Physical Sciences and Mathematics Commons^™

Advancements In Fractal Plasmonics: Structures, Optical Properties, And Applications., Gregory Q Wallace, Francois Lagugne-Labarthet

Chemistry Publications

The structural characteristics of plasmonic nanostructures directly influence their plasmonic properties, and therefore, their potential role in applications ranging from sensing and catalysis to light- and energy-harvesting. For a structure to be compatible with a selected application, it is critical to accurately tune the plasmonic properties over a specific spectral range. Fabricating structures that meet these stringent requirements remains a significant challenge as plasmon resonances are generally narrow with respect to the considered selected spectral range. Adapted from their well-established role in GHz applications, plasmonic fractal structures have emerged as architectures of interest due to their ability to support multiple …

Photo-Isomerizable Complementary Hydrogen Bond Arrays, Jeffrey S. Pleizier

Electronic Thesis and Dissertation Repository

The use of light as an external stimulus provides a non-invasive technique to induce large changes in physical and chemical properties of a substrate. The incorporation of a photochromic subunit into supramolecular polymeric systems therefore adds a potential "smart" quality for polymer manipulation. The azo moiety (-N=N-) is one of the most popular photochromic units as the trans to cis isomerization results in a large degree of spatial rearrangement. This present thesis exploits the azo group by its incorporation into complementary hydrogen bonded complexes. Hydrogen bonding acceptor groups attached to the periphery of the central azo photoswitch provided strong complexation …

Corrosion Dynamics Of Carbon Steel In Used Fuel Container Environments, Dan Guo

Electronic Thesis and Dissertation Repository

The current Canadian used nuclear fuel container (UFC) design uses a pressure‑grade carbon steel (CS) vessel with its outer surface coated with a thin layer of copper. One concern regarding the structural integrity of the UFC design is the potential internal corrosion of the CS vessel. Moisture trapped inside a UFC could condense within the gap between the hemispherical head and the cylindrical body of the vessel. The internal UFC environment will be exposed to a continuous flux of ionizing radiation arising from the decay of radionuclides trapped in the used UO₂ fuel matrix.

This thesis research project investigates …

Near-Infrared Photoluminescence And Electrochemiluminescence From An Exceptionally Simple Boron Difluoride Formazanate Dye, Ryan R. Maar, Ruizhong Zhang, David G. Stephens, Zhifeng Ding, Joe Gilroy

Chemistry Publications

Electrochemiluminescence involves the generation of light via electrochemical reactions and has recently shown utility for single-cell imaging. To further develop this novel imaging platform, it is necessary to produce readily available dyes that photoluminesce and electrochemiluminesce in the near-infrared region to limit absorption by biological tissue. To address this need, we prepared a boron difluoride formazanate dye that exhibits near-infrared photoluminescence and electrochemiluminescence in two straightforward synthetic steps. Examination of its solid-state structure suggests that the N-aryl substituents have significant quinoidal character, which narrows the S₁-S₀ energy gap and leads to near-infrared absorption and photoluminescence. Electrochemical …

Evidence For A Partially Stalled Γ Rotor In F, Angela Murcia Rios, Siavash Vahidi, Stanley D Dunn, Lars Konermann

Chemistry Publications

F₁-ATPase uses ATP hydrolysis to drive rotation of the γ subunit. The γ C-terminal helix constitutes the rotor tip that is seated in an apical bearing formed by α₃β₃. It remains uncertain to what extent the γ conformation during rotation differs from that seen in rigid crystal structures. Existing models assume that the entire γ subunit participates in every rotation. Here we interrogated E. coli F₁-ATPase by hydrogen-deuterium exchange (HDX) mass spectrometry. Rotation of γ caused greatly enhanced deuteration in the γ C-terminal helix. The HDX kinetics implied that most F_{1 …}

The Electrochemical Study Of Simulated Spent Nuclear Fuel (Simfuel) Corrosion Under Permanent Disposal Conditions, Ziyan Zhu

