1
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Okita K, Kasahara K, Matubayasi N. Diffusion theory of molecular liquids in the energy representation and application to solvation dynamics. J Chem Phys 2022; 157:244505. [PMID: 36586971 DOI: 10.1063/5.0125432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The generalized Langevin equation (GLE) formalism is a useful theoretical fundament for analyzing dynamical phenomena rigorously. Despite the systematic formulation of dynamics theories with practical approximations, however, the applicability of GLE-based methods is still limited to simple polyatomic liquids due to the approximate treatment of molecular orientations involved in the static molecular liquid theory. Here, we propose an exact framework of dynamics based on the GLE formalism incorporating the energy representation theory of solution, an alternative static molecular liquid theory. A fundamental idea is the projection of the relative positions and orientations of solvents around a solute onto the solute-solvent interaction, namely the energy coordinate, enabling us to describe the dynamics on a one-dimensional coordinate. Introducing systematic approximations, such as the overdamped limit, leads to the molecular diffusion equation in the energy representation that is described in terms of the distribution function of solvents on the energy coordinate and the diffusion coefficients. The present theory is applied to the solvation dynamics triggered by the photoexcitation of benzonitrile. The long-time behavior of the solvation time correlation function is in good agreement with that obtained by the molecular dynamics simulation.
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Affiliation(s)
- Kazuya Okita
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Kento Kasahara
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Nobuyuki Matubayasi
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
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2
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Tanaka S, Yamamoto N, Kasahara K, Ishii Y, Matubayasi N. Crystal Growth of Urea and Its Modulation by Additives as Analyzed by All-Atom MD Simulation and Solution Theory. J Phys Chem B 2022; 126:5274-5290. [DOI: 10.1021/acs.jpcb.2c01764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Senri Tanaka
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Naoki Yamamoto
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Kento Kasahara
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Yoshiki Ishii
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Nobuyuki Matubayasi
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
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3
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Matubayasi N. Solvation energetics of proteins and their aggregates analyzed by all-atom molecular dynamics simulations and the energy-representation theory of solvation. Chem Commun (Camb) 2021; 57:9968-9978. [PMID: 34505117 DOI: 10.1039/d1cc03395f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Solvation is a controlling factor for the structure and function of proteins. This article addresses the effects of solvation from an energetic perspective for the fluctuations and cosolvent-induced changes in protein structures and the equilibrium of aggregate formation for a peptide. A theoretical framework to analyze the solvation effects with an explicit solvent is introduced by adopting the energy-representation theory of solvation, and the connection of the solvation free energy to the protein structure and the aggregation tendency is quantitatively described in combination with all-atom molecular dynamics simulations. The interaction components that govern the solvation effects on the structural variations of proteins are further identified through correlation analysis, and a computational scheme to assess the shift of an aggregation equilibrium due to the addition of a cosolvent is provided.
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Affiliation(s)
- Nobuyuki Matubayasi
- Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan.
