Browsing by Subject "Redox"

Now showing 1 - 5 of 5
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    Development, Mechanism, and Application of Titanium(II/IV) Catalysed C-N Bond Forming Reactions
    (2018-09) Gilbert, Zachary
    This thesis describes the development of titanium catalysed C-N bond forming reactions of alkynes and diazenes. These reactions proceed through a TiIV/II catalytic cycle and a unique diazene cleavage step. Chapter 1 details previous titanium redox reactions for the formation of CX bonds. Chapters 2 and 3 describe the discovery, development, and mechanism of the titanium catalysed [2+2+1] coupling of alkynes and diazenes for the synthesis of multisubsituted pyrroles. Chapter 4 describes the 3-component coupling of alkenes, alkynes, and diazenes in the synthesis of α,β-unsaturated imines and α-(iminomethyl) cyclopropanes. Finally, Chapter 5 describes the development of a benchtop stable catalyst system for a series of titanium catalysed C-N and C-C bond forming reactions.
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    Ferric Iron Partitioning between Pyroxene and Melt: Experiments, Microbeam analysis, and Consequences for Mantle Redox
    (2021-12) Rudra, Avishek
    Pyroxene is the chief reservoir of Fe3+ in upper mantle peridotite, but experiments exploring pyroxene/melt Fe3+ partitioning have been restricted to 100 kPa and pyroxene with low alumina. Here we present Fe3+ partitioning experiments between clinopyroxenes (cpx) and mafic melt at elevated pressures (1–2.5 GPa). Experiments were conducted with fO2 buffered and modulated by Ru+RuO2 and Fe-Pt alloy capsules, respectively, between ∆QFM -2.68 and +5.13. Fe3+/FeT of both cpx and melt were determined by Fe K-edge X-ray absorption near edge structure spectroscopy. The experimentally synthesized cpx compositions (Al2O3 = 2.36–6.01 wt.%, CaO = 19.33–22.21 wt.%) approximate those expected in basalt source regions. We find that Fe3+ is moderately incompatible in cpx and correlates with cpx Al2O3 content, increasing from 0.05±0.09 to 0.81±0.04. Comparison between experimentally synthesized cpx with those from natural peridotites indicates influences of both temperature and composition on Fe3+/FeT for cpx in spinel and garnet peridotites. The combined effects of decreased pyroxene Al2O3 concentration and pyroxene mode with progressive partial melting of peridotite diminishes the bulk partition coefficients of Fe3+, leading to greater Fe2O3 contents in high degree partial melts, and this accounts for an inverse relationship between Na2O and Fe2O3 observed in mid-ocean ridge basalts (MORB). Comparison to numerical experiments with pMELTS and the model of Jennings and Holland (2015) show that these models overpredict for partial melting of the mantle, and so they do not accurately determine the relationship between the fO2 and Fe2O3 of peridotite in basalt source regions. To estimate the Fe3+/FeT ratio of the mantle source of MORB, we modeled liquid Fe2O3 during isentropic batch melting of peridotite at three potential temperatures (1320 °C, 1400 °C, and 1440 °C) for peridotitic sources with Fe3+/FeT ratios between 0.02–0.06. A source with an Fe3+/FeT ratio of 0.038±0.007 matches most of the span of natural MORB. This ratio is similar to that typical of continental lithospheric mantle sampled by xenoliths, but lower than that surmised by several recent experimental and thermodynamic studies. Considering this source Fe3+/FeT but extending the partial melting calculations to higher pressures (2.5–4 GPa) reveals that bulk significantly decreases for garnet peridotite relative to spinel peridotite because the cpx become significantly less aluminous with increasing pressure. This results in high pressure partial melts with greater liquid Fe3+/FeT ratios. Therefore, elevated Fe3+/FeT ratios observed from some oceanic island basalts (OIB), such as those from Hawaii and Iceland, reflect in part the differences in conditions of melting and may not require mantle source regions more oxidized than those that produce MORB.
