Nonequilibrium free-energy profile of charge-transfer reaction in polarizable solvent studied using solvent-polarizable three-dimensional reference interaction-site model theory

Tsuyoshi Yamaguchi; Norio Yoshida

doi:10.1063/5.0013083

Nonequilibrium free-energy profile of charge-transfer reaction in polarizable solvent studied using solvent-polarizable three-dimensional reference interaction-site model theory

The Journal of Chemical Physics ◽

10.1063/5.0013083 ◽

2020 ◽

Vol 153 (3) ◽

pp. 034502

Author(s):

Tsuyoshi Yamaguchi ◽

Norio Yoshida

Keyword(s):

Free Energy ◽

Charge Transfer ◽

Model Theory ◽

Transfer Reaction ◽

Three Dimensional ◽

Charge Transfer Reaction ◽

Energy Profile ◽

Interaction Site ◽

Free Energy Profile ◽

Site Model

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Free energy calculation using molecular dynamics simulation combined with the three-dimensional reference interaction site model theory. II. Thermodynamic integration along a spatial reaction coordinate

The Journal of Chemical Physics ◽

10.1063/1.3532078 ◽

2011 ◽

Vol 134 (4) ◽

pp. 044127 ◽

Cited By ~ 15

Author(s):

Tatsuhiko Miyata ◽

Yasuhiro Ikuta ◽

Fumio Hirata

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulation ◽

Model Theory ◽

Three Dimensional ◽

Dynamics Simulation ◽

Free Energy Calculation ◽

Energy Calculation ◽

Interaction Site ◽

Site Model

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Analysis of molecular dynamics simulations of 10-residue peptide, chignolin, using statistical mechanics: Relaxation mode analysis and three-dimensional reference interaction site model theory

Biophysics and Physicobiology ◽

10.2142/biophysico.16.0_407 ◽

2019 ◽

Vol 16 (0) ◽

pp. 407-429

Author(s):

Yutaka Maruyama ◽

Hiroshi Takano ◽

Ayori Mitsutake

Keyword(s):

Molecular Dynamics ◽

Statistical Mechanics ◽

Molecular Dynamics Simulations ◽

Model Theory ◽

Three Dimensional ◽

Mode Analysis ◽

Relaxation Mode ◽

Interaction Site ◽

Site Model ◽

Dynamics Simulations

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Comparison of DNA hydration patterns obtained using two distinct computational methods, molecular dynamics simulation and three-dimensional reference interaction site model theory

The Journal of Chemical Physics ◽

10.1063/1.2904865 ◽

2008 ◽

Vol 128 (18) ◽

pp. 185102 ◽

Cited By ~ 12

Author(s):

Yoshiteru Yonetani ◽

Yutaka Maruyama ◽

Fumio Hirata ◽

Hidetoshi Kono

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Computational Methods ◽

Model Theory ◽

Three Dimensional ◽

Dynamics Simulation ◽

Interaction Site ◽

Site Model ◽

Dna Hydration ◽

Reference Interaction Site

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Solvation free-energy pressure corrections in the three dimensional reference interaction site model

The Journal of Chemical Physics ◽

10.1063/1.4935065 ◽

2015 ◽

Vol 143 (18) ◽

pp. 184116 ◽

Cited By ~ 38

Author(s):

Volodymyr Sergiievskyi ◽

Guillaume Jeanmairet ◽

Maximilien Levesque ◽

Daniel Borgis

Keyword(s):

Free Energy ◽

Three Dimensional ◽

Solvation Free Energy ◽

Interaction Site ◽

Site Model ◽

Reference Interaction Site

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Development of a solvent-polarizable three-dimensional reference interaction-site model theory

The Journal of Chemical Physics ◽

10.1063/5.0004173 ◽

2020 ◽

Vol 152 (11) ◽

pp. 114108 ◽

Cited By ~ 1

Author(s):

Norio Yoshida ◽

Tsuyoshi Yamaguchi

Keyword(s):

Model Theory ◽

Three Dimensional ◽

Interaction Site ◽

Site Model ◽

Reference Interaction Site

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State-specific solvation effect on the intramolecular charge transfer reaction in solution: A linear-response free energy TDDFT method

Chemical Physics Letters ◽

10.1016/j.cplett.2014.05.104 ◽

2014 ◽

Vol 608 ◽

pp. 140-144 ◽

Cited By ~ 8

Author(s):

Noriyuki Minezawa

Keyword(s):

Free Energy ◽

Charge Transfer ◽

Linear Response ◽

Transfer Reaction ◽

Intramolecular Charge Transfer ◽

Solvation Effect ◽

Charge Transfer Reaction ◽

Specific Solvation ◽

Reaction In Solution ◽

Tddft Method

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Correction terms for the solvation free energy functional of three-dimensional reference interaction site model based on the reference-modified density functional theory

Journal of Molecular Liquids ◽

10.1016/j.molliq.2019.111160 ◽

2019 ◽

Vol 291 ◽

pp. 111160

Author(s):

Yutaka Maruyama

Keyword(s):

Density Functional Theory ◽

Free Energy ◽

Density Functional ◽

Three Dimensional ◽

Energy Functional ◽

Functional Theory ◽

Interaction Site ◽

Site Model ◽

Free Energy Functional ◽

Correction Terms

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Free energy profiles of electron transfer at water–electrode interface studied by the reference interaction site model theory

Chemical Physics Letters ◽

10.1016/s0009-2614(99)00372-3 ◽

1999 ◽

Vol 305 (3-4) ◽

pp. 251-257 ◽

Cited By ~ 9

Author(s):

Ryo Akiyama ◽

Masahiro Kinoshita ◽

Fumio Hirata

Keyword(s):

Electron Transfer ◽

Free Energy ◽

Model Theory ◽

Interaction Site ◽

Site Model ◽

Energy Profiles ◽

Electrode Interface ◽

Reference Interaction Site ◽

Free Energy Profiles

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Comparison of molecular mechanics-Poisson-Boltzmann surface area (MM-PBSA) and molecular mechanics-three-dimensional reference interaction site model (MM-3D-RISM) method to calculate the binding free energy of protein-ligand complexes: Effect of metal ion and advance statistical test

Chemical Physics Letters ◽

10.1016/j.cplett.2018.01.059 ◽

2018 ◽

Vol 695 ◽

pp. 69-78 ◽

Cited By ~ 8

Author(s):

Preeti Pandey ◽

Rakesh Srivastava ◽

Pradipta Bandyopadhyay

Keyword(s):

Free Energy ◽

Molecular Mechanics ◽

Surface Area ◽

Metal Ion ◽

Binding Free Energy ◽

Three Dimensional ◽

Statistical Test ◽

Interaction Site ◽

Site Model ◽

Poisson Boltzmann

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Non-linear effects in the free energy profile of electron transfer reaction: An integral equation approach

Studies in Physical and Theoretical Chemistry - Structure, Fluctuation, and relaxtion in solutions, Proceedings of the Yamada Conference XXXXII ◽

10.1016/s0167-6881(06)80806-2 ◽

1995 ◽

pp. 345-348

Author(s):

Song-Ho Chong ◽

Fumio Hirata

Keyword(s):

Integral Equation ◽

Electron Transfer ◽

Free Energy ◽

Transfer Reaction ◽

Electron Transfer Reaction ◽

Energy Profile ◽

Equation Approach ◽

Free Energy Profile ◽

Integral Equation Approach ◽

Linear Effects

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