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

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Oxygen mass transport parameters in ionomer films under controlled relative humidity

Author: 
Date created: 
2017-04-20
Abstract: 

Mass transport parameters are determined for the oxygen reduction reaction (ORR) at the electrochemical interface of a platinum microdisk electrode and five different series of polymer electrolyte membranes. The series included proton exchange polyfluorosulfonic acid (PFSA) based membranes (Nafion 117, Nafion 211), films cast from PFSA dispersions (DE2020), anion exchange quaternary ammonium based membranes (FAA-3), and films cast from hexamethyl-p-terphenyl polymethylbenzimidazole (HMT-PMBI) dispersions. The membranes differ in chemical structure, morphology, and water content controlled by relative humidity. The series of materials were investigated over a range of temperatures (50-70 °C) and relative humidities (30-98% RH) using a solid state electrochemical cell. Cyclic voltammetry yielded the potentials where ORR is mass transport limited, as well as the electrochemically active surface area of the platinum microdisk electrode. Chronoamperometry was performed at mass transport limiting potentials, where fitting the current transients to analytical models (Cottrell/Shoup-Szabo) allowed for the calculation of oxygen diffusion coefficient (Db), solubility (cb), and permeability (Db*cb) for the applied environmental conditions. A numerical model is also presented which highlights constraints in using the analytical models to determine mass transport parameters when the inherently-assumed infinite electrolyte thickness is not present. During chronoamperometric measurements, where the potential applied results in the generation of liquid water at the membrane/electrode interface (ORR), a reversible time-dependent behaviour was observed where Db and Db*cb increased over time to plateau values. The time-dependency responds to changes in relative humidity and is reversible, where mass transport parameters shift to a vapour equilibrated state over long periods of time. It is suggested that the electrochemically generated liquid water at the membrane/platinum interface during oxygen reduction results in a morphological change over repeated perturbations in the form of chronoamperometric analysis. The presence of interfacial liquid water causes hydrophilic channels, which are not present in substantial amounts at the interface in the vapour equilibrated-state, to reorient toward the surface. The increase in water-filled channels at the interface can explain the increase in Db and Db*cb, which are dependent on water content. Oxygen mass transport parameters for both proton and anion exchange membranes are reported as a function of relative humidity. In order to perform electrochemical measurements at < 70% RH (at 50 °C) for perfluorosulfonic acid membranes and for all conditions for anion exchange membranes, a modified twoelectrode setup was employed and compared to a three-electrode configuration. The oxygen diffusion coefficient is observed to depend on the water content. A lower relative humidity resulted in lower values of Db; significantly so for alkaline anion exchange samples compared to their acidic counterparts. cb was observed to exhibit an inverse relationship, which increases with decreasing relative humidity. The decrease in Db as the relative humidity was lowered was larger than the increase in cb, which lead to a decrease in Db*cb as the relative humidity was lowered for all membranes.

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

The G-quadruplex-hemin DNAzyme can tag itself with the reactive substrate biotin tyramide

Date created: 
2017-04-19
Abstract: 

Genomic database searches suggest that there are a large number of potentially G-quadruplex forming sequences present in the human genome, in addition to their well-established localization in telomeres. Novel imaging techniques support these data and have begun to indicate the extent to which G-quadruplexes are present in vivo. Information on any biological function of these sequences is less clear. This thesis presents the creation of an assay that could target G-quadruplexes for imaging or pulldown and potentially give information on their biological relevance. We utilize the inherent peroxidase activity of the quadruplex-hemin interaction to initiate a tagging reaction based upon a reactive tyramide substrate.

Document type: 
Thesis
File(s): 
Senior supervisor: 
Dipankar Sen
Department: 
Science: Department of Chemistry
Thesis type: 
(Thesis) M.Sc.

New Directions for Bis-Adamantane Chemistry and Reactivity

Author: 
Date created: 
2017-01-27
Abstract: 

Bulky chiral ligands have gained tremendous attention in metal coordination chemistry as they influence greatly coordination geometry and reactivity and are critical features of asymmetric catalysts. In this thesis, the design and synthesis of sterically congested chiral alcohol and amine ligands based on a bis-adamantane framework, are explored. Optimization of the ligand synthesis and purification were conducted on the racemic ketone, while the chiral synthetic pathway utilized an enzymatic hydrolysis as the key step. In another aspect of bis-adamantane chemistry, the bromonium ion of adamantylideneadamantane (Ad=Ad) has provided valuable mechanistic information about electrophilic addition of bromine and undergoes a fast “Br+” transfer process to alkenes. However, the Ad=Ad isomer SesquiAdAd only reacts with [AdAdBr+] and not with Br2. This thesis also investigated the rearrangement of SesquiAdAd to Ad=Ad catalyzed by [AdAdBr+] via the formation of the potentially high energy intermediate SesquiAdAdBr+, probed by 1H NMR spectroscopy and kinetics. Data analysis involved a series of 1H NMR spectral deconvolutions.

