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Item Development and characterization of a novel isothermal DNA amplification reaction(Montana State University - Bozeman, College of Engineering, 2021) Ozay, Burcu; Chairperson, Graduate Committee: Scott McCalla; This is a manuscript style paper that includes co-authored chapters.Isothermal nucleic acid amplification chemistries are gaining popularity as nucleic acid detection tools that can replace the current gold standard methods, PCR and its derivatives, with their simplicity, speed and applicability to point-of-care applications. In this work, we have developed and characterized a novel isothermal amplification chemistry, ultrasensitive DNA amplification reaction (UDAR). UDAR differs from similar chemistries with its unique, biphasic response with a high-gain output that can be captured with a cell-phone camera. The switch-like, nonlinear characteristics provide a definitive on/off signal for potential use in applications such as molecular diagnostics and DNA circuits. Tunability of the reaction was explored and the relationship between thermodynamic properties of the reaction templates and the reaction output was established. Limitations on fluorescent staining of reaction components by two popular commercial nucleic acid stains, SYBR Green II and SYBR Gold, were determined for a more accurate evaluation of the reaction output and reaction product analysis. A mathematical model of the reaction output was built and outputs from three different UDAR templates were successfully simulated. This model revealed important information on reaction pathways and helped identify the impact of individual reaction events. A comprehensive literature review of enhancement strategies for isothermal amplification reactions was conducted to serve as a guide to improve and modify these reactions according to different needs and applications. Lastly, UDAR was applied to microRNA detection, which are putative biomarkers for diseases such as cancer, malaria, and traumatic brain injury. Five different miRNAs were successfully detected by UDAR, down to 10 fM concentration. UDAR-based miRNA quantification is possible, with linear calibration curves provided between 10fM and 1 nM. This work has significant contributions to the growing field of isothermal nucleic acid amplification based-molecular detection systems by introducing a unique isothermal amplification chemistry, establishing design and manipulation techniques, and guiding improvement efforts of these technologies.Item Mechanistic studies and new methodologies relevant to palladium-catalyzed chemodivergent cross-coupling reactions(Montana State University - Bozeman, College of Letters & Science, 2021) Reeves, Emily Kathryn; Chairperson, Graduate Committee: Sharon NeufeldtPalladium-catalyzed cross-couplings are powerful methods for constructing new carbon-carbon bonds in organic molecules. While the mechanism of these reactions are generally well studied, complexities are introduced when the starting materials involved in the reaction contain several possible sites at which the new C-C bond can be made. It is often desirable for the palladium catalyst to facilitate (chemo)selective cross-coupling at just one of the reaction sites while leaving the other(s) intact. This can be challenging and often requires extensive tuning of the palladium catalyst and the reaction conditions. In this work, we describe efforts to better understand the properties causing palladium catalysts to react chemoselectively at aryl chloride (C-Cl) or triflate (C-OTf) reaction sites. Using a combined approach of computational and experimental chemistry, we demonstrate that solvent plays a critical role in the reaction selectivity by coordinating to the palladium catalyst and promoting reaction at C-OTf sites via formation of bisligated palladium. Anionic additives like inorganic bases play a complementary role in promoting reaction at C-OTf sites. We additionally describe efforts to develop new chemodivergent cross-coupling methodologies using palladium-N-heterocyclic carbene precatalysts. These catalysts demonstrate robust reactivity under mild conditions, allowing for a greatly expanded scope of chemoselective cross-coupling products, especially biaryl triflates.Item Gas-surface interactions with sp 2 carbon in extreme environments(Montana State University - Bozeman, College of Letters & Science, 2018) Murray, Vanessa Jean; Chairperson, Graduate Committee: Timothy Minton; Brooks C. Marshall, Philip J. Woodburn and Timothy K. Minton were co-authors of the article, 'Inelastic and reactive scattering dynamics of hyperthermal O and O 2 on hot vitreous carbon surfaces' in the journal 'Journal of physical chemistry C' which is contained within this thesis.; Eric J. Smoll Jr. and Timothy K Minton were co-authors of the article, 'Dynamics of graphite oxidation at high temperature' in the journal 'Journal of physical chemistry C' which is contained within this thesis.; Marcin D. Pilinski, Eric J. Smoll, Jr., Min Qian, Timothy K. Minton, Stojan M. Madzunkov and Murray R. Darrach were co-authors of the article, 'Gas-surface scattering dynamics applied to concentration of gases for mass spectrometry in tenuous atmospheres' in the journal 'Journal of physical chemistry C' which is contained