Chemistry

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

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Monitoring Ultrafast Lattice Dynamics in 2D NbTe2
(University of Waterloo, 2025-05-13) Viernes, Christian
The discovery and control of emergent phenomena in strongly-correlated materials is a cornerstone of modern condensed matter physics and materials science. Among these phenomena, charge density waves (CDWs) represent a striking example of how the coupling between electrons and the atomic lattice can give rise to new properties. Understanding the microscopic mechanisms behind CDW formation and their dynamical evolution is crucial not only for fundamental science, but also for the development of ultrafast, energy-efficient electronic and quantum devices. The idea behind controlling such phenomena has been propelled by the advent of ultrafast lasers which enables investigation of electron-lattice interactions and has lead to the realization of many phase transitions. In this thesis, the ultrafast lattice dynamics of the layered quasi-two-dimensional material niobium ditelluride (NbTe2) are explored, a system known to host a robust CDW phase. By employing both time-resolved transient reflectivity (TR) and ultrafast electron diffrac- tion (UED), the femtosecond response is revealed from two different perspectives. These techniques enable direct observations of the dynamical structural distortion and coherent phonon generation with sub-picosecond temporal resolution. These findings reveal a rapid, photoinduced suppression of the CDW order within 200 femtoseconds, followed by coherent lattice oscillations that reflect the material’s transient structural state. UED measurements quantify a transient 1.3% CDW order suppression, while TR data show fluence-dependent modulations of phonon frequencies and lifetimes, highlighting the complex nature of the lattice response. At high fluence, the CDW order of NbTe2 approaches a complete melting along with an irreversible tellurium crystallization on the sample surface—a phenomenon characterized by Raman spectroscopy and interpreted through density functional theory (DFT)-based calculations. Beyond characterizing the behavior of NbTe2, this thesis establishes a broader experimental framework for investigating symmetry-breaking transitions and metastable states in low- dimensional quantum materials. The work highlights the power of ultrafast techniques for unveiling non-equilibrium phenomena and offers insights into how light can be used to engineer and manipulate material properties on demand.
Development and Optimization of Analytical methods for Sulfolane and BTEX Quantification in Environmental samples
(University of Waterloo, 2025-04-29) Kobarfard, Merrik
Sulfolane is an industrial solvent widely used in various industries, particularly the petrochemical sector. It is highly mobile in the environment due to its water miscibility at slightly above room temperature and minimal adsorption onto most soil types. Furthermore, sulfolane is a relatively stable compound, with aerobic biodegradation serving as its primary degradation pathway. However, its high mobility allows it to contaminate groundwater, where anaerobic conditions can lead to prolonged persistence. Additionally, sulfolane can migrate into fractured rock structures within groundwater zones, where small pores may trap contaminants, further prolonging environmental contamination. Given the large annual volumes of sulfolane usage, accidental releases are inevitable. Despite significant gaps in toxicological research, sulfolane is recognized as a neurotoxin and may disrupt multiple physiological systems, including the circulatory, hepatic, and reproductive systems. Due to these potential health risks, it is crucial to conduct environmental risk assessments, beginning with the measurement of sulfolane concentrations in environmental matrices. Sulfolane is rarely used in isolation and is often co-released with other organic solvents and chemicals. Its physicochemical properties, particularly its high solubility in both water and organic solvents, can influence the environmental distribution of co-contaminants. One important group of such co-contaminants commonly associated with sulfolane in the petrochemical industry are BTEX (benzene, toluene, ethylbenzene, and xylenes). BTEX compounds are well-established environmental pollutants with documented adverse effects on human health, including neurotoxicity, hematologic malignancies and damage to multiple organ systems. Therefore, monitoring BTEX alongside sulfolane is essential to understanding potential interactions and cumulative risks. In this study, two gas chromatography-mass spectrometry (GC-MS) methods were developed, optimized, and validated for the quantification of sulfolane in rock and groundwater samples. The methods were designed to be simple and environmentally friendly, minimizing the use of organic solvents. Due to the distinct characteristics of each matrix, tailored extraction techniques were employed. For rock samples, a microwave-assisted extraction method using methanol was developed to expedite contaminants extraction. The method was validated, and sulfolane stability in methanol extracts was assessed, confirming its stability for up to one year post-collection. The method was applied to 109 rock core samples from a contaminated site in Alberta, Canada, revealing sulfolane contamination in only one sample, while toluene and ethylbenzene were the most prevalent contaminants. For groundwater samples, an in-vial extraction method utilizing dichloromethane was developed. The method was validated, and assessed for ruggedness. Benzene was identified as the most susceptible to loss during sample preparation. Stability assessments showed that sulfolane remained stable in refrigerated water samples for up to 23 days. The method was then applied to 97 surface water and groundwater samples collected from a contaminated site in Alberta, Canada. Results indicated that sulfolane concentrations exceeded Health Canada's maximum acceptable contamination levels in 17 out of 50 locations, whereas only a few samples exhibited BTEX concentrations exceeding regulatory guidelines. Overall, this study successfully developed and validated methods for detecting sulfolane in environmental samples, contributing to a better understanding of its distribution in contaminated sites. However, further sampling and analysis are required to comprehensively assess sulfolane’s fate and transport at the study site.
