| Chapter 22. Solvation (COSMO, SM5.2, SM5C) | ||
|---|---|---|
|
Part II. AMPAC™ 10 Examples |  |
| Chapter 22. Solvation (COSMO, SM5.2, SM5C) | ||
|---|---|---|
|
|
Part II. AMPAC™ 10 Examples | |
Table of Contents
AMPAC provides several keywords for incorporating solvation into a calculation. The simplest and most general is COSMO. (See Chapter 14, COSMO Solvation Model for details and related keywords.) For demonstration, the properties of alanine are calculated in water. (Water is assumed to be the solvent unless otherwise specified.)
am1 rhf singlet cosmo 1scf bonds grad t=auto Alanine COSMO C 0.000000 0 0.000000 0 0.000000 0 C 1.530000 1 0.000000 0 0.000000 0 O 2.154300 1 1.059800 1 0.000000 0 N 2.105600 1 -1.154500 1 0.000000 1 C 3.562000 1 -1.256300 1 0.000000 1 C 3.970900 1 -2.730700 1 0.000000 1 O 3.116500 1 -3.615500 1 0.000000 1 N 5.237200 1 -2.976800 1 0.000000 1 C 5.724600 1 -4.353100 1 0.000000 1 H -0.360500 1 1.018100 1 0.000000 1 H -0.360500 1 -0.509000 1 -0.881700 1 H -0.360500 1 -0.509000 1 0.881700 1 H 1.545000 1 -1.993400 1 0.000000 1 H 3.957200 1 -0.773700 1 -0.881700 1 H 5.895800 1 -2.212400 1 0.000000 1 H 6.804600 1 -4.353100 1 0.000000 1 H 5.365100 1 -4.862800 1 -0.881700 1 H 5.365100 1 -4.862800 1 0.881700 1 C 4.121800 1 -0.572600 1 1.249000 1 H 3.834800 1 0.468600 1 1.249300 1 H 5.199200 1 -0.648400 1 1.249300 1 H 3.727200 1 -1.054500 1 2.131300 1 0 0.000000 0 0.000000 0 0.000000 0
Timestamp: 2011-08-31-12-36-10-0000000360-win64
User Info: John Millam, Nahum,
SUMMARY OF AM1 CALCULATION
Aug-31-2011
AMPAC Version 10.0.1
Presented by:
Semichem, Inc.
www.semichem.com
FORMULA: C6H12N2O2
Alanine
COSMO
1SCF WAS SPECIFIED, SO NO OPTIMIZATION ATTEMPTED
SCF FIELD WAS ACHIEVED
FINAL HEAT OF FORMATION = -72.806427 kcal ** 
= -304.694896 kJ **
ELECTRONIC ENERGY = -9444.965712 eV
CORE-CORE REPULSION = 7456.602909 eV
TOTAL ENERGY = -1988.362803 eV **
COSMO TOTAL SURFACE = 117.112099 squared angstroms
COSMO POLARIZATION ENERGY = -0.560842 eV ( 200 SEGMENTS)
DIELECTRIC CONSTANT = 78.355000
GRADIENT NORM = 278.548752
RMS GRADIENT NORM = 35.960489
DIPOLE = 3.765386 debyes
MOLECULAR WEIGHT = 144.173000
MOLECULAR POINT GROUP = C1 0.100000
NO. OF FILLED LEVELS = 29 (OCC = 2)
TOTAL NUMBER OF ORBITALS = 52
COMPUTATION TIME = 0.34 SECONDS
** ENERGY INCLUDES SOLVATION ENERGY
FINAL GEOMETRY OBTAINED CHARGE
AM1 RHF SINGLET COSMO 1SCF BONDS GRAD T=AUTO
Alanine
COSMO
C 0.000000 0 0.000000 0 0.000000 0 0 0 0 -0.2496
C 1.530000 1 0.000000 0 0.000000 0 1 0 0 0.3159
O 1.230011 1 120.501208 1 0.000000 0 2 1 0 -0.4818
N 1.290033 1 116.499504 1 -180.000000 1 2 1 3 -0.3349
C 1.459953 1 120.497883 1 -180.000000 1 4 2 1 -0.0060
C 1.530051 1 109.498837 1 -180.000000 1 5 4 2 0.3077
O 1.229988 1 120.500930 1 0.000000 1 6 5 4 -0.4710
N 1.289993 1 116.498549 1 -180.000000 1 6 5 4 -0.3374
C 1.460055 1 120.499075 1 -180.000000 1 8 6 5 -0.0696
H 1.080041 1 109.498594 1 0.000000 1 1 2 3 0.1089
H 1.080017 1 109.499044 1 119.997576 1 1 2 3 0.1077
H 1.080017 1 109.499044 1 -119.997576 1 1 2 3 0.1078
H 1.008973 1 119.747429 1 0.000000 1 4 2 1 0.2696
H 1.080037 1 109.503566 1 -60.003303 1 5 4 2 0.1303
H 1.008990 1 119.749793 1 0.000000 1 8 6 5 0.2652
H 1.080000 1 109.500984 1 -180.000000 1 9 8 6 0.1014
H 1.080014 1 109.496406 1 60.001100 1 9 8 6 0.0889
H 1.080014 1 109.496406 1 -60.001100 1 9 8 6 0.0889
C 1.529975 1 109.501915 1 60.001401 1 5 4 2 -0.2328
H 1.080031 1 109.499686 1 -60.040097 1 19 5 4 0.1116
H 1.080063 1 109.502690 1 179.967663 1 19 5 4 0.0892
H 1.079995 1 109.501824 1 59.959724 1 19 5 4 0.0899
0 0.000000 0 0.000000 0 0.000000 0 0 0 0
Timestamp: 2011-08-31-12-36-10-0000000360-win64
User Info: John Millam, Nahum,
*******************************************************************************
AM1 CALCULATION RESULTS
*******************************************************************************
* AMPAC Version 10.0.1
* Presented by:
*
* Semichem, Inc.
