1
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Pederson JP, McDaniel JG. PyDFT-QMMM: A modular, extensible software framework for DFT-based QM/MM molecular dynamics. J Chem Phys 2024; 161:034103. [PMID: 39007371 DOI: 10.1063/5.0219851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Accepted: 06/24/2024] [Indexed: 07/16/2024] Open
Abstract
PyDFT-QMMM is a Python-based package for performing hybrid quantum mechanics/molecular mechanics (QM/MM) simulations at the density functional level of theory. The program is designed to treat short-range and long-range interactions through user-specified combinations of electrostatic and mechanical embedding procedures within periodic simulation domains, providing necessary interfaces to external quantum chemistry and molecular dynamics software. To enable direct embedding of long-range electrostatics in periodic systems, we have derived and implemented force terms for our previously described QM/MM/PME approach [Pederson and McDaniel, J. Chem. Phys. 156, 174105 (2022)]. Communication with external software packages Psi4 and OpenMM is facilitated through Python application programming interfaces (APIs). The core library contains basic utilities for running QM/MM molecular dynamics simulations, and plug-in entry-points are provided for users to implement custom energy/force calculation and integration routines, within an extensible architecture. The user interacts with PyDFT-QMMM primarily through its Python API, allowing for complex workflow development with Python scripting, for example, interfacing with PLUMED for free energy simulations. We provide benchmarks of forces and energy conservation for the QM/MM/PME and alternative QM/MM electrostatic embedding approaches. We further demonstrate a simple example use case for water solute in a water solvent system, for which radial distribution functions are computed from 100 ps QM/MM simulations; in this example, we highlight how the solvation structure is sensitive to different basis-set choices due to under- or over-polarization of the QM water molecule's electron density.
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Affiliation(s)
- John P Pederson
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA
| | - Jesse G McDaniel
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA
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2
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Jung J, Yagi K, Tan C, Oshima H, Mori T, Yu I, Matsunaga Y, Kobayashi C, Ito S, Ugarte La Torre D, Sugita Y. GENESIS 2.1: High-Performance Molecular Dynamics Software for Enhanced Sampling and Free-Energy Calculations for Atomistic, Coarse-Grained, and Quantum Mechanics/Molecular Mechanics Models. J Phys Chem B 2024; 128:6028-6048. [PMID: 38876465 PMCID: PMC11215777 DOI: 10.1021/acs.jpcb.4c02096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Revised: 05/15/2024] [Accepted: 05/21/2024] [Indexed: 06/16/2024]
Abstract
GENeralized-Ensemble SImulation System (GENESIS) is a molecular dynamics (MD) software developed to simulate the conformational dynamics of a single biomolecule, as well as molecular interactions in large biomolecular assemblies and between multiple biomolecules in cellular environments. To achieve the latter purpose, the earlier versions of GENESIS emphasized high performance in atomistic MD simulations on massively parallel supercomputers, with or without graphics processing units (GPUs). Here, we implemented multiscale MD simulations that include atomistic, coarse-grained, and hybrid quantum mechanics/molecular mechanics (QM/MM) calculations. They demonstrate high performance and are integrated with enhanced conformational sampling algorithms and free-energy calculations without using external programs except for the QM programs. In this article, we review new functions, molecular models, and other essential features in GENESIS version 2.1 and discuss ongoing developments for future releases.
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Affiliation(s)
- Jaewoon Jung
- Computational
Biophysics Research Team, RIKEN Center for
Computational Science, Kobe, Hyogo 650-0047, Japan
- Theoretical
Molecular Science Laboratory, RIKEN Cluster
for Pioneering Research, Wako, Saitama 351-0198, Japan
| | - Kiyoshi Yagi
- Theoretical
Molecular Science Laboratory, RIKEN Cluster
for Pioneering Research, Wako, Saitama 351-0198, Japan
| | - Cheng Tan
- Computational
Biophysics Research Team, RIKEN Center for
Computational Science, Kobe, Hyogo 650-0047, Japan
| | - Hiraku Oshima
- Laboratory
for Biomolecular Function Simulation, RIKEN
Center for Biosystems Dynamics Research, Kobe, Hyogo 650-0047, Japan
- Graduate
School of Life Science, University of Hyogo, Harima Science Park City, Hyogo 678-1297, Japan
| | - Takaharu Mori
- Theoretical
Molecular Science Laboratory, RIKEN Cluster
for Pioneering Research, Wako, Saitama 351-0198, Japan
- Department
of Chemistry, Tokyo University of Science, Shinjuku-ku, Tokyo 162-8601, Japan
| | - Isseki Yu
- Theoretical
Molecular Science Laboratory, RIKEN Cluster
for Pioneering Research, Wako, Saitama 351-0198, Japan
- Department
of Bioinformatics, Maebashi Institute of
Technology, Maebashi, Gunma 371-0816, Japan
| | - Yasuhiro Matsunaga
- Computational
Biophysics Research Team, RIKEN Center for
Computational Science, Kobe, Hyogo 650-0047, Japan
- Graduate
School of Science and Engineering, Saitama
University, Saitama 338-8570, Japan
| | - Chigusa Kobayashi
- Computational
Biophysics Research Team, RIKEN Center for
Computational Science, Kobe, Hyogo 650-0047, Japan
| | - Shingo Ito
- Theoretical
Molecular Science Laboratory, RIKEN Cluster
for Pioneering Research, Wako, Saitama 351-0198, Japan
| | - Diego Ugarte La Torre
- Computational
Biophysics Research Team, RIKEN Center for
Computational Science, Kobe, Hyogo 650-0047, Japan
| | - Yuji Sugita
- Computational
Biophysics Research Team, RIKEN Center for
Computational Science, Kobe, Hyogo 650-0047, Japan
- Theoretical
Molecular Science Laboratory, RIKEN Cluster
for Pioneering Research, Wako, Saitama 351-0198, Japan
- Laboratory
for Biomolecular Function Simulation, RIKEN
Center for Biosystems Dynamics Research, Kobe, Hyogo 650-0047, Japan
