Chemistry

Permanent URI for this collection

https://dspaceuiprd01.lib.uwaterloo.ca/handle/10012/9941

This is the collection for the University of Waterloo's Department of Chemistry.

Research outputs are organized by type (eg. Master Thesis, Article, Conference Paper).

Waterloo faculty, students, and staff can contact us or visit the UWSpace guide to learn more about depositing their research.

Browse

Now showing 1 - 20 of 842

A Curiosity Driven Exploration of Hypervalent Iodine(III) Reagents
(University of Waterloo, 2024-05-27) To, Avery Joseph
Hypervalent iodine (HVI) reagents have established themselves in the literature as reagents with diverse reactivity and utility in many different transformations. Their unique bonding structure often leads to divergent reactivity when compared to common oxidants, making them attractive reagents for study. They are typically easy-to-handle solids and require mild reaction conditions for activation. The field of hypervalent iodine is very active with many new transformations and even new reagents being reported annually. In Chapter 2 the use of diaryliodonium salts as catalysts for the Nazarov cyclization is discussed. In this study, the structure of the diaryliodonium salt catalyst was optimized for solubility and activity in the Nazarov reaction. Univariate optimization of the reaction for solvent, reaction temperature, and catalyst loading was completed. Using the optimized conditions a series of substrates were explored. Notably, many of the yields obtained were lower than those reported in the literature for the comparable Lewis and Brønsted acid-catalyzed reactions. A 1H-NMR study revealed a possible substrate degradation pathway to account for the lower yields. Control reactions were used to establish the necessity of oxygen in the reaction for catalyst activation and turnover. Overall, reaction conditions were developed for the use of a diaryliodonium salt in the Nazarov cyclization. In Chapter 3 we investigated the reactions of TolIF2 with styrenyl substrates containing a strained ring. This investigation uses the knowledge gained from previous reactions developed with TolIF 2 in the Murphy group. Three different reactions were explored, each giving a unique product, not obtained with classical fluorination methods. The first reaction, the reaction of TolIF2 with methylenecyclopropanes, produced a surprising product which incorporated the iodotoluene from TolIF2 into it, albeit in low yield. The second reaction was the ring expansion of a cyclobutanol to a fluorinated cyclopentanone. This reaction was optimized for Lewis acid activator, reaction solvent, temperature, as well as equivalents of reagent, but unfortunately still only gave the product in 61% yield with substantial side product. The final reaction explored was the gem-difluorination of alphacyclopropyl styrenes. Again, the conditions were optimized (Lewis acid, reaction temperature, reaction solvent, etc.) to produce the product in 51% yield. In this reaction, a persistent ketone byproduct was always observed. In Chapter 4 attention was turned to the design of new fluoroiodane derivatives. A survey of the hypervalent iodine literature revealed addition of steric bulk ortho to the iodine atom in HVI reagents led to improvements in reaction outcome. The key structural feature assessed was the torsion angle of the hypervalent bond. X-ray crystal structures of new derivatives were obtained and the torsion angle of the hypervalent bond of five fluoroiodanes and three chloroiodanes were compared. As expected, the torsion angle was larger in newly prepared derivatives (~8° vs. ~20°). A much larger torsion angle of ~55° was achieved with the homologated six-membered fluoroiodane. Unfortunately, preliminary investigations of the reactivity indicate that this series is less reactive compared to the parent reagent.
Exploring Ruthenium Nanoparticles Geometric Complexity to Boost Kellogg Advanced Ammonia Process Through Confinement Effect
(University of Waterloo, 2024-05-23) Radchanka, Aliaksandra
Ammonia consumption is expected to increase in the future due to its use as a zero-carbon fuel and as a material for hydrogen storage and shipping. Among all single metal catalysts, ruthenium has the highest catalytic activity for the synthesis of ammonia. This study investigates the catalytic performance of ruthenium nanocages (CGs) towards ammonia production. Additionally, the effect of spatial constraints on reaction kinetics has been investigated using CGs with large (20 nm) and small (2 nm) confinements. The kinetic parameters for NH3 synthesis were determined using temperature-programmed surface reaction and temperature programmed desorption experiments. The results of the ammonia production by the CGs were compared with those of control materials that would possess little to no confinement effects – nanospheres and nanoplates synthesized in the same conditions. It has been demonstrated that the uptake, activation energy and frequency factor of nitrogen desorption on ruthenium nanoparticles increases in the following order: no confinements < large confinements < large + small confinements. The nanoparticles with “small” confinements were shown to reach optimal temperatures for ammonia production at 310 °C, lower than both controls and CGs with larger confinements. The validity of attributing the potential catalytic improvement to the confinement effect, rather than to differences in morphology, structural defects, and alloying, is discussed.
Towards the Development of a Prototype Ion Mobility Spectrometer
(University of Waterloo, 2024-05-22) Rickert, Daniel
Ion mobility spectrometry (IMS) is an analytical technique that separates ions in the gas-phase based on differences in their mobility under the influence of an electric field. In traditional drift-tube IMS systems, an axial DC electric field pushes ions through a static bath gas, and the different ion subpopulations achieve averaged steady-state drift velocities that are dependent on their shape and size. Mobility separation is achieved due to multiple collisions between the molecular ions and gas molecules. Smaller, more compact ions will collide less frequently with the buffer gas in comparison to larger, more elongated ions. Consequently, the smaller ions have higher mobilities and therefore reach the detector faster. One of the most recent developments in IMS, which is referred to as trapped ion mobility spectrometry (TIMS) was reported first in 2011 by Park and coworkers. In contrast to the conventional drift tube approach described above, in the TIMS configuration, ions are trapped axially by balancing an applied DC electric field gradient against a parallel flow of neutral carrier gas flowing towards the detector. A radiofrequency induced quadrupolar field radially confines ions in the center of the TIMS separation region. Trapped ions are focused first and then eluted towards the mass analyzer from the separation region based on differences in their mobility by gradually reducing the electric field strength. The research described in this thesis covers the development and characterization of a prototype ion mobility spectrometer designed to improve upon the existing TIMS platform. This instrument, referred to as a variable flow trapped ion mobility spectrometer (vfTIMS), has a segmented mobility separation region comprised of four sectors with decreasing inner diameter. A gas flow velocity gradient that is generated through the decreasing sectors of the mobility region can be harnessed for high-resolution separations. Another improvement compared to the conventional TIMS is instead of a quadrupolar radially confining field, the vfTIMS employs a hexapolar field for improved ion focusing and increased ion capacity. Additionally, the DC electric field gradient that traps the ions is completely customizable by utilizing individually addressable electrodes, so the profile is not limited to a simple linear field gradient. The main research objectives of this thesis are as follows: 1. Construct a prototype ion mobility spectrometer, combining multiple commercial and in-house components. 2. Implement an improved electrical layout to drive the instrument, with the added ability to define all the electric fields within the analyzer. 3. Fully characterize the performance of the prototype instrument for ion trapping and ion mobility separation. In summary, this thesis aims to address the above objectives described in the chapters that make up its content. Chapter 2 and Chapter 3 focus on the design and construction of the vfTIMS. More specifically, Chapter 2 outlines the various hardware components of the vfTIMS that were either designed and built in-house or purchased commercially and modified. Chapter 3 details the design and testing of the electronics that power the system, along with the development of the user interface to control the instrument. Chapter 4 presents the extensive experimental optimization that was completed to get the instrument operational. Additionally, Chapter 4 also covers the experimental results that establish a baseline set of instrumental conditions that should be used for more complex experiments. Chapter 5 describes the first two proof of concept studies that demonstrate the feasibility of ion mobility separation experiments on the vfTIMS, building on the knowledge gleaned from the experiments in Chapter 4. Lastly, Chapter 6 serves as a roadmap for what must be done next to advance the project, in both the short term as well as the longer term.
