Mechanism of hydrogen production in [Fe–Fe]-hydrogenases: A quantum mechanics/molecular mechanics study

[Fe–Fe]-hydrogenases are a class of metalloenzymes that catalyze the production of H2 from two protons and two electrons. Crystal structures for [Fe–Fe]-hydrogenases found in two species – Clostridium pasteurianum (CpI) and Desulfovibrio desulfuricans (DdH) – show very similar active sites. However, the catalytic mechanism has not as yet been fully clarified. We employed density functional theory (DFT) within a QM/MM method to investigate proposed mechanisms of hydrogen production by DdH and CpI hydrogenases and their dependence on the protein environment of the active sites. For each mechanism investigated, we found only minor differences between the CpI and DdH hydrogenases in terms of the intermediate active site structures, although one mechanism follows a lower energy path for DdH hydrogenase, while the other mechanism follows a lower energy path for the CpI hydrogenase. We note, however, that the high activation energy we calculated for a step unique to one of the mechanisms might preclude it, making the energy-path comparison for the two mechanisms unnecessary.