担当区分：最終著者,　責任著者   記述言語：英語   掲載種別：研究論文（学術雑誌）  

DOI： 10.1016/j.molliq.2023.122503

担当区分：最終著者   記述言語：英語   掲載種別：研究論文（学術雑誌）  

DOI： 10.1063/5.0159130

担当区分：最終著者   記述言語：英語   掲載種別：研究論文（学術雑誌）  

DOI： https://doi.org/10.1063/5.0158046

担当区分：最終著者,　責任著者   記述言語：英語   掲載種別：研究論文（学術雑誌）  

DOI： 10.1016/j.molliq.2023.122503

担当区分：筆頭著者,　責任著者   記述言語：英語   掲載種別：研究論文（学術雑誌）  

DOI： 10.1016/j.molliq.2023.122418

担当区分：最終著者   記述言語：英語   掲載種別：研究論文（学術雑誌）  

DOI： 10.1016/j.molliq.2023.122311

担当区分：最終著者,　責任著者   記述言語：英語   掲載種別：研究論文（学術雑誌）  

DOI： https://doi.org/10.1021/acs.jpcb.3c00343

担当区分：最終著者   記述言語：英語   掲載種別：研究論文（学術雑誌）  

DOI： https://doi.org/10.1063/5.0142256

記述言語：英語  

DOI： 10.1002/jcc.27009

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記述言語：英語   掲載種別：研究論文（国際会議プロシーディングス）  

DOI： 10.1088/1757-899X/1280/1/012002

記述言語：英語   出版者・発行元：Journal of Chemical Physics  

A theoretical method for calculating the thermodynamic properties and phase equilibria of liquid-liquid mixtures using the integral equation theory is proposed. The solvation chemical potentials of the two components are evaluated by the integral equation theory and the isothermal-isobaric variation of the total density with composition is determined to satisfy the Gibbs-Duhem relation. Given the density of a pure component, the method can calculate the densities of the mixture at any composition. Furthermore, it can treat the phase equilibrium without thermodynamic inconsistency with respect to the Gibbs-Duhem relation. This method was combined with the reference interaction-site model integral equation theory and applied to mixtures of water + 1-alcohol by changing the alcohol from methanol to 1-butanol. The destabilization of the mixing Gibbs energy by increasing the hydrophobicity of the alcohol and demixing of the water-butanol mixture were reproduced. However, quantitative agreement with experiments is not satisfactory, and further improvements of the integral equation theory and the molecular models are required.

DOI： 10.1063/5.0131475

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担当区分：筆頭著者,　責任著者   記述言語：英語   掲載種別：研究論文（学術雑誌）  

DOI： 10.1021/acs.jcim.2c00192

PubMed

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：{MDPI} {AG}  

<jats:p>The protonation/deprotonation reaction is one of the most fundamental processes in solutions and biological systems. Compounds with dissociative functional groups change their charge states by protonation/deprotonation. This change not only significantly alters the physical properties of a compound itself, but also has a profound effect on the surrounding molecules. In this paper, we review our recent developments of the methods for predicting the Ka, the equilibrium constant for protonation reactions or acid dissociation reactions. The pKa, which is a logarithm of Ka, is proportional to the reaction Gibbs energy of the protonation reaction, and the reaction free energy can be determined by electronic structure calculations with solvation models. The charge of the compound changes before and after protonation; therefore, the solvent effect plays an important role in determining the reaction Gibbs energy. Here, we review two solvation models: the continuum model, and the integral equation theory of molecular liquids. Furthermore, the reaction Gibbs energy calculations for the protonation reactions require special attention to the handling of dissociated protons. An efficient method for handling the free energy of dissociated protons will also be reviewed.</jats:p>

DOI： 10.3390/j4040058

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掲載種別：研究論文（学術雑誌）   出版者・発行元：MDPI AG  

Water in the supercritical region of the phase diagram exhibits a markedly different structure and properties from that at ambient conditions, which is useful in controlling chemical reactions. Nonetheless, the experimental, as well as theoretical, characterization of the substance is not easy because the region is next to the critical point. This article reviews the experimental as well as theoretical studies on water in the supercritical region and its properties as a solvent for chemical reactions, as carried out by the authors and based on small-angle X-ray scattering and the statistical mechanics theory of molecular liquids, also known as reference interaction-site model (RISM) theory.

DOI： 10.3390/j4040049

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記述言語：日本語   掲載種別：研究論文（学術雑誌）   出版者・発行元：New Journal of Chemistry  

The angiotensin-converting enzyme 2 (ACE2) protein is a cell gate receptor for the SARS-CoV-2 virus, responsible for the development of symptoms associated with the Covid-19 disease. Pharmacological inhibition of the SARS-CoV-2 spike receptor binding domain (RBD) and ACE2 interaction is one of the most attractive ways to prevent viral replication in human cells. Unfortunately, at this stage there is no complete picture of this process and so the computational modelling might provide an important insight valuable for the development of new and efficient inhibitors. In this work we propose the use of the molecular theory of solvation to study the nanomorphology of the spike-ACE2 binding formed by a complex solvent (water, ions, and dissolved drug-like molecules) and leading to the viral protein with cell membrane receptors. In contrast to the typical molecular dynamics, the statistical-mechanical theory of solvation directly provides distributions of complex solvents around the binding location as well as the thermodynamics of solvation. We present an example of the application of the three-dimensional theory of solvation to model the nanomorphology formed by solvent environment around binding surfaces of interacting proteins. The results of our calculations are compared with the other published data. Our recent developments allow the application of the methodology to be extended to potential drug screening and virulence analysis.

