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Fukuda I, Nakamura H. Non-Ewald methods for evaluating the electrostatic interactions of charge systems: similarity and difference. Biophys Rev 2022; 14:1315-1340. [PMID: 36659982 PMCID: PMC9842848 DOI: 10.1007/s12551-022-01029-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 11/30/2022] [Indexed: 01/13/2023] Open
Abstract
In molecular simulations, it is essential to properly calculate the electrostatic interactions of particles in the physical system of interest. Here we consider a method called the non-Ewald method, which does not rely on the standard Ewald method with periodic boundary conditions, but instead relies on the cutoff-based techniques. We focus on the physicochemical and mathematical conceptual aspects of the method in order to gain a deeper understanding of the simulation methodology. In particular, we take into account the reaction field (RF) method, the isotropic periodic sum (IPS) method, and the zero-multipole summation method (ZMM). These cutoff-based methods are based on different physical ideas and are completely distinguishable in their underlying concepts. The RF and IPS methods are "additive" methods that incorporate information outside the cutoff region, via dielectric medium and isotropic boundary condition, respectively. In contrast, the ZMM is a "subtraction" method that tries to remove the artificial effects, generated near the boundary, from the cutoff sphere. Nonetheless, we find physical and/or mathematical similarities between these methods. In particular, the modified RF method can be derived by the principle of neutralization utilized in the ZMM, and we also found a direct relationship between IPS and ZMM.
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Affiliation(s)
- Ikuo Fukuda
- Graduate School of Information Science, University of Hyogo, 7-1-28 Minatojima, Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047 Japan
| | - Haruki Nakamura
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871 Japan
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2
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Matsumoto K, Kitabayashi R, Fukuchi N, Suka N. Preparation of Optically Active Biphenyl Compounds via an Albumin-
Mediated Asymmetric Nitroaldol Reaction. LETT ORG CHEM 2022. [DOI: 10.2174/1570178618666210531093928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Abstract:
Human serum albumin (HSA) was found to catalyze the asymmetric nitroaldol reaction
of biphenyl aldehydes with nitromethane to afford the corresponding optically active 2-nitro alcohols.
Careful optimization of the conditions for the reaction of 4-phenylbenzaldehyde with nitromethane
in water at a neutral pH improved both the reactivity and the enantioselectivity. Finally, the
reaction of 4-phenylbenzaldehyde (56 mg, 0.30 mmol) in nitromethane (2.8 mL) and water (1.1
mL) using HSA (68 mg) at 5 °C for 240 h gave (R)-1-([1,1'-biphenyl]-4-yl)-2-nitroethanol in 71%
yield (52 mg), with an ee up to 85% ee. Subsequent recrystallization improved the ee up to 95%.
The reaction was useful in a preparative-scale operation, and the biocatalyst could be reused several
times. The procedure was also applicable to other substrates with different substitution patterns.
Although the nitroaldol reaction of 2-phenylbenzaldehyde with nitromethane proceeded with low
enantioselectivity to afford the corresponding (R)-2-nitroalcohols (35% ee), the reactions of the
substrates bearing Br, Me, OMe, or CN group at the 4'-position of the benzene ring gave the corresponding
optically active compounds with high enantioselectivities (80-88% ee).
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Affiliation(s)
- Kazutsugu Matsumoto
- Department of Chemistry and Life Science, Meisei University, 2-1-1 Hodokubo, Hino, Tokyo 191-8506, Japan
| | - Ryota Kitabayashi
- Department of Chemistry and Life Science, Meisei University, 2-1-1 Hodokubo, Hino, Tokyo 191-8506, Japan
| | - Naoki Fukuchi
- Department of Chemistry and Life Science, Meisei University, 2-1-1 Hodokubo, Hino, Tokyo 191-8506, Japan
| | - Noriyuki Suka
- Department of Chemistry and Life Science, Meisei University, 2-1-1 Hodokubo, Hino, Tokyo 191-8506, Japan
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3
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Takahashi KZ, Nozawa T, Yasuoka K. A fast and accurate computational method for the linear-combination-based isotropic periodic sum. Sci Rep 2018; 8:11880. [PMID: 30089878 PMCID: PMC6082916 DOI: 10.1038/s41598-018-30364-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 07/16/2018] [Indexed: 12/13/2022] Open
Abstract
An isotropic periodic sum (IPS) is a powerful technique to reasonably calculate intermolecular interactions for wide range of molecular systems under periodic boundary conditions. A linear-combination-based IPS (LIPS) has been developed to attain computational accuracy close to an exact lattice sum, such as the Ewald sum. The algorithm of the original LIPS method has a high computational cost because it needs long-range interaction calculations in real space. This becomes a performance bottleneck for long-time molecular simulations. In this work, the combination of an LIPS and fast Fourier transform (FFT) was developed, and evaluated on homogeneous and heterogeneous molecular systems. This combinational approach of LIPS/FFT attained computational efficiency close to that of a smooth particle mesh Ewald while maintaining the same high accuracy as the original LIPS. We concluded that LIPS/FFT has great potential to extend the capability of IPS techniques for the fast and accurate computation of many types of molecular systems.
