Chemistry

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

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Design, Synthesis, and Characterization of Multimetallic Complexes Supported by an Imidazopyrimidine-Based Trinucleating Ligand
(University of Waterloo, 2025-10-17) Woods, Riley
Transition metal catalysis has revolutionized chemical synthesis for decades and has allowed for the development of several Nobel prize-winning chemical reactions and processes. These catalysts, however, usually rely on the use of rare Earth metals such as platinum-group metals, mainly palladium, leading to economic and sustainability concerns. Recent studies on the use of Earth-abundant elements nickel, cobalt, and copper have revealed that these metals have the potential of offering low-cost alternatives to the traditional catalysts. Furthermore, these metals can access many more states, allowing for new and complementary reactivities to be achieved. Whilst transition metal catalysis is a large and impactful field, the majority of known catalysts are monometallic in nature. A compelling yet much underexplored area is the use of multimetallic complexes. Several studies and reviews have highlighted the beneficial effect of having multiple metal centers held in proximity. These sorts of systems often display improved catalytic performances over their monometallic counterparts. Synergy or metal-metal cooperativity between the centers is usually responsible for these observations, sometimes allowing for multielectron processes that are simply not possible with traditional monometallic catalysts. In terms of trimetallics, there is a paucity of ligand systems that can reliably produce a precise and controlled arrangement of the three metal centers in a way that is useful in catalysis. This is due to most relying on flexible organic frameworks tied to a symmetric node, additionally excluding them from heterometallic applications. Herein is reported a new trinucleating ligand framework, bpipp, specifically designed to enforce close proximity among three metal centers upon complexation. Based on the inherently unsymmetric imidazopyridmine backbone, the ligand features a tridentate pincer-like binding pocket with two additional bidentate binding pockets. This approach utilizes scalable synthetic methods to create a rigid ligand scaffold that precisely controls the spatial arrangement of the metals. The versatility of this ligand is demonstrated through the synthesis of several trimetallic complexes of Ni(II), Cu(II), Co(II); fully characterized by NMR spectroscopy, ESI-HRMS, and X ray crystallography. Notably, our ligand design achieves remarkably short metal-metal distances ranging from 3.3–3.5 Å, significantly closer than most reported trimetallic systems. This structural feature establishes an ideal platform for investigating genuine three-metal cooperative effects in catalysis.
Dual Characterization of Hydrophobically Modified Polyamidoamine Dendrimers and their Surfactant Aggregate Hosts by Pyrene Excimer Fluorescence
(University of Waterloo, 2025-10-14) Liu, Donghan
This thesis explores why the conformational response of generation-0 polyamidoamine dendrimers end-labeled with four identical 1-pyrenealkanoyl groups (PyCX-PAMAM-G0 with X = 4, 6, 8, 10, and 12 for a butyroyl, hexanoyl, octanoyl, decanoyl, and dodecanoyl linker, respectively) to their local environment makes them excellent molecular probes to investigate surfactant aggregates. The conformation of the dendrimers was studied in polar organic solvents, spherical micelles, and non-spherical surfactant aggregates (NSSA) using pyrene excimer formation (PEF) and the model-free analysis (MFA) of the fluorescence decays. In N,N-dimethylformamide (DMF) and dimethyl sulfoxide (DMSO) and in micelles of sodium dodecyl sulfate (SDS) or dodecyltrimethylammonium bromide (DTAB), the dendrimers with shorter (X = 4, 6, 8) alkanoyl linkers adopted an ideal conformation. In contrast, the PyC10- and PyC12-PAMAM-G0 dendrimers experienced a conformational inversion in pure surfactant micelles driven by the hydrophobicity gradient (HG) generated between the polar surface and the hydrophobic interior of the micelles. The conformational inversion of the PyC10- and PyC12-PAMAM-G0 dendrimers was further investigated with mixed micelles prepared from SDS and DTAB mixtures. The decrease in conformational inversion as the micellar shape evolved from a sphere to an elongated ellipsoid with increasing DTAB content led to the idea of the spatial partitioning theory (SPT). The SPT attributes changes in the average conformation of the dendrimers to the change in the volume fractions of the two regions found inside the mixed micelles, between which the dendrimers partition themselves. These two regions were the polar edge region, which was made of ~ 70 charged SDS molecules, and had a curved surface and a high HG, and a more hydrophobic middle region with a lower surface curvature and a low HG formed by the remaining neutralized surfactants. The SPT provided a robust fundamental framework to predict how the average rate constant () for PEF, obtained from the MFA of the fluorescence decays acquired with the PyCX-PAMAM-G0 samples, was affected by the composition of the NSSA the dendrimers interacted with. The sensitivity of the conformational inversion of the PyC10- and PyC12-PAMAM-G0 dendrimers to their local environment shows the potential of these dendrimers as molecular probes for NSSA formed upon the addition of NaCl or DTAB to aqueous solutions of SDS micelles. Partitioning of the dendrimers with longer C10 and C12 linkers between the edge and middle regions rationalized the changes in observed as a function of salt concentration, DTAB content, or both. The generality of the SPT, which applied to all surfactant systems investigated in this thesis, provided strong support for the two regions coexisting in the NSSA, with the edge region being constituted of the same number of charged surfactants as that found in a pure SDS micelle. This insight led to a proposal for the mechanism leading to the formation of NSSA, when salt or oppositely charged surfactants are added to an SDS aqueous solution. Together, the results presented in this thesis suggest that the PyCX-PAMAM-G0 dendrimers constitute outstanding molecular probes to study NSSA in solution.
