Literature DB >> 30281307

Polarizable Drude Model with s-Type Gaussian or Slater Charge Density for General Molecular Mechanics Force Fields.

Mohammad Mehdi Ghahremanpour1, Paul J van Maaren1, Carl Caleman2,3, Geoffrey R Hutchison4, David van der Spoel1.   

Abstract

Gas-phase electric properties of molecules can be computed routinely using wave function methods or density functional theory (DFT). However, these methods remain computationally expensive for high-throughput screening of the vast chemical space of virtual compounds. Therefore, empirical force fields are a more practical choice in many cases, particularly since force field methods allow one to routinely predict the physicochemical properties in the condensed phases. This work presents Drude polarizable models, to increase the physical realism in empirical force fields, where the core particle is treated as a point charge and the Drude particle is treated either as a 1 s-Gaussian or a ns-Slater ( n = 1, 2, 3) charge density. Systematic parametrization to large high-quality quantum chemistry data obtained from the open access Alexandria Library ( https://doi.org/10.5281/zenodo.1004711 ) ensures the transferability of these parameters. The dipole moments and isotropic polarizabilities of the isolated molecules predicted by the proposed Drude models are in agreement with experiment with accuracy similar to DFT calculations at the B3LYP/aug-cc-pVTZ level of theory. The results show that the inclusion of explicit polarization into the models reduces the root-mean-square deviation with respect to DFT calculations of the predicted dipole moments of 152 dimers and clusters by more than 50%. Finally, we show that the accuracy of the electrostatic interaction energy of the water dimers can be improved systematically by the introduction of polarizable smeared charges as a model for charge penetration.

Entities:  

Year:  2018        PMID: 30281307     DOI: 10.1021/acs.jctc.8b00430

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


  8 in total

1.  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

2.  Synthesis, substitution kinetics, DNA/BSA binding and cytotoxicity of tridentate N^E^N (E = NH, O, S) pyrazolyl palladium(II) complexes.

Authors:  Reinner O Omondi; Adewale O Fadaka; Amos A Fatokun; Deogratius Jaganyi; Stephen O Ojwach
Journal:  J Biol Inorg Chem       Date:  2022-10-05       Impact factor: 3.862

3.  A collection of forcefield precursors for metal-organic frameworks.

Authors:  Taoyi Chen; Thomas A Manz
Journal:  RSC Adv       Date:  2019-11-13       Impact factor: 4.036

4.  Semi-automated Optimization of the CHARMM36 Lipid Force Field to Include Explicit Treatment of Long-Range Dispersion.

Authors:  Yalun Yu; Andreas Krämer; Richard M Venable; Andrew C Simmonett; Alexander D MacKerell; Jeffery B Klauda; Richard W Pastor; Bernard R Brooks
Journal:  J Chem Theory Comput       Date:  2021-02-23       Impact factor: 6.006

5.  Large scale relative protein ligand binding affinities using non-equilibrium alchemy.

Authors:  Vytautas Gapsys; Laura Pérez-Benito; Matteo Aldeghi; Daniel Seeliger; Herman van Vlijmen; Gary Tresadern; Bert L de Groot
Journal:  Chem Sci       Date:  2019-12-02       Impact factor: 9.825

6.  Deriving a Polarizable Force Field for Biomolecular Building Blocks with Minimal Empirical Calibration.

Authors:  Koen M Visscher; Daan P Geerke
Journal:  J Phys Chem B       Date:  2020-02-19       Impact factor: 2.991

7.  Rotational and Translational Diffusion of Proteins as a Function of Concentration.

Authors:  Zahedeh Bashardanesh; Johan Elf; Haiyang Zhang; David van der Spoel
Journal:  ACS Omega       Date:  2019-11-27

8.  Metallic Effects on p-Hydroxyphenyl Porphyrin Thin-Film-Based Planar Optical Waveguide Gas Sensor: Experimental and Computational Studies.

Authors:  Nuerguli Kari; Marco Zannotti; Rita Giovannetti; David Řeha; Babak Minofar; Shawket Abliz; Abliz Yimit
Journal:  Nanomaterials (Basel)       Date:  2022-03-13       Impact factor: 5.076

  8 in total

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