Synthesis of Deuterated Benzene for a Circular Deuterium Economy
(University of Waterloo, 2024-04-30) Kappheim, Benjamin Jacob
Deuterium is an important natural isotope; its unique properties can impart significant effects on molecules with emerging applications across electronics and medicinal industries. Aromatic hydrocarbons or arenes are one example of such compounds where deuterium proves advantageous, breaching limitations in commercial organic-based electronics. Current methods introduce deuterium into molecules through direct hydrogen/deuterium (H/D) exchange reactions which depend on a reliable and high supply of deuterium that has been slowly dwindling in recent years. To continue the exploration of deuterium-enriched compounds and their applications, new methods that use deuterium conservatively to achieve efficient H/D exchange are needed. The Canadian company deutraMed™ has responded to this demand by developing a D2O refinery capable of recycling deuterium waste. Working in partnership, the work herein will discuss the development of an H/D exchange procedure to deuterate benzene that is compatible with the D2O refinery. Benzene is a simple arene that is a common motif in compounds related to organic electronics and pharmaceuticals. The large-scale production of deuterated benzene fuels the demand for a versatile building block to access an assortment of compounds relevant to these industries. The development of the H/D exchange procedure found success using hydrothermal conditions to achieve 96% deuteration of benzene at laboratory scale. The results of this work will be beneficial in the further development of this process on an industrial scale.
Advancing Linear-Scaling Techniques in Computation of Exchange Matrices in Mean-Field and Cluster-in-Molecule Calculations
(University of Waterloo, 2024-04-30) Song, Nan
Quantum chemistry faces ongoing challenges in developing methods that combine efficiency with accuracy, especially for large molecular systems. The Cluster-in-Molecule (CiM) technique, integrated with Coupled Cluster theory (CC) methods, offers a promising solution by accurately computing correlated ground state energies through division into computations of small subsystems. These systems utilize a subset of localized natural orbitals (LNO) defined by localized orbital domains [1, 2, 3, 4, 5, 6]. The advantage of CiM-CC approach is that all subsystem calculations can trivially be computed in parallel with a relatively straightforward algorithm. The main challenges are in defining small orbital domains in accurate and efficient ways, and the required integral transformation from the global atomic orbitals (AO) basis to the subset of LNO. In this work, we enhance the efficiency of calculating two-electron repulsion integral (ERI) through advanced computational techniques that incorporate the Resolution of Identity (RI) metric matrix and a three-index short-range Coulomb potential with Gaussian-Type Geminal (GTG) correction. This aspect of the research, inspired by the thesis work of Dr.Michael J. Lecours in the Nooijen group, focuses on improving the efficiency of calculating the exchange matrices K while maintaining acceptable error margins [7, 8]. Our newly developed algorithms in the Python module for quantum chemistry platform (PySCF) program, especially for calculating Coulomb J and exchange K matrices through the JK-Engine, are shown to achieve a linear correlation between performance and the size of molecular systems. These improvements are not only vital for CiM but also for Hartree-Fock (HF) and (hybrid) Density Functional Theory (DFT) mean-field calculations, with accuracy controlled by a single parameter defining the short-range Coulomb potential’s range. Utilizing the exchange matrix, we present an efficient orbital domain construction scheme for occupied localized molecular orbitals (LMO) based on the pivoted Cholesky decomposition of the exchange matrix. This method improves the efficiency of the parti- tioning into LMO subspaces, crucial for CiM calculations. In summary, our advancements in linear-scaling exchange matrix calculations and or- bital domain construction mark significant progress toward more efficient and accurate electronic structure calculations for mean-field and CiM approaches, promising enhanced computational performance for large molecular systems.
Pyrene Excimer Formation: A Tool to Study Macromolecular Conformations in Solution
(University of Waterloo, 2024-04-26) Patel, Sanjay
The current view for fluorescence collisional quenching (FCQ) experiments is that no quantitative information can be retrieved from macromolecules containing more than a single dye-quencher pair attached at two specific positions on a macromolecule. This holds true for pyrene excimer formation (PEF), a well-established FCQ phenomenon, where an excimer is produced through the encounter between an excited and a ground-state pyrenyl labels attached onto a macromolecule. In contrast, recent studies suggest that the analysis of fluorescence decays acquired with macromolecules containing many pyrenyl labels with the model free analysis (MFA) and florescence blob model (FBM) yields quantitative information about the internal dynamics and local density of macromolecules in solution. The underlying physical principle enabling the MFA and FBM to probe macromolecules in this manner is based on the direct relationship existing between the average rate constant () for PEF and the local concentration ([Py]loc) of pyrenyl labels on the macromolecule. Yet, and despite its importance, no study has conclusively validated this relationship. This is due, in part, to the difficulty in determining [Py]loc for pyrene-labeled macromolecules (PyLM) and benchmarking this methodology against other experimental techniques. In the present thesis, this fundamental relationship was demonstrated with a series of polyamidoamine (PAMAM) dendrimers of generations GY (=0, 1, or 2) that had been labeled with pyrene derivatives having different numbers X (= 4, 8, or 12) of carbon atoms in the pyrenyl linker to yield the PyCX-PAMAM-GY samples. The fluorescence decays were acquired in N,Ndimethylformamide (DMF) and dimethylsulfoxide (DMSO) and analyzed with the MFA to retrieve , which was compared to [Py]loc obtained by assuming that the internal segments of the PyCX-PAMAM-GY samples linking the pyrenyl labels obeyed Gaussian statistics. The direct relationship found between and [Py]loc for the PyCX-PAMAM-GY samples provided a vi validation for this assumption and demonstrated that PEF can be employed to probe the conformation of macromolecules in solution. Subsequently, PEF was applied to probe the conformational changes induced by protonating the internal tertiary amines of the PyCX-PAMAM-GY samples, showcasing PEF's ability to study these conformational changes intramolecularly, a feat difficult to achieve by traditional methods used for characterizing macromolecular conformations in solution. Expanding beyond dendrimers, PEF was applied to study the conformation of larger macromolecules like poly(glutamic acid) (PGA) and polynorbornene (PNb) on different length scales by using 1-pyrenealkylamines with varied alkyl side chains. The fluorescence blob model (FBM) was applied to determine the number (Nblob exp) of structural units within a blob, the volume probed by an excited pyrenyl label, taken as a measure of the local macromolecular density. Comparison of Nblob exp with Nblob MMO obtained through molecular mechanic optimizations (MMOs) validated PEF's ability to probe macromolecular conformations over different length scales. The conformation of the Py-PGA constructs was found to remain unchanged when probed with 1-pyrenealkylamines having different linker lengths reflecting a homogeneous conformation over different length scales. In contrast, the Py-PNb samples appeared helical and randomly coiled for the 1-pyrenealkylamines with a shorter and longer linker, respectively, highlighting the potential of PEF at probing complex macromolecules with heterogeneous conformation across various length scales. In conclusion, this thesis further supports the applicability of PEF as a robust experimental technique for probing the conformations and internal dynamics of macromolecules in solution.
