Subject: re:ccl two unrelated questions

From: "Jeffrey J. Ayres" <[email-masked]>
Date: Thu, 29 May 1997 14:09:32 -0700

> Hr. Dr. S. Shapiro wrote:
> >
> > Dear Colleagues;
> >
> >         I have two quite unrelated questions for which perhaps some CCLers
> > might be able to provide useful replies:
> >
> > Question 1:  In order to obtain Mulliken partial atomic charges for some
> > work in which we are engaged, I prepared a Z-matrix for the molecule
> > p-tolylacetylene ("tolac.mop"), as follows:
> >
> > am1 nointer
> > p-tolylacetylene
> >
> > C     0.000000  0    0.000000  0    0.000000  0   0   0   0
> > C     1.401729  0    0.000000  0    0.000000  0   1   0   0
> > C     1.399999  0  120.081459  0    0.000000  0   2   1   0
> > C     1.399809  0  120.056900  0    0.000000  0   3   2   1
> > C     1.399806  0  119.942001  0    0.000000  0   4   3   2
> > C     1.400006  0  120.056679  0    0.000000  0   5   4   3
> > C     1.312333  0  120.109207  0  180.000000  0   1   2   3
> > C     1.200200  0  179.891647  0  180.000000  0   7   1   2
> > H     1.103619  0  119.699532  0  180.000000  0   2   3   1
> > H     1.103127  0  119.972672  0  180.000000  0   3   2   1
> > H     1.103111  0  120.028992  0  180.000000  0   4   3   2
> > H     1.103127  0  119.970596  0  180.000000  0   5   4   3
> > H     1.103619  0  119.699341  0  180.000000  0   6   5   4
> > H     1.059943  0  180.000000  0  180.000000  0   8   7   1
> >
> > When I tried running it in MOPAC 6.0, I got the following output:
> >
> >                      CALCULATION ABANDONED AT THIS POINT
> >
> >            THREE ATOMS BEING USED TO DEFINE THE
> >            COORDINATES OF A FOURTH ATOM, WHOSE BOND-ANGLE IS
> >            NOT ZERO OR 180 DEGREEES, ARE IN AN ALMOST STRAIGHT
> >            LINE.  THERE IS A HIGH PROBABILITY THAT THE
> >            COORDINATES OF THE ATOM WILL BE INCORRECT.
> >
> >                     THE FAULTY ATOM IS ATOM NUMBER  14
> >
> >                                 :
> >                                 :
> >
> >                          [some stuff omitted]
> >
> >                                 :
> >                                 :
> >
> >             CARTESIAN COORDINATES UP TO FAULTY ATOM
> >
> >      I            X            Y            Z
> >      1          .00000       .00000       .00000
> >      2         1.40173       .00000       .00000
> >      3         2.10345      1.21144       .00000
> >      4         1.40648      2.42540       .00000
> >      5          .00667      2.42736       .00000
> >      6         -.69623      1.21660       .00000
> >      7         -.65833     -1.13526       .00000
> >      8        -1.26237     -2.17238       .00000
> >      9         1.95719      -.95365       .00000
> >     10         3.20658      1.20934       .00000
> >     11         1.95985      3.37966       .00000
> >     12         -.54306      3.38375       .00000
> >     13        -1.79982      1.22503       .00000
> >     14          .00000       .00000       .00000
> >
> >        ATOMS  8,  7, AND  1 ARE WITHIN  .0025 ANGSTROMS OF A STRAIGHT LINE
> >
> >         Adding the keyword "geo-ok" didn't help.  Does anyone know of a
> > workaround to this so that I can obtain Mulliken partial atomic charges for
> > the atoms of p-tolylacetylee using MOPAC?
Dr. Shapiro,
        Both acetylbenzene (acebenz.mop) and tolylacetylyne
(tolylace.mop)
were successful using MOPAC 6.  Each file was separately
entered into the interface function of molgen, configured for mopac, and
input files written.  The arc files displayed successful completion of
the calculation (acebenz.arc, tolylace.arc).  The dummy atoms were
placed automatically using molgen/mopac6.

