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Free energy simulations: Applications to the study of liquid water, hydrophobic interactions and solvent effects on conformational stability
Author(s) -
Beveridge D. L.,
Mezei M.,
Ravishanker G.,
Jayaram B.
Publication year - 1986
Publication title -
international journal of quantum chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.484
H-Index - 105
eISSN - 1097-461X
pISSN - 0020-7608
DOI - 10.1002/qua.560290542
Subject(s) - chemistry , monte carlo method , molecular dynamics , solvent , umbrella sampling , dipeptide , alkyl , computational chemistry , solvent effects , hydrophobic effect , interaction energy , nucleic acid , potential of mean force , chemical physics , molecule , organic chemistry , amino acid , biochemistry , statistics , mathematics
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.