Chemistry

Permanent URI for this collectionhttps://hdl.handle.net/10315/26546

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Access status: Open Access ,
Design, Synthesis, and Characterization of Novel Phosphorus-Containing Conjugated Materials Based on Vat Orange 3
(2025-11-11) Dadgaryeganeh, Reza; Baumgartner, Thomas
As the global production and diversification of electronic devices—ranging from energyconversion to energy-storage applications—continues to surge, enhancing their efficiency has become a critical objective. While the well-built metal-based technology of these devices warrants recognition, the associated sustainability and toxicity issues must not be overlooked. This is where π-conjugated organic materials play a pivotal role. Research in the new millennium has provided numerous types of conjugated materials possessing properties that offer clear paths towards integrated electronic devices (e.g., Organic Light-Emitting Devices (OLEDs), Organic Solar Cells (OSCs), Organic Field-Effect Transistors (OFETs), organic batteries) with performances approaching those of their metal-based counterparts. Accordingly, a multitude of developed compounds such as Polycyclic Aromatic Hydrocarbons (PAHs) or strategies that embed main group elements into carbon-based synthons, have all been aimed at this common goal. However, the development of PAHs and incorporation of heaver main group elements such as phosphorus have rarely intersected until recently. This marriage is facilitated by the emergence of vat dyes as cost-effective precursors for organic semiconductors as their scaffolds provide a convenient route to PAH cores, such as anthanthrene and chrysene. Therefore, this thesis is focused on methods of merging phosphacycles with Vat Orange 3, along with investigating the photophysics of these functional materials, their capacity and ease of undergoing redox processes, and the role of phosphorus in modulating the systems’ electronics and impact on the overall functional properties. Through bridging heavier main group elements and large conjugated scaffolds, the emerging platform also attempts to overcome long-standing limitations in the literature, such as inefficient low-energy luminescence, restoration of the original keto groups in the vat dye-based frameworks, and doublet emission from phosphorus-containing conjugated materials.
Access status: Open Access ,
Synthesis and Characterization of Model Compounds For Self-Assembled Dithienophosphole-Based Phosphamides
(2025-11-11) Odagwe, Mary Ibukunola; Baumgartner, Thomas
On the path to synthesizing classes of dithienophosphole soft materials, this thesis documents the synthesis and characterization of model compounds for self-assembled dithienophosphole-based phosphinamides. Expanding upon the blue-emitting series within this class of compounds and targeting applications in white OLEDs, green and orange emitters, along with their corresponding model compounds, are reported. Taking advantage of the ease of functionalizing the α-position of the dithienophosphole core, the emitter compounds were synthesized via Suzuki cross-coupling reactions. The model compounds, incorporating hydrogen-bonding moieties, were prepared through substitution at the phosphorus center. Comprehensive characterization was performed, including optical and spectroscopic analyses, and full synthetic details are provided.
Access status: Open Access ,
A Modified Commercial Dynamic Chamber System for Measuring Soil Reactive Nitrogen Fluxes
(2025-11-11) Shah, Moxy Hemantkumar; VandenBoer, Trevor
Reactive nitrogen compounds (NO, NO2, HONO, and NH3; Nr) play an important role in atmospheric processes and pose environmental and health risks. Though studied individually, their interactions at the surface–atmosphere interface remain unexplored. To address this issue, a comprehensive Nr dynamic chamber setup was developed by modifying a commercially available system for GHGs. System modifications to minimize surface loss for Nr were implemented. Proof-of-concept measurements under controlled lab conditions demonstrated that NO, NO2, HONO, NH3, and N2O emissions can be quantified simultaneously. The p-values for the NO, NO2 and HONO within a specific soil volumetric water content range (20-24%) revealed heterogeneity, suggesting a need to reconsider the soil sampling and handling techniques used in laboratory studies. Emission trends from urea and synthetic magnesium/zinc ammonium carbonate fertilizers provide preliminary insights into Nr release from fertilized soils.
