Subject: Computational Chemistry

From: "Julie M. Desrosiers" <[email-masked]>
Date: Thu, 6 Jun 1996 13:40:01 -0400

ATTENTION:  Students and Educators of Computational Chemistry

Available as of June 1996

The first in a series of tutorials in computational chemistry, edited by
Dr. Tim Clark, author of the leading "Handbook of Computational Chemistry"
and editor of the "Journal of Molecular Modeling".

The first tutorial covers semiempirical molecular orbital theory and is
targeted at students, educators and experimental chemists.  It blends
theory and practical applications through the use of examples based on
widely used modeling programs.

Initially available in English, the tutorial will also be available in
Japanese, German and French later in 1996.

The initial introductory price will be US $49 per tutorial (US $39 in
electronic form) with a total price of US $250 for the whole set.  The
entire set consists of six tutorials covering semiempirical MO theory,
force fields, ab initio MO theory, spectroscopy, QSAR and application
examples in computational chemistry.

For more information and a list of contents/example chapter, please contact

                                 http://www.sciencelearn.com

Science Learning Ltd.
http://www.sciencelearn.com

---

From: A J Turner <[email-masked]>
Date: Thu, 6 Jun 1996 23:21:04 +0100 (BST)

Hi!

I have been approached by a couple of people over this mopac deck
that caused some problems for me. I include the .dat and .out files.
My concern is that the C to which the Cl is bonded has a charge (in
the esp calc) which is highly negative whilst the Cl has a small
positive  charge.

It has been brought to my attention that Mopac93 _revision_2_ should
have a bug fix (Dr J Stuart - thanks), But I have not had time to
check this out yet.

I will forward any more info should the ccl users be interested.

best wishes

Alex

PS I seem to have more luck using natural atomic charges in  VAMP.

			--==INPUT ==--

 AM1  esp

  C    0.00000000  0    0.0000000  0    0.0000000  0    0    0    0
-0.0998
  H    1.11678955  1    0.0000000  0    0.0000000  0    1    0    0
0.0901
  H    1.11860861  1  110.5001057  1    0.0000000  0    1    2    0
0.0965
  H    1.11804978  1  111.0078215  1  124.1366815  1    1    2    3
0.1255
  O    1.42977966  1  109.6919909  1 -121.1538376  1    1    2    3
-0.3183
  C    1.39974700  1  114.4456389  1   68.8811837  1    5    1    2
0.0316
  H    1.11840798  1  106.4911216  1  161.8104747  1    6    5    1
0.1699
  H    1.11884361  1  112.9830933  1   35.3301012  1    6    5    1
0.1476
 Cl    1.80283055  1  111.4239110  1  -83.0814824  1    6    5    1
-0.2448
  O    3.42808614  1   97.1266757  1   20.8564401  1    6    5    1
-0.4855
  H    0.96400805  1  126.7099492  1   68.1397632  1   10    6    5
0.2458
  H    0.96345463  1  101.2179497  1  -48.2960684  1   10    6    5
0.2415

			--== OUTPUT ==--

*******************************************************************************
 **                            MOPAC 93 (c) Fujitsu
**

*******************************************************************************

                                 AM1 CALCULATION RESULTS

*******************************************************************************
 *                   MOPAC  93.00               CALC'D. Thu Jun  6
21:13:03 1996
 *  ESP      - ELECTROSTATIC POTENTIAL CALCULATION
 *   T=      - A TIME OF  7200.0 SECONDS REQUESTED
 *  DUMP=N   - RESTART FILE WRITTEN EVERY   600.0 SECONDS
 *  AM1      - THE AM1 HAMILTONIAN TO BE USED

***********************************************************************050BY050
 AM1  ESP

    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      H         1.11679  *                                  1
      3      H         1.11861  *     110.50011  *                 1    2
      4      H         1.11805  *     111.00782  *  124.13668  *   1    2
3
      5      O         1.42978  *     109.69199  * -121.15384  *   1    2
3
      6      C         1.39975  *     114.44564  *   68.88118  *   5    1
2
      7      H         1.11841  *     106.49112  *  161.81047  *   6    5
1
      8      H         1.11884  *     112.98309  *   35.33010  *   6    5
1
      9     Cl         1.80283  *     111.42391  *  -83.08148  *   6    5
1
     10      O         3.42809  *      97.12668  *   20.85644  *   6    5
1
     11      H         0.96401  *     126.70995  *   68.13976  *  10    6
5
     12      H         0.96345  *     101.21795  *  -48.29607  *  10    6
5