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3
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Barnes TA, Ellis S, Chen J, Plimpton SJ, Nash JA. Plugin-based interoperability and ecosystem management for the MolSSI Driver Interface Project. J Chem Phys 2024; 160:214114. [PMID: 38832733 DOI: 10.1063/5.0214279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 05/15/2024] [Indexed: 06/05/2024] Open
Abstract
The MolSSI Driver Interface (MDI) Project is an effort to simplify and standardize the process of enabling tight interoperability between independently developed code bases and is supported by numerous software packages across the domain of chemical physics. It enables a wide variety of use cases, including quantum mechanics/molecular mechanics, advanced sampling, path integral molecular dynamics, machine learning, ab initio molecular dynamics, etc. We describe two major developments within the MDI Project that provide novel solutions to key interoperability challenges. The first of these is the development of the MDI Plugin System, which allows MDI-supporting libraries to be used as highly modular plugins, with MDI enforcing a standardized application programming interface across plugins. Codes can use these plugins without linking against them during their build process, and end-users can select which plugin(s) they wish to use at runtime. The MDI Plugin System features a sophisticated callback system that allows codes to interact with plugins on a highly granular level and represents a significant advancement toward increased modularity among scientific codes. The second major development is MDI Mechanic, an ecosystem management tool that utilizes Docker containerization to simplify the process of developing, validating, maintaining, and deploying MDI-supporting codes. Additionally, MDI Mechanic provides a framework for launching MDI simulations in which each interoperating code is executed within a separate computational environment. This eliminates the need to compile multiple production codes within a single computational environment, reducing opportunities for dependency conflicts and lowering the barrier to entry for users of MDI-enabled codes.
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Affiliation(s)
- T A Barnes
- Molecular Sciences Software Institute, Blacksburg, Virginia 24060, USA
| | - S Ellis
- Molecular Sciences Software Institute, Blacksburg, Virginia 24060, USA
| | - J Chen
- Molecular Sciences Software Institute, Blacksburg, Virginia 24060, USA
| | - S J Plimpton
- Temple University, Philadelphia, Pennsylvania 19122, USA
| | - J A Nash
- Molecular Sciences Software Institute, Blacksburg, Virginia 24060, USA
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4
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Saito T, Takano Y. Spin-projected QM/MM Free Energy Simulations for Oxidation Reaction of Guanine in B-DNA by Singlet Oxygen. Chemphyschem 2021; 22:561-568. [PMID: 33462992 PMCID: PMC8048875 DOI: 10.1002/cphc.202000978] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 01/17/2021] [Indexed: 12/11/2022]
Abstract
Guanine is the most susceptible base to oxidation damage induced by reactive oxygen species including singlet oxygen (1 O2 , 1 Δg ). We clarify whether the first step of guanine oxidation in B-DNA proceeds via either a zwitterionic or a diradical intermediate. The free energy profiles are calculated by means of a combined quantum mechanical and molecular mechanical (QM/MM) method coupled with the adaptive biasing force (ABF) method. To describe the open-shell electronic structure of 1 O2 correctly, the broken-symmetry spin-unrestricted density functional theory (BS-UDFT) with an approximate spin projection (AP) correction is applied to the QM region. We find that the effect of spin contamination on the activation and reaction free energies is up to ∼8 kcal mol-1 , which is too large to be neglected. The QM(AP-ULC-BLYP)/MM-based free energy calculations also reveal that the reaction proceeds through a diradical transition state, followed by a conversion to a zwitterionic intermediate. Our computed activation energy of 5.2 kcal mol-1 matches experimentally observed range (0∼6 kcal mol-1 ).
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Affiliation(s)
- Toru Saito
- Department of Biomedical Information Science, Graduate School of Information Science, Hiroshima City University, 3-4-1 Ozuka-Higashi, Asa-Minami-Ku, 731-3194, Hiroshima, Japan
| | - Yu Takano
- Department of Biomedical Information Science, Graduate School of Information Science, Hiroshima City University, 3-4-1 Ozuka-Higashi, Asa-Minami-Ku, 731-3194, Hiroshima, Japan
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5
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Pan X, Nam K, Epifanovsky E, Simmonett AC, Rosta E, Shao Y. A simplified charge projection scheme for long-range electrostatics in ab initio QM/MM calculations. J Chem Phys 2021; 154:024115. [PMID: 33445891 DOI: 10.1063/5.0038120] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
In a previous work [Pan et al., Molecules 23, 2500 (2018)], a charge projection scheme was reported, where outer molecular mechanical (MM) charges [>10 Å from the quantum mechanical (QM) region] were projected onto the electrostatic potential (ESP) grid of the QM region to accurately and efficiently capture long-range electrostatics in ab initio QM/MM calculations. Here, a further simplification to the model is proposed, where the outer MM charges are projected onto inner MM atom positions (instead of ESP grid positions). This enables a representation of the long-range MM electrostatic potential via augmentary charges (AC) on inner MM atoms. Combined with the long-range electrostatic correction function from Cisneros et al. [J. Chem. Phys. 143, 044103 (2015)] to smoothly switch between inner and outer MM regions, this new QM/MM-AC electrostatic model yields accurate and continuous ab initio QM/MM electrostatic energies with a 10 Å cutoff between inner and outer MM regions. This model enables efficient QM/MM cluster calculations with a large number of MM atoms as well as QM/MM calculations with periodic boundary conditions.
