Molecular mechanical potentials

Field, M.J., Bash, P.A., Karplus, M. A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations. J. Comput. Chem. 11 (1990) 700-733. 

To see the contributions to the molecular mechanics potential energy function and their mathematical representation... 

Many molecular mechanics potentials were developed at a time when it was computationally impractical to add large numbers of discrete water m olecules to ih e calcu la Lion to sim ulate th e effect of ac ueous media. As such, tech n iq ties cam e into place that were intended to Lake into account the effect of solvent in some fashion. These tech niqiieswcre difficult to justify physically but they were used n cvcrth eless. 

Amara P and M J Field 1998. Combined Quantum Mechanical and Molecular Mechanical Potentials. In Schleyer, P v R, N L Allinger, T Clark, J Gasteiger, P A Kolhnan H F Schaefer HI and P R Schreiner (Editors). The Encyclopedia of Computational Chemistry. Chichester, John Wiley Sons. 

Gao J 1995. Methods and Applications of Combined Quantum Mechanical and Molecular Mechanical Potentials. In Lipkowitz K B and D B Boyd (Editors) Reviews in Computational Chemistry Volume 7. New York, VCH Publishers, pp. 119-185. 

Field M J, P A Bash and M Karplus 1990. A Combined Quantum Mechanical and Molecular Mechanical Potential for Molecular Dynamics Simulations. Journal of Computational Chemistry 11 700-733. 

As motivation for the rest of the chapter, a few further observations can be made. Eirst, the calculation of full electrostatics is expensive. A typical molecular mechanics potential function is of the form... 

Bash, P. A., Field, M. J. and Karplus, M. Free energy perturbation method for chemical reactions in the condensed phase a dynamical approach based on a combined quantum and molecular mechanics potential,... 

Jiali Gao, Methods and Applications of Combined Quantum Mechanical and Molecular Mechanical Potentials. 

A concerted rather than a stepwise reaction involving a tetrahedral intermediate is supported for die papain-catalysed hydrolysis of amides. The TS for die hydrolysis has been determined by using a hybrid quantum mechanical/molecular mechanical potential, QM(AM1)/MM.216... 

J. Gao, Methods and applications of combined quantum mechanical and molecular mechanical potentials, in K. B. Lipkowitz and D. B. Boyd (eds), Reviews in Computational Chemistry, Vol. 7, VCH, New York, 1996. 

W. D, Cone]], A. G, Howant, and P, Kcdbimn. Molecular mechanical potential functions and their application to study molecular systems. Curr. Opin. Struct. Bid 7 201-212(1991). 

Bash, P.A., Field M.J. and Karplus M., Free Energy Perturbation Method for Chemical Reactions in the Condensed Phase A Dynamical Approach Based on a Combined Quantum and Molecular Mechanics Potential. J. Am. Chem.Soc. (1987) 109 8092-8094. 

---