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

Abstract

Here in this work, we report two polarizable molecular mechanics (polMM) force field models for estimating the polarization energy in hybrid quantum mechanical molecular mechanical (QM/MM) calculations. These two models, named the potential of atomic charges (PAC) and potential of atomic dipoles (PAD), are formulated from the ab initio quantum mechanical (QM) response kernels for the prediction of the QM density response to an external molecular mechanical (MM) environment (as described by external point charges). The PAC model is similar to fluctuating charge (FQ) models because the energy depends on external electrostatic potential values at QM atomic sites; the PAD energy depends on external electrostatic field values at QM atomic sites, resembling induced dipole (ID) models. To demonstrate their uses, we apply the PAC and PAD models to 12 small molecules, which are solvated by TIP3P water. The PAC model reproduces the QM/MM polarization energy with a R2 value of 0.71 for aniline (in 10,000 TIP3P water configurations) and 0.87 or higher for other eleven solute molecules, while the PAD model has a much better performance with R2 values of 0.98 or higher. The PAC model reproduces reference QM/MM hydration free energies for 12 solute molecules with a RMSD ofmore » 0.59 kcal/mol. The PAD model is even more accurate, with a much smaller RMSD of 0.12 kcal/mol, with respect to the reference. Lastly, this suggests that polarization effects, including both local charge distortion and intramolecular charge transfer, can be well captured by induced dipole type models with proper parametrization.« less

Authors:
; ; ; ; ; ORCiD logo; ORCiD logo; ORCiD logo; ; ORCiD logo
Publication Date:
Research Org.:
Brookhaven National Laboratory (BNL), Upton, NY (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES)
OSTI Identifier:
1342645
Report Number(s):
BNL-113460-2017-JA
Journal ID: ISSN 1549-9618; R&D Project: 16068; KC0403020
Grant/Contract Number:  
SC0012704; SC0011297; GM096678-02; GM072558; GM051501
Resource Type:
Accepted Manuscript
Journal Name:
Journal of Chemical Theory and Computation
Additional Journal Information:
Journal Volume: 13; Journal Issue: 2; Journal ID: ISSN 1549-9618
Publisher:
American Chemical Society
Country of Publication:
United States
Language:
English
Subject:
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSICS; 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY

Citation Formats

Huang, Jing, Mei, Ye, König, Gerhard, Simmonett, Andrew C., Pickard, Frank C., Wu, Qin, Wang, Lee-Ping, MacKerell, Alexander D., Brooks, Bernard R., and Shao, Yihan. An Estimation of Hybrid Quantum Mechanical Molecular Mechanical Polarization Energies for Small Molecules Using Polarizable Force-Field Approaches. United States: N. p., 2017. Web. doi:10.1021/acs.jctc.6b01125.
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Huang, Jing, Mei, Ye, König, Gerhard, Simmonett, Andrew C., Pickard, Frank C., Wu, Qin, Wang, Lee-Ping, MacKerell, Alexander D., Brooks, Bernard R., & Shao, Yihan. An Estimation of Hybrid Quantum Mechanical Molecular Mechanical Polarization Energies for Small Molecules Using Polarizable Force-Field Approaches. United States. https://doi.org/10.1021/acs.jctc.6b01125
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Huang, Jing, Mei, Ye, König, Gerhard, Simmonett, Andrew C., Pickard, Frank C., Wu, Qin, Wang, Lee-Ping, MacKerell, Alexander D., Brooks, Bernard R., and Shao, Yihan. Tue . "An Estimation of Hybrid Quantum Mechanical Molecular Mechanical Polarization Energies for Small Molecules Using Polarizable Force-Field Approaches". United States. https://doi.org/10.1021/acs.jctc.6b01125. https://www.osti.gov/servlets/purl/1342645.
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@article{osti_1342645,
title = {An Estimation of Hybrid Quantum Mechanical Molecular Mechanical Polarization Energies for Small Molecules Using Polarizable Force-Field Approaches},
author = {Huang, Jing and Mei, Ye and König, Gerhard and Simmonett, Andrew C. and Pickard, Frank C. and Wu, Qin and Wang, Lee-Ping and MacKerell, Alexander D. and Brooks, Bernard R. and Shao, Yihan},
abstractNote = {Here in this work, we report two polarizable molecular mechanics (polMM) force field models for estimating the polarization energy in hybrid quantum mechanical molecular mechanical (QM/MM) calculations. These two models, named the potential of atomic charges (PAC) and potential of atomic dipoles (PAD), are formulated from the ab initio quantum mechanical (QM) response kernels for the prediction of the QM density response to an external molecular mechanical (MM) environment (as described by external point charges). The PAC model is similar to fluctuating charge (FQ) models because the energy depends on external electrostatic potential values at QM atomic sites; the PAD energy depends on external electrostatic field values at QM atomic sites, resembling induced dipole (ID) models. To demonstrate their uses, we apply the PAC and PAD models to 12 small molecules, which are solvated by TIP3P water. The PAC model reproduces the QM/MM polarization energy with a R2 value of 0.71 for aniline (in 10,000 TIP3P water configurations) and 0.87 or higher for other eleven solute molecules, while the PAD model has a much better performance with R2 values of 0.98 or higher. The PAC model reproduces reference QM/MM hydration free energies for 12 solute molecules with a RMSD of 0.59 kcal/mol. The PAD model is even more accurate, with a much smaller RMSD of 0.12 kcal/mol, with respect to the reference. Lastly, this suggests that polarization effects, including both local charge distortion and intramolecular charge transfer, can be well captured by induced dipole type models with proper parametrization.},
doi = {10.1021/acs.jctc.6b01125},
journal = {Journal of Chemical Theory and Computation},
number = 2,
volume = 13,
place = {United States},
year = {Tue Jan 24 00:00:00 EST 2017},
month = {Tue Jan 24 00:00:00 EST 2017}
}
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  • Journal of Chemical Theory and Computation, Vol. 12, Issue 8
  • DOI: 10.1021/acs.jctc.6b00385

LICHEM: A QM/MM program for simulations with multipolar and polarizable force fields: A QM/MM Program for Simulations with Multipolar and Polarizable Force Fields
journal, January 2016

  • Kratz, Eric G.; Walker, Alice R.; Lagardère, Louis
  • Journal of Computational Chemistry, Vol. 37, Issue 11
  • DOI: 10.1002/jcc.24295

TINKTEP: A fully self-consistent, mutually polarizable QM/MM approach based on the AMOEBA force field
journal, September 2016

  • Dziedzic, Jacek; Mao, Yuezhi; Shao, Yihan
  • The Journal of Chemical Physics, Vol. 145, Issue 12
  • DOI: 10.1063/1.4962909
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    Works referencing / citing this record:

    Predicting partition coefficients of drug-like molecules in the SAMPL6 challenge with Drude polarizable force fields
    journal, January 2020

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