DFT investigation of the Ni-A inactive state of the [NiFe]-hydrogenases: inactivation mechanism under aerobic conditions

Because dihydrogen is considered as a future non polluting source of energy, Hydrogenase enzymes are of fundamental interest for their capability to catalyse the reversible interconversion of protons and reducing equivalents into molecular hydrogen. While the [FeFe]-hydrogenases are irreversibly inactivated by O2, the oxidized [NiFe]-hydrogenases can be reactivated by one-electron reduction and protonation. This property, in addition to the high catalytic efficiency and the absence of expensive metals in their active site, makes the [NiFe]-hydrogenases a very promising target for reverse engineering studies aimed at the development of bioinspired catalysts. In the active site of [NiFe]-hydrogenases, the iron and nickel atoms are bridged by two cysteine residues. Two further cysteine residues are terminally bounded to the Ni atom while two CN and one CO ligands coordinate the Fe atom. The inactive oxidized Ni-A state of this enzyme have been recently characterized by X-ray diffraction, as containing a bridging hydroxide ligand between the two metallic ions and a bridging cysteine oxidized to its sulfanated form. To investigate the mechanism of oxidation of active forms to this state, quantum mechanics calculations have been carried out in the framework of the Density Functional Theory (DFT) on a very large model of the active site. Under aerobic conditions, oxidation is promoted by binding to the active site of a O2 molecule, that provide the two oxygen atoms included in the Ni-A form.