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

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Interactions between hemin-binding DNA aptamers and hemin-graphene nanosheets: Reduced affinity but unperturbed catalytic activity

Author: 
Date created: 
2019-03-12
Abstract: 

Hemin-graphene nanosheets (H-GNs) were reported to exhibit peroxidase-like activity, salt-induced aggregation, and the ability to discriminate single-stranded and double-stranded DNA colorimetrically. In the meantime, hemin-binding DNA aptamers were isolated by in vitro selection, which bind hemin tightly and exhibit enhanced peroxidase activity. In this research, it was demonstrated that H-GNs can in fact discriminate hemin-binding DNA aptamers not only from nonspecific strands but also among different hemin-binding DNA sequences. As such, H-GNs can be used for the determination of the binding affinities of various hemin-binding DNA aptamers. Particularly, the H-GN/DNA interaction was examined by exploiting the peroxidase-like activity of the hypothesized H-GN/aptamer ternary complex. The binding of the aptamer to H-GNs was validated by the conformity of data obtained from kinetic assays to the specific ligand binding model. Although the binding affinity of the aptamer to H-GNs was weaker and the catalytic activity of the resulting complex is lower than that of hemin/aptamer complex in solution, the catalytic activity of the H-GN/aptamer complex is much higher compared to that of the “parent” H-GNs.

Document type: 
Thesis
File(s): 
Supervisor(s): 
Hua-Zhong Yu
Department: 
Science: Department of Chemistry
Thesis type: 
(Thesis) M.Sc.

Construction of an array of photonic crystal films for visual differentiation of water/ethanol mixtures

Author: 
Date created: 
2019-03-14
Abstract: 

A photonic crystals films (PCF) which consists of a porous layered structure with a highly ordered periodic arrangement of nanopores has been used to differentiate between various mixtures of water and ethanol (EtOH). Refractive index difference between the wall (silica) and air which occupies the empty pore results in the structural color of the PCF. This color disappears when the nanopores are infiltrated by a liquid with a similar refractive index to silica (or silicon dioxide). The disappearance of the structural color provides a means to construct a sensor to differentiate various water/EtOH mixtures based on their wettability of the nanopores in the PCF. In this study, an array of silica-based PCFs was synthesized on a silicon substrate with a precise control of nanopore properties using the co-assembly/sedimentation method. Using this method, we benefitted from having different PCFs on a single substrate. Chemical coatings, neck angles, and thicknesses on each PCF were the three factors used to adjust the wettability of the pores. Nanopore wetting by water/EtOH mixtures was studied in a systematic manner and combinations of the three factors were used to develop a sensor for differentiation of various water/EtOH mixtures. The final developed sensor consisting of an array of six PCFs was able to differentiate seven different water/EtOH mixtures: W10, W20, W30, W40, W50, W60 and W70, in which W10 means 10% of water in EtOH.

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

Coordination polymers incorporating gold(I) and platinum(II) cyanometallate linkers – chemical vapour sensors and beyond

Author: 
Date created: 
2018-09-25
Abstract: 

This thesis focuses on the use of heterobimetallic coordination polymers incorporating dicyanoaurate and tetracyanoplatinate linkers as photoluminescence based vapour sensors for S-donors and ammonia. Other applications include the use of these materials as nonlinear optical media and conductive solids. Cu2/3Au1/3CN was shown to exhibit a rapid, reversible luminescent response to thioether vapours. Exposing HgPt(CN)4 to some thiol vapours resulted in drastic changes to their luminescence. CuI(Bz2S2) (Bz=benzyl) and CuI(Me2S2) were synthesized and structurally characterized. ZnPt(CN)4 was shown to reversibly react with ammonia to form Zn(NH3)2.5Pt(CN)4 with an accompanying change in luminescence. Raman spectroscopy was also used to detect ammonia via the νCN bands of Zn[Au(CN)2]2 and ZnPt(CN)4. The structure of [NBu4]6(Cd4Cl4)2(Au(CN)2)12[CdCl4] was determined and it was shown to be a turn-on ammonia sensor. A series of isostructural 1D coordination polymers, [PPN]MX2Au(CN)2 (M=Zn,Cd,Hg; X=Cl,Br,I), were shown to exhibit second harmonic generation. A potentially conductive coordination polymer [TTF]CdCl2Au(CN)2 was synthesized.

