Theoretical Research On Biological Models Of Molecular Proton Transfer Mechanism And Its Auxiliary Group Effect

As one of the simplest and the most fundamental phenomena in the tautomeric equilibria and oxidation-reduction reactions, the intra- or intermolecular proton transfers (PTs) play an important role in many chemical and biochemical processes. The formation of hydrogen bonds and PT occur widely in the most important and frequent chemical processes. For instance, almost each reaction in organic chemistry involves a complete or partial proton transfer. Electron transfer and proton transfer widely exist in the various proceedings of the photosynthetic chain, respiratory chain and oxidase-promoting reaction, which produce the driving-force for motabolic transport, decide the direction and procedure of information transport and make the biological information code and transfer in the way of energy quantum.In this paper, we choose two systems, modeling arginine systems and guanine-Na~+ monohydrate, to theoretically investigate the proton transfer using density functional theory. Some important results have been obtained.The whole paper consists of five chapters. The first chapter is the preface. It briefly introduces the background of intermolecular or intramolecular proton transfers, the frequency characteristics of infrared spectra and the primary work of this paper. The second chapter introduces the related computational methods employed in this paper. By comparing the methods, finally we thought that the DFT method is the best one and we used it throughout the research. In brief, the former two chapters are the basis and background of our studies, which offer us useful and reliable quantum methods.On the basis of these theories, the proton transfer mechanisms of the modeling arginine systems have been investigated in the third chapter employing the DFT method, where the protonated cases have been also considered. We found that the proton can complete the internal transmission in the protein through the protonation or deprotonation processes. In conduction process, dueto the coexistence of these isomers, PT phenomenon also exists to realize the different proton transmission mechanisms in the proton pump process. The water-assisted PT processes should be easily observable at any temperature of biological importance experimentally. Obviously, the dihydrated case provides an optimal static condition among the water-assisted cases studied here.In the fourth chapter, we selected some representative modeling amino acids to simulate the amino acids-assisted PT. Similar with the water-assisted proton transfer isomerization, the auxiliary groups similarly have certain catalytic effects. In this chapter, various amino acid models have been considered with differently active sites to participate in the double proton transfer isomerization processes. Moreover, a pair of hydrogen bonds have been formed whose natures are similar to each other, where the double proton transfer proceeds with a concerted mechanism.In the fifth part, we investigate the coupling characteristics and proton transfer mechanism of Guanine-Na~+ monohydrate at the B3LYP/6-311+G* level of theory. Computational results show that the participation of the metal ion may hinder or promote the tautomerization of the base, and a water molecule has a little effect on this kind of function as compared to the metal ion. The interaction energy in the formation of monohydrated guanine-Na~+ is lower, therefore it may be more advantageous in the organism.