Literature DB >> 29149556

Evaluating Force-Field London Dispersion Coefficients Using the Exchange-Hole Dipole Moment Model.

Mohamad Mohebifar1, Erin R Johnson2, Christopher N Rowley1.   

Abstract

London dispersion interactions play an integral role in materials science and biophysics. Force fields for atomistic molecular simulations typically represent dispersion interactions by the 12-6 Lennard-Jones potential using empirically determined parameters. These parameters are generally underdetermined, and there is no straightforward way to test if they are physically realistic. Alternatively, the exchange-hole dipole moment (XDM) model from density-functional theory predicts atomic and molecular London dispersion coefficients from first principles, providing an innovative strategy to validate the dispersion terms of molecular-mechanical force fields. In this work, the XDM model was used to obtain the London dispersion coefficients of 88 organic molecules relevant to biochemistry and pharmaceutical chemistry and the values compared with those derived from the Lennard-Jones parameters of the CGenFF, GAFF, OPLS, and Drude polarizable force fields. The molecular dispersion coefficients for the CGenFF, GAFF, and OPLS models are systematically higher than the XDM-calculated values by a factor of roughly 1.5, likely due to neglect of higher order dispersion terms and premature truncation of the dispersion-energy summation. The XDM dispersion coefficients span a large range for some molecular-mechanical atom types, suggesting an unrecognized source of error in force-field models, which assume that atoms of the same type have the same dispersion interactions. Agreement with the XDM dispersion coefficients is even poorer for the Drude polarizable force field. Popular water models were also examined, and TIP3P was found to have dispersion coefficients similar to the experimental and XDM references, although other models employ anomalously high values. Finally, XDM-derived dispersion coefficients were used to parametrize molecular-mechanical force fields for five liquids-benzene, toluene, cyclohexane, n-pentane, and n-hexane-which resulted in improved accuracy in the computed enthalpies of vaporization despite only having to evaluate a much smaller section of the parameter space.

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Year:  2017        PMID: 29149556     DOI: 10.1021/acs.jctc.7b00522

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


  8 in total

1.  Computation of protein-ligand binding free energies using quantum mechanical bespoke force fields.

Authors:  Daniel J Cole; Israel Cabeza de Vaca; William L Jorgensen
Journal:  Medchemcomm       Date:  2019-02-27       Impact factor: 3.597

2.  Improving Force Field Accuracy by Training against Condensed-Phase Mixture Properties.

Authors:  Simon Boothroyd; Owen C Madin; David L Mobley; Lee-Ping Wang; John D Chodera; Michael R Shirts
Journal:  J Chem Theory Comput       Date:  2022-05-09       Impact factor: 6.578

3.  Simulating protein-ligand binding with neural network potentials.

Authors:  Shae-Lynn J Lahey; Christopher N Rowley
Journal:  Chem Sci       Date:  2020-01-23       Impact factor: 9.825

4.  A Simple Method for Including Polarization Effects in Solvation Free Energy Calculations When Using Fixed-Charge Force Fields: Alchemically Polarized Charges.

Authors:  Braden D Kelly; William R Smith
Journal:  ACS Omega       Date:  2020-07-07

5.  A QM/MM Derived Polarizable Water Model for Molecular Simulation.

Authors:  Koen M Visscher; William C Swope; Daan P Geerke
Journal:  Molecules       Date:  2018-11-29       Impact factor: 4.411

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.  Extension of an Atom-Atom Dispersion Function to Halogen Bonds and Its Use for Rational Design of Drugs and Biocatalysts.

Authors:  Wiktoria Jedwabny; Edyta Dyguda-Kazimierowicz; Katarzyna Pernal; Krzysztof Szalewicz; Konrad Patkowski
Journal:  J Phys Chem A       Date:  2021-02-23       Impact factor: 2.781

  8 in total

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