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Affiliation(s)
- Xiaoliang Pan
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Pkwy, Norman, Oklahoma 73019, USA
| | - Kwangho Nam
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington, Texas 76019, USA
| | - Evgeny Epifanovsky
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | - Andrew C Simmonett
- National Institutes of Health-National Heart, Lung and Blood Institute, Laboratory of Computational Biology, Bethesda, Maryland 20892, USA
| | - Edina Rosta
- Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom
| | - Yihan Shao
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Pkwy, Norman, Oklahoma 73019, USA
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Zhang B, Altarawy D, Barnes T, Turney JM, Schaefer HF. Janus: An Extensible Open-Source Software Package for Adaptive QM/MM Methods. J Chem Theory Comput 2019; 15:4362-4373. [DOI: 10.1021/acs.jctc.9b00182] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Boyi Zhang
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602, United States
| | - Doaa Altarawy
- The Molecular Sciences Software Institute, Virginia Tech, Blacksburg, Virginia 24060, United States
- Department of Computer and Systems Engineering, Alexandria University, Alexandria 21544, Egypt
| | - Taylor Barnes
- The Molecular Sciences Software Institute, Virginia Tech, Blacksburg, Virginia 24060, United States
| | - Justin M. Turney
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602, United States
| | - Henry F. Schaefer
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602, United States
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7
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Bistafa C, Kitamura Y, Martins-Costa MTC, Nagaoka M, Ruiz-López MF. Vibrational Spectroscopy in Solution through Perturbative ab Initio Molecular Dynamics Simulations. J Chem Theory Comput 2019; 15:4615-4622. [DOI: 10.1021/acs.jctc.9b00362] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Carlos Bistafa
- Department of Complex Systems Science, Graduate School of Informatics, Nagoya University, Chikusa Ku, Furo Cho, Nagoya, Aichi 4648601, Japan
| | - Yukichi Kitamura
- Department of Complex Systems Science, Graduate School of Informatics, Nagoya University, Chikusa Ku, Furo Cho, Nagoya, Aichi 4648601, Japan
| | - Marilia T. C. Martins-Costa
- Laboratoire de Physique et Chimie Théoriques, UMR CNRS 7019, Faculté des Sciences et Technologies, Université de Lorraine, CNRS, BP 70239, 54506 Vandoeuvre-lès-Nancy Cedex, France
| | - Masataka Nagaoka
- Department of Complex Systems Science, Graduate School of Informatics, Nagoya University, Chikusa Ku, Furo Cho, Nagoya, Aichi 4648601, Japan
- ESICB, Kyoto University, Kyodai Katsura, Nishikyo-ku, Kyoto 6158520, Japan
- Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Honmachi, Kawaguchi 3320012, Japan
- Future Value Creation Research Center, Graduate School of Informatics, Nagoya University, Chikusa Ku, Furo Cho, Nagoya, Aichi 4648601, Japan
| | - Manuel F. Ruiz-López
- Laboratoire de Physique et Chimie Théoriques, UMR CNRS 7019, Faculté des Sciences et Technologies, Université de Lorraine, CNRS, BP 70239, 54506 Vandoeuvre-lès-Nancy Cedex, France
- Future Value Creation Research Center, Graduate School of Informatics, Nagoya University, Chikusa Ku, Furo Cho, Nagoya, Aichi 4648601, Japan
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8
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Yagi K, Yamada K, Kobayashi C, Sugita Y. Anharmonic Vibrational Analysis of Biomolecules and Solvated Molecules Using Hybrid QM/MM Computations. J Chem Theory Comput 2019; 15:1924-1938. [PMID: 30730746 PMCID: PMC8864611 DOI: 10.1021/acs.jctc.8b01193] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
![]()
Quantum
mechanics/molecular mechanics (QM/MM) calculations are
applied for anharmonic vibrational analyses of biomolecules and solvated
molecules. The QM/MM method is implemented into a molecular dynamics
(MD) program, GENESIS, by interfacing with external electronic structure
programs. Following the geometry optimization and the harmonic normal-mode
analysis based on a partial Hessian, the anharmonic potential energy
surface (PES) is generated from QM/MM energies and gradients calculated
at grid points. The PES is used for vibrational self-consistent field
(VSCF) and post-VSCF calculations to compute the vibrational spectrum.
The method is first applied to a phosphate ion in solution. With both
the ion and neighboring water molecules taken as a QM region, IR spectra
of representative hydration structures are calculated by the second-order
vibrational quasi-degenerate perturbation theory (VQDPT2) at the level
of B3LYP/cc-pVTZ and TIP3P force field. A weight-average of IR spectra
over the structures reproduces the experimental spectrum with a mean
absolute deviation of 16 cm–1. Then, the method
is applied to an enzyme, P450 nitric oxide reductase (P450nor), with
the NO molecule bound to a ferric (FeIII) heme. Starting
from snapshot structures obtained from MD simulations of P450nor in
solution, QM/MM calculations have been carried out at the level of
B3LYP-D3/def2-SVP(D). The spin state of FeIII(NO) is likely
a closed-shell singlet state based on a ratio of N–O and Fe–NO
stretching frequencies (νN–O and νFe–NO) calculated for closed- and open-shell singlet
states. The calculated νN–O and νFe–NO overestimate the experimental ones by 120 and
75 cm–1, respectively. The electronic structure
and solvation of FeIII(NO) affect the structure around
the heme of P450nor leading to an increase in νN–O and νFe–NO.
