MOPAC output example from Molecular Modeling Pro and
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description
Figure 1. Starting geometry
for fluoxetine, the molecule used in the following example. After the molecule is drawn in, go to the
Tools menu and select "MOPAC". Atom types supported by
MOPAC v. 6 methods: MNDO: H, Li, Be, B, C, N, O, F, Na, Al, Si, P,
S, Cl, K, Cr, Zn, Ge, Br, Sn, I, Hg, Pb MINDO: H, C, N, O, F, P, S, Cl AM1: H, B, C, N, O, F, Na, Al, Si, P, S, Cl, K,
Zn, Ge, Br, I, Hg PM3: H, C, N, O, F, Na, Mg, Al, Si, P, S, Cl,
K, Zn, Ga, Ge, As, Se, Br, Cd, In, Sn, Sb, Te, I, Hg, Tl, Pb, Bi |
Figure 2. The MOPAC options panel. In this example we have checked the PM3 and
Force options. If the keyword does not
appear in the checkboxes, type it into the "Other options" text
box. Hit Done after you have selected
options. ROT = : C1 CI CS =
1; C2 C2V C2H = 2; C3 C3V C3H = 3; C4 C4V C4H = 4; C6 C6V C6H = 6; D2 D2D D2H
= 4; D3 D3D D3H = 6; D4 D4D D4H = 8; D6 D6D D6H =12; S6 = 3; C(INF)V =1 ;
D(INF)H =2; T TD =12; OH = 24. ROT =
the rotational contributions to the thermodynamic quantities of the symmetry
number of the molecule. The symmetry
number is the number of equivalent positions attainable by pure
rotation. No reflections or improper
rotations are allowed. THEMO (Thermodynamics)
calculations require the FORCE and ROT keywords. |
**
32-bit Microsoft Windows, Victor Lobanov, 1996, University of
Florida ** **
max number of heavy atoms = 50,
max number of light atoms = 100 ** ******************************************************************************* PM3
CALCULATION RESULTS ******************************************************************************* *
MOPAC: VERSION 6.00 CALC'D. *
T= - A TIME OF 3600.0 SECONDS REQUESTED *
DUMP=N - RESTART FILE WRITTEN
EVERY 3600.0 SECONDS *
FORCE - FORCE CALCULATION
SPECIFIED *
PM3 - THE PM3 HAMILTONIAN
TO BE USED ***********************************************************************050BY100 PM3
FORCE T=3600 fluoxetine MOPAC calculations:
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 1.40000 * 1
3 C 1.40000
* 120.04090 * 2 1
4 C 1.40000 *
120.00010 * .00000
* 3 2
1
5 C 1.40087 *
119.93860 * .00000
* 1 2
3
6 H 1.08400 *
120.03070 * 180.00000
* 1 2
3
7 O 1.36000 *
119.97960 * 180.00000
* 2 3
4
8 C 1.40000 *
120.02040 * .00000
* 5 1
2
9 H 1.08400 *
119.98980 * 180.00000
* 5 1
2
10 H 1.08400 *
120.00000 * 180.00000
* 3 2
1
11 C 1.42600 *
109.47120 * .00000
* 7 2
3
12 C 1.50500 *
120.00000 * 180.00000
* 8 5 1
13 H 1.08400 *
