- A fully optimized model for the resting state of the active site of the third type of phylogenetically unrelated (monoiron) hydrogenase, iron-sulfur cluster-free hydrogenase (Hmd), was constructed based on density functional calculations. This resting state structure shows good agreement with the experimental IR spectra. The calculations predict that the barrier for H2 cleavage in the presence of MPT+ is 18 kcal/mol lower than that in the absence of MPT+, a result that explains why the isotopic H2/D2O exchange catalyzed by Hmd is strictly dependent on the presence of MPT+. This difference is a result of the MPT+ triggering the pyridone to provide electron density to allow the Fe to take a proton while transferring a hydride to the MPT+. These active site models and catalytic mechanism are useful in understanding this hydrogen activation for the design of novel hydrogenation catalysts and for low cost, high efficiency hydrogen generation.