          CARTESIAN COORDINATES

    NO.       ATOM         X         Y         Z

     1         C        0.0000    0.0000    0.0000
     2         H        1.1168    0.0000    0.0000
     3         H       -0.3917    1.0478    0.0000
     4         H       -0.4008   -0.5857   -0.8639
     5         O       -0.4818   -0.6964    1.1520
     6         C       -0.2447   -0.0414    2.3661
     7         H       -0.9405   -0.4970    3.1138
     8         H       -0.3181    1.0720    2.2834
     9        Cl        1.4205   -0.3666    2.9756
    10         O        0.1850    3.1050    1.0748
    11         H       -0.4902    3.6560    0.6627
    12         H        0.8024    2.9300    0.3562
  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)
  O: (AM1): M.J.S. DEWAR ET AL, J. AM. CHEM. SOC. 107 3902-3909 (1985)
 Cl: (AM1): M.J.S. DEWAR AND E. G. ZOEBISCH, THEOCHEM, 180, 1 (1988).

      MOLECULAR POINT GROUP   :   C1

      RHF CALCULATION, NO. OF DOUBLY OCCUPIED LEVELS = 17

            INTERATOMIC DISTANCES
0
                  C  1       H  2       H  3       H  4       O  5       C
6

------------------------------------------------------------------------------
     C    1   0.000000
     H    2   1.116790   0.000000
     H    3   1.118609   1.836710   0.000000
     H    4   1.118050   1.841876   1.847881   0.000000
     O    5   1.429780   2.089878   2.092237   2.020582   0.000000
     C    6   2.379071   2.730157   2.608870   3.279261   1.399747
0.000000
     H    7   3.290513   3.765019   3.518993   4.015159   2.024576
1.118408
     H    8   2.542478   2.902057   2.284688   3.558119   2.105730
1.118844
    Cl    9   3.317631   3.013493   3.760213   4.255262   2.655746
1.802831
     O   10   3.291019   3.415375   2.391717   4.209939   3.860271
3.428086
     H   11   3.747723   4.048158   2.692852   4.508895   4.379802
4.078229
     H   12   3.058734   2.968291   2.257404   3.911132   3.928561
3.736989
0
                  H  7       H  8      Cl  9       O 10       H 11       H
12

------------------------------------------------------------------------------
     H    7   0.000000
     H    8   1.881153   0.000000
    Cl    9   2.368604   2.360434   0.000000
     O   10   4.289376   2.418034   4.146323   0.000000
     H   11   4.843314   3.054999   5.018147   0.964008   0.000000
     H   12   4.731432   2.902014   4.255730   0.963455   1.513882
0.000000
 CYCLE:   1 TIME:   1.69 TIME LEFT:   7197.2 GRAD.:    11.550
HEAT:-121.8725
 CYCLE:   2 TIME:   1.02 TIME LEFT:   7196.2 GRAD.:     8.108
HEAT:-122.0686
 CYCLE:   3 TIME:   1.00 TIME LEFT:   7195.1 GRAD.:     9.042
HEAT:-122.1418
 CYCLE:   4 TIME:   1.01 TIME LEFT:   7194.1 GRAD.:     7.788
HEAT:-122.2566
 CYCLE:   5 TIME:   1.01 TIME LEFT:   7193.1 GRAD.:     7.018
HEAT:-122.2919
 CYCLE:   6 TIME:   0.71 TIME LEFT:   7192.4 GRAD.:     7.065
HEAT:-122.4400
 CYCLE:   7 TIME:   0.71 TIME LEFT:   7191.7 GRAD.:     8.147
HEAT:-122.5202
 TEST ON GRADIENT SATISFIED
                    HOWEVER, A COMPONENT OF GRADIENT IS LARGER THAN  1.00