Access status: Open Access ,
Synthesis and Lewis Base-Catalyzed Functionalization of Carbamoyl Fluorides
(2025-11-11) Cadwallader, Dusty James; Le, Christine
Amides are extremely prevalent in the pharmaceutical, agrochemical and materials industries. Typically, amides are prepared by the combination of amines and carboxylic acids in the presence of an amide-coupling reagent. This dissertation describes the synthesis and reactivity of carbamoyl fluorides, a unique electrophilic class of molecules that form amides when treated with carbon-based nucleophiles. A synthesis of carbamoyl fluorides directly from secondary amines is described. This method relies on the reaction of difluorocarbene with an oxidant to generate difluorophosgene (COF2) in-situ. Several carbamoyl fluorides were prepared with this method, and the mechanism was supported by kinetic analysis and nuclear magnetic resonance (NMR) spectroscopy experiments. To prepare alkynamides, carbamoyl fluorides were paired with alkynyl silanes and the common laboratory reagent tetrabutylammonium fluoride (TBAF) was found to be the optimal catalyst. This reaction proceeded efficiently due to the thermodynamic driving force of forming extremely strong Si-F bonds in the by-products. A selection of alkynamides were synthesized using this method, including those bearing functional groups that may be problematic in other modern alkynamide syntheses. Using silyl ketene imine nucleophiles, α-cyanoamides were prepared from carbamoyl fluorides using either fluoride, phenanthrolines or P(V) compounds as catalysts. As the amide produced in this method contains a chiral quaternary carbon centre, this project was focused on identifying a chiral Lewis base for asymmetric catalysis. It is suspected that the fluoride released in this reaction acts as the active catalyst, outcompeting the chiral compounds and limiting asymmetric induction.
Access status: Open Access ,
Group 4 and 12 Complexes Bearing Guanidine-Phenolate or Amidine-Phenolate Ligands: Coordination Chemistry and Polymerization Studies
(2025-11-11) Flores Romero, Victor; Lavoie, Gino
This dissertation explored the synthesis of Group 4 and Zn catalysts bearing guanidine–phenolate or amidine–phenolate ligands and their ability to catalyze chemical transformations. Group 4 diisopropoxide and Zn complexes were evaluated for the homopolymerization of lactide, while titanium dichloride complexes were assessed for their ability to polymerize ethylene. Group 4 diisopropoxide catalysts were active towards the ring-opening polymerization (ROP) of lactide, in the absence of any solvent, at 130°C. All Zr complexes were more active than the corresponding titanium homologues. The rate constant of the bis(guanidine–phenolate) group 4 systems (1.17––3.21 × 10-4 s–1) were higher than those displayed with Ti(OiPr)4 (5.34 × 10-5 s–1), and Zr(OiPr)4·iPrOH (2.79 × 10-5 s–1 ). Polylactic acid produced by guanidine-based catalysts exhibited similar molecular weights and dispersity (Ð) values to those of the industrial standard catalyst Sn(Oct)2, as well as to the precursors Ti(OiPr)4 and Zr(OiPr)4. The guanidine–phenol ligand proved to be active for the ROP of lactide with a larger rate constant than the most active Zr-based catalysts. The bis(guanidine–phenolate) titanium dichloride complexes were successfully synthesized and evaluated for the homopolymerization of ethylene. The low activity (up to 1.1 kgPE mol–1h–1) of the titanium dichloride complexes was ascribed to the electron-donating ability of the guanidine fragment and the stereoarrangement imparted by the guanidine–phenolate ligand about the Ti center. Zn catalysts bearing guanidine– and amidine–phenolate ligands were synthesized and evaluated for the ROP of lactide under solvent-free conditions at 130°C. The catalyst with the best performance was only 3 times slower than the industrial standard Sn(Oct)2 when a 100 to 1 monomer to catalyst ratio was used. Most catalysts displayed heterotactic bias in the polylactic acid generated with molecular weights up to 4900 Da. Dispersity values (Ð) ranged from 1.2 to 2.3 and were considered acceptable. Proligands were tested for the ROP of lactide, proving that their participation in the polymerization process cannot be ruled out. This new class of ligands and the corresponding complexes offer great potential and have a great deal of room for improvement.