Document type: 
Thesis
Supervisor(s): 
Daniel Leznoff
Department: 
Science: Department of Chemistry
Thesis type: 
(Thesis) M.Sc.

Preparation and covalent surface modifications of silica coated spherical and rod-shaped gold nanoparticles

Author: 
Date created: 
2018-08-17
Abstract: 

The surface chemistry of silica-coated gold nanoparticles (Au NPs) was investigated by modifying these surfaces using alcohol-based reagents. Alcohol condensation reactions were facilitated by dielectric heating using a microwave reactor. The attachment of two alcohol-based reagents, a carboxylic acid functionalized alcohol and a chelating agent with a terminal alcohol functional group, was achieved on the surfaces of spherical gold nanoparticles and gold nanorods, respectively. A fluorescent probe was coupled to the carboxylic acid functionalized silica-coated Au NPs as a confirmation of the surface functionalization, and as a demonstration of an application for these nanoparticles. The silica-coated gold nanorods modified with a chelating species were evaluated for their ability to capture metal ions present in an aqueous solution. A wide range of surface chemistry for silica-based nanoparticles can be achieved using the methods presented herein to meet the requirements of their future applications.

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

Creating nano- and microstructure catalyst coated membrane interfaces for improving the performance of proton exchange membrane fuel cells

Author: 
Date created: 
2018-06-21
Abstract: 

Proton exchange membrane fuel cells (PEMFCs) are an important low-emission energy generation system that can be utilized for automotive applications. These systems are, however, limited by the use of Pt as the cathode catalyst, where the relatively expensive cost of Pt limits the competition of PEFMCs against petroleum based systems. Due to the unique characteristics of these PEMFC systems, an optimal balance of hydration of the PEM and the catalyst layers must be maintained within the fuel cell. The current densities achievable with the system can be impacted by an inefficient mass transport of the reactants and products that result in over- or under-hydration of the system. Improvements for increasing effective utilization of Pt and optimizing transport characteristics of PEMFCs could further propel this technology into the mainstream. The work presented in this thesis demonstrates an array of approaches to control the interfaces at or within the cathode catalyst layer (CCL). Architectures at the micro- and nanoscale were sought for improving the performance of PEMFCs. These approaches included creating microscale (5 to 50 µm) patterns of the PEM to CCL interface by the direct printing of CCLs and the hot-embossing of the PEMs. Catalyst materials with tuned pore sizes (1 to 0.05 µm) were also prepared with a coating of catalytic nanoparticles (NPs) through the use of polymeric sacrificial templates. Finally, CCLs containing mesoporous (<10 nm) Pt catalysts were prepared by electrodeposition. These CCL architectures were extensively characterized by electron microscopy and electrochemical techniques. Electron microscopy and related spectroscopy techniques were utilized for determining the morphologies and elemental compositions of the structured materials. The performances of these materials were analyzed using ex situ solution-based, three-electrode electrochemical cells. Some of the prepared catalysts were further analyzed with laboratory scale [membrane electrode assemblies (MEAs) with a geometric surface area of 5 cm2] and industrial relevant scale [MEAs with a geometric surface area of 40 cm2] fuel cell test stations. The goal of this thesis is to demonstrate the preparation of these materials with commercially available materials and industrially compatible processes, which can be extended to further catalytic materials in the future for further enhancing the efficiencies of PEMFC systems.

Document type: 
Thesis
Supervisor(s): 
Byron Gates
Department: 
Science: Department of Chemistry
Thesis type: 
(Thesis) Ph.D.

