Chemistry - Theses, Dissertations, and other Required Graduate Degree Essays

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Permeability of water through polymer membranes and porous electrodes

Author: 
Date created: 
2020-12-17
Abstract: 

Water sorption and transport through hydrocarbon (HC)-based polymer electrolyte membranes (PEMs) and porous electrodes are vital for water management and performance improvements of fuel cells. This thesis is the culmination of three research projects conducted into an extensive water sorption and transport study, including steady-state permeation, transient diffusion, and sorption isotherm on a series of novel HC-based PEMs. Numerical models, such as the Park model for sorption isotherm and the resistance model for steady-state permeation, were chosen and applied to interpret the membranes’ chemical and structural features. Conductive atomic force microscope (AFM) and surface roughness measurement were applied to examine the membranes’ physical properties. Collectively, transport measurements, numerical models, and characterizations were integrated to generate an insightful structure-transport correlation. The first project studies sulfonated phenylated poly(phenylene) biphenyl (SPPB) and compares it to a HC-based reference, sulfonated phenylated poly(arylene ether), and the commercial benchmark, Nafion. At thickness > ~30 μm, SPPB is the most permeable due to its lowest internal resistance coefficient. The second research involves four structurally controlled, one-element-variant, pyridyl-bearing sulfonated phenylated polyphenylenes. An increase in the number of pyridyl groups increases the fraction of neutralized protons in –SO3H groups, and decreases polymer’s ion exchange capacity, proton conductivity, liquid and vaporous water sorption, dimensional swelling, steady-state water permeability, and transient diffusivity. The third investigation expands the research focus to the catalyst layers incorporated with the novel HC-based ionomers. A lower ionomer content of SPPB in the catalyst layer favors a larger water vapor uptake and faster transient diffusion rate. Specifically, the catalyst layer of 15 wt% ionomer SPPB is found possessing the best electrochemical performance with the most hydrophilic and the roughest surface. Insights obtained in this thesis can direct further tuning of the HC-based polymer’s structure for desirable mass transport through both the membrane and the catalyst layers, which subsequently lead to electrochemical performance improvements of the fuel cell.

Document type: 
Thesis
File(s): 
Supervisor(s): 
Steven Holdcroft
Department: 
Science: Department of Chemistry
Thesis type: 
(Thesis) Ph.D.

Cytochrome P450cam (CYP101A1) mutants to study dehalogenation of endosulfan: A persistent organic pollutant, and oxidation of β-phellandrene: A monoterpene

Author: 
Date created: 
2021-05-06
Abstract: 

Cytochrome P450cam (CYP101A1) from the soil bacterium Pseudomonas putida oxidizes camphor regio- and stereoselectively at the 5-position, to give 5-exo¬-hydroxycamphor. In order to alter the substrate range of P450cam, it has to be mutated. Previously, we have randomly mutated P450cam and selected seven mutants on the bicyclic polychlorinated pollutant endosulfan (ES). Endosulfan is a pesticide and is a persistent organic pollutant (POP). Endosulfan diol (ES diol), which is the major hydrolysis product of endosulfan in the environment, is also persistent in the environment, along with endosulfan itself. Here, we describe the activity of the P450cam mutants towards biodegradation of endosulfan diol. The P450cam mutants convert these substrates to substituted ortho-quinones, which we detected using 4-aminoantipyrine (4-AAP) in the assays. Here, we have studied the dehalogenation of endosulfan diol catalyzed by the endosulfan – selected P450cam mutants, using in vitro kinetics, chloride release assays and 13C labeled endosulfan diol. ES7 (V247F/D297N/K314E) was found to be the most active mutant, significantly more active than the wild type (WT) towards biodegradation of ES diol. On average ~ 5.2 Cl- ions are released per aromatic product detected upon turnover of ES diol. Based on these findings, we propose a mechanism that begins with the epoxidation of the ES-substrate’s double bond on the norbornene system, proceeds with elimination of six chloride ions and loss of the bridge as CO2, to furnish the ortho-quinone. The monoterpene β-phellandrene is released by certain species of pine when placed under stress. Due to the limited supply of β-phellandrene available from natural sources, here we describe a short synthesis of racemic β-phellandrene from readily available β-pinene. Furthermore, oxidized monoterpenes are known to be released by plants and to function as attractants or repellents of insects, so it is of interest to find ways of selectively oxidizing β-phellandrene. The compound was found to be a substrate for WT-P450cam and the ES7 mutant. In in vitro assays with the cytochrome P450cam, β-phellandrene was hydroxylated.

