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Title: Multiple environment single system quantum mechanical/molecular mechanical (MESS-QM/MM) calculations. 1. Estimation of polarization energies

Abstract

In combined quantum mechanical/molecular mechanical (QM/MM) free energy calculations, it is often advantageous to have a frozen geometry for the quantum mechanical (QM) region. For such multiple-environment single-system (MESS) cases, two schemes are proposed here for estimating the polarization energy: the first scheme, termed MESS-E, involves a Roothaan step extrapolation of the self-consistent field (SCF) energy; whereas the other scheme, termed MESS-H, employs a Newton–Raphson correction using an approximate inverse electronic Hessian of the QM region (which is constructed only once). Both schemes are extremely efficient, because the expensive Fock updates and SCF iterations in standard QM/MM calculations are completely avoided at each configuration. Here, they produce reasonably accurate QM/MM polarization energies: MESS-E can predict the polarization energy within 0.25 kcal/mol in terms of the mean signed error for two of our test cases, solvated methanol and solvated β-alanine, using the M06-2X or ωB97X-D functionals; MESS-H can reproduce the polarization energy within 0.2 kcal/mol for these two cases and for the oxyluciferin–luciferase complex, if the approximate inverse electronic Hessians are constructed with sufficient accuracy.

Authors:
 [1];  [2];  [1];  [3];  [4];  [1];  [5]
+ Show Author Affiliations
  1. National Institutes of Health, Rockville, MD (United States)
  2. National Institutes of Health, Rockville, MD (United States); East China Normal Univ., Shanghai (China); NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai (China)
  3. Southern Methodist Univ., Dallas, TX (United States)
  4. Univ. of Utah, Salt Lake City, UT (United States)
  5. Q-Chem Inc., Pleasanton, CA (United States)
Publication Date:
Research Org.:
Q-Chem Inc., Pleasanton, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1346161
Grant/Contract Number:  
SC0011297
Resource Type:
Accepted Manuscript
Journal Name:
Journal of Physical Chemistry. A, Molecules, Spectroscopy, Kinetics, Environment, and General Theory
Additional Journal Information:
Journal Volume: 119; Journal Issue: 9; Journal ID: ISSN 1089-5639
Publisher:
American Chemical Society
Country of Publication:
United States
Language:
English
Subject:
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSICS; 74 ATOMIC AND MOLECULAR PHYSICS; 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY

Citation Formats

Sodt, Alexander J., Mei, Ye, Konig, Gerhard, Tao, Peng, Steele, Ryan P., Brooks, Bernard R., and Shao, Yihan. Multiple environment single system quantum mechanical/molecular mechanical (MESS-QM/MM) calculations. 1. Estimation of polarization energies. United States: N. p., 2014. Web. doi:10.1021/jp5072296.
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Sodt, Alexander J., Mei, Ye, Konig, Gerhard, Tao, Peng, Steele, Ryan P., Brooks, Bernard R., & Shao, Yihan. Multiple environment single system quantum mechanical/molecular mechanical (MESS-QM/MM) calculations. 1. Estimation of polarization energies. United States. https://doi.org/10.1021/jp5072296
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Sodt, Alexander J., Mei, Ye, Konig, Gerhard, Tao, Peng, Steele, Ryan P., Brooks, Bernard R., and Shao, Yihan. Thu . "Multiple environment single system quantum mechanical/molecular mechanical (MESS-QM/MM) calculations. 1. Estimation of polarization energies". United States. https://doi.org/10.1021/jp5072296. https://www.osti.gov/servlets/purl/1346161.
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@article{osti_1346161,
title = {Multiple environment single system quantum mechanical/molecular mechanical (MESS-QM/MM) calculations. 1. Estimation of polarization energies},
author = {Sodt, Alexander J. and Mei, Ye and Konig, Gerhard and Tao, Peng and Steele, Ryan P. and Brooks, Bernard R. and Shao, Yihan},
abstractNote = {In combined quantum mechanical/molecular mechanical (QM/MM) free energy calculations, it is often advantageous to have a frozen geometry for the quantum mechanical (QM) region. For such multiple-environment single-system (MESS) cases, two schemes are proposed here for estimating the polarization energy: the first scheme, termed MESS-E, involves a Roothaan step extrapolation of the self-consistent field (SCF) energy; whereas the other scheme, termed MESS-H, employs a Newton–Raphson correction using an approximate inverse electronic Hessian of the QM region (which is constructed only once). Both schemes are extremely efficient, because the expensive Fock updates and SCF iterations in standard QM/MM calculations are completely avoided at each configuration. Here, they produce reasonably accurate QM/MM polarization energies: MESS-E can predict the polarization energy within 0.25 kcal/mol in terms of the mean signed error for two of our test cases, solvated methanol and solvated β-alanine, using the M06-2X or ωB97X-D functionals; MESS-H can reproduce the polarization energy within 0.2 kcal/mol for these two cases and for the oxyluciferin–luciferase complex, if the approximate inverse electronic Hessians are constructed with sufficient accuracy.},
doi = {10.1021/jp5072296},
journal = {Journal of Physical Chemistry. A, Molecules, Spectroscopy, Kinetics, Environment, and General Theory},
number = 9,
volume = 119,
place = {United States},
year = {Thu Oct 16 00:00:00 EDT 2014},
month = {Thu Oct 16 00:00:00 EDT 2014}
}
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Evaluating and interpreting the chemical relevance of the linear response kernel for atoms II: open shell
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Dual-basis second-order Møller-Plesset perturbation theory: A reduced-cost reference for correlation calculations
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  • Steele, Ryan P.; DiStasio, Robert A.; Shao, Yihan
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Analysis of charge transfer effects in molecular complexes based on absolutely localized molecular orbitals
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Potentialphilicity and potentialphobicity: Reactivity indicators for external potential changes from density functional reactivity theory
journal, September 2009

  • Liu, Shubin; Li, Tonglei; Ayers, Paul W.
  • The Journal of Chemical Physics, Vol. 131, Issue 11
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Ewald mesh method for quantum mechanical calculations
journal, March 2012

  • Chang, Chun-Min; Shao, Yihan; Kong, Jing
  • The Journal of Chemical Physics, Vol. 136, Issue 11
  • DOI: 10.1063/1.3694829

Perspective on density functional theory
journal, April 2012

  • Burke, Kieron
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Kohn-Sham orbital formulation of the chemical electronic responses, including the hardness
journal, August 1997

  • Senet, P.
  • The Journal of Chemical Physics, Vol. 107, Issue 7
  • DOI: 10.1063/1.474591

Maintain rigid structures in Verlet based Cartesian molecular dynamics simulations
journal, October 2012

  • Tao, Peng; Wu, Xiongwu; Brooks, Bernard R.
  • The Journal of Chemical Physics, Vol. 137, Issue 13
  • DOI: 10.1063/1.4756796

Ab Initio Quantum Chemical and Mixed Quantum Mechanics/Molecular Mechanics (Qm/Mm) Methods for Studying Enzymatic Catalysis
journal, May 2005

QM/MM Approaches in Medicinal Chemistry Research
journal, January 2010

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    journal, September 2018

    • Huggins, David J.; Biggin, Philip C.; Dämgen, Marc A.
    • Wiley Interdisciplinary Reviews: Computational Molecular Science, Vol. 9, Issue 3
    • DOI: 10.1002/wcms.1393

    Biomolecular simulations: from dynamics and mechanisms to computational assays of biological activity
    text, January 2019

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