Quantum molecular dynamics simulation of proton transfer in cytochrome c oxidase

Biochimica et Biophysica Acta (BBA) - Bioenergetics ◽

10.1016/j.bbabio.2004.03.006 ◽

2004 ◽

Vol 1656 (2-3) ◽

pp. 189-202 ◽

Author(s):

R.I Cukier

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Cytochrome C ◽

Proton Transfer ◽

Cytochrome C Oxidase ◽

Dynamics Simulation ◽

Quantum Molecular Dynamics

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Molecular dynamics simulation of water in cytochrome c oxidase reveals two water exit pathways and the mechanism of transport

Biochimica et Biophysica Acta (BBA) - Bioenergetics ◽

10.1016/j.bbabio.2009.04.004 ◽

2009 ◽

Vol 1787 (9) ◽

pp. 1140-1150 ◽

Author(s):

Ryogo Sugitani ◽

Alexei A. Stuchebrukhov

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Cytochrome C ◽

Cytochrome C Oxidase ◽

Dynamics Simulation ◽

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Molecular Dynamics Simulation of the Excited-State Proton Transfer Mechanism in 3-Hydroxyflavone Using Explicit Hydration Models

The Journal of Physical Chemistry A ◽

10.1021/acs.jpca.1c03687 ◽

2021 ◽

Author(s):

Yingchao Li ◽

Farhan Siddique ◽

Adélia J. A. Aquino ◽

Hans Lischka

Keyword(s):

Molecular Dynamics ◽

Excited State ◽

Molecular Dynamics Simulation ◽

Proton Transfer ◽

Transfer Mechanism ◽

Dynamics Simulation ◽

Excited State Proton Transfer

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A quantum molecular dynamics simulation of an excess electron in methanol

The Journal of Chemical Physics ◽

10.1063/1.464883 ◽

1993 ◽

Vol 98 (7) ◽

pp. 5679-5693 ◽

Author(s):

Jianjun Zhu ◽

R. I. Cukier

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Excess Electron ◽

Dynamics Simulation ◽

Quantum Molecular Dynamics

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Quantum molecular dynamics simulation of hydrogen diffusion in zirconium hydride

Physics of the Solid State ◽

10.1134/s1063783414090315 ◽

2014 ◽

Vol 56 (9) ◽

pp. 1879-1885 ◽

Author(s):

A. V. Yanilkin

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Hydrogen Diffusion ◽

Dynamics Simulation ◽

Zirconium Hydride ◽

Quantum Molecular Dynamics

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Advanced analysis of laser-driven pulsed magnetic diffusion based on quantum molecular dynamics simulation

Matter and Radiation at Extremes ◽

10.1063/5.0053621 ◽

2021 ◽

Vol 6 (6) ◽

pp. 065901

Author(s):

Hiroki Morita ◽

Tadashi Ogitsu ◽

Frank R. Graziani ◽

Shinsuke Fujioka

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Dynamics Simulation ◽

Quantum Molecular Dynamics ◽

Magnetic Diffusion ◽

Advanced Analysis

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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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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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Efficient Free-Energy Calculation of Proton Transfer by Constrained Density Functional Theory and Geometrically Restrained Molecular Dynamics Simulation

Chemistry Letters ◽

10.1246/cl.210132 ◽

2021 ◽

Author(s):

Tatsuya Joutsuka ◽

Koji Ando

Keyword(s):

Molecular Dynamics ◽

Density Functional Theory ◽

Free Energy ◽

Molecular Dynamics Simulation ◽

Proton Transfer ◽

Density Functional ◽

Dynamics Simulation ◽

Free Energy Calculation ◽

Energy Calculation ◽

Functional Theory

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Conformational flexibility decreased due to Y67F and F82H mutations in cytochrome c: Molecular dynamics simulation studies

Journal of Molecular Graphics and Modelling ◽

10.1016/j.jmgm.2009.08.005 ◽

2009 ◽

Vol 28 (3) ◽

pp. 270-277 ◽

Author(s):

Sarkkarai Raja Singh ◽

Subash Prakash ◽

Veerapandy Vasu ◽

Chandran Karunakaran

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Cytochrome C ◽

Conformational Flexibility ◽

Dynamics Simulation ◽

Simulation Studies

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How ABA block polymers activate cytochrome c in toluene: molecular dynamics simulation and experimental observation

Physical Chemistry Chemical Physics ◽

10.1039/c5cp00418g ◽

2015 ◽

Vol 17 (16) ◽

pp. 10708-10714 ◽

Author(s):

Gong Chen ◽

Xian Kong ◽

Jingying Zhu ◽

Diannan Lu ◽

Zheng Liu

Keyword(s):

Molecular Dynamics ◽

High Temperature ◽

Molecular Dynamics Simulation ◽

Cytochrome C ◽

Experimental Observation ◽

Dynamics Simulation ◽

Block Polymers ◽

Dispersion Properties

The temperature responsiveness of ABA-polymer-conjugated Cyt c and its improved dispersion properties at high temperature have been investigated through both simulations and experiments.

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