Wall clock time and date at job start Tue Mar 31 2020 03:21:44
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.
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* 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 1.31511 * 1
3 3 Si 1.86801 * 120.00029 * 2 1
4 4 H 1.48496 * 109.47142 * 270.00287 * 3 2 1
5 5 H 1.48505 * 109.46946 * 30.00249 * 3 2 1
6 6 H 1.48501 * 109.47091 * 150.00126 * 3 2 1
7 7 C 1.37876 * 120.00243 * 180.02562 * 2 1 3
8 8 H 1.08000 * 119.99852 * 0.02562 * 7 2 1
9 9 S 1.76201 * 120.00224 * 179.97438 * 7 2 1
10 10 O 1.42092 * 106.40186 * 66.46000 * 9 7 2
11 11 O 1.42103 * 106.40024 * 293.54214 * 9 7 2
12 12 N 1.65604 * 107.21967 * 180.02562 * 9 7 2
13 13 C 1.46495 * 120.00014 * 64.99721 * 12 9 7
14 14 C 1.52998 * 109.47000 * 164.99966 * 13 12 9
15 15 N 1.46508 * 109.47135 * 179.97438 * 14 13 12
16 16 C 1.34780 * 119.99852 * 179.97438 * 15 14 13
17 17 O 1.21557 * 120.00061 * 0.02562 * 16 15 14
18 18 C 1.47845 * 119.99555 * 180.02562 * 16 15 14
19 19 C 1.39575 * 120.13807 * 180.02562 * 18 16 15
20 20 C 1.37966 * 119.85100 * 179.97438 * 19 18 16
21 21 C 1.38359 * 120.14194 * 359.97438 * 20 19 18
22 22 C 1.38356 * 120.29572 * 0.04433 * 21 20 19
23 23 C 1.37965 * 120.14354 * 359.95888 * 22 21 20
24 24 H 0.97001 * 120.00003 * 359.97438 * 1 2 3
25 25 H 0.96996 * 119.99679 * 245.00377 * 12 9 7
26 26 H 1.09002 * 109.47170 * 45.00204 * 13 12 9
27 27 H 1.08999 * 109.47764 * 285.00352 * 13 12 9
28 28 H 1.08996 * 109.46951 * 60.00588 * 14 13 12
29 29 H 1.08996 * 109.47668 * 300.00178 * 14 13 12
30 30 H 0.97002 * 119.99932 * 0.02562 * 15 14 13
31 31 H 1.07998 * 120.08057 * 359.70005 * 19 18 16
32 32 H 1.08000 * 119.93085 * 179.97438 * 20 19 18
33 33 H 1.08003 * 119.85292 * 180.02562 * 21 20 19
34 34 H 1.08001 * 119.93259 * 179.97438 * 22 21 20
35 35 H 1.08003 * 120.07139 * 180.02562 * 23 22 21
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 2.2491 1.6177 0.0000
4 1 2.4966 2.0464 -1.4000
5 1 1.4465 2.6527 0.7001
6 1 3.5467 1.4402 0.7000
7 6 2.0045 -1.1940 -0.0005
8 1 1.4646 -2.1293 -0.0014
9 16 3.7665 -1.1940 -0.0012
10 8 4.1683 -0.6499 1.2484
11 8 4.1673 -0.6492 -1.2510
12 7 4.2568 -2.7758 -0.0025
13 6 3.9610 -3.6334 -1.1527
14 6 4.8199 -4.8975 -1.0806
15 7 4.5237 -5.7555 -2.2306
16 6 5.1662 -6.9312 -2.3775
17 8 5.9912 -7.2798 -1.5556
18 6 4.8677 -7.7967 -3.5383
19 6 5.5309 -9.0150 -3.6931
20 6 5.2473 -9.8182 -4.7784
21 6 4.3074 -9.4187 -5.7117
22 6 3.6466 -8.2120 -5.5644
23 6 3.9209 -7.3994 -4.4838
24 1 -0.4850 0.8401 0.0004
25 1 4.7397 -3.1344 0.7585
26 1 4.1835 -3.0951 -2.0740
27 1 2.9066 -3.9093 -1.1388
28 1 4.5974 -5.4359 -0.1593
29 1 5.8743 -4.6218 -1.0946
30 1 3.8656 -5.4772 -2.8866
31 1 6.2677 -9.3262 -2.9674
32 1 5.7601 -10.7610 -4.8996
33 1 4.0887 -10.0513 -6.5593
34 1 2.9143 -7.9057 -6.2967
35 1 3.4042 -6.4579 -4.3697
RHF calculation, no. of doubly occupied orbitals= 52
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
ZINC001192987998.mol2 35
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 03:21:44
Heat of formation + Delta-G solvation = -119.968892 kcal
Electronic energy + Delta-G solvation = -20871.412284 eV
Core-core repulsion = 17380.947322 eV
Total energy + Delta-G solvation = -3490.464961 eV
No. of doubly occupied orbitals = 52
Molecular weight
(most abundant/longest-lived isotopes) = 298.082 amu
Computer time = 0.68 seconds
Orbital eigenvalues (eV)
-41.23459 -39.26759 -37.75412 -37.26133 -36.48622 -35.19672 -35.00780 -32.30338
-31.84715 -29.24025 -28.53544 -25.03259 -23.75582 -23.13477 -21.59868 -21.05516