Path integral and qubit encoding techniques for quantum simulations of discrete planar rotor lattices
(University of Waterloo, 2025-04-28) Moeed, Muhammad Shaeer
Typical path integral Monte Carlo approaches use the primitive approximation to compute the probability density for a given path. In this thesis, we investigate the utility of pair approximating the action in path integral ground state simulations targeting planar rotations. The pair propagator, which was initially introduced to study superfluidity in condensed Helium, is naturally well-suited for systems interacting with a pair-wise potential. Consequently, paths sampled using the pair action tend to be closer to the exact paths (compared to primitive Trotter paths) for such systems leading to convergence with less imaginary time steps. Our approach relies on using the pair factorization in conjunction with a rejection-free path integral ground state paradigm to study a chain of planar rotors interacting with a pair-wise dipole-dipole interaction. We first use a heat kernel expansion to analyze the asymptotics of the pair propagator in imaginary time. Then, we exhibit the utility of the pair factorization scheme via convergence studies comparing the pair and primitive propagators. Finally, we compute energetic and structural properties of this system including the orientational correlation and Binder ratio as functions of the coupling strength to examine the behavior of the pair-DVR method near criticality. Density matrix renormalization group calculations are used for benchmarking throughout. Near term quantum devices have recently garnered significant interest as promising candidates for investigating difficult-to-probe regimes in many-body physics. To this end, various qubit encoding schemes targeting second quantized Hamiltonians have been proposed and optimized. In this thesis, we also investigate two qubit representations of the planar rotor lattice Hamiltonian. The first representation is realized by decomposing the rotor Hamiltonian projectors in binary and mapping them to spin-1/2 projectors. The second approach relies on embedding the planar rotor lattice Hilbert space in a larger space and recovering the relevant qubit encoded system as a quotient space projecting down to the physical degrees of freedom. This is typically called the unary mapping and is used for bosonic systems. We establish the veracity of the two encoding approaches using sparse diagonalization on small chains and discuss quantum phase estimation resource requirements to simulate small planar rotor lattices on near-term quantum devices.
Grafting of Starch Nanoparticles with Polymers
(University of Waterloo, 2025-04-17) Fernandez, Joanne
As a biocompatible and biodegradable polysaccharide, starch has sparked significant interest for various industrial applications, but its poor mechanical properties limit its uses without chemical or physical modification. The work reported herein concerns the development of synthetic techniques to modify starch by graft polymerization via cerium (IV) activation. Starch nanoparticles (SNPs) were modified with acrylic acid (AA) in water under acidic conditions via activation with cerium (IV) in combination with potassium persulfate (KPS). The reactions were conducted with either the as-supplied SNPs containing glyoxal, or after purification (without glyoxal), for different target molar substitution (MS) values. A novel purification protocol using methanol extraction and centrifugation was implemented to purify the samples. This method proved to be selective to isolate the poly(acrylic acid) (PAA) homopolymer contaminant from the starch-g-PAA copolymer, and more reliable than the gravimetric analysis methods reported in the literature. The starch-g-PAA copolymers were characterized by dynamic light scattering (DLS), and degradation of the starch substrate allowed the determination of the molar mass of the PAA side chains via gel permeation chromatography (GPC) analysis. In the presence of aldehydes the rate of polymerization of AA increased significantly (by > 37 %), and the highest grafting efficiencies were obtained for glyoxal and butyraldehyde. The combination of cerium (IV) with glyoxal and KPS resulted in the highest polymerization rate and grafting efficiency. Increasing the glyoxal concentration also increased the rate of monomer conversion and the grafting efficiency. The increased rate of polymerization provided further insight into the grafting mechanism, as it was discovered that esterification reactions between starch and PAA also contributed significantly to the grafting process, particularly at longer reaction times. In the presence of aldehydes, the production of large amounts of PAA homopolymer resulted in esterification dominating the grafting process. Model reactions involving direct coupling of linear PAA samples with starch were investigated. All the reactions were characterized by high coupling efficiencies for a target MS = 3, and higher molar mass PAA samples (30 and 250 kDa) coupled faster than a lower molar mass sample (1.8 kDa), as expected in terms of reaction probabilities. The importance of esterification was also confirmed with model reactions using 2-hydroxyethyl acrylate, a monomer not containing a free carboxylic acid functional group, which yielded notably lower grafting efficiencies. Overall, the grafting mechanism for starch and acrylic acid promoted by cerium (IV) therefore appears more complex than described previously, particularly in the presence of aldehydes: The high overall grafting efficiencies observed result from two distinct reactions occurring concurrently, namely grafting via cerium (IV) activation, as well as the esterification of free PAA homopolymer. The additional insight gained for these reactions was possible due to the newly developed purification protocol, used in combination with NMR spectroscopy analysis, which provided detailed composition data for the different sample fractions and a better understanding of the grafting mechanism. Furthermore, preliminary results were obtained for starch modified with acrylonitrile and cerium (IV) in water under acidic conditions. Extraction of the polyacrylonitrile (PAN) homopolymer component was more difficult due to its solubility characteristics, but mixtures of dimethylacetamide with water (up to 10 % by volume) provided consistent results. High grafting efficiencies (> 67 %) were obtained for the starch-g-PAN copolymers, and characterization of the products was performed by Fourier transform-infrared spectroscopy, DLS, GPC, and atomic force spectroscopy. Hydrolysis of the starch substrate yielded hollow PAN shells or spheres, depending on the MS level of the copolymer, with potential applications in nanoencapsulation.
Development of Novel Human Aggrecanse-2 Dual-Binding Bis-Squaramide Inhibitors
(University of Waterloo, 2025-03-12) Ratto, Amanda; Honek, John
Osteoarthritis (OA) is a degenerative joint disease that affects millions of individuals worldwide. OA is characterized by the breakdown of articular cartilage, including the proteoglycan aggrecan, which plays a crucial role in enabling cartilage to withstand compressive loads. A Disintegrin and Metalloproteinase with Thrombospondin Motifs-5 (ADAMTS-5; aggrecanase-2), has been reported to be the predominant aggrecanase in mice, and in vitro studies revealed ADAMTS-5 exhibits high efficiency at cleaving aggrecan. Although no disease modifying OA drugs have been developed, it is hypothesized that inhibitors against ADAMTS-5 could slow the progression of OA. Typical inhibitors of ADAMTS-5 include zinc-binding groups (ZBGs) that interact with the catalytic zinc. Recently, an exosite that inhibitors can target has been identified at a nearby domain, not within the catalytic site. Here we present the development of novel potential dual-binding inhibitors which aim to target both the catalytic site and exosite of ADAMTS-5. The inhibitors investigated in this thesis incorporate a squaramide nucleus, which is an excellent molecular scaffold due to its ease of derivatization, known synthetic pathways, and commercial availability. To identify potential dual-binding bis-squaramide inhibitors, a large in silico library was constructed, consisting of the squaramide nucleus linking potential exosite binding groups and ZBGs. Numerous computational techniques were utilized to identify inhibitors, including molecular docking to evaluate potential interactions with both the binding pocket and exosite of ADAMTS-5, as well as molecular dynamics simulations to assess inhibitor stability and predict binding affinities. The four bis-squaramide molecules identified from the computational screening were successfully synthesized using a one-pot, microwave-assisted synthetic approach, which facilitated a high-throughput process through reaction automation. A range of bis-squaramide compounds were enzymatically screened with micromolar IC50’s for ADAMTS-5.
