Literature DB >> 19618944

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

Lingchun Song1, Jaebeom Han, Yen-lin Lin, Wangshen Xie, Jiali Gao.   

Abstract

The explicit polarization (X-Pol) method has been examined using ab initio molecular orbital theory and density functional theory. The X-Pol potential was designed to provide a novel theoretical framework for developing next-generation force fields for biomolecular simulations. Importantly, the X-Pol potential is a general method, which can be employed with any level of electronic structure theory. The present study illustrates the implementation of the X-Pol method using ab initio Hartree-Fock theory and hybrid density functional theory. The computational results are illustrated by considering a set of bimolecular complexes of small organic molecules and ions with water. The computed interaction energies and hydrogen bond geometries are in good accord with CCSD(T) calculations and B3LYP/aug-cc-pVDZ optimizations.

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Year:  2009        PMID: 19618944      PMCID: PMC2893562          DOI: 10.1021/jp902710a

Source DB:  PubMed          Journal:  J Phys Chem A        ISSN: 1089-5639            Impact factor:   2.781


  18 in total

1.  A Self-Consistent Space-Domain Decomposition Method for QM/MM Computations of Protein Electrostatic Potentials.

Authors:  Jose A Gascon; Siegfried S F Leung; Enrique R Batista; Victor S Batista
Journal:  J Chem Theory Comput       Date:  2006-01       Impact factor: 6.006

2.  Large-scale validation of a quantum mechanics based scoring function: predicting the binding affinity and the binding mode of a diverse set of protein-ligand complexes.

Authors:  Kaushik Raha; Kenneth M Merz
Journal:  J Med Chem       Date:  2005-07-14       Impact factor: 7.446

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.  Applications and assessment of QM:QM electronic embedding using generalized asymmetric Mulliken atomic charges.

Authors:  Priya V Parandekar; Hrant P Hratchian; Krishnan Raghavachari
Journal:  J Chem Phys       Date:  2008-10-14       Impact factor: 3.488

5.  Density-fragment interaction approach for quantum-mechanical/molecular-mechanical calculations with application to the excited states of a Mg(2+)-sensitive dye.

Authors:  Kazuhiro Fujimoto; Weitao Yang
Journal:  J Chem Phys       Date:  2008-08-07       Impact factor: 3.488

6.  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

7.  Dynamics of folded proteins.

Authors:  J A McCammon; B R Gelin; M Karplus
Journal:  Nature       Date:  1977-06-16       Impact factor: 49.962

8.  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

9.  Quantum mechanical study of the nonbonded forces in water-methanol complexes.

Authors:  K N Kirschner; R J Woods
Journal:  J Phys Chem A       Date:  2001-04-26       Impact factor: 2.781

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

Authors:  Wangshen Xie; Lingchun Song; Donald G Truhlar; Jiali Gao
Journal:  J Phys Chem B       Date:  2008-10-21       Impact factor: 2.991

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  21 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

Review 3.  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

4.  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

5.  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

6.  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

7.  Optimization of the explicit polarization (X-Pol) potential using a hybrid density functional.

Authors:  Jaebeom Han; Donald G Truhlar; Jiali Gao
Journal:  Theor Chem Acc       Date:  2012-03       Impact factor: 1.702

8.  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

9.  Quantum mechanical force fields for condensed phase molecular simulations.

Authors:  Timothy J Giese; Darrin M York
Journal:  J Phys Condens Matter       Date:  2017-08-17       Impact factor: 2.333

10.  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

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