1
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Okamoto R, Koga K. Theory of Gas Solubility and Hydrophobic Interaction in Aqueous Electrolyte Solutions. J Phys Chem B 2021; 125:12820-12831. [PMID: 34756051 DOI: 10.1021/acs.jpcb.1c08050] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ion-specific effects on the solubility of nonpolar solutes and on the solute-solute hydrophobic interaction in aqueous electrolyte solutions are studied on the basis of a continuum theory that incorporates the excluded volume of the molecules using the four-component (water, cations, anions, and solutes) Boublı́k-Mansoori-Carnahan-Starling-Leland model and ion hydration (electrostriction) using the Born model. We examine how the ordering of ions in the salt effect on the solubility as measured by the Sechenov coefficient KS changes with varying sizes of ions and solutes. Our calculation reproduces the general trend of experimentally measured KS and also provides insight into the irregular behavior of KS for lithium ion. The correlation between KS and the salt effect on the hydrophobic interaction that has been pointed out earlier is accounted for by an explicit connection between KS and the salt-enhanced-association coefficient CI in the expansion of the second osmotic virial coefficient B(ns) = B(0) - CIns + ··· in powers of the salt density ns at fixed pressure and temperature. The quadratic relation CI≈KS2/4 is derived for ions and solutes that are not very large.
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Affiliation(s)
- Ryuichi Okamoto
- Research Institute for Interdisciplinary Science, Okayama University, Okayama 700-8530, Japan
| | - Kenichiro Koga
- Research Institute for Interdisciplinary Science, Okayama University, Okayama 700-8530, Japan
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2
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Katsuto H, Okamoto R, Sumi T, Koga K. Ion Size Dependences of the Salting-Out Effect: Reversed Order of Sodium and Lithium Ions. J Phys Chem B 2021; 125:6296-6305. [PMID: 34102058 DOI: 10.1021/acs.jpcb.1c03388] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A general trend of the salting-out effect on hydrophobic solutes in aqueous solution is that the smaller the size of a dissolved ion, the larger the effect of reducing the solubility of a hydrophobe. An exception is that Li+, the smallest in alkali metal ions, has a notably weaker effect than Na+. To understand the reversed order in the cation series, we performed molecular dynamics simulations of aqueous solutions of salt ions and calculated the Setschenow coefficient of methane with the ionic radius of either a cation or an anion varied in a wide range. It is confirmed that the Setschenow coefficient is correlated with the packing fraction of salt solution, as observed in earlier studies, and also correlated with the partial molar volume of an ion. Analyses of correlation function integrals, packing fractions of solvation spheres, and orientations of water molecules surrounding an ion reveal the key differences in microscopic properties between the cation and anion series, which give rise to the reversed order in the cation series of the partial molar volumes of ions and ultimately that of the Setschenow coefficients.
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Affiliation(s)
- Hiroyuki Katsuto
- Research Institute for Interdisciplinary Science, Okayama University, Okayama 700-8530, Japan.,Department of Chemistry, Faculty of Science, Okayama University, Okayama 700-8530, Japan
| | - Ryuichi Okamoto
- Research Institute for Interdisciplinary Science, Okayama University, Okayama 700-8530, Japan.,Department of Chemistry, Faculty of Science, Okayama University, Okayama 700-8530, Japan
| | - Tomonari Sumi
- Research Institute for Interdisciplinary Science, Okayama University, Okayama 700-8530, Japan.,Department of Chemistry, Faculty of Science, Okayama University, Okayama 700-8530, Japan
| | - Kenichiro Koga
- Research Institute for Interdisciplinary Science, Okayama University, Okayama 700-8530, Japan.,Department of Chemistry, Faculty of Science, Okayama University, Okayama 700-8530, Japan
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3
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Fujita T, Yamamoto T. Assessing the accuracy of integral equation theories for nano-sized hydrophobic solutes in water. J Chem Phys 2017; 147:014110. [DOI: 10.1063/1.4990502] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Affiliation(s)
| | - Takeshi Yamamoto
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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4
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Kasahara K, Nakano H, Sato H. Theoretical Study of the Solvation Effect on the Reductive Reaction of Vinylene Carbonate in the Electrolyte Solution of Lithium Ion Batteries. J Phys Chem B 2017; 121:5293-5299. [DOI: 10.1021/acs.jpcb.7b02864] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kento Kasahara
- Department
of Molecular Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Hiroshi Nakano
- Department
of Molecular Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510, Japan
- Elements
Strategy Initiative for Catalysts and Batteries (ESICB), Kyoto University, Nishikyo-ku, Kyoto 615-8520, Japan
| | - Hirofumi Sato
- Department
of Molecular Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510, Japan
- Elements
Strategy Initiative for Catalysts and Batteries (ESICB), Kyoto University, Nishikyo-ku, Kyoto 615-8520, Japan
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5
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Murakami S, Hayashi T, Kinoshita M. Effects of salt or cosolvent addition on solubility of a hydrophobic solute in water: Relevance to those on thermal stability of a protein. J Chem Phys 2017; 146:055102. [DOI: 10.1063/1.4975165] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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6
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Kasahara K, Sato H. Dynamics theory for molecular liquids based on an interaction site model. Phys Chem Chem Phys 2017; 19:27917-27929. [DOI: 10.1039/c7cp05423h] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Dynamics theories for molecular liquids based on an interaction site model have been developed over the past few decades and proved to be powerful tools to investigate various dynamical phenomena.
