Free energy simulations: Applications to the study of liquid water,hydrophobic interactions and solvent effects on conformational stability

Free energy simulations using the Metropolis Monte Carlo method and the coupling parameter approach with umbrella sampling are described for several problems of interest in structural biochemistry: the liquid water, the hydrophobic interaction of alkyl and phenyl groups in water, and solvent effects on the conformational stability of the alanine dipeptide and the dimethyl phosphate anion in water. Proximity analysis of the results is employed to identify stabilizing factors. Implications of the result with respect to the structural chemistry of proteins and nucleic acids is considered.