Electronic Thesis and Dissertation Repository

The safety assessment of spent nuclear fuel under permanent disposal conditions requires examination of the corrosion of the spent fuel waste form (UO₂) inside a failed waste container. The objective of this research project was to develop a detailed mechanism of the UO₂ corrosion process when exposed to groundwater. The redox conditions within a failed container in a deep geologic repository will be complex. The oxidant, H₂O₂, produced by the α-radiolysis of groundwater, will be the main driving force for fuel corrosion. However, the efficiency of fuel dissolution will be determined by the …

Pressure Tuning Of Energy Storage Materials Probed By In-Situ Vibrational Spectroscopy And Synchrotron Radiation, Pan Wang

Electronic Thesis and Dissertation Repository

Clean and renewable energy has drawn much attention recently due to the increasing demand for more energy and environmental issues. New materials have been developed and the improved performance of such materials have been achieved in the past decades. It has been proved that application of external high pressure can significantly tune the structure of materials. Consequently, the properties of the materials could also be modified. Therefore, in this thesis, we focused on the high-pressure studies of two classes of energy storage materials, hydrogen storage materials and solar cell materials. Ammonia borane (AB) has been extensively investigated as an excellent …

Computational Studies On Nucleic Acid-Ion Interactions In Droplets And Bulk Solution, Mahmoud Sharawy

Electronic Thesis and Dissertation Repository

Interactions of macromolecules with ions in solution have a long history of study because of their ubiquitous nature. These interactions are essential for the stability and function of macromolecules such as nucleic acids. Nucleic acids are involved in many natural biochemical processes. For example, deoxyribonucleic acid (DNA) provides more than storage of genetic information. The guanine-rich structures, at the ends of the DNA, participate in regulating the gene expression in the living cell by forming guanine quadruplex (G-quadruplex) structures. These structures provide a possible drug target for the treatment of cancer. Nucleic acids are polyions under physiological pH of 7.4. …

Phosphonium Hydrogels For Controlled Release Of Ionic Cargo., Tristan D Harrison, Paul J Ragogna, Elizabeth R Gillies

Chemistry Publications

We describe the synthesis of three different phosphonium salts and their reaction with poly(ethylene glycol) dimethacrylate to create cationic hydrogels. The hydrogels were loaded with an anionic dye and an anionic anti-inflammatory drug through ionic interactions and compared with an analogous ammonium gel. The release rates of these anions depended on their structure and pKa values, as well as the pH and ionic strength of the release medium.

Layer-By-Layer Construction Strategies Towards Efficient Czts Solar Cells, Matthew J. Turnbull

Electronic Thesis and Dissertation Repository

Solar energy has very high potential for ensuring the world’s energy requirements for the long-term future. Earth-abundant materials like Cu₂ZnSnS₄ (CZTS) are especially desirable, with a non-toxic, low-cost nature, though the quaternary nature allows for a lot of crystal structure variability, and thus underwhelming performance. This Ph.D. thesis is devoted to deepening the understanding of the CZTS material formation, and the processes that can be used to control it, to construct a low-cost, high efficiency CZTS-based solar cell. The layer-by-layer approach presented within this thesis shows great potential for rectifying the problem. CZTS nanocrystal (NC) stoichiometric control …

Surprising Antibacterial Activity And Selectivity Of Hydrophilic Polyphosphoniums Featuring Sugar And Hydroxy Substituents., Tyler J Cuthbert, Benjamin Hisey, Tristan D Harrison, John F Trant, Elizabeth R Gillies, Paul J Ragogna

Chemistry Publications

There is currently an urgent need for the development of new antibacterial agents to combat the spread of antibiotic-resistant bacteria. We explored the synthesis and antibacterial activities of novel, sugar-functionalized phosphonium polymers. While these compounds exhibited antibacterial activity, we unexpectedly found that the control polymer poly(tris(hydroxypropyl)vinylbenzylphosphonium chloride) showed very high activity against both Gram-negative Escherichia coli and Gram-positive Staphylococcus aureus and very low haemolytic activity against red blood cells. These results challenge the conventional wisdom in the field that lipophilic alkyl substituents are required for high antibacterial activity and opens prospects for new classes of antibacterial polymers.