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Affiliation(s)
- Kento Kasahara
- Department of Molecular Engineering
- Kyoto University
- Japan
| | - Hirofumi Sato
- Department of Molecular Engineering and Elements Strategy for Catalysts and Batteries (ESICB)
- Kyoto University
- Japan
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7
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Misin M, Vainikka PA, Fedorov MV, Palmer DS. Salting-out effects by pressure-corrected 3D-RISM. J Chem Phys 2016; 145:194501. [DOI: 10.1063/1.4966973] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Affiliation(s)
- Maksim Misin
- Department of Physics, SUPA, University of Strathclyde, 107 Rottenrow, Glasgow G4 0NG, United Kingdom
| | - Petteri A. Vainikka
- Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
| | - Maxim V. Fedorov
- Department of Physics, SUPA, University of Strathclyde, 107 Rottenrow, Glasgow G4 0NG, United Kingdom
- Skolkovo Institute of Science and Technology, 3 Nobel Street, Moscow 143026, Russian Federation
| | - David S. Palmer
- Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
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8
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Hayashi T, Kinoshita M. Statistical thermodynamics of aromatic–aromatic interactions in aqueous solution. Phys Chem Chem Phys 2016; 18:32406-32417. [DOI: 10.1039/c6cp06000e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
To elucidate the interactions between aromatic rings, which are believed to play essential roles in a variety of biological processes, we analyze the water-mediated interactions between toluene molecules along face-to-face stacked (FF) and point-to-face T-shaped (TS) paths using a statistical-mechanical theory of liquids combined with a molecular model for water.
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9
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Oshima H, Kinoshita M. A highly efficient hybrid method for calculating the hydration free energy of a protein. J Comput Chem 2015; 37:712-23. [DOI: 10.1002/jcc.24253] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 10/28/2015] [Accepted: 10/29/2015] [Indexed: 11/10/2022]
Affiliation(s)
- Hiraku Oshima
- Institute of Advanced Energy, Kyoto University; Uji Kyoto 611-0011 Japan
| | - Masahiro Kinoshita
- Institute of Advanced Energy, Kyoto University; Uji Kyoto 611-0011 Japan
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10
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Matveev A, Li B, Rösch N. Uranyl Solvation by a Three-Dimensional Reference Interaction Site Model. J Phys Chem A 2015; 119:8702-13. [PMID: 26167741 DOI: 10.1021/acs.jpca.5b03712] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We report an implementation of the three-dimensional reference interaction site model (3D RISM) that in particular addresses the treatment of the long-range Coulomb field of charged species, represented by point charges and/or a distributed charge density. A comparison of 1D and 3D results for atomic ions demonstrates a reasonable accuracy, even for a moderate size of the unit cell and a moderate grid resolution. In an application to uranyl complexes with 4-6 explicit aqua ligands and an implicit bulk solvent modeled by RISM, we show that the 3D technique is not susceptible to the deficiencies of the 1D technique exposed in our previous work [Li, Matveev, Krüger, Rösch, Comp. Theor. Chem. 2015, 1051, 151]. The 3D method eliminates the artificial superposition of explicit aqua ligands and the RISM medium and predicts essentially the same values for uranyl and uranyl-water bond lengths as a state-of-the-art polarizable continuum model. With the first solvation shell treated explicitly, the observables are nearly independent of the order of the closure relationship used when solving the set of integral equations for the various distribution functions. Furthermore, we calculated the activation barrier of water exchange with a hybrid approach that combines the 3D RISM model for the bulk aqueous solvent and a quantum mechanical description (at the level of electronic density functional theory) of uranyl interacting with explicitly represented water molecules. The calculated result agrees very well with experiment and the best theoretical estimates.
