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Binninger T, Saraç D, Marsh L, Picard T, Doublet ML, Raynaud C. AMOEBA Polarizable Force Field for Molecular Dynamics Simulations of Glyme Solvents. J Chem Theory Comput 2023; 19:1023-1034. [PMID: 36692444 DOI: 10.1021/acs.jctc.2c00926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Classical molecular dynamics (MD) simulations of electrolyte systems are important to gain insight into the atom-scale properties that determine the battery-relevant performance. The recent Tinker-HP software release enables efficient and accurate MD simulations with the AMOEBA polarizable force field. In this work, we developed a procedure to construct a universal AMOEBA model for the solvent family of glymes (glycol methyl ethers), which involves a refinement scheme for valence parameters by fitting the AMOEBA-derived atomic forces to those computed at the DFT level. The refined AMOEBA model provides a good description of both local and nonlocal properties in terms of the spectroscopic response of glyme molecules, as well as the liquid glyme density and dielectric constant. In addition, the complexation energies of alkali and alkaline-earth metal cations with tetraglyme molecules obtained from AMOEBA calculations are in good agreement with DFT results, demonstrating the suitability of the developed AMOEBA model for an accurate simulation of glyme-based battery electrolytes. We also expect the procedure to be transferable to the development of AMOEBA models for other battery electrolyte systems.
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Affiliation(s)
- Tobias Binninger
- ICGM, Université de Montpellier, CNRS, ENSCM, 34095Montpellier, France
| | - Defne Saraç
- ICGM, Université de Montpellier, CNRS, ENSCM, 34095Montpellier, France.,Réseau sur le Stockage Electrochimique de l'Energie (RS2E), FR CNRS3459, Hub de l'Energie, 80039Amiens, France
| | - Liam Marsh
- ICGM, Université de Montpellier, CNRS, ENSCM, 34095Montpellier, France
| | - Tanguy Picard
- LEPMI, Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, Grenoble INP, 38000Grenoble, France
| | - Marie-Liesse Doublet
- ICGM, Université de Montpellier, CNRS, ENSCM, 34095Montpellier, France.,Réseau sur le Stockage Electrochimique de l'Energie (RS2E), FR CNRS3459, Hub de l'Energie, 80039Amiens, France
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2
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Szabadi A, Schröder C. Recent Developments in Polarizable Molecular Dynamics Simulations of Electrolyte Solutions. JOURNAL OF COMPUTATIONAL BIOPHYSICS AND CHEMISTRY 2022. [DOI: 10.1142/s2737416521420035] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Polarizable molecular dynamics simulations are a fast progressing field in the scientific research of ionic liquids. The fundamentals of polarizable simulations, as well as their application to ionic liquids, were summarized in a review [Bedrov, D.; Piquemal, J.-P.; Borodin, O.; MacKerell, Jr., A. D.; Roux, B.; Schröder, C. Molecular Dynamics Simulations of Ionic Liquids and Electrolytes Using Polarizable Force Fields. Chem. Rev. 2019, 119, 7940–7995] in 2019. Since then, new methods to treat intermolecular interaction of induced dipoles in these highly charged systems were developed. This concerns the damping of these interactions and additional charge transfer as well as the prediction of ionic materials with ultrahigh refractive indices. In addition to the progress of the polarizable force fields, also thermostats and barostats for polarizable simulations evolved recently.
