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

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Stabilizing proton exchange membranes using Cerium(III) ions

Author: 
Date created: 
2021-10-05
Abstract: 

Proton Exchange Membrane Fuel Cells (PEMFCs) represent an innovative and promising technology for transportation applications due to their low weight, lower operative temperature, and pressure ranges. One of the most challenging limiting factors for the adoption of PEMFC in everyday life is the durability of the Proton Exchange Membrane (PEM), the true core of this type of device. The internal environment of PEMFCs is naturally rich in free radicals (such as HO• and HOO•), which react with the PEM backbone, damage the PEM, and ultimately lead to the PEMFC failure. One way to improve the stability of PEMs against these species is the incorporation of an additive that can act as a radical scavenger and become the preferential site for radical oxidation. One of the most used radical scavengers for this kind of application is cerium in its Ce3+ oxidation state. In this thesis work, a set of sulfophenylated polyphenylenes (sPPB) membranes were synthesized by introducing different amounts of Ce3+ (sPPB-Ce3+), and efforts were made to identify the multiple degradation pathways (chemical, thermal, mechanical). The stability of sPPB-Ce3+ membranes to radical degradation was enhanced almost threefold, they maintained their structural integrity, shape, and thickness and their proton conductivity was comparable to that of the pristine materials. Several other properties such as dimensional stability, polydispersity and solubility also underwent important changes. As observed through these analyses, the effects of Ce3+ on the original material properties can be advantageous in improving the characteristics of proton exchange membranes.

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

Studies of bacterial and insect cytochromes P450 in degradation of pesticides

Author: 
Date created: 
2021-08-16
Abstract: 

Cytochromes P450 is a group of heme-containing enzymes with diverse catalytic activity that can be used for the biodegradation of environmental chemicals. Cytochrome P450cam (CYP101A1) from the soil bacterium Pseudomonas putida is known for hydroxylating camphor. Here, I have investigated the dehalogenation ability of two P450cam mutants, ES6 (G120S) and ES7 (V247F/D297N/K314E), in comparison to the wild-type (WT) enzyme. Six hexachlorinated persistent organic pollutants (POP), namely endosulfan (ES), ES diol, ES lactone, ES ether, ES sulfate and heptachlor, were tested since they are similarly structured to the native substrate. The mutated enzymes were capable of converting the selected substrates to phenols and o-quinones, which were detected using a colorimetric assay with 4-aminoantipyrine (4-AAP). Kinetic studies and statistical analysis were carried out and it was found that both ES6 and ES7 are significantly more active than the WT, with the highest activity noticed against ES ether and heptachlor. The western honey bee, Apis mellifera, is a vital pollinator of the ecosystem, however, its being threatened by the ectoparasitic mite, Varroa destructor. This pest is becoming immune towards commercially available pesticides, thus, new control agents have been previously synthesized that showed miticidal effects. Fortunately, insect cytochromes P450 are known to be responsible for the metabolism of such xenobiotics. Here, I have tested the ability of three potent dialkoxybenzene compounds, namely 1-allyloxy-4-propoxybenzene (3c{3,6}), 1,4-dipropoxybenzene (3c{3,3}) and 1,4-diallyloxybenzene (3c{6,6}), to get degraded by honey bee cytochromes P450. The formation of the dealkylated products was detected in abdomen extracts using a colorimetric assay with 4-aminoantipyrine (4-AAP). Kinetic studies and statistical analysis showed a downregulation of detectable P450 activity in the treated vs. the untreated extracts. Gas chromatography-mass spectrometry (GC-MS) quantitative assays were carried out and three dealkylated products were found, hydroquinone (HQ), 1-hydroxy-4-propoxybenzene (2c{3}) and 1-hydroxy-4-allyloxybenzene (2c{6}).

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

Design, synthesis and use of chiral pheromone-based probes to study pheromone enantiomer discrimination in the pheromone binding proteins from the gypsy moth, Lymantria dispar

Date created: 
2021-04-15
Abstract: 