Synthesis and Analysis of Daptomycin Analogues
(University of Waterloo, 2025-09-26) Brill, Robert
Daptomycin (Dap) is a naturally occurring, membrane-active, calcium-dependent cyclic lipodepsipeptide antibiotic (cLPA) which is used as a last-resort antibiotic to treat serious infections caused by Gram-positive (G+) bacteria including Staphylococcus aureus (S. aureus) and vancomycin-resistant enterococci (VRE). The appearance of Dap-resistant (Dap-R) bacteria with increasing frequency has motivated the search for Dap analogues that are active against Dap-R bacteria. Recently, it has been shown that appending hydrophobic groups to tryptophan (Trp) or kynurenine (Kyn) yielded some Dap analogues with improved activity and were active against Dap-R bacteria. Chapter 2 of this thesis describes the synthesis and evaluation of Dap analogues with hydrophobic modifications to the side chain of the D-asparagine (Asn) residue at position 2 to determine if appending hydrophobic groups to D-Asn2 will also result in Dap analogs with improved activity. Eight Asn derivatives were synthesized containing alkyl or hydroxyl groups appended to the primary amide nitrogen of the D-Asn side chain. Dap analogues containing these D-Asn derivatives at position 2 were synthesized using Fmoc (9-fluorenylmethyloxycarbonyl) solid-phase peptide synthesis (SPPS). Dap analogs containing methyl (Me), ethyl (Et), n-propyl (Pr), n-butyl (Bu) and n-hexyl (Hex) on the D-Asn exhibited minimum inhibitory concentration (MIC) values that were 2–4-fold higher than Dap while the n-octyl (Oct) and piperidinyl (Pip) analogs had MIC values that were 8- and 32-fold greater than Dap, respectively. These results demonstrate that the activity of Dap cannot be improved by appending hydrophobic groups to D-Asn2 and suggest that D-Asn2 may not be closely associated with the cell membrane. These results also show that the primary amide of D-Asn2 is not essential for activity while the presence of at least one hydrogen on the nitrogen of the D-Asn2 side chain is very important to activity. Membrane insertion studies using model membranes and fluorescence spectroscopy revealed that the hexyl and octyl analogues were able to insert into membranes even in the absence of Ca²⁺ consistent with their much-increased hydrophobicity compared to Dap. In chapter 3, we wished to determine if it is possible to convert Dap into a Zn+2-dependent antibiotic by substituting the two aspartate (Asp) residues in Dap’s calcium-binding motif, Asp7 and Asp9, with Nγ-hydroxyasparagine (Asn(OH)), an amino acid that has a hydroxamic acid side chain. Hydroxamic acids, known for strong Zn²⁺ chelation, have been used in medicinal chemistry to improve metal-dependent interactions. The synthesis of an Asn(OH) building block with the hydroxamic acid side chain protected with a trityl (Trt) group (Fmoc-Asn(OTrt)-OH) was achieved following a multi-step route starting from Fmoc-Asp(tBu)-OH. Attempts to synthesize Dap analogues containing Asn(OH) at positions 7 or 9 using this building block via Fmoc SPPS failed. However, the synthesis of a Dap analogue containing Asn(OH) at position 2 was successful indicating that incorporation of this residue using this building block is sequence dependent. A new Asn(OH) building block containing a protecting group that is smaller than the Trt group, the dimethoxybenzyl (DMB) group (Fmoc-Asn(ODMB)-OH), was prepared. Attempts to prepare the target peptides using this new building block also failed as were attempts using an Asn(OH) building block with the hydroxamic acid side chain unprotected.
Towards the synthesis of coinage metal chalcogen compounds stabilized by a bidentate N-heterocyclic carbene
(University of Waterloo, 2025-09-26) Alex, Alice
Group 11 metal chalcogen clusters have been of interest due to their potential applications in light emitting materials. Although group 11 metal chalcogen complexes with phosphine ligands have been extensively examined and most of them reported do not contain N-heterocyclic carbene (NHC) ligand. This thesis examines how the rigid bidentate NHC, 1,1’-(dibenzyl)-3,3’-(1,2-xylylene)dibenzo[d]imidazol-2-ylidene) (bisNHCBn) can be incorporated into the gold(I) metal – chalcogenolate (chalcogenolate = RSe-; R = organic moiety) and gold(I) chalcogenide (chalcogenide = Se2-) complexes. In these studies, the chalcogen reagents Se(SiMe3)2 or RSeSiMe3 are reacted with the gold coordination complex [(AuOAc)2(bisNHCBn)] to target Au(I) selenide and Au(I) selenolate clusters with bisNHCBn. The preparation, characterization, and UV-vis absorption studies of the resulting clusters are presented.
Multimetallic Complexes Supported by an Unsymmetrical Imidazopyrimidine-Based Ligand: Synthesis, Characterization, and Catalytic Studies
(University of Waterloo, 2025-09-23) Abaeva, Mila
Bimetallic catalysts containing two metals in close proximity harness cooperative effects that enable enhanced or unique reactivity in comparison to traditional monometallic catalysts. The development of such catalysts relies on the development of binucleating ligands that support their assembly and modulate key parameters, synthetic routes to access bimetallic complexes, and continued exploration of their catalytic properties. In this regard, heterobimetallic catalysts are particularly underdeveloped due to synthetic challenges associated with incorporating two different metal centers selectively. This thesis explores the synthesis of heterobimetallic complexes using a novel unsymmetrical ligand design. In ‎Chapter 2, imidazopyrimidine-based ligands are introduced as a novel motif for binucleating ligand design. The imidazopyrimidine motif was selected for its ease of synthesis and inherently unsymmetrical nature. A representative ligand was synthesized in high yield from readily available starting materials, and the route was successfully extended to multigram scale. In ‎Chapter 3, the coordination chemistry of this ligand was investigated through the synthesis of homobimetallic complexes. Dinickel(II), dicopper(II), and dipalladium(II) complexes were prepared and characterized to assess the structural influence of the imidazopyrimidine motif. Serendipitously, trinickel(II) and tricobalt(II) complexes were also prepared and characterized, demonstrating the ability of imidazopyrimidine-based ligands to potentially accommodate variable nuclearities. Key structural features, such as the metal-metal distances, were evaluated and compared with literature complexes. ‎Chapter 4 focuses on the synthesis of heterobimetallic complexes supported by an imidazopyrimidine-based ligand. One-step syntheses of nickel(II)/copper(II) and cobalt(II)/copper(II) complexes were achieved, including both binuclear and trinuclear complexes. NMR studies revealed that the heterometallic complexes were thermodynamically favoured. Competition reactions analyzed by ESI-MS demonstrated that the selective formation of heterometallic complexes was driven in part by the preferential binding of copper(II) to one of the coordination sites on the ligand. Attempts to access other heterobimetallic combinations, including nickel(II)/palladium(II) or copper(II)/palladium(II), were unsuccessful. In ‎Chapter 5, the Glaser-Hay coupling is explored using a dicopper complex supported by an imidazopyrimidine-based ligand. Compared to related monometallic catalysts, the dicopper complex exhibited a consistently reduced reaction rate, as determined by NMR studies.
