A DMol3study of the methanol addition–elimination oxidation mechanism by methanol dehydrogenase enzyme

The addition–elimination (A–E) mechanism proposed for the oxidation of methanol to formaldehyde by PQQ-containing methanol dehydrogenase (MDH) enzyme is investigated at the Becke–Lee–Yang–Parr/double numerical with polarisation density functional theory level with the DMol3 module of the Materials Studio® software. Two different models representing the Methylobacterium extorquens MDH (1H4I) active site are considered and tested upon methanol oxidation in gas phase. Model A consists of the PQQ molecule, the Ca2 + ion and aspartic acid (ASP-303), and model B contains also glutamic acid (GLU-177) and asparagine (ASN-261) in addition to the contents of model A. The first proton transfer from methanol to ASP-303 and from ASP-303 to PQQ is affected by the model size; however, the second proton transfer corresponding to the cleavage of Cmet–H17 is practically unaffected by the MDH active site model under consideration. The energy barrier for the cleavage of the C atom of methanol (Cmet) and H17 is 13 and 17 kcal/mol for models A and B, respectively, in good agreement with the general kinetic requirements of an enzymatic process. Step 1 as proposed in the literature is not kinetically favourable in the gas phase at this theory level. It is possible then, that either solvent effects are critical or that one or more intermediate steps leading to the formation of the first intermediate complex are missing from the proposed methanol A–E mechanism for the oxidation of methanol by MDH.