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    Interactions with Iron: Ferrous Iron Transport and Resistance in Shewanella oneidensis strain MR-1
    (2017-01) Bennett, Brittany
    All living cells have requirements for metals, largely for the catalytic functions of metalloenzymes and other metal-containing proteins. However, metals become toxic to cells at higher concentrations. Therefore, it is imperative that organisms maintain intracellular metal concentrations within a viable range. As such, cells have many means through which to import, export, store, and detoxify metals, in order to fine-tune the intracellular concentration and reduce the toxicity of each. Iron is one of the most-used metals in metalloproteins, due to both its abundance in the Earth’s crust and its redox flexibility. Easily reduced to the ferrous state (Fe2+) or oxidized to ferric state (Fe3+), iron is widely used in enzymes involved in electron transfer, such as cytochromes, or redox sensing, such as transcription factors. The importance of iron is underscored by the large number of cellular processes that have been discovered in all domains of life that regulate the concentration and usage of iron. Multiple transport systems, for example, mediate the influx and efflux of both Fe2+ and Fe3+. Additionally, the redox flexibility of iron and its midrange redox potentials make iron a potential substrate for anaerobic respiration. Shewanella oneidensis strain MR-1 is a dissimilatory metal-reducing bacterium that lives in the redox transition zones of aquatic sediments. S. oneidensis produces numerous cytochromes that allow it to respire a wide variety of substrates, including extracellular, insoluble Fe3+ compounds, which are reduced to Fe2+. Fe2+ is much more soluble than Fe3+ in physiologically relevant conditions; therefore, S. oneidensis must contend with increasing local concentrations of soluble Fe2+ as it continues to respire Fe3+. How S. oneidensis interacts with Fe2+ and resists Fe2+ toxicity is the subject of this thesis. The second and third chapters of this thesis describe two newly discovered Fe2+ transport proteins in S. oneidensis. The first, which has been named FeoE (ferrous iron export), is an Fe2+ exporter that reduces the intracellular Fe2+ concentration during Fe3+ respiration by S. oneidensis. FeoE belongs to the Cation Diffusion Facilitator superfamily of divalent metal efflux proteins, which includes transporters of Cd2+, Co2+, Cu2+, Fe2+, Ni2+, and Zn2+. Studies presented in this dissertation demonstrate that FeoE is exclusively an Fe2+ exporter. The transporter described in Chapter 3, which was named FicI (ferrous iron and cobalt importer), is an Fe2+ and Co2+ importer. FicI belongs to the Magnesium Transporter-E (MgtE) family of Mg2+ and Co2+ importers; this is the first discovery of an MgtE protein that imports Fe2+ and not Mg2+. FicI appears to represent a secondary Fe2+ importer active at higher Fe2+ concentrations. FicI doesn’t require nucleotide hydrolysis for Fe2+ import, unlike the primary Fe2+ importer FeoB, therefore allowing the cell to conserve energy under high Fe2+ conditions. The fourth chapter in this thesis concerns the ATP-dependent protease ClpXP. ClpXP has previously been found to be involved in various cellular functions in several bacterial species, including releasing stalled proteins from ribosomes and the regulation of sigma factors, which influence the transcription of large groups of genes. The work presented in Chapter 4 shows that ClpXP is needed for the resistance of S. oneidensis to higher concentrations of Fe2+, which does not appear to involve previously described functions of ClpXP. Data presented in Chapter 4 indicate that ClpXP may target metalloproteins during Fe2+ stress, a finding that implicates high Fe2+ concentrations in protein mismetallation and misfolding. Supplementary Tables S1 and S2 contain transposon screen and protein-trapping results, respectively, relevant to this chapter. The work in this thesis expands the knowledge of the ways in which S. oneidensis interacts with Fe2+, including its uptake and efflux, and presents a potential mode of Fe2+ toxicity under anoxic conditions. As iron is an essential metal to most living organisms, and as there are many microorganisms living in metal-rich environments, the work presented here is relevant both to the study of S. oneidensis and to microbiology in general. The protein families discussed here are highly conserved among many microorganisms, and their newly discovered functions in S. oneidensis are likely to apply in others as well. More broadly, this work presents several widely-conserved proteins that have been repurposed or given added functions to meet the needs of an organism in order for it to thrive in a particular environmental niche, which reflects the adaptive nature of evolution.
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    Natural products and their derivatives in cancer prevention and therapy: inositol phosphates and Illudin.
    (2009-10) Liu, Xiaodan
    Part I. Myo-inositol (Ins) and myo-inositol phosphates (InsPs) are widely distributed in plants and animals. The evaluation of Ins and InsPs distribution in cells and plant sources can impact the understanding of their role in nutrition, cellular processes and diseases, and how they may be modulated by diet. We developed an anion-exchange chromatography-tandem mass spectrometry (HPLC-ESI-MS/MS) method for the separation and simultaneous quantitation of Ins and different naturally occurring phosphorylated inositol compounds. Chromatographic separation was achieved in 30 min on a commercial anion exchange column (150 × 0.5 mm) using a gradient of 200 mM ammonium carbonate buffer (pH 9.0) and 5% methanol in H2O. Analytes were identified by selective reaction monitoring using a triple quadrupole mass spectrometer in negative ion electrospray mode. Adenosine 5'-monophosphate was used as a general internal standard for quantitation. Using this approach, Ins and InsPs were measured in three different plant samples and in cultured cell, illustrating significant differences in the distribution of inositol compounds in food sample compared to cells and between cell types. Ins and InsPs are cellular second messenger with potential roles in cancer prevention and therapy. It typically is difficult to attribute specific pharmacological activity to a single inositol phosphate because they are rapidly metabolized by phosphatases and kinases. We designed stable analogs of Ins(4,5)P2 and Ins(1,4,5)P3 that