Thesis advisor: Jianmin Gao / With the rapid evolution of antibiotic resistance, the need for more effective antibiotics is imminent. Bacterial membranes are an appealing target due to their accessibility and relatively conserved structures. Membrane targeting antibiotics, especially cationic antimicrobial peptides (CAMPs) such as host defense peptides, have been increasingly explored as novel antibiotics and tunable innate antimicrobials. The latter could be achieved by treatment with an antibiotic adjuvant: a compound that would increase the potency of host CAMPs without killing the bacteria on its own. Boosting the host’s own immune system with an adjuvant is beneficial over using antibiotics and would theoretically avoid triggering bacterial resistance. One mechanism of bacterial resistance is increasing the cationic charge of the membrane. As CAMPs are electrostatically attracted to anionic bacterial membranes, making the membrane more cationic decreases that attraction, rendering CAMPs less effective. To target this resistance mechanism chemically, two antibiotic adjuvant strategies were explored as co-treatments with various CAMPs: membrane targeting peptides used to bind and block surface amines, and small molecules used to either acetylate surface amines or convert a cationic membrane phospholipid to an anionic phospholipid. Co-treatment of the Staphylococcus aureus (S. aureus) membrane targeting peptide KAM-CT and various CAMPs increased S. aureus susceptibility to those CAMPs. Bacterial surface acetylation using sulfo-NHS-acetate followed by CAMP treatment caused up to 10 times increased CAMP potency. Hydrazine and hydroxylamine were shown to cleave the lysine moiety from the lysyl-phosphatidylglycerol (Lys-PG) phospholipid to generate phosphatidylglycerol (PG) in liposome models. S. aureus was treated with a hydroxylamine-CAMP conjugate, but it showed decreased antibiotic activity compared to the CAMP alone. To better understand what was happening in the bacteria, a novel Lys-PG quantification protocol was created by fluorophore labeling Lys-PG and quantifying the labeled Lys-PG via normal phase high-performance liquid chromatography (NP-HPLC). Cyclic peptides, such as KAM-CT, represent complex yet synthetically attainable moieties that could be used as novel antibiotics adjuvants. Expanding the repertoire of reversible covalent chemistries, especially those applied to peptide cyclization, is desirable due to the high potency and selectivity of such interactions. Herein, we also describe a novel reversible covalent chemistry between 2-formylphenylboronic acid (FPBA) and 2,3-diaminopropionic acid (Dap): the imidazolidino boronate (IzB) conjugate. It was found to be potent (Kd = 100 μM) and quickly reversible (t1 = ~6 sec) under physiological conditions. IzB formation was successfully employed as a peptide cyclization strategy as there was little interference from biologically relevant small molecules, except cysteine. Cysteine interference was utilized to create “smart” peptides that can linearize upon increasing cysteine concentrations via thiazolidino boronate (TzB) formation with the FPBA moiety in the peptide. Such “smart” peptides could be used as pH-responsive peptides or cysteine sensors able to report on the cysteine concentration in complex media. / Thesis (MS) — Boston College, 2017. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Chemistry.

This Thesis reports the synthesis, purification and characterisation of gold nanoparticles (NPs) functionalised with a monolayer of hydrazone ligands in order to perform post-synthetic manipulations of the NP-bound monolayer exploiting dynamic covalent chemistry. NP post-synthetic manipulation based on reversible non-covalent interactions between oligonucleotides represents a promising approach to achieve functionalisation and self-assembly for potential applications in biology and medicine. However, the stability of these nanosystems is ensured only in a narrow window of environmental conditions. On the other hand, irreversible covalent strategies potentially allow the full range of synthetic chemistry to be exploited but they provide poor control over the manipulation of the NP-bound monolayer and can only produce kinetically controlled amorphous NP aggregates. Dynamic covalent chemistry represents an interesting and an attractive alternative approach because it would combine the reversibility of non-covalent interactions with the stability of covalent bonds. By this way, ligand-functionalised NPs could be manipulated in order to introduce a large variety of molecular functionalities on the NP surface not only to subtly tune the NP physicochemical properties but also to access an entire range of novel nanomaterials.

