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Title: Efficient Computation of Free Energy Surfaces of Diels–Alder Reactions in Explicit Solvent at Ab Initio QM/MM Level

Abstract

For Diels–Alder (DA) reactions in solution, an accurate and converged free energy (FE) surface at ab initio (ai) quantum mechanical/molecular mechanical (QM/MM) level is imperative for the understanding of reaction mechanism. However, this computation is still far too expensive. In a previous work, we proposed a new method termed MBAR+wTP, with which the computation of the ai FE profile can be accelerated by several orders of magnitude via a three-step procedure: (I) an umbrella sampling (US) using a semi-empirical (SE) QM/MM Hamiltonian is performed; (II) the FE profile is generated using the Multistate Bennett Acceptance Ratio (MBAR) analysis; and (III) a weighted Thermodynamic Perturbation (wTP) from the SE Hamiltonian to the ai Hamiltonian is performed to obtain the ai QM/MM FE profile using weight factors from the MBAR analysis. In this work, this method is extended to the calculations of two-dimensional FE surfaces of two Diels–Alder reactions of cyclopentadiene with either acrylonitrile or 1-4-naphthoquinone at ai QM/MM level. The accurate activation free energies at the ai QM/MM level, which are much closer to the experimental measurements than those calculated by other methods, indicate that this MBAR+wTP method can be applied in the studies of complex reactions in condensed phase withmore » much-enhanced efficiency.« less

Authors:
ORCiD logo [1]; ORCiD logo [1]; ORCiD logo [1]; ORCiD logo [2];  [3];  [3]; ORCiD logo [4]
+ Show Author Affiliations
  1. East China Normal Univ., Shanghai (China). State Key Lab. of Precision Spectroscopy, School of Physics and Materials Science
  2. Univ. of Oklahoma, Norman, OK (United States)
  3. East China Normal Univ., Shanghai (China). Computer Center, School of Computer Science and Software Engineering
  4. East China Normal Univ., Shanghai (China). State Key Lab. of Precision Spectroscopy, School of Physics and Materials Science; Univ. of Oklahoma, Norman, OK (United States); NYU Shanghai, Shanghai (China). NYU-ECNU Center for Computational Chemistry
Publication Date:
Research Org.:
Q-Chem, Inc., Pleasanton, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC); National Natural Science Foundation of China (NSFC)
OSTI Identifier:
1611615
Grant/Contract Number:  
SC0011297; 21773066
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; Diels–Alder reaction; free energy surface; ab initio; reference-potential method; umbrella sampling

Citation Formats

Li, Pengfei, Liu, Fengjiao, Jia, Xiangyu, Shao, Yihan, Hu, Wenxin, Zheng, Jun, and Mei, Ye. Efficient Computation of Free Energy Surfaces of Diels–Alder Reactions in Explicit Solvent at Ab Initio QM/MM Level. United States: N. p., 2018. Web. doi:10.3390/molecules23102487.
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Li, Pengfei, Liu, Fengjiao, Jia, Xiangyu, Shao, Yihan, Hu, Wenxin, Zheng, Jun, & Mei, Ye. Efficient Computation of Free Energy Surfaces of Diels–Alder Reactions in Explicit Solvent at Ab Initio QM/MM Level. United States. https://doi.org/10.3390/molecules23102487
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Li, Pengfei, Liu, Fengjiao, Jia, Xiangyu, Shao, Yihan, Hu, Wenxin, Zheng, Jun, and Mei, Ye. Fri . "Efficient Computation of Free Energy Surfaces of Diels–Alder Reactions in Explicit Solvent at Ab Initio QM/MM Level". United States. https://doi.org/10.3390/molecules23102487. https://www.osti.gov/servlets/purl/1611615.
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@article{osti_1611615,
title = {Efficient Computation of Free Energy Surfaces of Diels–Alder Reactions in Explicit Solvent at Ab Initio QM/MM Level},
author = {Li, Pengfei and Liu, Fengjiao and Jia, Xiangyu and Shao, Yihan and Hu, Wenxin and Zheng, Jun and Mei, Ye},
abstractNote = {For Diels–Alder (DA) reactions in solution, an accurate and converged free energy (FE) surface at ab initio (ai) quantum mechanical/molecular mechanical (QM/MM) level is imperative for the understanding of reaction mechanism. However, this computation is still far too expensive. In a previous work, we proposed a new method termed MBAR+wTP, with which the computation of the ai FE profile can be accelerated by several orders of magnitude via a three-step procedure: (I) an umbrella sampling (US) using a semi-empirical (SE) QM/MM Hamiltonian is performed; (II) the FE profile is generated using the Multistate Bennett Acceptance Ratio (MBAR) analysis; and (III) a weighted Thermodynamic Perturbation (wTP) from the SE Hamiltonian to the ai Hamiltonian is performed to obtain the ai QM/MM FE profile using weight factors from the MBAR analysis. In this work, this method is extended to the calculations of two-dimensional FE surfaces of two Diels–Alder reactions of cyclopentadiene with either acrylonitrile or 1-4-naphthoquinone at ai QM/MM level. The accurate activation free energies at the ai QM/MM level, which are much closer to the experimental measurements than those calculated by other methods, indicate that this MBAR+wTP method can be applied in the studies of complex reactions in condensed phase with much-enhanced efficiency.},
doi = {10.3390/molecules23102487},
journal = {Molecules},
number = 10,
volume = 23,
place = {United States},
year = {Fri Sep 28 00:00:00 EDT 2018},
month = {Fri Sep 28 00:00:00 EDT 2018}
}
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QM/MM Methods for Biomolecular Systems
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journal, May 2007