Characterizing the Occurrence and Fate of Micropollutants in Aqueous and Environmental Samples: A Multidimensional Approach
(University of Waterloo, 2025-09-09) Lemmens, Shannon
Emerging contaminants such as pharmaceuticals and per-and polyfluoroalkyl substances (PFAS) present persistent challenges for environmental monitoring due to their chemical diversity, trace-level occurrence and limited removal in conventional wastewater treatment. This thesis presents a dual approach combining experimental two-dimensional separations with computational modelling to advance contaminant detection and mechanistic understanding. A targeted liquid chromatography-mass spectrometry (LCxDMS-MS/MS) method was developed and applied to complex pharmaceutical mixtures, revealing improved compound differentiation and class-based clustering across orthogonal retention time and compensation voltage dimensions. These trends demonstrate the potential of LCxDMS-MS/MS as a selective, high-throughput workflow for micropollutant screening in aqueous matrices. Complementary to this, quantum chemical calculations were performed on PFAS molecules, specifically perfluorosulfonic acids (PFSAs), to elucidate degradation pathways and assess the influence of molecular conformation on fragmentation energetics. Calculations identified several concerted and non-concerted reaction pathways that contribute to product selectivity. Together, these efforts establish a framework that integrates instrumentation and theory to support more informed contaminant analysis and method development.
Design, construction, and operation of a compact, ultrafast 100kV electron diffraction instrument
(University of Waterloo, 2025-09-08) Netzke, Samuel
Elucidating the structure and properties of nanomaterials at greater resolutions necessitates the continuing development of novel imaging techniques. Electron imaging methods (such as electron microscopy/diffraction) are well-suited for probing matter at the nanoscale; for a given energy, the electron scattering cross-section is ~10⁵⁻⁶ higher than X-rays and ~10³ times less damaging [1]. Ultrafast electron imaging techniques are capable of spatial and temporal resolutions down to ~0.1 nm and 100 fs (femtosecond), respectively. This enables the observation of fundamental dynamic processes including photoinduced phase transitions, electron-phonon energy transfer, and the evolution of coherent phonons [2]. At present, open user access to the incredible power of these ultrafast techniques is generally limited to one ultrafast electron diffraction (UED) facility. Existing, well-established methods used to study nanomaterials such as X-ray diffraction and conventional electron microscopy have a plethora of commercially available, laboratory scale instruments which can be used to carry out experiments. In contrast, there are no similar turn-key devices that enable the study of ultrafast dynamic processes. The construction of an in-house ultrafast electron diffraction apparatus is one solution to the problem of instrument accessibility and the realization of time-demanding experiments with proper controls. In this thesis, I document the design, assembly, and use of a compact laboratory scale UED instrument. The instrument is capable of stable operation at 100 kV, with subsequent development and testing suggesting that it can reach voltages in excess of ~130 kV. The instrument is able to produce electron pulses with a temporal length of ~200 fs while containing a sufficient number of electrons for adequate signal-to-noise level. Two experiments were then carried out using the UED apparatus in order to showcase its time and spatial resolutions: electron deflection by photoinduced plasma, and the investigation of the charge density wave (CDW) material NbTe2. Analysis of the time-resolved diffraction data collected from the NbTe2 measurements suggests at 60 kV demonstrate sub-picosecond resolution in agreement with the predicted instrument response obtained from N-particle tracer simulations.
Computational Methods for Inferring the Structures of Amorphous Materials and Understanding Ionic Diffusivities
(University of Waterloo, 2025-09-05) Gouws, Xander Andrew
The simulation of solid-state electrolytes (SSEs) has allows researchers to directly observe the migration paths of lithium ions, and so has played a pivotal role in elucidating the mechanisms of ionic conduction. Performing these simulations requires three steps: Structure determination, simulation, and analysis. Here, we have developed and tested new computational methods to address key challenges in two of these steps. First, we develop a gradient-based optimization method for determining the structures of amorphous materials from total scattering data. Unlike traditional reverse Monte Carlo approaches that rely on random atomic movements and suffer from slow convergence, our gradient-based method moves atoms to directly minimize the chi-squared goodness-of-fit and potential energy. Our approach was tested on amorphous silicon and a nickel--niobium metallic glass. Convergence was achieved in on the order of 5,000 steps, which is approximately one hundred times faster than existing hybrid Monte Carlo methods. Then, we introduce a method for detecting ion hopping events in SSEs without prior knowledge of site locations. This may be useful when simulating i) new materials, for which the positions of all lithium occupancy sites may be unknown, ii) structural changes (e.g. doping) that introduce local strains that shift site positions, or iii) amorphous materials, where lithium sites may be unknown prior to simulation. Testing our method on Li6PS5Cl and its BH4-doped variant, we recover the cage-forming nature of lithium sites in argyrodite structures, and find that the correlation factor for hops between cages is greater than one, indicating a forward-bias for intercage hops.
Impact of control noise on a variational quantum eigensolver
(University of Waterloo, 2025-08-21) Wang, Xinning
Quantum computers promise advantages over classical systems for problems such as molecular simulation, fueling the development of hybrid quantum-classical algorithms like the Variational Quantum Eigensolver (VQE). VQE is particularly attractive for noisy intermediate-scale quantum (NISQ) devices due to its shallow circuit depth and partial resilience to noise. Silicon-based spin qubits, with their compatibility with existing semiconductor technologies, are strong candidates for scalable quantum computation. However, their performance is constrained by hardware imperfections—chiefly charge noise and voltage miscalibration—that manifest as fluctuations or offsets in gate electrode voltages. These disturbances degrade quantum gate fidelities and, in turn, the accuracy of algorithmic results, presenting significant challenges for practical applications. In this thesis, we develop a comprehensive hardware-algorithm co-simulation framework to quantify the impact of voltage noise on silicon quantum dot systems. Charge noise is modeled using an ensemble of random telegraph noise processes to emulate realistic 1/f-like spectra. We systematically investigate the effects of stochastic noise and systematic miscalibration at both the gate level and algorithm level. For individual quantum gates—including RX, Hadamard, CZ, and RootSWAP—we characterize noise-induced fidelity loss and derive analytical expressions for error sensitivity, revealing contrasting robustness between detuning-driven and exchange-driven gates. Quantum process tomography and Kraus operator decomposition further elucidate dominant error channels, distinguishing coherent and incoherent contributions from different noise regimes. Extending the analysis to algorithm performance, we simulate VQE for the hydrogen molecule and identify a practical noise tolerance window within which high-accuracy energy estimation is maintained. These advances underscore the progress in bridging device physics and quantum algorithm implementation for silicon spin qubits, offering quantitative guidance on error budgeting, control calibration, and the development of noise-resilient algorithms for near-term quantum processors.
