Literature DB >> 34962789

Atomic Polarizabilities for Interactive Dipole Induction Models.

Jacob M Litman1, Chengwen Liu1, Pengyu Ren1.   

Abstract

Thole-style mutual induction models for molecular polarization have been adopted by several popular polarizable force fields (FFs) for their simplicity and transferability. The atomic polarizability parameters of these models are typically derived by fitting to ab initio or/and experimental molecular polarizabilities. In this work, we improve upon Thole polarizability parameters by employing both high-level quantum mechanics molecular polarizabilities and electrostatic potential (ESP) responses on three-dimensional grids. Our results indicate that the two approaches to derive atomic polarizability parameters are both effective, while the ESP approaches can also capture the polarization for the atoms with lone pair electrons. The resulting polarizability parameters have been validated on a set of over 7200 molecules covering the most common elements found in organic molecules (C, H, O, N, P, S, F, Cl, Br, and I). These parameters have also been tested on the experimentally measured molecular polarizabilities of 422 molecules. The final set of parameters derived in this work show notable improvement over the current AMOEBA set. The result is a highly transferable, expanded set of atomic polarizabilities defined by the local chemical environment in the form of SMARTS patterns. These parameters can be used directly in molecular mechanics polarizable potential energy functions such as AMOEBA, AMOEBA+, and other Thole-style models.

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Year:  2021        PMID: 34962789      PMCID: PMC8791008          DOI: 10.1021/acs.jcim.1c01307

Source DB:  PubMed          Journal:  J Chem Inf Model        ISSN: 1549-9596            Impact factor:   4.956


  32 in total

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Authors:  Florian Weigend
Journal:  Phys Chem Chem Phys       Date:  2006-01-03       Impact factor: 3.676

2.  Gaussian induced dipole polarization model.

Authors:  Dennis Elking; Tom Darden; Robert J Woods
Journal:  J Comput Chem       Date:  2007-05       Impact factor: 3.376

3.  Accurate molecular polarizabilities with coupled cluster theory and machine learning.

Authors:  David M Wilkins; Andrea Grisafi; Yang Yang; Ka Un Lao; Robert A DiStasio; Michele Ceriotti
Journal:  Proc Natl Acad Sci U S A       Date:  2019-02-07       Impact factor: 11.205

4.  Bond-Dependent Thole Model for Polarizability and Spectroscopy.

Authors:  Mark DelloStritto; Michael L Klein; Eric Borguet
Journal:  J Phys Chem A       Date:  2019-06-13       Impact factor: 2.781

5.  Polarizable Atomic Multipole-based Molecular Mechanics for Organic Molecules.

Authors:  Pengyu Ren; Chuanjie Wu; Jay W Ponder
Journal:  J Chem Theory Comput       Date:  2011-10-11       Impact factor: 6.006

6.  Polarizable Force Fields for Biomolecular Simulations: Recent Advances and Applications.

Authors:  Zhifeng Jing; Chengwen Liu; Sara Y Cheng; Rui Qi; Brandon D Walker; Jean-Philip Piquemal; Pengyu Ren
Journal:  Annu Rev Biophys       Date:  2019-03-27       Impact factor: 12.981

7.  Calculating binding free energies of host-guest systems using the AMOEBA polarizable force field.

Authors:  David R Bell; Rui Qi; Zhifeng Jing; Jin Yu Xiang; Christopher Mejias; Michael J Schnieders; Jay W Ponder; Pengyu Ren
Journal:  Phys Chem Chem Phys       Date:  2016-11-09       Impact factor: 3.676

8.  Consistent treatment of inter- and intramolecular polarization in molecular mechanics calculations.

Authors:  Pengyu Ren; Jay W Ponder
Journal:  J Comput Chem       Date:  2002-12       Impact factor: 3.376

9.  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

10.  AMOEBA binding free energies for the SAMPL7 TrimerTrip host-guest challenge.

Authors:  Yuanjun Shi; Marie L Laury; Zhi Wang; Jay W Ponder
Journal:  J Comput Aided Mol Des       Date:  2020-11-03       Impact factor: 3.686

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  2 in total

1.  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

2.  Computational study on the binding of Mango-II RNA aptamer and fluorogen using the polarizable force field AMOEBA.

Authors:  Xudong Yang; Chengwen Liu; Yu-An Kuo; Hsin-Chih Yeh; Pengyu Ren
Journal:  Front Mol Biosci       Date:  2022-09-02
  2 in total

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