The Development of Electrochemical Systems for the Oxidation of Organic Contaminants for Water Treatment
(University of Waterloo, 2025-01-16) Delva, Nyhenflore; Klinkova, Anna
1,4 dioxane, also known as dioxane, is a contaminant of emerging concern, with no natural methods of degradation and no established treatment methods. This study investigates the use of both direct and indirect electrochemical advanced oxidation processes to generate radicals for dioxane oxidation, and how adjusting electrochemical parameters may be used to tune dioxane oxidation towards target compounds, thus offering a pathway to combine wastewater treatment with the synthesis of valuable compounds. Ion chromatography and nuclear magnetic resonance were used to identify and quantify the liquid products. The electro-Fenton process was used to indirectly oxidize dioxane via the activation of H2O2 generated in situ. H2O2 was quantified using TiOSO4 in an acidic solution. It was found that perfluorinated sulfonic acid binders can tailor carbon materials towards H2O2 production in acidic media, with as little as 5 wt% of PFSA binder dramatically improving both current density and H2O2 selectivity. Fe2+ concentration was shown to shift product selectivity of the Electro-Fenton process, with higher concentration resulting in greater selectivity towards C1 products. Early analysis of anodic oxidation of dioxane on ZnO reveals that carbonate radicals- formed from the oxidation of the bicarbonate electrolyte- are also part of the oxidation pathway, resulting in a different range of products than previously documented in the literature.
Multi-dimensional Analysis of Molecular Clusters in the Gas-phase
(University of Waterloo, 2025-01-10) Lee, Tsun Hei Arthur Enoch; Hopkins, Scott
In this thesis, interactions and properties of novel gas-phase clusters are studied. These gas-phase clusters often possess unique geometries and unexpected properties, which are influenced by the forces and interactions between the moieties within the cluster. Spectroscopic methods and ion mobility methods are coupled with tandem mass spectrometry to elucidate the cluster properties and geometry. IRMPD provides insight toward the nature of the cluster by their IR fingerprints, which can be used in parallel with tandem mass spectrometry method such as CID to provide further information. In addition, ion mobility methods are used to differentiate conformational differences between isomeric clusters. In chapter 3, IRMPD and CID of deprotonated fluorinated propionic acids are studied. In analytical studies of short chain per- and polyfluoroalkyl substances (PFAS), the quantification and the identification of these carboxylic acids are done by monitoring the carbanion signal after the loss of CO2. The degree of fluorination influences fragmentation under IRMPD and CID, leading to fragmentation pathways such as formation of FCO2– and HF elimination. Fluorinated propionic acids with at least one fluorine atom bound to the terminal carbon yield FCO2–, whereas loss of HF is observed in polyfluorinated species with at least one fluorine bound to the α-carbon. The formation of FCO2– and HF elimination products occur through a four-membered ring transition state. Chapter 4 describes the study of aromatic organometallic compounds such as cyclopentadienyl that are known to form sandwich complexes with counter cations, because the dominant interactions between the cation and the anion are Coulombic interactions and ion-induced dipole interactions. This work focuses on studying the influence on the geometry of the cluster by reducing the symmetry of the aromatic compound through clustering 1,2,3–triazolide and 1,2,4–triazolide with various alkali metal cations (with an excess of one cation to preserve cationic states). Through a combination of IRMPD and DFT calculations, the primary interaction between the alkali metal cations and the triazolide is found to be dominantly ion-dipole interactions and lone-pair donation interactions. This results in the geometry of the 1,2,3–triazolide clusters to be a 3D compact structure, whereas the 1,2,4–triazolide analogues are found to be more open with longer distances between the cations. Potential overtone bands or combination bands associated with the C-H wagging motion and ring torsion motion are found between the 1500 – 1800 cm–1 region. Chapter 5 is a study on the clusters of perfluorinated dodecaborate cages, B12F122–, with protonated diaminoalkanes H2N(CH2)nH2N (n = 2 – 12) through a combination of IMRPD action spectroscopy and ion mobility spectrometry. I focus on characterizing the different singly-charged clusters of the form [B12F12 + H2N(CH2)nNH2 + H]– and doubly-charged clusters of the form [2(B12F12) + H2N(CH2)nH2N + 2H]2– (n = 2 – 12). Three unique geometries are found for the singly-charged clusters, a low energy proton-bound ring geometry where intramolecular hydrogen bonding occurs between the two amine functional groups, a bidentate geometry (where both amine groups bind to the B12F122– moiety), and a monodentate geometry. For the doubly-charged clusters, the doubly protonated diaminoalkane act as a tether between the B12F122– cages. The major fragmentation channels of the singly-charged and doubly-charged clusters are found to be: (i) proton-transfer leading to production of HB12F12– and (ii) the loss of B12F122–. Formation of HB12F12– likely leads to further gas-phase reactions that can yield compounds such as [B12F11 + N2]–. Travelling wave ion mobility spectrometry (TWIMS) analysis of HB12F12– finds CCSTWIMS = 142 ± 6.7 Å2. IRMPD spectroscopy, aided by computational modelling, indicates that the bidentate conformation is the major sub-population in the gas-phase ensemble.
