Examples: Path calculation

Examples: Path calculations

Path calculations, in which one variable is changed stepwise, are mostly used either to compare conformations (by rotating a dihedral angle), or to investigate a reaction (by changing a bond length).
The changing variable is flagged with the "-1" symbol.
Subsequent values for this variable can be provided in two ways:

using the keywords POINT=n STEP=m.mm,
by listing values at the end of the input file.

Both are shown in the examples below.

Example 1. Calculating the rotation barrier in butane.

The input file for this calculation would be:

 AM1 T=3600 STEP=15.0 POINT=24 NOINTER NOXYZ
 butane.dat
 rotation barrier
  C    0.0000000  0      0.000000  0      0.000000  0    0    0    0     -0.2106
  C    1.5063742  1      0.000000  0      0.000000  0    1    0    0     -0.1589
  C    1.5148539  1    111.573294  1      0.000000  0    2    1    0     -0.1590
  C    1.5071242  1    111.395741  1    179.493020 -1    3    2    1     -0.2108
  H    1.1169330  1    110.709122  1    -60.101300  1    1    2    3      0.0715
  H    1.1168898  1    110.338981  1    179.940403  1    1    2    3      0.0713
  H    1.1167861  1    110.743701  1     59.913852  1    1    2    3      0.0716
  H    1.1219264  1    109.644186  1   -121.306429  1    2    1    3      0.0776
  H    1.1219566  1    109.633533  1    121.320785  1    2    1    3      0.0777
  H    1.1218934  1    109.541874  1     58.087177  1    3    2    1      0.0777
  H    1.1219751  1    109.481812  1    -59.070562  1    3    2    1      0.0777
  H    1.1168833  1    110.341776  1    179.968300  1    4    3    2      0.0713
  H    1.1167637  1    110.730350  1     59.934203  1    4    3    2      0.0716
  H    1.1169092  1    110.696271  1    -60.072307  1    4    3    2      0.0715

The dihedral angle C4-C3-C2-C1 (the central bond) is rotated a full circle (24 steps of 15 degrees), starting from the minimum at 180.

The result (the .out file) can be viewed using MOLDEN. Activate 'Geom.conv.' which displays a plot of the energy vs. dihedral.
Then hit 'Movie' to see the change in the structures.

Example 2. An S_N2 reaction.

The input file for the reaction Cl^- + CH₃-CHBr-CH₃:

 AM1 CHARGE=-1 T=600 NOINTER NOXYZ
 sn2 reaction
 cl-  2-bromopropane
Br      0.0  
 C      1.9     1         0.0   0     0.0 0  1  0  0
 H      1.12    1       110.0   1     0.0 0  2  1  0
 C      1.42    1       110.0   1   120.0 1  2  1  3
 C      1.42    1       110.0   1   240.0 1  2  1  3
Cl      3.5    -1       154.0   1     0.0 0  2  1  3
 H      1.1     1       110.0   1    60.0 1  5  2  4
 H      1.1     1       110.0   1   180.0 1  5  2  4
 H      1.1     1       110.0   1   300.0 1  5  2  4
 H      1.1     1       110.0   1    60.0 1  4  2  5
 H      1.1     1       110.0   1   180.0 1  4  2  5
 H      1.1     1       110.0   1   300.0 1  4  2  5
 0 
3.0 2.9  2.8  2.7  2.6  2.5  2.4  2.3  2.2  2.1  2.0  1.9  1.8  1.7

The chloride anion is placed at 3.5 angstroms from the central carbon, and this distance is gradually shortened, using the values listed at the end of the file (note the zero line above it to close the coordinates).
The bromide anion will be pushed out automatically; the C-Br distance doesn't have to be treated as a reaction coordinate.
The zero dihedral angle for the Cl keeps the atom on the right track towards C2; it prevents the elimination reaction, in which Cl^- abstracts a proton.
The result can again be viewed using MOLDEN.

A maximum in the curve of a path search is a good starting point for a transition state calculation.

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Last updated on November 18, 1996