Structural chemistry of biomolecular hydration via computer simulation: The proximity criterion

This chapter deals with the analysis issue of biomolecular simulations and discusses the effort to formulate a structural chemistry of hydration and environmental effects in general from the results of molecular simulation. Three aspects of biomolecular simulations require attention as the field emerges from infancy and establishes a broad-based credibility: (1) the development of accurate intermolecular functions, (2) the improvement of simulation methodology within the context of the Monte Carlo and molecular dynamics procedures, and (3) the analysis of results in a form accessible to a larger community of structural biochemists, molecular pharmacologists, and others requiring information from computer models to apply to their research studies. The various atom–atom pair correlation or radial distribution functions (RDF), g(R), can in principle be deduced from diffraction experiments and theoretical calculations, and are thus the most important class of functions. Quasi-component distribution functions (QCDF) with respect to coordination number and binding energy is used extensively in conjunction with Monte Carlo computer simulation methodology on molecular liquids and solutions.