Document type: 
Thesis
File(s): 
Supervisor(s): 
Erika Plettner
Department: 
Science: Department of Chemistry
Thesis type: 
(Thesis) Ph.D.

Polymer self-assembly and thin film deposition in supercritical fluids

Author: 
Date created: 
2021-04-12
Abstract: 

Patterning of flexible electronic devices using large-area printing techniques is the focus of intense research due to their promise of producing low-cost, light-weight, and flexible devices. The successful integration of advanced materials like semiconductor nanocrystals, carbon nanotubes and polymer semiconductors into microscale electronic devices requires deposition techniques that are robust, scalable, and enable fine patterning. To this end, we have established a deposition technique that leverages the unique solubility properties of supercritical fluids. The technique is the solution-phase analog of physical vapour deposition and allows thin films of a semiconducting polymer to be grown without the need for in-situ chemical reactions. To demonstrate the flexibility of the technique, we demonstrated precise control over the location of material deposition using a combination of photolithography and resistive heating. The versatility of the technique is demonstrated by creating a patterned film on the concave interior of a silicone hemisphere, a substrate that cannot be patterned via any other technique. More generally, the ability to control the deposition of solution processed materials with lithographic accuracy provides the long sought-after bridge between top-down and bottom-up self-assembly. In addition, we investigated the self-assembly of polymers in supercritical fluids by depositing thin films and studying their morphology using polarized optical microscopy and grazing incidence wide angle x-ray scattering. We summarized our observations with a two-step model for film formation. The first step is pre-aggregation in solution whereby the local crystalline order is established, and the solution turbulence can easily disrupt the solution-phase self-assembly. The second step to film formation is the longer length scale organization that is influenced by the chain mobility on the surface. We identified pressure and solvent additive as two powerful tools to facilitate the local crystalline order and longer length scale organization. The work demonstrated key insights necessary to optimizing thin-film morphologies and principles for understanding self-assembly in supercritical fluids that could be applied to self-assembly of materials in other contexts. Finally, we developed a simple empirical model based on classical thermodynamics that highlights the interplay of intermolecular interactions and solvent entropy and describes both the temperature and pressure dependence of polymer solubility in supercritical fluids.

Document type: 
Thesis
File(s): 
Supervisor(s): 
Loren Kaake
Department: 
Science: Department of Chemistry
Thesis type: 
(Thesis) Ph.D.

Investigation of free radicals in clathrate hydrates using electron paramagnetic resonance spectroscopy

Author: 
Date created: 
2021-03-19
Abstract: 

Gas hydrates (or clathrate hydrates) are well-defined crystalline structures that consist of a host lattice of hydrogen-bonded water molecules partially or fully loaded with guest molecules. Guest molecules are located in the cavities formed by water molecules. In this research, the double hydrates of a thiol and another organic compound were synthesized in a gas handling system constructed in our lab. A UV diode was used to irradiate the sample hydrates mounted in an EPR spectrometer in order to produce isolated hydrogen atoms and other free radicals inside the hydrate cavities. Hydrogen atoms can diffuse freely between cages above the diffusion temperature and react with the organic molecules in other cages to produce organic radicals which can be detected by EPR. In this research, the temperature at which hydrogen radicals can be stabilized inside the cavities is determined. This is important because gas hydrates are being considered as a future storage material for hydrogen molecules.

