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SCIGRESS - Computational Tools - Molecular Mechanics

The term molecular mechanics refers to methods of determining molecular geometries using equations from classical Newtonian physics. These methods describe the forces acting on atoms in molecules using empirically derived equations. Currently, several different molecular mechanics force fields are widely used. You may also hear molecular mechanics methods called forcefield methods or Westheimer methods.

Most molecular mechanics force fields include terms describing bond stretching, angle bending, torsional, and nonbonded interactions such as van der Waals and hydrogen bond interactions. The sum of all these terms constitutes the steric energy of themolecule. Steric energy is a type of potential energy, and here the terms steric energy and potential energy are used interchangeably.

The SCIGRESS Mechanics application computes the net force acting on each atom in your molecule as the sum of the following energy terms:

  • Bond stretch
  • Bond angle
  • Dihedral angle
  • Improper torsion
  • van der Waals
  • Electrostatics (MM2/MM3 dipoles or partial charges)
  • Hydrogen bond
  • Torsion stretch (MM3 only)
  • Bend-bend interactions (MM3 only)

The electrostatic term is calculated from dipole-dipole interactions for the standard non-augmented force fields. For the augmented force fields, the dipoles are decomposed in to atomic charges before evaluation. Partial charges can only be added to a structure if they already exist in the structure file.

The potential energy of the molecule varies as the nuclear positions of the atoms change, and can be thought of as a multidimensional potential energy surface. The potential energy surface has hills corresponding to strained high energy conformations, and valleys corresponding to low energy conformations.

The goal of molecular mechanics optimization is to adjust the positions of the atoms until finding an optimum molecular geometry. This optimum geometry corresponds to a minimum, or valley, in the potential energy surface. Molecular mechanics optimization techniques find an optimum geometry by systematically moving all atoms until the net force acting on each atom approaches zero.

The SCIGRESS Mechanics application implements Allinger's standard MM2 force field and MM3 force fields. SCIGRESS significantly augments these force fields by providing rules that estimate the force field parameters for cases not addressed by the standard force fields. Augmentations enable minimization calculations for square planar, trigonal bipyramidal, and octahedral atoms.

To find more information about MM2 and MM3 force fields please refer to:

  • Allinger, N. L., J. Am. Chem. Soc. 1977, 99, 8127.
  • Allinger, N. L., Yuh, Y. H., Lii, J-H., J. Am. Chem. Soc., 1989, 111, 8551-8566.
  • Bowen, J. P., and Shim, J-Y., J. Comp. Chem., 1998, 19, 1370-1386.