Hybrid quantum/classical molecular dynamics for a proton transfer reaction coupled to a dissipative bath

The Journal of Chemical Physics ◽

10.1063/1.2206175 ◽

2006 ◽

Vol 124 (24) ◽

pp. 244102 ◽

Author(s):

Soo Young Kim ◽

Sharon Hammes-Schiffer

Keyword(s):

Molecular Dynamics ◽

Proton Transfer ◽

Transfer Reaction ◽

Proton Transfer Reaction ◽

Classical Molecular Dynamics

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Hybrid Quantum Classical Molecular Dynamics Simulation of the Proton-Transfer Reaction of HO-with HBr in Aqueous Clusters

The Journal of Physical Chemistry A ◽

10.1021/jp983678y ◽

1999 ◽

Vol 103 (26) ◽

pp. 5105-5112 ◽

Author(s):

M. Dolores Elola ◽

Dario A. Estrin ◽

Daniel Laria

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Proton Transfer ◽

Transfer Reaction ◽

Proton Transfer Reaction ◽

Dynamics Simulation ◽

Classical Molecular Dynamics

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Sampling the Proton Transfer Reaction Coordinate in Mixed Quantum-Classical Molecular Dynamics Simulations

The Journal of Physical Chemistry A ◽

10.1021/jp206772e ◽

2012 ◽

Vol 116 (2) ◽

pp. 832-838 ◽

Author(s):

Being J. Ka ◽

Ward H. Thompson

Keyword(s):

Molecular Dynamics ◽

Proton Transfer ◽

Molecular Dynamics Simulations ◽

Transfer Reaction ◽

Proton Transfer Reaction ◽

Reaction Coordinate ◽

Classical Molecular Dynamics ◽

Dynamics Simulations

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Molecular‐dynamics simulation for a model nonadiabatic proton transfer reaction in solution

The Journal of Chemical Physics ◽

10.1063/1.459733 ◽

1991 ◽

Vol 94 (5) ◽

pp. 3619-3628 ◽

Author(s):

Daniel Borgis ◽

James T. Hynes

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Proton Transfer ◽

Transfer Reaction ◽

Proton Transfer Reaction ◽

Dynamics Simulation ◽

Reaction In Solution

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Quantum semiempirical parametrization of the molecular dynamics thermodynamics integration method in a case of the proton transfer reaction in the 2-[N,N-dimethylaminomethyl]-phenol

Journal of Molecular Liquids ◽

10.1016/s0167-7322(00)00126-4 ◽

2000 ◽

Vol 87 (1) ◽

pp. 1-9 ◽

Author(s):

Adam Fedorowicz ◽

Aleksander Koll

Keyword(s):

Molecular Dynamics ◽

Proton Transfer ◽

Transfer Reaction ◽

Integration Method ◽

Proton Transfer Reaction

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Molecular Dynamics Simulations of the Proton Transfer Reaction Between the Catalytic Residues in HTLV-I Protease

Biophysical Journal ◽

10.1016/j.bpj.2013.11.3745 ◽

2014 ◽

Vol 106 (2) ◽

pp. 676a

Author(s):

Shuhua Ma ◽

Natalie Petrillo ◽

Kimberly Vogt

Keyword(s):

Molecular Dynamics ◽

Proton Transfer ◽

Molecular Dynamics Simulations ◽

Transfer Reaction ◽

Proton Transfer Reaction ◽

Catalytic Residues ◽

Dynamics Simulations

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A molecular dynamics study of intramolecular proton transfer reaction of malonaldehyde in solution based upon a mixed quantum–classical approximation. II. Proton transfer reaction in non-polar solvent

The Journal of Chemical Physics ◽

10.1063/1.4919635 ◽

2015 ◽

Vol 142 (17) ◽

pp. 174502 ◽

Author(s):

H. Kojima ◽

A. Yamada ◽

S. Okazaki

Keyword(s):

Molecular Dynamics ◽

Proton Transfer ◽

Transfer Reaction ◽

Polar Solvent ◽

Proton Transfer Reaction ◽

Intramolecular Proton Transfer ◽

Classical Approximation

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The chemical reaction molecular dynamics method and the dynamic transition state: proton transfer reaction in formamidine and water solvent system

Journal of the American Chemical Society ◽

10.1021/ja00003a007 ◽

1991 ◽

Vol 113 (3) ◽

pp. 769-778 ◽

Author(s):

Masataka Nagaoka ◽

Yoshishige Okuno ◽

Tokio Yamabe

Keyword(s):

Molecular Dynamics ◽

Proton Transfer ◽

Transition State ◽

Chemical Reaction ◽

Transfer Reaction ◽

Solvent System ◽

Proton Transfer Reaction ◽

Molecular Dynamics Method ◽

Water Solvent ◽

Dynamics Method

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Free-energy analyses of a proton transfer reaction by simulated-tempering umbrella sampling and first-principles molecular dynamics simulations

Physical Review E ◽

10.1103/physreve.87.023301 ◽

2013 ◽

Vol 87 (2) ◽

Author(s):

Yoshiharu Mori ◽

Yuko Okamoto

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Proton Transfer ◽

Molecular Dynamics Simulations ◽

First Principles ◽

Transfer Reaction ◽

Proton Transfer Reaction ◽

Umbrella Sampling ◽

Simulated Tempering ◽

Dynamics Simulations

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A molecular dynamics study of intramolecular proton transfer reaction of malonaldehyde in solutions based upon mixed quantum-classical approximation. I. Proton transfer reaction in water

The Journal of Chemical Physics ◽

10.1063/1.4893933 ◽

2014 ◽

Vol 141 (8) ◽

pp. 084509 ◽

Author(s):

Atsushi Yamada ◽

Hidekazu Kojima ◽

Susumu Okazaki

Keyword(s):

Molecular Dynamics ◽

Proton Transfer ◽

Transfer Reaction ◽

Proton Transfer Reaction ◽

Intramolecular Proton Transfer ◽

Classical Approximation ◽

Reaction In Water

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Chemical Reaction Molecular Dynamics Simulation and the Energy-Transfer Mechanism in the Proton-Transfer Reaction of Formamidine in Aqueous Solution

The Journal of Physical Chemistry ◽

10.1021/j100099a011 ◽

1994 ◽

Vol 98 (48) ◽

pp. 12506-12515 ◽

Author(s):

Masataka Nagaoka ◽

Yoshishige Okuno ◽

Tokio Yamabe

Keyword(s):

Molecular Dynamics ◽

Aqueous Solution ◽

Energy Transfer ◽

Molecular Dynamics Simulation ◽

Proton Transfer ◽

Chemical Reaction ◽

Transfer Reaction ◽

Proton Transfer Reaction ◽

Dynamics Simulation ◽

Energy Transfer Mechanism

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