Only within the last decade has supramolecular chemistry begun to adopt the Group 15 elements into its field of research. This dissertation presents a supramolecular approach to the self-assembly and reactivity of Group 15 metalloids, specifically arsenic and antimony, with organothiolate ligands. Investigating the self-assembly of pnictogen-based coordination complexes allows for in-depth characterization of the chemical behavior of arsenic, antimony and other Group 15 elements. Currently, the infiltration of arsenic into global groundwater systems has developed into a worldwide health concern. There are no chelating agents available for public use in the treatment of arsenic poisoning which are capable of binding arsenic (III) in its preferred coordination geometry thereby hindering the selectivity for rapid chelation. Chapter I is a review covering two important characteristics observed in the Group 15 elements: 1) a stabilizing, non-covalent cation-π interaction aiding in the formation of pnictogen-aryl thiolates, and 2) an observed lack of selectivity in environments containing multiple pnictogen ions which enables transmetalation of the complexes to occur or the generation of heterometallic assemblies. Based on the discovery of this new transmetalation reactivity, the remainder of the dissertation explores the effects of external additives during self-assembly in order to understand how they may affect the reactivity of these self-assembled complexes and provide insight into formation mechanisms. Chapter II identifies a catalyst for the acceleration of a slow self-assembly reaction between AsCl3 and a dithiolate ligand to give an As2L3 cryptand. Chapter III examines the oxidation of the arsenic cryptand using iodine, which leads to the self-assembly of a series of differently sized, discrete disulfide-bridged macrocycles. In Chapter IV, the self-assembly of the first trinuclear arsenic- and antimony-based coordination complexes was studied, revealing interesting solvent dependent conformational isomerism in solution. Chapter V applies the pnictogen-enhanced iodine oxidation to the synthesis of known and new cyclophanes using supramolecular chemistry, including the self-assembly and covalent capture of an unprecedented tetrahedral thiacyclophane. Additionally, an unusual trithioorthoformate capped tricyclophane cage was also synthesized and isolated by pnictogen-activated oxidation. Chapter VI includes the conclusion and future directions for the project. This dissertation includes co-authored material and previously published results. / 10000-01-01

En Science des colloïdes, il est fondamental de contrôler les interactions entre les particules et leur environnement pour obtenir les propriétés souhaitées. Dans ce travail de thèse, pour former des systèmes innovants, nous avons utilisé la chimie covalente réversible à l'interface particule/polymère dans deux domaines différents : les composites vitrimères et la nanocatalyse. Dans les composites, les liens réversibles permettent d'améliorer les propriétés mécaniques tout en limitant l'impact des charges sur les propriétés vitrimères des matériaux. Deux matrices vitrimères reposant sur des réactions d'échange de nature différente, la transestérification et la transimination, ont été étudiées. L'avantage du lien imine est d'être également dissociable dans certaines conditions douces, ce qui facilite le recyclage des matériaux. La réversibilité du lien imine peut aussi être exploitée pour contrôler la dispersion/agrégation de particules en solvant. Lorsqu'elles sont liées, les chaines polymères se déploient en bon solvant et confèrent aux particules une stabilisation stérique, stabilisation qui disparait lorsqu'elles sont détachées : les particules s'agrègent et peuvent être récupérées facilement. Ce concept a été développé sur un système catalytique composé de nanoparticules de palladium supportées sur des particules de silice. Les chaines greffées améliorent non seulement la dispersion des nanocatalyseurs et les taux de conversion du système catalytique, mais aussi stabilisent les nanoparticules de palladium à la surface de la silice, limitant leur lessivage et leur agrégation. L'efficacité catalytique du système est ainsi conservée sur plusieurs cycles. / The control of the interactions between particles and their environment is essential when dealing with colloids in order to reach desired properties. In this study, reversible covalent bonds were used as interfacial interactions in two systems: vitrimer composite materials and nanocatalysis in solution. The aim of this work was to develop materials which present original properties thanks to interfacial dynamic bonds. In composites, the introduction of dynamic covalent bonds between a vitrimer matrix and the fillers enables to improve mechanical properties while preserving vitrimer properties. Two vitrimer matrices based on two different exchange reactions, transesterification or transimination, have been studied. Imine bonds are reversible bonds that can dissociate in presence of water. We demonstrate that polyimine vitrimers can be reshaped and recycled under mild conditions. The reversibility of the imine bond can also be used to control the stability of a colloidal dispersion. Indeed, grafting of polymers on particles surface through reversible covalent bonds give them steric stabilization in good solvent of the chains. Dissocation of these bonds triggers detachment of the polymer chains and induces particle aggregation. This concept was applied to a catalytic system composed of palladium nanoparticles adsorbed onto silica particles. Polymer chains not only improve the dispersion of the whole catalytic system but also limit the leaching and aggregation of the palladium nanoparticles. As a consequence, the catalytic efficiency of the particles can be preserved over several cycles.