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Affiliation(s)
- András Szabadi
- University of Vienna, Faculty of Chemistry, Department of Computational Biological Chemistry, A-1090 Vienna, Austria
| | - Christian Schröder
- University of Vienna, Faculty of Chemistry, Department of Computational Biological Chemistry, A-1090 Vienna, Austria
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3
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Yao N, Chen X, Fu ZH, Zhang Q. Applying Classical, Ab Initio, and Machine-Learning Molecular Dynamics Simulations to the Liquid Electrolyte for Rechargeable Batteries. Chem Rev 2022; 122:10970-11021. [PMID: 35576674 DOI: 10.1021/acs.chemrev.1c00904] [Citation(s) in RCA: 67] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Rechargeable batteries have become indispensable implements in our daily life and are considered a promising technology to construct sustainable energy systems in the future. The liquid electrolyte is one of the most important parts of a battery and is extremely critical in stabilizing the electrode-electrolyte interfaces and constructing safe and long-life-span batteries. Tremendous efforts have been devoted to developing new electrolyte solvents, salts, additives, and recipes, where molecular dynamics (MD) simulations play an increasingly important role in exploring electrolyte structures, physicochemical properties such as ionic conductivity, and interfacial reaction mechanisms. This review affords an overview of applying MD simulations in the study of liquid electrolytes for rechargeable batteries. First, the fundamentals and recent theoretical progress in three-class MD simulations are summarized, including classical, ab initio, and machine-learning MD simulations (section 2). Next, the application of MD simulations to the exploration of liquid electrolytes, including probing bulk and interfacial structures (section 3), deriving macroscopic properties such as ionic conductivity and dielectric constant of electrolytes (section 4), and revealing the electrode-electrolyte interfacial reaction mechanisms (section 5), are sequentially presented. Finally, a general conclusion and an insightful perspective on current challenges and future directions in applying MD simulations to liquid electrolytes are provided. Machine-learning technologies are highlighted to figure out these challenging issues facing MD simulations and electrolyte research and promote the rational design of advanced electrolytes for next-generation rechargeable batteries.
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Affiliation(s)
- Nan Yao
- Beijing Key Laboratory of Green Chemical Reaction Engineering and Technology, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Xiang Chen
- Beijing Key Laboratory of Green Chemical Reaction Engineering and Technology, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Zhong-Heng Fu
- Beijing Key Laboratory of Green Chemical Reaction Engineering and Technology, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Qiang Zhang
- Beijing Key Laboratory of Green Chemical Reaction Engineering and Technology, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
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4
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Kee Soon N, Abdullah SB. Density functional theory on ionic liquid as carbonate scale dissolver in petroleum pipelines. COMPUT THEOR CHEM 2022. [DOI: 10.1016/j.comptc.2021.113576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Klajmon M, Červinka C. Does Explicit Polarizability Improve Simulations of Phase Behavior of Ionic Liquids? J Chem Theory Comput 2021; 17:6225-6239. [PMID: 34520200 DOI: 10.1021/acs.jctc.1c00518] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Molecular dynamics simulations are performed for a test set of 20 aprotic ionic liquids to investigate whether including an explicit polarizability model in the force field leads to higher accuracy and reliability of the calculated phase behavior properties, especially the enthalpy of fusion. A classical nonpolarizable all-atom optimized potentials for liquid simulations (OPLS) force-field model developed by Canongia Lopes and Pádua (CL&P) serves as a reference level of theory. Polarizability is included either in the form of Drude oscillators, resulting in the CL&P-D models, or in the framework of the atomic multipole optimized energetics for biomolecular application (AMOEBA) force field with polarizable atomic sites. Benchmarking of the calculated fusion enthalpy values against the experimental data reveals that overall the nonpolarizable CL&P model and polarizable CL&P-D models perform similarly with average deviations of about 30%. However, fusion enthalpies from the CL&P-D models exhibit a stronger correlation with their experimental counterparts. The least successful predictions are interestingly obtained from AMOEBA (deviation ca. 60%), which may indicate that a reparametrization of this force-field model is needed to achieve improved predictions of the fusion enthalpy. In general, all FF models tend to underestimate the fusion enthalpies. In addition, quantum chemical calculations are used to compute the electronic cohesive energies of the crystalline phases of the ionic liquids and of the interaction energies within the ion pair. Significant positive correlations are found between the fusion enthalpy and the cohesive energies. The character of the present anions predetermines the magnitude of individual mechanistic components of the interaction energy and related enthalpic and cohesive properties.
