Theses and Dissertations from UMD
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Item DESIGN AND SYNTHESIS OF NEW SULFONATED CNN LIGAND SCAFFOLDS FOR PLATINUM CATALYZED H/D EXCHANGE APPLICATIONS(2023) Kramer, Morgan; Vedernikov, Andrei N; Chemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)The use of platinum group metals for the activation and functionalization of C-H bonds has been a topic of substantial interest over the past 60 years. Specifically, platinum-based complexes represent a particularly promising avenue due to their ability to form air- and water-stable species that are capable of reacting with some of the most inert C-H bonds within organic substrates. Over the decades of research contributing to this field, platinum complexes have frequently been angled towards fundamental mechanistic analysis of homogeneous C-H bond activation. In turn, the development of homogenous PtII-based catalytic systems has remained underdeveloped for the practical applications in C-H bond functionalization and, in particular, deuteration of complex organic molecules, including pharmaceuticals. The latter direction is now attracting a significant interest by the pharmaceutical industry. In this work the kinetic and thermodynamic selectivity of our new catalyst, a Pt(II) sulfonated CNN-pincer complex 1.5, in the H/D exchange reaction between aromaticsubstrates and wet TFE-d1 was screened across thirty-four aromatic substrates with the catalysts TON up to 300 (Chapter 2). A kinetic preference of 1.5 for electron-rich C-H bonds and substrates was firmly established and a novel scale of Hammett-like σXM constants was introduced to characterize the reactivity of the substrates’ C(sp2)–H bonds in transition-metal-mediated C-H activation. To greatly enhance our PtII catalysts’ useful life, we used their rigid covalent immobilization to mesoporous silica nanoparticles (immobilized complex 3.5). The resulting robust material served as an efficient H/D exchange catalyst utilizing cheaper sources of exchangeable deuterium, AcOD-d4, and D2O, with the catalyst’s TON up to 1600 (Chapter 3). To understand our novel catalyst’s structure – activity relationship, a series of benzene fragment – R-substituted analogs of 1.5 (R = MeO, tBu, iPr, F, Cl, CF3) were synthesized and explored in the H/D exchange of a series of aromatic compounds (Chapter 4). Surprisingly, the complex 4.1-tBu (R = tBu) stood out as a most robust homogeneous catalyst compatible with AcOD-d4 and D2O at 120 oC as deuterium sources that can work under air. Thanks to this finding, the substrates scope for the H/D exchange with AcOD-d4 catalyzed by 4.1-tBu was expanded to include eight pharmaceuticals, some alkenes, with signs of engagement of some C(sp3)-H bond donors. A novel photo-induced (violet light) room temperature H/D exchange catalyzed by 4.1-OMe was discovered with a substantially different substrate selectivity, as compared to the thermal reaction at 80 oC. These observations may provide some important insight into the mechanism of PtII-mediated C-H activation. Finally, Chapter 5 summarizes the results of this work and suggests some future directions for this area of research.Item COMPUTATIONAL ANALYSIS OF METABOLIC NETWORKS AND ISOTOPE TRACER EXPERIMENTS FOR METABOLIC FLUX EVALUATION IN COMPLEX SYSTEMS(2021) Lugar, Daniel James; Sriram, Ganesh; Chemical Engineering; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Metabolic engineering endeavors seek to develop microorganisms as feedstocks for biofuels and commodity chemicals. Towards this, quantifying metabolic fluxes is an important step for characterizing an organism’s metabolism and designing effective engineering strategies. Metabolic fluxes are quantified using sophisticated techniques, namely flux balance analysis (FBA), an in silico technique, and isotope-assisted metabolic flux analysis (MFA), a hybrid experimental and computational technique. FBA uses a network’s stoichiometry with linear programming techniques to generate in silico flux predictions for genome-scale networks. MFA uses measurements from stable isotope (typically 13C) tracer experiments to estimate fluxes of central carbon metabolism. In MFA, fluxes are parameters to a model developed from the network’s carbon atom rearrangements, which is fit to isotope labeling data, typically acquired using mass spectrometry.We developed novel mathematical and computational techniques for quantifying and analyzing flux predictions obtained using MFA and FBA. FBA applications typically generate flux predictions for networks with on the order of 1000 [O(1000)] reactions and metabolites. We developed a network reduction algorithm that uses matrix algebra to reduce a large network and flux prediction to a smaller representation. From this reduced representation, a researcher may quickly gain holistic insights from the FBA model. In isotopically nonstationary MFA, time-series labeling measurements are acquired on the approach to steady state. A model consisting of a large system of typically O(1000) ordinary differential equations is fit to the measurements to estimate fluxes and pool sizes. For detailed networks, the number of parameters may be large. We developed a computationally effective framework for solving this problem having robust convergence and efficient scalability to large networks. In this approach, we formulate the problem as an equality-constrained nonlinear program (NLP), solved efficiently using a solver implemented on an algebraic modeling language. Finally, we apply this approach to a detailed model of Phaeodactylum tricornutum photoautotrophic and mixotrophic (on acetate) metabolism. Using the flux estimates, we characterized this organism’s metabolism under disparate growth conditions, which may inform future endeavors to engineer P. tricornutum as a chemical feedstock.Item Metabolic Flux Analysis for Metabolic Engineering of Marine Organisms(2018) Quinn, Andrew Higgins; Sriram, Ganesh; Chemical Engineering; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)We explored the metabolic pathways in two industrially relevant marine microorganisms to understand their core metabolic capabilities. It is necessary to track how an organism distributes organic building blocks throughout its metabolic pathways so that we can devise strategies to alter its metabolism and reroute substantial metabolic flux towards target compound(s). Though we cannot measure intracellular metabolic fluxes directly, we can retro-biosynthetically calculate them by supplying substrates labeled with non-radioactive isotopes to an organism. We then measure the resulting isotope labeling patterns of metabolites and calculate the fluxes that produced them. We addressed three goals with our research, (i) resolving questions surrounding organic carbon metabolism in the diatom Phaeodactylum tricornutum (P. tricornutum), (ii) identifying reactions in a putative photosynthetic carbon concentrating mechanism in P. tricornutum and (iii) mapping central carbon metabolism of the cellulolytic aerobe Saccharophagus degradans (S. degradans). Towards goal (i) we show that P. tricornutum predominantly consumes glucose, as opposed to atmospheric CO2, under mixotrophic conditions using the Entner-Doudoroff (ED) glycolytic pathway instead of the more common Embden-Meyerhof-Parnas pathway (EMP). We utilized metabolic flux analysis (MFA) to discover that acetate is metabolized for energy production instead of for biomass formation during mixotrophic growth on CO2 and acetate. Finally, we developed a method for measuring isotopic labeling in polyunsaturated fatty acids via gas chromatography-mass spectrometry (GC-MS), and demonstrated its utility in resolving outstanding questions about glucose metabolism by P. tricornutum. Towards goal (ii) we utilized isotope labeling and gene silencing in combination to identify pyruvate carboxylase as a key enzyme in a C4 carbon concentrating mechanism in P. tricornutum, while also ruling out phosphoenolpyruvate carboxylase as a key enzyme in the pathway. Towards goal (iii) we present 13C-MFA of aerobic consumption of glucose, xylose, and cellobiose by S. degradans. This is the first reported MFA of cellobiose metabolism and one of only a handful analyzing xylose metabolism in an aerobic microorganism.