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Affiliation(s)
- Kiyoshi Yagi
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Kenta Yamada
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Chigusa Kobayashi
- Computational Biophysics Research Team, RIKEN Center for Computational Science, 7-1-26 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Yuji Sugita
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Computational Biophysics Research Team, RIKEN Center for Computational Science, 7-1-26 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
- Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, 1-6-5 Minatojima-Minamimachi,
Chuo-ku, Kobe, Hyogo 650-0047, Japan
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9
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Bistafa C, Kitamura Y, Nagaoka M, Canuto S. Microscopic Origin of Different Hydration Patterns of para-Nitrophenol and Its Anion: A Study Combining Multiconfigurational Calculations and the Free-Energy Gradient Method. J Phys Chem B 2018; 122:9202-9209. [PMID: 30160963 DOI: 10.1021/acs.jpcb.8b06439] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A theoretical study of the solvatochromic shifts of para-nitrophenol ( pNP) and para-nitrophenolate anion ( pNP-) in aqueous solution is presented using a QM/MM methodology with molecular dynamics simulation. The optimized structures in aqueous solution are obtained using both the polarizable continuum and the free-energy gradient methods. For pNP, the calculated redshifts at the CASPT2 (12,10) level are, respectively, 0.71 and 0.94 eV, in good agreement with the experimental ones (0.80-0.83 eV), whereas for pNP-, they are small. The difference between the solvatochromic shifts of pNP and pNP- is calculated as 0.71 eV in good agreement with the experimental one (0.79-0.81 eV). Finally, these shifts are understood in terms of the solvent effect on the solute structure, accurately calculated by the present theoretical treatment.
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Affiliation(s)
- Carlos Bistafa
- Institute of Physics , University of São Paulo , Rua do Matão, 1371 , Cidade Universitária, São Paulo-SP 05508-090 , Brazil.,Graduate School of Informatics , Nagoya University , Furo-cho, Chikusa-ku, Nagoya , Aichi 464-8601 , Japan.,Core Research for Evolutional Science and Technology (CREST) , Japan Science and Technology Agency (JST) , Honmachi, Kawaguchi 332-0012 , Japan
| | - Yukichi Kitamura
- Graduate School of Informatics , Nagoya University , Furo-cho, Chikusa-ku, Nagoya , Aichi 464-8601 , Japan.,Core Research for Evolutional Science and Technology (CREST) , Japan Science and Technology Agency (JST) , Honmachi, Kawaguchi 332-0012 , Japan
| | - Masataka Nagaoka
- Graduate School of Informatics , Nagoya University , Furo-cho, Chikusa-ku, Nagoya , Aichi 464-8601 , Japan.,Core Research for Evolutional Science and Technology (CREST) , Japan Science and Technology Agency (JST) , Honmachi, Kawaguchi 332-0012 , Japan
| | - Sylvio Canuto
- Institute of Physics , University of São Paulo , Rua do Matão, 1371 , Cidade Universitária, São Paulo-SP 05508-090 , Brazil
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10
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Fujie T, Takenaka N, Suzuki Y, Nagaoka M. Red Moon methodology compatible with quantum mechanics/molecular mechanics framework: Application to solid electrolyte interphase film formation in lithium-ion battery system. J Chem Phys 2018; 149:044113. [PMID: 30068180 DOI: 10.1063/1.5034771] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The Red Moon (RM) method [a hybrid Monte Carlo (MC)/molecular dynamics reaction method] is capable of realizing the practical atomistic simulation for complex chemical reaction systems beyond the range of application of the traditional molecular simulation techniques. In the RM method, the chemical reaction is treated stochastically based on the MC method. In the present study, to extend the applicability of the RM methodology, a new energy estimation method for the MC procedure has been proposed by using the quantum mechanics (QM)/molecular mechanics (MM) method. To validate its calculation reliability, we have examined it in a typical dimerization reaction in electrolytes of lithium-ion batteries (LIBs) and found that both solute internal energy and short-range solute-solvent interaction energy are significantly improved in comparison to the conventional energy estimation method using the MM method. As a practical application, we have dealt with the solid electrolyte interphase film formation in LIB, focusing on the bifurcation of dimerization reactions between the reduction products, and were able to reproduce the tendency similar to that in the experimental observations. It is concluded that the present RM methodology compatible with the QM/MM framework is expected to make a significant contribution to a variety of materials design and function development involved in various complex chemical reactions.
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Affiliation(s)
- Takuya Fujie
- Graduate School of Informatics, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Norio Takenaka
- Graduate School of Informatics, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Yuichi Suzuki
- Graduate School of Informatics, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Masataka Nagaoka
- Graduate School of Informatics, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
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11
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Bistafa C, Kitamura Y, Martins-Costa MTC, Nagaoka M, Ruiz-López MF. Cost-Effective Method for Free-Energy Minimization in Complex Systems with Elaborated Ab Initio Potentials. J Chem Theory Comput 2018; 14:3262-3271. [DOI: 10.1021/acs.jctc.8b00271] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Carlos Bistafa
- Department of Complex Systems Science, Graduate School of Informatics, Nagoya University, Chikusa Ku, Furo Cho, Nagoya, Aichi 4648601, Japan
| | - Yukichi Kitamura
- Department of Complex Systems Science, Graduate School of Informatics, Nagoya University, Chikusa Ku, Furo Cho, Nagoya, Aichi 4648601, Japan
| | - Marilia T. C. Martins-Costa
- Laboratoire de Physique et Chimie Théoriques, UMR CNRS 7019, Faculté des Sciences et Technologies, Université de Lorraine, CNRS, BP 70239, 54506 Vandoeuvre-lès-Nancy Cedex,France
| | - Masataka Nagaoka