Coupling Scanning Electrochemical Microscopy And 3d Modelling To Probe Membrane Permeability Of Human Bladder Cancer (T24) Cells, Fraser Filice

Electronic Thesis and Dissertation Repository

Scanning electrochemical microscopy (SECM) scans a biased ultramicroelectrode (≤ 25 µm) probe over a sample to characterize topography, physical properties and chemical reactivity. In this dissertation, SECM was used to investigate the metal-induced changes in membrane response of single live human bladder cancer cells (T24). SECM imaging was coupled to 3D finite element method (FEM) simulations which were the first of their kind, providing advanced quantification of sample traits under conditions not previously usable.

The effects of Cd²⁺ on T24 cell membrane permeability were examined. Experimental depth-scan imaging was coupled with full 3D FEM simulations, eliminating many limitations of …

Hydrogen-Deuterium Exchange Mass Spectrometry And Molecular Dynamics Simulations For Studying Protein Structure And Dynamics, Yiming Xiao

Electronic Thesis and Dissertation Repository

Deciphering properties of proteins are essential for human health and aiding in the development of new pharmaceuticals. This dissertation uses hydrogen-deuterium exchange (HDX) mass spectrometry (MS) and molecular dynamics (MD) simulations to study protein dynamics, for improving the understanding of protein folding/unfolding mechanisms, and ligand binding and allosteric regulation.

Chapter 2 uses HDX-MS for probing the conformational dynamics of myoglobin in the presence of N₂ bubbles. We propose a dynamic model that reproduces the observed data: “semi-unfolded” “native” “globally unfolded” -> “aggregated”. Chapter 3 focuses on osteoprotegerin (OPG), which hinders bone resorption by inhibiting RANK/RANKL interactions. The dimerization of …

Mechanism Of Protein Charging And Supercharging In Electrospray Ionization: Molecular Dynamics Simulations And Experimental Investigations, Haidy S. Metwally

Electronic Thesis and Dissertation Repository

Electrospray ionization mass spectrometry (ESI-MS) is a powerful technique for investigating protein structures, conformations, and interactions. Despite its widespread use, many fundamental aspects of ESI remain poorly understood. In this thesis, we use a combination of molecular dynamics (MD) simulations and experiments to gain insights into the hidden complexities of ESI-MS.

Chapter 2 discusses the topic of salt-induced protein signal degradation. Salts such as NaCl, CsCl, and tetrabutyl ammonium chloride (NBu₄Cl) interfere with MS data acquisition, leading to adduct formation and signal suppression. MD simulations provide an explanation for these salt interferences. Signal suppression can be broken down …

Probing Trapped Extracellular Vesicles By Surface-Enhanced Raman Spectroscopy, Lauren Kaufman

Electronic Thesis and Dissertation Repository

Extracellular vesicles (EVs) are released by nearly all cell types within the human body and have been found to play important biological roles including cell-to-cell communication, apoptosis and tissue repair. Lacking cellular machinery, these nano-sized vesicles carry functional proteins and nucleic acids from their parent cells, providing insight into biomarkers present in healthy, cancerous and diseased cells. EVs may be isolated from biofluids such as from blood or urine. Their detection and characterization holds extreme potential in developing less invasive disease detection and treatment methods.