* www.semichem.com
*
* AM1 - THE AM1 HAMILTONIAN TO BE USED
* RHF - RESTRICTED HARTREE-FOCK CALCULATION
* 1SCF - READ KEYWORD BUT DO 1 SCF AND THEN STOP
* T=AUTO - AUTOMATIC DETERMINATION OF ALLOWED TIME
* COSMO - COSMO SOLVATION MODEL IN USE
* DIELEC= - THE DIELECTRIC CONSTANT IS 78.355
* or EPS=
* REFRACT= - THE SOLVENT INDEX OF REFRACTION IS 1.3328
* or IOFR=
* BONDS - PRINT NON-ZERO ELEMENTS OF FINAL BOND-ORDER MATRIX
* GRADIENTS- ALL GRADIENTS TO BE PRINTED
* SINGLET - IS THE REQUIRED SPIN MULTIPLICITY
*******************************************************************************
AM1 RHF SINGLET COSMO 1SCF BONDS GRAD T=AUTO
Alanine
COSMO
ATOM CHEMICAL BOND LENGTH BOND ANGLE TWIST ANGLE
NUMBER SYMBOL (ANGSTROMS) (DEGREES) (DEGREES)
(I) NA:I NB:NA:I NC:NB:NA:I NA NB NC
1 C
2 C 1.53000 * 1
3 O 1.23001 * 120.50121 * 2 1
4 N 1.29003 * 116.49950 * -180.00000 * 2 1 3
5 C 1.45995 * 120.49788 * -180.00000 * 4 2 1
6 C 1.53005 * 109.49884 * -180.00000 * 5 4 2
7 O 1.22999 * 120.50093 * 0.00000 * 6 5 4
8 N 1.28999 * 116.49855 * -180.00000 * 6 5 4
9 C 1.46005 * 120.49908 * -180.00000 * 8 6 5
10 H 1.08004 * 109.49859 * 0.00000 * 1 2 3
11 H 1.08002 * 109.49904 * 119.99758 * 1 2 3
12 H 1.08002 * 109.49904 * -119.99758 * 1 2 3
13 H 1.00897 * 119.74743 * 0.00000 * 4 2 1
14 H 1.08004 * 109.50357 * -60.00330 * 5 4 2
15 H 1.00899 * 119.74979 * 0.00000 * 8 6 5
16 H 1.08000 * 109.50098 * -180.00000 * 9 8 6
17 H 1.08001 * 109.49641 * 60.00110 * 9 8 6
18 H 1.08001 * 109.49641 * -60.00110 * 9 8 6
19 C 1.52997 * 109.50191 * 60.00140 * 5 4 2
20 H 1.08003 * 109.49969 * -60.04010 * 19 5 4
21 H 1.08006 * 109.50269 * 179.96766 * 19 5 4
22 H 1.08000 * 109.50182 * 59.95972 * 19 5 4
CARTESIAN COORDINATES READ IN BUT CALCULATION TO BE RUN IN INTERNAL COORDINATES.
MOLECULAR POINT GROUP SYMMETRY CRITERIA
C1 0.10000000
SINGLET STATE CALCULATION
RHF CALCULATION, NO. OF DOUBLY OCCUPIED LEVELS = 29
** REFERENCES TO PARAMETERS **
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).
-------------------------
* External Contributors *
-------------------------
COSMO Solvation Model:
----------------------
The COSMO solvation model found in AMPAC was contributed from
MOPAC-7 (public domain) by Jimmy Stewart.
Corrections and extensions by Daniel A. Liotard,
with recommendations and permission from Andreas Klamt.
CARTESIAN COORDINATES
ATOM X Y Z
1 C 0.00000000 0.00000000 0.00000000
2 C 1.53000000 0.00000000 0.00000000
3 O 2.15430000 1.05980000 0.00000000
4 N 2.10560000 -1.15450000 0.00000000
5 C 3.56200000 -1.25630000 0.00000000
6 C 3.97090000 -2.73070000 0.00000000
7 O 3.11650000 -3.61550000 0.00000000
8 N 5.23720000 -2.97680000 0.00000000
9 C 5.72460000 -4.35310000 0.00000000
10 H -0.36050000 1.01810000 0.00000000
11 H -0.36050000 -0.50900000 -0.88170000
12 H -0.36050000 -0.50900000 0.88170000
13 H 1.54500000 -1.99340000 0.00000000
14 H 3.95720000 -0.77370000 -0.88170000
15 H 5.89580000 -2.21240000 0.00000000
16 H 6.80460000 -4.35310000 0.00000000
17 H 5.36510000 -4.86280000 -0.88170000
18 H 5.36510000 -4.86280000 0.88170000
19 C 4.12180000 -0.57260000 1.24900000
20 H 3.83480000 0.46860000 1.24930000
21 H 5.19920000 -0.64840000 1.24930000
22 H 3.72720000 -1.05450000 2.13130000
COSMO VAN DER WAALS RADII (ANGSTROMS), WITH RSOLV= 1.000
H 1.300 OPTIMIZED COSMO VALUE 1998
C 2.000 OPTIMIZED COSMO VALUE 1998
N 1.830 OPTIMIZED COSMO VALUE 1998
O 1.720 OPTIMIZED COSMO VALUE 1998
STANDARD DEVIATION ON ENERGY (KCAL) 0.00000055521
STANDARD DEVIATION ON GRADIENT (KCAL/A,RD,RD) 0.12191694 0.34135363 0.24661650
AM1 RHF SINGLET COSMO 1SCF BONDS GRAD T=AUTO
Alanine
COSMO
1SCF WAS SPECIFIED, SO NO OPTIMIZATION ATTEMPTED
SCF FIELD WAS ACHIEVED
AM1 CALCULATION
VERSION 10.0.1
Aug-31-2011