- Department of Complex Systems Science, Graduate School of Informatics, Nagoya University, Chikusa Ku, Furo Cho, Nagoya, Aichi 4648601, Japan
- ESICB, Kyoto University, Kyodai Katsura, Nishikyo-ku, Kyoto 6158520, Japan
- Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Honmachi, Kawaguchi 3320012, Japan
| | - Manuel F. Ruiz-López
- Laboratoire de Physique et Chimie Théoriques, UMR CNRS 7019, Faculté des Sciences et Technologies, Université de Lorraine, CNRS, BP 70239, 54506 Vandoeuvre-lès-Nancy Cedex,France
- Future Value Creation Research Center, Graduate School of Informatics, Nagoya University, Chikusa Ku, Furo Cho, Nagoya, Aichi 4648601, Japan
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12
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Duster AW, Wang C, Garza CM, Miller DE, Lin H. Adaptive quantum/molecular mechanics: what have we learned, where are we, and where do we go from here? WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2017. [DOI: 10.1002/wcms.1310] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Adam W. Duster
- Chemistry Department University of Colorado Denver Denver CO USA
| | - Chun‐Hung Wang
- Chemistry Department University of Colorado Denver Denver CO USA
| | | | | | - Hai Lin
- Chemistry Department University of Colorado Denver Denver CO USA
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13
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Asada T, Ando K, Bandyopadhyay P, Koseki S. Free Energy Contribution Analysis Using Response Kernel Approximation: Insights into the Acylation Reaction of a Beta-Lactamase. J Phys Chem B 2016; 120:9338-46. [PMID: 27501066 DOI: 10.1021/acs.jpcb.6b06104] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A widely applicable free energy contribution analysis (FECA) method based on the quantum mechanical/molecular mechanical (QM/MM) approximation using response kernel approaches has been proposed to investigate the influences of environmental residues and/or atoms in the QM region on the free energy profile. This method can evaluate atomic contributions to the free energy along the reaction path including polarization effects on the QM region within a dramatically reduced computational time. The rate-limiting step in the deactivation of the β-lactam antibiotic cefalotin (CLS) by β-lactamase was studied using this method. The experimentally observed activation barrier was successfully reproduced by free energy perturbation calculations along the optimized reaction path that involved activation by the carboxylate moiety in CLS. It was found that the free energy profile in the QM region was slightly higher than the isolated energy and that two residues, Lys67 and Lys315, as well as water molecules deeply influenced the QM atoms associated with the bond alternation reaction in the acyl-enzyme intermediate. These facts suggested that the surrounding residues are favorable for the reactant complex and prevent the intermediate from being too stabilized to proceed to the following deacylation reaction. We have demonstrated that the free energy contribution analysis should be a useful method to investigate enzyme catalysis and to facilitate intelligent molecular design.
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Affiliation(s)
- Toshio Asada
- Department of Chemistry, Graduate School of Science, Osaka Prefecture University , 1-1 Gakuen-cho, Naka-ku, Sakai 599-8531, Japan.,The Research Institute for Molecular Electronic Devices (RIMED), Osaka Prefecture University , 1-1 Gakuen-cho, Naka-ku, Sakai 599-8531, Japan
| | - Kanta Ando
- Department of Chemistry, Graduate School of Science, Osaka Prefecture University , 1-1 Gakuen-cho, Naka-ku, Sakai 599-8531, Japan
| | - Pradipta Bandyopadhyay
- School of Computational and Integrative Sciences, Jawaharlal Nehru University , New Delhi, India 110067
| | - Shiro Koseki
- Department of Chemistry, Graduate School of Science, Osaka Prefecture University , 1-1 Gakuen-cho, Naka-ku, Sakai 599-8531, Japan.,The Research Institute for Molecular Electronic Devices (RIMED), Osaka Prefecture University , 1-1 Gakuen-cho, Naka-ku, Sakai 599-8531, Japan
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14
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Asada T, Ando K, Sakurai K, Koseki S, Nagaoka M. Efficient approach to include molecular polarizations using charge and atom dipole response kernels to calculate free energy gradients in the QM/MM scheme. Phys Chem Chem Phys 2016; 17:26955-68. [PMID: 26403576 DOI: 10.1039/c5cp04423e] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An efficient approach to evaluate free energy gradients (FEGs) within the quantum mechanical/molecular mechanical (QM/MM) framework has been proposed to clarify reaction processes on the free energy surface (FES) in molecular assemblies. The method is based on response kernel approximations denoted as the charge and the atom dipole response kernel (CDRK) model that include explicitly induced atom dipoles. The CDRK model was able to reproduce polarization effects for both electrostatic interactions between QM and MM regions and internal energies in the QM region obtained by conventional QM/MM methods. In contrast to charge response kernel (CRK) models, CDRK models could be applied to various kinds of molecules, even linear or planer molecules, without using imaginary interaction sites. Use of the CDRK model enabled us to obtain FEGs on QM atoms in significantly reduced computational time. It was also clearly demonstrated that the time development of QM forces of the solvated propylene carbonate radical cation (PC˙(+)) provided reliable results for 1 ns molecular dynamics (MD) simulation, which were quantitatively in good agreement with expensive QM/MM results. Using FEG and nudged elastic band (NEB) methods, we found two optimized reaction paths on the FES for decomposition reactions to generate CO2 molecules from PC˙(+), whose reaction is known as one of the degradation mechanisms in the lithium-ion battery. Two of these reactions proceed through an identical intermediate structure whose molecular dipole moment is larger than that of the reactant to be stabilized in the solvent, which has a high relative dielectric constant. Thus, in order to prevent decomposition reactions, PC˙(+) should be modified to have a smaller dipole moment along two reaction paths.
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Affiliation(s)
- Toshio Asada
- Department of Chemistry, Graduate School of Science, Osaka Prefecture University, 1-1 Gakuen-cho, Sakai 599-8531, Japan.