Development and biomedical applications of solid phase micro-extraction (bio-SPME) chemical biopsy devices
(University of Waterloo, 2024-02-22) Jiang, Runshan (Will)
Micro-sampling is a vital component in modern diagnostics and personalized medicine. In vivo SPME is a novel branch of biomedical applications of SPME (Bio-SPME) that offers unique advantages complementary to existing in vivo micro-sampling techniques such as micro tissue biopsy and microdialysis. When coupled with powerful modern detection methods, such as mass spectrometry, the minimally invasiveness and convenient sample-cleanup of in vivo chemical biopsy SPME enable the rapid analysis of exogenous and endogenous analytes from a biological system in vivo. In vivo SPME has seen success in numerous clinical applications from therapeutic drug monitoring (TDM) to untargeted metabolomic/lipidomic fingerprinting. While the scope of theoretical considerations extends deep into the realm of complex physical chemistry, bio- SPME and in vivo SPME can still be executed by medical personnel with limited theoretical knowledge as long as a few key experimental parameters are controlled, such as extraction time. Chapter 2 details the fabrication of a novel recessed SPME chemical biopsy probe and a push-pull microsyringe sampling device. Compared to conventional in vivo sampling tools, the latest devices offer superior physical robustness with a convenient chemical sorbent that does not require solvent activation. Such devices have been successfully implemented in human in vivo studies which are also included in this chapter. Chapter 3 presents a proof-of-concept study showing the importance of non-destructive sampling (ie. in vivo SPME) in untargeted metabolomics using ovine lung tissue as a model coupled with a commercial metabolomics kit. Chapter 4 is another proof-of-concept study which explores the applicability of bio-SPME in proteomics which was thought to be impossible. Various sample preparation and device fabrication strategies such as protein digestion and porous coating were employed to achieve protein identification in clinical SARS-CoV-2 patient saliva samples. Chapter 5 of the thesis addresses some of the flaws with previous in vivo applications of SPME, provides strategies to overcome them, and showcases numerous clinical in vivo applications with the improved calibration strategies. In short, this thesis work offers a comprehensive strategy for various in vivo and ex vivo bio-SPME applications.
Controlling Exciton Polarization in Transition Metal Doped Indium Oxide Nanocrystals
(University of Waterloo, 2024-02-20) Shao, Qinghao
The simultaneous manipulation of electronic charge and spin in dilute magnetic semiconductors (DMSs) doped with transition metal ions has been long considered a holy grail for advancing spintronics and quantum information processing technologies. Although room temperature (RT) ferromagnetism has been attained in multiple DMSs including DMS oxides (DMSOs), these results have inconsistency in reproducibility. Moreover, RT ferromagnetism has also been observed in several metal oxides in the absence of any transition metal dopants. This phenomenon has been attributed to intrinsic defects in the host lattice, which creates confusion over the nature of exchange interactions that lead to RT ferromagnetism in DMSs. Here, using a carefully designed series of Co2+-doped indium oxide (Co2+:In2O3) nanocrystals (NCs) with different doping concentrations, and employing magnetic circular dichroism spectroscopy, we unravel the dominant mechanism governing spin polarization of charge carriers as a function of doping concentration, and establish the contributions of intrinsic defects and dopants to Zeeman splitting in Co2+:In2O3 NCs. Furthermore, the exchange coupling between the excitonic states and Co2+ is strongly dependent on the NC volume for sizes approaching the quantum confinement regime, but largely independent on the radial position of the dopants for larger NCs due to spatially homogeneous wavefunction of the exciton. Our work provides a critical understanding on why DMSOs are so sensitive to the synthesis methodology and will aid in developing new DMSO NC systems whose magnetic properties can be consistently predicted and reproduced.
Development and Application of a Consumable-Free Modulator for Comprehensive Two-Dimensional Gas Chromatography
(University of Waterloo, 2024-02-16) Edwards, Matthew
Comprehensive two-dimensional gas chromatography (GC×GC), is a separation method recognized as offering far greater peak capacity than conventional one-dimensional separations. Today, the most frequently used GC×GC systems require consumables such as liquid N2 for the trapping function of the modulator. Although these systems are recognized as being very effective, their initial and running costs are a hindrance to more widespread use. A consumable-free, single-stage thermal modulator for GC×GC has been developed to overcome these problems. The device traps analytes through the use of a specially prepared coated stainless steel capillary compressed between two ceramic cooling pads. Analytes are thermally released from the trap into the secondary column via resistive heating. Thermal treatment of the trapping capillary plays an important role in the function of the device and advanced imaging and material characterization techniques were used to reveal changes in the stationary phase coating of the trap. These experiments revealed the polydimethylsiloxane stationary phase coating was being converted to carbon doped, oxygen rich silica nanoparticles. These spherical particles coated the internal surface of the capillary evenly and provided an effective and highly sorptive phase for use in GC×GC modulation. This modulator’s performance was evaluated by applying it to real world analytical challenges. Samples such as honeybush tea volatiles, polychlorinated biphenyls, perfumes and petroleum products were successfully analyzed with performance comparable to commercially available instruments. This work demonstrates the single-stage, consumable-free GC×GC modulation system described herein is an excellent instrumental option for analysts across a wide breadth of application areas in the world of complex volatile and semi-volatile analysis.
