Theoretical Investigation On The Transfer /Scavenging Mechanisms Of Several Small Groups In Vivo

The transfer/scavenging reactions of small groups are widely existed in vivo, such as the transfer of acetyl group and the scavenging of reactive carbonyl species. Although these reactions are very important to the natural metabolize of organism, the detailed reaction mechanisms have not yet been clarity. Along with the rapid progress of computational methods and computer technology, computational chemistry has become more and more important in modern chemistry. Due to its moderate computational consume and high precision, Density Functional Theory (DFT) has been widely used in biochemistry, pharmaceutical chemistry and material science, and has become one of the most important methods in computational chemistry. The combined quantum mechanics and molecule mechanics (QM/MM) method can not only take account of the accuracy of calculations, but also calculate the reaction system with more atoms, it has been successfully applied to many enzymatic systems and proved to be considerably efficient. In this thesis, the reactions of some small group in vivo have mostly been investigated by DFT (B3LYP) and QM/MM methods. The present thesis is organized as follows:The reactions of small groups in vivo such as the transfer of acetyl group, the metabolize process of reactive carbonyl species as well as N–acetyl–L–aspartate have been introduced in chapter 1. The major works of this thesis were investigating the mechanism of the reactions above and finally determining the preferred reaction pathway.In chapter 2, the theory elements and several computational methods of quantum chemistry including Hartree–Fock Theory and Density Functional Theory Method were described. Furthermore, the QM/MM method and its recent application were also introduced.In chapter 3, we investigated the acetyltransfer reaction mechanism of the active site cysteine residue and the acetyl donor, ethyl acetate. Furthermore, the methanol–assisted acetylation mechanism was also provided. The results indicated that this reaction could be achieved through two possible reaction pathways: one was concerted and the other was stepwise, and the latter was the minimum energy pathway on the potential energy surface due to the lower activation energy barriers. The assistance of one methanol molecule in the transition state can obviously decrease the energy barrier at a range of 38.1 to 85.9 kJ?mol-1, but the priority for the pathways still remained. All the results were consistent with the experimental data very well.In chapter 4, we studied the reaction mechanism of pyridoxamine with a dicarbonyl compound 4–oxopentanal, and the results were compared with those in water–assisted reaction. The results indicated that the reaction could be achieved through two continuous steps. Firstly, pyridoxamine and 4–oxopentanal would generate a tetrahydropyrrole compound via two possible reaction pathways. Subsequently, two molecules of water would be removed to achieve the final pyrrole–type compound through two parallel paths. In addition, it’s possible to form an imine intermediate in this reaction, which seems more like a by–product from our calculation. In the end, the steric hindrance of the substitute was discussed. The activation energy of all transition states and intermediates in water–assisted reaction were much lower than those in non water–assisted reaction.In chapter 5, the hydrolysis mechanisms of NAA and a potent inhibition of aspartoacylase, N–methylphosphono–L–aspartate, were investigated by means of DFT B3LYP as well as ONIOM method with a two–layered model. The calculated results indicated that the reaction could be achieved through two possible reaction pathways: one was concerted and the other was stepwise, and the latter was the preferred pathway in the competitive reaction. The activity energy for NMPA hydrolysis was much lower than that of NAA, indicating that if the NMPA occupied the active site, it could effectively inhibit the hydrolysis reaction of NAA. The hydrogen–bonding interactions between substrates and residues (especially Arg71 and Arg168) and the electrostatic interactions between zinc ion and substrates play a crucial role in stabilizing the reaction system.