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Title: Representation of the QM Subsystem for Long-Range Electrostatic Interaction in Non-Periodic Ab Initio QM/MM Calculations

Abstract

In QM/MM calculations, it is essential to handle electrostatic interactions between the QM and MM subsystems accurately and efficiently. To achieve maximal efficiency, it is convenient to adopt a hybrid scheme, where the QM electron density is used explicitly in the evaluation of short-range QM/MM electrostatic interactions, while a multipolar representation for the QM electron density is employed to account for the long-range QM/MM electrostatic interactions. In order to avoid energy discontinuity at the cutoffs, which separate the short- and long-range QM/MM electrostatic interactions, a switching function should be utilized to ensure a smooth potential energy surface. In this study, we benchmarked the accuracy of such hybrid embedding schemes for QM/MM electrostatic interactions using different multipolar representations, switching functions and cutoff distances. For test systems (neutral and anionic oxyluciferin in MM (aqueous and enzyme) environments), the best accuracy was acquired with a combination of QM electrostatic potential (ESP) charges and dipoles and two switching functions (long-range electrostatic corrections (LREC) and Switch) in the treatment of long-range QM/MM electrostatics. It allowed us to apply a 10Å distance cutoff and still obtain QM/MM electrostatics/polarization energies within 0.1 kcal/mol and time-dependent density functional theory (TDDFT)/MM vertical excitation energies within 10-3 eV from theoreticalmore » reference values.« less

Authors:
ORCiD logo [1]; ORCiD logo [2]; ORCiD logo [1]
+ Show Author Affiliations
  1. Univ. of Oklahoma, Norman, OK (United States)
  2. King’s College London, London (United Kingdom)
Publication Date:
Research Org.:
Q-Chem, Inc., Pleasanton, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1611616
Grant/Contract Number:  
SC0011297
Resource Type:
Accepted Manuscript
Journal Name:
Molecules
Additional Journal Information:
Journal Volume: 23; Journal Issue: 10; Journal ID: ISSN 1420-3049
Publisher:
MDPI
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; Biochemistry & Molecular Biology; Chemistry

Citation Formats

Pan, Xiaoliang, Rosta, Edina, and Shao, Yihan. Representation of the QM Subsystem for Long-Range Electrostatic Interaction in Non-Periodic Ab Initio QM/MM Calculations. United States: N. p., 2018. Web. doi:10.3390/molecules23102500.
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Pan, Xiaoliang, Rosta, Edina, & Shao, Yihan. Representation of the QM Subsystem for Long-Range Electrostatic Interaction in Non-Periodic Ab Initio QM/MM Calculations. United States. https://doi.org/10.3390/molecules23102500
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Pan, Xiaoliang, Rosta, Edina, and Shao, Yihan. Sat . "Representation of the QM Subsystem for Long-Range Electrostatic Interaction in Non-Periodic Ab Initio QM/MM Calculations". United States. https://doi.org/10.3390/molecules23102500. https://www.osti.gov/servlets/purl/1611616.
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@article{osti_1611616,
title = {Representation of the QM Subsystem for Long-Range Electrostatic Interaction in Non-Periodic Ab Initio QM/MM Calculations},
author = {Pan, Xiaoliang and Rosta, Edina and Shao, Yihan},
abstractNote = {In QM/MM calculations, it is essential to handle electrostatic interactions between the QM and MM subsystems accurately and efficiently. To achieve maximal efficiency, it is convenient to adopt a hybrid scheme, where the QM electron density is used explicitly in the evaluation of short-range QM/MM electrostatic interactions, while a multipolar representation for the QM electron density is employed to account for the long-range QM/MM electrostatic interactions. In order to avoid energy discontinuity at the cutoffs, which separate the short- and long-range QM/MM electrostatic interactions, a switching function should be utilized to ensure a smooth potential energy surface. In this study, we benchmarked the accuracy of such hybrid embedding schemes for QM/MM electrostatic interactions using different multipolar representations, switching functions and cutoff distances. For test systems (neutral and anionic oxyluciferin in MM (aqueous and enzyme) environments), the best accuracy was acquired with a combination of QM electrostatic potential (ESP) charges and dipoles and two switching functions (long-range electrostatic corrections (LREC) and Switch) in the treatment of long-range QM/MM electrostatics. It allowed us to apply a 10Å distance cutoff and still obtain QM/MM electrostatics/polarization energies within 0.1 kcal/mol and time-dependent density functional theory (TDDFT)/MM vertical excitation energies within 10-3 eV from theoretical reference values.},
doi = {10.3390/molecules23102500},
journal = {Molecules},
number = 10,
volume = 23,
place = {United States},
year = {Sat Sep 29 00:00:00 EDT 2018},
month = {Sat Sep 29 00:00:00 EDT 2018}
}
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https://doi.org/10.3390/molecules23102500
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QM/MM: What Have We Learned, Where Are We, and Where Do We Go from Here?
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journal, January 2008