Access status: Open Access ,
Properties of Crystalline and Amorphous Transition Metal Oxides with Enhanced Fe Content as OER Electrocatalysts
(2025-11-11) Rezaee, Bibisomaia; Morin, Sylvie
This work investigates the design of electrocatalysts for the oxygen evolution reaction (OER) using binary iron-cobaltites and ternary cobaltites containing Fe, Ni, and/or Cu, all synthesized by thermal decomposition in both the amorphous and spinel phases. The catalysts were characterized by numerous characterization methods to study their structure, composition, and morphology, while their surface area and electrochemical properties were also examined and corrected for the ohmic drop and film surface area. The catalytic activity and OER kinetics were also evaluated. Structural analysis confirmed the successful formation of amorphous and spinel oxides, where for the latter the crystallite sizes were in agreement across techniques. Electron microscopy and composition analysis demonstrated textural differences and stoichiometric consistency, while X-ray photoelectron Spectroscopy revealed distinct surface species and oxidation states. Overall, Fe incorporation enhanced the catalytic activity, whereas Ni-doping reduced the catalyst performance.
Access status: Open Access ,
Replacing Sp2 Hybridized Carbon Centers with Phosphorus
(2025-11-11) Torres, Lucas Christian; Caputo, Christopher
The striking parallels between the chemistry of molecular carbon and phosphorus compounds has fascinated chemists for decades and has even led to phosphorus being coined “the Carbon Copy.” A guiding tenet in organic chemistry is that carbon can be bonded to a maximum of four other atoms to satisfy the octet rule. By comparison, phosphorus, a heavier p-block element, can exist in hypervalent states and can form bonds with up to six other atoms. Apparent patterns in the bonding and reactivity of carbon and phosphorus compounds typically manifest when these elements are in lower coordination environments (bonded to few other atoms). Molecules featuring low-coordinate earth abundant p-block elements (C, P, Si, Al, etc) have generated considerable research interest as of late, with pivotal discoveries showing these systems can facilitate processes more traditionally distinctive of transition metal complexes. Such behavior includes the activation of thermodynamically strong chemical bonds, which in some cases is reversible, and the ability to directly perform catalytic transformations on organic molecules, overall pushing the needle towards more sustainable and cost-conscious chemistry. Low-coordinate phosphorus cations are one general group of compounds that show great promise in these domains. This thesis delineates the synthesis of cations that distinctly feature a sp2 hybridized phosphorus atom and are principally inspired from classic carbon motifs. Firstly, we explore a synthetic route to a phosphorus analog of a [3]cumulene (R2C=C=C=CR2). We found our target phospha-cumulene, also known as an allenylidene phosphonium cation, to be uniquely accessible when harnessing electron rich substituents known as N-heterocyclic imines (NHIs). The properties and reactivity of the allenylidene phosphonium cation are investigated, with one interesting reactivity pathway being a thermally reversible [2+2] cycloaddition which occurs between a P=C and C=C bond. This process is remarkable given that comparable [2+2] cycloadditions between two C=C functional groups typically requires photoexcitation. The NHI substituent platform is also used to prepare a series of phosphenium cations (the phosphorus analog of carbenes) and the reactivity of these species is subsequently disclosed.
Access status: Open Access ,
Vertical Structure And Surface Interactions Of Nitrous Acid Using A 1D Model
(2025-11-11) Ebrahimi-Iranpour, Yashar; VandenBoer, Trevor
This study was undertaken in order to study the vertical distribution and surface interactions of gas-phase HONO under non-ideal mixing conditions during the 2011 NACHTT campaign using the Platform for Atmospheric Chemistry and vertical Transport in One Dimension (PACT-1D) model. This work builds on a previous 0D modelling study from the NACHTT campaign, where the greatest unknown source rate of HONO was found during the early morning when a morning burst of HONO were observed and a stable nocturnal boundary layer formed. The 48-hour model was initialized using observational constraints selected during periods where a morning burst of HONO were observed and a stable nocturnal boundary formed. The modelled HONO showed excellent agreement with observations when heterogeneous ground surface processes of HONO, surface water, and vertical mixing were accounted for without the need to apply additional daytime sources of HONO.