In this work, we propose use of lithographic techniques to fabricate platforms to allow for …

Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Imaging Of Zp1609 And Amyloid Beta, Jasmine S. H. Wang

Electronic Thesis and Dissertation Repository

The revolutionary development of soft ionization techniques like matrix-assisted laser desorption/ionization (MALDI) has opened up the possibilities for mass spectrometry (MS) in protein detection, identification, and sequencing. The ability of MALDI MS to acquire images of intact tissue sections offer an additional dimension of analysis where location information can be attained. Visualization of biological systems help to unravel the complexities of cells, drug pathways, and disease pathology. However, the capabilities of MALDI MS imaging are often being questioned, as signals are typically biased towards the most abundant component within a complex sample. Within biological tissue samples, the most abundant components …

Synthesis And Characterization Of Alkynyl-Substituted Boron Formazanate Dyes, Alex Van Belois

Electronic Thesis and Dissertation Repository

This thesis outlines the synthesis and characterization of the first alkynyl-substituted boron formazanate complexes and explores the electronic and structural changes that occur in these systems as a result of chemical modification at the boron centre. An alkynyl-substituted complex appended with a redox-active handle is also described, and the chemical reduction and oxidation of this system is explored. Finally, a model reaction is examined as a proof of concept toward the post-synthetic modification of these boron formazanate systems through copper(I)-assisted alkyne-azide cycloaddition chemistry. Exploiting chemistry at the boron centre opens up new possibilities toward incorporating function onto the boron formazanate …

Exploring The Chemistry Of Asymmetric Phosphines & Phosphinidene Sulfides, Taylor E. Pritchard

Electronic Thesis and Dissertation Repository

The field of low-coordinate main group chemistry has seen huge development in the last 30 years, with novel compounds that demonstrate unique structures and reactivity. Isolation of these species has relied on thoughtfully designed substituents normally containing substructure steric bulk. The area of phosphinidene chalcogenide isolation and transfer remains poorly understood by comparison. In this context, the major focus of thesis was on the development of a room-temperature method for the transfer of RP=S moieties with and without sterically demanding substituents. The preparation and complete characterization of new asymmetric phosphines with m-terphenyl ligands was also reported. In Chapter 2, …

Multi-Stimuli-Responsive Self-Immolative Polymer Assemblies, Rebecca E. Yardley, Elizabeth R. Gillies

Chemistry Publications

Self-immolative polymers (SIPs) undergo depolymerization in response to the cleavage of stimuli-responsive end-caps from their termini. Some classes of SIPs, including polycarbamates, have depolymerization rates that depend on environmental factors such as solvent and pH. In previous work, hydrophobic SIPs have been incorporated into amphiphilic block copolymers and used to prepare nanoassemblies. However, stimuli-responsive hydrophilic blocks have not previously been incorporated. In the current work, we synthesized amphiphilic copolymers composed of a hydrophobic polycarbamate SIP block and a hydrophilic poly(2-dimethylaminoethyl methacrylate) (PDMAEMA) block connected by a UV light-responsive linker end-cap. It was hypothesized that after assembly of the block copolymers …

Electrospray Ionization Of Polypropylene Glycol: Rayleigh-Charged Droplets, Competing Pathways, And Charge State-Dependent Conformations., Quentin Duez, Haidy Metwally, Lars Konermann

Chemistry Publications

Recent molecular dynamics (MD) simulations from various laboratories have advanced the general understanding of electrospray ionization (ESI)-related processes. Unfortunately, computational cost has limited most of those previous endeavors to ESI droplets with radii of ∼3 nm or less, which represent the low end of the size distribution in the ESI plume. The current work extends this range by conducting simulations on aqueous ESI droplets with radii of 5.5 nm (∼23 000 water molecules). Considering that computational cost increases with r⁶, this is a significant step forward. We focused on the ESI process for polypropylene glycol (PPG) which is …

Chain Ejection Model For Electrospray Ionization Of Unfolded Proteins: Evidence From Atomistic Simulations And Ion Mobility Spectrometry., Haidy Metwally, Quentin Duez, Lars Konermann

