Department of Chemistry Graduate Theses

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    Synthesis of Mixed Ladder-Like Polysilsesquioxanes by Copolymerization of 2-(3,4-Epoxycyclohexyl)ethyltrimethoxysilane and Dodecyltrimethoxysilane
    (2024-03-27) Wolpert, Adam Michael; Chemistry; Liu, Guojun
    Epoxycyclohexyl- and dodecyl-bearing ladder-like polysilsesquioxanes (EDLASQs) are synthesized through the hydrolysis and co-condensation of 2-(3,4-epoxycyclohexyl)ethyltrimethoxysilane (ECTMS) and dodecyltrimethoxysilane (DTMS). Such copolymerization reactions are traditionally conducted in tetrahydrofuran and water containing K2CO3 as catalyst. The differing water compatibilities of the two monomers cause their reaction rates to differ drastically, making their random copolymerization impossible. In this work, we demonstrate that sodium dodecyl sulfate, a surfactant, can be used to improve water dispersion in monomers, thus increasing the area of the monomer/water interfaces and the reaction rates of the more hydrophobic DTMS monomer. This study presents results of polymerization kinetics from varying conditions and compositions as well as characterization data for the synthesized EDLASQs. Cured coatings of EDLASQs at E/D molar ratios of 8/1 and 6/1 exhibit both high hardness (> 1.0 GPa) and enhanced water repellency. The proposed method should be useful for synthesizing other co-LASQs.
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    Developing a Novel Antibiotic Resistance Detection Method for Water Systems using IDEXX TECTA Technologies
    Cole, Allison; Chemistry; Brown, R. Stephen; She, Zhe
    Regular surveillance of water in the environment is essential for identifying hazardous contaminants, including antimicrobial-resistant (AMR) bacteria. These bacteria not only present a significant risk to public health but also impose considerable economic costs. Traditional methods for detecting resistance, though effective, are hindered by slow results, the need for intensive labor, specialized training, costly equipment, and a lack of portable, dependable alternatives 26. Consequently, there exists a substantial gap in our understanding of current AMR prevalence in natural settings, which obscures the levels of human exposure. This thesis presented an adaptation of the IDEXX TECTA system, a device already instrumental in identifying fecal bacteria within 18 hours, bypassing the need for preliminary bacterial culture steps. By evaluating its capability to detect resistance in typical fecal indicators like E. coli and coliforms, specifically against the widely used antibiotic ampicillin, this research aimed to pioneer a novel, readily deployable approach. The TECTA was used to explore viable E. coli concentrations at varying antibiotic concentrations and to analyze different growth kinetics according to the degree of resistance. Compared to conventional tests, the TECTA device showed highly agreeable results, with simplified steps and turnaround times of 18 hours. The TECTA used with ampicillin was able to discriminate the relative resistance of three E. coli strains using the time-to-detection values provided by the device, as well as bacteria concentration and fraction of inhibition. The TECTA device also shows potential for use in real-world samples as determined by mixed culture experiments.
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    The Liquid Microjunction-Surface Sampling Probe as an Emerging Tool for Medicinal Mass Spectrometry
    McKeown, Mark J.; Chemistry; Oleschuk, Richard
    Ambient ionization mass spectrometry (AIMS) is an attractive technique for providing supplementary information that medical professionals can use to guide clinical decisions. The group of techniques includes ionization methods, such as desorption electrospray ionization (DESI) and rapid evaporative ionization mass spectrometry (REIMS) that, when combined with mass spectrometry (MS) analyze thousands of compounds (e.g., highly polar/non-volatile, non-polar/volatile analytes) within resected tissues. From these compound profiles, one can distinguish between healthy and diseased states on a cellular level. Tissue analysis by MS is difficult to perform as it is challenging to obtain the required data from these specimens while minimizing the loss of information from time-dependent metabolomic changes. Despite technological advances, many AIMS techniques are limited in processing speed, analyte extraction, and sample restraints for widespread clinical utility. Herein, the liquid microjunction- surface sampling probe (LMJ-SSP) is investigated in profiling and imaging MS to directly interrogate fresh tissue surrogates of various sizes/shapes/thicknesses. A previously developed conductive feedback system is enhanced and used with the probe to produce four-dimensional (4D) images that describe the topography and chemistry of uneven surfaces using the LMJ-SSP. The platform enables the analysis of these tissue specimens with absolute height variations of up to centimeters, and the ability to monitor the dynamics of changing surfaces. Secondly, the versatility of the LMJ-SSP is explored to profile underwater tissue surrogates. To this end, normal saline solutions (water and 0.9% sodium chloride, weight by volume [w/v]) are typically used to temporarily maintain tissue integrity before analysis. The two described workflows use a low miscible solvent to directly interrogate these specimens immersed in saline solutions or extract compounds from saline microenvironments. Submerged analytes are still identifiable for their molecular weights at high salt concentrations (0 - 3.5% NaCl, w/v). Underwater analysis of an insoluble compound reveals the effects of salt on electrospray ionization (ESI). The LMJ-SSP provides the speed of information needed to revolutionize patient care and outcomes.