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15
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Zhou Y, Wang S, Li Y, Zhang Y. Born-Oppenheimer Ab Initio QM/MM Molecular Dynamics Simulations of Enzyme Reactions. Methods Enzymol 2016; 577:105-18. [PMID: 27498636 PMCID: PMC4986621 DOI: 10.1016/bs.mie.2016.05.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
There are two key requirements for reliably simulating enzyme reactions: one is a reasonably accurate potential energy surface to describe the bond-forming/breaking process as well as to adequately model the heterogeneous enzyme environment; the other is to perform extensive sampling since an enzyme system consists of at least thousands of atoms and its energy landscape is very complex. One attractive approach to meet both daunting tasks is Born-Oppenheimer ab initio QM/MM molecular dynamics (aiQM/MM-MD) simulation with umbrella sampling. In this chapter, we describe our recently developed pseudobond Q-Chem-Amber interface, which employs a combined electrostatic-mechanical embedding scheme with periodic boundary condition and the particle mesh Ewald method for long-range electrostatics interactions. In our implementation, Q-Chem and the sander module of Amber are combined at the source code level without using system calls, and all necessary data communications between QM and MM calculations are achieved via computer memory. We demonstrate the applicability of this pseudobond Q-Chem-Amber interface by presenting two examples, one reaction in aqueous solution and one enzyme reaction. Finally, we describe our established aiQM/MM-MD enzyme simulation protocol, which has been successfully applied to study more than a dozen enzymes.
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Affiliation(s)
- Y Zhou
- Laboratory of Mesoscopic Chemistry, Collaborative Innovation Center of Chemistry for Life Sciences, Institute of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
| | - S Wang
- New York University, New York, NY, United States
| | - Y Li
- International Center of Quantum and Molecular Structures, and Shanghai Key Laboratory of High Temperature Superconductors, Shanghai University, Shanghai, China
| | - Y Zhang
- New York University, New York, NY, United States; NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai, China.
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16
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Takenaka N, Kitamura Y, Nagaoka M. Efficient Computational Research Protocol to Survey Free Energy Surface for Solution Chemical Reaction in the QM/MM Framework: The FEG-ER Methodology and Its Application to Isomerization Reaction of Glycine in Aqueous Solution. J Phys Chem B 2016; 120:2001-11. [PMID: 26794718 DOI: 10.1021/acs.jpcb.5b10061] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In solution chemical reaction, we often need to consider a multidimensional free energy (FE) surface (FES) which is analogous to a Born-Oppenheimer potential energy surface. To survey the FES, an efficient computational research protocol is proposed within the QM/MM framework; (i) we first obtain some stable states (or transition states) involved by optimizing their structures on the FES, in a stepwise fashion, finally using the free energy gradient (FEG) method, and then (ii) we directly obtain the FE differences among any arbitrary states on the FES, efficiently by employing the QM/MM method with energy representation (ER), i.e., the QM/MM-ER method. To validate the calculation accuracy and efficiency, we applied the above FEG-ER methodology to a typical isomerization reaction of glycine in aqueous solution, and reproduced quite satisfactorily the experimental value of the reaction FE. Further, it was found that the structural relaxation of the solute in the QM/MM force field is not negligible to estimate correctly the FES. We believe that the present research protocol should become prevailing as one computational strategy and will play promising and important roles in solution chemistry toward solution reaction ergodography.
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Affiliation(s)
- Norio Takenaka
- Graduate School of Information Science, Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan.,ESICB, Kyoto University , Kyodai Katsura, Nishikyo-ku, Kyoto 615-8520, Japan
| | - Yukichi Kitamura
- Graduate School of Information Science, Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan.,Core Research for Evolutional Science and Technology, Japan Science and Technology Agency , Honmachi, Kawaguchi 332-0012, Japan
| | - Masataka Nagaoka
- Graduate School of Information Science, Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan.,ESICB, Kyoto University , Kyodai Katsura, Nishikyo-ku, Kyoto 615-8520, Japan.,Core Research for Evolutional Science and Technology, Japan Science and Technology Agency , Honmachi, Kawaguchi 332-0012, Japan
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17
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Vilseck JZ, Kostal J, Tirado-Rives J, Jorgensen WL. Application of a BOSS-Gaussian interface for QM/MM simulations of Henry and methyl transfer reactions. J Comput Chem 2015; 36:2064-74. [PMID: 26311531 PMCID: PMC4575649 DOI: 10.1002/jcc.24045] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Revised: 07/17/2015] [Accepted: 07/20/2015] [Indexed: 01/06/2023]
Abstract
Hybrid quantum mechanics and molecular mechanics (QM/MM) computer simulations have become an indispensable tool for studying chemical and biological phenomena for systems too large to treat with QM alone. For several decades, semiempirical QM methods have been used in QM/MM simulations. However, with increased computational resources, the introduction of ab initio and density function methods into on-the-fly QM/MM simulations is being increasingly preferred. This adaptation can be accomplished with a program interface that tethers independent QM and MM software packages. This report introduces such an interface for the BOSS and Gaussian programs, featuring modification of BOSS to request QM energies and partial atomic charges from Gaussian. A customizable C-shell linker script facilitates the interprogram communication. The BOSS-Gaussian interface also provides convenient access to Charge Model 5 (CM5) partial atomic charges for multiple purposes including QM/MM studies of reactions. In this report, the BOSS-Gaussian interface is applied to a nitroaldol (Henry) reaction and two methyl transfer reactions in aqueous solution. Improved agreement with experiment is found by determining free-energy surfaces with MP2/CM5 QM/MM simulations than previously reported investigations using semiempirical methods.