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4
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5
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Yamada K, Matubayasi N. Chain-Increment Method for Free-Energy Computation of a Polymer with All-Atom Molecular Simulations. Macromolecules 2020. [DOI: 10.1021/acs.macromol.9b01952] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kazuo Yamada
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Nobuyuki Matubayasi
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
- Elements Strategy Initiative for Catalysts and Batteries, Kyoto University, Katsura, Kyoto 615-8520, Japan
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6
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Matubayasi N. Energy-Representation Theory of Solutions: Its Formulation and Application to Soft, Molecular Aggregates. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2019. [DOI: 10.1246/bcsj.20190246] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Nobuyuki Matubayasi
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
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7
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Gurina DL, Antipova ML, Petrenko VE. Hydroxycinnamic acids in supercritical carbon dioxide. The dependence of cosolvent-induced solubility enhancement on the selective solvation. J Supercrit Fluids 2019. [DOI: 10.1016/j.supflu.2019.04.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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8
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Masutani K, Yamamori Y, Kim K, Matubayasi N. Free-energy analysis of the hydration and cosolvent effects on the β-sheet aggregation through all-atom molecular dynamics simulation. J Chem Phys 2019; 150:145101. [DOI: 10.1063/1.5088395] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
- Keiichi Masutani
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Yu Yamamori
- Artificial Intelligence Research Center and Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Koto, Tokyo 135-0064, Japan
| | - Kang Kim
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Nobuyuki Matubayasi
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
- Elements Strategy Initiative for Catalysts and Batteries, Kyoto University, Katsura, Kyoto 615-8520, Japan
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9
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Urano R, Pantelopulos GA, Straub JE. Aerosol-OT Surfactant Forms Stable Reverse Micelles in Apolar Solvent in the Absence of Water. J Phys Chem B 2019; 123:2546-2557. [PMID: 30688469 DOI: 10.1021/acs.jpcb.8b07847] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Normal micelle aggregates of amphiphilic surfactant in aqueous solvents are formed by a process of entropically driven self-assembly. The self-assembly of reverse micelles from amphiphilic surfactant in a nonpolar solvent in the presence of water is considered to be an enthalpically driven process. Although the formation of normal and reverse surfactant micelles has been well characterized in theory and experiment, the nature of dry micelle formation, from amphiphilic surfactant in a nonpolar solvent in the absence of water, is poorly understood. In this study, a theory of dry reverse micelle formation is developed. Variation in free energy during micelle assembly is derived for the specific case of aerosol-OT surfactant in isooctane solvent using atomistic molecular dynamics simulation analyzed using the energy representation method. The existence and thermodynamic stability of dry reverse micelles of limited size are confirmed. The abrupt occurrence of monodisperse aggregates is a clear signature of a critical micelle concentration, commonly observed in the formation of normal surfactant micelles. The morphology of large dry micelles provides insight into the nature of the thermodynamic driving forces stabilizing the formation of the surfactant aggregates. Overall, this study provides detailed insight into the structure and stability of dry reverse micelles assembly in a nonpolar solvent.
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Affiliation(s)
- Ryo Urano
- Chemistry Department , Boston University , 590 Commonwealth Avenue , Boston , Massachusetts 02215 , United States
| | - George A Pantelopulos
- Chemistry Department , Boston University , 590 Commonwealth Avenue , Boston , Massachusetts 02215 , United States
| | - John E Straub
- Chemistry Department , Boston University , 590 Commonwealth Avenue , Boston , Massachusetts 02215 , United States
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10
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Yamamoto N, Nakakuki I, Matubayasi N. Free-energy analysis of physisorption on solid-liquid interface with the solution theory in the energy representation. J Chem Phys 2018; 149:014504. [PMID: 29981552 DOI: 10.1063/1.5027861] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Physisorption of urea on its crystal in contact with water was subject to energetics analysis with all-atom molecular dynamics simulation. The transfer free energy of urea to an adsorption site was treated in the framework of the energy-representation theory of solutions, which allows a fast computation of the free energy in an inhomogeneous environment with solid-liquid interface. The preference of adsorption was then compared between the (001) and (110) faces, and it was found that the physisorption is more favorable on (001) than on (110) in correspondence to the hydrogen bonding between the adsorbed urea and the crystal urea. Among the terrace configurations of adsorption, the attractive interaction governs the preferable site with a minor role of the repulsive interaction. The effect of an edge was also treated by examining the terrace and step and was shown to be strongly operative on the (110) face when the CO group of the adsorbed urea points toward the edge. The present work demonstrates that the solution theory can be a framework for analyzing the energetics of physisorption and addressing the roles of the crystal and liquid at the interface through the systematic decomposition of free energy.