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Affiliation(s)
- Martin Klajmon
- Department of Physical Chemistry, Faculty of Chemical Engineering, University of Chemistry and Technology, Prague, Technická 5, 166 28 Prague 6, Czech Republic
| | - Ctirad Červinka
- Department of Physical Chemistry, Faculty of Chemical Engineering, University of Chemistry and Technology, Prague, Technická 5, 166 28 Prague 6, Czech Republic
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Vázquez-Montelongo EA, Vázquez-Cervantes JE, Cisneros GA. Current Status of AMOEBA-IL: A Multipolar/Polarizable Force Field for Ionic Liquids. Int J Mol Sci 2020; 21:ijms21030697. [PMID: 31973103 PMCID: PMC7037047 DOI: 10.3390/ijms21030697] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 01/11/2020] [Accepted: 01/16/2020] [Indexed: 01/25/2023] Open
Abstract
Computational simulations of ionic liquid solutions have become a useful tool to investigate various physical, chemical and catalytic properties of systems involving these solvents. Classical molecular dynamics and hybrid quantum mechanical/molecular mechanical (QM/MM) calculations of IL systems have provided significant insights at the atomic level. Here, we present a review of the development and application of the multipolar and polarizable force field AMOEBA for ionic liquid systems, termed AMOEBA–IL. The parametrization approach for AMOEBA–IL relies on the reproduction of total quantum mechanical (QM) intermolecular interaction energies and QM energy decomposition analysis. This approach has been used to develop parameters for imidazolium– and pyrrolidinium–based ILs coupled with various inorganic anions. AMOEBA–IL has been used to investigate and predict the properties of a variety of systems including neat ILs and IL mixtures, water exchange reactions on lanthanide ions in IL mixtures, IL–based liquid–liquid extraction, and effects of ILs on an aniline protection reaction.
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Affiliation(s)
| | | | - G. Andrés Cisneros
- Department of Chemistry, University of North Texas, Denton, TX 76201, USA; (E.A.V.-M.); (J.E.V.-C.)
- Center for Advanced Scientific Computing and Modeling (CASCaM), University of North Texas, Denton, TX 76201, USA
- Correspondence:
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Bedrov D, Piquemal JP, Borodin O, MacKerell AD, Roux B, Schröder C. Molecular Dynamics Simulations of Ionic Liquids and Electrolytes Using Polarizable Force Fields. Chem Rev 2019; 119:7940-7995. [PMID: 31141351 PMCID: PMC6620131 DOI: 10.1021/acs.chemrev.8b00763] [Citation(s) in RCA: 284] [Impact Index Per Article: 56.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Indexed: 11/30/2022]
Abstract
Many applications in chemistry, biology, and energy storage/conversion research rely on molecular simulations to provide fundamental insight into structural and transport properties of materials with high ionic concentrations. Whether the system is comprised entirely of ions, like ionic liquids, or is a mixture of a polar solvent with a salt, e.g., liquid electrolytes for battery applications, the presence of ions in these materials results in strong local electric fields polarizing solvent molecules and large ions. To predict properties of such systems from molecular simulations often requires either explicit or mean-field inclusion of the influence of polarization on electrostatic interactions. In this manuscript, we review the pros and cons of different treatments of polarization ranging from the mean-field approaches to the most popular explicit polarization models in molecular dynamics simulations of ionic materials. For each method, we discuss their advantages and disadvantages and emphasize key assumptions as well as their adjustable parameters. Strategies for the development of polarizable models are presented with a specific focus on extracting atomic polarizabilities. Finally, we compare simulations using polarizable and nonpolarizable models for several classes of ionic systems, discussing the underlying physics that each approach includes or ignores, implications for implementation and computational efficiency, and the accuracy of properties predicted by these methods compared to experiments.
