Improvement of semiempirical response properties with charge-dependent response density

Giese, Timothy J.; York, Darrin M.

doi:doi:10.1063/1.2080007

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Fast evaluation of polarizable forces

Polarizability is considered to be the single most significant development in the next generation of force fields for biomolecular simulations. However, the self-consistent computation of induced atomic dipoles in a polarizable force field is expensive due to the cost of solving a large dense linear system at each step of a simulation. This article introduces methods that reduce the cost of computing the electrostatic energy and force of a polarizable model from about 7.5 times the cost of compu...

Coarse-grained free-energy-functional treatment of quasistatic multiscale processes in heterogeneous materials

A new treatment of quasistatic (reversible) multiscale processes in heterogeneous materials at nonzero temperature is presented. The system is coarse grained by means of a finite-element mesh. The coarse-grained free-energy functional (of the positions of the nodes of the mesh) appropriate to the thermodynamic-state variables controlled in the relevant process is minimized. Tests of the new procedure on a Lennard-Jonesium crystal yield thermomechanical properties in good agreement with the “exa...

The present work outlines a new method for treatment of charge-dependent polarizability in semiempirical quantum models for use in combined quantum-mechanical/molecular mechanical simulations of biological reactions. The method addresses a major shortcoming in the performance of conventional semiempirical models for these simulations that is tied to the use of a localized minimal atomic-orbital basis set. The present approach has the advantages that it uses a density basis that retains a set of linear-response equations, does not increase the atomic-orbital basis, and avoids the problem of artificial charge transfer and scaling of the polarizability seen in related models that allow atomic charges to fluctuate. The model introduces four new atom-based parameters and has been tested with the modified neglect of differential overlap d-orbital Hamiltonian against 1132 molecules and ions and shown to decrease the dipole moment and polarizability errors by factors of 2 and 10, respectively, with respect to density-functional results. The method performs impressively for a variety of charge states (from 2+ to 2−), and offers a potentially powerful extension in the design of next generation semiempirical quantum models for accurate simulations of highly charged biological reactions.

Article Outline

INTRODUCTION
METHODS
1. Chemical-potential equalization correction to the semiempirical energy
2. Reference data, semiempirical calculations, and parametrization
RESULTS AND DISCUSSION
1. Polarizability of atoms and monatomic ions
2. Dipole moments of neutral molecules
3. Polarizabilities of neutral molecules, cations, and anions
4. Na⁺⋯H₂O dipole and polarizability curves
CONCLUSION

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KEYWORDS and PACS

Keywords

biochemistry, molecular biophysics, polarisability, NDO calculations, density functional theory

PACS

87.15.R-

Reactions and kinetics
87.15.A-

Theory, modeling, and computer simulation

ARTICLE DATA

Digital Object Identifier

http://dx.doi.org/10.1063/1.2080007

PUBLICATION DATA

ISSN

0021-9606 (print)

1089-7690 (online)

Publisher

$abstract.society.value is a Member of CrossRef

American Institute of Physics

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