2. The MOPAC input file

The z-matrix forms the heart of the input file. It is preceeded by three lines: one line with keywords that control the calculation, and two lines with comment.
The z-matrix starts at the fourth line, and is closed by an empty line. After this, extra information may follow, e.g. describing symmetry in the structure, if any, or a series of values to be inserted where the -1 flag appears.

An input file with all options will serve as an example: 

 AM1 T=600 SYMMETRY
   rotatie om c-c binding
   met symmetrie
  C    0.00000000  0    0.0000000  0    0.0000000  0    0    0    0 
  C    1.51738930  1    0.0000000  0    0.0000000  0    1    0    0
  H    1.11721396  1  107.8021607  1    0.0000000  0    2    1    0
  H    1.11205843  0  111.3722406  0 -122.3562469  1    1    2    3
  H    1.11783779  0  107.4581078  0  115.7104335  1    1    2    3
  H    1.11692070  0  111.0770073  0    0.0000000 -1    1    2    3
  H    1.11712199  0  111.0150133  0    0.8782819  1    2    1    4 
  H    1.11702994  0  110.9935404  0  120.0975124  1    2    1    4
  0
   3  1  4  5  6  7  8
   3  2  4  5  6  7  8

 10. 20. 30. 40. 50. 60. 70. 80. 90. 100. 110. 120. 130. 140. 150. 
 160. 170. 180.
Only three keywords are present:
AM1 is the computational method selected here
Other methods are PM3 and MNDO
T=600 tells MOPAC that 600 seconds are available,
being the allowed time in our short queue.
SYMMETRY indicates that a symmetry statement follows after the z-matrix.
The format of this statement is: reference_atom symm_function affected_atoms.
Function 1 is the bond length. The value for H3 is transfered to all other hydrogens.
Function 2 is the bond angle, which is also made equal for all hydrogens. The derived parameters get the '0' flag.
An empty line closes the symmetry part. What follows at the bottom are values to be inserted, in turn, for the parameter marked with the '-1' flag, i.e. the torsion angle 6-1-2-3.
Apart from this torsion angle, all other parameters are minimized.
This results in 19 calculations, in which the torsion angle is increased in steps of 10 degrees, from 0 to 180 degrees.
Suitable programs (MOLDEN) can make a plot of the energy versus torsion angle, as we find them on the pages 80-85 in Morrison&Boyd.

3. How to perform mopac calculations and view the results

This is a very brief description of the MOPAC input file. More information can be found in an overview of keywords, which lists for instance the symmetry functions under the keyword symmetry.
Back to Organic Chemistry Modules.