2B: Grid searches in MOPAC

We continue with the Diels-Alder reaction (cyclopentadiene/ethene) from paragraph 1E as an example.
For the unsubstituted compound bond lengths of 2.1 angstroms were found. We use this structure as a starting point for a grid search around an asymmetric TS. We replace the H (10) at C3 by a methyl group.
We must keep in mind that in a grid search, the structure supplied is placed in the left upper corner of the grid. (By MOPAC93; Other programs (VAMP, AMPAC) place it in the center of the grid.)
So if we want to scan the range 1.9 - 2.3 for both bonds, we start with the structure 1.9/1.9.
The z-matrix for this point is extracted from the output (the .arc file) of the line search:
 AM1 T=3600 . . .
     point 1.9 from line search
     as starting point for grid
  C    0.00000000  0    0.0000000  0    0.0000000  0    0    0    0     -0.1714
  C    1.36463273  1    0.0000000  0    0.0000000  0    1    0    0     -0.1696
  C    1.47851177  1  108.7740230  1    0.0000000  0    2    1    0     -0.1142
  C    1.90000000 -1   99.3972493  1   72.5669970  1    3    2    1     -0.1766
  C    1.46395430  1  103.2007924  1  -68.9861040  1    4    3    2     -0.1766
  C    1.90000000  0  102.4708788  1    1.0393710  1    5    4    3     -0.1143
  C    1.52902961  1  104.0509156  1  -25.1975308  1    3    2    1     -0.1448
  H    1.08779133  1  128.0529101  1 -176.5439863  1    1    2    3      0.1387
  H    1.08870887  1  127.6075304  1  176.6225059  1    2    1    3      0.1378
  H    1.09060907  1  122.1631176  1 -167.6794797  1    3    2    1      0.1214
  H    1.10340154  1  102.2949693  1  170.2188338  1    4    3    2      0.0895
  H    1.10258615  1  103.4222897  1   52.5993732  1    4    3    2      0.0928
  H    1.10289667  1  116.1611708  1 -109.6610654  1    5    4    3      0.0901
  H    1.10238814  1  116.3952278  1  113.2431506  1    5    4    3      0.0932
  H    1.09104936  1  121.9170807  1  167.0272164  1    6    1    2      0.1202
  H    1.11379846  1  113.0546990  1  157.0081121  1    7    3    2      0.0924
  H    1.11698372  1  111.6136060  1  -79.6371307  1    7    3    2      0.0916

In an editor we take this block, replace H10 by a C (adjust the bond length), and add three hydrogens add the end.
For the grid search we have to add to the keyword line: the number of points, and the step size in each direction. The result will look like this:
 AM1 T=3600 POINT1=9 STEP1=0.05 POINT2=9 STEP2=0.05
     starting point for grid search
 
  C    0.00000000  0    0.0000000  0    0.0000000  0    0    0    0     -0.1714
  C    1.36463273  1    0.0000000  0    0.0000000  0    1    0    0     -0.1696
  C    1.47851177  1  108.7740230  1    0.0000000  0    2    1    0     -0.1142
  C    1.90000000 -1   99.3972493  1   72.5669970  1    3    2    1     -0.1766
  C    1.46395430  1  103.2007924  1  -68.9861040  1    4    3    2     -0.1766
  C    1.90000000 -1  102.4708788  1    1.0393710  1    5    4    3     -0.1143
  C    1.52902961  1  104.0509156  1  -25.1975308  1    3    2    1     -0.1448
  H    1.08779133  1  128.0529101  1 -176.5439863  1    1    2    3      0.1387
  H    1.08870887  1  127.6075304  1  176.6225059  1    2    1    3      0.1378
  C    1.50060907  1  122.1631176  1 -167.6794797  1    3    2    1      0.1214
  H    1.10340154  1  102.2949693  1  170.2188338  1    4    3    2      0.0895
  H    1.10258615  1  103.4222897  1   52.5993732  1    4    3    2      0.0928
  H    1.10289667  1  116.1611708  1 -109.6610654  1    5    4    3      0.0901
  H    1.10238814  1  116.3952278  1  113.2431506  1    5    4    3      0.0932
  H    1.09104936  1  121.9170807  1  167.0272164  1    6    1    2      0.1202
  H    1.11379846  1  113.0546990  1  157.0081121  1    7    3    2      0.0924
  H    1.11698372  1  111.6136060  1  -79.6371307  1    7    3    2      0.0916
  H    1.11698372  1  109.6136060  1  179.6371307  1    10   3    2      0.0916
  H    1.11698372  1  109.6136060  1   60.6371307  1    10   3    2      0.0916
  H    1.11698372  1  109.6136060  1  -60.6371307  1    10   3    2      0.0916

