Molecular mechanics potential functions

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... 

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). 

The basis of the QM/MM approach (Figure 1) is that the process or subsystem of most interest is localized in a fairly small part of a larger system. The computational effort is therefore focused on this small region, which most requires a quantum mechanical description. The bulk of the system is treated more simply by a molecular mechanics potential function. The combination of... 

Analytical expressions for the forces due to other terms in the molecular mechanics potential function have been published for most of the functional forms encountered in common force... 

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

As demonstrated in Table 5.3, the potential energy functions in side-chain prediction methods have varied tremendously from simple steric exclusion terms to full molecular mechanics potentials. In most cases, the potential energy function is a standard Lennard-Jones potential ... 

Tunon I, Martins-Costa MTC, Millot C, Ruiz-Lopez MF. Molecular dynamics simulations of elementary chemical processes in liquid water using combined density functional and molecular mechanics potential I. Proton transfer in strongly H-bonded complexes. J Chem Phys 1997 106 3633-3642. 

Methods are now emerging that can provide an accurate and practical alternative to explicit solvent inclusion. A common way to avoid dealing with this problem is to concentrate on differences between similar systems, each modeled without water. Assuming that solvent affects each system in the same way, it is hoped that errors will cancel. Another way is to treat the solvent as a statistical continuum,examining the interaction of each fully or partially exposed atom with solvent,and adding a solvation energy function to existing molecular mechanics potentials. ... 

Molecular mechanics potential energy functions have been used to calculate binding constants, protein folding kinetics, protonation equilibria, active site coordinates, and to design binding sites [4,5]. 

Another empirical method that has been extensively used by Warshel and co-workers is the empirical valence bond (EVB) theory. jn this approach, it is assumed that a reaction can be described by some VB resonance structures. The analytical form of these VB functions can be approximated by appropriate molecular mechanics potentials, and the parameters of these MM potentials are calibrated to reproduce experimental or ab initio MO data in the gas phase as well as in the condensed phase. The combined EVB/MM method and its unique calibration procedure have been recently reviewed. > 2 it should be noted that Kim and Hynes presented a similar method, yielding a nonlinear Schrodinger equation. However, the solvent was treated as a dielectric continuum in the Kim-Hynes theory. Nevertheless, an interesting feature in the latter method is a consideration of nonequilibrium coupling between the solute and solvent. ... 

H. Liu, F. Mulle Plathe, and W. F. van Gunsteren, /. Chem. Phys., 102, 1702 (1995). A Molecular Dynamics Simulation Study with a Combined Quantum Medianical and Molecular Mechanical Potential Energy Function Solvation Effects of the Conformational Equilibrium of Dimethoxyethane. 

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