AM1 NOINTER  T=100000
LINEARITY CHECK, W/O TOLYL GROUP

99     0.00000   0       0.00000   0         0.00000   0      0  0  0
 6     3.43972   1       0.00000   0         0.00000   0      1  0  0
 6     1.21234   1      64.66995   1         0.00000   0      2  1  0
99     1.00000   1      90.00001   1       180.00000   1      3  2  1
99     1.00000   1      90.00000   1       180.00000   1      3  2  1
99     1.00000   1      90.00000   1       180.00000   1      5  3  2
 6     1.31568   1      90.00011   1       359.99994   1      3  5  6
 6     1.39791   1     149.19049   1       119.94086   1      7  6  5
 6     1.39663   1     120.14005   1        72.87572   1      8  7  6
 6     1.39612   1     120.06921   1         0.00000   1      9  8  7
 6     1.39612   1     119.88985   1         0.00000   1     10  9  8
 6     1.39663   1     120.06889   1         0.00000   1     11 10  9
 1     1.10365   1     119.36862   1       180.00000   1     12 11 10
 1     1.10315   1     119.93962   1       180.00000   1     11 10  9
 1     1.10312   1     120.05508   1       180.00000   1     10  9  8
 1     1.10315   1     119.99132   1       180.00000   1      9  8  7
 1     1.10365   1     120.49116   1       252.87573   1      8  7  6
 1     1.08988   1     180.00000   1       329.12024   1      2  3  4
 0
99

AM1 NOINTER  T=100000
LINEARITY CHECK

99     0.00000   0       0.00000   0         0.00000   0      0  0  0
 6     3.48042   1       0.00000   0         0.00000   0      1  0  0
 6     1.21234   1      65.15163   1         0.00000   0      2  1  0
99     1.00000   1      90.00000   1       180.00000   1      3  2  1
99     1.00000   1      90.00000   1       180.00000   1      3  2  1
99     1.00000   1      90.00000   1       180.00000   1      5  3  2
 6     1.31563   1      89.99992   1         0.00000   1      3  5  6
 6     1.39705   1     149.14925   1       120.29477   1      7  6  5
 6     1.39659   1     120.22314   1        72.56248   1      8  7  6
 6     1.39913   1     120.88677   1       359.99326   1      9  8  7
 6     1.39902   1     118.43241   1         0.01592   1     10  9  8
 6     1.39633   1     120.99382   1       359.98410   1     11 10  9
 6     1.50826   1     121.44947   1       179.98825   1     10  9  8
 1     1.11359   1     112.38258   1       359.52576   1     13 10  9
 1     1.11378   1     110.22261   1       239.41864   1     13 10  9
 1     1.11377   1     110.19374   1       119.64949   1     13 10  9
 1     1.10366   1     119.40629   1       180.00584   1     12 11 10
 1     1.10282   1     119.58285   1       179.98978   1     11 10  9
 1     1.10264   1     119.11382   1       179.99895   1      9  8  7
 1     1.10369   1     120.40184   1       252.56161   1      8  7  6
 1     1.08988   1     180.00000   1       328.78256   1      2  3  4
 0
99

                     SUMMARY OF   AM1   CALCULATION

                                                            VERSION 
6.00

  C8  H6 
                                                      
Today                   
 AM1 NOINTER T=100000
 LINEARITY CHECK, W/O TOLYL GROUP

     HERBERTS TEST WAS SATISFIED IN BFGS                      
     SCF FIELD WAS ACHIEVED                                   

          HEAT OF FORMATION       =        76.494364 KCAL
          ELECTRONIC ENERGY       =     -4591.203173 EV
          CORE-CORE REPULSION     =      3486.776813 EV
          GRADIENT NORM           =         3.408224
          DIPOLE                  =          .25742 DEBYE
          NO. OF FILLED LEVELS    =        19
          IONIZATION POTENTIAL    =         9.289317 EV
          MOLECULAR WEIGHT        =       102.135
          SCF CALCULATIONS        =        27
          COMPUTATION TIME =  1 MINUTES AND  30.000 SECONDS

          FINAL GEOMETRY OBTAINED                                   
CHARGE
 AM1 NOINTER T=100000
 LINEARITY CHECK, W/O TOLYL GROUP
 
