Electron transfer calculation progress

Overview of Progress in Calculation of Electron-Transfer Rates... 

The problem of linking atomic scale descriptions to continuum descriptions is also a nontrivial one. We will emphasize here that the problem cannot be solved by heroic extensions of the size of molecular dynamics simulations to millions of particles and that this is actually unnecessary. Here we will describe the use of atomic scale calculations for fixing boundary conditions for continuum descriptions in the context of the modeling of static structure (capacitance) and outer shell electron transfer. Though we believe that more can be done with these approaches, several kinds of electrochemical problems—for example, those associated with corrosion phenomena and both inorganic and biological polymers—will require approaches that take into account further intermediate mesoscopic scales. There is less progress to report here, and our discussion will be brief. 

These preliminary calculations do not immediately provide an explanation for the unidirectionally of electron transfer in the RC. However, there are several potentially important factors which have been omitted. It is possible that residues that have been assumed to be charged in this analysis are actually neutral because they are buried in the protein or low dieletric material around the protein. Also, no partial charges have been placed on the bacteriochlorophyll and bacteriopheophytin acetyls, keto groups or esters. These are often close to neighboring cofactors. Further work on this problem is in progress. 

Since electron transfer is an activated process, the central quantity needed to determine the reaction rate is the activation free energy. To calculate this quantity in computer simulations, the reaction coordinate used to follow progress of the reaction has to be chosen. In statistical mechanics this choice is not unique and is usually motivated by the nature of the reaction of interest. Since solvent reorganization plays the major role in electron transfer, it was found that a very good, onedimensional reaction coordinate is the solvent coordinate ,... 

The older versions of the theory considered the electrode as a reservoir of electrons and hence could not explain catalysis. Substantial progress was achieved when two of us [6,7] connected electron transfer with ideas from the Anderson-Newns theory [8,9] and applied Green s function techniques. This made it possible to consider the electronic structure of the electrode, distinguish between d bands and sp bands, and treat the case of strong electronic interactions, which give rise to catalysis. Since it does not contain many-body effects, it requires input from DFT for quantitative calculations—this will be treated later (see Section 1.2.3). However, the theory by itself already does offer a nice way to understand qualitatively how a catalyst worics, which we proceed to present. 

The electronic transitions of silicalite and TS-1 in the UV-visible spectrum have provided significant information about the structure of TS-1. The diffuse reflectance spectra of the two materials (Fig. 11) show a strong transition at 48,000 cm-1 that is present in the spectrum of TS-1 and absent from that of silicalite. This transition must be associated with a charge-transfer process localized on Tiiv. The frequency of this transition is modified by the presence of H20 (Fig. 12). As the H20 partial pressure increases, the peak at 48,000 cm- is progressively eroded with formation of a lower-frequency absorption, which reaches a new stable maximum value at 42,000 cm. These frequencies come very close to those that can be calculated by the Jorgensen equation for Tiiv tetrahedrally and octahedrally coordinated to oxygen, respectively. Furthermore,... 

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