FINAL HEAT OF FORMATION = -72.806427 kcal ** 
= -304.694896 kJ **
ELECTRONIC ENERGY = -9444.965712 eV
CORE-CORE REPULSION = 7456.602909 eV
TOTAL ENERGY = -1988.362803 eV **
COSMO TOTAL SURFACE = 117.112099 squared angstroms 
COSMO POLARIZATION ENERGY = -0.560842 eV ( 200 SEGMENTS) 
DIELECTRIC CONSTANT = 78.355000
GRADIENT NORM = 278.548752
RMS GRADIENT NORM = 35.960489
MOLECULAR WEIGHT = 144.173000
MOLECULAR POINT GROUP = C1 0.100000
NO. OF FILLED LEVELS = 29 (OCC = 2)
TOTAL NUMBER OF ORBITALS = 52
SCF CALCULATIONS = 1
COMPUTATION TIME = 0.30 SECONDS
** ENERGY INCLUDES SOLVATION ENERGY
FINAL GEOMETRY AND DERIVATIVES
PARAMETER ATOM TYPE VALUE GRADIENT
1 2 C BOND 1.530000 -5.493963 kcal/angstrom
2 3 O BOND 1.230011 -80.073469 kcal/angstrom
3 3 O ANGLE 120.501208 9.999790 kcal/radian
4 4 N BOND 1.290033 -159.645884 kcal/angstrom
5 4 N ANGLE 116.499504 1.257687 kcal/radian
6 4 N DIHEDRAL -180.000000 -3.396084 kcal/radian
7 5 C BOND 1.459953 -16.099156 kcal/angstrom
8 5 C ANGLE 120.497883 -27.636755 kcal/radian
9 5 C DIHEDRAL -180.000000 -3.426254 kcal/radian
10 6 C BOND 1.530051 -41.893807 kcal/angstrom
11 6 C ANGLE 109.498837 -8.679523 kcal/radian
12 6 C DIHEDRAL -180.000000 -5.232405 kcal/radian
13 7 O BOND 1.229988 -84.559276 kcal/angstrom
14 7 O ANGLE 120.500930 -6.536370 kcal/radian
15 7 O DIHEDRAL 0.000000 -0.261660 kcal/radian
16 8 N BOND 1.289993 -147.803386 kcal/angstrom
17 8 N ANGLE 116.498549 -9.808434 kcal/radian
18 8 N DIHEDRAL -180.000000 3.131605 kcal/radian
19 9 C BOND 1.460055 13.683916 kcal/angstrom
20 9 C ANGLE 120.499075 -13.036869 kcal/radian
21 9 C DIHEDRAL -180.000000 -0.097037 kcal/radian
22 10 H BOND 1.080041 -31.422162 kcal/angstrom
23 10 H ANGLE 109.498594 1.637736 kcal/radian
24 10 H DIHEDRAL 0.000000 -0.001355 kcal/radian
25 11 H BOND 1.080017 -33.063555 kcal/angstrom
26 11 H ANGLE 109.499044 -1.388238 kcal/radian
27 11 H DIHEDRAL 119.997576 0.726147 kcal/radian
28 12 H BOND 1.080017 -33.054575 kcal/angstrom
29 12 H ANGLE 109.499044 -1.361800 kcal/radian
30 12 H DIHEDRAL -119.997576 -0.729647 kcal/radian
31 13 H BOND 1.008973 7.928248 kcal/angstrom
32 13 H ANGLE 119.747429 -9.603945 kcal/radian
33 13 H DIHEDRAL 0.000000 0.368550 kcal/radian
34 14 H BOND 1.080037 -40.482106 kcal/angstrom
35 14 H ANGLE 109.503566 3.389865 kcal/radian
36 14 H DIHEDRAL -60.003303 -0.025054 kcal/radian
37 15 H BOND 1.008990 10.777075 kcal/angstrom
38 15 H ANGLE 119.749793 -8.639904 kcal/radian
39 15 H DIHEDRAL 0.000000 0.499994 kcal/radian
40 16 H BOND 1.080000 -35.432597 kcal/angstrom
41 16 H ANGLE 109.500984 2.674084 kcal/radian
42 16 H DIHEDRAL -180.000000 0.004058 kcal/radian
43 17 H BOND 1.080014 -36.673098 kcal/angstrom
44 17 H ANGLE 109.496406 0.933668 kcal/radian
45 17 H DIHEDRAL 60.001100 0.873648 kcal/radian
46 18 H BOND 1.080014 -36.670301 kcal/angstrom
47 18 H ANGLE 109.496406 0.940267 kcal/radian
48 18 H DIHEDRAL -60.001100 -0.871263 kcal/radian
49 19 C BOND 1.529975 -21.697065 kcal/angstrom
50 19 C ANGLE 109.501915 -16.505387 kcal/radian
51 19 C DIHEDRAL 60.001401 -3.202284 kcal/radian
52 20 H BOND 1.080031 -32.886866 kcal/angstrom
53 20 H ANGLE 109.499686 -4.370304 kcal/radian
54 20 H DIHEDRAL -60.040097 1.962317 kcal/radian
55 21 H BOND 1.080063 -32.043182 kcal/angstrom
56 21 H ANGLE 109.502690 -3.362301 kcal/radian
57 21 H DIHEDRAL 179.967663 -1.957821 kcal/radian
58 22 H BOND 1.079995 -33.288518 kcal/angstrom
59 22 H ANGLE 109.501824 -3.427306 kcal/radian
60 22 H DIHEDRAL 59.959724 -0.637585 kcal/radian
ATOM CHEMICAL BOND LENGTH BOND ANGLE TWIST ANGLE
NUMBER SYMBOL (ANGSTROMS) (DEGREES) (DEGREES)
(I) NA:I NB:NA:I NC:NB:NA:I NA NB NC
1 C
2 C 1.53000 * 1
3 O 1.23001 * 120.50121 * 2 1
4 N 1.29003 * 116.49950 * -180.00000 * 2 1 3