Document type: 
Thesis
File(s): 
Supervisor(s): 
Paul Percival
Department: 
Science: Department of Chemistry
Thesis type: 
(Thesis) M.Sc.

The design of novel benzoin acetate photolabile protecting groups

Author: 
Date created: 
2021-01-14
Abstract: 

Photoremovable protecting groups are powerful tools for the release or deprotection of a wide range of molecules. Benzoin type photoremovable protecting groups are renowned for their exceptional properties but have been significantly underdeveloped. This thesis concerns the design, synthesis, and evaluation of four molecules in the benzoin class. A review of the benzoin photolabile protecting group is presented in Chapter 2. The first study, featured in Chapter 3, revisits the fundamental photochemistry of the 3’,5’-dimethoxybenzoin acetate photolabile protecting group and explores that of two polyaromatic derivatives. In a second study, Chapter 4, the unique photochemistry of a donor acceptor 4-dimethylamino-3’,5’-dimethoxybenzoin photocage is examined. The implications of the deviation of this photorelease from all known mechanistic pathways are discussed. A second donor-acceptor derivative 4-methoxy-3’,5’-dimethoxybenzoin was designed to combine the traditional photochemistry of dimethoxybenzoin acetate with the advantageous properties of the previous donor acceptor species

Document type: 
Thesis
File(s): 
Supervisor(s): 
Neil Branda
Department: 
Science: Department of Chemistry
Thesis type: 
(Thesis) M.Sc.

Chemical proteomics tools for probing carbohydrate processing enzymes

Author: 
Date created: 
2020-04-24
Abstract: 

The modification of proteins with O-linked N-acetylglucosamine (O-GlcNAc) is a nucleocytoplasmic modification that is present on over a thousand different protein targets. This post-translational modification is conserved among multicellular eukaryotes and has been found to play diverse physiological roles within cells. Remarkably, O- GlcNAc levels are globally controlled by only two enzymes; O-GlcNAcase (OGA) and O- GlcNAc transferase (OGT). How this modification is regulated on the large set of target substrates by just these two enzymes remains a topic of high interest within the field. In this thesis, I describe the development of a chemical proteomics method to interrogate OGA that help move the field toward elucidating the factors that regulate this enzyme. Specifically, I describe the creation of four distinct affinity-based probes that bind with high affinity to OGA and enable its precipitation at endogenous levels from tissues. These probes are designed to enable precipitation of OGA and its protein partners under gentle conditions followed by precipitation on streptavidin-coated beads. The disulfide linker that can be cleaved using gentle conditions enables release of OGA-containing protein complexes. Using these probes in a parallel series of experiments, I define a set of high confidence candidate OGA interacting proteins that are seen in multiple data sets from mass spectrometry-based proteomic analyses of the chemoproteomic precipitates obtained from bovine brain tissue. In addition, I detail targeted discovery of post- translational modifications on OGA from bovine brain tissue obtained using one of these new chemoproteomic probes. I envision this approach can ultimately be applied to identifying factors that regulate OGA activity within cells and provide a blueprint for robust chemoproteomics strategies that harness the use of multiple probes having distinct chemical structures.

Document type: 
Thesis
File(s): 
Supervisor(s): 
David Vocadlo
Leonard Foster
Department: 
Science: Department of Chemistry
Thesis type: 
(Thesis) M.Sc.

