Theses and Dissertations at Montana State University (MSU)
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Item Development of density functional methods for iron-sulfur clusters : application to the elusive structure of the iron-molybdenum cofactor of nitrogenase(Montana State University - Bozeman, College of Letters & Science, 2011) Harris, Travis Victor; Chairperson, Graduate Committee: Robert K. SzilagyiIron-sulfur proteins are found in all forms of life, performing key functions in many of the most important biological processes, such as nitrogen fixation, respiration, DNA repair, and photosynthesis. The functional centers of these metalloproteins are iron-sulfur clusters, which are efficient electron-transfer agents, and provide a range of other functions, from catalysis to iron sensing. The main focus of this dissertation is to eliminate the structural uncertainties of one of the most complex iron-sulfur clusters, the iron-molybdenum cofactor of nitrogenase. The long-term goal of nitrogenase research is to understand all of the molecular-level details that enable biological nitrogen fixation, which may lead to alternatives to the fossil fuel-reliant, high temperature and pressure Haber-Bosch process for industrial nitrogen fixation. The research presented here is all based on computational chemistry, using primarily density functional theory with comprehensive experimental support from the literature. Computational chemistry can help explain experimental findings, and it can be used to probe structural and mechanistic details that cannot be observed through experiment; however, methods for theoretical modeling of iron-sulfur clusters must be developed before accurate results can be obtained. In this work, the best available methods (functionals, basis sets, and population analyses) are developed by comparing calculated properties of a series of model iron-sulfur complexes with experimental reference data. The newly recommended methods are then applied to a protein-embedded cluster, and the effects of the network of hydrogen bonds, dipoles, and electrostatic interactions are systematically probed. In addition to new insights regarding the role of the protein in tuning iron-sulfur cluster properties, an algorithm is derived for constructing computational models that capture all significant environmental effects. Future work will benefit from the foundations developed in these first two studies. The final work is a computational evaluation of the uncertain composition, charge, magnetic structure, and protonation state of the iron-molybdenum cofactor, based on a series of criteria defined by all available experimental data. The results show that the [Mo IV -2Fe II -5Fe III -9S ²- -C ⁴-] composition with hydroxyl-protonated homocitrate ligand is favored over the [Mo IV -4Fe II -3Fe III -9S ²- -N ³- ] composition preferred in the literature, adding new context to the many proposed mechanisms for biological nitrogen fixation.Item Synchrotron radiation-based spectroscopic investigation of the electronic and geometric structures of iron-sulfur clusters, particles, and minerals(Montana State University - Bozeman, College of Letters & Science, 2012) Gardenghi, David Jeremiah; Chairperson, Graduate Committee: Robert K. SzilagyiIron-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.