Chemistry electronic theses and dissertations (MU)
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The items in this collection are the theses and dissertations written by students of the Department of Chemistry. Some items may be viewed only by members of the University of Missouri System and/or University of Missouri-Columbia. Click on one of the browse buttons above for a complete listing of the works.
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Item On the formation of a new full-length DNA with non-canonical backbone by spermine mediated strand cleavage at abasic (AP) site in duplex DNA(University of Missouri--Columbia, 2024) Mahbub, Md Selim; Gates, Kent S.[EMBARGOED UNTIL 12/01/2025] Abasic (Ap) sites are among the most prevalent DNA lesions, resulting from the loss of a nucleobase. These sites exhibit chemical reactivity and can lead to strand cleavage via ?-elimination, which is catalyzed by various factors, including biological amines. In this study, we investigate the products formed during spermine-mediated strand cleavage at Ap sites. Spermine, a naturally occurring polyamine, facilitates the formation of a reactive ?,?-unsaturated iminium ion intermediate (3'ddR-Sp+) at the strand break. This intermediate reacts with exocyclic amine groups of nucleobases to produce unique low-molecular-weight interstrand crosslinks (LMW ICLs). In this thesis, we report the discovery of a novel "re-ligated" product formed through the 1,4-Michael addition of guanine's exocyclic amine group to the iminium ion intermediate. The ligated product exhibits remarkable stability under physiological conditions and resists cleavage by most human DNA repair enzymes, including APE1 and Fpg, but is effectively processed by bacterial endonuclease IV. Our findings highlight the biochemical consequences of spermine-mediated Ap site cleavage and reveal a previously unrecognized DNA lesion with potential implications for genomic stability and cellular repair mechanisms. These results provide critical insights into the reactivity of Ap sites and their repair pathways, advancing our understanding of DNA damage and its biological consequences.Item Advancements in green chemistry approaches to chemical synthesis(University of Missouri--Columbia, 2024) Virdi, Jagdeep Kaur; Handa, Sachin[EMBARGOED UNTIL 12/01/2025] Green chemistry approaches in chemical synthesis aim to reduce environmental impact while improving the efficiency and sustainability of chemical processes. In this work, we present two significant advancements in this field. First, the introduction and development of a non-pyrophoric version of Raney-nickel (Ra- Ni) by modifying the catalyst's surface. Raney nickel is renowned for its high catalytic activity in a variety of transformations. Predominantly, it is used to reduce unsaturated hydrocarbons and various functional groups. However, in anhydrous form, it is highly flammable when exposed to air, which makes it unsafe to use. To mitigate this issue, we have developed a non-pyrophoric version of Ra-Ni that is easier to handle in powder form. It can be weighed easily and requires no pre-activation procedures. The modified version of Ra-Ni is recyclable and catalytically active under mild conditions in water. The catalyst structure was characterized by scanning transmission electron microscopy (STEM), high- resolution transmission electron microscopy (HRTEM), and X-ray photoelectron spectroscopy (XPS). Its activity was tested on various transformations, such as the hydrogenation of quinolines, chalcones, and substituted 1,10-phenanthroline. The catalytic process is safe and sustainable as we have mitigated its flammability hazard, making it more suitable for potential large-scale industrial applications. The second advancement was modifying the PS-750-M amphiphile by replacing its mPEG part with a sugar molecule to enable chemistry in water. Water is regarded as an eco- friendly, sustainable, and cost-effective solvent for organic synthesis. However, conducting organic reactions in water presents significant challenges, primarily due to the poor solubility of substrates and catalysts. To solve this issue, as of now numerous non-ionic designer surfactants are developed for efficient organic transformations in water. Notably, most of surfactant molecules contain polyethylene glycol as its hydrophilic part. For instance, in vitamin E derived TPGS-750-M by Lipshutz's group and L-proline based PS- 750-M from Handa's group, polyethylene glycol moiety as a hydrophilic part may not be biodegradable. Therefore, a second-generation PS-750-M (2nd Gen-PS) is developed as an alternative of polyethylene glycol (PEG)-based surfactant. The synthetic protocol for this newer version is simple, scalable, and derived from economical sources such as L-proline, lauroyl chloride, and N-methyl glucamine. This surfactant is compatible with various organic transformations in water and has been characterized by NMR spectroscopy and dynamic light scattering. By incorporating another sustainability feature to micellar catalysis, we contribute to sustainable and eco-friendly chemical processes as well as reducing reliance on toxic solvents by their usage.Item Light-mediated synthesis of azepine-linked peptide macrocycles(University of Missouri--Columbia, 2024) Heidarzadeh Vazifehkhorani, Hossein; Outlaw, Victor K.