Development of hydrophilic silicone-based ink for the 3D vat photopolymerization printing of biomedical devices
(University of Waterloo, 2025-08-19) Wong, Li Yan
Three-dimensional (3D) printing is a layer-by-layer additive manufacturing technique that continues to gain interest due to its ability to fabricate customized structures at low setup cost and quick turnaround time. In this thesis, advanced ink materials are developed for the fabrication of elastic biomedical devices using vat photopolymerization (VP) printing. In Chapter 1, an overview of various 3D printing techniques is presented, including their respective advantages, disadvantages, and requirements for ink material. Compared to other major 3D printing techniques, VP printing offers high printing accuracy, resolution, and superior surface quality. However, the fabrication of elastic structures using VP printing has long been a challenge due to the high viscosity and tackiness of elastomeric material. A review of various elastic materials and their current applicability in VP printing is also presented. Finally, recent materials and strategies for fabricating biomimetic implants and fluidic devices via VP printing are discussed. In Chapter 2, a VP-printable hydrophilic silicone-based material is developed, using aminosilicone methacryloyl (SilMA) incorporated with acrylamide (AA) and poly(ethylene glycol) dimethacrylate (PEGDMA) as reactive diluents. The incorporation of AA and PEGDMA addresses the issues of high pre-gel viscosity and slow curing rate of SilMA. Furthermore, the formation of a SilMA/AA/PEGDMA interpenetrating network (IPN) upon curing is novel as it differs from the existing acrylate and thiol-ene silicone network. By integrating hydrogel components, the material displayed distinct characteristics compared to conventional silicone, including hydrophilicity and good swelling properties. Additionally, compared to regular hydrogels, the material shows improved strength, elasticity, and durability suitable for the fabrication of biomimetic implants. Despite its excellent VP printability, the developed material exhibits signs of overcuring, which hinders the printing of ultra-fine features. Hence, in Chapter 3, cellulose nanocrystal (CNC) is used to improve printing accuracy and resolution. The use of CNC to tune photocuring depth is novel and, to the best of our knowledge, has not been reported in literature previously. Upon the integration of 1 wt% of CNC, the developed material exhibits a high printing accuracy and resolution down to 100 μm with a near-zero deviation in the X and Y direction. Most importantly, the incorporation of CNC results in a printed fluidic device with excellent surface detail, good fluid processibility, and minimal colour staining. Yet, with the SilMA-based material, it remains challenging to achieve one-step printing of fluidic devices with embedded channels. Therefore, in Chapter 4, ink formulation with siloxane oligomer instead of polymer is developed for an even lower pre-gel viscosity. In this ink formulation, amphiphilic siloxane oligomer (silmer) is complemented with AA and glycidyl methacrylate (GMA). The use of silmer as the primary component in resin formulations is uncommon due to the challenges in dissolving high concentrations of silmer. Herein, a novel approach using a solvent blend is introduced as a critical strategy for formulating the amphiphilic silicone-based ink materials for VP printing. Silmer conformation is solvent-dependent, resulting in tuneable pre-gel viscosity, transparency, and surface properties. Upon ink optimization, a silicone-based fluidic device with embedded channel is successfully produced with VP printing, and the printed device shows excellent capability in synthesizing drug-encapsulated hydrogel beads, demonstrating its feasibility for real-world biomedical applications. Taken all together, this thesis presents the formulation of VP-printable hydrophilic silicone-based resin material with two different strategies: (1) the addition of reactive diluents and (2) the use of lower-molecular-weight siloxane oligomers; offering new perspectives on the formulation of hydrophilic elastomeric resin material for VP printing. Furthermore, the successful fabrication of biomimetic scaffold implants and biomedical fluidic devices with VP printing reveals a significantly simpler and more cost-effective method for the fabrication of silicone-based biomedical devices, moving beyond the conventional method of soft- lithography and moulding.
Fundamental studies for small molecule aptamer selection using capture-SELEX
(University of Waterloo, 2025-08-11) Ding, Yuzhe
DNA aptamers for small molecules hold transformative promise in biosensing, diagnostics, and therapeutics, yet their in vitro evolution has been hampered by incomplete knowledge of the parameters that drive efficient enrichment. In recent years, the development of library-immobilization based method, so called capture-SELEX, has generated over 100 high-quality DNA aptamers for various types of small molecules. Importantly, capture-SELEX allows systematic investigation of fundamental problems in the selection of aptamers. This thesis studies the capture-SELEX platform by dissecting thermodynamic, kinetic, and methodological variables to accelerate the discovery of high-affinity DNA aptamers. Using adenosine/ATP as targets for selection has repeatedly produced the same guanine-rich aptamer motif that was first reported by the Szostak group in 1995. This aptamer has been considered as the adenosine/ATP aptamer by the field. First, by gradually increasing the selection stringency on classical targets (adenosine and ATP), we selected two new aptamers with Kd ≈ 230 nM, 35-fold tighter than that of the classical aptamer sequence. This was achieved through gradual reduction of target concentration from 5 mM to the low-micromolar range. The evolution of the sequence abundance cross different rounds was traced by deep sequencing, and the reason for the previous repeated report of the classical sequence was attributed to its short 12-nucleotide conserved binding regions, whereas the two new aptamers have approximately 16 conserved nucleotides. This study highlights the importance of using low target concentration in order to enrich high affinity aptamers. During aptamer selection, using a lower target concentration tends to favor the enrichment of higher affinity binders, raising the question of whether a practical lower limit exists. Next, we performed three capture-SELEX campaigns using 5 µM, 500 nM, and 50 nM guanine as the target, respectively, to investigate it. Both the 5 µM and 500 nM selections successfully enriched the same guanine aptamer-requiring eight rounds at 5 µM guanine versus 17 rounds at 500 nM guanine. However, the 50 nM selection failed to yield any aptamers. The highest affinity and most enriched aptamer from these selections displayed a Kd of 200 nM, indicating that if the target concentration is much lower than Kd can lead to failed selections. Mutation analysis further revealed a critical cytosine in the guanine binding pocket: substituting this cytosine with a thymine switched selectivity