Dataset Information

A polarizable force-field model for quantum-mechanical-molecular-mechanical Hamiltonian using expansion of point charges into orbitals.

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.

SUBMITTER: Biswas PK

PROVIDER: S-EPMC2736615 | biostudies-literature | 2008 Oct

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

A polarizable force-field model for quantum-mechanical-molecular-mechanical Hamiltonian using expansion of point charges into orbitals.

Biswas P K PK Gogonea Valentin V

The Journal of chemical physics 20081001 15

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 energ ...[more]

PMID: 19045177

Similar Datasets

Project description:A quantum mechanical force field (QMFF) for water is described. Unlike traditional approaches that use quantum mechanical results and experimental data to parameterize empirical potential energy functions, the present QMFF uses a quantum mechanical framework to represent intramolecular and intermolecular interactions in an entire condensed-phase system. In particular, the internal energy terms used in molecular mechanics are replaced by a quantum mechanical formalism that naturally includes electronic polarization due to intermolecular interactions and its effects on the force constants of the intramolecular force field. As a quantum mechanical force field, both intermolecular interactions and the Hamiltonian describing the individual molecular fragments can be parameterized to strive for accuracy and computational efficiency. In this work, we introduce a polarizable molecular orbital model Hamiltonian for water and for oxygen- and hydrogen-containing compounds, whereas the electrostatic potential responsible for intermolecular interactions in the liquid and in solution is modeled by a three-point charge representation that realistically reproduces the total molecular dipole moment and the local hybridization contributions. The present QMFF for water, which is called the XP3P (explicit polarization with three-point-charge potential) model, is suitable for modeling both gas-phase clusters and liquid water. The paper demonstrates the performance of the XP3P model for water and proton clusters and the properties of the pure liquid from about 900 × 10(6) self-consistent-field calculations on a periodic system consisting of 267 water molecules. The unusual dipole derivative behavior of water, which is incorrectly modeled in molecular mechanics, is naturally reproduced as a result of an electronic structural treatment of chemical bonding by XP3P. We anticipate that the XP3P model will be useful for studying proton transport in solution and solid phases as well as across biological ion channels through membranes.

Dataset Information

A polarizable force-field model for quantum-mechanical-molecular-mechanical Hamiltonian using expansion of point charges into orbitals.

Publications

A polarizable force-field model for quantum-mechanical-molecular-mechanical Hamiltonian using expansion of point charges into orbitals.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets