The Nickel-Iron  hydrogenase has been investigated by a variety of scientitsts.  It has been the focus of computational studies, spectroscopy studies, and biochemical studies for the past decade.  An article in the journal Nature has even given thie enzyme credit for playing a key role in eukaryotic evolution (1). This page is an introduction to the structure of the Nickel-Iron Hydrogenase.  By exploring this page, I hope you are able to find an appreciation for  the complexity of this biological system even though it catalyzes a seemingly simple reaction:

This page is currently under construction as we are using Jaguar 4.0  to investigate spin states, molecular orbitals, the reaction mechanism, and other molecular properties of this molecule. Updates will be posted as we arrive upon them.

Below is an image of the Nickel-Iron Hydrogenase. The molecule is in the triplet state with an overall charge of -2, iron and nickel are both in the +2 oxidation states. This molecule was optimized using B3LYP level of theory in Jaguar. The output file was transferred to gOpenMol where the .pdb was created to give the view below. gOpenMol was also used to view molecular orbitals, electron density plots, and electrostatic potential.

The Diversity of Prokaryotic Metabolism at UW-Madison
Bioenergetics of Respiratory Chain Hydrogenase
Amazing Microorganisms
An Introduction To DFT- Molecular Simulations
E Wimmer's Article on Computational Methods for Atomistic Simulation

View molecular orbitals, animation of the density plots, or electrostatic potential by clicking here.
 
 

This mechanism by which the active site of this enzyme works has been studied extensively (2 & 3) but many questions still remain. We are currently studiying a small part of the reaction mechanism in looking for the transition state between the reactant (top) and product (bottom) shown below. Electrons are transferred from the active site to a thiocubane structure which we have also studied using Jaguar 4.0.

1. Martin W., & Muller M., "The Hydrogen Hypothesis for the First Eukaryote" Nature 392, 37-41 (1998).

2. Pavlov M et al., "Mechanism of H-H Activation by Nickel-Iron Hydrogenase" J. Am. Chem. Soc. 120, 548-555 (1998).

3. Niu S., Thomson L., Hall M., "Theoretical Characterization of the Reaction Intermediates in a Model of the Nickel-Iron Hydrogenase of Desulfovibrio gigas" J. Am. Chem. Soc., 121, 4000-4007 (1999).