from guanine to adenine. A similar specificity switching was previously seen in the natural guanine riboswitches. These findings define a lower limit for target concentration in capture-SELEX and offer a practical guidance for selecting target levels to isolate high-affinity aptamers. Selection of high-affinity aptamers underpins all downstream applications, yet most protocols emphasize thermodynamic factors-such as target concentration-while overlooking binding kinetics. Third, we performed a library-immobilization selection against ampicillin to dissect these influences. Under typical gravity-flow conditions (1-2 min interaction), a low-affinity aptamer (Kd = 12.7 µM) dominated the enriched pool. In contrast, extending the incubation time to 10 min enriched a higher affinity sequence (Kd = 1.8 µM), differing by only three nucleotides from the weaker Kd aptamer. Systematic comparison of library immobilization efficiency, release fraction, and release kinetics confirmed that dissociation rate from the capture duplex was the primary determinant of the selection outcome. We observed the same kinetic bias in parallel adenosine selections, demonstrating the generality of this effect. Based on these findings, we recommend combining low target concentrations with extended incubation time to favor the enrichment of high-affinity aptamers. This study not only yields a robust, high affinity and selective ampicillin aptamer but also highlights a critical interplay between thermodynamics and kinetics during in vitro aptamer selection. Since 1990, numerous aptamer-selection techniques have been developed, yet quantitative comparisons of their enrichment efficiencies remain scarce. Finally, we evaluated three library‐immobilization SELEX methods, capture‐SELEX, GO‐SELEX, and gold‐SELEX, using a spiked library containing DNA aptamers with varying affinities for adenosine. Using 100 µM adenosine as target, all three methods showed that <1 % of the library was released by adenosine as revealed by qPCR, with gold‐SELEX showing virtually no DNA elution. Deep sequencing of three model aptamers (Ade1301, Ade1304, and the classical adenosine aptamer) revealed 30-50‐fold enrichment in capture-SELEX, whereas GO‐SELEX and gold‐SELEX both yielded enrichment factors below 1, indicating a lack of aptamer enrichment. Blocking the primer‐binding regions improved GO‐SELEX enrichment to ~14 % but still fell far short of capture‐SELEX’s performance. Finally, we compared nonspecific versus target‐induced release and elucidated why capture‐SELEX’s structural-switching mechanism offers superior aptamer enrichment. Overall, capture‐SELEX is a markedly more efficient strategy for isolating high‐affinity aptamers. Collectively, this work establishes a quantitative framework for capture-SELEX-balancing target concentration, kinetic control, and partitioning strategy-to reliably isolate nanomolar-class DNA aptamers for small molecules.
Exploration, Synthesis, and Characterization of Bioinspired Iron–Imide and Iron–Amide Clusters
(University of Waterloo, 2025-07-24) Shmordok, Justin
Iron-sulfur clusters with high-spin irons play a crucial role in various biological processes. These clusters are found in enzymes such as ferredoxins, aconitase, and nitrogenase, where they function as redox cofactors or active sites for catalysis. One particularly significant transformation is the reduction of atmospheric dinitrogen to ammonia, which occurs at a complex iron-sulfur cluster with core composition [MFe7S9C] where M = Mo, V or Fe. Notably, this cluster features a μ6-carbide, whose function in the cluster remains unclear. In synthetic iron-sulfur chemistry, Fe4S4 clusters have been extensively studied with various ligands and core compositions. To explore the effects of light 2p-element ligation, nitrogen anions in amide or imide motifs can be employed. Research in the Lee group has led to the synthesis of a series of iron-imide-sulfide clusters [Fe4(NtBu)nS4-nCl4]z (n = 1-4). This class of compounds extends from [Fe4S4] to [Fe4(NtBu)4] cores, with intermediate species in the series containing a mixture of imide and sulfide ligands. The [Fe4(NtBu)4] core is synthesized via the reaction of FeCl3 with two equivalents of LiNHtBu, yielding [Fe4(NtBu)4Cl4]1–, Fe4(NtBu)4Cl3(NtBu) and FeCl2(NH2tBu)2 as the primary iron-containing products, with an approximate combined in-situ yield of 50% based on starting iron content. The [Fe4(NtBu)4Cl4]1– species can be isolated in 24% yield and undergoes both chemical oxidation and reduction to form [Fe4(NtBu)4Cl4] and [Fe4(NtBu)4Cl4]2–, respectively. The [Fe4(NtBu)4Cl4]z series has been characterized using a range of spectroscopic and structural techniques to elucidate its solid-state and solution phase properties. LiNHtBu is synthesized via the lithiation of tBuNH2 with one equivalent of n-BuLi. Upon workup, this reaction affords white crystals which display an octameric ladder structure with eight molecules of LiNHtBu in the solid state. When excess tBuNH2 (ca. 1.1 equivalents) is used, a white colloidal solution forms, yielding an infinite polymeric ladder structure in the solid state. The cyclic ladder structure was determined to be the metastable polymorph and the infinite polymer ladder structure was determined to be the thermodynamic polymorph using DSC analysis and synthetic procedures. The cyclic ladder structure can be converted to the infinite polymer structure by heat or by addition of a donor ligand to catalyze the transformation The [Fe4(NtBu)S3Cl4]2– cluster is synthesized via a controlled synthetic protocol involving the formation of an iron-amide dinuclear intermediate, Fe2(μ-NHtBu)2[N(SiMe3)2]2. This intermediate arises from the protonolysis reaction of Fe[N(SiMe3)2]2 with tBuNH2. Notably, this transformation is unusual, as analogous reactions with Fe[N(SiMe3)2]2 typically proceed with ligands that are more acidic than HN(SiMe3)2. To explore the scope of this reactivity, a series of amines with varying acidity, steric hindrance and nitrogen substitution patterns were examined. The products that can form from reactivity of Fe[N(SiMe3)2]2 with amines include a mononuclear amine adduct, di– and tri–substituted dinuclear complexes and homo– and heteroleptic trinuclear complexes. The type of complex formed depended on the stoichiometry of amine to Fe[N(SiMe3)2]2 and the acidity, nitrogen substitution and steric hindrance around the nitrogen. Finally, the reduction of [Fe4(NtBu)S3(SPh)4]2– was attempted. Although reduction to the z = 3– cluster was achieved, the resulting product proved unstable in CD3CN, decomposing into a new species accompanied by thiolate release. Upon oxidation of the decomposition product, [Fe4(NtBu)S3(SPh)4]2– was regenerated, indicating that the Fe4(NtBu)S3 core likely remains intact. Further ligand tuning revealed that the use of p-methylbenzene thiolate allowed for the isolation of the reduced cluster; however, purification was hindered by its limited solubility. The synthesis of the oxidized, [Et4N][Fe4(NtBu)S3(SMes)4] cluster was achieved by oxidization of the z = 2– cluster by ferrocenium. Surprisingly, the oxidized cluster displayed a ground spin state of S = 3/2.