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Affiliation(s)
| | | | - Notker Rösch
- §Institute of High Performance Computing, Agency for Science, Technology and Research, 1 Fusionopolis Way, Connexis #16-16, Singapore 138632, Singapore
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11
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Kido K, Kasahara K, Yokogawa D, Sato H. A hybrid framework of first principles molecular orbital calculations and a three-dimensional integral equation theory for molecular liquids: multi-center molecular Ornstein-Zernike self-consistent field approach. J Chem Phys 2015; 143:014103. [PMID: 26156461 DOI: 10.1063/1.4923007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
In this study, we reported the development of a new quantum mechanics/molecular mechanics (QM/MM)-type framework to describe chemical processes in solution by combining standard molecular-orbital calculations with a three-dimensional formalism of integral equation theory for molecular liquids (multi-center molecular Ornstein-Zernike (MC-MOZ) method). The theoretical procedure is very similar to the 3D-reference interaction site model self-consistent field (RISM-SCF) approach. Since the MC-MOZ method is highly parallelized for computation, the present approach has the potential to be one of the most efficient procedures to treat chemical processes in solution. Benchmark tests to check the validity of this approach were performed for two solute (solute water and formaldehyde) systems and a simple SN2 reaction (Cl(-) + CH3Cl → ClCH3 + Cl(-)) in aqueous solution. The results for solute molecular properties and solvation structures obtained by the present approach were in reasonable agreement with those obtained by other hybrid frameworks and experiments. In particular, the results of the proposed approach are in excellent agreements with those of 3D-RISM-SCF.
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Affiliation(s)
- Kentaro Kido
- Nuclear Safety Research Center, Japan Atomic Energy Agency, 2-4 Shirane, Shirakata, Tokai-mura, Naka-gun, Ibaraki 319-1195, Japan
| | - Kento Kasahara
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Daisuke Yokogawa
- Department of Chemistry, Graduate School of Science, Nagoya University, Chikusa, Nagoya 464-8602, Japan
| | - Hirofumi Sato
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510, Japan
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12
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Ratkova EL, Palmer DS, Fedorov MV. Solvation thermodynamics of organic molecules by the molecular integral equation theory: approaching chemical accuracy. Chem Rev 2015; 115:6312-56. [PMID: 26073187 DOI: 10.1021/cr5000283] [Citation(s) in RCA: 135] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Ekaterina L Ratkova
- †G. A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences, Akademicheskaya Street 1, Ivanovo 153045, Russia.,‡The Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, Leipzig 04103, Germany
| | - David S Palmer
- ‡The Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, Leipzig 04103, Germany.,§Department of Chemistry, University of Strathclyde, Thomas Graham Building, 295 Cathedral Street, Glasgow, Scotland G1 1XL, United Kingdom
| | - Maxim V Fedorov
- ‡The Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, Leipzig 04103, Germany.,∥Department of Physics, Scottish Universities Physics Alliance (SUPA), University of Strathclyde, John Anderson Building, 107 Rottenrow East, Glasgow G4 0NG, United Kingdom
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13
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Chuev GN, Vyalov I, Georgi N. Exact site–site bridge functions for dielectric consistent reference interaction site model: A test for ambient water. J Mol Liq 2015. [DOI: 10.1016/j.molliq.2014.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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14
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Li B, Matveev AV, Krüger S, Rösch N. Uranyl solvation by a reference interaction site model. COMPUT THEOR CHEM 2015. [DOI: 10.1016/j.comptc.2014.10.032] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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15
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Kasahara K, Sato H. Development of three-dimensional site-site Smoluchowski-Vlasov equation and application to electrolyte solutions. J Chem Phys 2014; 140:244110. [PMID: 24985621 DOI: 10.1063/1.4884386] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Site-site Smoluchowski-Vlasov (SSSV) equation enables us to directly calculate van Hove time correlation function, which describes diffusion process in molecular liquids. Recently, the theory had been extended to treat solute-solvent system by Iida and Sato [J. Chem. Phys. 137, 034506 (2012)]. Because the original framework of SSSV equation is based on conventional pair correlation function, time evolution of system is expressed in terms of one-dimensional solvation structure. Here, we propose a new SSSV equation to calculate time evolution of solvation structure in three-dimensional space. The proposed theory was applied to analyze diffusion processes in 1M NaCl aqueous solution and in lithium ion battery electrolyte solution. The results demonstrate that these processes are properly described with the theory, and the computed van Hove functions are in good agreement with those in previous works.
