Literature DB >> 31136175

AMOEBA+ Classical Potential for Modeling Molecular Interactions.

Chengwen Liu1, Jean-Philip Piquemal1,2,3, Pengyu Ren1.   

Abstract

Classical potentials based on isotropic and additive atomic charges have been widely used to model molecules in computers for the past few decades. The crude approximations in the underlying physics are hindering both their accuracy and transferability across chemical and physical environments. Here we present a new classical potential, AMOEBA+, to capture essential intermolecular forces, including permanent electrostatics, repulsion, dispersion, many-body polarization, short-range charge penetration, and charge transfer, by extending the polarizable multipole-based AMOEBA (Atomic Multipole Optimized Energetics for Biomolecular Applications) model. For a set of common organic molecules, we show that AMOEBA+ with general parameters can reproduce both quantum mechanical interactions and energy decompositions according to Symmetry-Adapted Perturbation Theory (SAPT). Additionally, a new water model based on the AMOEBA+ framework captures various liquid-phase properties in molecular dynamics simulations while remaining consistent with SAPT energy decompositions, utilizing both ab initio data and experimental liquid properties. Our results demonstrate that it is possible to improve the physical basis of classical force fields to advance their accuracy and general applicability.

Entities:  

Year:  2019        PMID: 31136175      PMCID: PMC6615954          DOI: 10.1021/acs.jctc.9b00261

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


  93 in total

1.  Ion solvation thermodynamics from simulation with a polarizable force field.

Authors:  Alan Grossfield; Pengyu Ren; Jay W Ponder
Journal:  J Am Chem Soc       Date:  2003-12-17       Impact factor: 15.419

2.  Development of a polarizable force field for proteins via ab initio quantum chemistry: first generation model and gas phase tests.

Authors:  George A Kaminski; Harry A Stern; B J Berne; Richard A Friesner; Yixiang X Cao; Robert B Murphy; Ruhong Zhou; Thomas A Halgren
Journal:  J Comput Chem       Date:  2002-12       Impact factor: 3.376

3.  Inter- and intramolecular potential for the N-formylglycinamide-water system. A comparison between theoretical modeling and empirical force fields.

Authors:  Jose Manuel Hermida-Ramón; Steve Brdarski; Gunnar Karlström; Ulf Berg
Journal:  J Comput Chem       Date:  2003-01-30       Impact factor: 3.376

4.  Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew.

Authors:  Hans W Horn; William C Swope; Jed W Pitera; Jeffry D Madura; Thomas J Dick; Greg L Hura; Teresa Head-Gordon
Journal:  J Chem Phys       Date:  2004-05-22       Impact factor: 3.488

5.  The binding energies of the D2d and S4 water octamer isomers: high-level electronic structure and empirical potential results.

Authors:  Sotiris S Xantheas; Edoardo Aprà
Journal:  J Chem Phys       Date:  2004-01-08       Impact factor: 3.488

6.  Validation of the 53A6 GROMOS force field.

Authors:  Chris Oostenbrink; Thereza A Soares; Nico F A van der Vegt; Wilfred F van Gunsteren
Journal:  Eur Biophys J       Date:  2005-04-01       Impact factor: 1.733

7.  Towards a force field based on density fitting.

Authors:  Jean-Philip Piquemal; G Andrés Cisneros; Peter Reinhardt; Nohad Gresh; Thomas A Darden
Journal:  J Chem Phys       Date:  2006-03-14       Impact factor: 3.488

8.  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

9.  High-level ab initio calculations for the four low-lying families of minima of (H2O)20. I. Estimates of MP2/CBS binding energies and comparison with empirical potentials.

Authors:  George S Fanourgakis; Edoardo Aprà; Sotiris S Xantheas
Journal:  J Chem Phys       Date:  2004-08-08       Impact factor: 3.488

10.  Strike a balance: optimization of backbone torsion parameters of AMBER polarizable force field for simulations of proteins and peptides.