The gypsy moth is a widespread and harmful pest causing extensive damage to the Canada’s forest and orchard ecosystems. It uses (+)-disparlure as a sex pheromone. Discovery of the pheromone, including its absolute configuration, has enabled monitoring of gypsy moth populations. Disparlure of low enantiopurity is not attractive to the moths and, for this reason, enantiopure (+)-disparlure has been a synthetic target for many years. To access (+)-disparlure of high enantiopurity we have used a diastereoselective nucleophilic addition reaction with the enantiopure α-chloroaldehyde (2-chlorododecanal) that yields a stereocontrolled access to the 1,2-anti chlorohydrin core. The (+)-disparlure was prepared through a series of transformations that include a Mitsunobu inversion. We have successfully completed the synthesis of (+)-disparlure in 5 steps as compared to Iwaki’s first synthesis in 12 steps and Sharpless’s widely used synthesis in 6 steps. The same approach was used to produce 18-hydroxydisparlure enantiomers, which were coupled to a linker with an alkyne moiety at the end. The alkyne was then coupled to azide-based commercial fluorescent probes, to furnish fluorescent disparlure-based probes for physical studies. The gypsy moth has two different pheromone binding proteins, LdisPBP1 and LdisPBP2. Previously, our group has addressed the enantiomer selectivity of these two PBPs and found that PBP1 binds (-)-disparlure more strongly than (+)-disparlure, while PBP2 binds (+)-disparlure more strongly. Despite several binding assays, the interaction and discrimination of gypsy moth PBPs towards disparlure enantiomers are not fully understood due to lack of binding interaction and kinetic studies, which are technically demanding, due to the hydrophobicity of the pheromone. In this thesis, we have studied the binding interaction of deuterium-labelled (+)-disparlure and (-)-disparlure with LdisPBPs by 2H NMR spectroscopy. The results from NMR studies were correlated with the results from docking simulations of (+)-disparlure and (-)-disparlure bound to one internal site and multiple external sites of LdisPBP1 and LdisPBP2. These results indicated that (+)-disparlure and (-)-disparlure adopt different conformations and orientations in the binding pockets of LdisPBP1 and LdisPBP2. Most of the reported work on PBPs focuses on the pheromone binding affinities of PBPs. However, the pheromone-PBP interactions require more than half an hour to establish equilibrium, whereas male moths respond to female pheromones in milliseconds. Therefore, the interactions between pheromones and olfactory components such as PBPs and pheromone receptors may not be under thermodynamic control. In this thesis, we aimed to provide a dynamic perspective of pheromone-PBP interactions and to link these to the functions of PBPs. We have studied thermodynamic (Kd) and kinetic properties (kon and koff) of LdisPBPs-disparlure enantiomer interaction by fluorescence binding assays and kinetic experiments using fluorophore-tagged disparlure enantiomers. The result indicated that the binding preference of disparlure enantiomers to LdisPBPs. Based on the kinetic data of LdisPBPs with fluorophore-tagged disparlure enantiomers, we propose a kinetic model that includes a two-step binding process. Each of these two steps may contribute to a different function of the LdisPBPs.

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

Development of chemical tools for the study of intracellular glycosylation

Author: 
Date created: 
2020-06-04
Abstract: 

Intracellular protein O-glycosylation is an important post-translational modification in mammalian cells with critical regulatory functions relating to transcription, stress response, cell signalling, and cell cycle control. This process is controlled by two enzymes: O-GlcNAc transferase (OGT), which catalyzes the addition of a single O-linked N-acetylglucosamine (O-GlcNAc) to serine and threonine residues of proteins, and O-GlcNAcase (OGA), which hydrolyzes the glycosidic linkage on proteins. While notable progress has been made in the design and application of chemical tools for the study of OGA, methods and tool compounds to detect and modulate the activity of OGT remain limited. In this thesis, I describe the development of a fluorescent glycosyl donor analogue which is tolerated by OGT and transferred to peptides and proteins. This substrate was exploited to develop a convenient and direct in vitro activity assay, enabling the study of OGT catalysis in the presence of various substrates and inhibitors. After optimizing the assay for high-throughput screening, a collection of small molecule libraries encompassing approximately 64,000 compounds was screened, leading to the identification of a novel and selective inhibitor of OGT. This assay was further applied to the functional analysis of peptide-based inhibitors of OGT that were discovered through phage display and in vitro mRNA display technologies. These efforts enabled the development of chemical tools with potent nanomolar affinity for OGT. The in vitro assay was also used for the study of novel glycosylation activity by OGT towards cysteine-containing acceptor substrates, permitting a detailed kinetic analysis of this recently discovered phenomenon. Finally, I describe the biochemical characterization of human Hexosaminidase D (HexD), an intracellular glycoside hydrolase of unknown physiological function, and use this information in the design of potential selective inhibitors. The methods, results, and insights gained from this research should prove useful in advancing our understanding of intracellular glycosylation and for furthering the application of this knowledge for translational therapeutic benefit.

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

The applications of interaction between light and chemical reactivity in molecular systems

Author: 
Date created: 
2021-06-30
Abstract: 

This thesis presents a series of scientific examples that provide further insight into the connection of light and chemical reactivity for applications in catalysis, targeted drug delivery, and detection. Small organic molecules based on 1,2-dithienylethenes (DTEs) and noble metal-based nano-assemblies were incorporated into the system to impart control over their physical and chemical properties, and activity. The light was used as an external stimulus to initiate chemical reactions by causing either a structural, electronic, or chemical change in the chromophore or energy transformation (such as heat) in the system. In the first example (Chapter 2), light is employed to generate the variation in the activity of Karstedt’s catalyst by introducing a DTE-based inhibitor. It is demonstrated that the electronic changes that occur during the light-assisted isomerization of dithienylethene lead to changes in the binding strength of the inhibitor to the catalyst’s metal centre. This, in turn, leads to changes in the reaction progression of simple hydrosilylation reactions. In the second example (Chapter 3), a novel dual-mode (colourimetric and fluorescent) optical probe based on photoresponsive dithienylethene is developed for fast and user-friendly detection and consumption of hydrazine in the vapour and solution phase. The molecule reacts with hydrazine to induce an irreversible structural change in the 1,3,5-hexatriene system leading to deactivation of photochromic activity by quenching effects and simultaneously generating an emissive response. In the third example (Chapter 4), light is used as an external stimulus to indirectly gate the chemical reactivity for an on-demand release of therapeutics in aqueous environments by creating nanoassemblies based on gold nanoparticle core. The constructed nanoassemblies consist of the thermoresponsive Diels-Alder adducts of the molecules to be released close to gold nanoparticles enclosed in an amphiphilic polymer shell. The system uses the photothermal effect of gold nanoparticles to trigger thermo-responsive retro Diels-Alder reactions in the vicinity of nanoparticles to release therapeutic molecules in aqueous solutions.

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

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.