Literature DB >> 19606279

Simple Formulas for Improved Point-Charge Electrostatics in Classical Force Fields and Hybrid Quantum Mechanical/Molecular Mechanical Embedding.

G A Cisneros1, S Na-Im Tholander, O Parisel, T A Darden, D Elking, L Perera, J-P Piquemal.   

Abstract

We present a simple damping scheme for point-charge electrostatics that could be used directly in classical force fields. The approach acts at the charge (or monopole) level only and allows the inclusion of short-range electrostatic penetration effects at a very low cost. Results are compared with density functional theory Coulomb intermolecular interaction energies and with several other methods such as distributed multipoles, damped distributed multipoles, and transferable Hermite-Gaussian densities. Realistic trends in the interactions are observed for atom-centered Mertz-Kollman corrected point-charge distributions. The approach allows increasing the selectivity of parameters in the case of metal complexes. In addition, two QM/MM calculations are presented where the damping function is employed to include the MM atoms located at the QM/MM boundary. The first calculation corresponds to the gas-phase proton transfer of aspartic acid through water and the second is the first step of the reaction catalyzed by the 4-oxalocrotonate tautomerase (4OT) enzyme. First, improved agreement is observed when using the damping approach compared with the conventional excluded charge method or when including all charges in the calculation. Second, in the case of 4OT, the damped charge approach is in agreement with previous calculations, whereas including all charges gives a significantly higher energy barrier. In both cases, no reparameterization of the van der Waals part of the force field was performed.

Entities:  

Year:  2008        PMID: 19606279      PMCID: PMC2709874          DOI: 10.1002/qua.21675

Source DB:  PubMed          Journal:  Int J Quantum Chem        ISSN: 0020-7608            Impact factor:   2.444


  22 in total

1.  The protein backbone makes important contributions to 4-oxalocrotonate tautomerase enzyme catalysis: understanding from theory and experiment.

Authors:  G Andrés Cisneros; Min Wang; Peter Silinski; Michael C Fitzgerald; Weitao Yang
Journal:  Biochemistry       Date:  2004-06-08       Impact factor: 3.162

2.  A critical evaluation of different QM/MM frontier treatments with SCC-DFTB as the QM method.

Authors:  P H König; M Hoffmann; Th Frauenheim; Q Cui
Journal:  J Phys Chem B       Date:  2005-05-12       Impact factor: 2.991

3.  [Pb(H2O)]2+ and [Pb(OH)]+: four-component density functional theory calculations, correlated scalar relativistic constrained-space orbital variation energy decompositions, and topological analysis.

Authors:  Christophe Gourlaouen; Jean-Philip Piquemal; Olivier Parisel
Journal:  J Chem Phys       Date:  2006-05-07       Impact factor: 3.488

4.  Charge-dependent model for many-body polarization, exchange, and dispersion interactions in hybrid quantum mechanical/molecular mechanical calculations.

Authors:  Timothy J Giese; Darrin M York
Journal:  J Chem Phys       Date:  2007-11-21       Impact factor: 3.488

5.  Numerical fitting of molecular properties to Hermite Gaussians.

Authors:  G Andrés Cisneros; Dennis Elking; Jean-Philip Piquemal; Thomas A Darden
Journal:  J Phys Chem A       Date:  2007-11-01       Impact factor: 2.781

6.  Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density.

Authors: 
Journal:  Phys Rev B Condens Matter       Date:  1988-01-15

7.  Electrostatic energy in the effective fragment potential method: theory and application to benzene dimer.

Authors:  Lyudmila V Slipchenko; Mark S Gordon
Journal:  J Comput Chem       Date:  2007-01-15       Impact factor: 3.376

8.  Revisiting the geometry of nd10 (n+1)s0 [M(H2O)]p+ complexes using four-component relativistic DFT calculations and scalar relativistic correlated CSOV energy decompositions (M(p+) = Cu+, Zn2+, Ag+, Cd2+, Au+, Hg2+).

Authors:  Christophe Gourlaouen; Jean-Philip Piquemal; Trond Saue; Olivier Parisel
Journal:  J Comput Chem       Date:  2006-01-30       Impact factor: 3.376

9.  Quadratic string method for determining the minimum-energy path based on multiobjective optimization.

Authors:  Steven K Burger; Weitao Yang
Journal:  J Chem Phys       Date:  2006-02-07       Impact factor: 3.488

10.  Self-Consistent Polarization of the Boundary in the Redistributed Charge and Dipole Scheme for Combined Quantum-Mechanical and Molecular-Mechanical Calculations.

Authors:  Yan Zhang; Hai Lin; Donald G Truhlar
Journal:  J Chem Theory Comput       Date:  2007-07       Impact factor: 6.006

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  14 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

Review 2.  Biomolecular electrostatics and solvation: a computational perspective.

Authors:  Pengyu Ren; Jaehun Chun; Dennis G Thomas; Michael J Schnieders; Marcelo Marucho; Jiajing Zhang; Nathan A Baker
Journal:  Q Rev Biophys       Date:  2012-11       Impact factor: 5.318

3.  Directional Dependence of Hydrogen Bonds: a Density-based Energy Decomposition Analysis and Its Implications on Force Field Development.

Authors:  Zhenyu Lu; Nengjie Zhou; Qin Wu; Yingkai Zhang
Journal:  J Chem Theory Comput       Date:  2011-12-13       Impact factor: 6.006

4.  Improved parameterization of interatomic potentials for rare gas dimers with density-based energy decomposition analysis.

Authors:  Nengjie Zhou; Zhenyu Lu; Qin Wu; Yingkai Zhang
Journal:  J Chem Phys       Date:  2014-06-07       Impact factor: 3.488

5.  Gaussian Multipole Model (GMM).

Authors:  Dennis M Elking; G Andrés Cisneros; Jean-Philip Piquemal; Thomas A Darden; Lee G Pedersen
Journal:  J Chem Theory Comput       Date:  2010       Impact factor: 6.006

6.  An optimized charge penetration model for use with the AMOEBA force field.

Authors:  Joshua A Rackers; Qiantao Wang; Chengwen Liu; Jean-Philip Piquemal; Pengyu Ren; Jay W Ponder
Journal:  Phys Chem Chem Phys       Date:  2016-12-21       Impact factor: 3.676

7.  Polarizable intermolecular potentials for water and benzene interacting with halide and metal ions.

Authors:  Fabien Archambault; Christophe Chipot; Ignacio Soteras; F Javier Luque; Klaus Schulten; François Dehez
Journal:  J Chem Theory Comput       Date:  2009-01-01       Impact factor: 6.006

8.  Derivation of fixed partial charges for amino acids accommodating a specific water model and implicit polarization.

Authors:  David S Cerutti; Julia E Rice; William C Swope; David A Case
Journal:  J Phys Chem B       Date:  2013-02-18       Impact factor: 2.991

9.  Scalable improvement of SPME multipolar electrostatics in anisotropic polarizable molecular mechanics using a general short-range penetration correction up to quadrupoles.

Authors:  Christophe Narth; Louis Lagardère; Étienne Polack; Nohad Gresh; Qiantao Wang; David R Bell; Joshua A Rackers; Jay W Ponder; Pengyu Y Ren; Jean-Philip Piquemal
Journal:  J Comput Chem       Date:  2016-02-15       Impact factor: 3.376

10.  Ewald-based methods for Gaussian integral evaluation: application to a new parameterization of GEM.

Authors:  Robert E Duke; G Andrés Cisneros
Journal:  J Mol Model       Date:  2019-09-09       Impact factor: 1.810

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