DOI： 10.1039/d1nj02015c

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記述言語：日本語   掲載種別：研究論文（学術雑誌）  

DOI： 10.1039/d1sm00152c

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記述言語：日本語   掲載種別：研究論文（学術雑誌）   出版者・発行元：Journal of Computational Chemistry  

A computational method to investigate the global conformational change of a protein is proposed by combining the linear response path following (LRPF) method and three-dimensional reference interaction site model (3D-RISM) theory, which is referred to as the LRPF/3D-RISM method. The proposed method makes it possible to efficiently simulate protein conformational changes caused by either solutions of varying concentrations or the presence of cosolvent species by taking advantage of the LRPF and 3D-RISM. The proposed method is applied to the urea-induced denaturation of ubiquitin. The LRPF/3D-RISM trajectories successfully simulate the early stage of the denaturation process within the simulation time of 300 ns, whereas no significant structural change is observed even in the 1 μs standard MD simulation. The obtained LRPF/3D-RISM trajectories reproduce the mechanism of the urea denaturation of ubiquitin reported in previous studies, and demonstrate the high efficiency of the method.

DOI： 10.1002/jcc.26481

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掲載種別：研究論文（学術雑誌）   出版者・発行元：Wiley  

DOI： 10.1002/jcc.26502

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記述言語：日本語   掲載種別：研究論文（学術雑誌）   出版者・発行元：Journal of Chemical Physics  

The theory of solvation structure in an electronically polarizable solvent recently proposed by us, referred to as the "solvent-polarizable three-dimensional reference interaction-site model theory,"is extended to dynamics in this study through the combination with time-dependent density functional theory. Test calculations are performed on model charge-transfer systems in water, and the effects of electronic polarizability on solvation dynamics are examined. The electronic polarizability slightly retards the solvation dynamics. This is ascribed to the decrease in the curvature of the nonequilibrium free energy profile along the solvation coordinate. The solvent relaxation is bimodal, and the faster and the slower modes are assigned to the reorientational and the translational modes, respectively, as was already reported by the surrogate theory combined with the site-site Smoluchowski-Vlasov equation. The relaxation path along the solvation coordinate is a little higher than the minimum free energy path because the translational mode is fixed in the time scale of the reorientational relaxation.

DOI： 10.1063/5.0036289

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記述言語：日本語   掲載種別：研究論文（学術雑誌）   出版者・発行元：Molecules  

There are two molecular processes that are essential for living bodies to maintain their life: the molecular recognition, and the self-organization or self-assembly. Binding of a substrate by an enzyme is an example of the molecular recognition, while the protein folding is a good example of the self-organization process. The two processes are further governed by the other two physicochemical processes: solvation and the structural fluctuation. In the present article, the studies concerning the two molecular processes carried out by Hirata and his coworkers, based on the statistical mechanics of molecular liquids or the RISM/3D-RISM theory, are reviewed.

DOI： 10.3390/molecules26020271

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開催年月日： 2023年7月

記述言語：英語   会議種別：口頭発表（招待・特別）  

開催地：Patthaya   国名：タイ王国  

開催年月日： 2023年7月

記述言語：日本語   会議種別：口頭発表（招待・特別）  

開催地：名古屋国際会議場   国名：日本国  

開催年月日： 2023年3月

記述言語：英語   会議種別：口頭発表（招待・特別）  

開催年月日： 2023年2月

記述言語：英語   会議種別：口頭発表（招待・特別）  

開催地：Quy Nhon   国名：ベトナム社会主義共和国  

開催年月日： 2022年12月

記述言語：英語   会議種別：口頭発表（招待・特別）  

開催地：The Emerald Hotel, Bangkok   国名：タイ王国  

開催年月日： 2022年11月

記述言語：英語   会議種別：口頭発表（招待・特別）  

開催地：The Magellan Sutera Resort, Sabah   国名：マレーシア  

開催年月日： 2022年9月

記述言語：英語   会議種別：口頭発表（一般）  

開催地：函館アリーナ   国名：日本国  

開催年月日： 2022年9月

記述言語：英語   会議種別：口頭発表（招待・特別）  

開催地：Korea Institute for Advanced Study, Seoul   国名：大韓民国  

開催年月日： 2022年7月

記述言語：日本語   会議種別：口頭発表（招待・特別）  

国名：日本国  

開催年月日： 2022年7月

記述言語：英語   会議種別：口頭発表（招待・特別）  

国名：カナダ  

開催年月日： 2022年6月

記述言語：英語   会議種別：口頭発表（招待・特別）  

国名：タイ王国  

開催年月日： 2022年6月

記述言語：日本語   会議種別：口頭発表（招待・特別）  

開催地：つくば国際会議場  

開催年月日： 2022年6月

記述言語：日本語   会議種別：口頭発表（招待・特別）  

開催年月日： 2022年2月

記述言語：英語   会議種別：口頭発表（招待・特別）  

開催地：the International Centre for Interdisciplinary Science and Education (ICISE), Quy Nhon   国名：ベトナム社会主義共和国