Potential energy surface of the reaction of imidazole with peroxynitrite: Density functional theory study

摘要

This article presents a theoretical investigation of the reaction mechanism of imidazole nitration by peroxynitrite using density functional theory calculations. Understanding this reaction mechanism will help in elucidating the mechanism of guanine nitration by peroxynitrite, which is one of the assumed chemical pathways for damaging DNA in cells. This work focuses on the analysis of the potential energy surface (PES) for this reaction in the gas phase. Calculations were carried out using Hartree-Fock (HF) and density functional theory (DFT) Hamiltonians with double-zeta basis sets ranging from 6-31G(d) to 6-31 + + G(d,p), and the triple-zeta basis set 6-311G(d). The computational results reveal that the reaction of imidazole with peroxynitrite in gas phase produces the following species: (i) hydroxide ion and 2-nitroimidazole, (ii) hydrogen superoxide ion and 2-nitrosoimidazole, and (iii) water and 2-nitroimidazolide. The rate-determining step is the formation of a short-lived intermediate in which the imidazole C-2 carbon is covalently bonded to peroxynitrite nitrogen. Three short-lived intermediates were found in the reaction path. These intermediates are involved in a proton-hopping transport from C2 carbon to the terminal oxygen of the -O-O moiety of peroxynitrite via the nitroso (ON-) oxygen. Both HF and DFT calculations (using the Becke3-Lee-Yang-Parr functional) lead to similar reaction paths for proton transport, but the landscape details of the PES for HF and DFT calculations differ. This investigation shows that the reaction of imidazole with peroxynitrite produces essentially the same types of products (nitro- and nitroso-) as observed experimentally in the reaction of guanine with peroxynitrite, which makes the former reaction a good model to study by computation the essential characteristics of the latter reaction. Nevertheless, the computationally determined activation energy for imidazole nitration by peroxynitrite in the gas phase is 84.1 kcal/mol (calculated at the B3LYP/6-31++G(d,p) level), too large for an enzymatic reaction. Exploratory calculations on imidazole nitration in solution, and on the reaction of 9-methylguanine with peroxynitrite in the gas phase and solution, show that solvation increases the activation energy for both imidazole and guanine, and that the modest decrease (15 kcal mol(-1)) in the activation energy, due to the adjacent six member ring of guanine, is counterbalanced by solvation. These results lead to the speculation that proton tunneling may be at the origin of experimentally observed high reaction rate of guanine nitration by peroxynitrite in solution. (c) 2005 Wiley Periodicals, Inc.