Developing tools to study carbohydrate processing enzymes in AmpC β-lactamase antibiotic resistance and OGA-based neurodegenerative research

Author: 
Date created: 
2020-12-18
Abstract: 

Carbohydrates are one of the four main classes of biological macromolecules in nature, alongside lipids, proteins, and nucleic acids. They serve in a wide range of cellular functions fundamental to the existence of biological organisms. These functions include but are not limited to cellular metabolism, energy production and storage, structural support, signaling, and recognition. The ubiquitous presence of carbohydrates in organisms has led to the study of their role in various maladies, such as neurodegenerative and infectious diseases. Deciphering the role of carbohydrates in these diseases allows for the possibility of developing treatments for associated diseases. In this manner, it is necessary to develop tools to exploit and test our understanding of these mechanisms. Existing methodologies may need to be adapted for application to larger scale experimental designs, such as those used in chronic dosing studies using preclinical animal models or high-throughput automated screening assays. This thesis describes improvements to previously published methods in the synthesis of one such chemical tool, Thiamet-G, a small molecule inhibitor used to study the carbohydrate processing enzyme O-GlcNAcase, which has been linked to neurodegenerative diseases including Alzheimer’s and Parkinson’s Disease. This thesis also seeks to apply the concepts developed during creation of a live cell assay towards creation of a new experimental approach suitable for large scale high through-put screening of compound libraries. Such an application would allow for the efficient pursuit of inhibitors of the bacterial protein AmpG - a transporter that is essential for inducible AmpC β-lactamase-driven antibiotic resistance.

Document type: 
Thesis
File(s): 
Supervisor(s): 
David Vocadlo
Department: 
Science: Department of Chemistry
Thesis type: 
(Thesis) M.Sc.

Structure-property relationships in sterically-congested proton-conducting poly(phenylene)s: The impact of backbone linearity

Author: 
Date created: 
2020-04-09
Abstract: 

Decarbonatization of the World’s primary energy supply is becoming increasingly more important due to a rapidly changing climate. A hydrogen-based economy offers a potential means of zero-carbon energy production through the use of fuel cells and water electrolyzers. The development of robust, thermochemically-stable hydrocarbon-based proton exchange membrane materials that resist swelling for use in these devices represent a significant hurdle in their commercial adoption. In this thesis, the structure-property relationship of hydrocarbon-based sulfonated phenylated poly(phenylene) proton exchange membranes possessing either angled or linear backbone moieties is discussed. Polymers were synthesized using either bent (ortho or meta), or linear (para) biphenyl linkages and evaluated for differences in physical and electrochemical properties. Model compounds, structurally-analogous to the polymers, were prepared and characterized using spectroscopic and computational methods to elucidate structural differences and potential impacts on the properties of the respective polymers. A highly angled ortho biphenyl linkage resulted in a sterically hindered, rotationally-restricted molecule. When incorporated into a homo-polymer, the angled ortho biphenyl moiety was found to prevent membrane formation. The angled meta biphenyl-containing homo-polymer, while forming a membrane, exhibited a 74% increase in volumetric expansion, 31% reduction in tensile strength, and 72% reduction in the elongation at break when compared to the linear para biphenyl-containing analogue. The differences observed are attributed to a rotationally-restricted backbone in the angled biphenyl systems. Co-polymers containing a small fraction (≤5%) of the ortho or meta biphenyl linkage in an otherwise para biphenyl containing system were found to have a significantly lower degree of swelling than those containing solely para biphenyl linkages. Collectively, the work presented in this thesis suggests that incorporating angled biphenyl linkages into sulfonated phenylated poly(phenylene)s leads to highly rigid, inflexible backbones that prevents chain entanglement and the formation of free-standing membranes.

Document type: 
Thesis
File(s): 
Supervisor(s): 
Steven Holdcroft
Department: 
Science: Department of Chemistry
Thesis type: 
(Thesis) M.Sc.