maintain the biological activity, but are phosphatase and kinase-resistant LC/MS/MS analysis of the enzyme-catalyzed reaction products indicates the phosphorothioate analog of Ins(1,4,5)P3 is stable towards alkaline phosphatase, and under the same condition, the natural ligand was extensively hydrolyzed. Analogs developed in this study are potential chemical probes for understanding mechanisms of inositol phosphate actions that may be elucidated by eliciting specific and prolonged activation of the Ins(1,4,5)P3 receptor. Part II. Acylfulvenes (AFs) are a class of antitumor agents with favorable cytotoxic selectivity profiles compared to their natural product precursor, illudin S. Illudin S readily reacts with thiol-containing small molecules such as cysteine, glutathione, and cysteine-containing peptides in slightly acidic pH (pH 6) in aqueous solution; reduced cellular glutathione levels can affect illudin S toxicity. However, AFs are less reactive towards these small thiols under the same conditions. By analogy, these compounds were proposed to have similar reactivity towards thiol-containing proteins, which may be responsible for AFs improved anticancer selectivity. The glutathione system (GSH and glutathione reductase (GR)) and thioredoxin system (thioredoxin reductase (TrxR) and thioredoxin (Trx)) are the major cellular redox-regulating systems that maintain cellular redox homeostasis, offering protection against oxidative stress. Disrupting this system will affect cell viability and lead to apoptosis. Furthermore, overexpression of thioredoxin and thioredoxin reductase in certain tumors is associated with higher proliferation capacities and lower apoptosis rates. The enzymes involved in these systems all have critical cysteine residues at the active site. The reactivities of illudin S and AFs toward these thiol-containing proteins were evaluated. The inhibition potency of illudin S and AFs is in the same order for GR, TrxR, and Trx, which is opposite what was expected based on their reactivity with small thiols, i.e., HMAF > AF > illudin S, however, both AFs irreversibly inhibit TrxR and Trx by targeting the active site cysteines. For GR, HMAF is an irreversible inhibitor, while AF is a reversible inhibitor. GR and TrxR share great structural and activity similarity, but TrxR has a selenocysteine (Sec) at the active site, which makes TrxR more reactive toward electrophiles. The IC50s for TrxR were in low micromolar range, while that for GR were hundred-fold higher. However, the presence of Sec is not the only reason in dictating the difference reactivity towards these two enzymes, since no covalent interaction occurs between AFs and glutathione peroxidase (Gpx), another redox-regulating enzyme containing Sec at active site. Furthermore, the inhibition of cellular GR and TrxR activity and reduction of Trx cellular protein level upon AFs treament suggest that they are AFs' cellular targets. Quenching of intrinsic fluorescence of GR and Trx suggests extensive conformational changes of by illudin S and AFs, which may facilitate the interaction between AFs and enzymes, but not the same case for illudin S. The differential reactivity of illudin S anda AFs towards these thiol-containing enzymes suggests that compared to small thiol-containing molecules, accessibility and reactivity of the enzyme active sites account for the inhibitory effects of AFs. The disruption of cellular redox systems by AFs may contribute to their improved anticancer selectivity compared to illudin S. The data obtained in this study are valuable in further understanding the role of modulating cellular redox enzymes in the anticancer effects of alkylating agents.
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    Numerical modeling of transport phenomena in reactive porous structures for solar fuel applications
    (2013-08) Keene, Daniel Joseph
    The focus of this work is the development and use of a numerical model to study solar thermochemical fuel production using nonstoichiometric ceria in the form of a reactive porous medium. Volume averaging theorems are applied at the pore-level to obtain a set of governing equations that use effective transport properties to describe the heat and mass transfer processes in the reactive porous medium on the macroscale. Reaction rate expressions are formulated for both the thermal reduction and oxidation steps as an interphase mass flux whose dependence on the partial pressures, solid temperature, and nonstoichiometry is derived from the ionization state of the oxygen vacancies.The porosity and pore-level solid feature size (as represented by a Sauter mean diameter) of a porous monolith are varied from 0.6 to 0.9 and 10 to 1000 μm, respectively, to determine their impact on the rate of oxygen release and the solar-to-chemical energy conversion efficiency during thermal reduction while the macroscale geometry and operating conditions are held fixed. The process is carried out in a batch mode by placing the reactive medium inside a cavity where it is directly irradiated with a concentrated solar flux as a sweep gas passes through its pore network. The best performance is obtained with a non-uniform heating of the solid, which is attributed to the nonlinear temperature dependence of the equilibrium nonstoichiometry. The solar-to-chemical energy conversion efficiency attains its highest value of 10.9 % with a porosity of 0.9 and a Sauter mean diameter of 10 μm. These results imply that high porosities and small feature sizes are preferred, but it is recognized and discussed that these findings are strongly tied to the particular set of operating conditions considered.The mathematical model is also used in conjunction with available experimental data to develop a method for determining a reaction rate expression that characterizes the oxidation of ceria by carbon dioxide. The volume-averaged conservation equations for the porous medium are used to simulate a packed bed of porous particles and the axially-dispersed plug flow model is used to compare numerical predictions of the effluent composition with experimental measurements. Reaction rate expressions are developed and their kinetic parameters are determined by minimizing the difference between the numerical predictions and the experimental measurements as quantified by a root mean square error for a temperature of 1203 K. At this temperature, numerical results obtained using a reaction rate expression based on singly ionized oxygen vacancies provide excellent agreement with the experimental data.