Development of a Low-Cost Biosensor for Tuberculosis Diagnosis
(University of Waterloo, 2025-01-06) Mayry, Jonathan; Honek, John; Mitra, Sushanta
Tuberculosis is a deadly disease that is a major public health issue, especially in low-resource communities. However, there are shortcomings associated with current diagnostic tools that are hindering the eradication of this disease. The overarching goal of this research was to create a diagnostic device for tuberculosis that is inexpensive and easy to use while still exhibiting excellent diagnostic sensitivity. This thesis will describe the multifaceted approach that was taken to develop such a device. To begin, the rationale for choosing tuberculosis as a biosensing target will be provided, and the shortcomings of current tuberculosis diagnostic tools will be summarized. This information is included to provide context for the experimental work that was conducted, much of which focused on the construction and testing of a paper-based lateral flow assay for the detection of the tuberculosis antigen lipoarabinomannan. The assay was constructed using an anti-lipoarabinomannan DNA aptamer sequence that was previously identified in the literature, and various signal generation methods, including aptamer-labelled gold nanoparticles and the catalysis of chromogenic reactions by aptamerlabelled enzymes, were employed. Aptamers were chosen over antibodies in this research to increase the stability and reduce the cost of the lateral flow assay. Although the assay constructed in this research was ultimately unable to successfully detect lipoarabinomannan, this thesis will describe the many insights that were gained regarding the challenges of developing such a sensor and suggest potential solutions to these challenges. Additional experimental work described in this thesis focused on the testing of horse spleen ferritin loaded with synthetic ferrihydrite cores as a potential replacement for peroxidase enzymes that are commonly used in biosensing. To facilitate the implementation of these catalysts into biosensors such as lateral flow assays, the ferritin was also modified with biotin groups, and work was undertaken to formulate a stable aqueous formulation of a peroxidase substrate that was compatible with the ferritin. Catalysis studies showed the ferritin could successfully catalyze the same reactions as peroxidase enzymes. With some additional optimization of the substrate formulation, horse spleen ferritin holds great promise as a low-cost, highly stable alternative to these ubiquitous enzymes. In parallel with the experimental work that took place in the laboratory, in silico experiments were also conducted to analyze the aptamer that was utilized in this research. Docking and molecular dynamics studies involving the aptamer and a fragment of lipoarabinomannan revealed a potential binding site on the aptamer. However, inconsistencies between the results of these simulations and experimental work reported in the literature highlighted the shortcomings of the computational models of the aptamer and antigen that were generated in this research. Further work is required to produce more realistic simulations. Finally, a novel, easily multiplexable sensor architecture is proposed in this thesis, and the computational modelling that was conducted to construct this sensor in silico is described. The computational modelling allowed for optimization of the sensor design, and it is hoped that further computational studies will enable the eventual in vitro implementation of this sensor to create low-cost, highly sensitive diagnostic tools for diseases such as tuberculosis.
Enzymatic Oxidation of Polyethylene & Peptide-Based Detection of Microplastics
(University of Waterloo, 2024-12-17) Waldie, Alexander; Honek, John
As humanity nears a century of steadily rising polyethylene (PE) production the associated environmental and societal costs are drawing increased concern. The recalcitrant nature of PE, while a distinct material advantage, poses a challenge to biotic degradation leading to prolonged environmental persistence. Here we present a screening of commercially available oxidative enzymes previously reported to oxidize the surface of PE with analysis performed by high-temperature 1H-NMR. This screening was conducted with the perspective gained from having previously characterized catalytically oxidized PE, which verified the efficacy of the 1H-NMR analytical method. In total, five commercially sourced oxidoreductases and hemocyanin were tested on standardized PE and characterized by 1H-NMR. Despite multiple attempts with various radical mediators, only manganese peroxidase demonstrated potential oxidative activity against PE. These results underscore the need for carefully designed PE degradation experiments which utilize standardized PE, employ a range of analytical techniques, include the full spectra of the acquired data, and report all outcomes. In addition to the screening of oxidative enzymes, we designed and tested five fluorescent peptide probes, produced using previously reported plastic binding peptides, to selectively identify the polymeric material of microplastics. Using both experimentation and computational modeling, tryptophan and phenylalanine were identified as key residues that mediate the binding of the peptides to the plastic surface. However, the produced hydrophobic interactions were determined to be largely non-specific when tested against PE, polyethylene terephthalate, polypropylene, and polystyrene.
Characterizing the Structural Arrangement of Lipoplexes by Pyrene Excimer Formation
(University of Waterloo, 2024-12-04) Lloyd, Ryan; Duhamel, Jean
Lipoplexes formed through the complexation of cationic surfactants and DNA were investigated by a combination of steady-state and time-resolved fluorescence with the fluorescent probe PyO-3-12, dynamic light scattering (DLS), and transmission electron microscopy (TEM). PyO-3-12 is an asymmetric gemini surfactant consisting of two dimethylammonium bromide headgroups linked by a propyl spacer, with one headgroup bearing a dodecyl chain and the other a 1-pyrenemethoxyhexyl derivative. Its sensitivity to the local pyrene concentration and polarity of the local environment were utilized to probe the hydrophobic microdomains generated inside lipoplexes. The overarching goal of this thesis is to demonstrate how pyrene excimer formation (PEF) between an excited and a ground-state pyrenyl labels can be applied to probe the interactions between surfactants and DNA and the resulting morphology of the lipoplexes. The first chapter of the thesis presents a review of the interactions between surfactants and water-soluble polymers such as DNA and the fundamentals of PEF with the perspective of their application for the characterization of lipoplexes. Other techniques used to probe lipoplexes such as DLS and TEM are briefly described as well. In Chapter 2, the ability of PyO-3-12 to behave as a complexing agent for the formation of lipoplexes was investigated. The interactions between PyO-3-12 and DNA were monitored as PyO-3-12 was held at a fixed concentration of 16 and 56 µM and the DNA concentration was varied between 1/10th and a 10-fold excess of the PyO-3-12 concentration. In terms of (-/+) ratio, representing the concentration of negative phosphates divided by the concentration of positive ammonium ions, the (-/+) ratio ranged from 0.1 to 10 in these experiments. Upon complexation onto DNA, PyO-3-12 showed increased PEF and indicated a more hydrophobic environment as would be expected. These results reflect the morphology of the PyO-3-12/DNA lipoplexes at the molecular level were supported by TEM and DLS experiments, which described the lipoplexes at the macroscopic level. In Chapter 3, the integrity of the PyO-3-12/DNA lipoplexes prepared with a (-/+) ratio of 1.5 and a PyO-3-12 concentration of 16 and 56 mM was investigated as they interacted with sodium dodecyl sulfate (SDS) for SDS concentrations ranging from 0 to 100 mM. The anionic surfactant generated a competing interaction for PyO-3-12 to induce the release of the negatively charged DNA. The existence of tertiary aggregates between all three species was demonstrated by fluorescence at the equicharge point between PyO-3-12 and SDS, followed by the loss of electrostatic interactions between PyO-3-12 and CT-DNA at higher SDS concentrations resulting in the release of DNA from the lipoplex. The evolution of the complexes formed between PyO-3-12, DNA, and SDS could be followed by TEM but DLS was less informative due to the polydispersity of the system that hampered the analysis of the DLS data. Chapter 4 represents the first example in the literature where PyO-3-12 was employed to probe the hydrophobic domains generated inside a lipoplex by two cationic surfactants, namely dodecyltrimethylammonium bromide (DTAB) and the gemini surfactant 12-3-12 constituted of two dimethylammonium headgroups held together by a propyl linker and bearing one dodecyl chain each. Analysis of the fluorescence data indicated that the 12-3-12/DNA lipoplexes were denser than the DTAB/DNA lipoplexes which was confirmed by conducting DLS and TEM experiments. In summary, this thesis demonstrated that PyO-3-12 is an interesting fluorescent probe to characterize the interactions between PyO-3-12 and anionic molecules such as SDS and DNA and study the interactions of other cationic surfactants such as 12-3-12 and DTAB with DNA. It opens the path for using PyO-3-12 in the molecular level characterization of soft matter generated through the interactions between surfactants and macromolecules.