5 C 1.45995 * 120.49788 * -180.00000 * 4 2 1
6 C 1.53005 * 109.49884 * -180.00000 * 5 4 2
7 O 1.22999 * 120.50093 * 0.00000 * 6 5 4
8 N 1.28999 * 116.49855 * -180.00000 * 6 5 4
9 C 1.46005 * 120.49908 * -180.00000 * 8 6 5
10 H 1.08004 * 109.49859 * 0.00000 * 1 2 3
11 H 1.08002 * 109.49904 * 119.99758 * 1 2 3
12 H 1.08002 * 109.49904 * -119.99758 * 1 2 3
13 H 1.00897 * 119.74743 * 0.00000 * 4 2 1
14 H 1.08004 * 109.50357 * -60.00330 * 5 4 2
15 H 1.00899 * 119.74979 * 0.00000 * 8 6 5
16 H 1.08000 * 109.50098 * -180.00000 * 9 8 6
17 H 1.08001 * 109.49641 * 60.00110 * 9 8 6
18 H 1.08001 * 109.49641 * -60.00110 * 9 8 6
19 C 1.52997 * 109.50191 * 60.00140 * 5 4 2
20 H 1.08003 * 109.49969 * -60.04010 * 19 5 4
21 H 1.08006 * 109.50269 * 179.96766 * 19 5 4
22 H 1.08000 * 109.50182 * 59.95972 * 19 5 4
MOLECULAR POINT GROUP SYMMETRY CRITERIA
C1 0.10000000
RHF EIGENVALUES
-41.68368 -40.18358 -36.15342 -35.89006 -33.00138 -29.92766
-28.35555 -25.22744 -21.81477 -21.30652 -19.31586 -17.99560
-17.17887 -17.03657 -16.32856 -16.21849 -14.98548 -14.64471
-14.15248 -13.80503 -13.58265 -13.51659 -13.39446 -13.10711
-12.74447 -11.15014 -10.79516 -10.54982 -10.41146 1.35052
1.57939 1.75517 2.26308 3.20179 3.61231 3.84950
4.02437 4.23470 4.34850 4.44549 4.46401 4.48686
4.70759 4.82940 4.93272 4.98795 5.01905 5.17832
6.13749 6.30089 6.85452 7.05464
NET ATOMIC CHARGES AND DIPOLE CONTRIBUTIONS
ATOM CHARGE ATOM ELECTRON DENSITY
1 C -0.2496 4.2496
2 C 0.3159 3.6841
3 O -0.4818 6.4818
4 N -0.3349 5.3349
5 C -0.0060 4.0060
6 C 0.3077 3.6923
7 O -0.4710 6.4710
8 N -0.3374 5.3374
9 C -0.0696 4.0696
10 H 0.1089 0.8911
11 H 0.1077 0.8923
12 H 0.1078 0.8922
13 H 0.2696 0.7304
14 H 0.1303 0.8697
15 H 0.2652 0.7348
16 H 0.1014 0.8986
17 H 0.0889 0.9111
18 H 0.0889 0.9111
19 C -0.2328 4.2328
20 H 0.1116 0.8884
21 H 0.0892 0.9108
22 H 0.0899 0.9101
DIPOLE (DEBYE) X Y Z TOTAL
POINT-CHG. 2.873 -2.129 0.178 3.580
HYBRID 0.130 -0.138 -0.026 0.191
SUM 3.003 -2.267 0.151 3.765
CARTESIAN COORDINATES
ATOM X Y Z
1 C 0.00000000 0.00000000 0.00000000
2 C 1.53000000 0.00000000 0.00000000
3 O 2.15430000 1.05980000 0.00000000
4 N 2.10560000 -1.15450000 0.00000000
5 C 3.56200000 -1.25630000 0.00000000
6 C 3.97090000 -2.73070000 0.00000000
7 O 3.11650000 -3.61550000 0.00000000
8 N 5.23720000 -2.97680000 0.00000000
9 C 5.72460000 -4.35310000 0.00000000
10 H -0.36050000 1.01810000 0.00000000
11 H -0.36050000 -0.50900000 -0.88170000
12 H -0.36050000 -0.50900000 0.88170000
13 H 1.54500000 -1.99340000 0.00000000
14 H 3.95720000 -0.77370000 -0.88170000
15 H 5.89580000 -2.21240000 0.00000000
16 H 6.80460000 -4.35310000 0.00000000
17 H 5.36510000 -4.86280000 -0.88170000
18 H 5.36510000 -4.86280000 0.88170000
19 C 4.12180000 -0.57260000 1.24900000
20 H 3.83480000 0.46860000 1.24930000
21 H 5.19920000 -0.64840000 1.24930000
22 H 3.72720000 -1.05450000 2.13130000
ATOMIC ORBITAL ELECTRON POPULATIONS
1.22089 0.92092 1.05820 1.04962 1.19881 0.90793
0.83212 0.74526 1.90954 1.70322 1.31341 1.55561
1.45366 1.07030 1.10601 1.70493 1.21447 0.82551
0.94352 1.02252 1.19557 0.83271 0.90673 0.75728
1.90983 1.50461 1.49912 1.55748 1.45251 1.07830
1.11475 1.69179 1.21307 1.00868 0.81445 1.03340
0.89106 0.89232 0.89220 0.73042 0.86968 0.73476
0.89855 0.91111 0.91112 1.21849 1.01526 1.03764
0.96137 0.88840 0.91080 0.91008
BOND ORDERS AND VALENCIES
| 1 C
1 C | 3.935599
| 1 C 2 C
2 C | 0.928055 3.844765
| 1 C 2 C 3 O
3 O | 0.048071 1.639900 1.907659
| 1 C 2 C 3 O 4 N
4 N | 0.026250 1.225701 0.169822 3.275409
| 1 C 2 C 3 O 4 N 5 C
5 C | 0.020652 0.010047 0.005765 0.932166 3.903527
| 1 C 2 C 3 O 4 N 5 C 6 C
6 C | 0.000958 0.006496 0.000133 0.004141 0.898700 3.857585
| 1 C 2 C 3 O 4 N 5 C 6 C
