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Watanabe HC, Yamada M, Suzuki Y. Proton transfer in bulk water using the full adaptive QM/MM method: integration of solute- and solvent-adaptive approaches. Phys Chem Chem Phys 2021; 23:8344-8360. [PMID: 33875999 DOI: 10.1039/d1cp00116g] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The quantum mechanical/molecular mechanical (QM/MM) method is a hybrid molecular simulation technique that increases the accessibility of local electronic structures of large systems. The technique combines the benefit of accuracy found in the QM method and that of cost efficiency found in the MM method. However, it is difficult to directly apply the QM/MM method to the dynamics of solution systems, particularly for proton transfer. As explained in the Grotthuss mechanism, proton transfer is a structural interconversion between hydronium ions and solvent water molecules. Hence, when the QM/MM method is applied, an adaptive treatment, namely on-the-fly revisions on molecular definitions, is required for both the solute and solvent. Although several solvent-adaptive methods have been proposed, a full adaptive framework, which is an approach that also considers adaptation for solutes, remains untapped. In this paper, we propose a new numerical expression for the coordinates of the excess proton and its control algorithm. Furthermore, we confirm that this method can stably and accurately simulate proton transfer dynamics in bulk water.
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Affiliation(s)
- Hiroshi C Watanabe
- Quantum Computing Center, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan.
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Yang ZH. On-the-fly determination of active region centers in adaptive-partitioning QM/MM. Phys Chem Chem Phys 2020; 22:19307-19317. [PMID: 32820763 DOI: 10.1039/d0cp03034a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Quantum mechanics/molecular mechanics (QM/MM) methods are widely used in molecular dynamics (MD) simulations of large systems. By partitioning the system into active and environmental regions and treating them with different levels of theory, QM/MM methods achieve accuracy and efficiency at the same time. Adaptive-partitioning (AP) QM/MM allows the partition of the system to change during the MD simulation, making it possible to simulate processes in which the active and environmental regions exchange atoms or molecules, such as processes in solutions or solids. AP-QM/MM methods usually partition the system according to distances to centers of active regions. For energy-conserving AP-QM/MM methods, these centers are chosen beforehand and remain fixed during the MD simulation, making it difficult to simulate processes in which active regions may occur or vanish. In this paper, I develop an adaptive-center (AC) method that allows on-the-fly determination of the centers of active regions according to any geometrical criterion or any criterion dependent on the potential energy. The AC method is compatible with all existing energy-conserving AP-QM/MM methods, and the resulting potential energy surface is smooth. The application of the AC method is demonstrated with two examples in solid systems.
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Affiliation(s)
- Zeng-Hui Yang
- Microsystem and Terahertz Research Center, China Academy of Engineering Physics, Chengdu, 610200, China. and Institute of Electronic Engineering, China Academy of Engineering Physics, Mianyang, 621000, China
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Yang ZH. Extending scaled-interaction adaptive-partitioning QM/MM to covalently bonded systems. Phys Chem Chem Phys 2020; 22:17987-17998. [PMID: 32749442 DOI: 10.1039/d0cp02855j] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Quantum mechanics/molecular mechanics (QM/MM) is the method of choice for atomistic simulations of large systems that can be partitioned into active and environmental regions. Adaptive-partitioning (AP) methods extend the applicability of QM/MM, allowing active regions to change during the simulation. AP methods achieve continuous potential energy surface (PES) by introducing buffer regions in which atoms have both QM and MM characters. Most of the existing AP-QM/MM methods require multiple QM calculations per time step, which can be expensive for systems with many atoms in buffer regions. Although one can lower the computational cost by grouping atoms into fragments, this may not be possible for all systems, especially for applications in covalent solids. The SISPA method [Field, J. Chem. Theory Comput., 2017, 13, 2342] differs from other AP-QM/MM methods by only requiring one QM calculation per time step, but it has the flaw that the QM charge density and wavefunction near the buffer/MM boundary tend to those of isolated atoms/fragments. Besides, regular QM/MM methods for treating covalent bonds cut by the QM/MM boundary are incompatible with SISPA. Due to these flaws, SISPA in its original form cannot treat covalently bonded systems properly. In this work, I show that a simple modification to the SISPA method improves the treatment of covalently bonded systems. I also study the effect of correcting the charge density in SISPA by developing a density-corrected pre-scaled algorithm. I demonstrate the methods with simple molecules and bulk solids.