A Parameterized Vibronic Spin-Orbit Coupling Model Protocol Suitable for Spectroscopy
(University of Waterloo, 2024-11-14) Chen, Benny; Nooijen, Marcel; Zeng, Tao
A diabatization protocol constructing vibronic model Hamiltonians with inclusion of spin-orbit coupling was implemented in Python. This protocol has been extended to include spectroscopic applications. GAMESS package GMC-QDPT level of theory calculations carries out a proposed diabatization scheme to automatically compute a grid of diabatic states in expansions of displaced nuclear coordinates. Diabatic potential energy surfaces can subsequently be constructed through fitting parameters. Generated vibronic models can be used for input to quantum dynamical simulation approaches such as MCTDH and VECC alike, where auto and cross-correlation functions can be obtained after propagation. Simulated gas-phase photoelectron spectra were reproduced for H2O, NH3, and PH3, with excellent agreement to experimentally recorded spectra. Absorption spectra of transition metal trifluorides CoF3 and RhF3, along with iron pentacarbonyl Fe(CO)5, were studied with a triple zeta polarized Sapporo basis set. Both CoF3 and RhF3 showed pronounced splitting originating from spin-orbit coupling effect, whereas Fe(CO)5 only displayed minimal change due to spin-orbit coupling limited to its truncated constant-order spectrum. It is predicted that the Jahn-Teller effect plays a more dominant role over spin-orbit coupling in our Fe(CO)5 model simulated spectra. Streamlining of the protocol has increased its accuracy and robustness, in the interest of supporting future vibronic spin-orbit coupling model research.
Multi-pronged analysis of secondary lithium metal batteries with various cathode chemistries
(University of Waterloo, 2024-10-17) Kochetkov, Ivan; Nazar, Linda
Due to permanently growing demand for safe and affordable energy, the search for sustainable alternatives to fossil fuels has become one of the most critical challenges of the 21st century. Owing to their high energy density, state-of-the-art lithium-ion batteries are widely applied in different areas of human life, from military drones carrying up to 200 kg of payload to cardioverter-defibrillators. Since current Li-ion technologies have approached the edge of their applicability in electric vehicles, there is an emerging call for developing lithium batteries with better characteristics. Post-LIB technologies, including Li-O2, Li-S, and solid-state batteries with metallic Li anode, are among the most promising alternatives to replace LIBs. However, post-LIB technologies encounter different fundamental challenges that substantially reduce the capacity retention, safety, and rate capability. Understanding and resolving some of the challenges of post-LIBs is the focus of this dissertation, with particular attention paid to correlating readily measurable battery characteristics with interfacial processes. This thesis covers multiple topics, including Li-O2 batteries, Li metal batteries with liquid and solid-state electrolytes, Li-S batteries with hybrid/liquid electrolytes, and all-solid-state batteries with high-energy-density cathodes. This work establishes multi-pronged approaches to study the efficacy of various electrolytes. A novel approach is demonstrated for stabilizing a Li+-conducting garnet solid electrolyte in Li-S batteries with electron pair donor electrolytes. Chapter 3 of the thesis presents the study of LiI as a potential charge redox mediator for nonaqueous Li-O2 batteries. The effect of LiI on oxygen electrochemistry during battery charge and discharge is investigated by combining various characterization techniques. This chapter demonstrates that the battery performance becomes less reversible when the electrolyte contains LiI. The combination of DEMS and iodometric titrations indicates that LiI lowers the yield of the target discharge product, Li2O2, and triggers redox shuttling on charge. The simultaneous presence of LiI and H2O in the electrolyte results in the irreversible 4e reduction of oxygen to LiOH. Chapters 4 – 5 are devoted to developing lithium metal batteries with different battery configurations and cathode chemistries. In Chapter 4, a comprehensive study of the solvate ionic liquid electrolytes containing LiFSI, Gn, and TTE establishes the relationship between the length of glyme solvents and the stability of Li anodes. The combination of Raman spectroscopy, AIMD simulations, and EIS illustrates that the kinetics of lithium metal anodes in solvate ionic liquid electrolytes containing long-chain Gn (G3 and G4) is impeded by the formation of the [Li(Gn)]+ chelates. In contrast, the G1(G2)-based SILs’ solvation structure is primarily comprised of strongly associated Li+ and FSI-, which reduces the interfacial resistance and activation energy barriers. However, the lithium transference number of the solvate electrolytes is limited to ~0.2, which dictates the diffusion-limited rate capability of the Li anode. The chapter demonstrates that the rate capability limit observed in the asymmetric Cu-Li and full Li||LiNCA cells agrees with the values predicted by combining the EIS results and existing Li dendrite formation models. The stability of Li anodes in solid-state cells with sulfide-based solid electrolytes is investigated in Chapter 6. This case study demonstrates that the presence of Si4+ in the structure of sulfide solid-state electrolytes triggers continuous interphase growth, which may consume a 50 micron Li anode. Meanwhile, the solid electrolytes, devoid of reducible cations, facilitate Li deposition with a CE exceeding 99 % when the current density is limited to 0.1 mA.cm-2. However, Li deposition at higher current densities is interrupted by the formation of Li dendrites. Nevertheless, the performance of Li anodes may be temporarily improved by modifying