Access status: Open Access ,
Forensic Applications of Sandpaper Spray Ionization Mass Spectrometry (SPS-MS): Detection and Chemometric Profiling of Small Molecules for Prohibited Practices
(2025-11-11) Rodrillo, Karl Angelo Morales; Ifa, Demian Rocha
The illicit trade of pharmaceuticals and wood presents threats to public health, ecological stability, and global markets. This thesis examines Sandpaper Spray Ionization Mass Spectrometry (SPS-MS) as a rapid, field-deployable technique for direct analysis of solid samples in two distinct forensic applications. (1) SPS-MS was used to detect and identify active pharmaceutical ingredients (APIs) and excipients in pharmaceuticals, assessing product authenticity. (2) SPS-MS was further developed for direct sampling and analysis, obtaining chemical fingerprints for classification and origin tracing of Canadian and Brazilian wood samples, in the context of forestry crimes. Chemometric analysis using PCA revealed clear species differentiation, supporting its use in species-level classification. SPS-MS thus offers a versatile, cost-effective, and operationally simple screening method to supplement current MS techniques. Its portability, minimal reagent use, and possible integration into current analytical workflows make it well-suited for remote or resource-limited settings for frontline testing of fraudulent drugs and trafficked wood.
Access status: Open Access ,
Exploring the Versatility of Dithieno[2,3-b;3?,2?-e]-4-keto-1,4-dihydrophosphinines
(2025-11-11) Hussein, Amaar; Baumgartner, Thomas
A less studied alteration of the dithienophosphole is the dithieno[2,3-b;3’,2’-e]-4-keto-1,4-dihydrophosphinine. Its relatively untouched chemistry and various sites for functionalization, makes it an appealing scaffold that can be tailored to the needs of various applications. Herein we report a range of targeted approaches to functionalizing each site of the dithienoketophosphinine with an emphasis on understanding the resulting properties. Based on the innate ability of phosphorus to be functionalized and alter the properties of entire molecular scaffolds, the first series of compounds focuses on phosphorus functionalization. The second series is derived from the synthetic versatility of carbonyl groups wherein Knoevenagel condensation was performed to create a series of dicyanomethylene-dithienophosphinines with enhanced acceptor character. Finally, a third series focusing on extending the conjugation of the dithienoketophosphinine by various aryl groups differing in their donor/acceptor behaviour and unlocking emission are presented. For each of the three series we report the optical, electrochemical, structural and synthetic details.
Access status: Open Access ,
From Metabolite Profiling To Biomolecule Quantification: Modern Mass Spectrometry Techniques Applied To Biological Research
(2025-07-23) Parasecolo, Leonardo; Ifa, Demian
Mass spectrometry (MS) is a versatile and powerful analytical technique that has revolutionized our ability to analyze complex biological systems. In this dissertation, we explore novel applications of various MS methodologies, including paper spray ionization (PSI), sandpaper spray ionization (SSI), matrix-assisted laser desorption/ionization (MALDI), and liquid chromatography-tandem mass spectrometry (LC-MS/MS). These techniques were applied to profile, detect, and quantify a wide range of metabolites and biomolecules across different biological contexts. At York University, we employed sandpaper spray ionization mass spectrometry for the rapid and comprehensive analysis of maple leaves infected with distinct fungal species. This approach demonstrated the capability of this high-throughput and solvent-efficient screening technique to differentiate fungal infections by analyzing directly from the leaf surface without requiring sample preparation. The study highlighted SSI-MS as a powerful tool for in situ metabolomic analysis of plant-pathogen interactions, enabling the detection of key metabolic changes associated with different fungal infections. Additionally, we developed a MALDI-high resolution MS method for the absolute quantification of the phytoalexins camalexin and scopoletin in Arabidopsis thaliana, providing novel insights into the plant’s biochemical responses to environmental stressors. Furthermore, a semi-quantitative version of this method was employed to perform relative quantification of a broader set of phytoalexins in wild-type and mutant Arabidopsis thaliana plants lacking key transcription factors involved in their production. In collaboration with Nucro-Technics Laboratories, we developed an ultra-sensitive immunoprecipitation-LC-MS/MS method for the quantification of low-abundance proteins in rat serum. This approach significantly enhances detection precision and sensitivity, allowing for the accurate quantification of trace-level proteins (≥ 1 ng/mL) in plasma while requiring small sample volumes (≤ 50 μL). This method meets the increasing demand for highly sensitive and reliable biomolecular assays in clinical and pharmaceutical research. These applications underscore the adaptability and efficacy of modern mass spectrometry in tackling diverse biological questions, ranging from plant-pathogen interactions to clinical biomolecule analysis. The methodologies developed and optimized in this dissertation provide valuable tools for MS-based metabolite profiling, biomolecule quantification, and the exploration of complex biological matrices. This research lays the foundation for future advancements in high-throughput screening, precision medicine, and plant metabolic studies.