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Affiliation(s)
- Naoki Yamamoto
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Ippei Nakakuki
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Nobuyuki Matubayasi
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
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11
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Kawakami T, Shigemoto I, Matubayasi N. Structure and permeability of ionomers studied by atomistic molecular simulation combined with the theory of solutions in the energy representation. J Chem Phys 2018; 148:214903. [PMID: 29884036 DOI: 10.1063/1.5018884] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Ionomers play a key role in forming the catalyst layer of polymer electrolyte fuel cells. In the present work, we performed atomistic molecular dynamics simulations and free-energy calculations with the energy-representation method for sulfonated polyethersulfone (SPES) and its derivatives toward the rational design of ionomers for carbon alloy catalysts. It was observed that H2O aggregates strongly in the branched SPES systems with fluorocarbons and is located homogeneously in the systems without fluorocarbons. The O2 permeability was then examined within the framework of the solubility-diffusion mechanism. The permeability was seen to be large for the branched SPES with fluorocarbons, indicating that the performance of ionomers as a permeation medium for O2 may be tuned by the flexibility and branching of the polymer chain.
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Affiliation(s)
- Tomonori Kawakami
- Advanced Materials Research Laboratories, Toray Industries, Inc., 2-1 Sonoyama 3-chome, Otsu, Shiga 520-0842, Japan
| | - Isamu Shigemoto
- Advanced Materials Research Laboratories, Toray Industries, Inc., 2-1 Sonoyama 3-chome, Otsu, Shiga 520-0842, Japan
| | - Nobuyuki Matubayasi
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
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12
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Tokunaga Y, Yamamori Y, Matubayasi N. Probabilistic analysis for identifying the driving force of protein folding. J Chem Phys 2018; 148:125101. [PMID: 29604891 DOI: 10.1063/1.5019410] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Toward identifying the driving force of protein folding, energetics was analyzed in water for Trp-cage (20 residues), protein G (56 residues), and ubiquitin (76 residues) at their native (folded) and heat-denatured (unfolded) states. All-atom molecular dynamics simulation was conducted, and the hydration effect was quantified by the solvation free energy. The free-energy calculation was done by employing the solution theory in the energy representation, and it was seen that the sum of the protein intramolecular (structural) energy and the solvation free energy is more favorable for a folded structure than for an unfolded one generated by heat. Probabilistic arguments were then developed to determine which of the electrostatic, van der Waals, and excluded-volume components of the interactions in the protein-water system governs the relative stabilities between the folded and unfolded structures. It was found that the electrostatic interaction does not correspond to the preference order of the two structures. The van der Waals and excluded-volume components were shown, on the other hand, to provide the right order of preference at probabilities of almost unity, and it is argued that a useful modeling of protein folding is possible on the basis of the excluded-volume effect.
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Affiliation(s)
- Yoshihiko Tokunaga
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Yu Yamamori
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Nobuyuki Matubayasi
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
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13
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Mizuguchi T, Matubayasi N. Free-Energy Analysis of Peptide Binding in Lipid Membrane Using All-Atom Molecular Dynamics Simulation Combined with Theory of Solutions. J Phys Chem B 2018; 122:3219-3229. [DOI: 10.1021/acs.jpcb.7b08241] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Tomoko Mizuguchi
- Institute for Molecular Science, Okazaki, Aichi 444-8585, Japan
- Institute for the Promotion of University Strategy, Kyoto Institute of Technology, Kyoto 606-8585, Japan
| | - Nobuyuki Matubayasi
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
- Elements Strategy Initiative for Catalysts and Batteries, Kyoto University, Katsura, Kyoto 615-8520, Japan
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14
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Ingrosso F, Ruiz-López MF. Modeling Solvation in Supercritical CO 2. Chemphyschem 2017; 18:2560-2572. [PMID: 28719104 DOI: 10.1002/cphc.201700434] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2017] [Indexed: 11/10/2022]
Abstract
In recent decades, a microscopic understanding of solute-solvent intermolecular interactions has been key to advances in technologies based on supercritical carbon dioxide. In many cases, computational work has provided the impetus for new discoveries, shedding new light on important concepts such as the local structure around the solute in the supercritical medium, the influence of the peculiar properties of the latter on the molecular behavior of dissolved substances and, importantly, CO2 -philicity. In this Review, the theoretical work that has been relevant to these developments is surveyed and, by presenting some crucial open questions, the possible routes to achieving further progress based on the interplay between theory and experiments is discussed.