the solid electrolyte with a sacrificial dendrite scavenger or wetting the Li/solid electrolyte interface with a solvate, as developed in Chapter 4. The novel concept of the Li-S battery with a Li6.5La3Ta0.5Zr1.5O12 (LLZO) garnet solid electrolyte and an electron pair donor electrolyte, DMA, is demonstrated in Chapter 6. Numerous characterization techniques were employed to investigate the interfacial reactivity between LLZO and sulfur in DMA. Traces of LiOH and Li2CO3 at the surface of LLZO trigger the oxidation of sulfur and formation of trisulfur radical which further reacts with LLZO, yielding an insulating layer containing thiosulfate, polythionate and La-O/La-O-S species. The interfacial instability of LLZO results in a rise in the interfacial resistance (> 5000 Ohm.cm2) and rapid capacity fading of the Li-S batteries. Nonetheless, phosphorylating LLZO yields a thin (~ 10 nm) and conductive (~ 40 Ohm.cm2) layer containing Li, La, and Zr phosphates, which inhibits the side reactions. Therefore, Li-S batteries with phosphorylated LLZO and DMA deliver a stable capacity of 1400 mAh.g-1. Chapter 7 is devoted to all-solid-state batteries with LiNixCoyMn1-x-yO2 cathodes and Li-M-Cl (Li2.5Y0.5Zr0.5Cl6, Li3InCl6, L2Sc1/3In1/3Cl4) catholytes. The effect of M in Li-M-Cl on the battery performance is analyzed through DFT calculations, electrochemical methods, and ToF-SIMS. Cycling solid-state batteries with LiNi1/3Co1/3Mn1/3O2 and LiNi0.85Co0.1Mn0.05O2 demonstrates that capacity fading depends on oxygen evolution in LiNixMnyCo1-x-yO2 and the nature of M in Li-M-Cl. When LiNixMnyCo1-x-yO2 does not undergo an OER, the cell performance is dictated by the intrinsic electrochemical stability of Li-M-Cl. However, the interfacial reactivity between LiNixMnyCo1-x-yO2 and Li-M-Cl is more important when OER occurs. The chapter also establishes a multi-pronged approach to study the performance of new solid electrolytes in solid-state batteries with high-energy-density cathode active materials.
Developing quantum field theoretical computational methods for quantum dynamics and statistical mechanics simulations in quantum chemistry
(University of Waterloo, 2024-09-24) Bao, Songhao; Nooijen, Marcel
This thesis presents the development of two approaches—thermal normal-ordered exponential (TNOE) and thermofield coupled cluster (TFCC)—for simulating quantum dynamics and statistical mechanics in quantum chemistry, grounded in quantum field theoretical formulations. The TNOE approach employs a normal-ordered exponential ansatz to parameterize the thermal density operator, allowing the calculation of thermal properties through cluster expansions and imaginary time integration of equations of motion (EOMs). The TFCC approach introduces a fictitious space and Bogoliubov transformation to express the thermal density operator as a "pure state," similarly enabling thermal property calculations through imaginary time integration. The two approaches are verified to be mathematically equivalent and they are applied to two specific problems: the electronic structure problem and the vibronic coupling problem. The application on the thermal electronic structure problems encounters challenges due to N-representability issues. Modifications to the TNOE approach lead to the vibrational electronic coupled cluster (VECC) method, effectively simulating the quantum dynamics of vibronic coupling systems with impressive efficiency and accuracy. The statistical mechanics formulation of the VECC method, vibrational electronicthermofield coupled cluster (VE-TFCC), utilizes imaginary time integration to successfully calculate thermal properties of vibronic coupling systems with enhanced efficiency and accuracy compared to conventional methods. Overall, the VECC and VE-TFCC approaches, in combination with vibronic models, provides a robust framework for simulating quantum dynamics and thermal equilibrium properties of vibronic coupling systems.
Development and Electronic Characterization of Graphene-Based Hall Effect Devices
(University of Waterloo, 2024-09-24) Lacroix, Camille; Baugh, Jonathan
Graphene is a two-dimensional carbon material with a unique honeycomb lattice structure and exceptional electronic properties. Its band structure confines carriers to a single plane, allowing them to act like relativistic massless particles at low carrier densities. This has made graphene a focal point in condensed matter physics, particularly following the groundbreaking discovery of the first topological state using a graphene lattice. Research into graphene's potential as a platform for quantum topological computing has surged. In addition to its distinct band interactions, graphene is also being studied as a potential standard for electrical resistance. However, progress in its isolation since its initial synthesis in 2004 has been limited. This thesis focuses on the synthesis of single-layer graphene (SLG) through low-pressure chemical vapor deposition (LPCVD) on copper films at temperatures above 1000 °C. The graphene films are transferred using a wet transfer technique and characterized with atomic force microscopy (AFM) and Raman spectroscopy. Hall devices for electrical transport studies are patterned using maskless alignment photolithography, with palladium as ohmic contacts. Electronic transport measurements are conducted at cryogenic temperatures up to a magnetic field of 5T using 4-terminal measurement techniques. Moreover, this work explores electronic transport in twisted bilayer graphene (TBG) - tungsten diselenide WSe2 Hall devices. This structure facilitates the study of strongly correlated electronic states enhanced by spin-orbit coupling induced by WSe2. Preliminary experiments to detect unconventional Hall states in similar devices are carried out at millikelvin temperatures and in magnetic fields up to 18 Teslas.