 CYCLE:   8 TIME:   0.70 TIME LEFT:   7191.0 GRAD.:     3.310
HEAT:-122.6152
 TEST ON GRADIENT SATISFIED
                    HOWEVER, A COMPONENT OF GRADIENT IS LARGER THAN  1.00

 CYCLE:   9 TIME:   0.72 TIME LEFT:   7190.3 GRAD.:     3.743
HEAT:-122.6741
 TEST ON GRADIENT SATISFIED
                    HOWEVER, A COMPONENT OF GRADIENT IS LARGER THAN  1.00

 CYCLE:  10 TIME:   1.61 TIME LEFT:   7188.7 GRAD.:     3.376
HEAT:-122.6876
 TEST ON GRADIENT SATISFIED
                    HOWEVER, A COMPONENT OF GRADIENT IS LARGER THAN  1.00

 CYCLE:  11 TIME:   0.95 TIME LEFT:   7187.7 GRAD.:     2.627
HEAT:-122.6943
 TEST ON GRADIENT SATISFIED
                    HOWEVER, A COMPONENT OF GRADIENT IS LARGER THAN  1.00

           THERE HAVE BEEN 3 ATTEMPTS TO

REDUCE THE GRADIENT.
           DURING THESE ATTEMPTS THE ENERGY DROPPED BY LESS THAN 0.3
KCAL/MOLE
           FURTHER CALCULATION IS NOT JUSTIFIED AT THIS TIME.
           TO CONTINUE, START AGAIN WITH THE WORD "PRECISE"

-------------------------------------------------------------------------------
 AM1  ESP

     GRADIENT TEST NOT PASSED, BUT FURTHER WORK NOT JUSTIFIED
     SCF FIELD WAS ACHIEVED

                                AM1    CALCULATION
                                                       MOPAC 93.00
                                                       Thu Jun  6 21:13:19
1996

          FINAL HEAT OF FORMATION =       -122.70753 KCAL =   -513.40831
KJ

          TOTAL ENERGY            =      -1368.18421 EV
          ELECTRONIC ENERGY       =      -4002.53479 EV  POINT GROUP:
C1
          CORE-CORE REPULSION     =       2634.35058 EV

          GRADIENT NORM           =          2.20576
          IONIZATION POTENTIAL    =         10.93990
          NO. OF FILLED LEVELS    =         17
          MOLECULAR WEIGHT        =     98.529

