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Item Radical S-adenosyl-L-methionine enzymes: radical control and assembly of complex metallocofactors(Montana State University - Bozeman, College of Letters & Science, 2018) Byer, Amanda Shaw; Chairperson, Graduate Committee: Joan B. Broderick; Elizabeth C. McDaniel, Stella Impano, William E. Broderick and Joan B. Broderick were co-authors of the article, 'Mechanistic studies of radical SAM enzymes: pyruvate formate-lyase activating enzyme and lysine 2,3-aminomutase' in the journal 'Methods in enzymology' which is contained within this dissertation.; Masaki Horitani was an author and Krista A. Shisler, Tilak Chandra, Joan B. Broderick and Brian M. Hoffman were co-authors of the article, 'Why nature uses radical S-adenosyl-L-methionine enzymes so widely: electron nuclear double resonance studies of lysine 2,3-aminomutase show the 5'-dADO 'free radical' is never free' in the journal 'Journal of the American Chemical Society' which is contained within this dissertation.; Hao Yang, Elizabeth C. McDaniel, Venkatesian Kathiresan, Stella Impano, Adrien Pagnier, Hope Watts, Carly Denler, Anna Vagstad, Jorn Piel, Kaitlin S. Duschene, Eric M. Shepard, Thomas P. Shields, Lincoln G. Scott, Edward A. Lilla, Kenichi Yokoyama, William E. Broderick, Brian M. Hoffman, and Joan B. Broderick were co-authors of the article, 'New paradigm for radical SAM enzyme reactions: organometallic intermediate Omega is central to catalysis' in the journal 'Journal of the American Chemical Society' which is contained within this dissertation.; Eric M. Shepard was an author and Priyanka Aggarwal, Jeremiah N. Betz, Krista A. Shisler, Robert J. Usselman, Gareth R. Eaton, Sandra S. Eaton, Joan B. Broderick were co-authors of the article, 'Hydrogenase maturase HydF: insights into [2Fe-2S] and [4Fe-4S] cluster communication and hydrogenase activation' in the journal 'Biochemistry' which is contained within this dissertation.; Eric M. Shepard, William E. Broderick and Joan B. Broderick were co-authors of the article, 'Activation of [FeFe]-hydrogenase in the absence of HydG' which is contained within this dissertation.; Donald S. Wright, Michael W. Ratzloff, Yisong Guo, Paul W. King and Joan B. Broderick were co-authors of the article, '[FeFe]-hydrogenase metallocluster assmebly on HydF as influenced by HydG' which is contained within this dissertation.; Amanda Shaw Byer is not the main author of an article which is contained within this dissertation.Electrons, whether from carbon-based radicals or metals, can generate oxidative stress and disease in biological systems; however, when directed properly by a protein, these electrons are responsible for crucial life-sustaining reactions, including photosynthesis, oxygen transport in blood, and nitrogen fixation. Beneficial use of radicals and metallocofactors is abundant in nature, and both are essential in one of the largest superfamilies in biology - the radical SAM (RS) enzyme superfamily. Found in all kingdoms of life, RS enzymes contribute to critical processes such as DNA repair, complex metallocluster assembly, and vitamin synthesis. Understanding how metalloenzymes, such as RS enzymes, control electron flow is critical for comprehending biological system functionality and potentially improving productivity through rational design. This work examines radical control in RS enzyme mechanism and then expands scope to consider RS enzyme contribution to assembly of the complex metallocluster (Hcluster) of [FeFe]-hydrogenase. Focusing in on the fundamental chemistry of RS enzyme radical initiation, this work investigated intermediate states in 5'deoxyadenosyl radical formation by: 1) slowing the radical reaction with a SAM analogue, anSAM, and 2) swiftly stopping catalysis via rapid freeze quench techniques. Employing primarily EPR and ENDOR spectroscopies, two intermediate states were characterized: 1) an analogue of the 5'-deoxyadenosyl radical, formed from anSAM, and 2) an organometallic intermediate, Omega, formed during reaction with SAM. To probe how certain RS enzymes (HydE and HydG) contribute to build the 2Fe H-cluster subcluster precursor on the [FeFe]-hydrogenase scaffold HydF, FeS cluster intermediate states were analyzed using UV-Vis, EPR, FTIR, CD, Mossbauer spectroscopies and gas chromatography. These results demonstrate: 1) HydF initially binds a [4Fe-4S] and a [2Fe-2S] cluster, 2) HydG contributes small molecule diatomics and perturbs the [2Fe-2S] cluster environment, 3) HydE can generate a subcluster precursor on HydF capable of generating catalytically active HydA, and 4) the HydF dimer, not tetramer, delivers the 2Fe H-cluster subcluster precursor for activation. Collectively, this thesis illuminates key mechanistic states RS enzymes use to productively control the 5'deoxyadenosyl radical during catalysis and identifies [FeFe]-hydrogenase H-cluster precursor intermediates suggesting RS enzyme sequentiality.Item Biocorrosion of 1018 steel in sulfide rich marine environments: a correlation between strain and corrosion using electron backscatter diffraction(Montana State University - Bozeman, College of Engineering, 2014) Martin, Joshua Daniel; Chairperson, Graduate Committee: Paul E. GannonMicrobially induced corrosion (MIC) of steel due to the presence