Document type: 
Thesis
Senior supervisor: 
Daniel B Leznoff
Andrew J Bennet
Department: 
Science: Department of Chemistry
Thesis type: 
(Thesis) M.Sc.

Development of tools and methods for studying glycan processing proteins in living systems

Date created: 
2016-05-12
Abstract: 

Carbohydrates are a class of biomolecules present in all domains of life that provide energy for cellular processes, afford structural support, and take part in molecular recognition and signalling. Given the ubiquity of carbohydrates in living systems, gaining an improved understanding of the proteins that process them – glycosyl transferases, glycoside hydrolases, lectins, and sugar transporters – is of key interest. Compared to in vitro assays, few live-cell or in vivo assays of carbohydrate-processing proteins have been developed, despite the wealth of knowledge that they provide. This discrepancy is largely due to the difficulties associated with live-cell and in vivo examination of protein function, namely issues of substrate selectivity, sensitivity, reactivity, and cell permeability. This thesis aims to develop substrates and methods to study two carbohydrate-processing proteins: human O-GlcNAcase, a glycoside hydrolase involved in Alzheimer’s disease, cancer, and the stabilization of nascent proteins; and bacterial AmpG, a sugar transporter implicated in β-lactam antibiotic resistance. In doing so, I hope to not only provide insight into the function of these proteins, but to also lay a foundation for live-cell or in vivo study of these and related proteins in the years to come.

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

Design and synthesis of a photoaffinity labelling analogue of ivacaftor to probe its putative binding site on mutant CFTR

Date created: 
2017-03-06
Abstract: 

The cystic fibrosis (CF) therapeutic, ivacaftor, restores activity to certain cystic fibrosis transmembrane regulating protein (CFTR) mutations; however, the nature of ivacaftor's interaction with mutant CFTR is still under investigation. This study aimed to generate photoaffinity labelling (PAL) probes that will be used to elucidate putative ivacaftor binding sites on mutant CFTR. Structure activity relationship studies indicated retention of ivacaftor's potentiating activity despite deletion of either of the t-butyl groups from the ivacaftor structure. These results initiated a synthesis program to prepare PAL probes incorporating a carbene-generating diazirine moiety in place of a t-butyl group on the ivacaftor scaffold. Initial synthetic approaches towards creating the diazirine PAL probe were devised with the ability to afford diversification at a late stage in the synthesis to allow incorporation of reporter tags into the PAL probe. While these approaches were unsuccessful, ultimately a linear synthetic approach successfully afforded the target diazirine PAL probe.

Document type: 
Thesis
Senior supervisor: 
Robert Young
Department: 
Science: Department of Chemistry
Thesis type: 
(Thesis) M.Sc.

Growth and Characterization of Lead Zirconate-Titanate (PbZr1-xTixO3)-Based Novel Piezo-/Ferroelectric Single Crystals

Author: 
Date created: 
2016-04-18
Abstract: 

Piezo-/ferroelectric materials form an important class of functional materials that can transduce mechanical energy to electrical energy and vice versa. PbZr1-xTixO3 (PZT) ceramics are the most extensively used piezoelectric materials owing to their good piezoelectric and electromechanical properties near the morphotropic phase boundary (MPB). However, the microstructures of this class of materials and the atomistic phenomena that cause the outstanding performance have not been thoroughly understood yet. Therefore, it is of particular interest to grow single crystals of PZT, which are not only necessary for thorough characterization of the anisotropic properties of this system, but also are expected to exhibit superior piezo-/ferroelectric performance over their ceramic counterparts. In this work, PZT single crystals with compositions of x = 0.54 and 0.45 were grown successfully by a top-seeded solution growth (TSSG) method, and characterized by X-ray diffraction, polarized light microscopy (PLM), piezoresponse force microscopy (PFM), and dielectric, ferroelectric, and piezoelectric measurements. On the other hand, given that PZT ceramics used in industry are always chemically modified to obtain desired and enhanced properties for specific applications, we extended our work to grow donor (La3+ and Bi3+)- and acceptor (Mg2+ and Mn2+)-doped PZT single crystals and to investigate the effects of the doping on the structure and properties. The compositions and homogeneity of the as-grown doped PZT single crystals were investigated by laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) and energy dispersive spectroscopy (EDS). The dielectric, ferroelectric and piezoelectric properties of these single crystals were investigated. These very first set of data on doped PZT single crystals not only provide a better understanding of structure-property relationship of PZT-based single crystals and their doping mechanisms, but also points to the possible applications of doped PZT single crystals as a new high-TC, high-performance piezo-/ferroelectric material. Moreover, there have been pressing demands for lead-free or lead-reduced replacement materials because of the environment concerns arising from the potential toxicity of the lead in high-performance piezo-/ferroelectric material such as PZT. In our search for high-temperature, lead-reduced piezoelectric materials, novel ferroelectric single crystals of complex perovskite ternary solid solution Bi(Zn0.5Ti0.5)O3-PbZrO3-PbTiO3 (BZT-PZ-PT) have been grown for the first time. The structure and properties of these crytals suggest that the BZT-PZ-PT ternary single crystals constitute a new family of high-TC ferroelectric materials, which are promising for various applications such as high-power electromechanical transducers that can operate in a wide temperature range.