Access status: Open Access ,
Pioneering The Development Of CRISPR-Guided Photooxidation Of Guanine For Guanine-To-Cytosine Conversion In Cellular DNA
(2025-07-23) Frias, Nicole Adrianna; Hili, Ryan
Adapted as an RNA-guided genome-editing system, CRISPR/Cas9 has served promising potential in the treatment of human genetic diseases. Specifically, enzymatic base editors can effectively catalyze single-nucleotide conversions in cellular DNA through the use of a catalytically-dead Cas9 and a deaminase. Current base editors primarily consist of cytosine and adenine base editors, which can create C-to-T and A-to-G conversions through deamination of the substrate, respectively. However, the use of enzyme-based approaches can give rise to exasperated levels of non-specific editing. Therefore, new base editors are needed to expand the mutagenic repertoire of current base editing technologies, as well as reduce off-target effects associated with current editors. For this, the photooxidation of guanine was explored as a method of achieving precise G-to-C conversions in the cellular genome. The development of the first chemical base editor could therefore allow for the utmost spatiotemporal precision, potentially alleviating the off-target effects associated with enzymatic editors.
Access status: Open Access ,
Expanding the Scope of T3 DNA Ligase-Catalyzed Oligonucleotide Polymerizations (T3-LOOPER)
(2025-07-23) Khamissi, Natalie; Hili, Ryan
Antibodies are currently the gold standard in the field of therapeutics but are quite costly and chemically unstable. Nucleic acid polymers can mimic antibody therapeutics but are more cost effective to produce, can reversibly denature, and have a high synthesis reproducibility. These polymers are called ‘aptamers’. However, they lack in chemical diversity when compared to antibody-based therapeutics and are susceptible to renal filtration, making them inferior for specific binding. Chemical modifications can be attached to these DNA/RNA polymers to increase their diversity, though only four unique modifications can be incorporated into one polymer. Ligase-catalyzed oligonucleotide polymerization (LOOPER) is a method that synthesizes chemically modified nucleic acid libraries containing up to 16 unique chemical modifications. The method entails template directed ligations of chemically modified oligonucleotides. The purpose of this thesis is to push the boundaries of LOOPER to tolerate nucleobase modified oligonucleotides, sugar modified oligonucleotides, modification positioning on the oligonucleotide sequence, RNA oligonucleotides, and reverse transcription via LOOPER of a modified nucleic acid polymer back to its DNA form. A nucleobase modified library was synthesized to include predominantly hydrophobic modifications, allowing for an increased chance of developing an aptamer during in vitro selections against a protein target. The library generated a LOOPER yield of 19% with a fidelity of 94.8%, allowing this library to be a viable option for selections. When attempting LOOPER with sugar modified oligonucleotides, LOOPER was able to tolerate 2’-F at every position in the trinucleotide sequence and locked nucleic acids (LNA) at the middle position of the oligonucleotide. Fidelity analysis revealed that all 2’-F fidelities were over 90%. LNA oligonucleotide fidelities were unable to be characterized since the modification cannot be transcribed by commercially available polymerases. Luckily, we discovered that LOOPER can “reverse transcribe” the LNA-modified nucleic acid polymer back to DNA with a 99.0% fidelity. Lastly, the LOOPER system was not able to accurately ligate RNA oligonucleotides, as the fidelities were below 20%. LOOPER is a method that can “polymerize” and “reverse transcribe” modified nucleic acid polymers, making these libraries more accessible to the in vitro selection process.