7 O | 0.000016 0.000080 0.000168 0.003273 0.053289 1.637855
| 7 O
| 1.919096
| 1 C 2 C 3 O 4 N 5 C 6 C
8 N | 0.000367 0.000905 0.000069 0.003979 0.025696 1.250218
| 7 O 8 N
| 0.174827 3.291695
| 1 C 2 C 3 O 4 N 5 C 6 C
9 C | 0.000172 0.000454 0.000030 0.001314 0.019394 0.010867
| 7 O 8 N 9 C
| 0.005551 0.931298 3.887264
| 1 C 2 C 3 O 4 N 5 C 6 C
10 H | 0.973594 0.003065 0.000610 0.005024 0.001913 0.000113
| 7 O 8 N 9 C 10 H
| 0.000003 0.000039 0.000020 0.988133
| 1 C 2 C 3 O 4 N 5 C 6 C
11 H | 0.968127 0.006189 0.007579 0.002907 0.000014 0.000002
| 8 N 10 H 11 H
| 0.000001 0.001808 0.988405
| 1 C 2 C 3 O 4 N 5 C 6 C
12 H | 0.968076 0.006198 0.007584 0.002897 0.000009 0.000006
| 7 O 8 N 10 H 11 H 12 H
| 0.000001 0.000001 0.001807 0.001425 0.988380
| 1 C 2 C 3 O 4 N 5 C 6 C
13 H | 0.000622 0.009147 0.017207 0.872895 0.011643 0.000944
| 7 O 8 N 9 C 10 H 11 H 12 H
| 0.006166 0.000200 0.000030 0.000073 0.000230 0.000224
| 13 H
| 0.927325
| 1 C 2 C 3 O 4 N 5 C 6 C
14 H | 0.000037 0.003093 0.002590 0.006767 0.940213 0.007285
| 7 O 8 N 9 C 10 H 11 H 12 H
| 0.006210 0.002560 0.000088 0.000010 0.000047 0.000067
| 13 H 14 H
| 0.003618 0.983018
| 1 C 2 C 3 O 4 N 5 C 6 C
15 H | 0.000002 0.000001 0.000001 0.000030 0.000383 0.009467
| 7 O 8 N 9 C 13 H 14 H 15 H
| 0.017565 0.880493 0.012008 0.000009 0.000205 0.929648
| 1 C 2 C 3 O 4 N 5 C 6 C
16 H | 0.000015 0.000040 0.000003 0.000109 0.000922 0.007644
| 7 O 8 N 9 C 10 H 13 H 14 H
| 0.000047 0.003070 0.970723 0.000002 0.000001 0.000007
| 15 H 16 H
| 0.000514 0.989709
| 4 N 5 C 6 C 7 O 8 N 9 C
17 H | 0.000001 0.000013 0.004027 0.003023 0.006381 0.967402
| 14 H 15 H 16 H 17 H
| 0.000053 0.003502 0.003297 0.992098
| 2 C 4 N 5 C 6 C 7 O 8 N
18 H | 0.000001 0.000004 0.000024 0.004009 0.003007 0.006381
| 9 C 14 H 15 H 16 H 17 H 18 H
| 0.967417 0.000062 0.003526 0.003301 0.004294 0.992101
| 1 C 2 C 3 O 4 N 5 C 6 C
19 C | 0.000211 0.004223 0.004918 0.009987 0.972453 0.007775
| 7 O 8 N 9 C 10 H 11 H 12 H
| 0.006839 0.004480 0.000361 0.000012 0.000072 0.000073
| 13 H 14 H 15 H 16 H 17 H 18 H
| 0.003282 0.003721 0.000483 0.000006 0.000089 0.000070
| 19 C
| 3.937208
| 1 C 2 C 3 O 4 N 5 C 6 C
20 H | 0.000009 0.000352 0.002780 0.000331 0.002560 0.006411
| 7 O 8 N 9 C 10 H 12 H 13 H
| 0.001054 0.000526 0.000053 0.000003 0.000001 0.000052
| 14 H 15 H 16 H 17 H 18 H 19 C
| 0.000300 0.000008 0.000006 0.000013 0.000004 0.969216
| 20 H
| 0.987544
| 1 C 2 C 3 O 4 N 5 C 6 C
21 H | 0.000346 0.000544 0.000410 0.007273 0.004083 0.000116
| 7 O 8 N 9 C 10 H 11 H 12 H
| 0.000091 0.000140 0.000033 0.000031 0.000003 0.000010
| 13 H 14 H 15 H 19 C 20 H 21 H
| 0.000889 0.000019 0.001451 0.972471 0.001857 0.992043
| 1 C 2 C 3 O 4 N 5 C 6 C
22 H | 0.000018 0.000275 0.000019 0.000537 0.003589 0.000418
| 7 O 8 N 9 C 10 H 11 H 12 H
| 0.000030 0.000064 0.000048 0.000006 0.000001 0.000001
| 13 H 14 H 16 H 18 H 19 C 20 H
| 0.000091 0.006065 0.000002 0.000001 0.976466 0.002007
| 21 H 22 H
| 0.002277 0.991914
ELAPSED WALL CLOCK TIME : 0.28 SECONDS
FULL COMPUTATION TIME : 0.34 SECONDS
|
The Van der Waals radii for each element used in the COSMO calculation. These default values may be overridden using the VDW keyword. |
|
|
The solvation energy is directly included in the heat of formation and total energy. |
|
|
Total surface area in the COSMO calculation. |
|
|
COSMO polarization energy. |
The AMSOL module methods provide a powerful alternative to COSMO. AMSOL comes in several variants as described in Chapter 15, AMSOL Model Module. As an example, trichloroethane in cyclohexane using SM5.2R is shown.
mndo rhf singlet 1scf t=auto sm5.2r trues hgas=-4.746588 +
solvnt='cyclohexane'
* trichloroethene in cyclohexane using SM5.2R/MNDO//HF/MIDI!