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Affiliation(s)
- Kazuaki Z Takahashi
- Research Center for Computational Design of Advanced Functional Materials, National Institute of Advanced Industrial Science and Technology (AIST), Central 2, 1-1-1 Umezono, Tsukuba, Ibaraki, 305-8568, Japan.
| | - Takuma Nozawa
- Department of Mechanical Engineering, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa, 223-8522, Japan
| | - Kenji Yasuoka
- Department of Mechanical Engineering, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa, 223-8522, Japan
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Sakuraba S, Fukuda I. Performance evaluation of the zero-multipole summation method in modern molecular dynamics software. J Comput Chem 2018; 39:1551-1560. [PMID: 29727031 DOI: 10.1002/jcc.25228] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 03/19/2018] [Accepted: 03/21/2018] [Indexed: 11/10/2022]
Abstract
The zero-multiple summation method (ZMM) is a cutoff-based method for calculating electrostatic interactions in molecular dynamics simulations, utilizing an electrostatic neutralization principle as a physical basis. Since the accuracies of the ZMM have been revealed to be sufficient in previous studies, it is highly desirable to clarify its practical performance. In this paper, the performance of the ZMM is compared with that of the smooth particle mesh Ewald method (SPME), where the both methods are implemented in molecular dynamics software package GROMACS. Extensive performance comparisons against a highly optimized, parameter-tuned SPME implementation are performed for various-sized water systems and two protein-water systems. We analyze in detail the dependence of the performance on the potential parameters and the number of CPU cores. Even though the ZMM uses a larger cutoff distance than the SPME does, the performance of the ZMM is comparable to or better than that of the SPME. This is because the ZMM does not require a time-consuming electrostatic convolution and because the ZMM gains short neighbor-list distances due to the smooth damping feature of the pairwise potential function near the cutoff length. We found, in particular, that the ZMM with quadrupole or octupole cancellation and no damping factor is an excellent candidate for the fast calculation of electrostatic interactions. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Shun Sakuraba
- Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba, 277-8561, Japan
| | - Ikuo Fukuda
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita-shi, Osaka, 565-0871, Japan
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5
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Abstract
Truncation is still chosen for many long-range intermolecular interaction calculations to efficiently compute free-boundary systems, macromolecular systems and net-charge molecular systems, for example. Advanced truncation methods have been developed for long-range intermolecular interactions. Every truncation method can be implemented as one of two basic cut-off schemes, namely either an atom-based or a group-based cut-off scheme. The former computes interactions of “atoms” inside the cut-off radius, whereas the latter computes interactions of “molecules” inside the cut-off radius. In this work, the effect of group-based cut-off is investigated for isotropic periodic sum (IPS) techniques, which are promising cut-off treatments to attain advanced accuracy for many types of molecular system. The effect of group-based cut-off is clearly different from that of atom-based cut-off, and severe artefacts are observed in some cases. However, no severe discrepancy from the Ewald sum is observed with the extended IPS techniques.
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Takahashi KZ. Combined use of periodic reaction field and coarse-grained molecular dynamics simulations. I. phospholipid monolayer systems. MOLECULAR SIMULATION 2017. [DOI: 10.1080/08927022.2016.1271948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Kazuaki Z. Takahashi
- Multi-scale Soft-matter Simulation Team, Research Center for Computational Design of Advanced Functional Materials, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
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7
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Nozawa T, Takahashi KZ, Narumi T, Yasuoka K. Comparison of the accuracy of periodic reaction field methods in molecular dynamics simulations of a model liquid crystal system. J Comput Chem 2015; 36:2406-11. [PMID: 26525311 DOI: 10.1002/jcc.24222] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Revised: 07/22/2015] [Accepted: 09/07/2015] [Indexed: 11/09/2022]
Abstract
A periodic reaction field (PRF) method is a technique to estimate long-range interactions. The method has the potential to effectively reduce the computational cost while maintaining adequate accuracy. We performed molecular dynamics (MD) simulations of a model liquid-crystal system to assess the accuracy of some variations of the PRF method in low-charge-density systems. All the methods had adequate accuracy compared with the results of the particle mesh Ewald (PME) method, except for a few simulation conditions. Furthermore, in all of the simulation conditions, one of the PRF methods had the same accuracy as the PME method.
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Affiliation(s)
- Takuma Nozawa
- Department of Mechanical Engineering, Keio University, Yokohama, 223-8522, Japan
| | - Kazuaki Z Takahashi
- Department of Mechanical Engineering, Keio University, Yokohama, 223-8522, Japan.,Research Institute for Sustainable Chemistry, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, 305-8568, Japan
| | - Tetsu Narumi
- Department of Computer Science, University of Electro-Communications, Tokyo, 182-8585, Japan
| | - Kenji Yasuoka
- Department of Mechanical Engineering, Keio University, Yokohama, 223-8522, Japan
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Fischer NM, van Maaren PJ, Ditz JC, Yildirim A, van der Spoel D. Properties of Organic Liquids when Simulated with Long-Range Lennard-Jones Interactions. J Chem Theory Comput 2015; 11:2938-44. [DOI: 10.1021/acs.jctc.5b00190] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Nina M. Fischer
- Uppsala
Centre for Computational Chemistry, Science for Life Laboratory, Department
of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box
596, SE-75124 Uppsala, Sweden
| | - Paul J. van Maaren
- Uppsala
Centre for Computational Chemistry, Science for Life Laboratory, Department
of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box
596, SE-75124 Uppsala, Sweden
| | - Jonas C. Ditz
- Uppsala
Centre for Computational Chemistry, Science for Life Laboratory, Department
of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box
596, SE-75124 Uppsala, Sweden
| | - Ahmet Yildirim
- Department
of Physics, Faculty of Science and Art, Siirt University, 56100 Siirt, Turkey
| | - David van der Spoel
- Uppsala
Centre for Computational Chemistry, Science for Life Laboratory, Department
of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box
596, SE-75124 Uppsala, Sweden
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