Determination of electrostatic parameters for a polarizable force field based on the classical Drude oscillator

Victor M. Anisimov, Guillaume Lamoureux, Igor Vorobyov, Niu Huang, Benoît Roux, Alexander D. MacKerell

Research output: Contribution to journalArticle

214 Citations (Scopus)

Abstract

A procedure to determine the electrostatic parameters has been developed for a polarizable empirical force field based on the classical Drude oscillator model. Atomic charges and polarizabilities for a given molecule of interest were derived from restrained fitting to quantummechanical electrostatic potentials (ESP) calculated at the B3LYP/cc-pVDZ or B3LYP/aug-ccpVDZ levels on grid points located on concentric Connolly surfaces. The determination of the atomic polarizabilities requires a series of perturbed ESP maps, each one representing the electronic response of the molecule in the presence of a background charge placed on Connolly surfaces primarily along chemical bonds and lone pairs. Reference values for the partial atomic charges were taken from the CHARMM27 additive all-atom force field, and those for the polarizabilities were based on adjusted Miller's ahp atomic polarizability values. The fitted values of atomic polarizabilities were scaled to reflect the reduced polarization expected for the condensed media and/or to correct for the systematic underestimation of experimental molecular polarizabilities by B3LYP calculations. Following correction of the polarizabilities, the atomic charges were adjusted to reproduce gas-phase dipole moments. The developed scheme has been tested on a set of small molecules representing functional moieties of nucleic acids. The derived electrostatic parameters have been successfully applied in a preliminary polarizable molecular dynamics simulation of a DNA octamer in a box of water with sodium counterions. Thus, this study confirms the feasibility of the use of a polarizable force field based on a classical Drude model for simulations of biomolecules in the condensed phase.

Original languageEnglish (US)
Pages (from-to)153-168
Number of pages16
JournalJournal of Chemical Theory and Computation
Volume1
Issue number1
DOIs
StatePublished - Dec 1 2005
Externally publishedYes

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field theory (physics)
Electrostatics
oscillators
electrostatics
Molecules
molecules
Chemical bonds
Nucleic acids
Dipole moment
Biomolecules
nucleic acids
chemical bonds
Nucleic Acids
boxes
Molecular dynamics
dipole moments
DNA
deoxyribonucleic acid
simulation
Gases

ASJC Scopus subject areas

  • Computer Science Applications
  • Physical and Theoretical Chemistry

Cite this

Determination of electrostatic parameters for a polarizable force field based on the classical Drude oscillator. / Anisimov, Victor M.; Lamoureux, Guillaume; Vorobyov, Igor; Huang, Niu; Roux, Benoît; MacKerell, Alexander D.

In: Journal of Chemical Theory and Computation, Vol. 1, No. 1, 01.12.2005, p. 153-168.

Research output: Contribution to journalArticle

Anisimov, Victor M. ; Lamoureux, Guillaume ; Vorobyov, Igor ; Huang, Niu ; Roux, Benoît ; MacKerell, Alexander D. / Determination of electrostatic parameters for a polarizable force field based on the classical Drude oscillator. In: Journal of Chemical Theory and Computation. 2005 ; Vol. 1, No. 1. pp. 153-168.
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