Document type: 
Thesis
File(s): 
Senior supervisor: 
Zuo-Guang Ye
Department: 
Science: Department of Chemistry
Thesis type: 
(Thesis) Ph.D.

The investigation of the beta decay of 46K: Detailed spectroscopy of the low-lying structure of 46Ca with the GRIFFIN Spectrometer

Date created: 
2016-11-25
Abstract: 

The calcium region is currently a new frontier for modern shell model calculations, and detailed experimental data from these nuclei is critical for a comprehensive understanding of the region.Due to its very low natural abundance of 0.004%, the structure of the magic nucleus 46Ca has not been studied in great detail. Some excited states were previously identified by various reaction mechanisms, and few gamma rays were placed in the level scheme from results of beta-decay experiments equipped with limited detection capabilities. A high-statistics data set of the beta decay of the 46K 2- ground state into the excited states of 46Ca was measured with the GRIFFIN spectrometer located at TRIUMF-ISAC in December of 2014. A radioactive beam consisting almost entirely of 46K was implanted at the center of the GRIFFIN array, and the emitted gamma rays were detected by 15 high-purity germanium clover detectors. From forty hours of data collection, 430 million gamma-gamma coincidences were observed and analysed to construct the 46Ca level scheme. In total, 194 gamma rays were identified and placed into the level scheme; 150 of these transitions were observed for the first time. Angular correlations between pairs of gamma rays were analysed to investigate the spin assignments of the observed excited states. Correlations were investigated for 18 of the 42 observed excited states, and it was possible to confirm 7 previously reported spin assignments, and assign 3 new spins of 3-, 2-, and 3- for the 4435, 5052, and 5535 keV states, respectively. The measured half-life of the 96.41(10) s is in agreement with previous results. From the observed beta feeding intensities of this work, it is suggested that the 46K 2- ground state may contain more proton s1/2 character than has been previously believed. This is due to the strong population of the 5052 keV 2$^-$ state and the absence of observed feeding to the 46Ca ground state.

Document type: 
Thesis
File(s): 
Senior supervisor: 
Corina Andreoiu
Department: 
Science: Department of Chemistry
Thesis type: 
(Dissertation) Ph.D.

Oxidation of 3-Chloroindole and Biodegradation of Dialkoxybenzenes with Cytochrome P450cam (CYP101A1)

Author: 
Date created: 
2016-12-06
Abstract: 

Cytochrome P450cam (a camphor hydroxylase) isolated from soil bacterium Pseudomonas putida shows potent importance in environmental applications such as the degradation of chlorinated organic pollutants and insect control agents. Introducing such chemicals can be hazardous to the environment due to their lack of biodegradation. In this thesis, I have studied the role of several P450cam mutants in the oxidation of 3-chloroindole to isatin and the role of wild type P450cam in the dealkylation of 1,4-dibutoxybenzene, a potent feeding-deterrent against stored product pests. Mutant (E156G/V247F/V253G/F256S) was the most active in the conversion of 3-chloroindole by P450cam. We propose two mechanisms for the dechlorination of 3-chloroindole by P450cam. To investigate structure-activity patterns of 1,4-dialkoxybenzenes against beetles, the octanol-water partition coefficients of selected dialkoxybenzenes were investigated. Furthermore, P. putida strain ATCC17453 was able to metabolize 1,4-dibutoxybenzene. Results revealed that cytochrome P450cam catalyzed the first and second dealkylation steps in the biodegradation mechanism.