Comment
C 0.000000 0 0.000000 0 0.000000 0 0 0 0
C 1.311640 1 0.000000 0 0.000000 0 1 0 0
Cl 1.730281 1 124.579000 1 0.000000 0 2 1 0
Cl 1.728890 1 124.400000 1 0.000000 1 1 2 3
Cl 1.739642 1 120.664000 1 180.000000 1 1 2 3
H 1.069610 1 120.689000 1 180.000000 1 2 1 3
0 0.000000 0 0.000000 0 0.000000 0 0 0 0
|
SM5.2R has been specified as the solvation method. Keyword 1SCF is required because SM5.2R specifies a rigid solvation model. TRUES specifies that the true solvation free energy is to be computed and requires HGAS to be specified as well. HGAS gives gas phase heat of formation, which is determined by a gas-phase MNDO calculation. (The input geometry, which is used for both the gas-phase and the liquid-phase MNDO calculations, was calculated at the HF/MIDI! level.) |
Timestamp: 2011-08-31-12-53-47-00000012E8-win64
User Info: John Millam, Nahum,
SUMMARY OF MNDO CALCULATION
Aug-31-2011
AMPAC Version 10.0.1
Presented by:
Semichem, Inc.
www.semichem.com
FORMULA: C2H1Cl3
* trichloroethene in cyclohexane using SM5.2R/MNDO//HF/MIDI!
Comment
1SCF WAS SPECIFIED, SO NO OPTIMIZATION ATTEMPTED
SCF FIELD WAS ACHIEVED
FINAL HEAT OF FORMATION = -8.011427 kcal **
= -33.527822 kJ **
ELECTRONIC ENERGY = -3262.832096 eV
CORE-CORE REPULSION = 1929.372898 eV
TOTAL ENERGY = -1333.459198 eV **
SM5.2 POLARIZATION ENERGY = -0.020335 eV
G-CDS ENERGY = -0.124203 eV
DIELECTRIC CONSTANT = 2.016500
GRADIENT NORM = 0.000000
RMS GRADIENT NORM = 0.000000
DIPOLE = 1.257532 debyes
MOLECULAR WEIGHT = 131.388900
MOLECULAR POINT GROUP = Cs 0.100000
NO. OF FILLED LEVELS = 15 (OCC = 2)
TOTAL NUMBER OF ORBITALS = 21
COMPUTATION TIME = 0.25 SECONDS
** ENERGY INCLUDES SOLVATION ENERGY
Atom Chemical Partial Polarization Area G-CDS G-P + M
number symbol charge free energy G-CDS value
(kcal) (Ang**2) (kcal) (kcal)
1 C 0.02 -0.01 6.92 0.04 0.02 11
2 C 0.03 -0.05 10.36 0.06 0.01 11
3 Cl -0.07 0.03 28.76 -1.21 -1.18 11
4 Cl -0.04 -0.02 28.50 -1.20 -1.22 11
5 Cl -0.06 0.01 28.90 -1.22 -1.21 11
6 H 0.12 -0.42 7.97 -0.28 -0.71 11
Total: 0.00 -0.47 111.40 -3.82 -4.29
1SCF run. The solvation energy has been calculated at the input geometry.
If that was an optimized gas-phase geometry, the result may be denoted SM5.2R.
If the input geometry was not an optimized gas-phase geometry,
the result should be labeled as a non-optimized SM5.2 calculation.
This is a breakdown of the solvation energy calculated
without geometric relaxation in solution:
(0) E-EN(g) gas-phase electronic-nuclear energy -4.747 kcal
This is a breakdown of the true solvation energy:
(1) E-EN(s) electronic-nuclear energy of solute -4.678 kcal
(2) G-P(s) polarization free energy of solvation -0.469 kcal
(3) G-ENP(s) elect.-nuc.-pol. free energy of system = (1) + (2) -5.147 kcal
(4) G-CDS(s) cavity-dispersion-solvent structure free energy -2.864 kcal
(5) G-P-CDS(s) = G-P(s) + G-CDS(s) = (2) + (4) -3.333 kcal
(6) G-S(s) free energy of system = (1) + (5) -8.011 kcal
(7) DeltaE-EN(s) elect.-nuc. reorganization energy of solute 0.068 kcal
(7) = (1) - (0)
(8) DeltaG-ENP(s) elect.-nuc.-pol. free energy of solvation -0.401 kcal
(8) = (3) - (0)
(9) DeltaG-S(s) free energy of solvation -3.265 kcal
(9) = (6) - (0) = (5) + (7)
FINAL GEOMETRY OBTAINED CHARGE
MNDO RHF SINGLET 1SCF T=AUTO SM5.2R TRUES HGAS=-4.746588 +
SOLVNT='CYCLOHEXANE'
* trichloroethene in cyclohexane using SM5.2R/MNDO//HF/MIDI!
