Molecular modeling and dynamics studies with explicit inclusion of electronic polarizability. Theory and applications.

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TitleMolecular modeling and dynamics studies with explicit inclusion of electronic polarizability. Theory and applications.
Publication TypeJournal Article
Year of Publication2009
AuthorsLopes, PEM, Roux, B, Mackerell, AD
JournalTheor Chem Acc
Volume124
Issue1-2
Pagination11-28
Date Published2009 Sep
ISSN1432-881X
Abstract

A current emphasis in empirical force fields is on the development of potential functions that explicitly treat electronic polarizability. In the present article, the commonly used methodologies for modelling electronic polarization are presented along with an overview of selected application studies. Models presented include induced point-dipoles, classical Drude oscillators, and fluctuating charge methods. The theoretical background of each method is followed by an introduction to extended Langrangian integrators required for computationally tractable molecular dynamics simulations using polarizable force fields. The remainder of the review focuses on application studies using these methods. Emphasis is placed on water models, for which numerous examples exist, with a more thorough discussion presented on the recently published models associated with the Drude-based CHARMM and the AMOEBA force fields. The utility of polarizable models for the study of ion solvation is then presented followed by an overview of studies of small molecules (e.g. CCl(4), alkanes, etc) and macromolecule (proteins, nucleic acids and lipid bilayers) application studies. The review is written with the goal of providing a general overview of the current status of the field and to facilitate future application and developments.

DOI10.1007/s00214-009-0617-x
Alternate JournalTheor Chem Acc
PubMed ID20577578
PubMed Central IDPMC2888514
Grant ListR01 GM072558 / GM / NIGMS NIH HHS / United States
R01 GM072558-06 / GM / NIGMS NIH HHS / United States
R01 GM051501-13 / GM / NIGMS NIH HHS / United States
R01 GM051501 / GM / NIGMS NIH HHS / United States
R29 GM051501 / GM / NIGMS NIH HHS / United States