Master of Science / Department of Chemistry / Mark Hollingsworth / The crystal structures of the inclusion compounds 1,6-diisocyanohexane/urea and 1,6-dicyanohexane/urea were refined at several temperatures from X-ray data. These urea inclusion compounds are commensurate structures with host:guest ratios of 6:1. In contrast with the ordinary helical topology of the urea host, these structures have stacked loop topologies of the host hydrogen bonds and crystallize in space group P21/n. At room temperature, both structures are distorted along [001] from hexagonal metric symmetry. As in earlier studies of 1-chloro-6-cyanohexane/urea, cooling 1,6-diisocyanohexane/urea gives rise to an exothermic phase transition (Hº = -856 cal mol 1, Sº = -5 cal mol-1 K-1) at 175 K that results in the cooperative translation of guest molecules by 5.5 Å along the channel axis. In the low temperature form, 1,6-diisocyanohexane/urea is distorted along [100], much like X(CH2)6Y, where X, Y = Br, Cl. Although the crystal structure of 1,6-dicyanohexane/urea is essentially isomorphous with that of the high temperature form of 1,6-diisocyanohexane/urea, it does not undergo an equivalent phase transition at low temperatures. Both of these systems exhibit dynamic disorder between two gauche conformers of the guest, which have mean planes of the alkyl chains lying within 1º of [100] (major conformer) and approximately 14º from [001] (minor conformer). The temperature dependence of site occupancy factors for the disordered sites yielded enthalpy differences between major and minor sites in 1,6-diisocyanohexane/urea and 1,6-dicyanohexane/urea of 216 and 127 cal mol 1, respectively. Since the low temperature form of 1,6-diisocyanohexane/urea is distorted along [100], this is favored at low temperatures by an increased concentration of the major conformer, which predominates in 1,6-dibromohexane/urea and congeners. In 1,6-diisocyanohexane/urea, the phase transition to the low temperature form occurs at a threshold concentration for the major conformer of 67%. With its shallower temperature dependence, 1,6-dicyanohexane/urea should not reach this threshold population until approximately 92 K, at which temperature the system cannot overcome the barrier for cooperative translation of guests along the channel axis.

Doctor of Philosophy / Department of Chemistry / Viktor Chikan / This dissertation reports the colloidal synthesis of iron silicide, hafnium oxide core-gold shell and water soluble iron-gold alloy for the first time. As the first part of the experimentation, plasmonic and superparamagnetic nanoparticles of gold and iron are synthesized in the form of core-shell and alloy. The purpose of making these nanoparticles is that the core-shell and alloy nanoparticles exhibit enhanced properties and new functionality due to close proximity of two functionally different components. The synthesis of core-shell and alloy nanoparticles is of special interest for possible application towards magnetic hyperthermia, catalysis and drug delivery. The iron-gold core-shell nanoparticles prepared in the reverse micelles reflux in high boiling point solvent (diphenyl ether) in presence of oleic acid and oleyl amine results in the formation of monodisperse core-shell nanoparticles. The second part of the experimentation includes the preparation of water soluble iron-gold alloy nanoparticles. The alloy nanoparticles are prepared for the first time at relatively low temperature (110 oC). The use of hydrophilic ligand 3-mercapto-1-propane sulphonic acid ensures the aqueous solubility of the alloy nanoparticles. Next, hafnium oxide core-gold shell nanoparticles are prepared for the first time using high temperature reduction method. These nanoparticles are potentially important as a high κ material in semiconductor industry. Fourth, a new type of material called iron silicide is prepared in solution phase. The material has been prepared before but not in a colloidal solution. The Fe3Si obtained is superparamagnetic. Another phase β-FeSi2 is a low band gap (0.85 eV) semiconductor and is sustainable and environmentally friendly. At last, the iron monosilicide (FeSi) and β-FeSi2 are also prepared by heating iron-gold core-shell and alloy nanoparticles on silicon (111) substrate. The nucleation of gaseous silicon precursor on the melted nanoparticles results the formation of nanodomains of FeSi and β-FeSi2. A practical application of these nanoparticles is an important next step of this research. Further improvement in the synthesis of β-FeSi2 nanoparticles by colloidal synthetic approach and its application in solar cell is a future goal.

