Literature DB >> 18937511

Incorporation of a QM/MM buffer zone in the variational double self-consistent field method.

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

Abstract

The explicit polarization (X-Pol) potential is an electronic-structure-based polarization force field, designed for molecular dynamics simulations and modeling of biopolymers. In this approach, molecular polarization and charge transfer effects are explicitly treated by a combined quantum mechanical and molecular mechanical (QM/MM) scheme, and the wave function of the entire system is variationally optimized by a double self-consistent field (DSCF) method. In the present article, we introduce a QM buffer zone for a smooth transition from a QM region to an MM region. Instead of using the Mulliken charge approximation for all QM/MM interactions, the Coulombic interactions between the adjacent fragments are determined directly by electronic structure theory. The present method is designed to accelerate the speed of convergence of the total energy and charge density of the system.

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Year:  2008        PMID: 18937511      PMCID: PMC2725410          DOI: 10.1021/jp804512f

Source DB:  PubMed          Journal:  J Phys Chem B        ISSN: 1520-5207            Impact factor:   2.991


  9 in total

1.  Specific force field parameters determination for the hybrid ab initio QM/MM LSCF method.

Authors:  Nicolas Ferré; Xavier Assfeld; Jean-Louis Rivail
Journal:  J Comput Chem       Date:  2002-04-30       Impact factor: 3.376

2.  A priori evaluation of aqueous polarization effects through Monte Carlo QM-MM simulations.

Authors:  J Gao; X Xia
Journal:  Science       Date:  1992-10-23       Impact factor: 47.728

3.  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

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

Authors:  Wangshen Xie; Lingchun Song; Donald G Truhlar; Jiali Gao
Journal:  J Chem Phys       Date:  2008-06-21       Impact factor: 3.488

6.  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

7.  Proton shuttles and phosphatase activity in soluble epoxide hydrolase.

Authors:  Marco De Vivo; Bernd Ensing; Matteo Dal Peraro; German A Gomez; David W Christianson; Michael L Klein
Journal:  J Am Chem Soc       Date:  2007-01-17       Impact factor: 15.419

8.  Redistributed charge and dipole schemes for combined quantum mechanical and molecular mechanical calculations.

Authors:  Hai Lin; Donald G Truhlar
Journal:  J Phys Chem A       Date:  2005-05-05       Impact factor: 2.781

9.  QM/MM Minimum Free Energy Path: Methodology and Application to Triosephosphate Isomerase.

Authors:  Hao Hu; Zhenyu Lu; Weitao Yang
Journal:  J Chem Theory Comput       Date:  2007-03       Impact factor: 6.006

  9 in total
  9 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

2.  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

3.  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

4.  On the Interfragment Exchange in the X-Pol Method.

Authors:  Alessandro Cembran; Peng Bao; Yingjie Wang; Lingchun Song; Donald G Truhlar; Jiali Gao
Journal:  J Chem Theory Comput       Date:  2010       Impact factor: 6.006

5.  Polarized Molecular Orbital Model Chemistry. I. Ab Initio Foundations.

Authors:  Luke Fiedler; Jiali Gao; Donald G Truhlar
Journal:  J Chem Theory Comput       Date:  2011-03-03       Impact factor: 6.006

6.  X-Pol Potential: An Electronic Structure-Based Force Field for Molecular Dynamics Simulation of a Solvated Protein in Water.

Authors:  Wangshen Xie; Modesto Orozco; Donald G Truhlar; Jiali Gao
Journal:  J Chem Theory Comput       Date:  2009-02-17       Impact factor: 6.006

7.  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

8.  Explicit polarization (X-Pol) potential using ab initio molecular orbital theory and density functional theory.

Authors:  Lingchun Song; Jaebeom Han; Yen-lin Lin; Wangshen Xie; Jiali Gao
Journal:  J Phys Chem A       Date:  2009-10-29       Impact factor: 2.781

9.  Explicit polarization: a quantum mechanical framework for developing next generation force fields.

Authors:  Jiali Gao; Donald G Truhlar; Yingjie Wang; Michael J M Mazack; Patrick Löffler; Makenzie R Provorse; Pavel Rehak
Journal:  Acc Chem Res       Date:  2014-08-06       Impact factor: 22.384

  9 in total

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