Literature DB >> 21113276

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

Fabien Archambault1, Christophe Chipot, Ignacio Soteras, F Javier Luque, Klaus Schulten, François Dehez.   

Abstract

A complete derivation of polarizable intermolecular potentials based on high-level, gas-phase quantum-mechanical calculations is proposed. The importance of appreciable accuracy together with inherent simplicity represents a significant endeavor when enhancement of existing force fields for biological systems is sought. Toward this end, symmetry-adapted perturbation theory (SAPT) can provide an expansion of the total interaction energy into physically meaningful e.g. electrostatic, induction and van der Waals terms. Each contribution can be readily compared with its counterpart in classical force fields. Since the complexity of the different intermolecular terms cannot be fully embraced using a minimalist description, it is necessary to resort to polyvalent expressions capable of encapsulating overlooked contributions from the quantum-mechanical expansion. This choice results in consistent force field components that reflect the underlying physical principles of the phenomena. This simplified potential energy function is detailed and definitive guidelines are drawn. As a proof of concept, the methodology is illustrated through a series of test cases that include the interaction of water and benzene with halide and metal ions. In each case considered, the total energy is reproduced accurately over a range of biologically relevant distances.

Entities:  

Year:  2009        PMID: 21113276      PMCID: PMC2990227          DOI: 10.1021/ct9004189

Source DB:  PubMed          Journal:  J Chem Theory Comput        ISSN: 1549-9618            Impact factor:   6.006


  28 in total

1.  The Cationminus signpi Interaction.

Authors:  Jennifer C. Ma; Dennis A. Dougherty
Journal:  Chem Rev       Date:  1997-08-05       Impact factor: 60.622

2.  CHARMM fluctuating charge force field for proteins: II protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model.

Authors:  Sandeep Patel; Alexander D Mackerell; Charles L Brooks
Journal:  J Comput Chem       Date:  2004-09       Impact factor: 3.376

3.  A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6.

Authors:  Chris Oostenbrink; Alessandra Villa; Alan E Mark; Wilfred F van Gunsteren
Journal:  J Comput Chem       Date:  2004-10       Impact factor: 3.376

4.  Developing Improved Charge Sets for the Modeling of the KcsA K(+) Channel Using QM/MM Electrostatic Potentials.

Authors:  Denis Bucher; Leonardo Guidoni; Patrick Maurer; Ursula Rothlisberger
Journal:  J Chem Theory Comput       Date:  2009-08-11       Impact factor: 6.006

5.  Accurate Induction Energies for Small Organic Molecules:  1. Theory.

Authors:  Alston J Misquitta; Anthony J Stone
Journal:  J Chem Theory Comput       Date:  2008-01       Impact factor: 6.006

6.  Molecular dynamics simulations of DNA with polarizable force fields: convergence of an ideal B-DNA structure to the crystallographic structure.

Authors:  Volodymyr Babin; Jason Baucom; Thomas A Darden; Celeste Sagui
Journal:  J Phys Chem B       Date:  2006-06-15       Impact factor: 2.991

7.  Two-stage folding of HP-35 from ab initio simulations.

Authors:  Hongxing Lei; Yong Duan
Journal:  J Mol Biol       Date:  2007-04-20       Impact factor: 5.469

8.  Force field bias in protein folding simulations.

Authors:  Peter L Freddolino; Sanghyun Park; Benoît Roux; Klaus Schulten
Journal:  Biophys J       Date:  2009-05-06       Impact factor: 4.033

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

Authors:  G A Cisneros; S Na-Im Tholander; O Parisel; T A Darden; D Elking; L Perera; J-P Piquemal
Journal:  Int J Quantum Chem       Date:  2008       Impact factor: 2.444

10.  CHARMM fluctuating charge force field for proteins: I parameterization and application to bulk organic liquid simulations.

Authors:  Sandeep Patel; Charles L Brooks
Journal:  J Comput Chem       Date:  2004-01-15       Impact factor: 3.376

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  4 in total

1.  Improved Modeling of Cation-π and Anion-Ring Interactions Using the Drude Polarizable Empirical Force Field for Proteins.

Authors:  Fang-Yu Lin; Alexander D MacKerell
Journal:  J Comput Chem       Date:  2019-09-13       Impact factor: 3.376

2.  Challenges in protein folding simulations: Timescale, representation, and analysis.

Authors:  Peter L Freddolino; Christopher B Harrison; Yanxin Liu; Klaus Schulten
Journal:  Nat Phys       Date:  2010-10-01       Impact factor: 20.034

Review 3.  Cation-π Interactions and their Functional Roles in Membrane Proteins.

Authors:  Daniel T Infield; Ali Rasouli; Grace D Galles; Christophe Chipot; Emad Tajkhorshid; Christopher A Ahern
Journal:  J Mol Biol       Date:  2021-05-04       Impact factor: 5.469

4.  Non-covalent interactions from a Quantum Chemical Topology perspective.

Authors:  Paul L A Popelier
Journal:  J Mol Model       Date:  2022-08-25       Impact factor: 2.172

  4 in total

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