Resulting grid, .arc file:
 ARCHIVE FILE FOR GRID CALCULATION
GRID OF HEATS

 AM1 T=3600 POINT1=9 STEP1=0.05 POINT2=9 STEP2=0.05
     starting point for grid search
 

 TOTAL CPU TIME IN FLEPO :    492.970

  58.54  61.74  64.76  67.56  70.13  72.45  74.48  76.25  77.73
  61.52  64.56  67.36  69.89  72.21  74.12  75.69  76.87  77.70
  64.23  67.10  69.67  71.92  73.79  75.20  76.14  76.67  76.83
  66.81  69.48  71.73  73.52  74.83  75.57  75.75  75.58  75.29
  69.08  71.39  73.30  74.60  75.22  75.17  74.72  74.07  73.35
  71.14  73.13  74.45  75.10  74.95  74.23  73.27  72.24  71.30
  72.95  74.42  75.17  75.10  74.23  73.07  71.75  70.48  69.36
  74.53  75.43  75.43  74.62  73.35  71.77  70.20  68.76  67.39
  75.73  75.97  75.38  74.09  72.43  70.64  68.87  67.23  65.83
The .ump file contains the data in a suitable format for plotting programs, like Gnuplot.
The TS is not exactly at the center, but near the two 75.10 values; one bond is slightly shorter, the other (C4 - C3) longer than 2.10 A.
The point 2.15/2.05 seems a good starting point for a TS refinement. It is not available from the .arc file, but can be obtained in a few seconds by a short calculation.
Edit the previous input file: enter the values 2.15 and 2.05 as constants (flag 0) in the input file and remove the grid related keywords.
This should result in a structure with a Heat of Formation of 75.10 kcal/mol.

From the new .arc file the input file for the TS calculation can be made: change the two '0' flags back to '1' and add the keywords TS, PRECISE and AIGOUT. The latter is required to obtain a file with a gaussian type of z-matrix (see paragraph 2D).

 AM1 T=3600 TS PRECISE AIGOUT NOINTER 
     starting point for ts optimization
 
  C    0.00000000  0    0.0000000  0    0.0000000  0    0    0    0     -0.1780
  C    1.40208483  1    0.0000000  0    0.0000000  0    1    0    0     -0.1609
  C    1.42259991  1  109.1668993  1    0.0000000  0    2    1    0     -0.0875
  C    2.15000000  1   95.2886004  1   72.3355385  1    3    2    1     -0.2117
  C    1.39345295  1  102.7414566  1  -68.9908735  1    4    3    2     -0.2003
  C    2.05000000  1  102.9376995  1    0.5014035  1    5    4    3     -0.1265
  C    1.52065200  1  106.6468717  1  -17.8627955  1    3    2    1     -0.1270
  H    1.08931724  1  125.8188251  1 -174.9635358  1    1    2    3      0.1381
  H    1.08951451  1  125.7796415  1  174.6084539  1    2    1    3      0.1376
  C    1.46768153  1  126.0338633  1 -174.4468082  1    3    2    1     -0.1710
  H    1.09908711  1   91.8502269  1  169.2505342  1    4    3    2      0.1030
  H    1.09782732  1   94.6228112  1   53.7146024  1    4    3    2      0.1057
  H    1.10096177  1  119.6664730  1 -102.0221978  1    5    4    3      0.1005
  H    1.09996024  1  119.9161149  1  105.9591396  1    5    4    3      0.1036
  H    1.08959020  1  125.3591475  1  172.7286299  1    6    1    2      0.1294
  H    1.11277814  1  113.6664178  1  149.3557267  1    7    3    2      0.1002
  H    1.12081000  1  110.3418915  1  -88.5033910  1    7    3    2      0.1045
  H    1.11840183  1  110.7890571  1 -174.2195130  1   10    3    2      0.0781
  H    1.11969567  1  110.6708390  1   65.7090700  1   10    3    2      0.0797
  H    1.11846345  1  110.5804688  1  -53.9527720  1   10    3    2      0.0825

It is now up to the reader to check the result with a FORCE calculation. (You can submit the file above and subsequent ones through our MOPAC submit page.)
Take the .arc file, extract the input file, and replace TS PRECISE AIGOUT by FORCE.
The continuation in Gamess (that is why AIGOUT is included as a keyword) is the subject of paragraph 2D: From MOPAC to Gamess
More examples of input files for path or grid searches are listed separately.


2C: The MOPAC Saddle algorithm
Back to beginning of chapter 2, How to locate a Transition State.