Variations in Laser-Induced Carbon from Structurally Varied Poly(furfuryl alcohol)
(University of Waterloo, 2025-07-17) Yip, Emily
The laser-induced graphene technique, wherein a polymer precursor is irradiated by a CO2 IR laser, provides a simple method for patterning of carbon materials like graphene or glassy carbon under ambient conditions. This is a highly attractive method of carbonization for applications in electronics and energy storage devices, and fine tuning of the laser-induced carbon’s properties is permitted by the choice of precursor. For example, glassy carbon with its disordered structure and defects is desirable for high-performance supercapacitors and so an appropriate precursor can be selected to form glassy carbon by laser irradiation instead of graphene. However, direct structure-property correlations between the precursor and the nature of the resulting laser-induced carbon as well as its quality are unclear. To investigate this, poly(furfuryl alcohol) (PFA), a glassy carbon precursor that is infamously comprised of several structural motifs aside from its monomer unit, was synthesized under a variety of reaction conditions to create three series with different key structural features and then laser irradiated to analyze the resulting carbon material. Typical laser-induced carbon formed from PFA is more akin to glassy carbon, though varied lasing parameters and structures can potentially enable graphenization. Three series of PFA were prepared which exhibit varying degrees of polymerization, extents of ring opening, and high thermal stability. The PFA chemistry had a notable influence on the quality of the resulting laser-induced carbon, which demonstrated a broad range of ordering from an amorphous structure to that with more crystalline graphitic domains. Correlations between the PFA structure and laser-induced carbon quality showed that the most ordered carbon material formed when the PFA crosslinking was minimal and had high thermal resistance. Further structural engineering of the PFA with these properties may then enable laser-induced graphenization of the precursor.
Monitoring Ultrafast Lattice Dynamics in 2D NbTe2
(University of Waterloo, 2025-05-13) Viernes, Christian
The discovery and control of emergent phenomena in strongly-correlated materials is a cornerstone of modern condensed matter physics and materials science. Among these phenomena, charge density waves (CDWs) represent a striking example of how the coupling between electrons and the atomic lattice can give rise to new properties. Understanding the microscopic mechanisms behind CDW formation and their dynamical evolution is crucial not only for fundamental science, but also for the development of ultrafast, energy-efficient electronic and quantum devices. The idea behind controlling such phenomena has been propelled by the advent of ultrafast lasers which enables investigation of electron-lattice interactions and has lead to the realization of many phase transitions. In this thesis, the ultrafast lattice dynamics of the layered quasi-two-dimensional material niobium ditelluride (NbTe2) are explored, a system known to host a robust CDW phase. By employing both time-resolved transient reflectivity (TR) and ultrafast electron diffrac- tion (UED), the femtosecond response is revealed from two different perspectives. These techniques enable direct observations of the dynamical structural distortion and coherent phonon generation with sub-picosecond temporal resolution. These findings reveal a rapid, photoinduced suppression of the CDW order within 200 femtoseconds, followed by coherent lattice oscillations that reflect the material’s transient structural state. UED measurements quantify a transient 1.3% CDW order suppression, while TR data show fluence-dependent modulations of phonon frequencies and lifetimes, highlighting the complex nature of the lattice response. At high fluence, the CDW order of NbTe2 approaches a complete melting along with an irreversible tellurium crystallization on the sample surface—a phenomenon characterized by Raman spectroscopy and interpreted through density functional theory (DFT)-based calculations. Beyond characterizing the behavior of NbTe2, this thesis establishes a broader experimental framework for investigating symmetry-breaking transitions and metastable states in low- dimensional quantum materials. The work highlights the power of ultrafast techniques for unveiling non-equilibrium phenomena and offers insights into how light can be used to engineer and manipulate material properties on demand.
Development and Optimization of Analytical methods for Sulfolane and BTEX Quantification in Environmental samples
(University of Waterloo, 2025-04-29) Kobarfard, Merrik
Sulfolane is an industrial solvent widely used in various industries, particularly the petrochemical sector. It is highly mobile in the environment due to its water miscibility at slightly above room temperature and minimal adsorption onto most soil types. Furthermore, sulfolane is a relatively stable compound, with aerobic biodegradation serving as its primary degradation pathway. However, its high mobility allows it to contaminate groundwater, where anaerobic conditions can lead to prolonged persistence. Additionally, sulfolane can migrate into fractured rock structures within groundwater zones, where small pores may trap contaminants, further prolonging environmental contamination. Given the large annual volumes of sulfolane usage, accidental releases are inevitable. Despite significant gaps in toxicological research, sulfolane is recognized as a neurotoxin and may disrupt multiple physiological systems, including the circulatory, hepatic, and reproductive systems. Due to these potential health risks, it is crucial to conduct environmental risk assessments, beginning with the measurement of sulfolane concentrations in environmental matrices. Sulfolane is rarely used in isolation and is often co-released with other organic solvents and chemicals. Its physicochemical properties, particularly its high solubility in both water and organic solvents, can influence the environmental distribution of co-contaminants. One important group of such co-contaminants commonly associated with sulfolane in the petrochemical industry are BTEX (benzene, toluene, ethylbenzene, and xylenes). BTEX compounds are well-established environmental pollutants with documented adverse effects on human health, including neurotoxicity, hematologic malignancies and damage to multiple organ systems. Therefore, monitoring BTEX alongside sulfolane is essential to understanding potential interactions and cumulative risks. In this study, two gas chromatography-mass spectrometry (GC-MS) methods were developed, optimized, and validated for the quantification of sulfolane in rock and groundwater samples. The methods were designed to be simple and environmentally friendly, minimizing the use of organic solvents. Due to the distinct characteristics of each matrix, tailored extraction techniques were employed. For rock samples, a microwave-assisted extraction method using methanol was developed to expedite contaminants extraction. The method was validated, and sulfolane stability in methanol extracts was assessed, confirming its stability for up to one year post-collection. The method was applied to 109 rock core samples from a contaminated site in Alberta, Canada, revealing sulfolane contamination in only one sample, while toluene and ethylbenzene were the most prevalent contaminants. For groundwater samples, an in-vial extraction method utilizing dichloromethane was developed. The method was validated, and assessed for ruggedness. Benzene was identified as the most susceptible to loss during sample preparation. Stability assessments showed that sulfolane remained stable in refrigerated water samples for up to 23 days. The method was then applied to 97 surface water and groundwater samples collected from a contaminated site in Alberta, Canada. Results indicated that sulfolane concentrations exceeded Health Canada's maximum acceptable contamination levels in 17 out of 50 locations, whereas only a few samples exhibited BTEX concentrations exceeding regulatory guidelines. Overall, this study successfully developed and validated methods for detecting sulfolane in environmental samples, contributing to a better understanding of its distribution in contaminated sites. However, further sampling and analysis are required to comprehensively assess sulfolane’s fate and transport at the study site.