Human lung cell responses caused by roadside particle types

Author: 
Date created: 
2019-01-22
Abstract: 

Particulate matter (PM), especially traffic-derived particles, is associated with adverse effects on human health. An in vitro dose-response methodology using human lung cells A549 was adopted to investigate lung cell culture responses [cytokine expression Interleukin (IL) –6, IL-8, and cell death] following incubation with traffic-derived particles. The basis of this study was to investigate interactions between the known components on ambient particles proximal to roadways. In using ambient particle type ERM-CZ120, and laboratory mimics of PM, cellular responses clearly indicate the importance of insoluble particle types that are internalized via endocytosis. Particle size appears to not be a principal factor, but particle-air interface chemistries, while not investigated in this work, are likely important. The soluble species used herein did not effect a response when introduced alone, but when combined with insoluble particle types, the cellular response in excess of the insoluble particle alone was measured. A probable mechanism is that the insoluble particles function as carriers, via endocytosis, and that process provides an access route for internalization of soluble species. As evidenced by one set of experiments, prediction of overall cellular response to a given dose of a specific particle type is not trivial. Ferrous iron, when introduced with silica particles, effected significant down-regulation of expressed cytokines, whereas lead ions effected significant up-regulation, but when ferrous iron and lead ions were co-administered with silica particles, cytokine expression was down-regulated. These results indicate the necessity to measure specific cellular responses as an outcome following a dose with a specific particle composition of insoluble and soluble components for which detailed physical and chemical composition information is known, and not to extrapolate to other particle types.

Document type: 
Thesis
File(s): 
Supervisor(s): 
Dr. George R. Agnes
Department: 
Science: Department of Chemistry
Thesis type: 
(Thesis) Ph.D.

Applications of numerical linear algebra to protein structural analysis: the case of methionine-aromatic motifs

Author: 
Date created: 
2018-12-07
Abstract: 

Linear algebraic algorithms uncovered a preponderance of protein methionine residues interacting with two or more aromatic residues. The average geometric relationship between transition metals and methionine-aromatic interactions in PDB crystal structures was assessed with a nearest neighbours-like algorithm (“Met-aromatic”) developed for finding and classifying methionine-aromatic interactions. Here, we assumed that a methionine could interact with one to six midpoints between aromatic carbon atoms in any of phenylalanine, tyrosine, and tryptophan; an integer we termed “Order of Interaction.” Serendipitously, an oversight in Met-aromatic led to the discovery of a significant number of interactions of order exceeding VI, suggesting a large number of methionine residues interacting with two or more aromatics. This was termed the “Bridging Interaction.” Herein, the methioninearomatic and bridging interactions are discussed in light of their possible redox roles.

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

Physical modeling of local reaction conditions inside of cathode catalyst layer of polymer electrolyte fuel cells

Author: 
Date created: 
2018-12-06
Abstract: 

The foremost practical objective in research on polymer electrolyte fuel cells is to design catalyst layers with high performance at markedly reduced platinum loading. The overarching goal is thus to enhance the effectiveness factor of platinum utilization inside the cathode catalyst layer. This requires design modifications in fuel cell components, understanding of local reaction conditions inside the cathode catalyst layer, accounting for the impact of surface charging phenomena at pore walls on catalyst activity, as well as understanding water distribution and fluxes in porous electrode media and how the water balance affects all the aforementioned effects. As a contribution towards this objective, this thesis presents models to understand the local reaction conditions inside the cathode catalyst layer. This refers to rationalizing the oxygen and proton density in the cathode catalyst layer from the macroscopic level to the nanopore level. This work has been divided into three parts. The first part focuses on understanding of surface charging phenomena and catalytic activity in water-filled pores that are bounded on one side by an ionomer-skin layer. The model-based analysis reveals that the density of charged side chains at the ionomer shell exerts a pronounced impact on the surface charge density at the Pt surface and thereby on the activity of the pore for the oxygen reduction reaction. In the second part, we employed physical models of catalyst layer operation to analyze large sets of experimental performance data of fuel cells with gradually decreased Pt loading. The analysis reveals systematic variations in physical properties of cathode catalyst layers with Pt loading that can be consistently explained with a variation in the fuel cell water balance. A correlation exponent was introduced, which can be used to assess the design of a catalyst layer in terms of the propensity to flooding. The last part serves the need for a comprehensive water balance model as revealed by research described in the previous paragraph. We present a basic 1D +1D model to rationalize variations in water distribution and water fluxes in catalyst layers, diffusion media, and flow fields in response to changes in structure, composition and operating conditions. The model-based analysis consistently reproduces major trends in performance upon a systematic reduction in Pt loading. The tools and analyses provided in this thesis could thus inform strategies for minimizing the Pt loading without running into the water trap.