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Affiliation(s)
- Kento Kasahara
- Department of Molecular Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Hirofumi Sato
- Department of Molecular Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510, Japan
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16
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Tanaka Y, Yoshida N, Nakano H. Solvent effect on excited states of merocyanines: A theoretical study using the RISM–SCF method. Chem Phys Lett 2013. [DOI: 10.1016/j.cplett.2013.08.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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17
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Joung IS, Luchko T, Case DA. Simple electrolyte solutions: comparison of DRISM and molecular dynamics results for alkali halide solutions. J Chem Phys 2013; 138:044103. [PMID: 23387564 DOI: 10.1063/1.4775743] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Using the dielectrically consistent reference interaction site model (DRISM) of molecular solvation, we have calculated structural and thermodynamic information of alkali-halide salts in aqueous solution, as a function of salt concentration. The impact of varying the closure relation used with DRISM is investigated using the partial series expansion of order-n (PSE-n) family of closures, which includes the commonly used hypernetted-chain equation (HNC) and Kovalenko-Hirata closures. Results are compared to explicit molecular dynamics (MD) simulations, using the same force fields, and to experiment. The mean activity coefficients of ions predicted by DRISM agree well with experimental values at concentrations below 0.5 m, especially when using the HNC closure. As individual ion activities (and the corresponding solvation free energies) are not known from experiment, only DRISM and MD results are directly compared and found to have reasonably good agreement. The activity of water directly estimated from DRISM is nearly consistent with values derived from the DRISM ion activities and the Gibbs-Duhem equation, but the changes in the computed pressure as a function of salt concentration dominate these comparisons. Good agreement with experiment is obtained if these pressure changes are ignored. Radial distribution functions of NaCl solution at three concentrations were compared between DRISM and MD simulations. DRISM shows comparable water distribution around the cation, but water structures around the anion deviate from the MD results; this may also be related to the high pressure of the system. Despite some problems, DRISM-PSE-n is an effective tool for investigating thermodynamic properties of simple electrolytes.
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Affiliation(s)
- In Suk Joung
- Department of Chemistry and Chemical Biology and BioMaPS Institute, Rutgers University, Piscataway, New Jersey 08854, USA
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18
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Hayaki S, Kimura Y, Sato H. Ab Initio Study on an Excited-State Intramolecular Proton-Transfer Reaction in Ionic Liquid. J Phys Chem B 2013; 117:6759-67. [DOI: 10.1021/jp311883f] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Seigo Hayaki
- Department of Molecular Engineering, Kyoto University, Kyoto Daigaku Katsura, Kyoto 615-8510,
Japan
| | - Yoshifumi Kimura
- Department of Chemical
Science
and Technology, Hosei University, Koganei,
184-8584, Japan
| | - Hirofumi Sato
- Department of Molecular Engineering, Kyoto University, Kyoto Daigaku Katsura, Kyoto 615-8510,
Japan
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19
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Fukami K, Koda R, Sakka T, Ogata Y, Kinoshita M. Electrochemical deposition of platinum within nanopores on silicon: Drastic acceleration originating from surface-induced phase transition. J Chem Phys 2013; 138:094702. [DOI: 10.1063/1.4793526] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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20
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Iida K, Sato H. An extended formula of site-site Smoluchowski-Vlasov equation for electrolyte solution and infinitely dilute solution. J Chem Phys 2012; 137:034506. [DOI: 10.1063/1.4732760] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
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21
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Fukami K, Koda R, Sakka T, Urata T, Amano KI, Takaya H, Nakamura M, Ogata Y, Kinoshita M. Platinum electrodeposition in porous silicon: The influence of surface solvation effects on a chemical reaction in a nanospace. Chem Phys Lett 2012. [DOI: 10.1016/j.cplett.2012.05.078] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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22
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Ratkova EL. A comparative analysis of models for hydration free energy calculations using the RISM theory of integral equations. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2012. [DOI: 10.1134/s0036024412060222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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23
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Luchko T, Joung IS, Case DA. Integral Equation Theory of Biomolecules and Electrolytes. INNOVATIONS IN BIOMOLECULAR MODELING AND SIMULATIONS 2012. [DOI: 10.1039/9781849735049-00051] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The so-called three-dimensional version (3D-RISM) can be used to describe the interactions of solvent components (here we treat water and ions) with a chemical or biomolecular solute of arbitrary size and shape. Here we give an overview of the current status of such models, describing some aspects of “pure” electrolytes (water plus simple ions) and of ionophores, proteins and nucleic acids in the presence of water and salts. Here we focus primarily on interactions with water and dissolved salts; as a practical matter, the discussion is mostly limited to monovalent ions, since studies of divalent ions present many difficult problems that have not yet been addressed. This is not a comprehensive review, but covers a few recent examples that illustrate current issues.
