Calculation of the Proton Transfer Rate Using Density Matrix Evolution and Molecular Dynamics Simulations: Inclusion of the Proton Excited States

1995 ◽  
Vol 99 (34) ◽  
pp. 12711-12717 ◽  
Author(s):  
Janez Mavri ◽  
Herman J. C. Berendsen
Keyword(s):  
Molecular Dynamics ◽  
Proton Transfer ◽  
Density Matrix ◽  
Molecular Dynamics Simulations ◽  
Excited States ◽  
Transfer Rate ◽  
Dynamics Simulations ◽  
Matrix Evolution

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.

scholarly journals Electronic density-matrix algorithm for nonadiabatic couplings in molecular dynamics simulations

2001 ◽  
Vol 85 (4-5) ◽  
pp. 225-238 ◽  
Author(s):  
M. Tommasini ◽  
V. Chernyak ◽  
S. Mukamel
Keyword(s):  
Molecular Dynamics ◽  
Density Matrix ◽  
Molecular Dynamics Simulations ◽  
Electronic Density ◽  
Matrix Algorithm ◽  
Dynamics Simulations

Semiclassical molecular dynamics simulations of excited state double-proton transfer in 7-azaindole dimers

1999 ◽  
Vol 110 (20) ◽  
pp. 9922-9936 ◽  
Author(s):  
Victor Guallar ◽  
Victor S. Batista ◽  
William H. Miller
Keyword(s):  
Molecular Dynamics ◽  
Excited State ◽  
Proton Transfer ◽  
Molecular Dynamics Simulations ◽  
Double Proton Transfer ◽  
Dynamics Simulations

scholarly journals Key role of water in proton transfer at the Qo-site of the cytochrome bc1 complex predicted by atomistic molecular dynamics simulations

2013 ◽  
Vol 1827 (6) ◽  
pp. 761-768 ◽  
Author(s):  
Pekka A. Postila ◽  
Karol Kaszuba ◽  
Marcin Sarewicz ◽  
Artur Osyczka ◽  
Ilpo Vattulainen ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Proton Transfer ◽  
Molecular Dynamics Simulations ◽  
Cytochrome Bc1 ◽  
Bc1 Complex ◽  
Cytochrome Bc1 Complex ◽  
Qo Site ◽  
Dynamics Simulations

Photorelaxation of imidazole and adenine via electron-driven proton transfer along H2O wires

2016 ◽  
Vol 195 ◽  
pp. 237-251 ◽  
Author(s):  
Rafał Szabla ◽  
Robert W. Góra ◽  
Mikołaj Janicki ◽  
Jiří Šponer
Keyword(s):  
Molecular Dynamics ◽  
Excited State ◽  
Potential Energy ◽  
Proton Transfer ◽  
Potential Energy Surface ◽  
Molecular Dynamics Simulations ◽  
Gas Phase ◽  
Energy Surface ◽  
Water Molecules ◽  
Dynamics Simulations

Photochemically created πσ* states were classified among the most prominent factors determining the ultrafast radiationless deactivation and photostability of many biomolecular building blocks. In the past two decades, the gas phase photochemistry of πσ* excitations was extensively investigated and was attributed to N–H and O–H bond fission processes. However, complete understanding of the complex photorelaxation pathways of πσ* states in the aqueous environment was very challenging, owing to the direct participation of solvent molecules in the excited-state deactivation. Here, we present non-adiabatic molecular dynamics simulations and potential energy surface calculations of the photoexcited imidazole–(H2O)5 cluster using the algebraic diagrammatic construction method to the second-order [ADC(2)]. We show that electron driven proton transfer (EDPT) along a wire of at least two water molecules may lead to the formation of a πσ*/S0 state crossing, similarly to what we suggested for 2-aminooxazole. We expand on our previous findings by direct comparison of the imidazole–(H2O)5 cluster to non-adiabatic molecular dynamics simulations of imidazole in the gas phase, which reveal that the presence of water molecules extends the overall excited-state lifetime of the chromophore. To embed the results in a biological context, we provide calculations of potential energy surface cuts for the analogous photorelaxation mechanism present in adenine, which contains an imidazole ring in its structure.

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