Literature DB >> 27305996

Determining polarizable force fields with electrostatic potentials from quantum mechanical linear response theory.

Hao Wang1, Weitao Yang1.   

Abstract

We developed a new method to calculate the atomic polarizabilities by fitting to the electrostatic potentials (ESPs) obtained from quantum mechanical (QM) calculations within the linear response theory. This parallels the conventional approach of fitting atomic charges based on electrostatic potentials from the electron density. Our ESP fitting is combined with the induced dipole model under the perturbation of uniform external electric fields of all orientations. QM calculations for the linear response to the external electric fields are used as input, fully consistent with the induced dipole model, which itself is a linear response model. The orientation of the uniform external electric fields is integrated in all directions. The integration of orientation and QM linear response calculations together makes the fitting results independent of the orientations and magnitudes of the uniform external electric fields applied. Another advantage of our method is that QM calculation is only needed once, in contrast to the conventional approach, where many QM calculations are needed for many different applied electric fields. The molecular polarizabilities obtained from our method show comparable accuracy with those from fitting directly to the experimental or theoretical molecular polarizabilities. Since ESP is directly fitted, atomic polarizabilities obtained from our method are expected to reproduce the electrostatic interactions better. Our method was used to calculate both transferable atomic polarizabilities for polarizable molecular mechanics' force fields and nontransferable molecule-specific atomic polarizabilities.

Entities:  

Year:  2016        PMID: 27305996      PMCID: PMC4912555          DOI: 10.1063/1.4953558

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  30 in total

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

Review 2.  Molecular dynamics simulations of biomolecules.

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Journal:  Nat Struct Biol       Date:  2002-09

3.  Toward a Separate Reproduction of the Contributions to the Hartree-Fock and DFT Intermolecular Interaction Energies by Polarizable Molecular Mechanics with the SIBFA Potential.

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Journal:  J Chem Theory Comput       Date:  2007-05       Impact factor: 6.006

4.  Revised Parameters for the AMOEBA Polarizable Atomic Multipole Water Model.

Authors:  Marie L Laury; Lee-Ping Wang; Vijay S Pande; Teresa Head-Gordon; Jay W Ponder
Journal:  J Phys Chem B       Date:  2015-02-26       Impact factor: 2.991

5.  Development of polarizable models for molecular mechanical calculations. 4. van der Waals parametrization.

Authors:  Junmei Wang; Piotr Cieplak; Jie Li; Qin Cai; Meng-Juei Hsieh; Ray Luo; Yong Duan
Journal:  J Phys Chem B       Date:  2012-06-06       Impact factor: 2.991

6.  Development of polarizable models for molecular mechanical calculations I: parameterization of atomic polarizability.

Authors:  Junmei Wang; Piotr Cieplak; Jie Li; Tingjun Hou; Ray Luo; Yong Duan
Journal:  J Phys Chem B       Date:  2011-03-10       Impact factor: 2.991

7.  Development of polarizable models for molecular mechanical calculations II: induced dipole models significantly improve accuracy of intermolecular interaction energies.

Authors:  Junmei Wang; Piotr Cieplak; Jie Li; Jun Wang; Qin Cai; MengJuei Hsieh; Hongxing Lei; Ray Luo; Yong Duan
Journal:  J Phys Chem B       Date:  2011-03-10       Impact factor: 2.991

8.  Specificity of acyl transfer from 2-mercaptobenzamide thioesters to the HIV-1 nucleocapsid protein.

Authors:  Lisa M Miller Jenkins; Toshiaki Hara; Stewart R Durell; Ryo Hayashi; John K Inman; Jean-Philip Piquemal; Nohad Gresh; Ettore Appella
Journal:  J Am Chem Soc       Date:  2007-08-18       Impact factor: 15.419

9.  The Polarizable Atomic Multipole-based AMOEBA Force Field for Proteins.

Authors:  Yue Shi; Zhen Xia; Jiajing Zhang; Robert Best; Chuanjie Wu; Jay W Ponder; Pengyu Ren
Journal:  J Chem Theory Comput       Date:  2013       Impact factor: 6.006

10.  General Model for Treating Short-Range Electrostatic Penetration in a Molecular Mechanics Force Field.

Authors:  Qiantao Wang; Joshua A Rackers; Chenfeng He; Rui Qi; Christophe Narth; Louis Lagardere; Nohad Gresh; Jay W Ponder; Jean-Philip Piquemal; Pengyu Ren
Journal:  J Chem Theory Comput       Date:  2015-04-28       Impact factor: 6.006

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  4 in total

1.  An Estimation of Hybrid Quantum Mechanical Molecular Mechanical Polarization Energies for Small Molecules Using Polarizable Force-Field Approaches.

Authors:  Jing Huang; Ye Mei; Gerhard König; Andrew C Simmonett; Frank C Pickard; Qin Wu; Lee-Ping Wang; Alexander D MacKerell; Bernard R Brooks; Yihan Shao
Journal:  J Chem Theory Comput       Date:  2017-01-24       Impact factor: 6.006

2.  Mapping the Drude polarizable force field onto a multipole and induced dipole model.

Authors:  Jing Huang; Andrew C Simmonett; Frank C Pickard; Alexander D MacKerell; Bernard R Brooks
Journal:  J Chem Phys       Date:  2017-10-28       Impact factor: 3.488

3.  Predicting partition coefficients of drug-like molecules in the SAMPL6 challenge with Drude polarizable force fields.

Authors:  Ye Ding; You Xu; Cheng Qian; Jinfeng Chen; Jian Zhu; Houhou Huang; Yi Shi; Jing Huang
Journal:  J Comput Aided Mol Des       Date:  2020-01-20       Impact factor: 3.686

4.  Deep Neural Network Model to Predict the Electrostatic Parameters in the Polarizable Classical Drude Oscillator Force Field.

Authors:  Anmol Kumar; Poonam Pandey; Payal Chatterjee; Alexander D MacKerell
Journal:  J Chem Theory Comput       Date:  2022-02-11       Impact factor: 6.006

  4 in total

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