Chem3D Users Manual - CambridgeSoft

Appendix I: MM2
Overview
This appendix contains miscellaneous information
about the MM2 parameters and force field.
MM2 Parameters
The original MM2 parameters include the elements
commonly used in organic compounds: carbon,
hydrogen, nitrogen, oxygen, sulfur and halogens.
The atom type numbers for these atom types range
from 1 to 50.
The MM2 parameters were derived from three
sources:
1. Most of the parameters were provided by
Dr. N. L. Allinger.
2. Several additional parameters were provided by
Dr. Jay Ponder, author of the TINKER
program.
3. Some commonly used parameters that were
not provided by Dr. Allinger or Dr. Ponder are
provided by CambridgeSoft Corporation.
However, most of these parameters are
estimates which are extrapolated from other
parameters.
The best source of information on the MM2
parameter set is Molecular Mechanics, Burkert, Ulrich
and Allinger, Norman L., ACS Monograph 177,
American Chemical Society, Washington, DC,
1982.
A method for developing reasonable guesses for
parameters for non-MM2 atom types can be found
in “Development of an Internal Searching
Algorithm for Parameterization of the MM2/MM3
Force Fields”, Journal of Computational
Chemistry, Vol 12, No. 7, 844-849 (1991).
Other Parameters
The rest of the parameters consist of atom types
and elements in the periodic table which were not
included in the original MM2 force field, such as
metals. The rectification type of all the non-MM2
atom types in the Chem3D Parameter tables is
Hydrogen (H). The atom type numbers for these
atom types range from 111 to 851. The atom type
number for each of the non-MM2 atom types in the
MM2 Atom Type Parameters table is based on the
atomic number of the element and the number of
ligands in the geometry for that atom type. To
determine an atom type number, the atomic
number is multiplied by ten, and the number of
ligands is added.
For example, Co Octahedral has an atomic number
of 27 and six ligands. Therefore the atom type
number is 276.
In a case where different atom types of the same
element have the same number of ligands (Iridium
Tetrahedral, Atom Type # 774 and Iridium Square
Planar, Atom Type # 779), the number nine is used
for the second geometry.
Viewing Parameters
To view the parameters used by Chem3D to
perform MM2 computations:
• From the View menu, point to Parameter
Tables, and choose a table.
The table you chose opens in a window.
Appendices
ChemOffice 2005/Appendix MM2 • 289
MM2 Parameters