Path integral and qubit encoding techniques for quantum simulations of discrete planar rotor lattices
(University of Waterloo, 2025-04-28) Moeed, Muhammad Shaeer
Typical path integral Monte Carlo approaches use the primitive approximation to compute the probability density for a given path. In this thesis, we investigate the utility of pair approximating the action in path integral ground state simulations targeting planar rotations. The pair propagator, which was initially introduced to study superfluidity in condensed Helium, is naturally well-suited for systems interacting with a pair-wise potential. Consequently, paths sampled using the pair action tend to be closer to the exact paths (compared to primitive Trotter paths) for such systems leading to convergence with less imaginary time steps. Our approach relies on using the pair factorization in conjunction with a rejection-free path integral ground state paradigm to study a chain of planar rotors interacting with a pair-wise dipole-dipole interaction. We first use a heat kernel expansion to analyze the asymptotics of the pair propagator in imaginary time. Then, we exhibit the utility of the pair factorization scheme via convergence studies comparing the pair and primitive propagators. Finally, we compute energetic and structural properties of this system including the orientational correlation and Binder ratio as functions of the coupling strength to examine the behavior of the pair-DVR method near criticality. Density matrix renormalization group calculations are used for benchmarking throughout. Near term quantum devices have recently garnered significant interest as promising candidates for investigating difficult-to-probe regimes in many-body physics. To this end, various qubit encoding schemes targeting second quantized Hamiltonians have been proposed and optimized. In this thesis, we also investigate two qubit representations of the planar rotor lattice Hamiltonian. The first representation is realized by decomposing the rotor Hamiltonian projectors in binary and mapping them to spin-1/2 projectors. The second approach relies on embedding the planar rotor lattice Hilbert space in a larger space and recovering the relevant qubit encoded system as a quotient space projecting down to the physical degrees of freedom. This is typically called the unary mapping and is used for bosonic systems. We establish the veracity of the two encoding approaches using sparse diagonalization on small chains and discuss quantum phase estimation resource requirements to simulate small planar rotor lattices on near-term quantum devices.
Grafting of Starch Nanoparticles with Polymers
(University of Waterloo, 2025-04-17) Fernandez, Joanne
As a biocompatible and biodegradable polysaccharide, starch has sparked significant interest for various industrial applications, but its poor mechanical properties limit its uses without chemical or physical modification. The work reported herein concerns the development of synthetic techniques to modify starch by graft polymerization via cerium (IV) activation. Starch nanoparticles (SNPs) were modified with acrylic acid (AA) in water under acidic conditions via activation with cerium (IV) in combination with potassium persulfate (KPS). The reactions were conducted with either the as-supplied SNPs containing glyoxal, or after purification (without glyoxal), for different target molar substitution (MS) values. A novel purification protocol using methanol extraction and centrifugation was implemented to purify the samples. This method proved to be selective to isolate the poly(acrylic acid) (PAA) homopolymer contaminant from the starch-g-PAA copolymer, and more reliable than the gravimetric analysis methods reported in the literature. The starch-g-PAA copolymers were characterized by dynamic light scattering (DLS), and degradation of the starch substrate allowed the determination of the molar mass of the PAA side chains via gel permeation chromatography (GPC) analysis. In the presence of aldehydes the rate of polymerization of AA increased significantly (by > 37 %), and the highest grafting efficiencies were obtained for glyoxal and butyraldehyde. The combination of cerium (IV) with glyoxal and KPS resulted in the highest polymerization rate and grafting efficiency. Increasing the glyoxal concentration also increased the rate of monomer conversion and the grafting efficiency. The increased rate of polymerization provided further insight into the grafting mechanism, as it was discovered that esterification reactions between starch and PAA also contributed significantly to the grafting process, particularly at longer reaction times. In the presence of aldehydes, the production of large amounts of PAA homopolymer resulted in esterification dominating the grafting process. Model reactions involving direct coupling of linear PAA samples with starch were investigated. All the reactions were characterized by high coupling efficiencies for a target MS = 3, and higher molar mass PAA samples (30 and 250 kDa) coupled faster than a lower molar mass sample (1.8 kDa), as expected in terms of reaction probabilities. The importance of esterification was also confirmed with model reactions using 2-hydroxyethyl acrylate, a monomer not containing a free carboxylic acid functional group, which yielded notably lower grafting efficiencies. Overall, the grafting mechanism for starch and acrylic acid promoted by cerium (IV) therefore appears more complex than described previously, particularly in the presence of aldehydes: The high overall grafting efficiencies observed result from two distinct reactions occurring concurrently, namely grafting via cerium (IV) activation, as well as the esterification of free PAA homopolymer. The additional insight gained for these reactions was possible due to the newly developed purification protocol, used in combination with NMR spectroscopy analysis, which provided detailed composition data for the different sample fractions and a better understanding of the grafting mechanism. Furthermore, preliminary results were obtained for starch modified with acrylonitrile and cerium (IV) in water under acidic conditions. Extraction of the polyacrylonitrile (PAN) homopolymer component was more difficult due to its solubility characteristics, but mixtures of dimethylacetamide with water (up to 10 % by volume) provided consistent results. High grafting efficiencies (> 67 %) were obtained for the starch-g-PAN copolymers, and characterization of the products was performed by Fourier transform-infrared spectroscopy, DLS, GPC, and atomic force spectroscopy. Hydrolysis of the starch substrate yielded hollow PAN shells or spheres, depending on the MS level of the copolymer, with potential applications in nanoencapsulation.