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Affiliation(s)
- Tyler Luchko
- Department of Chemistry and Chemical Biology and BioMaPS Institute Rutgers University Piscataway NJ 08854, USA
| | - In Suk Joung
- Department of Chemistry and Chemical Biology and BioMaPS Institute Rutgers University Piscataway NJ 08854, USA
| | - David A. Case
- Department of Chemistry and Chemical Biology and BioMaPS Institute Rutgers University Piscataway NJ 08854, USA
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24
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Iida K, Sato H. Theoretical study on ionization process in aqueous solution. J Chem Phys 2012; 136:144510. [DOI: 10.1063/1.3700225] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
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25
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26
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Santosh MS, Lyubartsev AP, Mirzoev AA, Bhat DK. Molecular dynamics investigation of dipeptide-transition metal salts in aqueous solutions. J Phys Chem B 2010; 114:16632-40. [PMID: 21086976 DOI: 10.1021/jp108376j] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Molecular dynamics (MD) simulations of glycylglycine dipeptide with transition metal ions (Mn(2+), Fe(2+), Co(2+), Ni(2+), Cu(2+), and Zn(2+)) in aqueous solutions have been carried out to get an insight into the solvation structure, intermolecular interactions, and salt effects in these systems. The solvation structure and hydrogen bonding were described in terms of radial distribution function (RDF) and spatial distribution function (SDF). The dynamical properties of the solvation structure were also analyzed in terms of diffusion and residence times. The simulation results show the presence of a well-defined first hydration shell around the dipeptide, with water molecules forming hydrogen bonds to the polar groups of the dipeptide. This shell is, however, affected by the strong electric field of divalent metal ions, which at higher ion concentrations lead to the shift in the dipeptide-water RDFs. Higher salt concentrations lead also to increased residence times and slower diffusion rates. In general, smaller ions (Cu(2+), Zn(2+)) demonstrate stronger binding to dipeptide than the larger ones (Fe(2+), Mn(2+)). Simulations do not show any stronger association of peptide molecules indicating their dissolution in water. The above results may be of potential interest to future researchers on these molecular interactions.
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Affiliation(s)
- M S Santosh
- Physical Chemistry Division, Department of Chemistry, National Institute of Technology Karnataka, Surathkal, Mangalore-575025, India
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27
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Hayaki S, Kido K, Sato H, Sakaki S. Ab initio study on SN2 reaction of methyl p-nitrobenzenesulfonate and chloride anion in [mmim][PF6]. Phys Chem Chem Phys 2010; 12:1822-6. [DOI: 10.1039/b920190b] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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28
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Kido K, Sato H, Sakaki S. First Principle Theory for pKa Prediction at Molecular Level: pH Effects Based on Explicit Solvent Model. J Phys Chem B 2009; 113:10509-14. [DOI: 10.1021/jp903610p] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kentaro Kido
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Hirofumi Sato
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Shigeyoshi Sakaki
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510, Japan
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29
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Hayaki S, Kido K, Yokogawa D, Sato H, Sakaki S. A Theoretical Analysis of a Diels−Alder Reaction in Ionic Liquids. J Phys Chem B 2009; 113:8227-30. [DOI: 10.1021/jp902599b] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Seigo Hayaki
- Department of Molecular Engineering, Kyoto University, Kyoto Daigaku Katsura, Kyoto 615-8510, Japan
| | - Kentaro Kido
- Department of Molecular Engineering, Kyoto University, Kyoto Daigaku Katsura, Kyoto 615-8510, Japan
| | - Daisuke Yokogawa
- Department of Molecular Engineering, Kyoto University, Kyoto Daigaku Katsura, Kyoto 615-8510, Japan
| | - Hirofumi Sato
- Department of Molecular Engineering, Kyoto University, Kyoto Daigaku Katsura, Kyoto 615-8510, Japan
