Department of Chemistry Graduate Theses
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Item Surfaces with Switchable Wettability for Anti-Smudge and Antimicrobial Applications(2025-01-03) Shum, Rachel Lok-Ting; Chemistry; Liu, GuojunThe increase in surface disinfectant usage has raised concerns regarding overexposure and environmental contamination, driving a growing interest in developing antimicrobial coatings. For long-lasting antimicrobial performance, coatings should incorporate contact-active, surface-attached biocides and exhibit durability. Surfaces equipped with immobilized biocides eliminate bacteria on contact without releasing harmful agents, addressing the limitations of conventional disinfectants that require frequent reapplication and contribute to environmental pollution. These coatings provide a more sustainable and long-lasting alternative to traditional surface disinfectants. In this work, we explore the synthesis, formulation, and functional properties of inorganic-organic hybrid coatings engineered to deliver dual functionalities: anti-smudge and antimicrobial performance, while achieving high hardness and flexibility. The coatings are based on a photocurable, double-grafted copolymer system, [L-(QAS)], where the graft copolymer AS consists of poly(dimethyl siloxane) (PDMS, S) grafted onto quaternized (Q) poly(dimethylaminoethyl methacrylate) (PDMAEMA, A), which is then grafted onto a ladder-like polysilsesquioxane (ELASQ, L) backbone. Formulated from 2-(3,4-epoxycyclohexyl)ethyltrimethoxysilane, L-based coatings exhibit enhanced hardness combined with flexibility, characteristic of inorganic-organic hybrid materials. The double-grafted copolymer architecture enables controlled surface reconstruction upon exposure to moisture, allowing the coating’s surface properties to adapt in response to environmental conditions. In air, the coatings demonstrate effective anti-smudge properties, attributed to the presence of hydrophobic PDMS chains at the surface. Upon contact with droplets carrying bacterial E. coli cells, the surface undergoes reconstruction, exposing quaternary ammonium groups that disrupt bacterial membranes, providing potent antimicrobial activity. This work comprehensively examines the factors influencing the formulation, smudge resistance, surface reconstruction, and antimicrobial performance of these hybrid coatings, positioning them as promising candidates for durable, multifunctional surface protection in diverse applications.Item Sequential Enantioselective Iridium-Catalyzed Allylic Alkylation/Cope Rearrangement for the Construction of Acyclic γ-Tertiary or Quaternary Stereocenters(2024-12-16) Xie, Hengmu; Chemistry; Evans, P. AndrewFunctionalized carbonyl compounds with extended chiral carbon chains are commonly found in natural and synthetic bioactive molecules. However, catalytic asymmetric γ-functionalization of carbonyl derivates is challenging because of the issues with ontrolling chemo- (O vs. C), regio- (α vs. γ), and enantioselectivity. In this way, enantioselective transition metal-catalyzed γ-allylic alkylation reactions have attracted increasing attention, albeit they are typically restricted to cyclic nucleophiles. A direct strategy to construct acyclic γ-allylated carbonyl derivates is underdeveloped due to the challenging regio- and enantiocontrol, especially for constructing quaternary stereocenters. In this regard, an innovative strategy that sequential enantioselective iridium-catalyzed allylic alkylation/Cope rearrangement to provide an efficient method approach to acyclic γ-tertiary and quaternary stereocenters. The following thesis is divided into four chapters, which encompass a comprehensive literature review followed by two research chapters, further divided based on the type of transformation discussed. Chapter 1 commences with a brief introduction to the enantioselective catalytic γ-functionalization of carbonyl derivates, which is followed by a comprehensive review divided into two major subsections based on the type of pronucleophiles, namely homoenolate and dienolate equivalents, which are further subdivided into cyclic and acyclic nucleophiles. Chapter 2 highlights the development of enantioselective iridium-catalyzed γ-allylic alkylation of acyclic pronucleophiles. This chapter begins with a review of the iridium-catalyzed allylic substitution reactions, which includes seminal examples. While direct enantioselective iridiumγcatalyzed allylic alkylation at γ-position remains a significant challenge. Hence, we developed an indirect enantioselective iridium-catalyzed γ-allylic alkylation with a broad range of acyclic α,β-iii unsaturated cyanoacetates, and allylic carbonates, which can efficiently construct acyclic γ-tertiary stereocenters at mild conditions. Chapter 3 illustrates the development of a sequential enantioselective iridium-catalyzed allylic alkylation/Cope rearrangement for the construction of acyclic γ-quaternary stereocenters. This chapter opens with a review of the historical development of the construction of acyclic quaternary stereocenters, which are limited to adjacent positions of carbonyl groups. Then, our approach involves iridium-catalyzed γ-allylic alkylation of a series of acyclic disubstituted α,β-unsaturated malononitrile for the construction of quaternary stereocenters via a sequential α-allylic alkylation and in situ Cope rearrangement. Chapter 4 highlights some future works.Item Discovery and Characterization of New Thermostable Nylon-Degrading Enzyme from Thermomicrobiales bacterium(2024-12-05) Heo, Jun; Chemistry; Howe, GraemeA crucial step in the biodegradation of solid polymers is their conversion to soluble oligomers or monomers. In the context of polyamide hydrolysis, NylB, one of the three types of nylonase, functions as an Ahx-oligomer exohydrolase. This thesis reports the characterization of a novel thermostable NylB from an unclassified Thermomicrobiales bacterium, dubbed TmbB, which was identified through targeted genome mining for thermostable polyamide-degrading enzymes. To confirm that our targeted genome mining led to the identification of a thermostable protein, melting