Literature DB >> 19045177

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

P K Biswas1, Valentin Gogonea.   

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.

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Year:  2008        PMID: 19045177      PMCID: PMC2736615          DOI: 10.1063/1.2992527

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  8 in total

Review 1.  Tetrahydrobiopterin radical enzymology.

Authors:  Chin-Chuan Wei; Brian R Crane; Dennis J Stuehr
Journal:  Chem Rev       Date:  2003-06       Impact factor: 60.622

2.  Car-Parrinello molecular dynamics with Vanderbilt ultrasoft pseudopotentials.

Authors: 
Journal:  Phys Rev B Condens Matter       Date:  1993-04-15

3.  Unified approach for molecular dynamics and density-functional theory.

Authors: 
Journal:  Phys Rev Lett       Date:  1985-11-25       Impact factor: 9.161

4.  A regularized and renormalized electrostatic coupling Hamiltonian for hybrid quantum-mechanical-molecular-mechanical calculations.

Authors:  P K Biswas; V Gogonea
Journal:  J Chem Phys       Date:  2005-10-22       Impact factor: 3.488

5.  VMD: visual molecular dynamics.

Authors:  W Humphrey; A Dalke; K Schulten
Journal:  J Mol Graph       Date:  1996-02

6.  Electronic structure, ionization potential, and electron affinity of the enzyme cofactor (6R)-5,6,7,8-tetrahydrobiopterin in the gas phase, solution, and protein environments.

Authors:  Valentin Gogonea; Jacinto M Shy; Pradip K Biswas
Journal:  J Phys Chem B       Date:  2006-11-16       Impact factor: 2.991

7.  From dimer to condensed phases at extreme conditions: accurate predictions of the properties of water by a Gaussian charge polarizable model.

Authors:  Patrice Paricaud; Milan Predota; Ariel A Chialvo; Peter T Cummings
Journal:  J Chem Phys       Date:  2005-06-22       Impact factor: 3.488

8.  Crystal structure of constitutive endothelial nitric oxide synthase: a paradigm for pterin function involving a novel metal center.

Authors:  C S Raman; H Li; P Martásek; V Král; B S Masters; T L Poulos
Journal:  Cell       Date:  1998-12-23       Impact factor: 41.582

  8 in total
  2 in total

Review 1.  Classical electrostatics for biomolecular simulations.

Authors:  G Andrés Cisneros; Mikko Karttunen; Pengyu Ren; Celeste Sagui
Journal:  Chem Rev       Date:  2013-08-27       Impact factor: 60.622

2.  Polarization effects in molecular mechanical force fields.

Authors:  Piotr Cieplak; François-Yves Dupradeau; Yong Duan; Junmei Wang
Journal:  J Phys Condens Matter       Date:  2009-07-24       Impact factor: 2.333

  2 in total

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