Quantum-Classical Molecular Dynamics Simulations of Proton Transfer Processes in Molecular Complexes and in Enzymes

1996 ◽  
Vol 100 (7) ◽  
pp. 2535-2545 ◽  
Author(s):  
P. Bała ◽  
P. Grochowski ◽  
B. Lesyng ◽  
J. A. McCammon
Keyword(s):  
Molecular Dynamics ◽  
Proton Transfer ◽  
Molecular Dynamics Simulations ◽  
Molecular Complexes ◽  
Transfer Processes ◽  
Classical Molecular Dynamics ◽  
Dynamics Simulations

scholarly journals Explicit proton transfer in classical molecular dynamics simulations

2014 ◽  
Vol 35 (8) ◽  
pp. 657-671 ◽  
Author(s):  
Maarten G. Wolf ◽  
Gerrit Groenhof
Keyword(s):  
Molecular Dynamics ◽  
Proton Transfer ◽  
Molecular Dynamics Simulations ◽  
Classical Molecular Dynamics ◽  
Dynamics Simulations

Applications of quantum-classical and quantum-stochastic molecular dynamics simulations for proton transfer processes

1994 ◽  
Vol 180 (2-3) ◽  
pp. 271-285 ◽  
Author(s):  
P. Bala ◽  
B. Lesyng ◽  
J.A. McCammon
Keyword(s):  
Molecular Dynamics ◽  
Proton Transfer ◽  
Molecular Dynamics Simulations ◽  
Transfer Processes ◽  
Dynamics Simulations

scholarly journals Characterization of amorphous Si generated through classical molecular dynamics simulations

2017 ◽  
Author(s):  
Ivan Santos ◽  
Pedro Lopez ◽  
Maria Aboy ◽  
Luis A. Marques ◽  
Lourdes Pelaz
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Classical Molecular Dynamics ◽  
Amorphous Si ◽  
Dynamics Simulations

scholarly journals Cavity hydration dynamics in cytochrome c oxidase and functional implications

2017 ◽  
Vol 114 (42) ◽  
pp. E8830-E8836 ◽  
Author(s):  
Chang Yun Son ◽  
Arun Yethiraj ◽  
Qiang Cui
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Proton Transfer ◽  
Molecular Dynamics Simulations ◽  
Transmembrane Protein ◽  
Wetting Transition ◽  
Protonation State ◽  
Hydration Level ◽  
Level Change ◽  
Dynamics Simulations

Cytochrome c oxidase (CcO) is a transmembrane protein that uses the free energy of O2 reduction to generate the proton concentration gradient across the membrane. The regulation of competitive proton transfer pathways has been established to be essential to the vectorial transport efficiency of CcO, yet the underlying mechanism at the molecular level remains lacking. Recent studies have highlighted the potential importance of hydration-level change in an internal cavity that connects the proton entrance channel, the site of O2 reduction, and the putative proton exit route. In this work, we use atomistic molecular dynamics simulations to investigate the energetics and timescales associated with the volume fluctuation and hydration-level change in this central cavity. Extensive unrestrained molecular dynamics simulations (accumulatively ∼4 μs) and free energy computations for different chemical states of CcO support a model in which the volume and hydration level of the cavity are regulated by the protonation state of a propionate group of heme a3 and, to a lesser degree, the redox state of heme a and protonation state of Glu286. Markov-state model analysis of ∼2-μs trajectories suggests that hydration-level change occurs on the timescale of 100–200 ns before the proton-loading site is protonated. The computed energetic and kinetic features for the cavity wetting transition suggest that reversible hydration-level change of the cavity can indeed be a key factor that regulates the branching of proton transfer events and therefore contributes to the vectorial efficiency of proton transport.

On the structure of biomedical silver-doped phosphate-based glasses from molecular dynamics simulations

2014 ◽  
Vol 16 (39) ◽  
pp. 21135-21143 ◽  
Author(s):  
Richard I. Ainsworth ◽  
Jamieson K. Christie ◽  
Nora H. de Leeuw
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
First Principles ◽  
Classical Molecular Dynamics ◽  
Dynamics Simulations

First-principles and classical molecular dynamics simulations have been carried out on undoped and silver-doped phosphate-based glasses with 50 mol% P2O5, 0–20 mol% Ag2O, and varying amounts of Na2O and CaO.

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