<p> Ligands play a vital role in transition metal catalysis: they modulate the steric and electronic properties of the metal catalysts, thus enabling the desired reactivity and selectivity. The dominant ligand classes include phosphines, amines, and NHCs, which render the metal centers more electron-rich through &sigma;-donation. On the contrary, although the &pi;-accepting, electron-deficient olefins (EDOs) are known to promote bond-forming reductive elimination, they have not been widely utilized as ligands for catalysis. Development of these EDOs into a modular class of ligands would allow for novel reactivity that cannot be achieved with existing ligand classes.</p><p> In an effort to develop cross couplings with non-traditional electrophiles, we discovered that an electron-deficient olefin, dimethylfumarate, is the optimal ligand for nickel-catalyzed Negishi alkylation of styrenyl aziridines. Mechanistic studies revealed a stereoablative mechanism of this reaction and that the sulfonamide group is involved in directing the C&ndash;C formation. Furthermore, the critical role of dimethylfumarate is most likely be promoting the reductive elimination.</p><p> To expand the substrate scope to the less activated alkyl aziridines, we designed an N-protecting group, cinsyl (Cn), which contains an electron-deficient olefin as the directing group. Effective arylations and alkylations of Cn-aziridines can be achieved utilizing the nickel catalyst and organozinc reagents. The stereoablative mechanism going through radical intermediates was again observed. </p><p> The modular framework of dimethylfumarate allows us to modify the ligand structure and achieve more challenging transformation. We found that an indenylsultam-derived ligand, Fro-DO, enables cross coupling with 1,1-disubstituted styrenyl aziridines to generate all-carbon quaternary centers. Solid-state analysis revealed a unique U-shape structure of this ligand, which may be responsible for the improved reactivity and selectivity. Additionally, utilization of a chiral camphorsultam-derived EDO ligand provided modest but promising enantioselectivity of this reaction.</p><p> In this thesis work, we have demonstrated that EDOs can be developed into a novel ligand class for transition metal catalysis. The structural platform allows for rapid ligand modification and reaction evaluation. We expect that future exploration of these EDO ligands will unlock new reactivity and selectivity that has not been possible with current technology.</p>

Gold nanoparticles (AuNPs) hold a great promise for biomedical applications. The inert inorganic core provides a scaffold to hold organic ligands and their payloads, while the diversity of monolayers provide a means to tailor AuNP surface properties for particular purposes. Based on our synthethic approach to ligand fabrication, our group has been able to control the chemical properties of AuNPs at the nanoscale level. These properties have made AuNPs an excellent scaffold for delivery applications. In this dissertation, it has been demonstrated how the properties of monolayers play a crucial role in achieving a desired biological goal. In each case, the monolayer of AuNPs has been tailored using organic synthesis as a strategy to afford stable and biocompatible biological tools. These engineered AuNPs demonstrate numerous biomedical applications, including a controlled release of payload, cellular uptake, gene regulations, cytosolic delivery, and cytotoxicity.