Materials science today is a multidisciplinary effort comprising an accelerated convergence of diverse fields spanning the physical, applied, and engineering sciences. This diversity promises to deliver the next generation of advanced functional materials for a wide range of specific applications. In particular, the past decade has seen a growing interest in the development of nanoscale materials for sophisticated technologies. Aqueous colloidal microgels have emerged as a promising class of soft materials for multiple biotechnology applications. The amalgamation of physical, chemical and mechanical properties of microgels with optical properties of nanostructures in hybrid composite particles further enhances the capabilities of these materials. This work covers the general areas of responsive polymer microgels and their composites, and encompasses methods of fabricating microgel-based drug delivery systems for controlled and targeted therapeutic applications. The first part of this thesis is devoted to acquainting the reader with the fundamental aspects of the synthesis, functionalization and characteristic properties of stimulus-responsive microgels constructed from poly(N-isopropylacrylamide) (poly(NIPAm)) and other functional comonomers. In particular, the role of electrostatics on the swelling-deswelling transitions of polyampholyte microgels upon exposure to a range of environmental stimuli including pH, temperature, and salt concentration are discussed. The templated synthesis of bimetallic gold and silver nanoparticles in zwitterionic microgels is also described. The latter part of this thesis focuses on the rational development of microgel-based drug delivery systems for controlled and targeted drug release. Specifically, the development of a biofunctionalized, pH-responsive drug delivery system (DDS) is illustrated, and shown to effectively suppress cancer cells when loaded with an anticancer agent. In another chapter, the design of tailored hybrid particles that combine the thermal response of microgels with the light-sensitive properties of gold nanorods to create a DDS for photothermally-induced drug release is discussed. The photothermally-triggered volume transitions of hybrid microgels under physiological conditions are reported, and their suitability for the said application evaluated. In another component of this work, it is explicitly shown that electrostatic interactions were not needed to deposit gold nanorods on poly(NIPAm)-derived particles, thereby eliminating the need for incorporation of charged functional groups in the microgels that are otherwise responsible for large, undesirable shifts and broadening of the phase transition.

Tyrosyl phosphorylation plays an important role in many fundamental cellular processes, including cell growth, differentiation and proliferation. The levels of phosphotyrosine (pY) are regulated by the opposing actions of protein-tyrosine kinases (PTKs) and protein-tyrosine phosphatases (PTPs). A limitation to understanding the roles of PTPs in physiological and pathological cell signaling has been the absence of global proteomic approaches that enable the systematic and comprehensive analysis of PTP expression, regulation and function. This dissertation describes the development and application of novel proteomic methodologies that permit the global analysis of PTP expression (qPTPome), regulation (by oxidation and nitrosylation; q-oxPTPome) and substrates/binding proteins. These methods provide a workflow to begin assessing PTP function at a systems level, rather than its current targeted format. Application of these techniques will provide invaluable information to begin bridging the gap in our understanding of PTP and PTK function in normal and malignant cell signaling.

Développer de nouveaux nanomatériaux, interrupteurs et machines nanométriques sensibles à de petites variations de température spécifiques devrait être de grande utilité pour une multitude de domaines œuvrant dans la nanotechnologie. De plus, l’objectif est de convaincre le lecteur que les nanotechnologies à base d’ADN offrent d’énormes possibilités pour la surveillance de température en temps réel à l’échelle nanométrique. Dans la section Résultats, nous exploitons les propriétés de l’ADN pour créer des thermomètres versatiles, robustes et faciles à employer. En utilisant une série de nouvelles stratégies inspirées par la nature, nous sommes en mesure de créer des nanothermomètres d’ADN capables de mesurer des températures de 25 à 95°C avec une précision de <0.1°C. En créant de nouveaux complexes d’ADN multimériques, nous arrivons à développer des thermomètres ultrasensibles pouvant augmenter leur fluorescence 20 fois sur un intervalle de 7°C. En combinant plusieurs brins d’ADN avec des plages dynamiques différentes, nous pouvons former des thermomètres montrant une transition de phase linéaire sur 50°C. Finalement, la vitesse de réponse et la précision des thermomètres développés et leur réversibilité sont illustrées à l’aide d’une expérience de surveillance de température à l’intérieur d’un unique puits d’un appareil de qPCR. En conclusion, les applications potentielles de tels nanothermomètres en biologie synthétique, imagerie thermique cellulaire, nanomachines d’ADN et livraison contrôlée seront considérées. / Developing nanomaterials, probes, switches or nanomachines that are able to respond to specific temperature changes should prove of utility for several applications in the fields of in vivo imaging, clinical diagnostics, and drug-delivery. Here, we describe various bio- inspired strategies to engineer DNA thermoswitches with programmable linear response ranges for precise temperature sensing between 25 to 95°C with thermal precision <0.1°C. Using multimeric switch architectures, we are able to create ultrasensitive thermometers that display large 20-fold, quantitative signal changes within only 7°C. Lastly, by combining thermoswitches of different stabilities, or a mix of stabilizers of various strengths, we can create extended thermometers that respond linearly in a 50°C temperature window. Using these programmable DNA thermometers we measured, for the first time, the temperature equilibration time inside PCR wells using a fluorescent readout. Their potential applications in in vivo imaging, DNA nanomachines, drug delivery systems and synthetic biology are further discussed.