within this thesis.; Neil A. Mehta is an author and Chenbiao Xu, Deborah A. Levin and Timothy K. Minton were co-authors of the article, 'Scattering dynamics of N 2 from highly oriented pyrolytic graphite' in the journal 'Journal of physical chemistry C' which is contained within this thesis.; Chenbiao Xu, Savio Poovatthingal and Timothy K. Minton were co-authors of the article, 'Scattering dynamics of nitromethane and methyl formate on HOPG' submitted to the journal 'Journal of physical chemistry C' which is contained within this thesis.Molecular beam scattering experiments can determine the relative importance of reactive and non-reactive processes that occur when a surface is bombarded with high energy atoms and molecules. The mechanisms by which these processes proceed are inferred by analyzing the angle-resolved flux and energy distributions of the scattered products. The studies presented in this thesis have been conducted with a crossed molecular beams machine reconfigured for surface scattering. Two molecular beam sources were used. One uses a laser detonation process to produce high translational energy O atoms in the ground electronic state, and the other uses a supersonic expansion to produce continuous beams of N 2, nitromethane, or methyl formate. In the first two studies presented in this thesis, the oxidation of dynamics vitreous carbon and highly oriented pyrolytic graphite (HOPG) held at surface temperatures in the range of 800 - 2300 K by O atoms with a translational energy of ~ 500 kJ mol -1 are presented. These two studies revealed that the reactivity is suppressed at high temperature because O atoms desorb from the surface before they react to form CO and CO 2. Even though the translational energy of the O atoms was high, the surface reactions proceeded primarily through reactions that occurred in thermal equilibrium with the surface. The third study focuses on the scattering dynamics of O, O 2, and Ar with the surfaces of a gold thin-film, SiO 2, and HOPG. The results of the experiments were used to evaluate the efficacy of a proposed gas concentrator. The strong forward scattering on the HOPG surface made it the most suitable surface for the gas concentrator. The fourth study examines the non-reactive scattering dynamics of N 2 with HOPG. At high surface temperature, the residence time of N 2 is too short for the molecule to fully accommodate to the surface. Thus, even if the molecule suffers multiple collisions with the surface, it will scatter into the vacuum before it can come into thermal equilibrium with the surface. The results have been used in conjunction with theoretical calculations by a collaborator to investigate the relationship between the potential energy surface and the scattering dynamics. In order determine the usefulness of an HOPG concentrator with complex molecules, the scattering dynamics of methyl formate and nitromethane on HOPG were studied. These molecules do not shatter upon impact with the surface and they both scatter strongly in the forward direction through direct and indirect mechanisms, suggesting that the proposed HOPG concentrator should perform as desired. In all studies described in this thesis, the fundamental gas-surface scattering dynamics were elucidated from molecular beam experiments, and these fundamental results have direct links to modeling the performance of hypersonic vehicles and designing a gas concentrator for mass spectrometry in tenuous atmospheres.Item Interactions of Rh(I) and Pd(II) with cyclopropanes in rigid systems : kinetics, product analyses and mechanisms(Montana State University - Bozeman, College of Letters & Science, 1984) Taylor, Richard BruceItem Ethereal oxygen influences on solvomercuration and hydrogenation reactions(Montana State University - Bozeman, College of Letters & Science, 1983) Glancy, Steven BenItem A study of the kinetics of the oxidation of maleic hydrazide by ferricyanide in basic aqueous solution \ Robert Baxter Miller.(Montana State University - Bozeman, College of Letters & Science, 1969) Miller, Robert BaxterItem Reaction of iridium with cyclopropanes contained in rigid ring systems(Montana State University - Bozeman, College of Letters & Science, 1983) Campbell, William Henry; Chairperson, Graduate Committee: Paul W. JenningsThe reaction of IrCl(CO)(Ph 3P) 2 (Vaska's catalyst) with cyclopropane moieties contained within rigid ring systems was investigated. A variety of substrates were investigated, and several were labeled with deuterium. The results show that exocyclic methylene products predominate in most cases, but a diversity of other products was also obtained. Analysis of products demonstrates a great deal of regioselectivity of reaction. Further, mechanistic pathways leading to products are varied and highly dependent on the electronic and steric environment provided by the substrate. Endocyclopropane compounds seem to be more reactive (when chloroform is used as the reaction solvent) than their exo-counterparts. Catalytic reaction is enhanced in the presence of oxygen and when chloroform is used as the reaction solvent, but regioselectivity of reaction is somewhat decreased. Olefin products and substrates are capable of reaction with Vaska's catalyst and have been shown to establish a dynamic equilibrium in some cases.