Development of Novel Human Aggrecanse-2 Dual-Binding Bis-Squaramide Inhibitors
(University of Waterloo, 2025-03-12) Ratto, Amanda; Honek, John
Osteoarthritis (OA) is a degenerative joint disease that affects millions of individuals worldwide. OA is characterized by the breakdown of articular cartilage, including the proteoglycan aggrecan, which plays a crucial role in enabling cartilage to withstand compressive loads. A Disintegrin and Metalloproteinase with Thrombospondin Motifs-5 (ADAMTS-5; aggrecanase-2), has been reported to be the predominant aggrecanase in mice, and in vitro studies revealed ADAMTS-5 exhibits high efficiency at cleaving aggrecan. Although no disease modifying OA drugs have been developed, it is hypothesized that inhibitors against ADAMTS-5 could slow the progression of OA. Typical inhibitors of ADAMTS-5 include zinc-binding groups (ZBGs) that interact with the catalytic zinc. Recently, an exosite that inhibitors can target has been identified at a nearby domain, not within the catalytic site. Here we present the development of novel potential dual-binding inhibitors which aim to target both the catalytic site and exosite of ADAMTS-5. The inhibitors investigated in this thesis incorporate a squaramide nucleus, which is an excellent molecular scaffold due to its ease of derivatization, known synthetic pathways, and commercial availability. To identify potential dual-binding bis-squaramide inhibitors, a large in silico library was constructed, consisting of the squaramide nucleus linking potential exosite binding groups and ZBGs. Numerous computational techniques were utilized to identify inhibitors, including molecular docking to evaluate potential interactions with both the binding pocket and exosite of ADAMTS-5, as well as molecular dynamics simulations to assess inhibitor stability and predict binding affinities. The four bis-squaramide molecules identified from the computational screening were successfully synthesized using a one-pot, microwave-assisted synthetic approach, which facilitated a high-throughput process through reaction automation. A range of bis-squaramide compounds were enzymatically screened with micromolar IC50’s for ADAMTS-5.
The Development of Electrochemical Systems for the Oxidation of Organic Contaminants for Water Treatment
(University of Waterloo, 2025-01-16) Delva, Nyhenflore; Klinkova, Anna
1,4 dioxane, also known as dioxane, is a contaminant of emerging concern, with no natural methods of degradation and no established treatment methods. This study investigates the use of both direct and indirect electrochemical advanced oxidation processes to generate radicals for dioxane oxidation, and how adjusting electrochemical parameters may be used to tune dioxane oxidation towards target compounds, thus offering a pathway to combine wastewater treatment with the synthesis of valuable compounds. Ion chromatography and nuclear magnetic resonance were used to identify and quantify the liquid products. The electro-Fenton process was used to indirectly oxidize dioxane via the activation of H2O2 generated in situ. H2O2 was quantified using TiOSO4 in an acidic solution. It was found that perfluorinated sulfonic acid binders can tailor carbon materials towards H2O2 production in acidic media, with as little as 5 wt% of PFSA binder dramatically improving both current density and H2O2 selectivity. Fe2+ concentration was shown to shift product selectivity of the Electro-Fenton process, with higher concentration resulting in greater selectivity towards C1 products. Early analysis of anodic oxidation of dioxane on ZnO reveals that carbonate radicals- formed from the oxidation of the bicarbonate electrolyte- are also part of the oxidation pathway, resulting in a different range of products than previously documented in the literature.
Multi-dimensional Analysis of Molecular Clusters in the Gas-phase
(University of Waterloo, 2025-01-10) Lee, Tsun Hei Arthur Enoch; Hopkins, Scott
In this thesis, interactions and properties of novel gas-phase clusters are studied. These gas-phase clusters often possess unique geometries and unexpected properties, which are influenced by the forces and interactions between the moieties within the cluster. Spectroscopic methods and ion mobility methods are coupled with tandem mass spectrometry to elucidate the cluster properties and geometry. IRMPD provides insight toward the nature of the cluster by their IR fingerprints, which can be used in parallel with tandem mass spectrometry method such as CID to provide further information. In addition, ion mobility methods are used to differentiate conformational differences between isomeric clusters. In chapter 3, IRMPD and CID of deprotonated fluorinated propionic acids are studied. In analytical studies of short chain per- and polyfluoroalkyl substances (PFAS), the quantification and the identification of these carboxylic acids are done by monitoring the carbanion signal after the loss of CO2. The degree of fluorination influences fragmentation under IRMPD and CID, leading to fragmentation pathways such as formation of FCO2– and HF elimination. Fluorinated propionic acids with at least one fluorine atom bound to the terminal carbon yield FCO2–, whereas loss of HF is observed in polyfluorinated species with at least one fluorine bound to the α-carbon. The formation of FCO2– and HF elimination products occur through a four-membered ring transition state. Chapter 4 describes the study of aromatic organometallic compounds such as cyclopentadienyl that are known to form sandwich complexes with counter cations, because the dominant interactions between the cation and the anion are Coulombic interactions and ion-induced dipole interactions. This work focuses on studying the influence on the geometry of the cluster by reducing the symmetry of the aromatic compound through clustering 1,2,3–triazolide and 1,2,4–triazolide with various alkali metal cations (with an excess of one cation to preserve cationic states). Through a combination of IRMPD and DFT calculations, the primary interaction between the alkali metal cations and the triazolide is found to be dominantly ion-dipole interactions and lone-pair donation interactions. This results in the geometry of the 1,2,3–triazolide clusters to be a 3D compact structure, whereas the 1,2,4–triazolide analogues are found to be more open with longer distances between the cations. Potential overtone bands or combination bands associated with the C-H wagging motion and ring torsion motion are found between the 1500 – 1800 cm–1 region. Chapter 5 is a study on the clusters of perfluorinated dodecaborate cages, B12F122–, with protonated diaminoalkanes H2N(CH2)nH2N (n = 2 – 12) through a combination of IMRPD action spectroscopy and ion mobility spectrometry. I focus on characterizing the different singly-charged clusters of the form [B12F12 + H2N(CH2)nNH2 + H]– and doubly-charged clusters of the form [2(B12F12) + H2N(CH2)nH2N + 2H]2– (n = 2 – 12). Three unique geometries are found for the singly-charged clusters, a low energy proton-bound ring geometry where intramolecular hydrogen bonding occurs between the two amine functional groups, a bidentate geometry (where both amine groups bind to the B12F122– moiety), and a monodentate geometry. For the doubly-charged clusters, the doubly protonated diaminoalkane act as a tether between the B12F122– cages. The major fragmentation channels of the singly-charged and doubly-charged clusters are found to be: (i) proton-transfer leading to production of HB12F12– and (ii) the loss of B12F122–. Formation of HB12F12– likely leads to further gas-phase reactions that can yield compounds such as [B12F11 + N2]–. Travelling wave ion mobility spectrometry (TWIMS) analysis of HB12F12– finds CCSTWIMS = 142 ± 6.7 Å2. IRMPD spectroscopy, aided by computational modelling, indicates that the bidentate conformation is the major sub-population in the gas-phase ensemble.

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