We start with the upper dummy, then the central one. These 'atoms' get XX as a label (in MOPAC nomenclature).

XX 0.00 0.00 0.00 0 0 0 XX 1.00 0.00 0.00 1 0 0 C 0.90 90.00 0.00 2 1 0 C 0.90 90.00 120.00 2 1 3 C 0.90 90.00 240.00 2 1 3 H 1.10 125.00 0.00 3 2 1 H 1.10 125.00 180.00 3 2 1 H 1.10 125.00 0.00 4 2 1 H 1.10 125.00 180.00 4 2 1 H 1.10 125.00 0.00 5 2 1 H 1.10 125.00 180.00 5 2 1*************************************

Questions

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The three angles of 90 degrees are not variables, but constants.

The same holds for all the dihedral angles. They follow from the definition of the dummy atoms.

XX 0.00 0 0.00 0 0.00 0 0 0 0 XX 1.00 0 0.00 0 0.00 0 1 0 0 C 0.90 1 90.00 0 0.00 0 2 1 0 C 0.90 1 90.00 0 120.00 0 2 1 3 C 0.90 1 90.00 0 240.00 0 2 1 3 H 1.10 1 125.00 1 0.00 0 3 2 1 H 1.10 1 125.00 1 180.00 0 3 2 1 H 1.10 1 125.00 1 0.00 0 4 2 1 H 1.10 1 125.00 1 180.00 0 4 2 1 H 1.10 1 125.00 1 0.00 0 5 2 1 H 1.10 1 125.00 1 180.00 0 5 2 1The number of variables is now 15.

All three C-XX2 distances will be equal because of the symmetry in the molecule. In MOPAC this is indicated at the bottom of the z-matrix (which is closed by a zero line) and SYMMETRY as a keyword on the first line:

XX 0.00 0 0.00 0 0.00 0 0 0 0 XX 1.00 0 0.00 0 0.00 0 1 0 0 C 0.90 1 90.00 0 0.00 0 2 1 0 C 0.90 0 90.00 0 120.00 0 2 1 3 C 0.90 0 90.00 0 240.00 0 2 1 3 H 1.10 1 125.00 1 0.00 0 3 2 1 H 1.10 1 125.00 1 180.00 0 3 2 1 H 1.10 1 125.00 1 0.00 0 4 2 1 H 1.10 1 125.00 1 180.00 0 4 2 1 H 1.10 1 125.00 1 0.00 0 5 2 1 H 1.10 1 125.00 1 180.00 0 5 2 1 0 0.00 3, 1, 4, 5 which means that for atom 3, variable 1 (the distance) is transferred to the atoms 4 and 5 as well. The corresponding flags have to be changed from 1 to 0.This symmetry could not have been implemented using the definition path suggested in the question above.

So the format is: reference atom, variable function, related atom(s).

See the MOPAC manual for the complete list of functions.

The most important ones are:

**1 ** the distance

** 2 ** the angle

** 3 ** the dihedral angle

** 9 ** dihedral angle varies as 180 degrees plus reference dihedral

**14 ** dihedral angle varies as negative of reference dihedral

**17 ** bond angle varies as 180 degrees minus reference bond angle

For the hydrogens 7 to 11, both the distances and the angles can be
taken from the values for H6:

6, 1, 7, 8, 9, 10, 11 6, 2, 7, 8, 9, 10, 11So the complete input file, with z-matrix, looks like:

AM1 T=600 SYMMETRY .... (keyword line) Cyclopropane input file (comment line) with symmetry (comment line) XX 0.00 0 0.00 0 0.00 0 0 0 0 XX 1.00 0 0.00 0 0.00 0 1 0 0 C 0.90 1 90.00 0 0.00 0 2 1 0 C 0.90 0 90.00 0 120.00 0 2 1 3 C 0.90 0 90.00 0 240.00 0 2 1 3 H 1.10 1 125.00 1 0.00 0 3 2 1 H 1.10 0 125.00 0 180.00 0 3 2 1 H 1.10 0 125.00 0 0.00 0 4 2 1 H 1.10 0 125.00 0 180.00 0 4 2 1 H 1.10 0 125.00 0 0.00 0 5 2 1 H 1.10 0 125.00 0 180.00 0 5 2 1 0 0.00 (blank or zero line) 3, 1, 4, 5 6, 1, 7, 8, 9, 10, 11 6, 2, 7, 8, 9, 10, 11Note that there are now only

**Exercise**: construct a z-matrix for the chair conformation of cyclohexane
with the minimum number of variables.

Check your answer.

This chapter is continued in:

1E: Creating MOPAC input files

This is the first chapter: Types of coordinates, z-matrices, input files

Next chapter How to locate a Transition State.

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