Doctor of Philosophy / Department of Chemical Engineering / Keith L. Hohn / Amorphous silica-alumina is widely used as a solid acid catalyst for various reactions in oil refining and the petrochemical industry. The strength and the number of the acid sites in the material are most often believed to arise from the alumina atoms inserted into the silica lattice. The existence of the acidity distribution across the framework is a result of the local composition or the short-range interactions on the silica-alumina surface. Conventional techniques used to characterize silica-alumina provide effective information on the average acidity, but may not reflect the heterogeneity of surface acidity within the material. Recently, it is possible to study individual catalytic sites on solid catalysts by single molecule fluorescence microscopy with high time and space resolution. Fluorophores can be chosen that emit at different wavelengths depending on the properties of the local environment. By doping these fluorophores into a solid matrix at nanomolar concentrations, individual probe molecules can be imaged. Valuable information can be extracted by analyzing changes in the fluorescence spectrum of the guest molecules within a host matrix. In this research, silica-alumina thin films were studied with single molecule fluorescence microscopy. The samples were prepared by a sol-gel method and a wide-field fluorescence microscope was used to locate and characterize the fluorescent behaviors of pH sensitive probes. In mesoporous thin films, the ratio of the dye emission at two wavelengths provides an effective means to sense the effective pH of the microenvironment in which each molecule resides. The goal of this work was to develop methods to quantify the acidity of individual micro-environments in heterogeneous networks. Pure silica films treated with external phosphate solutions of different pH values were used to provide references of the fluorescence signals from individual dye molecules. SM emission data were obtained from mesoporous Al-Si films as a function of Al content in films ranging from 0% to 20% alumina. Histograms of the emission ratio revealed that films became more acidic with increasing Al content. The acidity on interior surfaces in zeolite pores was also of interest in this work. A microfluidic device was built to isolate the interior surface from the exterior surface. Some preliminary results showed the potential of using SM fluorescence method to study the acidic properties inside the pores of zeolite crystals.

Doctor of Philosophy / Department of Chemistry / Viktor Chikan / The research work in this thesis aims at investigating the basic physic-chemical properties of magnetic and metal nanoparticles (NPs) for biomedical applications such as magnetic hyperthermia and controlled drug release. Magneto-plasmonic properties of magnetic NPs are important to evaluate potential applications of these materials. Magnetic property can be used to control, monitor and deliver the particles using a magnetic field while plasmonic property allows the tracking of the position of the particles, but aggregation of NPs could pose a problem. Here, the aggregation of NPs is investigated via the Faraday rotation of gold coated Fe[subscript]2O[subscript]3 NPs in alternating magnetic fields. In addition, the Faraday rotation of the particles is measured in pulsed magnetic fields, which can generate stronger magnetic fields than traditional inductive heaters used in the previous experiments. In the second project, the formation of protein-NPs complexes is investigated for hyperthermia treatment. The interactions between gold and iron-platinum NPs with octameric mycobacterial porin A from Mycobacterium smegmatis (MspA) and MspA[superscript])cys protein molecules are examined to assemble a stable, geometrically suitable and amphiphilic proteins-NPs complex. Magnetic NPs show promising heating effects in magnetic hyperthermia to eliminate cancer cells selectively in the presence of alternating magnetic field. As a part of investigation, the heating capacity of a variety of magnetic NPs and the effects of solvent viscosity are investigated to obtain insight into the heating mechanism of these particles. Finally, the controlled drug release of magnetic NPs loaded liposomes by pulsed magnetic field is investigated. The preliminary data indicate about 5-10% release of drug after the application of 2 Tesla magnetic pulses. The preliminary experiments will serve as the initial stage of investigation for more effective magnetic hyperthermia treatment with the help of short magnetic pulses.