-19.48840 -19.23519 -18.58878 -17.44364 -17.30103 -16.87829 -16.68485 -16.59328
-15.77782 -15.74211 -15.47964 -15.33753 -15.19939 -14.90482 -14.65183 -14.25678
-13.66047 -13.58996 -13.39829 -13.21305 -12.92277 -12.69978 -12.63930 -12.56388
-12.54327 -11.99624 -11.82532 -11.31748 -11.22493 -11.13574 -10.38661 -10.24434
-9.93131 -9.86866 -8.94682 -7.50616 -0.13402 0.11831 0.43624 1.08024
1.16937 1.24572 1.82430 1.91107 1.97988 2.44672 2.66643 2.91951
3.32490 3.59956 3.73184 3.94778 4.03909 4.04800 4.23978 4.27695
4.42330 4.48947 4.55596 4.62356 4.86896 4.88591 4.98176 5.08230
5.27254 5.37085 5.40384 5.47145 5.53226 5.96939 6.03464 6.24457
6.41951 6.56291 7.08569 8.22481
Molecular weight = 298.08amu
Principal moments of inertia in cm(-1)
A = 0.029171 B = 0.002999 C = 0.002824
Principal moments of inertia in units of 10**(-40)*gram-cm**2
A = 959.611179 B = 9332.657512 C = 9911.096090
Net atomic charges, atomic populations, and dipole contributions
calculated with CM2
Atom NO. Type Charge No. of electrons
1 N -0.853 5.853
2 C 0.109 3.891
3 Si 0.824 3.176
4 H -0.238 1.238
5 H -0.225 1.225
6 H -0.229 1.229
7 C -1.035 5.035
8 H 0.110 0.890
9 S 2.703 3.297
10 O -1.028 7.028
11 O -1.026 7.026
12 N -1.109 6.109
13 C 0.110 3.890
14 C 0.120 3.880
15 N -0.712 5.712
16 C 0.556 3.444
17 O -0.581 6.581
18 C -0.157 4.157
19 C -0.079 4.079
20 C -0.131 4.131
21 C -0.091 4.091
22 C -0.130 4.130
23 C -0.089 4.089
24 H 0.291 0.709
25 H 0.422 0.578
26 H 0.086 0.914
27 H 0.080 0.920
28 H 0.079 0.921
29 H 0.075 0.925
30 H 0.416 0.584
31 H 0.123 0.877
32 H 0.151 0.849
33 H 0.156 0.844
34 H 0.156 0.844
35 H 0.145 0.855
For the charges calculated by CM2:
Dipole moment (debyes) X Y Z Total
from point charges 5.847 -17.447 -12.219 22.088
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 -0.484 5.484
2 C -0.107 4.107
3 Si 0.642 3.358
4 H -0.161 1.161
5 H -0.147 1.147
6 H -0.152 1.152
7 C -1.168 5.168
8 H 0.128 0.872
9 S 2.803 3.197
10 O -1.018 7.018
11 O -1.015 7.015
12 N -0.870 5.870
13 C -0.017 4.017
14 C -0.005 4.005
15 N -0.365 5.365
16 C 0.345 3.655
17 O -0.462 6.462
18 C -0.160 4.160
19 C -0.098 4.098
20 C -0.149 4.149
21 C -0.109 4.109
22 C -0.147 4.147
23 C -0.108 4.108
24 H 0.101 0.899
25 H 0.257 0.743
26 H 0.104 0.896
27 H 0.099 0.901
28 H 0.097 0.903
29 H 0.093 0.907
30 H 0.255 0.745
31 H 0.141 0.859
32 H 0.169 0.831
33 H 0.174 0.826
34 H 0.173 0.827
35 H 0.163 0.837
Dipole moment (debyes) X Y Z Total
from point charges 6.709 -16.752 -11.781 21.551
hybrid contribution -0.706 0.485 0.424 0.955
sum 6.004 -16.267 -11.357 20.728
Atomic orbital electron populations
1.70007 1.07454 1.30441 1.40466 1.25131 0.95570 1.01391 0.88640
0.87498 0.82847 0.82915 0.82578 1.16124 1.14705 1.15151 1.30941
1.17850 1.01737 1.66226 0.87153 1.00379 0.75706 0.71321 0.72327
1.93448 1.85284 1.77190 1.45927 1.93382 1.84720 1.77246 1.46199
1.54887 1.74021 1.30107 1.28000 1.21386 1.00204 0.91035 0.89041
1.21403 0.99864 0.89611 0.89620 1.45676 1.43628 1.19646 1.27569
1.18695 0.80118 0.81135 0.85565 1.90746 1.35726 1.74110 1.45589
1.19903 1.02408 0.97093 0.96608 1.21393 0.97747 0.92703 0.98003
1.21461 0.98934 1.00648 0.93874 1.21820 0.93978 0.96229 0.98858
1.21527 1.00643 0.94596 0.97977 1.21631 0.95294 1.00470 0.93402
0.89884 0.74305 0.89601 0.90130 0.90321 0.90687 0.74548 0.85857
0.83138 0.82591 0.82683 0.83719
Number of geometries 1
Number of calculations of the screened coulomb radii 1
The total number of SCF iterations 24.