Access status: Open Access ,
Discerning Trends in Wintertime Reactive Chlorine Chemistry and Air Quality
(2025-07-23) Angelucci, Andrea Antonio; Young, Cora
Reactive chlorine species (Cl*) are crucial to atmospheric chemistry, impacting oxidative cycles, pollutant formation, and air quality. However, their behavior, particularly in urban winter environments, remains underexplored. This thesis investigates the sources, transformations, and impacts of reactive chlorine in urban settings using high-time-resolution measurements, size-resolved aerosol analysis, and advanced modeling techniques. High-time-resolution measurements of hydrogen chloride (HCl) were conducted in coastal (St. John’s, NL) and continental (Toronto, ON) regions. In the coastal environment, HCl variability was influenced by photochemical and acid displacement processes, while in Toronto, direct emissions dominated, with road salting contributing to particulate chloride but not directly to HCl production. Simulations using GEOS-Chem captured coastal variability but significantly underestimated urban HCl levels, indicating the complexity of urban chlorine sources. Size-resolved aerosol analysis during road salt application revealed that chloride levels in urban aerosols were similar to marine environments, with road salt-derived chloride redistributed into finer aerosol modes. These findings suggest that acid displacement and heterogeneous reactions play a critical role in sustaining HCl production over time. Simulations with the E-AIM model underscored the need for improved representation of ammonia and ammonium chloride chemistry to predict HCl partitioning more accurately. Indoor sources, particularly chloramines (NH₂Cl, NHCl₂) from hypochlorite-based cleaning products, were identified as significant outdoor contributors to reactive chlorine budgets. These sources were found to rival smaller industrial emissions. Mobile and vertical gradient measurements quantified spatial variability in HCl emissions, highlighting the influence of local meteorological conditions on HCl fluxes and deposition. These findings advance our understanding of urban chlorine chemistry, providing insights into sources, transformations, and their implications for air quality and atmospheric models.
Access status: Open Access ,
Investigation of Phosphatidylinositols and Phosphoinositides Using Matrix- Assisted Laser Desorption/Ionization Mass Spectrometry Imaging
(2025-07-23) Dabija, Laurentiu Gabriel; Ifa, Demian
Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) is a powerful analytical technique that captures the spatial distribution of biomolecules directly from tissue surfaces. Widely used in lipidomics, MALDI-MSI provides label-free, high-resolution imaging of lipid species in situ, making it invaluable for studying lipid dynamics in health and disease. This thesis focuses on phosphatidylinositols (PIs) and their phosphorylated forms, phosphoinositides (PIPs), which are critical regulators of cellular signaling, membrane dynamics, and cytoskeletal organization. Dysregulation of PIs and PIPs are implicated in various diseases, including atypical hemolytic uremic syndrome (aHUS), necessitating a deeper understanding of their spatial distribution and abundance. Given the low concentration of PIs and PIPs, the study aimed to optimize MALDI-MSI for their detection. Thus, various chemical matrices necessary for the desorption and subsequent ionization processes in MALDI, were systematically evaluated to enhance the ionization and improve the detectability of these species, identifying 2,5-dihydroxyacetophenone and 1,5-diaminonaphthalene as optimal matrices. Additionally, we explored the limitation of MALDI-MS, specifically investigating the in-source fragmentation (ISF) of phosphatidylinositol triphosphate using the survival yield method, confirming that ISF occurs within the high energy conditions of MALDI.
Access status: Open Access ,
Protein Structure Dynamics In Gram Negative Bacterial Secretion Systems
(2025-04-10) Nicholas Joseph Bragagnolo; Audette, Gerald F.
Bacteria use a variety of secretion systems that enhance their virulence. The conjugative type IV secretion system attributes transmission of mobile DNA elements in bacteria, whereas type IV pili are akin to the type II secretion system and are responsible for host adhesion and twitching motility. Understanding the structure and function of components in these systems has the potential to elucidate the mechanisms of bacterial commensalism and antagonism, and would aid in the development of inhibitors to bacterial pathogenesis by disrupting the tools virulent species use for stable, long-term infections. The entry exclusion protein of the F-like type IV secretion system, TraG, consists of a membrane-bound N-terminal domain and a periplasmic C-terminal domain, denoted TraG*. TraG* is essential in preventing redundant DNA transfer through interaction with a cognate TraS in the inner membrane of the recipient cell to prevent conjugation when the recipient cell carries the same plasmid. Using a multitude of biophysical methods including thermofluor, circular dichroism, collision induced unfolding mass spectrometry, and small angle X-ray scattering, the structural dynamics of TraG* was investigated. This allowed for the characterisation of the 50 N-terminal residues, the 77 C-terminal residues, and the TraS-interacting region of the protein as highly dynamic, providing evidence for the mechanism of the long-distance interactions made by TraG. This dissertation also describes the 1.3 Å crystal structure of the N-terminally truncated Type IV pilin of Pseudomonas aeruginosa from strain P1 (ΔP1), the first structure of its phylogenetically linked group (group Ia) to be reported. The structure was solved from X-ray diffraction data collected 20 years ago with a molecular replacement search model generated using AlphaFold. Comparisons of the ΔP1 structure to other Type IV pilins using ProSMART indicated that there are cases of higher structural homology between different phylogenetic groups of P. aeruginosa than there are between pilins from the same phylogenetic group, indicating that the classification of pilins based on structural homology may be necessary in developing anti-virulence drugs and vaccines.
