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Molecular modeling and dynamics studies with explicit inclusion of electronic polarizability: theory and applications

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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 modeling 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 Lagrangian 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., CCl4, 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.

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Acknowledgments

Financial support from the NIH (GM 51501 to A.D.M. and GM 072558 to B.R. and A.D.M.) is acknowledged.

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Authors and Affiliations

  1. Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, MD, 21230, USA

    Pedro E. M. Lopes & Alexander D. MacKerell Jr

  2. Institute of Molecular Pediatric Sciences, Gordon Center for Integrative Science, University of Chicago, 929 E. 57th St., Chicago, IL, 60637, USA

    Benoit Roux

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  1. Pedro E. M. Lopes
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  2. Benoit Roux
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  3. Alexander D. MacKerell Jr
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Correspondence to Alexander D. MacKerell Jr.

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Lopes, P.E.M., Roux, B. & MacKerell, A.D. Molecular modeling and dynamics studies with explicit inclusion of electronic polarizability: theory and applications. Theor Chem Acc 124, 11–28 (2009). https://doi.org/10.1007/s00214-009-0617-x

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