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    The Study of the Activation of Primary Terminal C-H Bonds by Rieske Oxygenase Enzymes and the Identification of a Serine Protease with Anti-nociceptive Activity
    Ramachandra, Manasa; Chemistry; Ross, Avena
    The first project in this thesis focused on the study of the activity of Rieske oxygenase enzymes, TamC and PtTamC. Tambjamines are methoxy-bipyrrole alkaloids isolated from marine invertebrates and bacteria, and possess several biologically useful properties. The first cyclic analogue, tambjamine MYP1, was isolated from a marine bacterium, Pseudoalteromonas citrea (also proposed to exist in Pseudoalteromonas tunicata). TamC and PtTamC, both Rieske oxygenase enzymes (ROs), are proposed to catalyse the cyclisation of tambjamine YP1, a linear analogue, to tambjamine MYP1. The macrocyclisation in MYP1 would involve a C-C bond formation at a primary carbon atom (terminal methyl) of the alkyl chain in YP1. This cyclisation activity was successfully demonstrated by the heterologous co-expression of TamC or PtTamC along with the identified redox partner enzymes of TamC, PcFdx and PcRed, in Escherichia coli, followed by substrate-feeding assays with synthesised tambjamine YP1 and tambjamine BE-18591 as substrates. These are the first reported C-C bond formations being initiated at the terminal methyl group of an alkyl chain in oxidative cyclisations and therefore, the first successful activation of an unreactive terminal C(sp3)-H bond in an oxidative carbocyclisation reaction catalysed by the RO enzymes, TamC and PtTamC. TamC, PtTamC, and PcRed were also successfully heterologously expressed and purified. The goal of the second project was the identification of serine proteases with anti-nociceptive activity from Faecalibacterium prausnitzii. Inflammatory bowel disease (IBD) induces hyperexcitability in dorsal root ganglion (DRG) nociceptors contributing to abdominal pain. Proteases modulate nociceptive signals in abdominal pain via activation of cell-surface receptors present on sensory neurons. Recent findings indicate that serine proteases from F. prausnitzii, a gut commensal bacterium, can reduce DRG neuron excitability, thereby suppressing abdominal pain. Genome mining and structure simulation tools led to the heterologous expression and purification of three proteases with potential anti-nociceptive activity. Patch clamp experiments conducted by our collaborators at Queen’s University led to the identification of a single protease with anti-nociceptive activity. The successful identification, expression, and purification of the anti-nociceptive serine protease, Clp-fp, from F. prausnitzii is the first step in the microbial modulation of IBD-related abdominal pain.
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    The Development of the Controlled-Atmosphere Flame Fusion Methodology for the Growth of Nickel Single Crystals and the Interplay between the Oxidation of Nickel and the Hydrogen Oxidation Reaction in Alkaline Media
    Esau, Derek M.; Chemistry; Jerkiewicz, Gregory
    Nickel (Ni) and Ni-based materials have become promising alternatives to the platinum group metals that are currently used in sustainable energy technologies. To improve the fundamental knowledge of Ni electrochemistry, Ni single crystal electrodes that have highly ordered surface arrangements of atoms were used. The development of the controlled atmosphere flame fusion methodology as part of this thesis work has allowed for bench top growth of poly-oriented spherical single crystals (POSSCs) of non-noble metals. Ni POSSCs were oriented, cut, and polished to produce hemispherical monocrystalline electrodes (Ni(hkl)), namely, Ni(111), Ni(100) and Ni(110). The surfaces were then characterised using cyclic voltammetry (CV) in solutions outgassed with nitrogen gas (N2(g)) in 0.10 M aqueous NaOH solution at a potential scan rate (s) of 50.0 mV s-1 and temperature (T) of 295 K. Each Ni(hkl) had a unique electrochemical response for the formation and reduction of α‒Ni(OH)2 and β‒NiOOH. Due to the importance of inductive heating for the pre-treatment of Ni(hkl), the technique was described in detail, including the relevant theory of electromagnetism, heat conduction and radiation emission with temperature. This was followed by a discussion of practical, experimental considerations to best utilize inductive heating and examples of the electrochemical response of a Ni(111) with varying degrees of surface oxidation. Lastly, the influence of s on the formation and reduction of α‒Ni(OH)2, and the hydrogen oxidation reaction (HOR) in 0.10 aqueous NaOH at T = 298 K was studied. The CV response in electrolyte that was outgassed with N2(g) and saturated with hydrogen gas (H2(sat.)) with s = 1.00, 2.00, 5.00, 10.0, 20.0, 50.0 and 100 mV s-1 in the potential range of ‒0.20 V ≤ E ≤ 0.50 V was studied. In solution outgassed with N2(g), the analysis suggests that Ni is likely partially covered by α‒Ni(OH)2 with sections of metallic Ni at the peak. In H2(sat.) electrolyte, the HOR occurs after the formation α‒Ni(OH)2 and allowed us to propose the “bifunctional mechanism” for the HOR. This work has provided valuable experimental methodology to produce Ni(hkl) cheaply and effectively, but also valuable fundamental information about the electrochemistry of monocrystalline Ni electrodes.