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

Mechanisms of new Ru-ferrocene and binuclear Ru metallochemotherapeutics and the Ru metastasis inhibitor NAMI-A

Author: 
Date created: 
2016-11-14
Abstract: 

Ruthenium-based anticancer compounds have become a leading area of development in medicinal chemistry. Ru(III) complexes, such as the antimetastatic compound imidazolium [trans-RuCl4(1H-imidazole)(DMSO-S)] (NAMI-A), where DMSO = dimethyl sulfoxide, have shown promising results in clinical trials. Furthermore, reports of organometallic Ru(II) arene complexes, such as [RuCl2(η6-p-cymene)(pta)] (RAPTA-C), where pta = 1,3,5-triaza-7-phosphatricyclo[3.3.1.13,7]decane, demonstrate that these types of compounds also have excellent chemotherapeutic potential. In this work, three families of new bimetallic drug candidates based on these types of Ru anticancer compounds have been developed, with the goal of generating multifunctional complexes with new biological activities. The first type of complex is ferrocene-functionalized pyridine analogues of NAMI-A. Inclusion of ferrocene generates bifunctional complexes with cytotoxicity from the ferrocene groups and antimetastatic activity from the Ru center. The second family of complexes described in this work is analogues of RAPTA-C with the pta ligand replaced with ferrocene-functionalized pyridine, imidazole, and piperidine ligands. These compounds have strong anticancer and antibiotic activities, which correlate quantitatively with the reduction potential of the ferrocene centers, implicating generation of reactive oxygen species as the origin of activity. The third family of complexes, asymmetric bimetallic complexes comprised of a Ru(III) NAMI-A-type center coupled to Ru(III) DNA intercalating groups via pyrimidine, have been synthesized. Functionalization with dipyrido[3,2-a:2’, 3’-c]phenazine (dppz) in particular led to strong DNA interactions and high cytotoxic activity. In this work, electron paramagnetic resonance (EPR) and NMR have been used to study the ligand-exchange processes of the complexes and their interactions with proteins. In particular, NMR was used to investigate the complicated solution behavior of NAMI-A. Furthermore, NMR studies of the complex with human serum albumin and human serum transferrin indicate non-specific coordination to histidine residues and changes in ligand exchange kinetics due to protein interactions.

Document type: 
Thesis
Senior supervisor: 
Dr. Charles J. Walsby
Department: 
Science: Department of Chemistry
Thesis type: 
(Thesis) Ph.D.

Physical modeling of water fluxes in the catalyst layers of polymer electrolyte fuel cells

Author: 
Date created: 
2016-12-02
Abstract: 

The ability to predict the electrochemical performance of the catalyst layer (CL) in polymer electrolyte fuel cells (PEFCs) hinges on a precise knowledge of the water balance. The key effective properties of this layer, like gas diffusivity and vaporization exchange rate constant, control water distribution and fluxes in the complete cell. Unfortunately, the knowledge of relevant properties of CLs is rare and not available with sufficient accuracy. A physical model of water fluxes in CLs is proposed to develop a methodology for the determination of the effective properties of CLs. For the purpose of this work, the CL is considered exclusively as a medium for vapor diffusion, liquid water permeation, and vaporization exchange. The presented model exploits an analogy of the water transport problem to the processes involved in charge transfer in a porous electrode, which is represented by the famous transmission line model (TLM). The expectation is that this analogy could lead to a diagnostic tool with similar capabilities as electrochemical impedance spectroscopy (EIS) in rationalizing the response of CLs to varying conditions and in extracting parameters of water transport and vaporization exchange. An analytical solution under steady state and isothermal conditions is presented that rationalizes the relation between controlled environmental conditions and the net water flux under partial saturation. The analysis of water flux data using this solution provides a method for the extraction of the net vaporization exchange rate, the activation energy of vaporization, vapor diffusivity, and the temperature exponent of the vapor diffusivity, which allows the transport mechanism of vapor diffusion in the CL to be identified. Transient analysis with a periodic perturbation is then explored. The overall impedance of water transport and the response function of a voltage change to a vapor change are analyzed for a specific scenario, where no effluence of liquid water from the CL is permitted. The methodology based on the transient analysis provides not only a way to extracting the effective properties of the CL, but also a way to estimate the liquid saturation in the CL.

Document type: 
Thesis
File(s): 
Senior supervisor: 
Michael H. Eikerling
Department: 
Science: Department of Chemistry
Thesis type: 
(Thesis) Ph.D.