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

Expanding the organocatalyzed α-chlorination-aldol reaction

Author: 
Date created: 
2018-12-14
Abstract: 

Organocatalysis, while still a relatively new field in organic chemistry, now plays an indispensable role in organic synthesis. Transformations not accessible by classical synthetic methods are now not only routine, but mild, high yielding and increasingly sophisticated in what they can achieve. One such reaction is the α-chlorination-aldol reaction developed by the Britton group in 2013. This reaction has been demonstrated to provide access to stereochemically rich chlorohydrins from readily available and achiral starting materials. The reaction has found extensive utility in the concise synthesis of imino-cyclitols and carbohydrate analogues. In this thesis a more general approach to the tandem α-chlorination-aldol with different electrophiles or ketones is investigated. Within, we show that azodicarboxylates can be used as electrophiles to functionalize aldehydes prior to submission to an aldol reaction. These aminated aldol adducts are further investigated for their utility in synthesizing imino-cyclitols, and their ability to form cyclic, polyhydroxylated hydrazones. As well, new substrates are investigated for their propensity to engage in an α-chlorination-aldol reaction. Four new substrates are demonstrated to form the corresponding chlorinated aldol adducts in moderate yields and high enantioselectivity. Furthermore, we demonstrate that these new aldol adducts can provide access to novel, natural product-like scaffolds.

Document type: 
Thesis
File(s): 
Supervisor(s): 
Robert A. Britton
Department: 
Science: Department of Chemistry
Thesis type: 
(Thesis) M.Sc.

Fully hydrocarbon ionomer catalyst layers in proton- and anion-exchange membrane fuel cells

Author: 
Date created: 
2018-09-17
Abstract: 

The structure and morphology of fuel cell catalyst layers and concomitant system properties, particularly mass transport, were investigated through electrochemical and physical characterization techniques. Catalyst layers designed for proton-exchange membrane fuel cells (PEMFCs) incorporated a hydrocarbon ionomer (sP4c) soluble in low-boiling solvents. These were used to probe the property alterations effected by increasing ionomer coverage within the catalyst layer, and also to measure the impact an extremely small quantities (0.38 wt%) of a commonly employed high-boiling solvent, DMF, in the catalyst ink. High-boiling solvents are difficult to eliminate during electrode formation, and resultant solvent-annealed catalyst layers lost electrocatalytic surface area, resulting in markedly greater kinetic losses compared to catalyst layers formed without high-boiling solvents. Catalyst layers designed for anion-exchange membrane fuel cells (AEMFCs) incorporating hydrocarbon ionomer in the catalyst layer (FAA-3) requiring high-boiling solvent (NMP, 2.3 wt% of total solvent) were formed over a broad array of conditions. Catalyst layers formed slowly at high temperatures to drive off high-boiling solvent displayed significantly enhanced mesoporosity, relating to enhanced transport characteristics, over solvent-annealed analogues with low mesoporosity, despite comparable total volumes. The impacts of solvent annealing on AEMFC electrode properties and resultant achievable power density and degradation were disproportionate compared to the similar PEMFC study. A new methodology for fuel cell membrane-electrode assembly construction, direct membrane deposition (DMD), enables lower interfacial resistances and enhanced water transport for a given thickness of membrane. These are desired properties for both PEMFCs and AEMFCs. Initially developed with inkjet printers designed for single-cell biological printing applications, this method was adapted to spray-coating systems in order to address issues with fuel and electrical crossover, suitability for hydrocarbon ionomers, and scalability / large-scale reproducibility. A perfluorinated sulfonic acid ionomer reference material (Nafion D520) was employed for direct comparison to initial methods. Highly reproducible DMDs with low fuel and electrical crossover resulted.

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