Literature DB >> 18570492

The variational explicit polarization potential and analytical first derivative of energy: Towards a next generation force field.

Wangshen Xie1, Lingchun Song, Donald G Truhlar, Jiali Gao.   

Abstract

A previous article proposed an electronic structure-based polarizable potential, called the explicit polarization (X-POL) potential, to treat many-body polarization and charge delocalization effects in polypeptides. Here, we present a variational version of the X-POL potential, in which the wave function of the entire molecular system is variationally optimized to yield the minimum total electronic energy. This allows the calculation of analytic gradients, a necessity for efficient molecular dynamics simulations. In this paper, the detailed derivations of the Fock matrix and analytic force are presented and discussed. The calculations involve a double self-consistent-field procedure in which the wave function of each fragment is self-consistently optimized in the presence of other fragments, and in addition the polarization of the entire system is self-consistently optimized. The variational X-POL potential has been implemented in the Chemistry at Harvard Molecular Mechanics (CHARMM) package and tested successfully for small model compounds.

Mesh:

Year:  2008        PMID: 18570492      PMCID: PMC2671662          DOI: 10.1063/1.2936122

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


  5 in total

Review 1.  Force fields for protein simulations.

Authors:  Jay W Ponder; David A Case
Journal:  Adv Protein Chem       Date:  2003

2.  Generalized hybrid-orbital method for combining density functional theory with molecular mechanicals.

Authors:  Jingzhi Pu; Jiali Gao; Donald G Truhlar
Journal:  Chemphyschem       Date:  2005-09-05       Impact factor: 3.102

Review 3.  Mechanisms and free energies of enzymatic reactions.

Authors:  Jiali Gao; Shuhua Ma; Dan T Major; Kwangho Nam; Jingzhi Pu; Donald G Truhlar
Journal:  Chem Rev       Date:  2006-08       Impact factor: 60.622

4.  The Design of a Next Generation Force Field: The X-POL Potential.

Authors:  Wangshen Xie; Jiali Gao
Journal:  J Chem Theory Comput       Date:  2007-11       Impact factor: 6.006

5.  Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme.

Authors:  A Warshel; M Levitt
Journal:  J Mol Biol       Date:  1976-05-15       Impact factor: 5.469

  5 in total
  29 in total

1.  Communication: variational many-body expansion: accounting for exchange repulsion, charge delocalization, and dispersion in the fragment-based explicit polarization method.

Authors:  Jiali Gao; Yingjie Wang
Journal:  J Chem Phys       Date:  2012-02-21       Impact factor: 3.488

Review 2.  Structural features of mammalian histidine decarboxylase reveal the basis for specific inhibition.

Authors:  A A Moya-García; A Pino-Angeles; R Gil-Redondo; A Morreale; F Sánchez-Jiménez
Journal:  Br J Pharmacol       Date:  2009-05       Impact factor: 8.739

3.  Fragment-based quantum mechanical methods for periodic systems with Ewald summation and mean image charge convention for long-range electrostatic interactions.

Authors:  Peng Zhang; Donald G Truhlar; Jiali Gao
Journal:  Phys Chem Chem Phys       Date:  2012-05-02       Impact factor: 3.676

Review 4.  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

5.  Quantum mechanical force field for water with explicit electronic polarization.

Authors:  Jaebeom Han; Michael J M Mazack; Peng Zhang; Donald G Truhlar; Jiali Gao
Journal:  J Chem Phys       Date:  2013-08-07       Impact factor: 3.488

6.  Incorporation of charge transfer into the explicit polarization fragment method by grand canonical density functional theory.

Authors:  Miho Isegawa; Jiali Gao; Donald G Truhlar
Journal:  J Chem Phys       Date:  2011-08-28       Impact factor: 3.488

7.  Multilevel X-Pol: a fragment-based method with mixed quantum mechanical representations of different fragments.

Authors:  Yingjie Wang; Carlos P Sosa; Alessandro Cembran; Donald G Truhlar; Jiali Gao
Journal:  J Phys Chem B       Date:  2012-03-19       Impact factor: 2.991

8.  A combined experimental and theoretical study of ion solvation in liquid N-methylacetamide.

Authors:  Haibo Yu; Christopher L Mazzanti; Troy W Whitfield; Roger E Koeppe; Olaf S Andersen; Benoît Roux
Journal:  J Am Chem Soc       Date:  2010-08-11       Impact factor: 15.419

9.  Using multipole point charge distributions to provide the electrostatic potential in the variational explicit polarization (X-Pol) potential.

Authors:  Hannah R Leverentz; Jiali Gao; Donald G Truhlar
Journal:  Theor Chem Acc       Date:  2011-01-26       Impact factor: 1.702

10.  Polarized Molecular Orbital Model Chemistry 3. The PMO Method Extended to Organic Chemistry.

Authors:  Miho Isegawa; Luke Fiedler; Hannah R Leverentz; Yingjie Wang; Santhanamoorthi Nachimuthu; Jiali Gao; Donald G Truhlar
Journal:  J Chem Theory Comput       Date:  2013-01-08       Impact factor: 6.006

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