 0.019 3.981
3 Si 0.970 3.030
4 H -0.272 1.272
5 H -0.276 1.276
6 H -0.270 1.270
7 C -0.548 4.548
8 H 0.054 0.946
9 C 0.272 3.728
10 N -0.343 5.343
11 C 0.054 3.946
12 C -0.291 4.291
13 C 0.264 3.736
14 N -0.612 5.612
15 C 0.522 3.478
16 O -0.527 6.527
17 C 0.149 3.851
18 H 0.162 0.838
19 C -0.622 4.622
20 S 2.463 3.537
21 O -0.943 6.943
22 O -0.943 6.943
23 C -0.620 4.620
24 C 0.546 3.454
25 O -0.572 6.572
26 N -0.701 5.701
27 N -0.339 5.339
28 H 0.272 0.728
29 H 0.022 0.978
30 H 0.057 0.943
31 H 0.198 0.802
32 H 0.170 0.830
33 H 0.431 0.569
34 H 0.173 0.827
35 H 0.195 0.805
36 H 0.203 0.797
37 H 0.186 0.814
38 H 0.415 0.585
For the charges calculated by CM2:
Dipole moment (debyes) X Y Z Total
from point charges 13.647 -18.651 -6.398 23.980
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 -0.560 5.560
2 C -0.182 4.182
3 Si 0.794 3.206
4 H -0.197 1.197
5 H -0.201 1.201
6 H -0.195 1.195
7 C -0.586 4.586
8 H 0.073 0.927
9 C 0.154 3.846
10 N -0.125 5.125
11 C -0.094 4.094
12 C -0.322 4.322
13 C 0.009 3.991
14 N -0.262 5.262
15 C 0.306 3.694
16 O -0.401 6.401
17 C 0.040 3.960
18 H 0.179 0.821
19 C -0.750 4.750
20 S 2.643 3.357
21 O -0.940 6.940
22 O -0.940 6.940
23 C -0.750 4.750
24 C 0.332 3.668
25 O -0.450 6.450
26 N -0.354 5.354
27 N -0.170 5.170
28 H 0.081 0.919
29 H 0.040 0.960
30 H 0.075 0.925
31 H 0.215 0.785
32 H 0.188 0.812
33 H 0.270 0.730
34 H 0.191 0.809
35 H 0.213 0.787
36 H 0.220 0.780
37 H 0.204 0.796
38 H 0.253 0.747
Dipole moment (debyes) X Y Z Total
from point charges 13.741 -18.144 -7.184 23.867
hybrid contribution -0.322 0.637 1.432 1.600
sum 13.419 -17.507 -5.753 22.796
Atomic orbital electron populations
1.69983 1.07242 1.28835 1.49894 1.25725 0.95802 1.02709 0.93915
0.85424 0.78292 0.77921 0.78963 1.19668 1.20055 1.19531 1.21375
0.93446 0.90905 1.52867 0.92732 1.19334 0.85676 0.81494 0.98128
1.48850 1.24044 1.20215 1.19370 1.23182 1.00612 0.88866 0.96752
1.21708 1.01984 1.06583 1.01916 1.19358 0.91740 0.93441 0.94557
1.42351 1.28531 1.24686 1.30653 1.20823 0.84455 0.79425 0.84680
1.90723 1.62405 1.60438 1.26523 1.20329 0.92232 0.95081 0.88398
0.82135 1.30693 1.21411 1.15924 1.06989 1.06990 0.76418 0.76241
0.76083 1.93641 1.81400 1.70374 1.48595 1.93632 1.53456 1.62541
1.84389 1.30448 1.18336 1.16563 1.09631 1.18724 0.78476 0.79814
0.89830 1.90842 1.43025 1.66153 1.45028 1.44926 1.51928 1.22536
1.16007 1.77268 1.04641 1.18110 1.16978 0.91857 0.95962 0.92495
0.78513 0.81249 0.73005 0.80894 0.78725 0.77981 0.79636 0.74678
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 -0.92 -50.81 13.29 21.45 0.28 -50.52 16