120.00010 * 180.00000
* 4 3
2
14 C 1.51000 *
109.47120 * 180.00000
* 11 7
2
15 C 1.54450 *
109.47120 * 59.99978
* 11 7
2
16 H
1.09100 * 109.47120 *
-59.99980 * 11
7 2
17 C 1.40000 *
120.03070 * 180.00000
* 14 11
7
18 C 1.40087 *
120.03070 * .00000
* 14 11
7
19 C 1.40000 *
120.04090 * 180.00000
* 17 14
11
20 H 1.08400 *
119.97950 * .00000
* 17 14
11
21 C 1.40000 *
120.02050 * 180.00000
* 18 14
11
22 H 1.08400 *
119.98980 * .00000
* 18 14
11
23 C 1.40000 *
120.00000 * .00000
* 19 17
14
24 H 1.08400 *
120.00000 * 180.00000
* 19 17
14
25 H 1.08400 *
120.00000 * 180.00000
* 21 18
14
26 H 1.08400 *
120.00000 * 180.00000
* 23 19
17
27 C 1.53700 *
109.47120 * 180.00000
* 15 11
7
28 H 1.09100 *
109.47120 * 59.99978
* 15 11
7
29 H 1.09100 *
109.47120 * -59.99980
* 15 11
7
30 N 1.47200 *
108.00000 * 180.00000
* 27 15
11
31 H 1.09100 *
109.83780 * 60.22756
* 27 15
11
32 H 1.09100 *
110.32770 * -59.34290
* 27 15
11
33 C 1.47200 *
108.00000 * 180.00000
* 30 27
15
34 H 1.00800 *
109.83770 * 60.22758
* 30 27
15
35 H 1.09100 *
109.47120 * 180.00000
* 33 30
27
36 H 1.09100 *
109.47130 * 59.99981
* 33 30
27
37 H 1.09100 *
109.47120 * -59.99980
* 33 30
27
38 F 1.33300 *
109.47120 * 180.00000
* 12 8
5
39 F 1.33300 *
109.47120 * 59.99978
* 12 8
5
40 F 1.33300 *
109.47130 * -59.99970
* 12 8
5
CARTESIAN COORDINATES
NO. ATOM X Y
Z
1 C .0000 .0000
.0000
2 C 1.4000 .0000
.0000
3 C 2.1009 1.2119
.0000
4 C 1.4017 2.4249
.0000
5 C -.6991 1.2139
.0000
6 H -.5425 -.9385
.0000
7 O 2.0796 -1.1780
.0000
8 C .0017 2.4259
.0000
9 H -1.7831 1.2149
.0000
10 H 3.1849 1.2112
.0000
11 C 3.4817 -.9180
.0000
12 C -.7498 3.7298
.0000
13 H 1.9444 3.3633
.0000
14 C 4.2362 -2.2259
.0000
15 C 3.8551 -.1082
1.2611
16 H 3.7454 -.3460
-.8908
17 C 5.6362 -2.2272
.0000
18 C 3.5360 -3.4392
.0000
19 C 6.3360 -3.4397
.0000
20 H 6.1787 -1.2887
.0000
21 C 4.2358 -4.6518
.0000
22 H 2.4520 -3.4392
.0000
23 C 5.6358 -4.6521
.0000
24 H 7.4200 -3.4399
.0000
25 H 3.6936 -5.5905
.0000
26 H 6.1776 -5.5909
.0000
27 C 5.3663 .1721
1.2611
28 H 3.5913 -.6802
2.1519
29 H 3.3099 .8368
1.2611
30 N 5.6859 .9433
2.4735
31 H 5.6361 .7476
.3744
32 H 5.9255 -.7646
1.2493
33 C 7.1332 1.2118
2.4735
34 H 5.4366 .4116
3.2927
35 H 7.3970 1.7838
3.3643
36 H 7.3970 1.7838
1.5827
37 H 7.6784 .2668
2.4735
38 F .1171 4.7423
.0000
39 F -1.5161 3.8009
1.0884
40 F -1.5162 3.8009
-1.0884 H:
(PM3): J. J. P. STEWART, J. COMP. CHEM.
10, 209 (1989). C:
(PM3): J. J. P. STEWART, J. COMP. CHEM.
10, 209 (1989). N:
(PM3): J. J. P. STEWART, J. COMP. CHEM.
10, 209 (1989). O: (PM3):