Comment
C 0.000000 0 0.000000 0 0.000000 0 0 0 0 0.0220
C 1.311640 1 0.000000 0 0.000000 0 1 0 0 0.0299
Cl 1.730281 1 124.579000 1 0.000000 0 2 1 0 -0.0693
Cl 1.728890 1 124.400000 1 0.000000 1 1 2 3 -0.0444
Cl 1.739642 1 120.664000 1 180.000000 1 1 2 3 -0.0559
H 1.069610 1 120.689000 1 180.000000 1 2 1 3 0.1178
0 0.000000 0 0.000000 0 0.000000 0 0 0 0
|
The solvation energy is directly included in the heat of formation and total energy. |
|
|
Table of the atom-by-atom solvent-accessible surface area and the atom-by-atom solvation free energy. This output can be suppressed by specifying AMSPRNT=0. |
|
|
Summary information about the solvation calculation including the total solvation free energy. |
Timestamp: 2011-08-31-12-53-47-00000012E8-win64
User Info: John Millam, Nahum,
*******************************************************************************
MNDO CALCULATION RESULTS
*******************************************************************************
* AMPAC Version 10.0.1
* Presented by:
*
* Semichem, Inc.
* www.semichem.com
*
* MNDO - THE MNDO HAMILTONIAN TO BE USED
* RHF - RESTRICTED HARTREE-FOCK CALCULATION
* 1SCF - READ KEYWORD BUT DO 1 SCF AND THEN STOP
* T=AUTO - AUTOMATIC DETERMINATION OF ALLOWED TIME
* SM5.2R - SOLVATION MODEL IN USE
* SOLVNT - CYCLOHEXANE
* TRUES - TRUE SOLVATION FREE ENERGY CALCULATED USING
* HGAS= - GAS-PHASE HEAT OF FORMATION = -4.746588
* SINGLET - IS THE REQUIRED SPIN MULTIPLICITY
*******************************************************************************
MNDO RHF SINGLET 1SCF T=AUTO SM5.2R TRUES HGAS=-4.746588 +
SOLVNT='CYCLOHEXANE'
* trichloroethene in cyclohexane using SM5.2R/MNDO//HF/MIDI!
Comment
ATOM CHEMICAL BOND LENGTH BOND ANGLE TWIST ANGLE
NUMBER SYMBOL (ANGSTROMS) (DEGREES) (DEGREES)
(I) NA:I NB:NA:I NC:NB:NA:I NA NB NC
1 C
2 C 1.31164 * 1
3 Cl 1.73028 * 124.57900 * 2 1
4 Cl 1.72889 * 124.40000 * 0.00000 * 1 2 3
5 Cl 1.73964 * 120.66400 * 180.00000 * 1 2 3
6 H 1.06961 * 120.68900 * 180.00000 * 2 1 3
MOLECULAR POINT GROUP SYMMETRY CRITERIA
Cs 0.10000000
SINGLET STATE CALCULATION
RHF CALCULATION, NO. OF DOUBLY OCCUPIED LEVELS = 15
** REFERENCES TO PARAMETERS **
H (MNDO): M.J.S. DEWAR, W. THIEL, J. AM. CHEM. SOC., 99, 4899, (1977)
C (MNDO): M.J.S. DEWAR, W. THIEL, J. AM. CHEM. SOC., 99, 4899, (1977)
Cl (MNDO): M.J.S.DEWAR, H.S.RZEPA, J. COMP. CHEM., 4, 158, (1983)
-------------------------
* External Contributors *
-------------------------
SMx Solvation Models:
---------------------
The SMx solvation models found in AMPAC were contributed from the University
of Minnesota by Gregory D. Hawkins, Daniel A. Liotard, Christopher J. Cramer,
and Donald G. Truhlar.
CARTESIAN COORDINATES
ATOM X Y Z
1 C 0.00000000 0.00000000 0.00000000
2 C 1.31164000 0.00000000 0.00000000
3 Cl 2.29364716 1.42461724 0.00000000
4 Cl -0.97676580 1.42653048 0.00000000
5 Cl -0.88722187 -1.49639288 0.00000000
6 H 1.85754523 -0.91981141 0.00000000
SM5x. SOLVENT= CYCLOHEXANE
DIELEC= 2.0165 REFRCT=1.4266 ALPHA=0.00 BETA=0.00 GAMMA=35.48
FACARB= 0.00 FEHALO= 0.00
MNDO RHF SINGLET 1SCF T=AUTO SM5.2R TRUES HGAS=-4.746588 +
SOLVNT='CYCLOHEXANE'
* trichloroethene in cyclohexane using SM5.2R/MNDO//HF/MIDI!