point assays conducted with SYPRO Orange revealed TmbB to have a melting temperature of 59 °C. It exhibited a half-life of thermal inactivation of 1.89 hours at 60 °C and the optimal conditions for hydrolyzing Ahx oligomers were found to be pH 8.0 and 50 °C. The catalytic ability to hydrolyze amide bonds was first measured using p-nitrophenyl hexanamide as the amide substrate and the kinetic analysis demonstrated that TmbB has a KM of 0.4 ± 0.09 mM and a kcat of 0.08 ± 0.008 s-1 with this small molecule. To evaluate the hydrolytic activity of TmbB on nylon mimics and authentic nylon substrates, a UPLC-MS-based assay was used to characterize the degradation of several substrates harboring different amide bonds, including nylon-6 and nylon-6,6 polymers, the dimer of nylon-6 and related small molecule (6-hexanamido-N-hexylhexanamide), and laurolactam. TmbB demonstrated activity towards all linear amides but not laurolactam, suggesting that TmbB, like other NylBs, cannot catalyze the hydrolysis of cyclic amides. TmbB hydrolyzed 2.3 % of a 10 mM solution of nylon-6 dimer in 24 hours, whereas complete conversion was observed with 6-(hexanoyl amino) hexanoic acid. Although TmbB is unlikely to be efficient enough to make bio-based nylon recycling competitive with the production of fresh nylons, enzyme engineering and directed evolution could be used to develop variant TmbBs that are catalytically efficient enough to be employed as nylon-degrading biocatalysts.Item Towards Creating Methods to Enzymatically Degrade Plastic Waste(2024-11-21) Yamoa, Maame Yaa Safoa; Chemistry; Zechel, DavidPlastics are versatile and durable materials with a wide range of uses. A lot of plastics are designed to be discarded, and the reusable plastics are eventually worn out and are also discarded. Their durability has caused a problem as they are difficult to dispose of when they are out of use. The bulk of the created plastic waste remains in landfills and can run into water sources. Recycling and chemical methods of managing plastic waste can be energy intensive processes and can require the use of chemicals that are also difficult to dispose of after use.Their durability has caused a problem as they are difficult to dispose of when they are out of use. Biological degradation could be included as a less energy intensive method of plastic disposal. Bacteria and fungi that can be sustainedmetabolize by compounds similar to with structures similar to the structures of plastics (e.g. oil and polyethylene having similar structures) contain enzymes that can be modified to degrade plastic. Plastic degradation starts can startwith eitherby hydrolysing the larger polymer structurstructure (hydrolytically sensitive plastics), or by functionalising polymers that cannot be hydrolysed (hydrolytically inert plastics). Plastics such as polyethylene terephthalate and polyamides have carbonyl groups that can be targeted for hydrolysis. Plastics such as polyethylene and polypropylene need to be hydroxylated and oxidised to be hydrolysed. Cytochrome P450 enzymes are a diverse class of enzymes that function primarily as monooxygenases. The P450 enzyme isolated from Bacillus megaterium was found to hydroxylate fatty acids and BM3 has been engineered to hydroxylate alkanes and has the promiscuity to act on substrates with longer carbon chains similar to polyethylene. We fused the enzyme to a phosphite dehydrogenase to regenerate NADPH which the P450 uses as a cofactor. It is has been found to hydroxylate alkanes. Some esterases and lipases have been shown to hydrolyse polyethylene terephthalate. As more polyethylene terephthalate hydrolyzing enzymes are discovered and engineered, a visual plate screening system can be used to streamline the selection procedure for enzymes that are tested. Agar homogenised with polyethylene terephthalate PET can be used to show enzyme degradation. Expressing and purifying the enzyme might be too time consuming, so the enzymes were fused to protein with a secretion tag, YebF, to be expressed in E. coli. This fusion protein gets secreted onto a plate 3-PET supplemented plate. The active polyethylene terephthalate hydrolyzing enzymes enzymes formed a halo around the E. coli. colonies.Item Approaching the Complexity of Biological Specimen: New Mass Spectrometry Concepts in Ambient Ionization and Proteomics(2024-10-28) McPhail, Julia; Chemistry; Oleschuk, RichardMass spectrometry (MS) is a powerful analytical technique that allows for the identification and quantification of molecules within a sample and therefore a valuable technique when analyzing complex biological specimen. Herein, two MS techniques in ambient ionization and proteomics are utilized to explore new concepts in food samples. First, a proof-of-concept is carried out with the liquid micro-junction surface sampling probe (LMJ-SSP), a liquid extraction-based ambient ionization probe, by replacing the tip with a 21-gauge needle. This creates the sharpened-LMJ-SSP, allowing for subsurface and depth profiling of limes. Lime layer characterization is performed using data-dependent acquisition, identifying important compounds such as malic acid, citric acid, and quinic acid. Depth profiling is performed by constructing an automated syringe pump system, where the sharpened-LMJ-SSP can be inserted into a lime at a constant speed, while monitoring the change in product ion at m/z 133.0 and m/z 191.0. The change in product ion is successfully monitored and this investigation shows promise for the sharpened probe. Second, different sample preparation methods are performed for high-throughput high-resolution mass spectrometry protein characterization of human milk. Human milk samples are fractioned into skim milk, milk fat globule membrane, whey, and casein using low and ultra centrifugation methods. In-gel digest, in-solution digest, and filter aided sample preparation (FASP) methods are performed. Additional variations in sample preparation were explored such as performing an acetone precipitation prior to digestion, different size filter membranes, and utilizing sodium dodecyl sulfate in FASP to determine the optimal sample preparation method.