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:
-
- National Institutes of Health, Rockville, MD (United States)
- 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)
- Southern Methodist Univ., Dallas, TX (United States)
- Univ. of Utah, Salt Lake City, UT (United States)
- 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.
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
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.
@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}
}
Web of Science
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On the Convergence of QM/MM Energies
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Evaluating and Interpreting the Chemical Relevance of the Linear Response Kernel for Atoms
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Multiscale Free Energy Simulations: An Efficient Method for Connecting Classical MD Simulations to QM or QM/MM Free Energies Using Non-Boltzmann Bennett Reweighting Schemes
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- König, Gerhard; Hudson, Phillip S.; Boresch, Stefan
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Computing the Free Energy along a Reaction Coordinate Using Rigid Body Dynamics
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Variational Principles for Describing Chemical Reactions. Reactivity Indices Based on the External Potential
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Dynamics on the Electronically Excited State Surface of the Bioluminescent Firefly Luciferase–Oxyluciferin System
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Dual-Basis Analytic Gradients. 1. Self-Consistent Field Theory
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- Steele, Ryan P.; Shao, Yihan; DiStasio,, Robert A.
- The Journal of Physical Chemistry A, Vol. 110, Issue 51
Long-range corrected hybrid density functionals with damped atom–atom dispersion corrections
journal, January 2008
- Chai, Jeng-Da; Head-Gordon, Martin
- Physical Chemistry Chemical Physics, Vol. 10, Issue 44
Computational enzymology
journal, January 2010
- Lonsdale, Richard; Ranaghan, Kara E.; Mulholland, Adrian J.
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Density functional triple jumping
journal, January 2010
- Deng, Jia; Gilbert, Andrew T. B.; Gill, Peter M. W.
- Physical Chemistry Chemical Physics, Vol. 12, Issue 36
Convergence of QM/MM free-energy perturbations based on molecular-mechanics or semiempirical simulations
journal, January 2012
- Heimdal, Jimmy; Ryde, Ulf
- Physical Chemistry Chemical Physics, Vol. 14, Issue 36
Evaluating and interpreting the chemical relevance of the linear response kernel for atoms II: open shell
journal, January 2014
- Boisdenghien, Zino; Fias, Stijn; Van Alsenoy, Christian
- Physical Chemistry Chemical Physics, Vol. 16, Issue 28
Dual-basis second-order Møller-Plesset perturbation theory: A reduced-cost reference for correlation calculations
journal, August 2006
- Steele, Ryan P.; DiStasio, Robert A.; Shao, Yihan
- The Journal of Chemical Physics, Vol. 125, Issue 7
Analysis of charge transfer effects in molecular complexes based on absolutely localized molecular orbitals
journal, May 2008
- Khaliullin, Rustam Z.; Bell, Alexis T.; Head-Gordon, Martin
- The Journal of Chemical Physics, Vol. 128, Issue 18
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
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
Perspective on density functional theory
journal, April 2012
- Burke, Kieron
- The Journal of Chemical Physics, Vol. 136, Issue 15
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
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
Ab Initio Quantum Chemical and Mixed Quantum Mechanics/Molecular Mechanics (Qm/Mm) Methods for Studying Enzymatic Catalysis
journal, May 2005
- Friesner, Richard A.; Guallar, Victor
- Annual Review of Physical Chemistry, Vol. 56, Issue 1
Free Energies of Chemical Reactions in Solution and in Enzymes with Ab Initio Quantum Mechanics/Molecular Mechanics Methods
journal, May 2008
- Hu, Hao; Yang, Weitao
- Annual Review of Physical Chemistry, Vol. 59, Issue 1
QM/MM Approaches in Medicinal Chemistry Research
journal, January 2010
- Menikarachchi, Lochana; Gascon, Jose
- Current Topics in Medicinal Chemistry, Vol. 10, Issue 1
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