Chemistry Publications

The ion evaporation model (IEM) and the charged residue model (CRM) represent cornerstones of any discussion related to the mechanism of electrospray ionization (ESI). Molecular dynamics (MD) simulations have confirmed that small ions such as Na⁺ are ejected from the surface of aqueous ESI droplets (IEM), while folded proteins in native ESI are released by water evaporation to dryness (CRM). ESI of unfolded proteins yields [M + zH] ^z+ ions that are much more highly charged than their folded counterparts. A chain ejection model (CEM) has been proposed to account for the protein ESI behavior under such non-native conditions …

Plant Stimuli-Responsive Biodegradable Polymers For The Use In Timed Release Fertilizer Coatings, Spencer Heuchan

Electronic Thesis and Dissertation Repository

The use of nitrogen-based fertilizers continues to accelerate with human population growth and increases in global food requirements. Enhanced efficiency fertilizers (EEFs) have been developed to improve the synchronization between nutrient supply and crop nutrient demand. However, many of the current controlled release fertilizers are coated with non-degradable polymers that contribute to accumulation of microplastics within ecosystems. This thesis describes research towards the development of a new class of fertilizer coatings using a self-immolative polymer known as poly (ethyl glyoxylate) (PEtG). PEtG itself does not have suitable properties to produce a viable coating but once blended with another degradable polyester …

Design, Synthesis, And Evaluation Of Novel Protease-Activated Receptor 2 (Par2)-Targeting Imaging Agents For Cancer, Jordan C. Lesarge

Electronic Thesis and Dissertation Repository

Aberrant function and over-expression of protease-activated receptor 2 (PAR2), a GPCR, is associated with various cancers and inflammatory diseases. PAR2-targeting ligands have been developed with therapeutic applications but the development of imaging probes is lacking. A series of PAR2-targeted fluorescent and ¹⁸F-PET imaging agents were synthesized and assessed for PAR2-binding. A novel dye-conjugated peptide, Isox-Cha-Chg-ARK(Sulfo-Cy5)-NH₂ (EC₅₀=16nM, K_D=38nM), showed >10-fold increase in potency and binding affinity for PAR2 compared to the leading known fluorescent probe. A novel PET imaging ¹⁸F-labeled peptide, Isox-Cha-Chg-AR-Dpr([¹⁸F]4-FB)-NH₂, is the first PAR2-targeted in vivo imaging agent. …

The Development Of Metal Complexes As Components Of Fluorescent And Nuclear Imaging Probes, William Turnbull

Electronic Thesis and Dissertation Repository

The advent of molecular imaging as a discipline has drastically improved our ability to understand the biochemical and cellular events that drive life, death and disease. This thesis will document the discovery of new metal chelators for Re/^99mTc, new methods of incorporating these metals into peptide structures, as well as new fluorescent compounds. These novel methods and compounds may be used in the development of molecular imaging probes for single photon emission computed tomography (SPECT) and optical imaging techniques, with applications for differentiating cancerous tissue from benign and healthy.

Chapter 2 discusses the development of a dual modality …

Investigating Non-Targeted Screening And Accurate Quantitation Of Trace Surface Water Contaminants Using High-Resolution Mass Spectrometry, Lucas M. Morrison

Electronic Thesis and Dissertation Repository

The human impact on surface water is a growing concern and the chemical surveying of contaminants including pharmaceuticals and pesticides is currently lacking. Neonicotinoids in particular, are among the most widely used insecticides that have prompted environmental concern and require monitoring. Chemical contaminants in environmental water samples are commonly analyzed by targeted tandem mass spectrometry. However, this requires a prior knowledge of the contaminants in the area of interest. Here, surface water samples were screened by utilizing optimized data-independent acquisition (DIA) methods and the spectra were databased for future retrospective analysis. This circumvents the requirement for target analytes prior to …

Design, Synthesis, And Oxidation Reactivity Of Palladacyclic Complexes Containing N-Donor Ligands, Ava Behnia

Electronic Thesis and Dissertation Repository

This thesis describes the synthesis and reactivity of complexes containing the cycloneophyl-Pd(II) group, PdCH₂CMe₂C₆H₄, in combination with N-donor ligands. These compounds contain both alkyl- and arylpalladium bonds and the selectivity of bond cleavage in reactions with oxidants and protic reagents is studied, often involving oxidative addition and reductive elimination reaction sequences.

