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Project Progress

A main focus of this thrust was the development a new generation of coordination chemical models for catalytic sites of iron-sulfur minerals, mineral surfaces, and particles. We consider the surface defects of minerals, the perturbed surface structure of iron-sulfur particles embedded in an organic matrix, and the active sites of metalloenzymes as coordination compounds with localized electronic and geometric structures that are being greatly modified by the mineral, organic, and protein environment. This hypothesis allows us to break away from the traditional periodic boundary conditions-based modeling strategies. Using the molecular orbital-based, localized electronic structure description we can employ a large set of theoretical methods that have already been validated for numerous systems. An essential stepping-stone for this work was to utilize virtual chemical models of the FeFe-hydrogenase active site. We have found that protein environment via the orientation of the coordinated amino acid residues can control the cluster’s electron density and thus affecting the cluster electronic and magnetic properties. These protein/cluster interactions also influence the catalytic pathways and rates as key factors in small molecule activation chemistry. A parallel computational work utilizing a multi-edge X-ray absorption spectrochemical library of biomimetic compounds provided the definition of the most reasonable level of theory for molecular size Fe-S motifs.

Using the above insights, we created coordination chemistry-based models for the bulk pyrite and the [100] surface of pyrite. We hypothesize that the bulk environment, similarly to protein environment can be considered as electronic and geometric perturbations to a defect site. By gradually expanding the bulk environment around a central 'active site’ moiety of pyrite, we defined three layers of interactions of the immediately covalently bound 'ligands’ (1st layer), the electrostatic polarizing layer (2nd later), and the terminating bulk with steric constraints (3rd layer) (Figure 1A). By performing a [100] cut to this bulk pyrite model, we can obtain two virtual chemical model of the surface with either S or Fe/S termination as demonstrated in Figure 1B. With the development of these models we are now poised for mapping the potential energy surface of small molecule activation, condensation, and substitution reactions that are relevant to the formation of the building blocks of life.