| | - Shigeyoshi Sakaki
- Department of Molecular Engineering, Kyoto University, Kyoto Daigaku Katsura, Kyoto 615-8510, Japan
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30
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Iida K, Yokogawa D, Sato H, Sakaki S. A systematic understanding of orbital energy shift in polar solvent. J Chem Phys 2009; 130:044107. [DOI: 10.1063/1.3068531] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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31
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Holzmann J, Ludwig R, Geiger A, Paschek D. Temperature and Concentration Effects on the Solvophobic Solvation of Methane in Aqueous Salt Solutions. Chemphyschem 2008; 9:2722-30. [DOI: 10.1002/cphc.200800544] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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32
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Thomas AS, Elcock AH. Molecular Dynamics Simulations of Hydrophobic Associations in Aqueous Salt Solutions Indicate a Connection between Water Hydrogen Bonding and the Hofmeister Effect. J Am Chem Soc 2007; 129:14887-98. [DOI: 10.1021/ja073097z] [Citation(s) in RCA: 135] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Andrew S. Thomas
- Contribution from the Department of Biochemistry, University of Iowa, Iowa City, Iowa 52242
| | - Adrian H. Elcock
- Contribution from the Department of Biochemistry, University of Iowa, Iowa City, Iowa 52242
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33
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Woelki S, Kohler HH, Krienke H. A Singlet-RISM Theory for Solid/Liquid Interfaces Part I: Uncharged Walls. J Phys Chem B 2007; 111:13386-97. [DOI: 10.1021/jp068998t] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Stefan Woelki
- Institute of Analytical Chemistry, Chemo- and Biosensors, University of Regensburg, D-93040 Regensburg, Germany, and Institute of Physical and Theoretical Chemistry, University of Regensburg, D-93040 Regensburg, Germany
| | - Hans-Helmut Kohler
- Institute of Analytical Chemistry, Chemo- and Biosensors, University of Regensburg, D-93040 Regensburg, Germany, and Institute of Physical and Theoretical Chemistry, University of Regensburg, D-93040 Regensburg, Germany
| | - Hartmut Krienke
- Institute of Analytical Chemistry, Chemo- and Biosensors, University of Regensburg, D-93040 Regensburg, Germany, and Institute of Physical and Theoretical Chemistry, University of Regensburg, D-93040 Regensburg, Germany
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34
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Yamaguchi T, Matsuoka T, Koda S. Mode-coupling study on the dynamics of hydrophobic hydration. J Chem Phys 2006; 120:7590-601. [PMID: 15267671 DOI: 10.1063/1.1687319] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The molecular motion of water in water-hydrophobic solute mixtures was investigated by the mode-coupling theory for molecular liquids based on the interaction-site description. When the model Lennard-Jones solute was mixed with water, both the translational and reorientational motions of solvent water become slower, in harmony with various experiments and molecular dynamics simulations. We compared the mechanism of the slowing down with that of the pressure dependence of the molecular motion of neat water [T. Yamaguchi, S.-H. Chong, and F. Hirata, J. Chem. Phys. 119, 1021 (2003)]. We found that the decrease in the solvent mobility caused by the solute can essentially be elucidated by the same mechanism: That is, the fluctuation of the number density of solvent due to the cavity formation by the solute strengthens the friction on the collective polarization through the dielectric friction mechanism: We also employed the solute molecule that is the same as solvent water except for the amount of partial charges, in order to alter the strength of the solute-solvent interaction continuously. The mobility of the solvent water was reduced both by the hydrophobic and strongly hydrophilic solutes, but it was enhanced in the intermediate case. Such a behavior was discussed in connection with the concept of positive and negative hydrations.
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Affiliation(s)
- T Yamaguchi
- Department of Molecular Design and Engineering, Graduate School of Engineering, Nagoya University, Chikusa, Nagoya, Aichi 464-8603, Japan.
