Improved electrostatic properties using combined Mulliken and hybridization-displaced charges for radicals

Quantum theoretical study of cleavage of the glycosidic bond of 2'-deoxyadenosine: base excision-repair mechanism of DNA by MutY

The enzyme adenine DNA glycosylase, also called MutY, is known to catalyze base excision repair by removal of adenine from the abnormal 2'-deoxyadenosine:8-oxo-2'-deoxyguanosine pair in DNA. The active site of the enzyme was considered to consist of a glutamic acid residue along with two water molecules. The relevant reaction mechanism involving different barrier energies was studied theoretically. Molecular geometries of the various molecules and complexes involved in the reaction, e.g., the reactant, intermediate, and product complexes as well as transition states, were optimized employing density functional theory at the B3LYP/6-31G(d,p) level in the gas phase. It was followed by single-point energy calculations at the B3LYP/AUG-cc-pVDZ, BHandHLYP/AUG-cc-pVDZ, and MP2/AUG-cc-pVDZ levels in the gas phase. Single-point energy calculations were also carried out at the B3LYP/AUG-cc-pVDZ and BHandHLYP/AUG-cc-pVDZ levels in aqueous media as well as in the solvents chlorobenzene and dichloroethane. For the solvation calculations, the integral equation formalism of the polarizable continuum model (IEF-PCM) was employed. It is found that glutamic acid along with two water molecules would effectively cleave the glycosidic bond of adenosine by a new two-step reaction mechanism proposed here which is different from the three-step mechanism proposed by other authors earlier regarding the working mechanism of MutY.

Mechanism of scavenging action of N-acetylcysteine for the OH radical: a quantum computational study

N-Acetylcysteine, a precursor of glutathione, is an effective antioxidant present in biological systems. The mechanism of scavenging action of N-acetylcysteine for the OH radical was studied theoretically. For this purpose, reactions of the OH radical at the different sites of N-acetylcysteine were investigated. All the relevant extrema on the potential energy surfaces were located by optimizing the geometries of the reactant and product complexes as well as those of the transition states at the BHandHLYP/AUG-cc-pVDZ level of density functional theory in the gas phase. The solvent effect of aqueous media was treated by performing single point energy calculations at the BHandHLYP/AUG-cc-pVDZ and MP2/AUG-cc-pVDZ levels of theory employing the polarizable continuum model. Correction for basis set superposition error (BSSE) was made by the counterpoise method. Rate constants for all the reaction mechanisms were calculated including the tunneling contributions. Our calculations show that the hydrogen atom of the SH group of N-acetylcysteine would be most efficiently abstracted by the OH group, which is in agreement with experimental observations.