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A comparative theoretical study of dipeptide solvation in water
KTH, School of Biotechnology (BIO), Theoretical Chemistry.ORCID iD: 0000-0001-8748-3890
2006 (English)In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 27, no 5, 672-684 p.Article in journal (Refereed) Published
Abstract [en]

Molecular dynamics studies have been performed on the zwitterionic form of the dipeptide glycine-alanine in water, with focus oil 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 call 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 -NH3+ and -CO2- 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).

Place, publisher, year, edition, pages
2006. Vol. 27, no 5, 672-684 p.
Keyword [en]
theoretical, ab initio, first-principles, molecular dynamics, density functional theory, dipeptide, solvation, QM/MM, Car-Parrinello, force fields, solvation, molecular-dynamics simulations, density-functional theory, particle mesh ewald, ab-initio, aqueous-solution, alanine dipeptide, force-field, bond formation, liquid water, amino-acids
URN: urn:nbn:se:kth:diva-15510ISI: 000235931800012OAI: diva2:333551
QC 20100525Available from: 2010-08-05 Created: 2010-08-05Bibliographically approved

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