Access status: Open Access ,
Chemical Approaches To Study Modified Nucleic Acids
(2025-04-10) Cauley-Le Fevre, Morgan Beatty Pierre; Hili, Ryan
Chemical modifications govern the fate and function of nucleic acids. The methylation of the N-6 position of adenosine (m6A) in RNA is the most studied naturally occurring modification. Methylation of this position is regulated by a complex, dynamic interplay between enzymes known as methyltransferases (writers) and demethylases (erasers). Modifications on functional nucleic acid polymers (aptamers), have also been reported to increase binding affinity and stability in vivo towards a particular target. Ligase-catalyzed OligOnucleotide polymERization (LOOPER) is a method to access hetermultivalent aptamers, and the method was successful in the evolution of a modified aptamer towards human α-thrombin. However, LOOPER requires a platform to produce these modified aptamers at scale. Chapter 2 of this thesis focusses on my work to create such a platform, using solid-phase DNA synthesis and orthogonal protecting groups. Two protecting groups were synthesized, and one, allyloxy carbonyl (alloc) was taken forward for this platform due to the ease of the solution-phase deprotection step. Synthesis of the modified phosphoramidite equipped with alloc was undertaken, and the phosphoramidite was eventually incorporated into an oligonucleotide. The protecting group was successfully removed on-instrument, however several coupling protocols to install the chemical modifiers for the aptamer were ultimately unsuccessful. In Chapter 3 of this thesis, I focussed on the optimisation of some hit compounds towards m6A demethylase ALKBH5, which has been shown to be up- or down-regulation in a variety of cancerous and non-cancerous disease. Selective inhibition of the protein would greatly facilitate knowledge generation around its associated pathologies. From two DNA-encoded library hits towards the protein, hit optimization synthesis of two molecules was performed. A fluorescence polarization (FP) assay to determine IC50 data from these compounds was produced and was successfully validated. Unfortunately, with little material of the two compounds generated, only limited FP data was generated, and the results were inconclusive.
Access status: Open Access ,
Photo-Oxidative Sequencing Approach For Methylated Guanosine In RNA
(2025-04-10) Chung Kim Chung, Kimberley Alexandra; Hili, Ryan
In recent years, RNA-modifying enzymes have gained significant attention due to their impact on critical RNA-based processes, and consequently human pathology. However, identifying sites of modifications throughout the cellular transcriptome remains challenging largely due to the lack of accurate and sensitive detection technologies. Indeed, N2-methylation at guanosine such as N2-methylated guanosine (m2G) and N2,N2-dimethylated guanosine (m22G) are prevalent modifications found in RNA but their functional studies are limited due to the absence of sequencing methods. While m22G creates termination during reverse transcription and can often be detected during sequencing due to its high error signature, m2G does not affect Watson−Crick−Franklin base pairing, and therefore cannot be distinguished from unmodified guanosine. Although computational predictors exist for m2G, there are no direct sequencing method available. In this thesis, the first chemistry-based sequencing method for N2-methylated guanosine at the single-nucleotide level is described. This method takes advantage of the chemoselectivity of photoredox chemistry to enable selective photo-oxidation of m2G and m22G in the presence of guanosine. Under blue light, using riboflavin as a photocatalyst and selectfluor as an oxidant, N2-methylated guanosines convert into their respective 2,5-diamino-4H-imidazol-4-one (Iz) and 8-oxoguanine (OG) products resulting in different mutation signature after sequencing. The limitation and scope of this method were further evaluated and extended to explore other methylated guanosine types such as m1G and generate the first database of high confidence m2G sites in multiple RNA types in human lung cancer cell line.