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Affiliation(s)
- Zeng-Hui Yang
- Microsystem and Terahertz Research Center, China Academy of Engineering Physics, Chengdu, 610200, China. and Institute of Electronic Engineering, China Academy of Engineering Physics, Mianyang, 621000, China
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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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5
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Watanabe HC, Cui Q. Quantitative Analysis of QM/MM Boundary Artifacts and Correction in Adaptive QM/MM Simulations. J Chem Theory Comput 2019; 15:3917-3928. [DOI: 10.1021/acs.jctc.9b00180] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Hiroshi C. Watanabe
- Quantum Computing Center, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
- Japan Science and Technology Agency, PRESTO, 4-18, Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Qiang Cui
- Departments of Chemistry, Physics, and Biomedical Engineering, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
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6
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Development of a new parameter optimization scheme for a reactive force field based on a machine learning approach. J Comput Chem 2019; 40:2000-2012. [DOI: 10.1002/jcc.25841] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 02/17/2019] [Accepted: 03/27/2019] [Indexed: 12/14/2022]
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Improvement of Performance, Stability and Continuity by Modified Size-Consistent Multipartitioning Quantum Mechanical/Molecular Mechanical Method. Molecules 2018; 23:molecules23081882. [PMID: 30060503 PMCID: PMC6222491 DOI: 10.3390/molecules23081882] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 07/25/2018] [Accepted: 07/25/2018] [Indexed: 11/17/2022] Open
Abstract
For condensed systems, the incorporation of quantum chemical solvent effects into molecular dynamics simulations has been a major concern. To this end, quantum mechanical/molecular mechanical (QM/MM) techniques are popular and powerful options to treat gigantic systems. However, they cannot be directly applied because of temporal and spatial discontinuity problems. To overcome these problems, in a previous study, we proposed a corrective QM/MM method, size-consistent multipartitioning (SCMP) QM/MM and successfully demonstrated that, using SCMP, it is possible to perform stable molecular dynamics simulations by effectively taking into account solvent quantum chemical effects. The SCMP method is characterized by two original features: size-consistency of a QM region among all QM/MM partitioning and partitioning update. However, in our previous study, the performance was not fully elicited compared to the theoretical upper bound and the optimal partitioning update protocol and parameters were not fully verified. To elicit the potential performance, in the present study, we simplified the theoretical framework and modified the partitioning protocol.
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Morzan UN, Alonso de Armiño DJ, Foglia NO, Ramírez F, González Lebrero MC, Scherlis DA, Estrin DA. Spectroscopy in Complex Environments from QM–MM Simulations. Chem Rev 2018; 118:4071-4113. [DOI: 10.1021/acs.chemrev.8b00026] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Uriel N. Morzan
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Diego J. Alonso de Armiño
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Nicolás O. Foglia
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Francisco Ramírez
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Mariano C. González Lebrero
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Damián A. Scherlis
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Darío A. Estrin
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
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Dutta D, Mishra S. Active Site Dynamics in Substrate Hydrolysis Catalyzed by DapE Enzyme and Its Mutants from Hybrid QM/MM-Molecular Dynamics Simulation. J Phys Chem B 2017; 121:7075-7085. [DOI: 10.1021/acs.jpcb.7b04431] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Debodyuti Dutta
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Sabyashachi Mishra
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
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Watanabe HC, Kubillus M, Kubař T, Stach R, Mizaikoff B, Ishikita H. Cation solvation with quantum chemical effects modeled by a size-consistent multi-partitioning quantum mechanics/molecular mechanics method. Phys Chem Chem Phys 2017; 19:17985-17997. [DOI: 10.1039/c7cp01708a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In the condensed phase, quantum chemical properties such as many-body effects and intermolecular charge fluctuations are critical determinants of the solvation structure and dynamics.
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Affiliation(s)
- Hiroshi C. Watanabe
- Research Center for Advanced Science and Technology
- The University of Tokyo
- Tokyo 153-8904
- Japan
- Department of Applied Chemistry
| | - Maximilian Kubillus
- Institute of Physical Chemistry and Center for Functional Nanostructures
- Karlsruhe Institute of Technology
- Karlsruhe 73131
- Germany
| | - Tomáš Kubař
- Institute of Physical Chemistry and Center for Functional Nanostructures
- Karlsruhe Institute of Technology
- Karlsruhe 73131
- Germany
| | - Robert Stach
- Institute of Analytical Bioanalytical Chemistry
- Ulm University
- Ulm 89081
- Germany
| | - Boris Mizaikoff
- Institute of Analytical Bioanalytical Chemistry
- Ulm University
- Ulm 89081
- Germany
| | - Hiroshi Ishikita
- Research Center for Advanced Science and Technology
- The University of Tokyo
- Tokyo 153-8904
- Japan
- Department of Applied Chemistry
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