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Affiliation(s)
- Dmitry Bedrov
- Department
of Materials Science & Engineering, University of Utah, 122 South Central Campus Drive, Room 304, Salt Lake City, Utah 84112, United States
| | - Jean-Philip Piquemal
- Laboratoire
de Chimie Théorique, Sorbonne Université,
UMR 7616 CNRS, CC137, 4 Place Jussieu, Tour 12-13, 4ème étage, 75252 Paris Cedex 05, France
- Institut
Universitaire de France, 75005, Paris Cedex 05, France
- Department
of Biomedical Engineering, The University
of Texas at Austin, Austin, Texas 78712, United States
| | - Oleg Borodin
- Electrochemistry
Branch, Sensors and Electron Devices Directorate, Army Research Laboratory, 2800 Powder Mill Road, Adelphi, Maryland 20703, United
States
| | - Alexander D. MacKerell
- Department
of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, Maryland 21201, United
States
| | - Benoît Roux
- Department
of Biochemistry and Molecular Biology, Gordon Center for Integrative
Science, University of Chicago, 929 57th Street, Chicago, Illinois 60637, United States
| | - Christian Schröder
- Department
of Computational Biological Chemistry, University
of Vienna, Währinger Strasse 17, A-1090 Vienna, Austria
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Vázquez-Montelongo EA, Vázquez-Cervantes JE, Cisneros GA. Polarizable ab initio QM/MM Study of the Reaction Mechanism of N- tert-Butyloxycarbonylation of Aniline in [EMIm][BF₄]. Molecules 2018; 23:E2830. [PMID: 30384470 PMCID: PMC6278528 DOI: 10.3390/molecules23112830] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 10/27/2018] [Accepted: 10/29/2018] [Indexed: 12/25/2022] Open
Abstract
N-t e r t-butoxycarbonylation of amines in solution (water, organic solvents, or ionic liquids) is a common reaction for the preparation of drug molecules. To understand the reaction mechanism and the role of the solvent, quantum mechanical/molecular mechanical simulations using a polarizable multipolar force field with long⁻range electrostatic corrections were used to optimize the minimum energy paths (MEPs) associated with various possible reaction mechanisms employing the nudged elastic band (NEB) and the quadratic string method (QSM). The calculated reaction energies and energy barriers were compared with the corresponding gas-phase and dichloromethane results. Complementary Electron Localization Function (ELF)/NCI analyses provide insights on the critical structures along the MEP. The calculated results suggest the most likely path involves a sequential mechanism with the rate⁻limiting step corresponding to the nucleophilic attack of the aniline, followed by proton transfer and the release of CO 2 without the direct involvement of imidazolium cations as catalysts.
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Affiliation(s)
| | | | - G Andrés Cisneros
- Department of Chemistry, University of North Texas, Denton, TX 76201, USA.
- The Center for Advanced Scientific Computing and Modeling (CASCaM), University of North Texas, Denton, TX 76201, USA.
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Liyana-Arachchi TP, Haskins JB, Burke CM, Diederichsen KM, McCloskey BD, Lawson JW. Polarizable Molecular Dynamics and Experiments of 1,2-Dimethoxyethane Electrolytes with Lithium and Sodium Salts: Structure and Transport Properties. J Phys Chem B 2018; 122:8548-8559. [DOI: 10.1021/acs.jpcb.8b03445] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
| | | | - Colin M. Burke
- Department of Chemical and Bimolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Kyle M. Diederichsen
- Department of Chemical and Bimolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Bryan D. McCloskey
- Department of Chemical and Bimolecular Engineering, University of California, Berkeley, California 94720, United States
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10
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Piquemal JP, Jordan KD. Preface: Special Topic: From Quantum Mechanics to Force Fields. J Chem Phys 2018; 147:161401. [PMID: 29096449 DOI: 10.1063/1.5008887] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
This Special Topic issue entitled "From Quantum Mechanics to Force Fields" is dedicated to the ongoing efforts of the theoretical chemistry community to develop a new generation of accurate force fields based on data from high-level electronic structure calculations and to develop faster electronic structure methods for testing and designing force fields as well as for carrying out simulations. This issue includes a collection of 35 original research articles that illustrate recent theoretical advances in the field. It provides a timely snapshot of recent developments in the generation of approaches to enable more accurate molecular simulations of processes important in chemistry, physics, biophysics, and materials science.
