Chemistry

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

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Characterizing the Structural Arrangement of Lipoplexes by Pyrene Excimer Formation
(University of Waterloo, 2024-12-04) Lloyd, Ryan
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.
Multi-pronged analysis of secondary lithium metal batteries with various cathode chemistries
(University of Waterloo, 2024-10-17) Kochetkov, Ivan
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
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
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
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
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
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
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
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
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.
Proteolysis and Mass Spectrometry for Structural Characterization of Adnectin Inclusion Bodies
(University of Waterloo, 2024-08-29) Liu, Xiaoyue
Inclusion bodies (IBs) are cellular aggregates that commonly form upon overexpression of protein in heterologous hosts. The formation of IBs is of broad interest for protein production for research, medical or biotechnological applications, and soluble or insoluble forms such as self-immobilized catalysts, drug delivery systems, and functional protein release systems. These aggregates are known to be heterogeneous, containing different conformations of the constituent protein. Adnectins are engineered binding proteins with high global thermostability and expression levels but varying propensity to form IBs, providing an attractive system for studying IB formation. A single-point mutation and two sets of multiple-point mutations with increasing charged residues were designed to alter the Adnectin IB structure. Fourier Transform Infrared spectroscopy (FTIR) showed an increased amyloid-like signal for the four-point mutations. To further analyze IB structure, we combined protease digestion with mass spectrometry (MS). Proteinase K, as a non-specific protease, can serve as an analytical tool by conducting parallel experiments digesting unlabeled and 15N-labelled IBs, followed by matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) MS. This procedure facilitated the identification of digested fragments. Comparing the fragments from the Adnectin variant IBs reveals both similarities between the IBs as well as different protease-accessible sites indicating structural differences. This new procedure for protease digestion analysis provides a valuable complementary tool to help overcome challenges in characterizing heterogeneous aggregation processes and advance the understanding and, ultimately, control of IB structure.
Selection and Characterization of DNA Aptamers for the Detection of Antibiotics
(University of Waterloo, 2024-08-28) Zhao, Yichen
DNA is a naturally occurring biomacromolecule that plays many roles in living organisms. While the majority of natural DNA is double stranded, chemical synthesis allows the production of single-stranded DNA oligonucleotides that can carry chemical functions for molecular recognition, and these are known as DNA aptamers. There is wide range of targets that DNA can bind, from metabolites, drugs, toxins, and other small molecules to proteins and even cells and tissues. Aptamers are generally selected through an iterative process called Systematic Evolution of Ligands by Exponential Enrichment (SELEX). After this process is completed, the newly selected aptamers can then be subject to binding assays for characterization before finally becoming useful for sensing. Compared to the traditional methods of sensing such as HPLC, mass spectroscopy, or antibodies, aptamers are cheaper, easier to transport and use, have longer shelf lives, and can have a wider range of targets. This focus of this thesis is to use a method called capture-SELEX to isolate new aptamers for a few important antibiotics. While aptamers have been reported for them, they were mostly obtained by the immobilization of target molecules. In capture-SELEX, the DNA library is immobilization allowing the use of free target molecules. In Chapter 1, background information is given about nucleic acid structure, DNA, and the current state of aptamers. The SELEX process is also discussed in detail as well as some characterization methods and sensor applications. In Chapter 2, a new DNA aptamer for the family of tetracycline antibiotics was selected using capture-SELEX and oxytetracycline (OTC) as the target. This new aptamer was called OTC5 and had a dissociation constant (Kd) of 150 nM OTC measured using ITC. This aptamer could also enhance the intrinsic fluorescence of the tetracycline antibiotics and this property could be exploited for label free and dye free sensing. Follow-up studies were done on the OTC5 aptamer. vii It was found that metal ions (specifically Mg2+) had an effect on the binding of OTC5 to the tetracyclines. pH also affected binding with pH 6 promoting binding more than higher pH values. Studies were also done on splitting the OTC5 aptamer. The split aptamer retained its binding with doxycycline. In Chapter 3, from the remaining SELEX pool of the selection in Chapter 2, 10 other aptamers were identified to have binding with the tetracyclines. Some of these could distinguish between tetracycline, doxycycline, and oxytetracycline which led to the development of an aptamer sensor array that could differentiate these antibiotics with statistical significance. In Chapter 4, a new aptamer called CAP1 was selected for chloramphenicol (CAP) using capture- SELEX. Previous aptamers for CAP were selected by target immobilization which omitted a portion of the CAP molecule. When subjected to ITC, this previous aptamer did not show any indications of binding to the full CAP molecule. The newly selected CAP1 showed a fitted Kd of 9.8 μM using ITC. A sensor was also developed using Thioflavin-T fluorescence and had a limit of detection of 1.8 μM in lake water and 3.8 μM in wastewater. In Chapter 5, the effect of pH on aptamer selection was studied by a parallel selection at pH 6 and pH 8 for the aminoglycoside antibiotic kanamycin A. The selection at pH 6 showed better convergence than pH 8 and yielded an aptamer (KAN6-1). This aptamer had a Kd of around 300 nM from ITC. pH and salt studies were done using Thioflavin-T fluorescence assays and the optimal condition for binding was at pH 6 with no added salts. When KAN6-1 was tried with thioflavin-T under pH 8 selection conditions, there was no evidence of any binding. A sensor was then designed using KAN6-1 and had a limit of detection of 0.1 μM in lake water.
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.

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