Guidelines for the analysis of free energy calculations
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  • Klimovich, Pavel V.; Shirts, Michael R.; Mobley, David L.
  • Journal of Computer-Aided Molecular Design, Vol. 29, Issue 5
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Efficient Strategy for the Calculation of Solvation Free Energies in Water and Chloroform at the Quantum Mechanical/Molecular Mechanical Level
journal, October 2017

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Calculations of Solvation Free Energy through Energy Reweighting from Molecular Mechanics to Quantum Mechanics
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  • Journal of Chemical Theory and Computation, Vol. 12, Issue 2
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Computational Insights into an Enzyme-Catalyzed [4+2] Cycloaddition
journal, November 2017

QM/QM′ Direct Molecular Dynamics of Water-Accelerated Diels–Alder Reaction
journal, April 2016

  • Liu, Fengjiao; Yang, Zhongyue; Mei, Ye
  • The Journal of Physical Chemistry B, Vol. 120, Issue 26
  • DOI: 10.1021/acs.jpcb.6b02336

Free energy calculations: a breakthrough for modeling organic chemistry in solution
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  • Accounts of Chemical Research, Vol. 22, Issue 5
  • DOI: 10.1021/ar00161a004

Combined Quantum Mechanics/Molecular Mechanics (QM/MM) Methods in Computational Enzymology
journal, April 2013

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  • Biochemistry, Vol. 52, Issue 16
  • DOI: 10.1021/bi400215w

Simulation of the Enzyme Reaction Mechanism of Malate Dehydrogenase †
journal, April 1997

  • Cunningham, Mark A.; Ho, L. Lawrence; Nguyen, Dzung T.
  • Biochemistry, Vol. 36, Issue 16
  • DOI: 10.1021/bi962734n

Understanding Rate Accelerations for Diels−Alder Reactions in Solution Using Enhanced QM/MM Methodology
journal, May 2007

  • Acevedo, Orlando; Jorgensen, William L.
  • Journal of Chemical Theory and Computation, Vol. 3, Issue 4
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Solvent effects on a Diels-Alder reaction from computer simulations
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  • Jorgensen, William L.; Lim, Dongchul; Blake, James F.
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  • DOI: 10.1021/ja00060a048

Theoretical examination of the SN2 reaction involving chloride ion and methyl chloride in the gas phase and aqueous solution
journal, January 1985

  • Chandrasekhar, Jayaraman; Smith, Scott F.; Jorgensen, William L.
  • Journal of the American Chemical Society, Vol. 107, Issue 1
  • DOI: 10.1021/ja00287a028