Low-Dimensional Nanostructured Catalysts of Copper Oxides and Nickel Oxides Supported on Graphene and Their Applications in Biosensing and Photoelectrochemical Hydrogen Evolution
(University of Waterloo, 2024-01-22) Gao, Wenyu
Cuprous oxide (Cu2O) nanomaterials provide a versatile platform for building non-enzymatic glucose sensors. In particular, Cu2O nanocubes with controllable sizes and distributions can be deposited electrochemically on a conductive graphene strip as a soft substrate under different conditions, including overpotential, temperature, copper ion electrolyte concentration, and deposition time. The graphene substrate provides a promising condition for sensing because of its high conductivity, high specific surface area, and unique thermal and mechanical properties. A more negative overpotential is found to produce smaller nanocubes with a large number density, while the deposition temperature could affect the morphology of nanocubes. The size of the nanocubes increases with increasing copper ion concentration and deposition time. Using an optimal condition of –1.0 V vs Ag/AgCl, 1 mM [Cu2+], and 100 s deposition time at room temperature, we obtain a near-homogeneous monolayer of Cu2O-shell Cu-core nanocubes, ~50 nm in size, on a graphene strip substrate. The Cu2O nanocubes/graphene is used as a high-performance sensor with a wide detection range of 0.002-17.1 mM and a high sensitivity appropriate for saliva-range glucose sensing. It is also used to test saliva glucose in the real sample with 95% accuracy. This non-enzymatic glucose sensor is considerably better in performance than other non-enzymatic sensors, including those based on bare graphene, and graphene sputter-coated with a Cu film, and conventional enzymatic sensors such as glucose oxidase immobilized on graphene. For the glucose oxidase/graphene sensor, the addition of the enzyme increases the resistance of the graphene substrate, which leads to poorer performance. Even with an added Nafion film, the glucose oxidase/Nafion/graphene sensor only has a slightly increased detection range. In addition to being an excellent catalyst, Cu2O nanocubes have a large specific surface area and a large number of active sites. These nanomaterial properties, along with the use of a high-conductivity substrate like graphene, make the Cu2O nanocubes/graphene sensor among the best saliva-range glucose sensors reported to date. Photoelectrochemical hydrogen evolution (HER), a half reaction of water splitting, is crucial to the low-cost, environmentally friendly production of clean H2 fuel as part of the solution for transitioning away from a fossil fuel economy. Electrodeposition of a controllable Cu film on graphene followed by thermal oxidation at 200-400 °C has been used to produce copper oxide (CuxO, x=1,2) nanowires. The relative compositions of CuO and Cu2O layers in CuxO-Cu/graphene system form a heterojunction structure enabling high efficiency for electron-hole separation and a fast charge transfer rate, where the CuO layer with a proper thickness enhances light absorption, improves the charge separation, and serves as a protective layer for Cu2O photocorrosion while graphene serves as a flexible high conductive substrate. A high-performance dual Z-scheme heterojunction photocatalyst to greatly improve charge carrier separation, increase carrier density, and reduce electron-hole recombination is obtained by decorating this CuxO-Cu/graphene system with an efficient co-catalyst based on Cu-based ternary CuFe2O4 nanoparticles, obtained by a solvothermal method. The addition of CuFe2O4 nanoparticles on the best optimized CuxO-Cu/graphene is found to nearly double the photocurrent from –2.64 mA cm-2 to –4.91 mA cm-2, making this dual heterojunction catalyst the best catalyst system for HER reported to date. Electrodeposition of nickel nanoparticles, achieved through potentiostatic amperometry, followed by thermal annealing at 200-400 °C has produced nickel oxide nanoparticles on flexible graphene substrates. Using transmission electron microscopy and depth-profiling X-ray photoelectron spectroscopy, we show that the resulting NiO¬x nanoparticles exhibit several Ni oxidation states and a core-shell heterostructure, with a metallic Ni crystalline core and a NiO crystalline shell with a mixed crystalline-amorphous NiOOH/Ni(OH)2 skin. The composition of NiOOH/Ni(OH)2 redox couple relative to NiO is found to vary with the annealing temperature and annealing time. Besides, the high conductive graphene substrate enhances the electron transfer. The NiOx nanoparticle samples obtained with selected annealing temperature-time combinations are used for lactate detection, with the best sample showing an excellent linear range of 0.02-65.1 mM, a high sensitivity of 80.0 μA mM-1 cm-2, and an impressive limit of detection of 0.00015 mM. NiOx nanoparticle sample is also tested for lactate sensing in an artificial sweat electrolyte, and it exhibits a reduced linear range of 0.02-53.1 mM and a lower limit of detection of 0.00013 mM, but the same high sensitivity of 80.0 μA mM-1 cm-2. This sensing performance can be optimized by controlling the NiOOH + Ni(OH)2 relative composition to NiO, with the sample obtained with a higher relative content at a lower annealing temperature found to provide more reactive sites for sweat-range lactate detection and therefore higher sensitivity.
