Metalloenzymes catalyze many different types of biological reactions with high efficiency and remarkable selectivity. The quantum chemical cluster approach and the combined quantum mechanics/molecular mechanics methods have proven very successful in the elucidation of the reaction mechanism and rationalization of selectivities in enzymes. In this review, recent progress in the computational understanding of various selectivities including chemoselectivity, regioselectivity, and stereoselectivity, in metalloenzymes, is discussed.

The class II benzoyl-coenzyme A reductase (BCR) is a tungsten-dependent enzyme that catalyzes the Birch reduction of benzoyl-CoA to a cyclic diene. The reaction mechanism and regioselectivity of benzoyl-CoA were explored through QM/MM calculations using two different QM regions (124 atoms and 223 atoms) on the solvated enzyme. The reduction reaction involves two major chemical steps that both proceed in the triplet state or in the broken-symmetry singlet state. First, the tungsten-bound water molecule delivers a proton to the C4 of the benzoyl-CoA substrate, coupled with an electron transfer from the W center to the substrate. This leads to the formation of a W-radical intermediate, with a barrier of 23.2 kcal/mol in the broken-symmetry singlet state at the B3LYP-D3/def2-TZVPP:Charmm level. Subsequently, the protonated His260 residue delivers a second proton to C3 of the benzoyl-CoA substrate, concomitantly with the shift of the second electron from the pyranopterin cofactor rather than the W ion to the substrate, which has a barrier of 19.1 kcal/mol at the B3LYP-D3/def2-TZVPP:Charmm level and produces the cyclohexa-1,5-diene-1-carboxyl-CoA product. The reduction of the aromatic ring at other positions has also been considered; however, the barriers are much higher, which shows that the cyclohexa-1,5-diene-1-carboxyl-CoA product is exclusively formed during the benzoyl-CoA reduction. Moreover, molybdenum, tungsten's lighter congener, has also been considered to replace the tungsten ion in the benzoyl-CoA reductase. The molybdenum substituted enzyme (Mo-BCR) was found to have a quite higher barrier for the reduction reaction, but a feasible barrier for the reverse oxidation reaction.