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35
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Paschek D, Geiger A, Hervé MJ, Suter D. Adding salt to an aqueous solution of t-butanol: Is hydrophobic association enhanced or reduced? J Chem Phys 2006; 124:154508. [PMID: 16674243 DOI: 10.1063/1.2188398] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Recent neutron scattering experiments on aqueous salt solutions of amphiphilic t-butanol by Bowron and Finney [Phys. Rev. Lett. 89, 215508 (2002); J. Chem. Phys. 118, 8357 (2003)] suggest the formation of t-butanol pairs, bridged by a chloride ion via O-H...Cl- hydrogen bonds, leading to a reduced number of intermolecular hydrophobic butanol-butanol contacts. Here we present a joint experimental/theoretical study on the same system, using a combination of molecular dynamics (MD) simulations and nuclear magnetic relaxation measurements. Both MD simulation and experiment clearly support the more classical scenario of an enhanced number of hydrophobic contacts in the presence of salt, as it would be expected for purely hydrophobic solutes. [T. Ghosh et al., J. Phys. Chem. B 107, 612 (2003)]. Although our conclusions arrive at a structurally completely distinct scenario, the molecular dynamics simulation results are within the experimental error bars of the Bowron and Finney data.
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Affiliation(s)
- Dietmar Paschek
- Physikalische Chemie, Universität Dortmund, D-44227 Dortmund, Germany.
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36
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Yamaguchi T, Matsuoka T, Koda S. Mode-coupling study on the dynamics of hydrophobic hydration II: Aqueous solutions of benzene and rare gases. Phys Chem Chem Phys 2006; 8:737-45. [PMID: 16482314 DOI: 10.1039/b514196f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The dynamic properties of both the solute and solvent of the aqueous solution of benzene, xenon and neon are calculated by the mode-coupling theory for molecular liquids based on the interaction-site model. The B-coefficients of the reorientational relaxation and the translational diffusion of the solvent are evaluated from their dependence on the concentration of the solute, and the reorientational relaxation time of water within the hydration shell is estimated based on the two-state model. The reorientational relaxation times of water in the bulk and within the hydration shell, that of solute, and the translational diffusion coefficients of solute and solvent, are calculated at 0-30 degrees C. The temperature dependence of these dynamic properties is in qualitative agreement with that of NMR experiment reported by Nakahara et al. (M. Nakahara, C. Wakai, Y. Yoshimoto and N. Matubayasi, J. Phys. Chem., 1996, 100, 1345-1349, ref. 36), although the agreement of the absolute values is not so good. The B-coefficients of the reorientational relaxation times for benzene, xenon and neon solution are correlated with the hydration number and the partial molar volume of the solute. The proportionality with the latter is better than that with the former. These results support the mechanism that the retardation of the mobility of water is caused by the cavity formation of the solute, as previously suggested by us (T. Yamaguchi, T. Matsuoka and S. Koda, J. Chem. Phys., 2004, 120, 7590-7601, ref. 34), rather than the conventional one that the rigid hydration structure formed around the hydrophobic solute reduces the mobility of water.
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Affiliation(s)
- T Yamaguchi
- Department of Molecular Design and Engineering, Graduate School of Engineering, Nagoya University, Chikusa, Nagoya, Aichi 464-8603, Japan.
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37
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Kinoshita M, Harano Y. Potential of Mean Force between Solute Atoms in Salt Solution: Effects Due to Salt Species and Relevance to Conformational Transition of Biomolecules. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2005. [DOI: 10.1246/bcsj.78.1431] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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38
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Abstract
The hydrophobic effects on partial molar volume (PMV) are investigated as a PMV change in the transfer of a benzenelike nonpolar solute from the nonpolar solvent to water, using an integral equation theory of liquids. The volume change is divided into two effects. One is the "packing" effect in the transfer from the nonpolar solvent to hypothetical "nonpolar water" without hydrogen bonding networks. The other is the "iceberg" effect in the transfer from nonpolar water to water. The results indicate that the packing effect is negative and a half compensated by the positive iceberg effect. The packing effect is explained by the difference in the solvent compressibility. Further investigation shows that the sign and magnitude of the volume change depend on the solute size and the solvent compressibility. The finding gives a significant implication that the exposure of a hydrophobic residue caused by protein denaturation can either increase or decrease the PMV of protein depending on the size of the residue and the fluctuation of its surroundings.