Size-Specific ZrO₂ and HfₓZr₁₋ₓO₂ Nanoclusters and Their Magnetic and Nanodevice Applications
(University of Waterloo, 2024-01-22) Guan, Xiaoyi
Nanoclusters, generally defined as assemblies of a discrete number of atoms or molecules in the size range of 1-10 nm, have attracted a lot of attention due to their unique properties that bridge the gap between isolated atoms or molecules and bulk materials. Nanoclusters possess distinct electronic, optical, magnetic, and catalytic characteristics, which are often profoundly different from those observed in bulk materials or even larger nanoparticles. These notable differences arise from quantum confinement effects, high surface-to-volume ratios, and the specific atomic arrangements in these nanoscale clusters that often include the presence of defects. The understanding and manipulation of these properties are pivotal for harnessing nanoclusters in diverse fields, ranging from nanoelectronics to catalysis, biomedicine, and advanced material design. The oxides of group IV-B transition metals, notably ZrO2 and HfO2, have attracted significant research interest due to their high dielectric constants, wide bandgaps, pronounced refractive indices, and superior thermal stability. Additionally, oxygen vacancy defects within these oxides, particularly in the nanocrystalline forms, contribute to the manifestation of intriguing phenomena. The present work delves deeply into the synthesis methodologies, precise characterization techniques, and the multifaceted application potential of the ZrO2 and HfxZr1-xO2 (x≤1) nanoclusters. Through this exploration, we aim to elucidate the intricate relationship between the defects in the physical structure of the nanocluster, composition, and their resulting macroscopic behaviors, with a special focus on the ferromagnetism, providing insights that could pave the way for future innovations in nanotechnology. Monosized ZrO2 nanoclusters (NCs) are deposited over a large area by using gas- phase condensation followed by in-situ size selection by a quadrupole mass filter. These size-specific NCs exhibit sub-oxide photoemission features at binding energies that are dependent on the cluster size (from 3 to 9 nm), which are attributed to different oxygen vacancy defect states. These dopant- free ZrO2 NCs also show strong size-dependent ferromagnetism, which provides distinct advantages in solubility and homogeneity of magnetism when compared to traditional dilute magnetic semiconductors. A defect-band hybridization-induced magnetic polaron model is proposed to explain the origin of this size-dependent ferromagnetism. This work demonstrates a new protocol of magnetization manipulation by nanocluster size control and promises potential applications based on these defect-rich size-selected NCs. Using two metal targets in the gas-phase condensation technique, we synthesize, for the first time, size-specific hybrid HfxZr1-xO2 (x ≤ 1) NCs that can be precisely tuned from 5 nm to 14 nm in size while adjusting the Zr and Hf composition. The crystallinity of the hybrid NCs is found to vary with the NC size obtained under specific deposition conditions, from amorphous for small NCs < 6 nm, to single crystalline for 6-10 nm NCs, to core-shell for NCs with higher Hf content and to polycrystalline for larger NCs > 10 nm with high Zr content. For the single-crystalline HfxZr1-xO2 NCs, we observe, for the first time for NCs, the special orthorhombic (Pca21) structure found only in the HfZrO2 film prepared under extreme conditions. Surprisingly, the measured bandgaps of these NCs are found to increase with the cluster size, in contrast to expected increasing band gap with decreasing NC size. The XPS spectra clearly show that the Zr 3d components can be attributed to oxygen vacancy defects and substitution of Hf for Zr in the lattice. A new model involving Hf induced polaron is proposed to describe the physical and electronic structures of these novel bimetallic hybrid oxide NCs. This work establishes a general formation protocol for other hybrid semiconductor NCs, while the HfxZr1-xO2 (x<1) NCs with novel phase and polarization could provide promising electrical properties for the next generation non-volatile memory device applications. To understand the behavior of the electrons within the defects of these NCs and explore their electronic properties, we fabricate nano-electrodes, including nano interdigital electrodes and nanogaps. As one of the most crucial procedures in the electronic device fabrication, patterning is studied by comparing the results obtained by maskless optical lithography, electron beam lithography, and ion beam lithography with a gas field He ion source and with a SiAu liquid metal alloy ion source. Helium ion beam lithography is found to offer the most refined feature resolution, while the Si ion beam lithography demonstrates its fastest patterning speed in creating nanofeatures, particularly by taking advantage of its unique direct-write capability. Using ion beam lithography, a nano-IDE with a 43-nm gap is created with direct writing of Au++ ion beam on a Pt film. This technology also enables precise nanogap device production with sharp edges that are crucial for tunneling and electron hopping studies. The spacing of these nanogaps can be fine-tuned through ion beam exposure. We also fabricate a single-nanocluster device, for the first time, by integrating HfxZr1- xO2 NCs into these nanogap devices. Such nano-electrodes serve as platforms for measuring the electronic properties of NCs, with promising potential for other nano and quantum device applications.
Advanced Electrolyte Design for Long-Life and High-Areal-Capacity Divalent Metal Batteries
(University of Waterloo, 2024-01-22) Li, Chang
Net-zero carbon dioxide emission demands clean renewable energy, while harnessing it requires electrochemical storage devices with high energy density, safety and affordability. To achieve decarbonization, much effort is being devoted to new battery technologies beyond lithium-ion batteries (LIBs), which suffer from limited lithium resources and low safety. Rechargeable batteries based on divalent metal anodes (Zn, Mg and Ca) are promising systems due to their high abundance, high volumetric capacity and potentially high safety. Zn anode has a high standard redox potential (-0.76 V vs. standard hydrogen electrode (SHE)), resulting in its relatively good compatibility with aqueous electrolytes. Such inherent safety and potential low-cost make aqueous Zn metal batteries (AZMBs) desirable candidates for small and large-scale stationary grid storage. Mg or Ca anode, on the other hand, has a much lower standard redox potential (-2.37 V or -2.87 V vs. SHE, respectively) that is even comparable to lithium (-3.04 V vs. SHE). Therefore, high-voltage rechargeable Mg or Ca metal batteries (MMBs or CMBs) are potential alternatives to LIBs in a variety of areas ranging from portable electronic devices to electrical vehicles. However, the study of these divalent metal batteries is still at the early stages. Among many unaddressed challenges for practical divalent metal batteries, designing better electrolytes is one key to their successful commercialization. This thesis presents a comprehensive investigation on designing new electrolytes for both AZMBs (chapters 3, 4 and 5) and MMBs (chapters 6 and 7), by tuning the solvation structure of Zn2+ or Mg2+ ions and their interaction with solvents or anions. A series of electrolytes with precisely controlled interfacial electrolyte/electrode chemistry are developed to achieve rechargeable AZMBs and MMBs under practical conditions. Chapter 3 reports a novel additive - N,N-dimethylformamidium trifluoromethanesulfonate (DOTf) - in a low-cost aqueous electrolyte that enable near 100% coulombic efficiency of Zn plating/striping at a combined high current density of 4 mA cm-2 and areal capacity of 4 mAh cm-2 over long-term cycling. The water-assisted dissociation of DOTf into triflic superacid creates a robust nanostructured SEI - as revealed by operando spectroscopy and cryo-microscopy - which excludes water and enables dense Zn deposition. Zn||Zn0.25V2O5·nH2O (ZVO) full cells based on this modified electrolyte retain ~83% of their capacity after 1000 cycles with mass-limited Zn anodes. By restricting the depth of discharge, the cathodes exhibit less proton intercalation and LDH formation with an extended lifetime of 2000 