[EMBARGOED UNTIL 12/01/2025] Conformationally constrained macrocyclic peptides exhibit improved stability, target affinity, and cell permeability compared to their linear counterparts, making them excellent candidates for drug development. This unique class of compounds holds significant pharmaceutical promise, and consequently, numerous peptide cyclization methods have been developed to optimize these properties. In this work, we introduce a straightforward, visible light-induced cyclization method that selectively creates a covalent bond between a seven-membered ring ketenimine intermediate and a lysine residue, yielding an azepine-linked cyclic peptide. We successfully synthesized a library of cyclic peptides ranging from 4 to 10 residues with good to moderate isolated yields. To further demonstrate the chemoselectivity of this method, several cyclic peptides containing various reactive side chains were synthesized and isolated, also achieving good to moderate yields. Additionally, we tested the compatibility of our method with a more complex 13-residue p53-derived peptide, which resulted in successful cyclization. Finally, three cilengitide-type cyclic peptides containing RGD residues were designed and synthesized using our method and are set to be evaluated for anti-cancer activity. Each starting linear peptide, and its corresponding cyclic product was characterized by high-resolution mass spectrometry, and purity was confirmed through analytical HPLC. H1NMR experiment was conducted for one of the Linear peptides and its cyclic peptide counterparts, proving the successful formation of cyclic form peptide.Item State specific collision dynamics of vibrationally excited nitric oxide at collision energies over five orders of magnitude(University of Missouri--Columbia, 2024) Perera, Dissanayakege Chatura Anuranga; Suits, Arthur G.[EMBARGOED UNTIL 12/01/2025] This thesis presents studies on rotationally inelastic collisions of highly vibrationally excited NO molecules prepared in single rotational and parity levels at v=9 and v=10 using stimulated emission pumping (SEP). This state preparation is employed in a recently developed crossed molecular beam apparatus. This thesis reports scattering studies involving three different beam geometries: near- copropagating, near-counterpropagating, and intrabeam configurations. These configurations enabled tuning collision energies spanning over five orders of magnitude. The near-copropagating and intrabeam geometry of the molecular beams permitted very wide tuning of the collision energy, from far above room temperature down to 1 K where we test the theoretical treatment of the attractive part of the potential and the difference potential. Two superthermal collision energies ~ 1 eV were achieved using near-copropagating beam geometry. We have obtained differential cross sections for state-to-state collisions of vibrationally excited NO with Argon (Ar), Neon (Ne) and Krypton (Kr) in both spin-orbit manifolds using velocity map imaging (VMI). in general, overall good agreement of the experimental results was seen with quantum mechanical close- coupling calculations done on both coupled-cluster and multi-reference configuration interaction potential energy surfaces. Probing cold collisions of NO carrying a ~2 eV of vibrational excitation allows us to test state-of-the-art theory in this extreme nonequilibrium regime.Item Computational study of ionic liquids/electrode interfacial reactions for environmental and energy applications(University of Missouri--Columbia, 2024) Glossmann, Tobias; Zeng, Xiangqun[EMBARGOED UNTIL 12/01/2025] Electrochemistry in Ionic Liquid (IL) electrolytes is an area of research with significant opportunity for innovation and of high relevance for environmental and energy applications. While computational chemistry methods exist and have continuously evolved over recent decades and contributed significantly to providing complementary information and insight for experimental physical science, there is relatively limited knowledge about applying them for electrochemical problems. This is due to the complication of the heterogeneous electrochemical interface and system. It is more challenging to apply computational methods to understand electrode/IL interface reactions and processes since ILs and/or IL containing electrolytes, owing to their unique nature of ions interacting with other ions, analytes, solvent molecules, and electrodes, add additional complexity to the current methods. This dissertation addresses important aspects of this challenge by taking three topics of electrochemistry with IL-based electrolytes and systematically leverages computational tools to advance the fundamental understanding of these IL based electrochemical systems. This approach leads to advancements of theoretical considerations regarding IL electrochemistry and to progress in the practical implementation of respective calculations. The first research subject is to understand the detail mechanisms of the dissociative reduction of trichloroethylene (TCE), which is important for TCE remediation. Computational approaches are proposed and used for the study of reaction pathways of TCE in an IL/acetonitrile mixed electrolyte. Systematic considerations of the thermodynamics, kinetics, and electrolyte structure related issues are included in the computational study. The second research subject is understanding the CO2 physical chemistry such as conductivity, mass density, and structure of the IL and their impact on CO2 solubility and adsorption that are valuable for the development of real time and continuous CO2 sensor applications. Computational methods are utilized to understand the mechanism that leads to selective impedance variation upon CO2 and methane exposure. The third research topic is dedicated to further computational methods for the study of CO2 and N2O reduction in IL electrolytes. Bulk, and surface structures of electrolyte, as well as the reaction pathways of CO2 and N2O reductions in these electrochemical systems are investigated, and novel methods to study gaseous molecules' redox chemistry in the IL electrolytes are developed, based on computational chemistry. With each of the model problems based on IL and/or IL containing electrolytes, calculation methods were proposed, implemented, and refined. The results of this work contribute to the advancement of computational chemistry to the complex field of IL and electrode interface electrochemistry, which offers solutions to critical environmental and energy related challenges.