          SCF CALCULATIONS  =               24
          COMPUTATION TIME =  13.600 SECONDS

       FINAL  POINT  AND  DERIVATIVES

   PARAMETER     ATOM    TYPE            VALUE       GRADIENT
      1          2  H    BOND            1.116799    -0.347593
KCAL/ANGSTROM
      2          3  H    BOND            1.120076     0.407521
KCAL/ANGSTROM
      3          3  H    ANGLE         110.201716     0.074788
KCAL/RADIAN
      4          4  H    BOND            1.116863    -0.991954
KCAL/ANGSTROM
      5          4  H    ANGLE         110.840081     0.200704
KCAL/RADIAN
      6          4  H    DIHEDRAL      123.221995     0.128332
KCAL/RADIAN
      7          5  O    BOND            1.421809     0.164988
KCAL/ANGSTROM
      8          5  O    ANGLE         110.321667     0.350172
KCAL/RADIAN
      9          5  O    DIHEDRAL     -121.967634     0.050739
KCAL/RADIAN
     10          6  C    BOND            1.404161     0.128443
KCAL/ANGSTROM
     11          6  C    ANGLE         114.195889    -0.100895
KCAL/RADIAN
     12          6  C    DIHEDRAL       65.471263     0.003608
KCAL/RADIAN
     13          7  H    BOND            1.118260    -0.098713
KCAL/ANGSTROM
     14          7  H    ANGLE         105.190162    -0.378939
KCAL/RADIAN
     15          7  H    DIHEDRAL      163.674507    -0.219790
KCAL/RADIAN
     16          8  H    BOND            1.119373     0.187760
KCAL/ANGSTROM
     17          8  H    ANGLE         112.681286     0.217125
KCAL/RADIAN
     18          8  H    DIHEDRAL       39.404522    -0.521225
KCAL/RADIAN
     19          9 Cl    BOND            1.779814    -0.117866
KCAL/ANGSTROM
     20          9 Cl    ANGLE         112.526966    -0.023789
KCAL/RADIAN
     21          9 Cl    DIHEDRAL      -80.506317    -0.426767
KCAL/RADIAN
     22         10  O    BOND            3.319322     0.249271
KCAL/ANGSTROM
     23         10  O    ANGLE          95.957251    -0.086942
KCAL/RADIAN
     24         10  O    DIHEDRAL       39.579346     0.051399
KCAL/RADIAN
     25         11  H    BOND            0.962387     1.115069
KCAL/ANGSTROM
     26         11  H    ANGLE         133.471007    -0.153652
KCAL/RADIAN
     27         11  H    DIHEDRAL       76.061552    -0.160365
KCAL/RADIAN
     28         12  H    BOND            0.960775    -0.753557
KCAL/ANGSTROM
     29         12  H    ANGLE         113.642023    -0.670582
KCAL/RADIAN
     30         12  H    DIHEDRAL      -64.740217     0.467094
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      H         1.11680  *                                  1
      3      H         1.12008  *     110.20172  *                 1    2
      4      H         1.11686  *     110.84008  *  123.22200  *   1    2
3
      5      O         1.42181  *     110.32167  * -121.96763  *   1    2
3
      6      C         1.40416  *     114.19589  *   65.47126  *   5    1
2
      7      H         1.11826  *     105.19016  *  163.67451  *   6    5
1
      8      H         1.11937  *     112.68129  *   39.40452  *   6    5
1
      9     Cl         1.77981  *     112.52697  *  -80.50632  *   6    5
1
     10      O         3.31932  *      95.95725  *   39.57935  *   6    5
1
     11      H         0.96239  *     133.47101  *   76.06155  *  10    6
5
     12      H         0.96078  *     113.64202  *  -64.74022  *  10    6
5

            INTERATOMIC DISTANCES
0
                  C  1       H  2       H  3       H  4       O  5       C
6

------------------------------------------------------------------------------
     C    1   0.000000
     H    2   1.116799   0.000000
     H    3   1.120076   1.834597   0.000000
     H    4   1.116863   1.839052   1.843059   0.000000
     O    5   1.421809   2.090858   2.092413   2.011092   0.000000
     C    6   2.372705   2.704175   2.635443   3.276064   1.404161
0.000000
     H    7   3.275812   3.735572   3.538804   4.003017   2.011229
1.118260
     H    8   2.554999   2.899303   2.330511   3.574457   2.106380
1.119373
    Cl    9   3.286910   2.963818   3.759574   4.216619   2.656001
1.779814
     O   10   3.378845   3.773155   2.404553   4.231754   3.735911
3.319322
     H   11   4.014383   4.550134   2.962808   4.718526   4.359106
4.042227
     H   12   3.378241   3.584533   2.375677   4.189580   4.062166
3.807729
0
                  H  7       H  8      Cl  9       O 10       H 11       H
12

------------------------------------------------------------------------------
     H    7   0.000000
     H    8   1.872377   0.000000
    Cl    9   2.358833   2.350628   0.000000
     O   10   4.007611   2.270271   4.376918   0.000000
     H   11   4.587674   3.028018   5.258932   0.962387   0.000000
     H   12   4.655196   2.836527   4.639448   0.960775   1.513877
0.000000

      MOLECULAR POINT GROUP   :   C1

                  EIGENVALUES

 -39.11753 -36.83630 -36.40134 -28.71722 -25.76450 -18.62597 -17.66089
-16.97551
 -16.88852 -15.40277 -13.81211 -13.59482 -13.05199 -12.69105 -11.52742
-11.01570
 -10.93990   1.57179   2.87550   3.73085   3.92118   4.08913   4.24695
4.38370
   4.45035   5.82484   5.95909

              NET ATOMIC CHARGES AND DIPOLE CONTRIBUTIONS

         ATOM NO.   TYPE          CHARGE        ATOM  ELECTRON DENSITY
           1          C          -0.083582        4.0836
           2          H           0.075457        0.9245
           3          H           0.068466        0.9315
           4          H           0.100983        0.8990
           5          O          -0.256087        6.2561
           6          C           0.010013        3.9900
           7          H           0.128095        0.8719
           8          H           0.129190        0.8708
           9         Cl          -0.173892        7.1739
          10          O          -0.394315        6.3943
          11          H           0.198865        0.8011
          12          H           0.196806        0.8032
 DIPOLE           X         Y         Z       TOTAL
 POINT-CHG.    -1.434     2.369    -1.575     3.186
 HYBRID         0.083     0.743    -0.534     0.919
 SUM           -1.351     3.112    -2.109     3.995