cycles. Chapter 4 presents the electrochemical degradation mechanism of LiV2(PO4)3 (LVP) as a host cathode in AZMBs. Phase conversion of LVP induced by H+ intercalation is observed in 4 m Zn(OTf)2 whereas dominant Zn2+ insertion is confirmed in ZnCl2 water-in-salt electrolyte (WiSE). This disparity is ascribed to the complete absence of free water and the strong Zn2+-H2O interaction in the latter that interrupts the H2O hydrogen bonding network, thus suppressing H+ intercalation. Based on this strategy, a novel PEG-based hybrid electrolyte is designed to replace the corrosive ZnCl2 WiSE. This system exhibits an optimized Zn2+ solvation sheath with a similar low free water content, showing not only much better suppression of H+ intercalation but also highly reversible Zn plating/stripping with a CE of ~99.7% over 150 cycles. Chapter 5 reveals the competition between Zn2+ vs proton intercalation chemistry of typical ZVO cathode using ex-situ/operando techniques, and alleviate side reactions by developing a cost-effective and non-flammable hybrid eutectic electrolyte. A fully hydrated Zn2+ solvation structure facilitates fast charge transfer at the solid/electrolyte interface, enabling dendrite-free Zn plating/stripping with a remarkably high average coulombic efficiency of 99.8% at commercially relevant areal capacities of 4 mAh cm-2 and function up to 1600 hours at 8 mAh cm-2. By concurrently stabilizing Zn redox at both electrodes, we achieve a new benchmark in Zn-ion battery performance of 4 mAh cm-2 anode-free cells that retain 85% capacity over 100 cycles at 25 C. Using this eutectic-design electrolyte, Zn||Iodine full cells are further realized with 86% capacity retention over 2500 cycles. The approach represents a new avenue for long-duration energy storage. Chapter 6 reports a low-cost inorganic membrane that forms an effective protection film on the Mg surface to stabilize Mg plating/stripping. It significantly reduces the population (and hence decomposition) of free diglyme (G2) molecules at the Mg/interface, while allowing facile transport of Mg2+ cations, leading to dendrite-free Mg deposition in a magnesium tetrakis(hexafluoroisopropyloxy)borate/G2 electrolyte. We demonstrate very stable Mg plating/stripping performance with a 750-fold extended lifetime (over 6000 hours) with a high coulombic efficiency of ~98%. The prototype Mo3S4 cathode paired with inorganic membrane-protected Mg anode shows 91% capacity retention over 200 cycles. More importantly, this membrane also protects soluble species in a high-voltage organic polymer cathode from being reduced at the anode via shuttling, achieving a full cell with a 3.5 V cutoff voltage and 1.4 V average discharge voltage. This results a high specific energy density of 320 Wh kg-1 and power density of 1320 W kg-1 based on cathode mass. Chapter 7 report a new and easily accessible co-ethereal phosphate electrolyte system for high-voltage rechargeable MMBs, which very effectively solves the difficulty of ion pair dissociation and facilitates fast nanoscale Mg nucleation/growth for the first time, enabling facile interfacial charge transfer at current densities up to 10 mA cm-2. Dendrite-free Mg plating/stripping is achieved for over 6000 hours (8.3 months) at a practical areal capacity of 2 mAh cm-2. The four-volt oxidative stability of these electrolytes - in conjunction with a polyaniline cathode with an upper potential of 3.5 V and a Mg metal anode - enables cells with stable cycling at a 2C rate for over 400 cycles at 25 C. We believe our work opens up new frontiers in developing low-cost and fast-charging MMBs with long life and high energy densities.
Oxygen Reduction Reaction on Doped Lanthanum Chromate Perovskites
(University of Waterloo, 2024-01-19) Liu, Xinran
The oxygen reduction reaction (ORR) plays a pivotal role in fuel cell technology and the generation of clean oxidizing agents. This reaction can proceed via two distinct pathways. The complete ORR pathway involves reducing oxygen to water through a four-electron transfer process. Alternatively, a two-electron transfer path- way leads to the partial reduction of oxygen, yielding hydrogen peroxide (H2O2) as the product. The perovskite CaSnO3 has demonstrated stability and selectivity in electrochemically oxidizing H2O to H2O2. In a similar vein, other perovskite oxides have demonstrated good selectivity in the complete ORR. Their catalytic perfor- mance can be analyzed through microkinetic analysis and the application of scaling relations. In this study, we explore a series of perovskites based on LaMO3, where ’M’ denotes a combination of Cr, Co, and Ni. Changes in the type and concentra- tion of doping lead to contraction in the perovskite lattice, along with alterations in B-O-B bond length and angle. These structural changes contribute to differences in their catalytic performance towards the ORR. The inclusion of Co in the catalyst tends to favor the four-electron ORR pathway, while the addition of Ni shows a predilection for the two-electron pathway.
Facilitating the Formation of Intermetallic Compounds in Al-Si Coatings on Steel during Hot Stamping
(University of Waterloo, 2023-12-14) Zhang, Jixi
Hot-stamped ultrahigh strength steel (UHSS) components are pivotal to automotive light-weighting. Steel blanks, often coated with an aluminum-silicon (Al-Si) layer to protect them from oxidation and decarburization, are austenitized within a furnace and then simultaneously quenched and formed into shape. The Al-Si coating melts within the furnace and reacts with iron from the steel to yield an intermetallic phase that provides some long-term corrosion protection. During the intermediate liquid phase, some of the coatings may transfer to the furnace components, leading to maintenance costs and operational downtime. This document describes the development of a rapid analysis method using Raman microscopy mapping to investigate the reaction mechanisms of Al-Si coating and steel during heating. A new surface modification strategy was applied on the Al-Si coating to facilitate intermetallic phase formation. This strategy provides the possibility of expediting the solidification during the heating, thus providing a method to mitigate furnace rollers’ contamination caused by melted high-temperature liquids in the industrial hot stamping process.
Hydride Generation as a Sample Introduction Technique for Detection of Arsenic by Microplasma
(University of Waterloo, 2023-12-08) Qadeer, Laiba
Microplasma can be used as a portable analytical instrument for elemental analysis of samples due to their small size, low power consumption, low carrier gas consumption, and low cost. This is specifically important for areas where contamination of water by arsenic is prevalent (e.g., because arsenic is indigenous to the soil). Due to the volatility of arsenic and its organic compounds, it is only chemical vapor generation (CVG) that can be used to introduce the sample into the microplasma. In this project, equipment for hydride generation (a type of CVG) was designed and used to test this sample introduction technique for microplasma. It was found that response of microplasma towards water vapors and hydrogen released from the hydride generation reaction was different when it was operated in each of three different carrier gases, namely helium, argon, and mixture of argon with 1000 ppm hydrogen. Similarly, the best observation position for arsenic over the microplasma tube was also different for helium microplasma and argon microplasma (0.84 cm and 1.34 cm away from the front electrode where carrier gas and analyte are introduced, respectively). Arsenic signals were also found to be more intense in helium microplasma, as compared to that in argon microplasma and argon – 1000 ppm hydrogen microplasma. Afterwards, the arsenic peaks at 197.3 nm and 228.8 nm were used to estimate the detection limit for arsenic in helium microplasma and argon microplasma, respectively. The detection limit for arsenic in helium and argon microplasma were estimated to be 31 ppb and 40 ppb, respectively. Although this project proved the feasibility of microplasma for detecting arsenic in liquid samples, it was concluded that more research is needed in this field to improve the reproducibility in the measurement of emission signal and the detection limit for arsenic, by making changes in the equipment and the design of gas-liquid separator.