Authors:  Zhi-Xiang Wang; Wei Zhang; Chun Wu; Hongxing Lei; Piotr Cieplak; Yong Duan
Journal:  J Comput Chem       Date:  2006-04-30       Impact factor: 3.376

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  21 in total

1.  Psi4 1.4: Open-source software for high-throughput quantum chemistry.

Authors:  Daniel G A Smith; Lori A Burns; Andrew C Simmonett; Robert M Parrish; Matthew C Schieber; Raimondas Galvelis; Peter Kraus; Holger Kruse; Roberto Di Remigio; Asem Alenaizan; Andrew M James; Susi Lehtola; Jonathon P Misiewicz; Maximilian Scheurer; Robert A Shaw; Jeffrey B Schriber; Yi Xie; Zachary L Glick; Dominic A Sirianni; Joseph Senan O'Brien; Jonathan M Waldrop; Ashutosh Kumar; Edward G Hohenstein; Benjamin P Pritchard; Bernard R Brooks; Henry F Schaefer; Alexander Yu Sokolov; Konrad Patkowski; A Eugene DePrince; Uğur Bozkaya; Rollin A King; Francesco A Evangelista; Justin M Turney; T Daniel Crawford; C David Sherrill
Journal:  J Chem Phys       Date:  2020-05-14       Impact factor: 3.488

2.  Molecular Dynamics Simulations of Ionic Liquids and Electrolytes Using Polarizable Force Fields.

Authors:  Dmitry Bedrov; Jean-Philip Piquemal; Oleg Borodin; Alexander D MacKerell; Benoît Roux; Christian Schröder
Journal:  Chem Rev       Date:  2019-05-29       Impact factor: 60.622

3.  Atomic Polarizabilities for Interactive Dipole Induction Models.

Authors:  Jacob M Litman; Chengwen Liu; Pengyu Ren
Journal:  J Chem Inf Model       Date:  2021-12-28       Impact factor: 4.956

4.  Accurate description of molecular dipole surface with charge flux implemented for molecular mechanics.

Authors:  Xudong Yang; Chengwen Liu; Brandon D Walker; Pengyu Ren
Journal:  J Chem Phys       Date:  2020-08-14       Impact factor: 3.488

5.  High Order Ab Initio Valence Force Field with Chemical Pattern Based Parameter Assignment.

Authors:  Xudong Yang; Chengwen Liu; Pengyu Ren
Journal:  J Comput Biophys Chem       Date:  2021-12-29

6.  Automation of AMOEBA polarizable force field for small molecules: Poltype 2.

Authors:  Brandon Walker; Chengwen Liu; Elizabeth Wait; Pengyu Ren
Journal:  J Comput Chem       Date:  2022-07-01       Impact factor: 3.672

7.  Implementation of Geometry-Dependent Charge Flux into the Polarizable AMOEBA+ Potential.

Authors:  Chengwen Liu; Jean-Philip Piquemal; Pengyu Ren
Journal:  J Phys Chem Lett       Date:  2019-12-30       Impact factor: 6.475

8.  Implicit Solvents for the Polarizable Atomic Multipole AMOEBA Force Field.

Authors:  Rae A Corrigan; Guowei Qi; Andrew C Thiel; Jack R Lynn; Brandon D Walker; Thomas L Casavant; Louis Lagardere; Jean-Philip Piquemal; Jay W Ponder; Pengyu Ren; Michael J Schnieders
Journal:  J Chem Theory Comput       Date:  2021-03-26       Impact factor: 6.006

9.  Testing the Limitations of MD-Based Local Electric Fields Using the Vibrational Stark Effect in Solution: Penicillin G as a Test Case.

Authors:  Jacek Kozuch; Samuel H Schneider; Chu Zheng; Zhe Ji; Richard T Bradshaw; Steven G Boxer
Journal:  J Phys Chem B       Date:  2021-04-26       Impact factor: 2.991

10.  Advanced Electrostatic Model for Monovalent Ions Based on Ab Initio Energy Decomposition.

Authors:  Zhifeng Jing; Chengwen Liu; Pengyu Ren
Journal:  J Chem Inf Model       Date:  2021-06-07       Impact factor: 6.162

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