Enzymatic Reduction of Nitrate to Nitrite: Insight from Density Functional Calculations

Abstract

The oxidative half-reaction of oxygen atom transfer from nitrate to the MoIV complex has been investigated by the density functional approach, based on the model cluster [(Me2C2S2)2Mo(MeS2)]− derived from the newly identified structure of nitrate reductase. Calculations show that the reduction of nitrate to nitrite can occur through an association of nitrate to the Mo center, followed by rupture of the Mo−O−NO2− bond. In reaction mechanism i, Mo−SCys bond cleavage coupling with the coordination of nitrate to Mo is the rate-determining step with a barrier of 19.8 kcal mol−1. In reaction mechanism iii, the direct coordination of nitrate to Mo is an almost barrier-free process, and the barrier for the rate-determining step of the Mo−O−NO2− bond cleavage is about 11.7 kcal mol−1, significantly lower than those in other plausible mechanisms. Present calculations lend support to the notion that the presence of a disulfide bond in the active site can influence the interconversion of MoIV to MoVI.