Evaluating the effects of 1-allyloxy-4-propoxybenzene on the parasitic mite Varroa destructor and synthesis of fluorescent probes to visualize the binding location(s) of the active compound in the mite

Author: 
Date created: 
2020-12-16
Abstract: 

Varroa destructor is a serious threat to the eastern honey bees, Apis melliferra. The available varroa controls are either ineffective due to resistance of varroa mites or require correct temperatures for efficacy and are labour intensive. To search new effective varroa control agents, 15 compounds were assesed for the acaricidal activities like paralysis and death, against varroa mites in laboratory bioassays. The data from structure-activity assays revealed that allyloxy and propoxy groups at the para position of a benzene-based structure, are necessary for the acaricidal activities tested. Compound 1-allyloxy-4-propoxybenzene, known as 3c{3,6}, showed the highest acaricidal activites from a group of 15 compounds tested . Activity of 3c{3,6} was the same as that of thymol, a widely used varroa control agent in structure-activity relationship studies. 3c{3,6} prevented the mites from staying on the abdomen of bees, which is a major feeding site of the mites. The active compound 3c{3,6} initially paralyzed the mites and eventually a high number of the mites were observed on the surface of the glass dishes used for bioassays. The varroa acetylcholine esterase (VdAChE) was not inhibited by 3c{3,6} and hence, we conclude that VdAChE is not a target of 3c{3,6}. Fluorescent probes in which the structure of 3c{3,6} was modified with a linker, and the linker was attached either to a fluorescein or a rhodamine fluorophore, were synthesized to visualise the target binding location(s) in the mites. All probes showed variable acaricidal activies against varroa mites. The fluorescein-containing compound, 6-FAM probe-2, had similar acaricidal activities as 3c{3,6}. The confocal images highlighted fluorescent signals in the regions of the central nervous system (CNS) in the mites, suggest that there may be a binding target of 3c{3,6} in the CNS. Compound 3c{3,6} could be a potential varroa control agent that could be used in combination with the current varroa controls in an integrated pest management (IPM) system.

Document type: 
Thesis
File(s): 
Supervisor(s): 
Erika Plettner
Department: 
Science: Department of Chemistry
Thesis type: 
(Thesis) M.Sc.

Controlling redox processes in metal complexes and multifunctional materials

Date created: 
2020-12-17
Abstract: 

Transition metal complexes incorporating redox-active ligands have the potential to facilitate controlled multielectron chemistry, enabling their use in catalysis and energy storage applications. Moreover, the use of transition metal complexes containing redox-active ligands has been extended to two- (2D) and three-dimensional (3D) materials, such as supramolecular assemblies (i.e., metallacycles, molecular cages, or macrocycles) and metal-organic frameworks (MOFs) for catalytic, magnetic, electronic, and sensing applications. Salens (N2O2 bis(Schiff-base)-bis(phenolate) are an important class of redox-active ligands, and have been investigated in detail as they are able to stabilize both low and high metal oxidation states for the above-mentioned applications. The work in this thesis focuses on the synthesis and electronic structure elucidation of metal salen complexes in monomeric form, as discrete supramolecular assemblies and 3D MOFs. Structural and spectroscopic characterization of the neutral and oxidized species was completed using mass spectrometry, cyclic voltammetry, X-ray diffraction, NMR, UV-Vis-NIR, and EPR spectroscopies, as well as theoretical (DFT) calculations. Chapter 2 discusses the synthesis and electronic structure evaluation of a series of oxidized uranyl complexes, containing redox-active salen ligands with varying para-ring substituents (tBu, OMe, NMe2). Chapters 3 and 4 discuss the incorporation of a redox-active nickel salen complex equipped with pyridyl groups on the peripheral positions of the ligand framework into supramolecular structures via coordination-driven self-assembly. The self-assembly results in formation of a number of distinct metallacycles, affording di-, tetra-, and octa-ligand radical species. Finally, the design, synthesis, and incorporation of metal salen units into MOFs is discussed in Chapter 5. Preliminary assembly and oxidation experiments are presented as an opportunity to explore the redox-properties of salen complexes incorporated into a solid-state 3D framework. Overall, the work described in this thesis provides a pathway for salen ligand radical systems to be used in redox-controlled host-guest chemistry, catalysis, and sensing.

Document type: 
Thesis
File(s): 
Supervisor(s): 
Tim Storr
Daniel B. Leznoff
Department: 
Science: Department of Chemistry
Thesis type: 
(Thesis) Ph.D.