J. J. P. STEWART, J. COMP. CHEM.
10, 209 (1989). F: (PM3): J. J. P. STEWART, J. COMP. CHEM. 10, 209 (1989). |
Figure 3. The first part of the MOPAC output contains
the header with the keywords used and the original starting geometry. Here we specified the PM3 and FORCE
keywords. |
CYCLE:
54 TIME: .71 TIME LEFT: 3582.6 GRAD.: 1.984 HEAT:-148.5333 HERBERTS TEST SATISFIED - GEOMETRY OPTIMIZED |
Figure 4. Make sure that you see the word
"satisfied" somewhere in the section describing optimization of
geometry in the print-out. Otherwise
you may want to re-run the job with a different starting geometry or use the
GEO-OK keyword. |
FINAL HEAT OF FORMATION =
-148.53332 KCAL
TOTAL ENERGY = -4068.76037 EV
ELECTRONIC ENERGY = -26504.69534 EV
CORE-CORE REPULSION = 22435.93497 EV
IONIZATION POTENTIAL = 9.43788
NO. OF FILLED LEVELS = 59
MOLECULAR WEIGHT = 309.331
SCF CALCULATIONS = 70
COMPUTATION TIME = 17.520
SECONDS |
Figure 5. Some molecular
properties are calculated and listed in the MOPAC output. Total energy is obtained by adding the
electronic and nuclear (core-core repulsion) terms. |
EIGENVALUES -42.13589 -40.07828 -37.73502 -36.18697
-33.31150 -32.15972 -30.38707 -29.91798 -29.17670
-27.80775 -25.52086 -24.43056 -24.11096 -22.89517 -22.55156 -22.03164 -21.91026 -21.17663 -20.35929 -20.11519
-19.29631 -18.92290 -18.84656 -18.73410 -18.53598 -17.30181 -16.89974 -16.87843
-16.78064 -16.53757 -16.40417 -16.16978 -16.02944
-15.88430 -15.81132 -15.72932 -15.56671 -15.29560 -15.23757 -15.13248 -14.90351 -14.63184 -14.29400 -14.05873
-13.83685 -13.56941 -13.32018 -13.18359 -13.05904 -12.91737 -12.65500 -12.48564
-12.29419 -11.98834 -10.39627 -10.01499
-9.88280 -9.70706 -9.43788
-.38791 -.16249 .01144
.15362 1.28122
1.69908 2.07155 2.38452
2.44376 2.54428 2.67768
2.76329 2.83535
2.94947 3.06670 3.08419
3.11271 3.17194 3.20430
3.31893 3.36635
3.43797 3.52969 3.57431
3.64486 3.70275 3.78035
3.84691 3.94869
4.13230 4.15338 4.25532
4.31244 4.38297 4.45546
4.68703 4.73059
4.76490 4.93038 5.00820
5.08249 5.38298 5.45135
5.55310 5.84846 5.91692 6.08812 |
Figure 6. From the Eigenvalue table you can obtain
the HOMO and LUMO values of the molecule in EV. Usually there is an obvious break point in
the eigenvalues, typically where the number goes from positive to negative. However above these numbers are both
negative (HOMO = -9.43788 EV, LUMO = -0.16249 EV)(HOMO = highest occupied
molecular orbital, LUMO = lowest unoccupied molecular orbital). These eigenvalues are solutions of the
Shrodinger equation. |
NET ATOMIC CHARGES AND DIPOLE
CONTRIBUTIONS ATOM NO.
TYPE CHARGE ATOM
ELECTRON DENSITY
1 C -.1519 4.1519
2 C .1339 3.8661
3 C -.2006 4.2006
4 C .0045 3.9955
5 C -.0083 4.0083
6 H .1280 .8720
7 O -.1804 6.1804
8 C -.2287 4.2287
9 H .1160 .8840
10 H .1272 .8728
11 C .1087 3.8913
12 C .4084 3.5916
13 H .1177 .8823
14 C -.0991 4.0991
15 C -.1349 4.1349
16 H .0706 .9294
17 C -.1110 4.1110
18 C -.0726 4.0726
19 C -.0989 4.0989
20 H .1107 .8893
21 C -.1016 4.1016
22 H .1180 .8820
23 C -.0965 4.0965
24 H .1045 .8955
25 H .1052 .8948
26 H .1048 .8952
27 C -.1022 4.1022
28 H .0703 .9297
29 H .0787 .9213
30 N -.0561 5.0561
31 H .0548 .9452
32 H .0409 .9591
33 C -.0998 4.0998
34 H .0474 .9526
35 H .0483 .9517
36 H .0463 .9537
37 H .0199 .9801
38 F -.1386 7.1386
39 F -.1417 7.1417
40 F -.1419 7.1419 DIPOLE X Y Z TOTAL POINT-CHG. 2.380
-2.468 .174 3.433 HYBRID 1.255 -.742
-.647 1.595 SUM 3.636 -3.209