An empirical valence bond approach for comparing reactions in solutions and in enzymes
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  • Warshel, Arieh; Weiss, Robert M.
  • Journal of the American Chemical Society, Vol. 102, Issue 20
  • DOI: 10.1021/ja00540a008

Walden-Inversion-Enforced Transition-State Stabilization in a Protein Tyrosine Phosphatase
journal, April 1998

  • Alhambra, Cristobal; Wu, Li; Zhang, Zhong-Yin
  • Journal of the American Chemical Society, Vol. 120, Issue 16
  • DOI: 10.1021/ja972578n

Combined ab initio and Free Energy Calculations To Study Reactions in Enzymes and Solution:  Amide Hydrolysis in Trypsin and Aqueous Solution
journal, April 1998

  • Stanton, Robert V.; Peräkylä, Mikael; Bakowies, Dirk
  • Journal of the American Chemical Society, Vol. 120, Issue 14
  • DOI: 10.1021/ja972723x

Enhanced Hydrogen Bonding of Water to Diels-Alder Transition States. Ab Initio Evidence
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  • Blake, James F.; Lim, Dongchul; Jorgensen, William L.
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  • DOI: 10.1021/jo00083a021

QM/MM Simulations for Diels−Alder Reactions in Water:  Contribution of Enhanced Hydrogen Bonding at the Transition State to the Solvent Effect †
journal, August 2002

  • Chandrasekhar, Jayaraman; Shariffskul, Shane; Jorgensen, William L.
  • The Journal of Physical Chemistry B, Vol. 106, Issue 33
  • DOI: 10.1021/jp020326p

Exploring, Refining, and Validating the Paradynamics QM/MM Sampling
journal, August 2012

  • Plotnikov, Nikolay V.; Warshel, Arieh
  • The Journal of Physical Chemistry B, Vol. 116, Issue 34
  • DOI: 10.1021/jp304678d

Hybrid ab Initio Quantum Mechanics/Molecular Mechanics Calculations of Free Energy Surfaces for Enzymatic Reactions:  The Nucleophilic Attack in Subtilisin
journal, March 1998

  • Bentzien, J.; Muller, R. P.; Florián, J.
  • The Journal of Physical Chemistry B, Vol. 102, Issue 12
  • DOI: 10.1021/jp973480y

Solvent effects on Diels-Alder reactions. The use of aqueous mixtures of fluorinated alcohols and the study of reactions of acrylonitrile
journal, January 1997

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  • DOI: 10.1039/a601717g

High‐Temperature Equation of State by a Perturbation Method. I. Nonpolar Gases
journal, August 1954

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  • The Journal of Chemical Physics, Vol. 22, Issue 8
  • DOI: 10.1063/1.1740409

A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu
journal, April 2010

  • Grimme, Stefan; Antony, Jens; Ehrlich, Stephan
  • The Journal of Chemical Physics, Vol. 132, Issue 15
  • DOI: 10.1063/1.3382344

A pseudobond approach to combining quantum mechanical and molecular mechanical methods
journal, January 1999

  • Zhang, Yingkai; Lee, Tai-Sung; Yang, Weitao
  • The Journal of Chemical Physics, Vol. 110, Issue 1
  • DOI: 10.1063/1.478083

Free energy calculation on enzyme reactions with an efficient iterative procedure to determine minimum energy paths on a combined ab initio QM/MM potential energy surface
journal, February 2000

  • Zhang, Yingkai; Liu, Haiyan; Yang, Weitao
  • The Journal of Chemical Physics, Vol. 112, Issue 8
  • DOI: 10.1063/1.480503

Quantum Mechanical Free Energy Barrier for an Enzymatic Reaction
journal, April 2005

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

QM/MM Geometry Optimization on Extensive Free-Energy Surfaces for Examination of Enzymatic Reactions and Design of Novel Functional Properties of Proteins
journal, May 2017

Diels-Alder reactions in water: Enforced hydrophobic interaction and hydrogen bonding
journal, January 1995

Statistically optimal analysis of samples from multiple equilibrium states
text, January 2008

Amber 2017, University of California, San Francisco
dataset, January 2017

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