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Affiliation(s)
- Takashi Imai
- Department of Bioscience and Bioinformatics, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
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39
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Shinto H, Morisada S, Higashitani K. Potentials of Mean Force for Hydrophilic-Hydrophobic Solute Pairs in Water. JOURNAL OF CHEMICAL ENGINEERING OF JAPAN 2005. [DOI: 10.1252/jcej.38.465] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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40
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Vlachy V, Hribar-Lee B, Kalyuzhnyi Y, Dill KA. Short-range interactions: from simple ions to polyelectrolyte solutions. Curr Opin Colloid Interface Sci 2004. [DOI: 10.1016/j.cocis.2004.05.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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41
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Kinoshita M, Sugai Y. Methodology of predicting approximate shapes and size distribution of micelles: illustration for simple models. J Comput Chem 2002; 23:1445-55. [PMID: 12370946 DOI: 10.1002/jcc.10144] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
We propose an efficient methodology for predicting approximate shapes and size distribution of micelles. The methodology is a judicious combination of a conventional thermodynamic approach, the reference interaction site model (RISM) theory, and the Monte Carlo (MC) simulated annealing technique. Solvent effects are fully incorporated using the RISM theory with our robust and very efficient algorithm for solving the RISM equations, and the MC technique is applied only to surfactant molecules. The methodology is potentially applicable to realistic models of surfactant and solvent molecules with all-atom potentials. As the first step, however, it is illustrated for simplified models having only essential characteristics of the amphiphiles. We estimate the critical micelle concentration, approximate shapes, and size distributions at some surfactant concentrations. Roles of the solvent and effects due to the type of the surfactant molecule are discussed in detail.
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Affiliation(s)
- Masahiro Kinoshita
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan.
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42
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Imai T, Nomura H, Kinoshita M, Hirata F. Partial Molar Volume and Compressibility of Alkali−Halide Ions in Aqueous Solution: Hydration Shell Analysis with an Integral Equation Theory of Molecular Liquids. J Phys Chem B 2002. [DOI: 10.1021/jp014504a] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Takashi Imai
- Department of Theoretical Studies, Institute for Molecular Science, Okazaki, Aichi, 444-8585 Japan
| | - Hiroyasu Nomura
- Department of Natural Sciences, Tokyo Denki University, Hatoyama, Hiki, Saitama, 350-0394 Japan
| | - Masahiro Kinoshita
- Advanced Energy Utilization Division, Institute of Advanced Energy, Kyoto University, Uji, Kyoto, 611-0011 Japan
| | - Fumio Hirata
- Department of Theoretical Studies, Institute for Molecular Science, Okazaki, Aichi, 444-8585 Japan
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43
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Cui Q, Smith VH. Solvation Structure, Thermodynamics, and Molecular Conformational Equilibria for n-Butane in Water Analyzed by Reference Interaction Site Model Theory Using an All-Atom Solute Model. J Phys Chem B 2002. [DOI: 10.1021/jp020191n] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Qizhi Cui
- Department of Chemistry, Queen's University, Kingston, Ontario, Canada K7L 3N6
| | - Vedene H. Smith
- Department of Chemistry, Queen's University, Kingston, Ontario, Canada K7L 3N6
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44
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Thermodynamic Quantities of Surface Formation of Aqueous Electrolyte Solutions. J Colloid Interface Sci 2001. [DOI: 10.1006/jcis.2001.7890] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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45
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Cui Q, Smith VH. Analysis of solvation structure and thermodynamics of ethane and propane in water by reference interaction site model theory using all-atom models. J Chem Phys 2001. [DOI: 10.1063/1.1384421] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
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46
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Kinoshita M. Long-range interaction between hydrophilic surfaces immersed in a hydrophobic fluid containing a hydrophilic component at low concentration. Chem Phys Lett 2001. [DOI: 10.1016/s0009-2614(00)01373-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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47
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Kovalenko A, Hirata F, Kinoshita M. Hydration structure and stability of Met-enkephalin studied by a three-dimensional reference interaction site model with a repulsive bridge correction and a thermodynamic perturbation method. J Chem Phys 2000. [DOI: 10.1063/1.1321039] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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48
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Kovalenko A, Truong TN. Thermochemistry of solvation: A self-consistent three-dimensional reference interaction site model approach. J Chem Phys 2000. [DOI: 10.1063/1.1313388] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
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49
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Mitsutake A, Kinoshita M, Okamoto Y, Hirata F. Multicanonical algorithm combined with the RISM theory for simulating peptides in aqueous solution. Chem Phys Lett 2000. [DOI: 10.1016/s0009-2614(00)01018-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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50
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Kovalenko A, Hirata F. Hydration free energy of hydrophobic solutes studied by a reference interaction site model with a repulsive bridge correction and a thermodynamic perturbation method. J Chem Phys 2000. [DOI: 10.1063/1.1305885] [Citation(s) in RCA: 141] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
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