Photosynthetic reaction center applications

A more complete list of early applications of QM/MM methods to enzymatic reactions can be found elsewhere [18, 35, 83, 84], Gao [85] has reviewed QM/MM studies of a variety of solution phenomena. QM/MM methods have also been used to study the spectra of small molecules in different solvents [86] and electrochemical properties of photosynthetic reaction centers within a protein environment [87-89], An approach has also been developed for calculation of NMR shielding tensors by use of a QM/ MM method [90]. 

The next two chapters are devoted to ultrafast radiationless transitions. In Chapter 5, the generalized linear response theory is used to treat the non-equilibrium dynamics of molecular systems. This method, based on the density matrix method, can also be used to calculate the transient spectroscopic signals that are often monitored experimentally. As an application of the method, the authors present the study of the interfadal photo-induced electron transfer in dye-sensitized solar cell as observed by transient absorption spectroscopy. Chapter 6 uses the density matrix method to discuss important processes that occur in the bacterial photosynthetic reaction center, which has congested electronic structure within 200-1500cm 1 and weak interactions between these electronic states. Therefore, this biological system is an ideal system to examine theoretical models (memory effect, coherence effect, vibrational relaxation, etc.) and techniques (generalized linear response theory, Forster-Dexter theory, Marcus theory, internal conversion theory, etc.) for treating ultrafast radiationless transition phenomena. 

A microscopic theory for describing ultrafast radiationless transitions in particular for, photo-induced ultrafast radiationless transitions is presented. For this purpose, one example system that well represents the ultrafast radiationless transaction problem is considered. More specifically, bacterial photosynthetic reaction centers (RCs) are investigated for their ultrafast electronic-excitation energy transfer (EET) processes and ultrafast electron transfer (ET) processes. Several applications of the density matrix method are presented for emphasizing that the density matrix method can not only treat the dynamics due to the radiationless transitions but also deal with the population and coherence dynamics. Several rate constants of the radiationless transitions and the analytic estimation methods of those rate... 

Recent rapid developments in ultrashort pulse laser [1-5] make it possible to probe not only the dynamics of population of the system but also the coherence (or phase) of the system. To treat these problems, the density matrix method is an ideal approach. The main purpose of this paper is to briefly describe the application of the density matrix method in molecular terms and show how to apply it to study the photochemistry and photophysics [6-9]. Ultrafast radiationless transactions taking place in bacterial photosynthetic reaction centers (RCs) are very important examples to which the proposed theoretical approach can be applied. 

The three-dimensional structures of the photosynthetic reaction centers from two purple bacteria have been determined, permitting scientists to trace the detailed paths of electrons during and after the absorption of light. Similar proteins and pigments compose photosystem II of plants as well, and the conclusions drawn from studies on this simple photosystem have proven applicable to plant systems. 

P. Beroza, D. R. Fredkin, M. Y. Okamura, and G. Feher, Proc. Natl. Acad. Sci. U.S.A., 88, 5804 (1991). Protonation of Interacting Residues in a Protein by a Monte Carlo Method Application to Lysozyme and the Photosynthetic Reaction Center of Rhodobacter sphaeroides. 

This volume grew out of an American Chemical Society (ACS) symposium titled Bioenergetics. The ACS Division of Computers in Chemistry sponsored the symposium, whose goal was to bring together scientists from different disciplines to discuss current achievements and future directions in molecular-level simulations of electron and proton transfer. This volume provides a sampling of recently developed simulation methods, as well as their applications to prototypical biochemical systems such as the photosynthetic reaction center and bacteriorhodopsin. 

In this review, we explain the SAC-CI applications to molecular spectroscopy with some examples. In Section 2, we briefly explain the theoretical and computational aspects of the SAC-CI method. Then, we show some SAC-CI applications to molecular spectroscopy the excitation and ionization spectra of tt-conjugated organic molecules (Section 3), collision-induced absorption spectra of van der Waals complex (Section 4), excitation spectra and NMR chemical shifts of transition metal complexes (Section 5), photofragmentation reaction of Ni(CO)4 (Section 6), absorption spectrum of free-base phthalocyanine (FBPc) and bacterial photosynthetic reaction center... 

In this section, we briefly review the SAC-Cl applications to the excited states of porphyrin compounds EBPc [106] and bacterial photosynthetic reaction center of Rhodopseudomonas viridis [107]. Phthalocyanine is a famous chromophore that has a large absorbance in the visible region of the spectrum. By systematically comparing... 

Great attention has been paid to the application of thylakoid membranes and photosynthetic microorganisms in environmental pollution control. The biorecognition system based on the binding of certain herbicides to the photosynthetic reaction center of plants and microorganisms seems to be the most direa and simple method for herbicide detection. These systems used as sensor s recognition elements allow the detection of a broad range of herbicides. Unfortunately, their stability and sensitivity are insufficient in the most cases. From this point of view, the DI protein, which binds specifically... 

Beroza, R, Fredkin, D.R., Okamura, M.Y., Feher, G. Protonation of interacting residues in a protein by a Monte Carlo method Application to lysozyme and the photosynthetic reaction center of Rhodobacter sphaeroides. Proc. Natl. Acad. Sci. USA 1991, 88, 5804-8. 

Early reports on interactions between redox enzymes and ruthenium or osmium compounds prior to the biosensor burst are hidden in a bulk of chemical and biochemical literature. This does not apply to the ruthenium biochemistry of cytochromes where complexes [Ru(NH3)5L] " , [Ru(bpy)2L2], and structurally related ruthenium compounds, which have been widely used in studies of intramolecular (long-range) electron transfer in proteins (124,156-158) and biomimetic models for the photosynthetic reaction centers (159). Applications of these compounds in biosensors are rather limited. The complex [Ru(NHg)6] has the correct redox potential but its reactivity toward oxidoreductases is low reflecting a low self-exchange rate constant (see Tables I and VII). The redox potentials of complexes [Ru(bpy)3] " and [Ru(phen)3] are way too much anodic (1.25 V vs. NHE) ruling out applications in MET. The complex [Ru(bpy)3] is such a powerful oxidant that it oxidizes HRP into Compounds II and I (160). The electron-transfer from the resting state of HRP at pH <10 when the hemin iron(III) is five-coordinate generates a 7i-cation radical intermediate with the rate constant 2.5 x 10 s" (pH 10.3)... 

The intensity of fluorescence from an immobilized, isotropic sample of photosynthetic reaction centers (RCs) increases upon application of an electric field at 77 K [IJ. The change in fluorescence was found to be quadratic with the applied field strength, and the fluorescence in the field was found to become polarized [2]. The fluorescence increase is ascribed to a net decrease in the rate of the forward electron transfer reaction which competes with fluorescence from P. The field alters the free energy change for electron transfer, AG, and thus the rate because the energy of the dipolar product state... 

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