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Affiliation(s)
- Francesca Ingrosso
- SRSMC UMR 7565, Université de Lorraine, BP 70239, 54506, Vandoeuvre-lès-Nancy, France.,SRSMC UMR 7565, CNRS, BP 70239, 54506, Vandoeuvre-lès-Nancy, France
| | - Manuel F Ruiz-López
- SRSMC UMR 7565, Université de Lorraine, BP 70239, 54506, Vandoeuvre-lès-Nancy, France.,SRSMC UMR 7565, CNRS, BP 70239, 54506, Vandoeuvre-lès-Nancy, France
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15
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The study of peculiarities of parabens solvation in methanol- and acetone-modified supercritical carbon dioxide by computer simulation. J Supercrit Fluids 2017. [DOI: 10.1016/j.supflu.2017.02.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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16
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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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17
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Yamamori Y, Matubayasi N. Interaction-component analysis of the effects of urea and its alkylated derivatives on the structure of T4-lysozyme. J Chem Phys 2017; 146:225103. [DOI: 10.1063/1.4985222] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Yu Yamamori
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Nobuyuki Matubayasi
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
- Elements Strategy Initiative for Catalysts and Batteries, Kyoto University, Katsura, Kyoto 615-8520, Japan
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18
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Gurina DL, Odintsova EG, Golubev VA, Antipova ML, Petrenko VE. Features of solvation of phenolic acids in supercritical carbon dioxide modified by methanol and acetone. J Supercrit Fluids 2017. [DOI: 10.1016/j.supflu.2017.01.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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19
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Noroozi J, Paluch AS. Microscopic Structure and Solubility Predictions of Multifunctional Solids in Supercritical Carbon Dioxide: A Molecular Simulation Study. J Phys Chem B 2017; 121:1660-1674. [DOI: 10.1021/acs.jpcb.6b12390] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Javad Noroozi
- Department
of Chemical and Petroleum Engineering, Sharif University of Technology, Tehran, Iran
| | - Andrew S. Paluch
- Department
of Chemical, Paper and Biomedical Engineering, Miami University, Oxford, Ohio 45056, United States
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20
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Harris RC, Deng N, Levy RM, Ishizuka R, Matubayasi N. Computing conformational free energy differences in explicit solvent: An efficient thermodynamic cycle using an auxiliary potential and a free energy functional constructed from the end points. J Comput Chem 2016; 38:1198-1208. [PMID: 28008630 DOI: 10.1002/jcc.24668] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 09/02/2016] [Accepted: 10/26/2016] [Indexed: 01/17/2023]
Abstract
Many biomolecules undergo conformational changes associated with allostery or ligand binding. Observing these changes in computer simulations is difficult if their timescales are long. These calculations can be accelerated by observing the transition on an auxiliary free energy surface with a simpler Hamiltonian and connecting this free energy surface to the target free energy surface with free energy calculations. Here, we show that the free energy legs of the cycle can be replaced with energy representation (ER) density functional approximations. We compute: (1) The conformational free energy changes for alanine dipeptide transitioning from the right-handed free energy basin to the left-handed basin and (2) the free energy difference between the open and closed conformations of β-cyclodextrin, a "host" molecule that serves as a model for molecular recognition in host-guest binding. β-cyclodextrin contains 147 atoms compared to 22 atoms for alanine dipeptide, making β-cyclodextrin a large molecule for which to compute solvation free energies by free energy perturbation or integration methods and the largest system for which the ER method has been compared to exact free energy methods. The ER method replaced the 28 simulations to compute each coupling free energy with two endpoint simulations, reducing the computational time for the alanine dipeptide calculation by about 70% and for the β-cyclodextrin by > 95%. The method works even when the distribution of conformations on the auxiliary free energy surface differs substantially from that on the target free energy surface, although some degree of overlap between the two surfaces is required. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Robert C Harris
- Department of Chemistry and Center for Biophysics and Computational Biology and Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania, 19122
| | - Nanjie Deng
- Department of Chemistry and Center for Biophysics and Computational Biology and Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania, 19122.,Department of Chemistry and Physical Sciences, Dyson College of Arts and Sciences, Pace University, New York, New York, 10038
