Quantum chemical modeling of methanol oxidation mechanisms by methanol dehydrogenase enzyme: effect of substitution of calcium by barium in the active site

Abstract

Previous experimental studies have shown that the activation energy for methanol oxidation by naturally occurring Ca(2+)-containing methanol dehydrogenase (MDH) enzyme is double the methanol activation energy by Ba(2+)-MDH. However, neither the reason for this difference nor the specific transition states and intermediates involved during the methanol oxidation by Ba(2+)-MDH have been clearly stated. Hence, an MDH active site model based on the well-documented X-ray crystallographic structure of Ca(2+)-MDH is selected, where the Ca(2+) is replaced by a Ba(2+) ion at the active site center, and the addition-elimination (A-E) and hydride-transfer (H-T) methanol oxidation mechanisms, already proposed in the literature for Ca(2+)-MDH, are tested for Ba(2+)-MDH at the BLYP/DNP theory level. Changes in the geometries and energy barriers for all the steps are identified, and qualitatively, similar (when compared to Ca(2+)-MDH) intermediates and transition states associated with each step of the mechanisms are found in the case of Ba(2+)-MDH. For both the A-E and H-T mechanisms, almost all the free-energy barriers associated with all of the steps are reduced in the presence of Ba(2+)-MDH, and they are kinetically feasible. The free energy barriers for methanol oxidation by Ba(2+)-MDH, particularly for the rate-limiting steps of both mechanisms, are almost half the corresponding barriers calculated for the case of Ca(2+)-MDH, which is in agreement with experimental observations.