 XX     .0000000  0       .000000  0       .000000  0    0    0    0
  C    3.4420049  1       .000000  0       .000000  0    1    0   
0      -.1964
  C    1.1970294  1     56.641236  1       .000000  0    2    1   
0      -.1280
 XX     .9949193  1     89.708910  1   -178.211018  1    3    2    1
 XX    1.0314086  1     90.561397  1   -179.649559  1    3    2    1
 XX    1.0312117  1     91.796755  1   -178.745409  1    5    3    2
  C    1.4082800  1     89.641007  1      1.183807  1    3    5   
6       .0244
  C    1.4046426  1    150.539338  1    118.976516  1    7    6   
5      -.1065
  C    1.3929953  1    120.068775  1     75.174986  1    8    7   
6      -.1338
  C    1.3962067  1    120.142186  1      -.010894  1    9    8   
7      -.1217
  C    1.3939876  1    119.995132  1      -.061412  1   10    9   
8      -.1337
  C    1.3932708  1    120.308968  1      -.013960  1   11   10   
9      -.1064
  H    1.0996732  1    120.271218  1   -179.971165  1   12   11  
10       .1389
  H    1.0995514  1    119.955001  1    179.985241  1   11   10   
9       .1336
  H    1.0991887  1    120.075223  1    179.756408  1   10    9   
8       .1325
  H    1.0996151  1    119.852421  1    179.928846  1    9    8   
7       .1340
  H    1.1002619  1    120.153389  1   -104.967368  1    8    7   
6       .1387
  H    1.0602610  1    179.663366  1    -32.668745  1    2    3   
4       .2244

                     SUMMARY OF   AM1   CALCULATION

                                                            VERSION 
6.00

  C9  H8 
                                                      
Today                   
 AM1 NOINTER T=100000
 LINEARITY CHECK

     HERBERTS TEST WAS SATISFIED IN BFGS                      
     SCF FIELD WAS ACHIEVED                                   

          HEAT OF FORMATION       =        68.807359 KCAL
          ELECTRONIC ENERGY       =     -5708.507321 EV
          CORE-CORE REPULSION     =      4448.209853 EV
          GRADIENT NORM           =         8.420059
          DIPOLE                  =          .59447 DEBYE
          NO. OF FILLED LEVELS    =        22
          IONIZATION POTENTIAL    =         9.060931 EV
          MOLECULAR WEIGHT        =       116.162
          SCF CALCULATIONS        =        19
          COMPUTATION TIME =  1 MINUTES AND  15.000 SECONDS

          FINAL GEOMETRY OBTAINED                                   
CHARGE
 AM1 NOINTER T=100000
 LINEARITY CHECK
 
 XX     .0000000  0       .000000  0       .000000  0    0    0    0
  C    3.5326280  1       .000000  0       .000000  0    1    0   
0      -.1990
  C    1.1976710  1     64.343847  1       .000000  0    2    1   
0      -.1256
 XX     .9950910  1     89.718735  1   -179.799558  1    3    2    1
 XX    1.0631774  1     90.499463  1   -179.548425  1    3    2    1
 XX    1.0671355  1     93.240342  1    178.738851  1    5    3    2
  C    1.4083877  1     89.614201  1     -1.067792  1    3    5   
6       .0185
  C    1.4028014  1    148.269348  1    120.465800  1    7    6   
5      -.1030
  C    1.3912395  1    120.347943  1     71.689079  1    8    7   
6      -.1344
  C    1.3993752  1    120.943731  1      -.065872  1    9    8   
7      -.0594
  C    1.4006745  1    118.564109  1      -.007479  1   10    9   
8      -.1366
  C    1.3922484  1    121.050539  1       .148925  1   11   10   
9      -.1023
  C    1.4796965  1    121.182156  1    179.957555  1   10    9   
8      -.1804
  H    1.1171995  1    111.396064  1      -.329014  1   13   10   
9       .0825
  H    1.1187774  1    110.236680  1   -120.707040  1   13   10   
9       .0868
  H    1.1188312  1    110.222303  1    120.041819  1   13   10   
9       .0868
  H    1.0998633  1    120.262222  1    179.778452  1   12   11  
10       .1387
  H    1.1004308  1    119.254943  1   -179.985301  1   11   10   
9       .1326
  H    1.1011481  1    119.402368  1    179.852623  1    9    8   
7       .1328
  H    1.1004635  1    119.741479  1   -108.339046  1    8    7   
6       .1381
  H    1.0595952  1    179.883562  1    -31.417881  1    2    3   
4       .2240