The detection of chemical explosives is an important problem that poses unique challenges for chemists. Common explosives such as nitro-organics and peroxides lack chromophores, and differ greatly in chemical structures and properties. A family of Zn(salicylaldimine) (ZnL) complexes were prepared, and investigated for fluorescence sensory applications. ZnLs are strong fluorophores, Φ = 0.3, with sub-nanosecond lifetimes and highly reducing excited states. The fluorescence of ZnL is effectively quenched by both nitroaromatics and nitroalkanes. Quenching occurs via photoinduced electron transfer from the phenolate ring of ZnL, creating a phenoxyl radical species that was observed with EPR. ZnL was synthetically varied with electron withdrawing and donating substituents, and Stern-Volmer quenching experiments revealed mixed quenching pathways, depending upon the steric bulk of the substituent. The energetic contributions from the electron withdrawing or donating substituents changed the driving force for electron transfer, and high steric bulk favored dynamic quenching over the static pathway. The kinetics of dynamic quenching were treated with Marcus theory, predicting a modest reorganization energy, λ = 24 kcal/mol, governed by solvent effects. A sensor array was formulated for the discrimination of structurally similar nitro-organic compounds. Fingerprint patterns were generated for each quencher based on the unique interactions with each ZnL. Using statistical analysis, 100% of unknown samples were accurately identified. Solid state structural investigations reveal a penta-coordinate Zn with solvent bound axially. The axial ligand, EtOH, THF and pyr, influenced the degree of π-stacking in the unit cell, and shifted the solid state λ em. Preliminary investigations into solid state sensors involved formation and characterization of polycrystalline structures, ZnL doped thin films, and ZnL polymers. Fluorescence turn-on methods are highly sensitive compared to fluorescence quenching. A fluorescence turn-on sensor was developed for peroxide based explosives using the oxidative deboronation of a masked prochelator to form H2L, which chelated Zn2+ and produced fluorescent ZnL. The rate of fluorophore formation was limited both by peroxide concentration and structure of the diamine backbone of the prochelator. Limits of detection for H2O2, benzoyl peroxide and triacetone triperoxide, a highly energetic peroxide-based explosive, were below 10nM in solution.

Self-assembly of nanoparticles presents an excellent tool in the development of novel nanoscale structures and materials for creating high sensitive sensors, electronic and diagnostic devices, ultrahigh-density magnetic storage devices and many more. In these systems, the nanoparticle core imparts exceptional physical properties while their organic coatings regulate the assembly process. Moreover, organic coatings improve particle stability and solubility, as well as regulate charge and hydrophobicity. This thesis has focused on the engineering of nanoparticles’ surfaces using organic molecules and assembly of these particles through supramolecular interactions for various applications. Morphology of the nanoparticle assembly was tuned simply by varying the degree of fluorinated coating on particles’ surfaces and thus controlling their hydrophobicity. Surface engineered particles were also assembled at oil-water interfaces alone and with enzymes creating colloidal microcapsules for controlled release and catalysis respectively. The combination of the unique attributes of the nanoparticle cores and the function of the organic coating provides ample opportunities in the creation of multi-functional nano-materials that are useful in biological and materials applications.

Over the past few decades, tremendous efforts have been made to develop nanomaterials for biotechnological applications such as therapeutics. Understanding and engineering interfaces between biomacromolecules and nanomaterials is a key to the creation of successful therapeutic systems. My research has been oriented toward developing therapeutic systems using gold nanoparticles (AuNPs) incorporating material science, organic synthesis, and biology. For this purpose, mixed monolayer protected AuNPs (∼2 nm core size) with various functional groups have been employed for triggering therapeutic effects. Several strategies have been accomplished using anticancer drugs that non-covalently and covalently incorporate onto AuNPs as a drug delivery carrier. Alternatively, AuNPs were developed by regulating host-guest complexation processes inside the cell, allowing control of the therapeutic effect of the AuNP. In addition, by using host-guest chemical events on the AuNPs, exocytosis of the AuNPs was controlled, enabling their prolonged retention inside of the cells, providing new strategies for improving conventional drug delivery systems. Therefore, engineering of the AuNP surface can afford new pathways for designing and improving therapeutics.