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Affiliation(s)
- Jean-Philip Piquemal
- Laboratoire de Chimie Théorique, UMR 7616 CNRS, UPMC, Sorbonne Universités, 75252 Paris Cedex 05, France
| | - Kenneth D Jordan
- Department of Chemistry, The University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, USA
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Lourenço TC, Zhang Y, Costa LT, Maginn EJ. A molecular dynamics study of lithium-containing aprotic heterocyclic ionic liquid electrolytes. J Chem Phys 2018; 148:193834. [DOI: 10.1063/1.5016276] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Tuanan C. Lourenço
- Instituto de Química, Universidade Federal Fluminense–Outeiro de São João Batista, s/n CEP:24020-141, Niterói, RJ, Brazil
| | - Yong Zhang
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Luciano T. Costa
- Instituto de Química, Universidade Federal Fluminense–Outeiro de São João Batista, s/n CEP:24020-141, Niterói, RJ, Brazil
| | - Edward J. Maginn
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, USA
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12
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McDaniel JG. Polarization Effects in Binary [BMIM+][BF4–]/1,2-Dichloroethane, Acetone, Acetonitrile, and Water Electrolytes. J Phys Chem B 2018; 122:4345-4355. [DOI: 10.1021/acs.jpcb.8b01714] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jesse G. McDaniel
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
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13
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Chu H, Peng X, Li Y, Zhang Y, Min H, Li G. Polarizable atomic multipole-based force field for DOPC and POPE membrane lipids. Mol Phys 2018. [DOI: 10.1080/00268976.2018.1436201] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Huiying Chu
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, Liaoning, China
| | - Xiangda Peng
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, Liaoning, China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Yan Li
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, Liaoning, China
| | - Yuebin Zhang
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, Liaoning, China
| | - Hanyi Min
- Chinese Academy of Medical Science & Peking Union Medical College Hospital, Ophthalmology, Beijing, China
| | - Guohui Li
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, Liaoning, China
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Blanco-Díaz EG, Vázquez-Montelongo EA, Cisneros GA, Castrejón-González EO. Computational investigation of non-covalent interactions in 1-butyl 3-methylimidazolium/bis(trifluoromethylsulfonyl)imide [bmim][Tf2N] in EMD and NEMD. J Chem Phys 2018; 148:054303. [DOI: 10.1063/1.5017987] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Edgar G. Blanco-Díaz
- Departamento de Ingeniería Química, Tecnológico Nacional de México en Celaya, Celaya, Guanajuato 38010,
Mexico
| | | | - G. Andrés Cisneros
- Department of Chemistry, University of North Texas, Denton, Texas 76206, USA
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15
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Lagardère L, Jolly LH, Lipparini F, Aviat F, Stamm B, Jing ZF, Harger M, Torabifard H, Cisneros GA, Schnieders MJ, Gresh N, Maday Y, Ren PY, Ponder JW, Piquemal JP. Tinker-HP: a massively parallel molecular dynamics package for multiscale simulations of large complex systems with advanced point dipole polarizable force fields. Chem Sci 2018; 9:956-972. [PMID: 29732110 PMCID: PMC5909332 DOI: 10.1039/c7sc04531j] [Citation(s) in RCA: 130] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 11/24/2017] [Indexed: 12/23/2022] Open
Abstract