The diimine ligand in [Pd(CH₂CMe₂C₆H₄)(MesN=CH-CH=NMes)] does not support formation of stable palladium(IV) complexes, but reactions with Br₂ or I₂ lead to reductive elimination by C-C bond formation of 1,1-dimethylcyclobutabenzene while …

Imaging The Surface Of A Hand-Colored 19th Century Daguerreotype., Madalena S Kozachuk, Maria O Avilés, Ronald R Martin, Brianne Potts, Tsun-Kong Sham, François Lagugné-Labarthet

Chemistry Publications

Daguerreotypes are valued artifacts that constitute a unique historical photographic memory of the 19th century. Understanding their surface chemistry is important in order to conserve and, when necessary, to restore them. Colored highlights were often added by hand to emphasize different features on the daguerreotype's subjects. In the present work, we report on a daguerreotype that was hand-colored with a red pigment that was added to the cheeks of the two individuals. A series of experiments using micro-Raman and micro-Fourier transform infrared spectroscopy and synchrotron-based X-ray fluorescence microscopy and absorption spectroscopy are used to analyze the surface and to determine …

Effects Of High Pressure On Photochemical Reactivity Of Organic Molecular Materials Probed By Vibrational Spectroscopy, Jiwen Guan

Electronic Thesis and Dissertation Repository

Chemical transformations of molecular materials induced by high pressure and light radiation exhibit novel and intriguing aspects that have attracted much attention in recent years. Particularly, under the two stimuli, entire transformations of molecular species can be realized in condensed phases without employing additional chemical constraints, e.g., the need of solvents, catalysts or radical initiators. This new synthetic approach in chemistry therefore satisfies increasing need for production methods with reduced environmental impacts. Motivated by these promises, my Ph. D thesis focuses on this state-of-the-art branch of high-pressure photochemistry. Specifically, high pressure is employed to create the necessary reaction conditions to …

Computational And Spectroscopic Studies In The Design Of Tetrapyrrole Dyes For Dye-Sensitized Solar Cells, Angel (Qi Wen) Zhang

Electronic Thesis and Dissertation Repository

Cyclic tetrapyrroles, like porphyrins, phthalocyanines, and chlorins, are of great interest for dye-sensitized solar cell (DSSC) applications due to their highly versatile structure, tunable π based spectroscopic and electrochemical properties, and excellent stabilities. As well, they have a structural analogy with chlorophyll, a natural photosensitizer. Chlorophylls exhibit a red and intense lowest energy absorption band that is one of the ideal properties of a dye for application in DSSCs. However, because chlorophylls are unstable, it is necessary to design similar but more stable tetrapyrroles with these ideal properties. The relationship between chlorophyll’s geometric structure and spectral properties were first explored …

Synthesis Of 2-Thiouracil And 2-Thiothymine Peptide Nucleic Acid Monomers Compatible With Fmoc-Based Oligomerization, Timothy Martin-Chan

Electronic Thesis and Dissertation Repository

Pseudo-complementary nucleobases are modified nucleobases which exhibit normal base pairing with unmodified complementary nucleobases; however, will not undergo stable base pairing with other pseudo-complementary nucleobases. The pseudo-complementary nature of these bases is of interest for the synthesis of pseudo-complementary peptide nucleic acid (pcPNA) oligomers, which are capable of binding targets in double-stranded DNA through a double duplex strand invasion. Until recently, pcPNAs were synthesized via Boc-based oligomerization chemistry which is currently less popular than the Fmoc-based strategy.

This research describes the development of a Fmoc protected thiouracil PNA monomer with an acid labile protecting group for use in standard SPPS. …