Computer simulation of phosphate ester hydrolysis reactions
Phosphate esters and their hydrolysis reactions underpin many of the most important reactions in biology and have therefore been the focus of continued research. In this thesis, a range of theoretical studies on two phosphate ester hydrolysis reactions is presented. Particular attention is paid to the role of solvent in these reactions. The first reaction studied is the hydrolysis of dimethyl phosphate. A study using density functional theory examines three possible mechanisms for this reaction in the gas phase and the presence of solvent is also considered through the use of reaction field methods. The base-catalysed mechanism for this reaction receives further attention and the reaction energy profile in solution is adiabatically mapped using two different hybrid QM/MM potentials. The use of a QM/MM potential facilitates an atomistic representation of the solvent. Another study determines the potential of mean force for this reaction by simulating the reaction using QM/MM molecular dynamics simulations in conjunction with umbrella sampling methods. Both QM/MM studies demonstrate that, in solution, the rate-determining step for the base-catalysed reaction is the cleavage of the bond between the phosphorous and the leaving group. The QM/MM studies also established that the reaction proceeds via the formation of a short-lived pentacoordinated intermediate species. The second reaction studied was the base-catalysed hydrolysis of methyl ribose phosphate, a realistic model of the nonenzymatic hydrolysis of RNA. Since the hydrolysis of thio-substituted analogues of RNA have been the study of many experimental studies probing the mechanism of RNA hydrolysis, theoretical studies of the hydrolysis of two thio analogues of methyl ribose phosphate are also presented. The results of these studies provide valuable insight into the mechanism of RNA hydrolysis and concludes that the cleavage of P-O5' bond corresponds to the reaction transition state.