Investigation of Crystal Structures and Ultra-Low Thermal Conductivities in Novel Group 14 and 15 Chalcogenides
(University of Waterloo, 2023-12-04) Menezes, Luke
The crystal structures and physical properties of several new group 14 and 15 chalcogenides are discussed in this thesis. The thesis discusses the chalcoantimonates TlLa2Sb3Se9 and La12+zSb9-ySe38-z (simplified as La12Sb9Se38). TlLa2Sb3Se9 crystallizes in an ordered variant of the KLa2Sb3S9 structure type (space group = P212121). The thermoelectric properties of TlLa2Sb3Se9 were enhanced through p-type doping by replacing La3+ with Ca2+. The largest thermoelectric figure-of-merit was 0.078 at 623 K in the TlLa0.95Ca0.05Sb3Se9 sample. The La12Sb9Se38 (Pm3 ̅) structure type features La3+/Sb3+ disorder and S2-/S22- disorder, making it possible to produce nonstoichiometric compounds within a narrow phase width. The low thermal conductivities of samples with the nominal compositions La12.17Sb8.5S38 and La12.17Sb8.5S37.75 were around 1 W m-1 K-1. The latter half of this document focusses on Si, Ge, and Sn selenides. Ba6Ge2Se12 (P21/c) and Ba7Ge2Se17 (Pnma) adopt new structure types—both possess positional disorder confirmed via a single crystal, Rietveld, and pair distribution function models. The Ba6Ge2Se12 structure contains disordered Se22- dumbbells which may align for quasi-infinite 1D chains, whereas the Ba7Ge2Se17 structure contains disordered [GeSe5]4- anions. The thermal conductivities of Ba6Ge2Se12 and Ba7Ge2Se17 range from 0.3 – 0.4 W m-1 K-1. Substituting Si into the Ge compound Ba6Ge2Se12 compounded produced the new compound Ba6Si2Se12 (P1 ̅). Up to 75% of the Si atoms in the Ba6Si2Se12 structure may be replaced with Ge while preserving the triclinic structure. The Si4+/Ge4+ disorder and the positional disorder in the Se22- dumbbells were studied using powder X-ray diffraction patterns collected using synchrotron radiation. The ultra-low thermal conductivity of Ba6Si2Se12 ranges from 0.3 to 0.5 W m-1 K-1. The final chapters discuss Sr compounds as well as Ba compounds. Sr8Ge4Se17 (P1 ̅) and Ba8Sn4Se17 (C2/c) share stoichiometries but adopt different structure types. The Ba8Sn4Se17 unit cell may be regarded as a 2 × 1 × 4 supercell of the Sr8Ge4Se17 unit cell. The structures of these two compounds were finalized using Rietveld refinements on powder X-ray diffraction data collected using synchrotron radiation, as no disorder was observed in these structures. Despite not having structural disorder, the ultra-low thermal conductivity of Ba8Sn4Se17 was found to be as low as 0.3 W m-1K 1 due to its complex structure. The final compound discussed is the noncentrosymmetric compound Sr6Ge3OSe11 (P3m1). This chapter explores partial isovalent substitution to design noncentrosymmetric structures by promoting the alignment of [GeOSe3]4- anions. The second-order nonlinear susceptibilities (dil) of Sr6Ge3OSe11 were calculated to be d15 = -12.9 pm V-1, d22 = -15.4 pm V-1, d33 = 15.0 pm V-1 and deff = 17.0 pm V-1. Size-dependent second harmonic generation intensity experiments revealed that Sr6Ge3OSe11 is phase matchable at 1064 nm with an intensity equal to 0.62 × KH2PO4.
Controlled nanometer liquid layer thicknesses for the study of nanomaterials and biospecimens in liquid-cell transmission electron microscopy
(University of Waterloo, 2023-09-22) Lott, Tyler
Liquid-cell transmission electron microscopy (LC-TEM) is an in-situ microscopy technique which aims to image nanomaterials and biospecimens in their native liquid phase environment. To accomplish this task, miniature vessels known as nanofluidic cells (NFCs) are utilized to enclose the liquid sample droplet and protect it from evaporating in the high or ultra-high vacuum of the electron microscope. These NFCs must conform to strict requirements so that a small volume of liquid sample is hermetically sealed between two ultrathin windows. Although the technique has seen significant growth in recent years with the utilization of hybrid material window membranes for improved imaging resolution, the incorporation of machine learning techniques for image processing, and advancements in bio-imaging in the liquid phase, the establishment of uniform thin liquid layers in the absence of membrane bulging has remained a challenge. The bulging of window membranes causes inhomogeneity across the viewing area of the assembled NFC. Since conventional NFCs are structurally sensitive to handling and are assembled in the atmosphere of the laboratory environment before being inserted into the electron microscope for imaging, bulging of the thin window membranes occurs. Researchers thus have been led to collect their LC-TEM data along the edges of the windows where bulging is minimized and therefore resolution is maximized. In this thesis a complete suite of instrumentation is presented, comprising: i) proprietary shape-engineered NFCs, ii) LC-TEM holders, and iii) a proprietary sample loading method/station that allows the enclosure of liquid in the absence of air. This combined technology enables the formation of uniform thin liquid layers for LC-TEM measurements in the absence of window membrane bulging. The capabilities of this method to achieve uniform thin liquid layers in assembled NFCs are demonstrated through the high-resolution imaging of gold (Au) nanorods, polystyrene (PS) nanospheres, and 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) liposomes as model sample specimens. In addition to these high-resolution images, electron energy loss spectroscopy (EELS) measurements were conducted within the electron microscope as a means to quantify the liquid layer thickness. The developed instrumentation and methodology resolves a long-standing issue in the LC-TEM community, conferring high-throughput imaging and establishing uniform thin liquid layers across the complete viewing area of the assembled NFC, enabling lattice resolution for crystalline materials and high-contrast for biospecimens.
Investigation of the Electronic Structure and Magnetic Properties of CeO2-X
(University of Waterloo, 2023-09-19) Zorn, Scott
In literature, it has been reported that undoped CeO2 exhibits a room-temperature ferromagnetic-like ordering that does not follow Curie-type behaviour, typically found in magnetic materials. However, none of the proposed mechanisms have yet to be proven experimentally. So, the goal of this thesis was to study the magnetic and magneto-optical properties of CeO2 to determine the potential mechanism causing the ferromagnetic-like ordering. This was done by systematically annealing undoped CeO2 from nanocrystals (NCs) into bulk powders under different annealing time, temperature, and atmosphere to observe grain size and defect concentration impacts on the magnetic properties. Structural characterization, optical, magnetic, and magneto-optical measurements were then conduct on colloidal CeO2-X NCs and annealed CeO2-X powders to contrast the systems. The origin of the ferromagnetic-like ordering was determined by comparing the samples using magnetic circular dichroism (MCD) spectroscopy. It was found that the origin of d0 ferromagnetic-like ordering in CeO2 may be caused by charge transfer-mediated magnetism. Where a delocalized charge transfer from either electrons trapped in oxygen vacancies or O 2p valence electrons to Ce 4f mid-band gaps states causes Stoner splitting to polarize the spins at the Fermi level, creating an uneven number of unpaired spins, and an overall net magnetic moment. The magnetic ordering can be enhanced by annealing CeO2 into bulk powders, where the magnetic signal was controlled directly by the grain size of the crystals and indirectly supported by the concentration of Ce3+/oxygen vacancy defects. With further characterization using temperature dependent XRD, SEM analysis of grain sizes, additional PPMS data, and temperature dependent MCD, the room temperature ferromagnetic-like ordering in CeO2 can ultimately be confirmed and CeO2 could become a promising candidate material for spintronic applications.
