Molecular Mechanics

Background

The "mechanical" molecular model was developed out of a need to describe molecular structures and properties in as practical a manner as possible. The range of applicability of molecular mechanics includes: The great computational speed of molecular mechanics allows for its use in procedures such as molecular dynamics, conformational energy searching, and docking, that require large numbers of energy evaluations.

Molecular mechanics methods are based on the following principles:

Note how these principles differ from those of quantum mechanics.


The Anatomy of a Molecular Mechanics Force-Field

The mechanical molecular model considers atoms as spheres and bonds as springs. The mathematics of spring deformation can be used to describe the ability of bonds to stretch, bend, and twist:

Non-bonded atoms (greater than two bonds apart) interact through van der Waals attraction, steric repulsion, and electrostatic attraction/repulsion. These properties are easiest to describe mathematically when atoms are considered as spheres of characteristic radii.

The object of molecular mechanics is to predict the energy associated with a given conformation of a molecule. However, molecular mechanics energies have no meaning as absolute quantities. Only differences in energy between two or more conformations have meaning. A simple molecular mechanics energy equation is given by:

Energy =
Stretching Energy +
Bending Energy +
Torsion Energy +
Non-Bonded Interaction Energy

These equations together with the data (parameters) required to describe the behavior of different kinds of atoms and bonds, is called a force-field. Many different kinds of force-fields have been developed over the years. Some include additional energy terms that describe other kinds of deformations. Some force-fields account for coupling between bending and stretching in adjacent bonds in order to improve the accuracy of the mechanical model.

The mathematical form of the energy terms varies from force-field to force-field. The more common forms will be described.