<p> In this work the redox properties of cytochrome c nitrite reductase (CcNiR), a decaheme homodimer that was isolated from <i>S. oneidensis,</i> were determined in the presence and absence of the strong-field ligands cyanide and nitrite. Four hemes per CcNiR protomer are hexa-coordinate with tightly bound axial histidines, while the fifth (active site) has one tightly bound lysine and a distal site that can be open, or contain exogenous ligands such as the substrate nitrite. Controlled potential electrolysis in combination with UV/visible absorption (UV-vis) and electron paramagnetic resonance (EPR) spectroscopies allowed for assignment of all heme midpoint potentials under each set of conditions. The studies show that the active-site heme is the first to be reduced under all conditions. The midpoint redox potential of that heme shifts approximately 70mV to the positive upon binding a strong field ligand such as nitrite or cyanide. When controlled potential electrolysis was carried out in the presence of nitrite, a concerted two electron reduction was observed by UV-vis, and a {Fe(NO)}⁷ reduced product was revealed in EPR. In addition, an asymmetry in ligand binding between active sites was revealed. This information is relevant for the interpretation of planned and ongoing mechanistic studies of CcNiR. </p><p> Over-expression, partial purification and characterization of another <i> S. oneidensis</i> multiheme enzyme, known as octaheme tetrathionate reductase (OTR), is also described herein. Though of unknown cellular function, OTR was previously reported to have tetrathionate reductase activity, in addition to nitrite and hydroxylamine reductase activities. The new results indicate that the expression of OTR has no effect on tetrathionate or nitrite reductase activities in the whole cell lysate, and only hydroxylamine reductase activity was substantially elevated in the overexpressing bacteria. OTR was stable in buffered solutions, but substantial activity loss during all attempts at column chromatography was a major obstacle to the complete purification. OTR also proved quite hydrophobic, so possible membrane association should be considered in future attempts to purify this protein. </p><p> Finally, this dissertation also reports attempts to improve <i> S. oneidensis'</i> ability to express foreign proteins. Though ideally suited to expressing c-hemes, it proved difficult to express carboxy his-tagged proteins in <i>S. oneidensis</i> because of persistent tag degradation. Attempts to knock out lon protease, a cytoplasmic carboxypeptidase, as well as the result of redirecting ccNiR from the SecA to the possibly more protected signal particle recognition (SRP) secretion pathway, are described. </p><p> Iron heme cofactors are single-electron transport moieties that play a crucial role in respiration. While oxygen is the electron acceptor of choice in aerobic atmospheres, microorganisms that live in anaerobic environments utilize other molecules with similarly high reduction potentials. <i> S. oneidensis</i> can utilize numerous terminal electron acceptors, including nitrite, dimethylsulfoxide and even uranium, thanks to a particularly rich array of multi c-heme respiratory proteins. Understanding of how the midpoint potentials and heme arrangements within the proteins influence these exotic respiratory processes is of interest in the fields of bioremediation and fuel development.</p>

Monolayer protected nanoparticles (NPs) include an inorganic core and a monolayer of organic ligands. The wide variety of core materials and the tunable surface monolayers make NPs promising materials for numerous applications. Concerns related to unforeseen human health and environmental impacts of NPs have also been raised. In this thesis, new analytical methods based on mass spectrometry are developed to understand the fate, transport, and biodistributions of NPs in the complex biological systems. A laser desorption/ionization mass spectrometry (LDI-MS) method has been developed to characterize the monolayers on NP surface. LDI-MS allows multiple NPs taken up by cells to be measured and quantified in a multiplexed fashion. The correlations between surface properties of NPs and cellular uptake have also been explored. LDI-MS is further coupled with inductively coupled plasma mass spectrometry (ICP-MS) to quantitatively measure monolayer stability of gold NPs (AuNPs) and quantum dots (QDs), respectively, in live cells. This label-free approach allows correlating monolayer structure and particle size with NP stability in various cellular environments. Finally, uptake, distribution, accumulation, and excretion of NPs in higher order organisms, such as fish and plants, have been investigated to understand the environmental impact of nanomaterials. The results indicate that surface chemistry is a primary determinant. NPs with hydrophilic surfaces are substantially less toxic and present a lower degree of bioaccumulation, making these nanomaterials attractive for sustainable nanotechnology.