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Affiliation(s)
- Jonah Z. Vilseck
- Department of Chemistry, Yale University, New Haven, CT 06520-8107USA
| | - Jakub Kostal
- Department of Chemistry, Yale University, New Haven, CT 06520-8107USA
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18
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Saito T, Kawakami T, Yamanaka S, Okumura M. QM/MM study of hydrolysis of arginine catalysed by arginase. Mol Phys 2015. [DOI: 10.1080/00268976.2015.1078506] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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19
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Studies of binding interactions between Dufulin and southern rice black-streaked dwarf virus P9-1. Bioorg Med Chem 2015; 23:3629-37. [DOI: 10.1016/j.bmc.2015.04.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 04/03/2015] [Accepted: 04/04/2015] [Indexed: 01/08/2023]
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20
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Saito T, Kawakami T, Yamanaka S, Okumura M. Computational Study of Catalytic Reaction of Quercetin 2,4-Dioxygenase. J Phys Chem B 2015; 119:6952-62. [PMID: 25990020 DOI: 10.1021/acs.jpcb.5b03564] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present a quantum mechanics/molecular mechanics (QM/MM) and QM-only study on the oxidative ring-cleaving reaction of quercetin catalyzed by quercetin 2,4-dioxygenase (2,4-QD). 2,4-QD has a mononuclear type 2 copper center and incorporates two oxygen atoms at C2 and C4 positions of the substrate. It has not been clear whether dioxygen reacts with a copper ion or a substrate radical as the first step. We have found that dioxygen is more likely to bind to a Cu(2+) ion, involving the dissociation of the substrate from the copper ion. Then a Cu(2+)-alkylperoxo complex can be generated. Comparison of geometry and stability between QM-only and QM/MM results strongly indicates that steric effects of the protein environment contribute to maintain the orientation of the substrate dissociated from the copper center. The present QM/MM results also highlight that a prior rearrangement of the Cu(2+)-alkylperoxo complex and a subsequent hydrogen bond switching assisted by the movement of Glu73 can facilitate formation of an endoperoxide intermediate selectively.
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Affiliation(s)
- Toru Saito
- †Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan.,‡Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology (JST) Agency, Kawaguchi, Saitama 332-0012, Japan
| | - Takashi Kawakami
- †Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Shusuke Yamanaka
- †Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan.,‡Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology (JST) Agency, Kawaguchi, Saitama 332-0012, Japan
| | - Mitsutaka Okumura
- †Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan.,‡Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology (JST) Agency, Kawaguchi, Saitama 332-0012, Japan
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21
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Free Energy Gradient Method and Its Recent Related Developments: Free Energy Optimization and Vibrational Frequency Analysis in Solution. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2015. [DOI: 10.1007/978-3-319-21626-3_8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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22
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Kitamura Y, Takenaka N, Koyano Y, Nagaoka M. Dual Approach to Vibrational Spectra in Solution: Microscopic Influence of Hydrogen Bonding to the State of Motion of Glycine in Water. J Chem Theory Comput 2014; 10:3369-79. [PMID: 26588305 DOI: 10.1021/ct500235a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We have proposed a new theoretical methodology to clarify the microscopic nature of the vibrational properties in solution, which consists of a combination of the vibrational frequency analyses (VFAs) with two kinds of Hessian matrices, that is, the effective Hessian on the free energy surface (free energy Hessian: "FE-Hessian") and the instantaneous one (instantaneous normal mode Hessian: "INM-Hessian") within QM/MM framework. In these VFAs, the Hessians were obtained by the analytical approach, having the advantages from the aspect of both the computational efficiency and accuracy in comparison to those obtained by the numerical one. In the present study, we have applied them to the glycine aqueous solution. First, by using the VFA with the FE-Hessian (VFA-FEH), we estimated the vibrational frequency shifts induced by solvent water molecules. The calculated values were quantitatively in agreement with experimental ones. It was clearly demonstrated that such vibrational shifts are attributed to not only the structural relaxation but also the explicit solute-solvent interactions (i.e., interatomic interactions). Second, by using the VFA with the INM-Hessian (VFA-INMH), the vibrational spectra in solution were investigated through the vibrational INM densities of states (DOS). By the comparison between the spectroscopic features and the microscopic solvation structure around glycine molecule, it was found that the frequency shifts and bandwidths in IR spectra are closely correlated with the hydrogen bonding (HB) network formations. In particular, the instantaneous changes of vibrational states of the hydroxyl group and carbonyl one, showing apparently inverse tendency on the strength of the HB interaction, can be explained very well on the basis of two different mechanisms, that is, the direct change of electron density in the bonding orbitals and the indirect one due to hyperconjugation between the lone electron pair and the antibonding orbitals, respectively. In conclusion, the present dual VFA approach is a quite useful strategy to interpret the microscopic origin of the experimental vibrational spectra.
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Affiliation(s)
- Yukichi Kitamura
- Graduate School of Information Science, Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan.,Japan Society for the Promotion of Science (JSPS), Tokyo 102-0083, Japan
| | - Norio Takenaka
- Graduate School of Information Science, Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan.,Elements Strategy Initiative for Catalysts and Batteries (ESICB), Kyoto University Katsura , Kyoto 615-8520, Japan
| | - Yoshiyuki Koyano
- Graduate School of Information Science, Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Masataka Nagaoka
- Graduate School of Information Science, Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan.,Elements Strategy Initiative for Catalysts and Batteries (ESICB), Kyoto University Katsura , Kyoto 615-8520, Japan.,Core Research for Evolutional Science and Technology, Japan Science and Technology Agency , Honmachi, Kawaguchi 332-0012, Japan
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23
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Saito T, Thiel W. Quantum mechanics/molecular mechanics study of oxygen binding in hemocyanin. J Phys Chem B 2014; 118:5034-43. [PMID: 24762083 DOI: 10.1021/jp5003885] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We report a combined quantum mechanics/molecular mechanics (QM/MM) study on the mechanism of reversible dioxygen binding in the active site of hemocyanin (Hc). The QM region is treated by broken-symmetry density functional theory (DFT) with spin projection corrections. The X-ray structures of deoxygenated (deoxyHc) and oxygenated (oxyHc) hemocyanin are well reproduced by QM/MM geometry optimizations. The computed relative energies strongly depend on the chosen density functional. They are consistent with the available thermodynamic data for oxygen binding in hemocyanin and in synthetic model complexes when the BH&HLYP hybrid functional with 50% Hartree-Fock exchange is used. According to the QM(BH&HLYP)/MM results, the reaction proceeds stepwise with two sequential electron transfer (ET) processes in the triplet state followed by an intersystem crossing to the singlet product. The first ET step leads to a nonbridged superoxo CuB(II)-O2(•-) intermediate via a low-barrier transition state. The second ET step is even more facile and yields a side-on oxyHc complex with the characteristic Cu2O2 butterfly core, accompanied by triplet-singlet intersystem crossing. The computed barriers are very small so that the two ET processes are expected to very rapid and nearly simultaneous.
