Electron transfer direct molecular dynamics

Wigner rotation/adiabatic-to-diabatic transformation matrices, 92 Electronic structure theory, electron nuclear dynamics (END) structure and properties, 326-327 theoretical background, 324-325 time-dependent variational principle (TDVP), general nuclear dynamics, 334-337 Electronic wave function, permutational symmetry, 680-682 Electron nuclear dynamics (END) degenerate states chemistry, xii-xiii direct molecular dynamics, structure and properties, 327 molecular systems, 337-351 final-state analysis, 342-349 intramolecular electron transfer,... 

Intraanchor reactions, conical intersection, two-state systems, 437-438 Intramolecular electron transfer, electron nuclear dynamics (END), 349-351 Intrinsic reaction coordinate (IRC), direct molecular dynamics, theoretical background, 358-361... 

Following the early studies on the pure interface, chemical and electrochemical processes at the interface between two immiscible liquids have been studied using the molecular dynamics method. The most important processes for electrochemical research involve charge transfer reactions. Molecular dynamics computer simulations have been used to study the rate and the mechanism of ion transfer across the water/1,2-dichloroethane interface and of ion transfer across a simple model of a liquid/liquid interface, where a direct comparison of the rate with the prediction of simple diffusion models has been made. ° ° Charge transfer of several types has also been studied, including the calculations of free energy curves for electron transfer reactions at a model liquid/liquid... 

As pointed out by Warshel and co-workers, the derivation of the important relation (14) is based on the assumption of non-saturation of the dielectric medium, which does not necessarily applies in the case of a macromolecule in solution [43]. These authors have shown that the validity of relation (14) could be directly tested by simulating the dipole motions through molecular dynamics models [43, 44, 45]. Detailed numerical calculations were carried out for the selfexchange reaction of cytochrome c [43], and for the electron transfer between two benzene-like molecules in water [45]. A similar approach was recently developed for the system (Fe " ", Fe ) in aqueous solution [46]. From these calculations, it was concluded that relation (14) applies provided that X is evaluated from a microscopic model. 

In addition to the development of new methods, new applications of molecular dynamics computer simulation are also needed in order to make comparisons with experimental results. In particular, more complicated chemical reactions, beyond the relatively simple electron transfer reaction, could be studied. Examples include the study of chemical adsorption, hydrogen evolution reactions, and chemical modification of the electrode surface. All of the above directions and opportunities promise to keep this area of research very active ... 

In order to interpret the results of our experiments, optimal-control calculations were performed where a GA controlled 40 independent degrees of freedom in the laser pulses that were used in a molecular dynamics simulation of the laser-cluster interactions for Xejv clusters with sizes ranging from 108 to 5056 atoms/cluster. These calculations, which are reported in detail elsewhere [67], showed optimization of the laser-cluster interactions by a sequence of as many as three laser pulses. Detailed inspection of the simulations revealed that the first pulse in this sequence initiates the cluster ionization and starts the expansion of the cluster, while the second and third pulse optimize two mechanisms that are directly related to the behaviour of the electrons in the cluster. We consistently observe that the second pulse in the three-pulse sequence arrives a time delay where the conditions for enhanced ionization are met. In other words, the second pulse arrives at a time where the ionization of atoms is assisted by the proximity of surrounding ions. The third peak is consistently observed at a delay where the collective oscillation of the quasi-free electrons in the cluster is 7t/2 out of phase with respect to the driving laser field. For a driven and damped oscillator this phase-delay represents an optimum for the energy transfer from the driving force to the oscillator. 

With site-directed mutation and femtosecond-resolved fluorescence methods, we have used tryptophan as an excellent local molecular reporter for studies of a series of ultrafast protein dynamics, which include intraprotein electron transfer [64-68] and energy transfer [61, 69], as well as protein hydration dynamics [70-74]. As an optical probe, all these ultrafast measurements require no potential quenching of excited-state tryptophan by neighboring protein residues or peptide bonds on the picosecond time scale. However, it is known that tryptophan fluorescence is readily quenched by various amino acid residues [75] and peptide bonds [76-78]. Intraprotein electron transfer from excited indole moiety to nearby electrophilic residue(s) was proposed to be the quenching... 

The discussion above must be modified if the acceptor molecules adsorb onto the electrode surface. Under these circumstances, the electrons are captured by the acceptor directly rather than through an intermediary solvated electron, and such direct photoassisted electron transfer has been much studied recently with the advent of dye-sensitized solar cells and molecular electronic devices. The normal approach is to use two-photon excitation both to probe the existence of localized states at the surface and to explore their dynamics. In experiments of this nature, which have been mostly carried out on ad-... 

Such preference in molecular orientation for electron transfer certainly should show up in the reaction dynamics, especially when seeking to direct reactions. This was exemplified for the first time in the reaction of sodium with a different molecule... 

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