          CARTESIAN COORDINATES

    NO.       ATOM               X         Y         Z

     1         C                  0.0000    0.0000    0.0000
     2         H                  1.1168    0.0000    0.0000
     3         H                 -0.3868    1.0512    0.0000
     4         H                 -0.3973   -0.5719   -0.8732
     5         O                 -0.4938   -0.7059    1.1311
     6         C                 -0.1950   -0.1009    2.3625
     7         H                 -0.8848   -0.5813    3.1000
     8         H                 -0.2824    1.0145    2.3279
     9        Cl                  1.4626   -0.4493    2.9091
    10         O                 -0.7042    3.0178    1.3466
    11         H                 -1.4959    3.5363    1.1715
    12         H                 -0.0847    3.3095    0.6726

          ATOMIC ORBITAL ELECTRON POPULATIONS

   1.24445   0.99238   0.96549   0.88127   0.92454   0.93153   0.89902
1.87677
   1.73882   1.50611   1.13439   1.26336   0.85007   1.00299   0.87357
0.87190
   0.87081   1.98669   1.32144   1.96727   1.89850   1.86117   1.28456
1.67282
   1.57576   0.80114   0.80319

NAICAS DUMPED:   8.33 PERCENT COMPLETE
NAICAS DUMPED:  16.67 PERCENT COMPLETE
NAICAS DUMPED:  25.00 PERCENT COMPLETE
NAICAS DUMPED:  33.33 PERCENT COMPLETE
NAICAS DUMPED:  41.67 PERCENT COMPLETE
NAICAS DUMPED:  50.00 PERCENT COMPLETE
NAICAS DUMPED:  58.33 PERCENT COMPLETE
NAICAS DUMPED:  66.67 PERCENT COMPLETE
NAICAS DUMPED:  75.00 PERCENT COMPLETE
NAICAS DUMPED:  83.33 PERCENT COMPLETE
NAICAS DUMPED:  91.67 PERCENT COMPLETE
NAICAS DUMPED: 100.00 PERCENT COMPLETE

NAICAP DUMPED:  10.00 PERCENT COMPLETE
NAICAP DUMPED:  20.00 PERCENT COMPLETE
NAICAP DUMPED:  30.00 PERCENT COMPLETE
NAICAP DUMPED:  40.00 PERCENT COMPLETE
NAICAP DUMPED:  50.00 PERCENT COMPLETE
NAICAP DUMPED:  60.00 PERCENT COMPLETE
NAICAP DUMPED:  70.00 PERCENT COMPLETE
NAICAP DUMPED:  80.00 PERCENT COMPLETE
NAICAP DUMPED:  90.00 PERCENT COMPLETE
NAICAP DUMPED: 100.00 PERCENT COMPLETE

            ELECTROSTATIC POTENTIAL CHARGES

               ATOM NO.    TYPE    CHARGE
                  1          C    -0.4073
                  2          H     0.1575
                  3          H     0.1508
                  4          H     0.1626
                  5          O     0.0241
                  6          C    -0.7417
                  7          H     0.3030
                  8          H     0.3827
                  9         Cl    -0.0028
                 10          O    -0.5600
                 11          H     0.2721
                 12          H     0.2590

            THE NUMBER OF POINTS IS:       775
            THE RMS DEVIATION IS:       1.1970
            THE RRMS DEVIATION IS:      0.1496

     DIPOLE MOMENT EVALUATED FROM THE POINT CHARGES

             X        Y        Z       TOTAL
          -1.1010  37.1058  -1.4698  37.1513

         TIME TO CALCULATE ESP:  160.15 SECONDS

 TOTAL CPU TIME:           173.89 SECONDS

 == MOPAC DONE ==
 JOB FINISHED

PPS - sorry that pine has reformatted this rather badly

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