2 C 0.02 1.02 5.46 84.65 0.46 1.48 16
3 Si 0.97 42.13 29.54 68.60 2.03 44.16 16
4 H -0.27 -11.63 7.11 99.48 0.71 -10.92 16
5 H -0.28 -11.49 7.11 99.48 0.71 -10.79 16
6 H -0.27 -11.47 7.11 99.48 0.71 -10.76 16
7 C -0.55 -29.60 9.24 25.60 0.24 -29.36 16
8 H 0.05 3.04 7.81 -2.91 -0.02 3.02 16
9 C 0.27 13.42 6.26 85.63 0.54 13.96 16
10 N -0.34 -14.86 3.66 -351.83 -1.29 -16.15 16
11 C 0.05 1.94 11.44 83.52 0.96 2.90 16
12 C -0.29 -9.81 9.60 22.11 0.21 -9.60 16
13 C 0.26 8.82 8.11 133.32 1.08 9.90 16
14 N -0.61 -12.97 5.45 -307.51 -1.68 -14.65 16
15 C 0.52 9.26 6.85 87.66 0.60 9.86 16
16 O -0.53 -13.12 13.42 -3.06 -0.04 -13.16 16
17 C 0.15 1.32 3.18 44.52 0.14 1.47 16
18 H 0.16 0.52 8.14 -2.39 -0.02 0.50 16
19 C -0.62 -2.30 5.78 71.91 0.42 -1.88 16
20 S 2.46 16.49 5.43 -56.49 -0.31 16.18 16
21 O -0.94 -12.38 18.11 -127.41 -2.31 -14.69 16
22 O -0.94 -12.68 17.92 -127.41 -2.28 -14.97 16
23 C -0.62 -3.68 6.51 71.04 0.46 -3.22 16
24 C 0.55 7.83 7.64 87.91 0.67 8.51 16
25 O -0.57 -13.70 17.60 -3.05 -0.05 -13.76 16
26 N -0.70 -8.78 4.63 -454.68 -2.11 -10.89 16
27 N -0.34 -14.07 12.43 -54.45 -0.68 -14.75 16
28 H 0.27 14.13 8.31 -92.71 -0.77 13.36 16
29 H 0.02 1.18 8.14 -2.39 -0.02 1.16 16
30 H 0.06 2.76 8.07 -2.39 -0.02 2.74 16
31 H 0.20 5.56 8.06 -2.91 -0.02 5.54 16
32 H 0.17 5.38 5.92 -2.91 -0.02 5.37 16
33 H 0.43 6.19 8.82 -92.71 -0.82 5.37 16
34 H 0.17 0.16 8.13 -2.39 -0.02 0.15 16
35 H 0.20 -0.29 8.14 -2.39 -0.02 -0.31 16
36 H 0.20 0.02 8.14 -2.39 -0.02 0.00 16
37 H 0.19 0.68 8.14 -2.39 -0.02 0.66 16
38 H 0.42 6.22 7.97 -92.71 -0.74 5.48 16
Total: -1.00 -85.59 346.66 -3.06 -88.65
By element:
Atomic # 1 Polarization: 10.96 SS G_CDS: -0.41 Total: 10.55 kcal
Atomic # 6 Polarization: -1.78 SS G_CDS: 5.77 Total: 3.99 kcal
Atomic # 7 Polarization: -101.49 SS G_CDS: -5.46 Total: -106.96 kcal
Atomic # 8 Polarization: -51.88 SS G_CDS: -4.69 Total: -56.57 kcal
Atomic # 14 Polarization: 42.13 SS G_CDS: 2.03 Total: 44.16 kcal
Atomic # 16 Polarization: 16.49 SS G_CDS: -0.31 Total: 16.18 kcal
Total: -85.59 -3.06 -88.65 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.
ZINC001361502687.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 23.438 kcal
(2) G-P(sol) polarization free energy of solvation -85.588 kcal
(3) G-ENP(sol) elect.-nuc.-pol. free energy of system -62.150 kcal
(4) G-CDS(sol) cavity-dispersion-solvent structure free energy -3.060 kcal
(5) G-P-CDS(sol) = G-P(sol) + G-CDS(sol) = (2) + (4) -88.648 kcal
(6) G-S(sol) free energy of system = (1) + (5) -65.210 kcal
1SCF WAS SPECIFIED, SO GEOMETRY OPTIMIZATION WAS NOT USED
Total computer time = 0.58 seconds