Comment
1SCF WAS SPECIFIED, SO NO OPTIMIZATION ATTEMPTED
SCF FIELD WAS ACHIEVED
MNDO CALCULATION
VERSION 10.0.1
Aug-31-2011
FINAL HEAT OF FORMATION = -8.011427 kcal **
= -33.527822 kJ **
ELECTRONIC ENERGY = -3262.832096 eV
CORE-CORE REPULSION = 1929.372898 eV
TOTAL ENERGY = -1333.459198 eV **
SM5.2 POLARIZATION ENERGY = -0.020335 eV
G-CDS ENERGY = -0.124203 eV
DIELECTRIC CONSTANT = 2.016500
GRADIENT NORM = 0.000000
RMS GRADIENT NORM = 0.000000
MOLECULAR WEIGHT = 131.388900
MOLECULAR POINT GROUP = Cs 0.100000
NO. OF FILLED LEVELS = 15 (OCC = 2)
TOTAL NUMBER OF ORBITALS = 21
SCF CALCULATIONS = 1
COMPUTATION TIME = 0.23 SECONDS
** ENERGY INCLUDES SOLVATION ENERGY
ATOM CHEMICAL BOND LENGTH BOND ANGLE TWIST ANGLE
NUMBER SYMBOL (ANGSTROMS) (DEGREES) (DEGREES)
(I) NA:I NB:NA:I NC:NB:NA:I NA NB NC
1 C
2 C 1.31164 * 1
3 Cl 1.73028 * 124.57900 * 2 1
4 Cl 1.72889 * 124.40000 * 0.00000 * 1 2 3
5 Cl 1.73964 * 120.66400 * 180.00000 * 1 2 3
6 H 1.06961 * 120.68900 * 180.00000 * 2 1 3
MOLECULAR POINT GROUP SYMMETRY CRITERIA
Cs 0.10000000
RHF EIGENVALUES
-37.37318 -27.46030 -26.22117 -25.69276 -22.69433 -18.41297
-17.45721 -15.41691 -14.97508 -13.88174 -13.48097 -13.38916
-13.10565 -12.84526 -10.70397 -0.35773 -0.27620 0.17690
1.30988 3.78079 4.56681
NET ATOMIC CHARGES AND DIPOLE CONTRIBUTIONS
ATOM CHARGE ATOM ELECTRON DENSITY
1 C 0.0220 3.9780
2 C 0.0299 3.9701
3 Cl -0.0693 7.0693
4 Cl -0.0444 7.0444
5 Cl -0.0559 7.0559
6 H 0.1178 0.8822
DIPOLE (DEBYE) X Y Z TOTAL
POINT-CHG. 0.922 -0.897 0.000 1.287
HYBRID -0.066 -0.024 0.000 0.071
SUM 0.856 -0.921 0.000 1.258
CARTESIAN COORDINATES
ATOM X Y Z
1 C 0.00000000 0.00000000 0.00000000
2 C 1.31164000 0.00000000 0.00000000
3 Cl 2.29364716 1.42461724 0.00000000
4 Cl -0.97676580 1.42653048 0.00000000
5 Cl -0.88722187 -1.49639288 0.00000000
6 H 1.85754523 -0.91981141 0.00000000
ATOMIC ORBITAL ELECTRON POPULATIONS
1.21309 0.87937 0.79291 1.09268 1.21713 0.88199
0.87543 0.99558 1.98131 1.70277 1.41961 1.96562
1.98121 1.71124 1.38043 1.97154 1.98197 1.76503
1.33432 1.97457 0.88219
POLARIZATION FREE ENERGY
= -0.2520*Sum-over-k-and-k'(q(k)*q(k')*gamma(k,k'))
= -83.7 kcal*Angstrom*Sum-over-k-and-k'(q(k)*q(k')/f(k,k'))
Atom Chemical Partial Polarization Area G-CDS G-P + M
number symbol charge free energy G-CDS value
(kcal) (Ang**2) (kcal) (kcal)
1 C 0.02 -0.01 6.92 0.04 0.02 11
2 C 0.03 -0.05 10.36 0.06 0.01 11
3 Cl -0.07 0.03 28.76 -1.21 -1.18 11
4 Cl -0.04 -0.02 28.50 -1.20 -1.22 11
5 Cl -0.06 0.01 28.90 -1.22 -1.21 11
6 H 0.12 -0.42 7.97 -0.28 -0.71 11
CS Contribution 111.40 8.60 8.60
Total: 0.00 -0.47 111.40 4.78 4.31
By element:
Atomic # 1 Polarization: -0.42 CDS: -0.28 Total: -0.71 kcal
Atomic # 6 Polarization: -0.06 CDS: 0.10 Total: 0.03 kcal
Atomic # 17 Polarization: 0.02 CDS: -3.63 Total: -3.61 kcal
Total CS contribution 8.60 Total: 8.60 kcal
Total: -0.47 -2.86 -3.33 kcal
* trichloroethene in cyclohexane using SM5.2R/MNDO//HF/MIDI!
Comment
1SCF run. The solvation energy has been calculated at the input geometry.
If that was an optimized gas-phase geometry, the result may be denoted SM5.2R.
If the input geometry was not an optimized gas-phase geometry,
the result should be labeled as a non-optimized SM5.2 calculation.
This is a breakdown of the solvation energy calculated
without geometric relaxation in solution:
(0) E-EN(g) gas-phase electronic-nuclear energy -4.747 kcal
This is a breakdown of the true solvation energy:
(1) E-EN(s) electronic-nuclear energy of solute -4.678 kcal
(2) G-P(s) polarization free energy of solvation -0.469 kcal
(3) G-ENP(s) elect.-nuc.-pol. free energy of system = (1) + (2) -5.147 kcal
(4) G-CDS(s) cavity-dispersion-solvent structure free energy -2.864 kcal
(5) G-P-CDS(s) = G-P(s) + G-CDS(s) = (2) + (4) -3.333 kcal
(6) G-S(s) free energy of system = (1) + (5) -8.011 kcal
(7) DeltaE-EN(s) elect.-nuc. reorganization energy of solute 0.068 kcal
(7) = (1) - (0)
(8) DeltaG-ENP(s) elect.-nuc.-pol. free energy of solvation -0.401 kcal
(8) = (3) - (0)
(9) DeltaG-S(s) free energy of solvation -3.265 kcal
(9) = (6) - (0) = (5) + (7)
ELAPSED WALL CLOCK TIME : 0.23 SECONDS
FULL COMPUTATION TIME : 0.25 SECONDS
|
Parameters for the specified solvent. This will appear only for named organic solvents
( SOLVNT=' |
|
|
The solvation energy is directly included in the heat of formation and total energy. |
|
|
Table of the atom-by-atom solvent-accessible surface area and the atom-by-atom solvation free energy. This output can be suppressed by specifying AMSPRNT=0. |
|
|
Summary information about the solvation calculation including the total solvation free energy. |
 |
Copyright © 1992-2013 Semichem, Inc. All rights reserved. |
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 |
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| Chapter 21. A Simple Example of Using Configuration Interaction |  |
Chapter 23. Cartesian Frequencies and Thermodynamics (FORCE) |