Free energy simulations: Applications to the study of liquid water,hydrophobic interactions and solvent effects on conformational stability |
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| Authors: | D L Beveridge M Mezei G Ravishanker B Jayaram |
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| Institution: | (1) Department of Chemistry, Hunter College of the City University of New York, 695 Park Avenue, Hunter College, 10021 New York, USA |
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| Abstract: | 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 results is employed to identify stabilizing factors. Implications of result
with respect to the structural chemistry of proteins and nucleic acids is considered. |
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| Keywords: | Free energy simulations hydrophobic interactions solvent effects in conformation |
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