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A comparative theoretical study of dipeptide solvation in water
Author(s) -
Hugosson Håkan W.,
Laio Alessandro,
Maurer Patrick,
Rothlisberger Ursula
Publication year - 2006
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.20360
Subject(s) - solvation , dipeptide , molecular dynamics , chemistry , quantum , chemical physics , computational chemistry , solvation shell , molecule , peptide , physics , organic chemistry , quantum mechanics , biochemistry
Molecular dynamics studies have been performed on the zwitterionic form of the dipeptide glycine–alanine in water, with focus on the solvation and electrostatic properties using a range of theoretical methods, from purely classical force fields, through mixed quantum mechanical/molecular mechanical simulations, to fully quantum mechanical Car–Parrinello calculations. The results of these studies show that the solvation pattern is similar for all methods used for most atoms in the dipeptide, but can differ substantially for some groups; namely the carboxy and aminoterminii, and the backbone amid NH group. This might have implications in other theoretical studies of peptides and proteins with charged —NH 3 +and —CO 2 −side chains solvated in water. Hybrid quantum mechanical/molecular mechanical simulations successfully reproduce the solvation patterns from the fully quantum mechanical simulations (PACS numbers: 87.14.Ee, 87.15.Aa, 87.15.He, 71.15.Pd). © 2006 Wiley Periodicals, Inc. J Comput Chem 27:672–684, 2006