Molecular Mechanics

Introduction
In molecular mechanics, an empirical method is used to represent the potential energy of a molecule as a function of geometric variables. Electrons are not considered explicitly, and the potential energy function depends on the positions of the nuclei. This energy function is an approximation of the Born-Oppenheimer type in that it represents the potential energy surface at the nuclear level. That is, electron motion is averaged out during nuclear motion. However, the electronic system is included implicitly by correct choice of parameters.

In this method a molecule is described as a collection of atoms that interact with one another by simple analytical functions that are based on the equations of classical mechanics. The parameters that are used in the energy calculations are derived from a database of structures that has been developed by experimental and quantum mechanical methods. The equations and parameters that are used to define the potential energy surface of a molecule in molecular mechanics are referred to collectively as a force field.

Force Fields
Force fields generally are developed to handle specific classes of molecules, and as yet a force field that is applicable to all classes of molecules does not exist. These force fields differ in the functional form of the analytic expressions and in the parameter sets. Listed below are examples of some force fields and the programs in which they are implemented.

On-Line Resources

The Australian Computational Chemistry via the Internet Project Team

The NIH Guide to Molecular Modeling

Printed References
Allinger, N.L., Yuh, Y.H., and Lii, J.-H. (1989) Molecular Mechanics. The MM3 Force Field for Hydrocarbons, J. Am. Chem. Soc. 111: 8551-8566.

Bowen, J.P. and Allinger, N.L. (1991) Molecular Mechanics: The Art and Science of Parameterization, in, New Approaches to Empirical Force Fields, in, Reviews in Computational Chemistry, Vol.2, Lipkowitz, K.B. and Boyd, D.B., eds. VCH Publishers, New York, pp. 81-97.

Boyd, D.B. and Lipkowitz, K.B. (1982) Molecular Mechanics - The Methods and Its Underlying Philosophy, J. Chem. Ed. 59: 269-277.

Brooks, B.R., Bruccoleri, R.E., Olafson, B.D., States, D.J., Swaminathan, S., and Karplus, M. (1983) CHARMM: A Program for Macromolecular Energy, Minimization, and Dynamics Calculations, J. Comp. Chem. 4: 187-217.

Burkert, U. and Allinger, N.L. (1982) Molecular Mechanics, ACS Monograph 177, American Chemical Society, Washington, D.C., 339pp.

Cornell, W.D., Cieplak, P., Bayly, C.I., Gould, I.R., Merz, K.M. Jr., Ferguson, D.M., Spellmeyer, D.C., Fox, T., Caldwell, J.W., and Kollman, P.A. (1995) A second generation force field for the simulation of proteins and nucleic acids, J. Amer. Chem. Soc. 117: 5179-5197.

Dinur, U. and Hagler, A.T. (1991) New Approaches to Empirical Force Fields, in, Reviews in Computational Chemistry, Vol.2, Lipkowitz, K.B. and Boyd, D.B., eds. VCH Publishers, New York, pp. 99-164.

Hirst, D.M. (1990) A Computational Approach to Chemistry, Blackwell Scientific Publications, Oxford, pp. 101-120.

Mohamadi, F., Richards, N.G.J., Guida, W.C., Liskamp, R., Lipton, M., Caufield, C., Chang, G., Hendrickson, T., and Still, W.C. (1990) MacroModel - An Integrated Software System for Modeling Organic and Bioorganic Molecules Using Molecular Mechanics, J. Comp. Chem. 11: 440-467.

Weiner, S.J., Kollman, P.A., Case, D.A., Singh, U.C., Ghio, C., Alagona, G., Profeta, S., and Weiner, P. (1984) A New Force Field for Molecular Mechanical Simulation of Nucleic Acids and Proteins, J. Am. Chem. Soc. 106: 765-784.