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An approach to computing electrostatic charges for molecules
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  • Journal of Computational Chemistry, Vol. 5, Issue 2
  • DOI: 10.1002/jcc.540050204

New spherical-cutoff methods for long-range forces in macromolecular simulation
journal, July 1994

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  • Journal of Computational Chemistry, Vol. 15, Issue 7
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journal, November 1994

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QM/MM studies of enzymes
journal, April 2007

Periodic Boundary Conditions in QM/MM Calculations: Implementation and Tests
journal, July 2016

  • Vasilevskaya, Tatiana; Thiel, Walter
  • Journal of Chemical Theory and Computation, Vol. 12, Issue 8
  • DOI: 10.1021/acs.jctc.6b00269

Classical Electrostatics for Biomolecular Simulations
journal, August 2013

  • Cisneros, G. Andrés; Karttunen, Mikko; Ren, Pengyu
  • Chemical Reviews, Vol. 114, Issue 1
  • DOI: 10.1021/cr300461d

An Efficient Linear-Scaling Ewald Method for Long-Range Electrostatic Interactions in Combined QM/MM Calculations
journal, October 2004

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  • DOI: 10.1021/ct049941i

Including Charge Penetration Effects in Molecular Modeling
journal, October 2010

  • Wang, Bo; Truhlar, Donald G.
  • Journal of Chemical Theory and Computation, Vol. 6, Issue 11
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Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ 1 and χ 2 Dihedral Angles
journal, August 2012

  • Best, Robert B.; Zhu, Xiao; Shim, Jihyun
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  • DOI: 10.1021/ct300400x

Fitting Molecular Electrostatic Potentials from Quantum Mechanical Calculations
journal, March 2007

  • Hu, Hao; Lu, Zhenyu; Yang, Weitao
  • Journal of Chemical Theory and Computation, Vol. 3, Issue 3
  • DOI: 10.1021/ct600295n

A General Boundary Potential for Hybrid QM/MM Simulations of Solvated Biomolecular Systems
journal, October 2009

  • Benighaus, Tobias; Thiel, Walter
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  • DOI: 10.1021/ct900437b

Toward the Accurate Modeling of DNA: The Importance of Long-Range Electrostatics
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All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins †
journal, April 1998

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Structural basis for the spectral difference in luciferase bioluminescence
journal, March 2006

  • Nakatsu, Toru; Ichiyama, Susumu; Hiratake, Jun
  • Nature, Vol. 440, Issue 7082
  • DOI: 10.1038/nature04542

NAMD goes quantum: an integrative suite for hybrid simulations
journal, March 2018

  • Melo, Marcelo C. R.; Bernardi, Rafael C.; Rudack, Till
  • Nature Methods, Vol. 15, Issue 5
  • DOI: 10.1038/nmeth.4638

Generalized solvent boundary potential for computer simulations
journal, February 2001

  • Im, Wonpil; Bernèche, Simon; Roux, Benoı̂t
  • The Journal of Chemical Physics, Vol. 114, Issue 7
  • DOI: 10.1063/1.1336570

A Hamiltonian electrostatic coupling scheme for hybrid Car–Parrinello molecular dynamics simulations
journal, April 2002

  • Laio, Alessandro; VandeVondele, Joost; Rothlisberger, Ursula
  • The Journal of Chemical Physics, Vol. 116, Issue 16
  • DOI: 10.1063/1.1462041

The Fourier transform Coulomb method: Efficient and accurate calculation of the Coulomb operator in a Gaussian basis
journal, November 2002

  • Füsti-Molnár, László; Pulay, Peter
  • The Journal of Chemical Physics, Vol. 117, Issue 17
  • DOI: 10.1063/1.1510121

Comparison of simple potential functions for simulating liquid water
journal, July 1983

  • Jorgensen, William L.; Chandrasekhar, Jayaraman; Madura, Jeffry D.
  • The Journal of Chemical Physics, Vol. 79, Issue 2
  • DOI: 10.1063/1.445869

A new smoothing function to introduce long-range electrostatic effects in QM/MM calculations
journal, July 2015

  • Fang, Dong; Duke, Robert E.; Cisneros, G. Andrés
  • The Journal of Chemical Physics, Vol. 143, Issue 4
  • DOI: 10.1063/1.4926652

A priori evaluation of aqueous polarization effects through Monte Carlo QM-MM simulations
journal, October 1992

Progress in Time-Dependent Density-Functional Theory
text, January 2011

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    Mutually polarizable QM/MM model with in situ optimized localized basis functions
    journal, February 2019

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    • The Journal of Chemical Physics, Vol. 150, Issue 7
    • DOI: 10.1063/1.5080384
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