Proximity Superconductivity in Indium Arsenide Two-Dimensional Electron Gas Devices
(University of Waterloo, 2024-09-23) Thompson, Fiona; Baugh, Jonathan
Of the many theoretical proposals for quantum computers, topological quantum computing is unique in its resistance to decoherence and the reliability of its gate operations. One proposed method for achieving these topological qubits is to harness the unusual non-Abelian exchange statistics of quasiparticle excitations known as Majorana bound states. Historically, research devoted to realizing these states has primarily been in nanowires, but purely one-dimensional devices are limited in their applications. Two-dimensional electron gas devices are an alternative with the benefit of future scalability and increased options for device geometries. To this end, we developed InAs/AlGaSb surface quantum well devices compatible with the proximity-induced superconductivity required to realize a Majorana device. Magnetotransport measurements investigating mobility-density relationships, I-V characteristics, the Shubnikov de Haas effect, and the quantum Hall effect confirm the very high quality of our dielectric deposition method and growths. Even with quantum wells so near the surface of the device, we achieve high mobilities and stable, reproducible gating characteristics. These devices have high spin-orbit coupling coefficients, confirming that we can simultaneously benefit from the inherent bulk properties of InAs and properties imparted by the rest of the growth and lithography steps. Analytical comparisons of devices with different quantum well widths, interface characters, and dielectric deposition methods reinforce the need for the rigorous optimization of numerous factors. From this analysis, we conclude that devices with smooth surface morphologies, SiO2 dielectric deposited by atomic layer deposition, and InSb-like interfaces provide the ingredients necessary to achieve near-record mobilities and consistent gating properties. On these same excellent wafers, we fabricated superconductor-normal-superconductor (SNS)-type devices of three different normal region dimensions with ex-situ deposited niobium as the proximitizing superconductor. The universally high quality of these devices challenges the long-held norm that epitaxial aluminum is the best choice for the superconductor in these types of devices. Specifically, we achieved figures of merit much higher than those previously reported in Nb-InAs-Nb devices and on par with those using epitaxial aluminum. Using two separate mathematical models, we found that our devices have very high transparencies, indicating high-quality interfaces. Detailed plans for future devices are also discussed in this thesis, including gated SNS devices, quantum point contacts, and an attempt at observing Majorana signatures.
Magneto-Optical Investigations of Lead-Free Metal Halide Perovskite Nanocrystals
(University of Waterloo, 2024-09-23) Feng, Lin; Radovanovic, Pavle
Inorganic lead-free metal halide perovskites have garnered much attention as low-toxicity alternatives to lead halide perovskite for luminescence and photovoltaic applications. However, the electronic structure and properties of these materials, including the composition dependence of the band structure, spin-orbit coupling, and Zeeman effects remain poorly understood. In this thesis, we focus on two specific systems: Cs3Bi2X9 (X = Cl, Br) and double perovskite, including Cs2AgBiX6 (X = Cl, Br), Cs2AgInCl6 and its Bi-alloyed analogue (Cs2AgIn0.5Bi0.5Cl6). Using magnetic circular dichroism (MCD) spectroscopy, we investigate the electronic structure, magneto-optical properties, and excitonic transitions in these lead-free perovskite NCs. Our results reveal that the excitonic spectra of Cs3Bi2X9 are predominantly characterized by both direct and indirect band-gap transitions, with only a minor contribution from excitons localized on Bi3+ sites. In contrast, the excitonic transitions in Cs2AgBiX6 are primarily derived from direct free- and bound- exciton transition. Additionally, our results demonstrate that halide composition significantly influences the Zeeman splitting energy and g-factors, with Cs3Bi2Br9 and Cs2AgBiBr6 exhibiting stronger spin-orbit coupling compared to their chloride counterparts. Moreover, introducing bismuth ion (Bi3+) into Cs2AgInCl6 NCs can enhance the spin-orbit coupling and modify the electronic structure, demonstrating the potential for compositional tuning to optimize these materials for specific applications. Furthermore, temperature-dependent MCD measurements were conducted to further explore the excitonic behavior of these materials, providing insights into their suitability for further applications. In conclusion, this thesis provides detailed insights into lead-free halide perovskite NCs, emphasizing their potential as environmentally friendly alternatives to lead-based perovskite. These findings offer valuable guidance for the design of low-toxicity, high-performance materials for applications in spintronics, photovoltaics, and optoelectronics.
Synthesis and Study of a Lithium-Selective Chelator
(University of Waterloo, 2024-09-17) Brutto, Mark; Schipper, Derek
Lithium, the lightest metal on the periodic table, serves as a very valuable resource due to its many applications in things such as glass and ceramics, greases, and most importantly, batteries. The battery industry consumes the majority of our collected lithium, and this trend is expected to continue with increased electric vehicle usage. An increased awareness for our carbon footprint and greenhouse gas emissions, along with governmental legislation has led to an exponential increase in our lithium demand. Unfortunately, current lithium collection processes are unable to keep up with this increased demand, thus creating a need for new or improved lithium collection processes. The majority of lithium is collected from two major sources, lithium-rich brines in the ABC (Argentina, Bolivia, Chile) region and China, as well as minerals and ores typically found in China and Australia. Current techniques include expensive processes such as roasting and leaching from minerals and ores, or lengthy precipitation processes from pre-evaporated brines, both of which have proven to be unfit for future industrial demands. This research aims to develop and study a lithium-selective ligand that will eliminate lengthy evaporation processes typically associated with lithium collection from brines. Chapter 1 begins with a literature review on lithium and its societal and economic importance. It will explore current lithium isolation processes and their drawbacks preventing more expansive and efficient collection. Chapter 2 will include the inspiration behind our ligand design, starting with a preliminary direction and a complete adjustment upon computational calculations. Chapter 3 will include the synthesis and study of our proposed motif, illustrating a cheap and efficient synthesis, and promising preliminary lithium selectivity when compared with other 1st group cations.