We present Tinker-HP, a massively MPI parallel package dedicated to classical molecular dynamics (MD) and to multiscale simulations, using advanced polarizable force fields (PFF) encompassing distributed multipoles electrostatics. Tinker-HP is an evolution of the popular Tinker package code that conserves its simplicity of use and its reference double precision implementation for CPUs. Grounded on interdisciplinary efforts with applied mathematics, Tinker-HP allows for long polarizable MD simulations on large systems up to millions of atoms. We detail in the paper the newly developed extension of massively parallel 3D spatial decomposition to point dipole polarizable models as well as their coupling to efficient Krylov iterative and non-iterative polarization solvers. The design of the code allows the use of various computer systems ranging from laboratory workstations to modern petascale supercomputers with thousands of cores. Tinker-HP proposes therefore the first high-performance scalable CPU computing environment for the development of next generation point dipole PFFs and for production simulations. Strategies linking Tinker-HP to Quantum Mechanics (QM) in the framework of multiscale polarizable self-consistent QM/MD simulations are also provided. The possibilities, performances and scalability of the software are demonstrated via benchmarks calculations using the polarizable AMOEBA force field on systems ranging from large water boxes of increasing size and ionic liquids to (very) large biosystems encompassing several proteins as well as the complete satellite tobacco mosaic virus and ribosome structures. For small systems, Tinker-HP appears to be competitive with the Tinker-OpenMM GPU implementation of Tinker. As the system size grows, Tinker-HP remains operational thanks to its access to distributed memory and takes advantage of its new algorithmic enabling for stable long timescale polarizable simulations. Overall, a several thousand-fold acceleration over a single-core computation is observed for the largest systems. The extension of the present CPU implementation of Tinker-HP to other computational platforms is discussed.
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Affiliation(s)
- Louis Lagardère
- Sorbonne Université , Institut des Sciences du Calcul et des Données , Paris , France
- Sorbonne Université , Institut Parisien de Chimie Physique et Théorique , CNRS , FR 2622 , Paris , France
- Sorbonne Université , Laboratoire de Chimie Théorique , UMR 7616 , CNRS , Paris , France .
| | - Luc-Henri Jolly
- Sorbonne Université , Institut Parisien de Chimie Physique et Théorique , CNRS , FR 2622 , Paris , France
| | - Filippo Lipparini
- Universita di Pisa , Dipartimento di Chimica e Chimica Industriale , Pisa , Italy
| | - Félix Aviat
- Sorbonne Université , Laboratoire de Chimie Théorique , UMR 7616 , CNRS , Paris , France .
| | - Benjamin Stamm
- MATHCCES , Department of Mathematics , RWTH Aachen University , Aachen , Germany
| | - Zhifeng F Jing
- The University of Texas at Austin , Department of Biomedical Engineering , TX , USA
| | - Matthew Harger
- The University of Texas at Austin , Department of Biomedical Engineering , TX , USA
| | - Hedieh Torabifard
- Department of Chemistry , Wayne State University , Detroit , MI 48202 , USA
| | - G Andrés Cisneros
- Department of Chemistry , University of North Texas , Denton , TX 76202 , USA
| | - Michael J Schnieders
- The University of Iowa , Department of Biomedical Engineering , Iowa City , IA , USA
| | - Nohad Gresh
- Sorbonne Université , Laboratoire de Chimie Théorique , UMR 7616 , CNRS , Paris , France .
| | - Yvon Maday
- Sorbonne Université , Laboratoire Jacques-Louis Lions , UMR 7598 , CNRS , Paris , France
- Institut Universitaire de France , Paris , France
- Brown University , Division of Applied Maths , Providence , RI , USA
| | - Pengyu Y Ren
- The University of Texas at Austin , Department of Biomedical Engineering , TX , USA
| | - Jay W Ponder
- Washington University in Saint Louis , Department of Chemistry , Saint Louis , MI , USA
| | - Jean-Philip Piquemal
- Sorbonne Université , Laboratoire de Chimie Théorique , UMR 7616 , CNRS , Paris , France .
- The University of Texas at Austin , Department of Biomedical Engineering , TX , USA
- Institut Universitaire de France , Paris , France
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