Synchrotron radiation-based spectroscopic investigation of the electronic and geometric structures of iron-sulfur clusters, particles, and minerals
Gardenghi, David Jeremiah.
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Iron-sulfur systems are ubiquitous in biological and geological environments. They range from molecular scale [2Fe-2S] clusters to nanometer scale particles to micrometer scale minerals. Across the length scale, each system has unique structural and functional roles with respect to its environment, such as metalloproteins or hydrothermal vents. Therefore, it is of great interest to understand the electronic and geometric structural properties that give a wide range of reactivity. The main focus of this dissertation is to investigate the possible connections among the different size scales using a primary technique, X-ray absorption spectroscopy (XAS), by gaining an understanding into the relationship between the system size and properties. X-ray absorption spectroscopy is a powerful tool to probe geometric and electronic structures across the entire length scale. In this work, extend x-ray absorption fine structure (EXAFS) analysis method was applied to determine geometric structure of the protein bound, molecular iron-sulfur cluster of HydA. It was found to contain a preformed [4Fe-4S] cluster. This method combined with Fe/S K-edge XANES analysis was applied to spore photoproduct lyase metalloprotein to structurally characterize the [4Fe-4S] cluster and its interaction with SAM. The Fe K-edge EXAFS and Fe/S K-edge XANES provide evidence for a cluster distortion upon interacting with SAM as a new EXAFS feature, indicating the presence of longer Fe-Fe distances and this provides new insights into the structure of radical SAM enzymes. At the nanometer scale, mineral and protein encapsulated particles were investigated with a possible link between molecular and micrometer scale. A reference library of FeS systems was established to describe the variation in bonding and structure. Also, a considerable amount was learned about XAS detection methods, and this was applied to the micrometer scale systems. From EXAFS and XANES analysis, the modified surface of pyrite was revealed to have an intermediate layer of Fe(I)-S phase with a metallic iron surface, and a reaction scheme was proposed. These studies of the different size iron-sulfur systems provide insights into the change in the electronic and geometric structures, and a model was proposed to describe the effects of size on the electronic and geometric structure.