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Affiliation(s)
- Toru Saito
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
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24
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Götz AW, Clark MA, Walker RC. An extensible interface for QM/MM molecular dynamics simulations with AMBER. J Comput Chem 2014; 35:95-108. [PMID: 24122798 PMCID: PMC4063945 DOI: 10.1002/jcc.23444] [Citation(s) in RCA: 117] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Revised: 08/05/2013] [Accepted: 08/31/2013] [Indexed: 11/09/2022]
Abstract
We present an extensible interface between the AMBER molecular dynamics (MD) software package and electronic structure software packages for quantum mechanical (QM) and mixed QM and classical molecular mechanical (MM) MD simulations within both mechanical and electronic embedding schemes. With this interface, ab initio wave function theory and density functional theory methods, as available in the supported electronic structure software packages, become available for QM/MM MD simulations with AMBER. The interface has been written in a modular fashion that allows straight forward extensions to support additional QM software packages and can easily be ported to other MD software. Data exchange between the MD and QM software is implemented by means of files and system calls or the message passing interface standard. Based on extensive tests, default settings for the supported QM packages are provided such that energy is conserved for typical QM/MM MD simulations in the microcanonical ensemble. Results for the free energy of binding of calcium ions to aspartate in aqueous solution comparing semiempirical and density functional Hamiltonians are shown to demonstrate features of this interface.
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Affiliation(s)
- Andreas W. Götz
- San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0505, USA
| | - Matthew A. Clark
- San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0505, USA
| | - Ross C. Walker
- San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0505, USA
- Department of Chemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0505, USA
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25
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A hybrid MC/MD reaction method with rare event-driving mechanism: Atomistic realization of 2-chlorobutane racemization process in DMF solution. Chem Phys Lett 2013. [DOI: 10.1016/j.cplett.2013.08.017] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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26
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Okamoto T, Ishikawa T, Koyano Y, Yamamoto N, Kuwata K, Nagaoka M. A Minimal Implementation of the AMBER-PAICS Interface for Ab Initio FMO-QM/MM-MD Simulation. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2013. [DOI: 10.1246/bcsj.20120216] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Takuya Okamoto
- Graduate School of Information Science, Nagoya University
| | - Takeshi Ishikawa
- Division of Prion Research, Center for Emerging Infectious Disease, Gifu University
| | | | | | - Kazuo Kuwata
- Division of Prion Research, Center for Emerging Infectious Disease, Gifu University
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27
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Takenaka N, Kitamura Y, Koyano Y, Nagaoka M. An improvement in quantum mechanical description of solute-solvent interactions in condensed systems via the number-adaptive multiscale quantum mechanical/molecular mechanical-molecular dynamics method: Application to zwitterionic glycine in aqueous solution. J Chem Phys 2012; 137:024501. [DOI: 10.1063/1.4732307] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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28
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Roberts BP, Seabra GM, Roitberg AE, Merz KM, Deumens E, Torras J, Trickey SB. Comment on "A minimal implementation of the AMBER-GAUSSIAN interface for ab initio QM/MM-MD simulation". J Comput Chem 2012; 33:1643-4. [PMID: 22570199 DOI: 10.1002/jcc.23003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2010] [Revised: 03/05/2012] [Accepted: 03/16/2012] [Indexed: 11/09/2022]
Abstract
We comment upon the recent critique of use of the Program for User Package Interfacing and Linking (PUPIL) system for linking AMBER and GAUSSIAN in a multiscale quantum mechanical/molecular mechanics (QM/MM) simulation (Okamoto et al., J. Comput. Chem. 2011, 32, 932). Specifically, their method for computing forces on the MM particles from the QM region via the GAUSSIAN-03 electrical field was already implemented in PUPIL version 1.3, publicly available beginning December 2009. Some other doubtful characterizations of PUPIL are discussed briefly in the context of current awareness of open-source codes more generally.
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Affiliation(s)
- Benjamin P Roberts
- Quantum Theory Project, Department of Physics, University of Florida, Gainesville, Florida 32611-8435, USA
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29
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Takenaka N, Kitamura Y, Koyano Y, Nagaoka M. The number-adaptive multiscale QM/MM molecular dynamics simulation: Application to liquid water. Chem Phys Lett 2012. [DOI: 10.1016/j.cplett.2011.12.053] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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30
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On the smoothing of free energy landscape of solute molecules in solution: A demonstration of the stability of glycine conformers via ab initio QM/MM free energy calculation. Chem Phys Lett 2011. [DOI: 10.1016/j.cplett.2011.08.061] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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31
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Yamada K, Koyano Y, Okamoto T, Asada T, Koga N, Nagaoka M. Toward a new approach for determination of solute's charge distribution to analyze interatomic electrostatic interactions in quantum mechanical/molecular mechanical simulations. J Comput Chem 2011; 32:3092-104. [DOI: 10.1002/jcc.21893] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2010] [Revised: 06/17/2011] [Accepted: 06/24/2011] [Indexed: 01/15/2023]
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32
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Takenaka N, Kitamura Y, Koyano Y, Asada T, Nagaoka M. Reaction path optimization and vibrational frequency analysis via ab initio QM/MM free energy gradient (FEG) method: application to isomerization process of glycine in aqueous solution. Theor Chem Acc 2011. [DOI: 10.1007/s00214-011-0962-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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