Access status: Open Access ,
Zinc And Aluminum Complexes Bearing Monoanionic Bidentate Cyclic Guanidine-Ethenolate Or Amidine-Ethenolate Ligands For The Ring Opening Polymerization Of Lactide
(2025-04-10) Campos Rivera, Lya Evelyn; Lavoie, Gino G.
Aluminum and zinc complexes bearing bidentate guanidine-ethenolate ligands are reported and used in the solvent-free polymerization of rac-lactide at 130 °C. Solid-state structures of the zinc complexes showed a distorted tetrahedral geometry. Solid-state structures of the bischelated aluminum complex showed dynamic trigonal pyramidal and square-based pyramidal geometries. The spectra provide evidence of hydroxy and L1H end group for PLA generated from Zn(L1)2 with and without BnOH, as well as from Zn(L1)Et with BnOH. These terminated PLA chains result from water contaminants present in LA. However, it remains challenging to determine whether AMM or CIM is the dominant mechanism. In contrast, Zn(OBn)2, both with and without BnOH, generated polymers with hydroxy, OBn, and macrocycles sodium adducted cationized open chain polymers. The presence of OBn end groups indicates that the polymerization proceeded through CIM. All spectra indicated transesterification side reactions present due to peak separations of m/z 72 g/mol. The π-accepting properties of the guanidine moiety in the Zn(Lx)2 complexes, as estimated by the 31P NMR chemical shift of the corresponding N-heterocyclic carbene–phosphinidene adduct, resulted in a negative correlation in the rate for the ROP of LA polymerization using zinc complexes produced polylactic acid (PLA) with a heterotactic bias (Pr = 0.52–0.65) with molecular weights comparable to those obtained in the SnOct2 control experiment. The most active zinc catalyst reported herein, Zn(L1)2 is only about three times less active than SnOct2, for the ROP of rac-LA at 130 ℃. For the polymerization of L-LA under industrial conditions, at 150 ℃, Zn(L1)2 is only about 14.4 times slower compared to Sn(Oct)2, and about only 2.5 times slower compared to Herres-Pawlis et al. zinc(II) Schiff base complex. Interestingly, the addition of benzyl alcohol as a co-initiator for the polymerization using Zn(L1)Et readily produced Zn(L1)2 and Zn(OBn)2, with both complexes giving comparable activities. Polymerization studies showed that Zn(OBn)2 is only 2.5 times less active than Sn(Oct)2 but with twice as large molecular weights. The Zn(L5)Et complex, in the presence of BnOH, resulted in a reaction rate three times faster than the monochelated guanidine-ethenolate Zn(L1)Et complex, due to the enhanced Lewis acidity of the metal center caused by the presence of the CAAI fragment. MALDI-TOF MS was used to determine the end groups of the polymer chain.
Access status: Open Access ,
Exploring The Evolution Process And Requirements For Molecular Recognition Via Highly Functionalized Aptamers
(2025-04-10) Movahedi, Matina; Hili, Ryan
Expanding the chemical diversity of oligonucleotide libraries has allowed the evolution of synthetic nucleic acid polymers with enhanced molecular recognition and catalytic abilities. Thus, synthetic methods that enable the sequence-defined incorporation of diverse chemical modifications in developing novel or improved nucleic acid polymers and selection methods that facilitate efficient enrichment of high-quality aptamers are of particular importance in identifying novel or improved nucleic acid polymers for diagnostics and therapeutics. In this thesis, the advancement of ligase-catalyzed oligonucleotide polymerization (LOOPER) is discussed as a method to increase the chemical diversity of oligonucleotide libraries and its application towards the evolution of modified aptamers. An evaluation of the use of different ligases, scope and number of modifications, sequence space, and evolutionary outcomes from in vitro selections is provided, along with a critical lens on challenges to be addressed for the method to mature into a more widely adapted technology. Further to this, a variety of selection methods are discussed striving towards efficient single-round aptamer selection. The successful single-round aptamer selection against Thrombin is an inspiring outcome for future selections.

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