of sulfide is a leading cause of pit formation of carbon steel in fuel-seawater environments. While extensively studied, the exact causes of pitting corrosion in naval fuel tanks when exposed to MIC in the presence of fuel and seawater are not completely understood. This thesis focuses on the role that cold-rolling of carbon steel plays on corrosion while subjected to sulfidogenic, suboxic corrosive environments. Particularly, the effects of microscopic residual strain found within 1018 steel on the anodic dissolution of the metal is studied in different MIC sulfide environments using EBSD, AFM, FE-SEM, EDX, and electrochemistry. It is found that regions of increased plastic deformation of the crystalline lattice as a result of cold rolling correlate to an increase in anodic dissolution rates of 1018 steel coupons cut parallel to rolling direction. Image overlay provides a verification of the location of corrosion of samples to the same locations found in EBSD mapping taken prior to corrosion, ensuring the predictive value of EBSD analysis in establishing locations of accelerated corrosion. The effect of different corrosion environments on the corrosion rate of steel is measured through electrochemistry. Values obtained through these measurements are applied using mechanochemical theories to predict the localized dissolution rate of the steel due to strain using computational methods. Mechanochemical analysis of the strained areas results in predicted corrosion rates within an order of magnitude of the corrosion rates measured using AFM for the exposed time period at the same locations. Areas exhibiting increased corrosion rates occur in areas exhibiting increased strain as measured by EBSD analysis. Further electrochemical results show an increase in corrosion rates for suboxic sulfide rich systems containing low levels of oxygen, when compared to anaerobic sulfide environments. Variations in corrosion current density as a function of oxygen presence, as measured by electrochemistry, accurately predict variations in mechanochemical corrosion rates of strained areas well within an order of magnitude. Results from this study support the use of EBSD as a means to further the understanding of pitting corrosion as a function of material properties.Item Epitaxial thin film deposition of magnetostrictive materials and its effect on magnetic anisotropy(Montana State University - Bozeman, College of Letters & Science, 2012) McClure, Adam Marc; Chairperson, Graduate Committee: Yves U. Idzerda; Steven Albert, Tino Jaeger, Hongyan Li, Paul Rugheimer, Juergen A. Schaefer and Yves U. Idzerda were co-authors of the article, 'Properties of single crystal Fe 1-xGa x thin films' in the journal 'Journal of applied physics' which is contained within this thesis.; Elke Arenholz and Yves U. Idzerda were co-authors of the article, 'Ferrimagnetic ordering of single crystal Fe 1-xGa x thin films' in the journal 'Journal of vacuum science and technology A' which is contained within this thesis.; Hongyan Li and Yves U. Idzerda were co-authors of the article, 'Magnetostrictive effect in single crystal Fe 1-xGa x thin films' in the journal 'Journal of applied physics' which is contained within this thesis.; Paul Rugheimer and Yves U. Idzerda were co-authors of the article, 'Magnetic and structural properties of single crystal Fe 1-xZn x thin films' in the journal 'Journal of applied physics' which is contained within this thesis.Magnetostriction means that the dimensions of a material depend on its magnetization. The primary goal of this dissertation was to understand the effect of magnetostriction on the magnetic anisotropy of single crystal magnetostrictive thin films, where the epitaxial pinning of the material to a substrate could inhibit its conversion to new dimensions. In order to address this goal, several Fe-based binary alloys were deposited onto various substrates by molecular beam epitaxy. The samples were characterized by an array of techniques including electron diffraction, Rutherford backscattering, vibrating sample magnetometry, ferromagnetic resonance, and x-ray absorption spectroscopies. The attempted growths of crystalline magnetostrictive thin films resulted in successful depositions of Fe 1-xGa x and Fe 1-xZn x. Depositions onto MgO(001) substrates result in an in-plane cubic magnetic anisotropy, as expected from the cubic symmetry of the Fe-based thin films, and a strong out-of-plane uniaxial anisotropy that forces the magnetization to lie in the plane of the films. Depositions onto ZnSe/GaAs(001) substrates feature an additional in-plane uniaxial anisotropy. The magnitudes and signs of the in-plane anisotropies depend on the Ga content. Furthermore, the cubic anisotropy constant of Fe 1-xGa x samples deposited onto MgO substrates switches sign at a lower Ga concentration than is seen in bulk Fe 1-xGa x. The effect on the magnetic anisotropy of depositing a magnetostrictive material as an epitaxial thin film is influenced by the material's magnetostrictive properties and the substrate upon which it is deposited. In particular, pinning a magnetoelastic material to a substrate will modify its cubic anisotropy, and depositions on substrates compliant to an anisotropic strain relaxation may result in a strong in-plane uniaxial anisotropy.