The extensive agricultural usage of organohalogenated pesticides has raised many concerns about their potential hazards especially in the soil environment. Environmental metabolomics is an emerging field that investigates the changes in the metabolic profile of native organisms in their environment due to the presence of an environmental stressor. Research presented here explores the potential of Nuclear Magnetic Resonance (NMR)-based metabolomics to examine the sub-lethal exposure of the earthworm, Eisenia fetida to sub-lethal concentrations of organohalogenated pesticides. Various one-dimensional (1-D) and two dimensional (2-D) NMR techniques were compared in a contact filter paper test earthworm metabolomic study using endosulfan, a prevalent pesticide in the environment. The results determined that both the 1H Presaturation Utilizing Gradients and Echos (PURGE) and the 1H-13C Heteronuclear Single Quantum Coherence (HSQC) NMR techniques were most effective in discriminating and identifying significant metabolites in earthworms due to contaminant exposure. These two NMR techniques were further explored in another metabolomic study using various sub-lethal concentrations of endosulfan and an organofluorine pesticide, trifluralin to E. fetida. Principal component analysis (PCA) tests showed increasing separation between the exposed and unexposed earthworms as the concentrations for both contaminants increased. A neurotoxic mode of action (MOA) for endosulfan and a non-polar narcotic MOA for trifluralin were delineated as many significant metabolites, arising from exposure, were identified. The earthworm tissue extract is commonly used as the biological medium for metabolomic studies. However, many overlapping resonances are apparent in an earthworm tissue extract NMR spectrum due to the abundance of metabolites present. To mitigate this spectral overlap, the earthworm’s coelomic fluid (CF) was tested as a complementary biological medium to the tissue extract in an endosulfan exposure metabolomic study to identify additional metabolites of stress. Compared to tests on the tissue extract, a plethora of different metabolites were identified in the earthworm CF using 1-D PURGE and 2-D HSQC NMR techniques. In addition to the neurotoxic MOA identified previously, an apoptotic MOA was also postulated due to endosulfan exposure. This thesis also explored the application of 1-D and 2-D NMR techniques in a soil metabolomic study to understand the exposure of E. fetida to sub-lethal concentrations of endosulfan and its main degradation product, endosulfan sulfate. The earthworm’s CF and tissue extract were both analyzed to maximize the significant metabolites identified due to contaminant exposure. The PCA results identified similar toxicity for both organochlorine contaminants as the same separation, between exposed to the unexposed earthworms, were detected at various concentrations. Both neurotoxic and apopotic MOAs were observed as identical fluctuations of significant metabolites were found. This research demonstrates the potential of NMR-based metabolomics as a powerful environmental monitoring tool to understand sub-lethal organohalogenated pesticide exposure in soil using earthworms as living probes.

Climate change is predicted to be the most pronounced in high latitude ecosystems, however very little is known about their vulnerability to the projected warmer temperatures. In particular, natural organic matter (NOM) in the high latitude cryosphere which includes dissolved organic matter (DOM) and cryoconite organic matter (COM) from glaciers and soil organic matter (SOM) in permafrost, is highly susceptible to climate change which may lead to severe consequences on both local and global carbon biogeochemical cycles. Examination of DOM in glacier ice by a novel 1H nuclear magnetic resonance (NMR) water suppression pulse sequence at its natural abundance revealed and quantified the composition and the organic constituents in ice samples from Antarctica. 1H NMR spectra of samples from several glaciers were acquired and compared to the dominant fluorescent DOM fraction. This comprehensive approach showed that glacier ice DOM was mainly composed of small, labile biomolecules associated with microbes. Examination of the organic debris found on glacier surfaces (COM) from both Arctic and Antarctic glaciers were determined to be derived from microbes. Samples from Arctic glaciers were more chemically heterogeneous with small inputs of plant-derived material detected after targeted extractions. Therefore the COM carbon composition was determined to be dependent on the local glacier environment, suggesting a site specific contribution to the carbon cycle. Finally, the distribution of extracted branched glycerol dialkyl glycerol tetraether (GDGT)microbial membrane lipids and the deuterium incorporation of plant-wax n-alkane biomarkers extracted from dated permafrost SOM (paleosols) were independently applied for Canadian Arctic climate reconstruction during the last glacial maximum. Overall, the branched GDGT based temperature reconstructions from the Arctic paleosols reconstruct higher temperatures, likely when bacterial activity was optimal. The deuterium composition of the C29 n-alkane plant lipids appears to integrate an average annual signal. Further analysis by both non-selective NMR spectroscopic and targeted biomarker techniques on these paleosol samples revealed that the major vegetative sources from this paleoecosystem originated from woody and non-woody angiosperms. This thesis demonstrates several novel analytical characterization techniques, along with the major sources and composition of NOM in the cryosphere while demonstrating its use in paleoclimate applications.

The air-water interface is abundant in the environment, thus it is an important proxy for atmospheric processes such as the uptake and transfer of molecules, heterogeneous reactions, photochemistry, and cloud condensation. This thesis aims to elucidate the role of semi-soluble and insoluble organic coatings on atmospheric processes at the air-water interface. Using glancing-angle LIF it was found that monolayer coatings of 1-octanol and of octanoic acid have opposing effects on the ozonation rate of pyrene at the air-water interface. LIF was also coupled with a Profile Analysis Tensiometer (PAT-1) to measure the effect of stearic acid coating compression on the uptake of HCl to a water droplet. Due to preliminary issues with this novel technique, no significant uptake suppression was observed. The oxidation of benzene by OH radical was also explored briefly, as were the photophysics of photosensitizers and the angle dependence of Raman signal from a D2O pendent droplet.