Document Type

Article

Publication Date

2008

Publication Title

The Journal of Chemical Physics

Abstract

We present an ab initio polarizable representation of classical molecular mechanics (MM) atoms by employing an angular momentum-based expansion scheme of the point charges into partial wave orbitals. The charge density represented by these orbitals can be fully polarized, and for hybrid quantum-mechanical-molecular-mechanical (QM/MM) calculations, mutual polarization within the QM/MM Hamiltonian can be obtained. We present the mathematical formulation and the analytical expressions for the energy and forces pertaining to the method. We further develop a variational scheme to appropriately determine the expansion coefficients and then validate the method by considering polarizations of ions by the QM system employing the hybrid GROMACS-CPMD QM/MM program. Finally, we present a simpler prescription for adding isotropic polarizability to MM atoms in a QM/MM simulation. Employing this simpler scheme, we present QM/MM energy minimization results for the classic case of a water dimer and a hydrogen sulfide dimer. Also, we present single-point QM/MM results with and without the polarization to study the change in the ionization potential of tetrahydrobiopterin (BH(4)) in water and the change in the interaction energy of solvated BH(4) (described by MM) with the P(450) heme described by QM. The model can be employed for the development of an extensive classical polarizable force-field.

Comments

The authors acknowledge the financial support from the Department of Energy Grant No. DE-FG02-03ER15462, the National Institutes of Health Grant No. 1R15GM070469-01, and the National Center on Minority Health and Health Disparities Grant No. P20MD002725, and Computational support from the National Center for Supercomputer Applications NCSA at University of Illinois and Ohio Supercomputer Center, OH.

DOI

10.1063/1.2992527

Version

Publisher's PDF

Volume

129

Issue

15

Included in

Chemistry Commons

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