Date of Award


Degree Type




First Advisor

Gogonea, Valentin

Subject Headings

Hydrogenase, Enzyme kinetics, Hydrogenase, DFT, QM/MM, Inactivation, Catalysis


[Fe-Fe]-hydrogenases are enzymes that reversibly catalyze the reduction of protons to molecular hydrogen, which occurs in anaerobic media. In living systems, [Fe-Fe]-hydrogenases shift the reversible reaction towards H2 formation. The [Fe-Fe]-hydrogenase H-cluster is the active site, which contains two iron atoms (Fep-Fed, i.e., proximal and distal iron). Because most experimental and theoretical investigations confirm that the structure of di-iron air inhibited species is FepII-FedII-O-O-H-, O2 has to be prevented from binding to Fed in all di-iron subcluster oxidation states in order to retain a catalytically active enzyme. By understanding the catalytic processes of metalloenzymes, researches are enabled to produce an excellent source of fuel and energy storage (H2) for the future, which is clean and highly energetic when reacted with oxygen. H-cluster oxidation in gas phase, and in aqueous enzyme phase, has been investigated by means of quantum mechanics (QM) and combined quantum mechanics-molecular mechanics (QM/MM). The inhibitory process occurs at the coordination site, distal iron (Fed), of the catalytic H-cluster. The processes involved in the H-cluster oxidative pathways are O2 binding, e-transfer, protonation, and H2O removal. We found that oxygen binding is non-spontaneous in gas phase, and spontaneous for aqueous enzyme phase where both Fe atoms have oxidation state II however, it is spontaneous for the partially oxidized and reduced clusters in both phases. Hence, in the protein environment the O2-inhibited H-cluster is obtained by means of exergonic reaction pathways. A unifying endeavor has been carried out for the purpose of understanding the thermodynamic results vis-a-vis several other performed electronic structural methods, such as frontier molecular orbitals (FMO), natural bond orbital partial charges (NBO), and H-cluster geometrical analysis. Since hydrogenases become O2 inactivated, residue mutations were carried out in order to make them O2 resistant. Residue mutations consist of deleti

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