Towards Understanding Differential Ion Mobility and its Applications for Analytical and Medicinal Chemistry
(University of Waterloo, 2023-08-30) Ieritano, Christian
This PhD thesis, titled “Towards Understanding Differential Ion Mobility Spectrometry and its Applications in Analytical and Medicinal Chemistry,” encompasses a broad effort to understand the principles that underpin differential mobility spectrometry (DMS), and how the DMS technique can be employed within the analytical and medicinal facets of chemistry. Specifically, this work highlights the components of the ion-neutral interaction potential that are pertinent to rationalize an ion’s DMS behaviour and how such information can be modelled using in silico and machine-learning approaches. Understanding the nature of ion-neutral interactions is especially important when DMS experiments are conducted in microsolvating environments (i.e., those in which the carrier gas is seeded with small amounts of a volatile solvent vapour), as components of the interaction potential can be used to predict molecular properties that are routinely screened during drug discovery. In the Chapter 1, we introduce the ion-solvent interactions that are intrinsic to DMS experiments and how microsolvation can impact an ion’s mobility. We specifically emphasize the significance of ion solvent clusters and how the waveform used in DMS separations fosters a dynamic solvation environment. Because field-induced heating is modulated such that an analyte undergoes many cycles of solvent condensation and evaporation at charge-dense regions of the analyte, DMS effectively samples interactions that may resemble the dynamics of solvation within the analyte’s primary solvation shell. In this regard, DMS can be utilized to probe characteristics of a molecule related to its insipient solvation, which, when used in conjunction with quantum-chemical calculations and/or machine learning algorithms, affords accurate predictions of that molecule’s physicochemical properties. In addition to the information regarding an analyte’s physicochemical properties that can be gleaned from DMS measurements in microsolvating environments (Chapter 2), ion microsolvation can help alleviate complications related to field-induced heating. This phenomenon is explored in Chapter 3, where microsolvation was found to stabilize analytes through the formation of localized ion-solvent clusters. In particular, the chapter explores the DMS behaviour of the MP1 peptide, which, when exposed to a microsolvation partner, underwent chemical transformations that reduced the observed charge state of MP1 from [MP1 + 3H]3+ to [MP1 + 2H]2+, and shielded protonated MP1 from fragmentation induced by collisional activation within the DMS cell. This behaviour suggests that microsolvation provides analytes with a solvent “air-bag,” which could play a role in retaining native-like ion configurations during DMS separations that operate well above the low-field limit. Chapter 4, titled Protonation-Induced Chirality Drives Separation by DMS, explores a fascinating phenomenon that can be probed by DMS. In short, chiral species possessing a permanent stereocenter and a prochiral, tertiary amine can form two diastereomers upon protonation during electrospray ionization. The resulting diastereomers exhibit distinct conformations that are resolvable by DMS, constituting the first measurement of this behaviour in the gas phase. Protonation-induced chirality appears to be a general phenomenon, as N-protonation at the tertiary amino moiety of 13 chiral compounds that contained a prochiral, tertiary amine moiety. The analytical utility of DMS is further exemplified in Chapter 5, where DMS and tandem mass spectrometry (MS) were used to distinguish a set of seven cannabinoids. Detection of analytes as argentinated species (i.e., [M + Ag]+ adducts) also led to the discovery that argentination promotes distinct fragmentation patterns for each cannabinoid, enabling their partial distinction by tandem-MS. By adding DMS to the tandem-MS workflow, each cannabinoid was resolved in a pure N2 DMS environment, allowing for accurate assessment of cannabinoid levels within commercial products with excellent accuracy and limits of detection/quantitation. In addition to the analytical utility provided by DMS and the other ion mobility spectrometry (IMS) techniques, IMS-based separation prior to mass spectrometry has become an invaluable tool in the structural elucidation of gas phase ions and in the characterization of complex mixtures. Application of ion mobility to structural studies requires an accurate methodology to bridge theoretical modelling of chemical structure with experimental determination of an ion’s collision cross section (CCS). Chapter 6 discusses the software package MobCal-MPI, which was developed to calculate CCSs efficiently and accurately at arbitrary field strengths via the trajectory method, including those accessed during DMS experiments. While significant progress has been made towards modelling the phenomenon of differential mobility, there are still several properties that have yet to be captured by in silico models. This thesis concludes with Chapter 7, which outlines unresolved issues in the field and suggests several directions in which future research endeavours can be directed.
Improving Biospecimen Imaging in Liquid Phase Electron Microscopy
(University of Waterloo, 2023-08-24) Shaw, Nicolette
This thesis highlights the progress made in LPEM and the study of biosamples. The introduction provides a comprehensive overview of the challenges encountered in investigating molecular processes and traces the historical evolution of microscopy, leading up to the development of transmission electron microscopy (TEM), cryogenic electron microscopy (cryo EM), and LPEM. Two major hurdles in LPEM are outlined and addressed in this thesis: LC transmissibility, and electron-induced biosample damage. Low electron transmission in thick silicon nitride (SiNx) LCs reduces the achievable resolution during imaging. To address this, I developed a technique to fabricate thin SiNx windows. These windows exhibit reduced bulging, higher transmission, and higher resolution imaging in the liquid phase than currently available SiNx cells. Implementation of thin SiNx LCs was demonstrated through imaging of apoferritin, adeno-associated virus (AAV), pAAV, and vesicles at high resolution. Though future work remains to produce thin LCs of reproducible liquid thickness, this work demonstrates a breakthrough in the capabilities of LPEM imaging. Another principal hurdle in LPEM lies in sample damage inflicted by the electron beam. The concept of radiolysis and its impact on biosamples is elucidated and demonstrated, showing the need to mitigate sample damage during imaging. The thesis addresses this challenge through the evaluation of inpainting techniques, which can be used to perform reduced-dose imaging. In silico analysis showed that algorithmic inpainting can be used to inpaint biosample images up to 80% with high accuracy. The analysis also showed that spiral inpainting does not significantly compromise image quality, indicating its potential v for performing low-dose imaging when spiral distortion is corrected. Overall, this thesis provides invaluable technical insights into LPEM and the cutting edge advancements made in this work. It sets the stage for future research endeavours and groundbreaking discoveries in the realm of in situ bioimaging.

Browse

Recent Submissions