| | - Ronald M Levy
- Department of Chemistry and Center for Biophysics and Computational Biology and Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania, 19122
| | - Ryosuke Ishizuka
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka, 560-8531, Japan
| | - Nobuyuki Matubayasi
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka, 560-8531, Japan.,Elements Strategy Initiative for Catalysts and Batteries, Kyoto University, Katsura, Kyoto, 615-8520, Japan
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21
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Matubayasi N. Free-energy analysis of protein solvation with all-atom molecular dynamics simulation combined with a theory of solutions. Curr Opin Struct Biol 2016; 43:45-54. [PMID: 27835803 DOI: 10.1016/j.sbi.2016.10.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 10/07/2016] [Indexed: 11/25/2022]
Abstract
The structure of a protein is strongly influenced by solvation. In the present review, the solvation effect is treated within the framework of statistical thermodynamics. The key quantity is the solvation free energy of protein and a fast method for its computation with explicit solvent is introduced. The applications of the method to the structural fluctuation of protein in water, structure determination of protein-protein complex, and urea effect on protein structure are then described, and the roles of solvent water and cosolvent are discussed from the standpoint of energetics.
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Affiliation(s)
- Nobuyuki Matubayasi
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan; Elements Strategy Initiative for Catalysts and Batteries, Kyoto University, Katsura, Kyoto 615-8520, Japan.
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22
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Solvation free energy and solubility of acetaminophen and ibuprofen in supercritical carbon dioxide: Impact of the solvent model. J Supercrit Fluids 2016. [DOI: 10.1016/j.supflu.2015.11.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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23
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Yamamori Y, Ishizuka R, Karino Y, Sakuraba S, Matubayasi N. Interaction-component analysis of the hydration and urea effects on cytochrome c. J Chem Phys 2016; 144:085102. [DOI: 10.1063/1.4941945] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Yu Yamamori
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Ryosuke Ishizuka
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Yasuhito Karino
- RIKEN Quantitative Biology Center, Kobe, Hyogo 650-0047, Japan
| | - Shun Sakuraba
- Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba 277-8568, Japan
| | - Nobuyuki Matubayasi
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
- Elements Strategy Initiative for Catalysts and Batteries, Kyoto University, Katsura, Kyoto 615-8520, Japan
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24
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Kamo F, Ishizuka R, Matubayasi N. Correlation analysis for heat denaturation of Trp-cage miniprotein with explicit solvent. Protein Sci 2015; 25:56-66. [PMID: 26189564 DOI: 10.1002/pro.2754] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 07/15/2015] [Indexed: 11/10/2022]
Abstract
Energetics was analyzed for Trp-cage miniprotein in water to elucidate the solvation effect in heat denaturation. The solvation free energy was computed for a set of protein structures at room and high temperatures with all-atom molecular dynamics simulation combined with the solution theory in the energy representation, and its correlations were investigated against the intramolecular (structural) energy of the protein and the average interaction energy of the protein with the solvent water. It was observed both at room and high temperatures that the solvation free energy is anticorrelated to the structural energy and varies in parallel to the electrostatic component of the protein-water interaction energy without correlations to the van der Waals and excluded-volume components. When the set of folded structures sampled at room temperature was compared with the set of unfolded ones at high temperature, it was found that the preference order of the two sets is in correspondence to the van der Waals and excluded-volume components in the sum of the protein intramolecular and protein-water intermolecular interactions and is not distinguished by the electrostatic component.
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Affiliation(s)
- Fumitaka Kamo
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka, 560-8531, Japan
| | - Ryosuke Ishizuka
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka, 560-8531, Japan.,Elements Strategy Initiative for Catalysts and Batteries, Kyoto University, Katsura, Kyoto, 615-8520, Japan
| | - Nobuyuki Matubayasi
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka, 560-8531, Japan.,Elements Strategy Initiative for Catalysts and Batteries, Kyoto University, Katsura, Kyoto, 615-8520, Japan
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25
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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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