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 -0.85 -48.09 13.96 21.45 0.30 -47.79 16
2 C 0.11 6.10 5.47 84.65 0.46 6.56 16
3 Si 0.82 40.05 26.54 68.60 1.82 41.88 16
4 H -0.24 -11.16 7.11 99.48 0.71 -10.45 16
5 H -0.22 -9.73 7.11 99.48 0.71 -9.03 16
6 H -0.23 -11.45 5.61 99.48 0.56 -10.89 16
7 C -1.03 -55.44 10.26 67.73 0.69 -54.75 16
8 H 0.11 5.97 8.06 -2.91 -0.02 5.95 16
9 S 2.70 126.86 4.24 -56.49 -0.24 126.62 16
10 O -1.03 -52.90 16.02 -128.00 -2.05 -54.95 16
11 O -1.03 -51.24 16.30 -128.00 -2.09 -53.33 16
12 N -1.11 -38.17 6.00 -187.50 -1.12 -39.29 16
13 C 0.11 3.13 6.34 86.38 0.55 3.68 16
14 C 0.12 2.98 5.82 86.38 0.50 3.48 16
15 N -0.71 -15.67 5.51 -465.96 -2.57 -18.23 16
16 C 0.56 14.40 7.77 86.79 0.67 15.07 16
17 O -0.58 -19.40 16.35 -3.89 -0.06 -19.47 16
18 C -0.16 -3.26 5.87 -20.09 -0.12 -3.38 16
19 C -0.08 -1.53 9.60 22.53 0.22 -1.32 16
20 C -0.13 -1.73 10.03 22.23 0.22 -1.51 16
21 C -0.09 -0.95 10.04 22.33 0.22 -0.73 16
22 C -0.13 -1.48 10.03 22.23 0.22 -1.26 16
23 C -0.09 -1.35 9.54 22.53 0.21 -1.13 16
24 H 0.29 14.79 8.31 -92.71 -0.77 14.02 16
25 H 0.42 12.29 8.65 -96.75 -0.84 11.45 16
26 H 0.09 2.43 7.75 -2.39 -0.02 2.41 16
27 H 0.08 2.17 8.14 -2.39 -0.02 2.15 16
28 H 0.08 1.94 8.14 -2.39 -0.02 1.92 16
29 H 0.07 1.92 8.14 -2.39 -0.02 1.90 16
30 H 0.42 6.79 6.51 -92.71 -0.60 6.19 16
31 H 0.12 2.57 7.65 -2.91 -0.02 2.55 16
32 H 0.15 1.23 8.06 -2.91 -0.02 1.20 16
33 H 0.16 0.69 8.06 -2.91 -0.02 0.66 16
34 H 0.16 0.96 8.06 -2.91 -0.02 0.94 16
35 H 0.15 1.57 6.41 -2.91 -0.02 1.55 16
Total: -1.00 -74.72 317.43 -2.60 -77.31
By element:
Atomic # 1 Polarization: 22.97 SS G_CDS: -0.45 Total: 22.52 kcal
Atomic # 6 Polarization: -39.13 SS G_CDS: 3.87 Total: -35.27 kcal
Atomic # 7 Polarization: -101.93 SS G_CDS: -3.39 Total: -105.32 kcal
Atomic # 8 Polarization: -123.54 SS G_CDS: -4.20 Total: -127.74 kcal
Atomic # 14 Polarization: 40.05 SS G_CDS: 1.82 Total: 41.88 kcal
Atomic # 16 Polarization: 126.86 SS G_CDS: -0.24 Total: 126.62 kcal
Total: -74.72 -2.60 -77.31 kcal
The number of atoms in the molecule is 35
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.
ZINC001192987998.mol2 35
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 -42.656 kcal
(2) G-P(sol) polarization free energy of solvation -74.717 kcal
(3) G-ENP(sol) elect.-nuc.-pol. free energy of system -117.373 kcal
(4) G-CDS(sol) cavity-dispersion-solvent structure free energy -2.596 kcal
(5) G-P-CDS(sol) = G-P(sol) + G-CDS(sol) = (2) + (4) -77.313 kcal
(6) G-S(sol) free energy of system = (1) + (5) -119.969 kcal
1SCF WAS SPECIFIED, SO GEOMETRY OPTIMIZATION WAS NOT USED
Total computer time = 0.68 seconds