Dans l'optique de préparer des vitrimères à partir des thermoplastiques communément utilisés, tels le PMMA et le PS, des réactions d'échange dynamiques reposant les liens imine et esters boroniques ont été étudiées. Des paramètres importants comme la constante de dissociation de certaines molécules, la constante de vitesse et l'énergie d'activation ont été mesurées. Des monomères porteurs de liaisons échangeables ont été synthétisés et polymérisés. Des vitrimères, avec des liaisons C-C dans la chaine principale, ont été créés par différentes stratégies (PMMA et PS). Ces matériaux sont réticulés et insolubles avec un plateau caoutchouteux mais également façonnables et recyclables par moulage par compression ou par injection. Ces vitrimères peuvent relaxer les contraintes et couler à une température supérieure à celle de leur transition vitreuse. Des viscosités de 105-107 Pa.s ont été estimées pour les vitrimères PMMA reposant sur la chimie des esters boroniques. Des tests de traction montrent que leurs propriétés mécaniques de ces matériaux ne subissent pas de baisse significative après plusieurs cycles de recyclage par moulage par injection. Même après plusieurs cycles de moulage, les vitrimères basés sur la chimie des esters boroniques peuvent être complètement dé-réticulés, signe de leur stabilité à haute température lors du moulage. Ces vitrimères ont une résistance supérieure dans les conditions "d'environmental stress cracking" comme des réseaux polymères conventionnels. / With the aim to generate vitrimers from commonly used thermoplastics with carbon-carbon based backbones, such as PMMA and PS, dynamic covalent exchange reactions relying on Schiff’s bases and boronic esters were investigated. Two different approaches, i.e. crosslinking in solution or in extrusion, were used. These materials are processable via extrusion, compression and injection molding like their thermoplastic counterparts. The crosslinked nature of these systems was confirmed by solubility tests and DMA. Rheological measurements revealed the vitrimers ability to flow and viscosities between 105-107 Pa.s for boronic ester based PMMA vitrimers were measured. Consecutive tensile testing/reprocessing sequences proved the full recyclability of these vitrimers, and selective cleavage of the vitrimer networks followed by precise chemical analyses showed the thermal and chemical stabilities of vitrimers relying on boronic ester bonds. The stress cracking resistance of these vitrimers was significantly higher than that of parent thermoplastics, as can be expected for crosslinked systems.

Gas-phase ion/ion covalent modification was coupled to ion mobility/mass spectrometry analysis to directly correlate the structure of gaseous ubiquitin to its solution structures with selective covalent structural probes. Collision cross section (CCS) distributions were measured prior to ion/ion reactions to ensure the ubiquitin ions were not unfolded when they were introduced to the gas phase. Ubiquitin ions were electrosprayed from aqueous and methanolic solutions yielding a range of different charge states that were analyzed by ion mobility and time-of-flight mass spectrometry. Aqueous solutions stabilizing the native state of ubiquitin generated folded ubiquitin structures with CCS values consistent with the native state. Denaturing solutions favored several families of unfolded conformations for most of the charge states evaluated. Gas-phase covalent labeling via ion/ion reactions was followed by collision induced dissociation of the intact, labeled protein to determine which residues were labeled. Ubiquitin 5+ and 6+ electrosprayed from aqueous solutions were covalently modified preferentially at the lysine 29 and arginine 54 residues, indicating that elements of secondary structure as well as tertiary structure were maintained in the gas phase. On the other hand, most ubiquitin ions produced in denaturing conditions were labeled at various other lysine residues, likely due to the availability of additional sites following methanol and low pH-induced unfolding. These data support the conservation of ubiquitin structural elements in the gas phase. The research presented here provides the basis for residue-specific characterization of biomolecules in the gas phase

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The fluorination of porous materials often leads to the enhancement of properties such as stability, crystallinity and selective adsorption. Although there has been much interest in the fluorination of many types of porous materials, little research has been done on the fluorination of macrocycles, specifically trianglimine and leaning pillararene based materials. In this work, we introduce for the first time highly fluorinated trianglimine and leaning pillararene and show the enhancement effects brought about by the inclusion of fluorinated-phenyl moieties, such as increased stability, surface area, and tendency for self-assembly in our systems. We then show how our fluorinated macrocycles open the door for the formation of extended macrocycle-based polymetric materials simply and in high yields via nucleophilic aromatic substitution. We show for the first time the formation of a trianglimine-based cross-linked polymer and demonstrate its use for micropollutant and gas separation.

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