-.473 4.873 |
Figure 7. The calculated
dipole moment is 4.873 debyes. If you
line the molecule up so that its maximum length is along the x axis and
maximum width along the y axis, then comparison of the X, Y and Z components
of this molecule to other similarly oriented molecules becomes
meaningful. The point charges and
electron densities for each atom are also listed. Note the relationship between position on
the periodic table, electron density and partial charge (e.g. positive core
charge [H=1, C=4, O=6 etc.] - number of valence electrons [electron density
number] = partial charge in
electrons). |
CARTESIAN COORDINATES
NO. ATOM X Y Z
1 C .0000 .0000
.0000
2 C 1.4062 .0000
.0000
3 C 2.1172 1.2070
.0000
4 C 1.4261 2.4115
.0035
5 C -.6763 1.2091
.0005
6 H -.5565 -.9447
-.0029
7 O 1.9643 -1.2542
-.0312
8 C .0345 2.4118
.0043
9 H -1.7727 1.2274
-.0006
10 H 3.2177 1.1984
-.0042
11 C 3.3870 -1.3492
.1285
12 C -.7617 3.7114
.0089
13 H 1.9866 3.3539
.0051
14 C 3.8672 -2.5610
-.6357
15 C 3.7380 -1.4650
1.6267
16 H 3.8757 -.4350
-.3081
17 C 5.2370 -2.6539
-.9039
18 C 3.0163 -3.5780
-1.0664 19
C 5.7445 -3.7352
-1.6108
20 H 5.9136 -1.8725
-.5234
21 C 3.5296 -4.6602
-1.7763
22 H 1.9411 -3.5401
-.8573
23 C 4.8888 -4.7394
-2.0538
24 H 6.8177 -3.7969
-1.8185
25 H 2.8551 -5.4530
-2.1172
26 H 5.2868 -5.5903
-2.6163
27 C 5.1214 -.8800
1.8915
28 H 3.6858 -2.5267
1.9418
29 H 2.9802 -.9370
2.2412
30 N 5.5156 -1.0773
3.3083
31 H 5.1193 .2128
1.6985
32 H 5.8607 -1.3166
1.1727
33 C 6.8645 -.5674
3.6064
34 H 5.4588 -2.0468
3.5411
35 H 7.0849 -.7459
4.6664
36 H 6.8922 .5161
3.4301
37 H 7.6633 -1.0287
3.0047
38 F -.0272 4.8472
.0127
39 F -1.5828 3.8430
1.0779
40 F -1.5828 3.8502
-1.0592 |
Figure 8. The coordinates of the optimized molecular
geometry. These are the coordinates
that are read back into Molecular Modeling Pro and Molecular Modeling Pro
Plus. |
ATOMIC ORBITAL ELECTRON POPULATIONS
1.17777 .93382 .98517
1.05514 1.17027 .92239
.85530 .91812
1.18126 .99733 .93329
1.08871 1.16830 .92037
.97230 .93454
1.17148 .98254 .91515
.93913 .87198 1.83669
1.21582 1.25008
1.87786 1.18511 .96280
.93826 1.14257 .88397
.87284 1.17043
.81764 .96052 .94267
1.15914 .80623 .84733
.77887 .88229
1.18551 .95183 .96277
.99895 1.17177 .97993
1.03218 .95104
.92937 1.18149 .94734
.98787 .99432 1.17574
.98706 .93688
.97294 1.17824 .98281
.95239 .98544 .88930
1.18042 .95770
.97703 .98644 .88202
1.17971 .94726 .97903
.99051 .89554 .89478
.89521 1.18210 .96264
1.00971 .94776 .92975
.92134
1.47891 1.23345 1.18742
1.15628 .94515 .95907
1.15078 .93273
1.00868 1.00757 .95256
.95172 .95372 .98014
1.77175 1.82297
1.57213 1.97180 1.77394
1.76453 1.96898 1.63421
1.77398 1.76468
1.96829 1.63497 |
Figure 9. The atomic orbital electron populations in
electrons. |
PRINCIPAL MOMENTS OF INERTIA IN CM(-1)
A = .014222 B =
.003855 C = .003252
PRINCIPAL MOMENTS OF INERTIA IN UNITS OF 10**(-40)*GRAM-CM**2
A = 1968.332005 B =
7260.768676 C = 8606.615691 |
Figure 10. Since we specified the FORCE keyword, the moments
of inertia are printed out. Following
these number are the matrices and vibrational contributions from which the
moments of inertia are derived. |
NOTICE of the Public Domain nature of MOPAC version 6:
the MOPAC computer program is a work of the United
States Government and as such is not subject to protection by copyright. You may freely distribute the MOPAC.EXE file
packaged with this program.