Two-Dimensional Separation via Hybrid Liquid Chromatography and Differential Ion Mobility Spectrometry for PFAS Characterization
(University of Waterloo, 2024-09-17) Ryan, Christopher; Hopkins, W. Scott
This thesis details the development and implementation of differential mobility spectrometry (DMS) methods for the separation of per- and polyfluoroalkyl substances (PFAS). PFAS have become ubiquitous environmental pollutants, posing significant risks to ecosystems and human health. The complexity of PFAS matrices in environmental samples necessitates separation prior to mass spectrometric analysis because co-elution of compounds can cause ion suppression and compromise analyte identification and quantification accuracy. Although liquid chromatography (LC) is commonly used in PFAS analyses, some PFAS species co-elute and could benefit from an additional orthogonal dimension of separation. In Chapter 3 I explore the effects of solvent modifier on DMS behaviour for 224 compounds in negative mode electrospray ionization (ESI) mass spectrometry (MS). The data procured from these measurements will be used for machine learning (ML) purposes to predict the DMS behaviour of emerging environmental pollutants. Prior to this study, our library of DMS data was composed entirely of compounds that were measured in positive mode ESI MS and the distribution of observed dispersion behaviour was heavily skewed towards one behaviour type. Incorporation of the negative mode ESI data not only provided a better overall distribution of dispersion behaviour, but also allows for future ML models to be applicable for anions and cations alike. The results of this chapter also provide insight into the ion-neutral interactions that occur as analytes transit the DMS cell. From this it can be determined how different classes of compounds interact with various solvent modifiers, and how their analytical separation is influenced by the choice of modifier. This allowed us to determine the instrument conditions that lead to the optimal separation of the studied PFAS. In Chapter 4, I utilize the optimal separation conditions determined in Chapter 3 in a hybrid LC×DMS-MS2 method. Here, I employ DMS following LC separation to analyse 34 PFAS species. Upon incorporating DMS in a 2D separation scheme, I observed baseline resolution of 29 compounds in the 2D space, with only two and three compounds co-eluting, respectively. In comparison, only 5 compounds were baseline resolved in 1-dimensional LC experiments. Because DMS measurements are acquired within seconds, targeted 2D LC×DMS-MS2 analyses operate on the same timescale as 1D LC-MS2 analysis. Additionally, limits of quantitation approach those observed in state-of-the-art LC-MS2 methods. Moreover, distinct trends observed in the 2D separation space for the various PFAS subclasses could enable analyte identification in future non-targeted analyses.
Identifying Electrostatic Interactions Controlling pH-switching in Myristoylated Hisactophilin
(University of Waterloo, 2024-08-30) McDonald, Iain; Meiering, Elizabeth
Myristoyl-switching in proteins is an essential form of functional regulation that controls fundamental biological processes such as signal transduction, protein-membrane interactions, and viral infection. In this form of functional regulation, the reversible switching of a saturated C14 fatty-acyl chain covalently attached to the N-terminus of a protein switches between two states: 1) a sequestered state where the myristoyl group is buried in a hydrophobic environment and 2) a state with increased solvent accessibility where the myristoyl group is available for interaction with binding partners. Myristoyl-switching controls protein function by modulating affinity for membrane and protein binding partners, depending on the accessibility of the hydrophobic myristoyl group. Hisactophilin is a membrane binding protein found in Dictyostelium discoideum responsible for binding and bundling actin in a pH-dependent manner, largely driven by the reversible exposure of its myristoyl group. This protein’s myristoyl switch is controlled by an intramolecular network of electrostatic-hydrophobic interactions; at low pH ~1.5 protons are bound by some of the many ionizable groups, resulting in a conformational shift where the sequestered myristoyl group is made more accessible for insertion into cellular membranes. Through a combination of implicit solvent molecular dynamics simulations and experimental methods, residues D57, H89 and H91 were hypothesized to be the residues controlling myristoyl-switching in hisactophilin. Mutation of these residues indicates that the proposed mechanism of pH-switching in hisactophilin is not fully correct. Design and experimental characterization of follow-up mutants indicates that pH-switching may be controlled through an alternative mechanism. Further investigating the molecular mechanisms of myristoyl-switching in this protein will provide valuable insight into how hydrophobic-electrostatic networks regulate function in allosteric proteins.
Investigation into the Chiral Selectivity of DNA Aptamers for Essential Biomolecule Targets
(University of Waterloo, 2024-08-30) Zia, David; Liu, Juewen
In nature, chiral molecules are typically represented as a single enantiomer for most biomolecules. This aspect of homochirality is said to be connected to prehistoric RNA which led to the dominance of sugar and amino acids to exist exclusively as one chiral form. With the advent of geomatics technology becoming more prominent in therapeutics like biosensing and drug delivery, understanding a deeper aspect on nucleic acid chemistry can help with both improving efficiency and expanding applications. In this thesis, the focus will be on DNA, specifically aptamer technology and how their affinity to ligands can be influenced by chirality. The chiral biomolecules of both lactate and tryptophan are explored by conducting various selections for the different isomers. Both targets are important in clinical applications. Tryptophan is an essential biomolecule responsible for the production of neurological hormones in the body, while lactate is an unique biomolecule in that both of its enantiomers have distinct role in the body. In our lactate selection, even using only D-lactate as a target, high specificity aptamers for L-lactate were obtained. The aptamers showed capabilities of reaching KD of 0.23 mM and a limit of detection (LOD) of 0.21 mM in blood serum. These concentrations nicely cover the physiological range of lactate (1-20 mM), which demonstrates its potential for therapeutics applications. Additionally, the aptamer also demonstrates a 5-fold enantioselectivity for L-lactate compared to D-lactate. From the evidence present of this experiment, it is likely that DNA aptamer exhibit a preference towards L-chirality for lactate. For the selection with tryptophan, two separate experiments were conducted using racemic and homochiral solution of tryptophan as the selection targets. The obtained aptamers from these selections demonstrated high enantioselectivity for both L-tryptophan and D-tryptophan. One of the D-tryptophan aptamer exhibited a KD of 11 μM and a 7-fold greater affinity compared to L-tryptophan. We can compare this affinity to that of aptamers specific to L-tryptophan reported in other studies, which displayed similar affinity and selectivity for the opposite enantiomer. Due to this result, we proposed that DNA’s affinity for both enantiomers stems from the greater complexity and binding features presented in tryptophan’s molecular structure. By studying the sequences that were obtained from the selections, we observed two distinct cases of chiral bias in DNA for different biomolecules. We demonstrated how using a homochiral target solution can be applied to improve the selection of high affinity aptamers, as seen by the lactate study. Additionally, we demonstrated that highly selective DNA aptamers can also be obtained for both enantiomer of a target, as seen by the tryptophan study. Although the exact reason for the chiral preference in some targets remains uncertain, our findings suggests that variance in size may be a plausible reason to explain this phenomenon. Future studies should be taken to explore this case further by selecting other essential biomolecules that are similar in size to the two targets used. Exploring how DNA interacts with targets that have varying functional groups would help provide some more insight on the underlying mechanism of DNA’s chiral binding.

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