Hierarchically structured inorganic materials are everywhere in nature. From unicellular aquatic algae such as diatoms to the bones and/or cartilage that comprise the skeletal systems of vertebrates. Complex mechanisms involving site-specific chemistries and precision kinetics are responsible for the formation of such structures. In the synthetic realm, reproduction of even the most basic hierarchical structure effortlessly produced in nature is difficult. However, through the utilization of self-assembling structures or "templates", such as polymers or amphiphilic surfactants, combined with some favorable interaction between a chosen inorganic, the potential exists to imprint an inorganic material with a morphology dictated via synthetic molecular self-assembly. In doing so, a very basic hierarchical structure is formed on the angstrom and nanometer scales. The work presented herein utilizes the self-assembly of either surfactants or block copolymers with the desired inorganic or inorganic precursor to form templated inorganic structures. Specifically, mesoporous silica spheres and copolymer directed calcium phosphate-polymer composites were formed through the co-assembly of an organic template and a precursor to form the desired mesostructured inorganic. For the case of the mesoporous silica spheres, a silica precursor was mixed with cetyltrimethylammonium bromide and cysteamine, a highly effective biomimetic catalyst for the conversion of alkoxysilanes to silica. Through charge-based interactions between anionic silica species and the micelle-forming cationic surfactant, ordered silica structures resulted. The incorporation of a novel, effective catalyst was found to form highly condensed silica spheres for potential application as catalyst supports or an encapsulation media. Ordered calcium phosphate-polymer composites were formed using two routes. Both routes take advantage of hydrogen bonding and ionic interactions between the calcium and phosphate precursors and the self-assembling copolymer template. Some evidence suggests that the copolymer morphology remained in the composite despite the known tendency for calcium phosphates to form highly elongated crystalline structures with time, as is commonly the case for synthetic hydroxyapatites. Such materials have obvious application as bone grafts and bone coatings due, in part, to the osteoconductive nature of calcium phosphate as well as to the mesoporosity generated through the cooperative assembly of the block copolymer and the inorganic. Future work, including potential experiments to determine osteoconductivity of as-prepared composites, is also presented herein.

This thesis describes the synthesis of halogen bonding receptors for integration within interlocked anion host systems. Chapter 1 introduces the field of supramolecular chemistry, with a particular focus on anion recognition and sensing, halogen bonding, and the synthesis of mechanically interlocked structures. Chapter 2 describes the preparation and anion binding properties of carbazole-based receptor molecules. A systematic anion binding study on a series of halogen- and hydrogen-bonding 3,6-bis-triazolium carbazole acyclic receptors is described initially, followed by the development of a halogen bonding rotaxane. The anion and metal complexation properties of acyclic and macrocyclic systems incorporating the 1,8-bis-triazole carbazole motif are also presented. Chapter 3 details the synthesis and anion complexation investigations of halogen and hydrogen bonding naphthalene-based acyclic and interlocked rotaxane host molecules. Chapter 4 presents receptors based on the 4,4'-bis-triazole-2,2'-bipyridyl motif. A halogen bonding rhenium(I) bipyridyl complex is exploited in the development of a rotaxane host system which optically senses anions via luminescence purely through halogen bonding interactions. The anion recognition and sensing properties of diquat-based receptors are also investigated, and shown to exhibit optical and electrochemical responses to anions. Chapter 5 summarises the major conclusions from Chapters 2-4. Chapter 6 describes the experimental procedures used in the work, and includes characterisation data for the synthesised compounds. Supplementary information relating to crystallographic data, and absorption, luminescence and electrochemical studies, is provided in the Appendices.

This thesis presents the development and redesign of a commercial electrochemical quartz crystal microbalance with dissipation (E–QCM–D). This was used to study factors affecting the efficiency of the four electron reduction catalysed by the fuel cell enzyme bilirubin oxidase from Myrothecium verrucaria immobilised on thiol modified gold surfaces. Within this thesis, the E–QCM–D was used to show that application of a constant potential to bilirubin oxidase adsorbed to thiol-modified gold surfaces causes activity loss that can be attributed to a change in structural arrangement. Varying the load by potential cycling distorts the enzyme by inducing rapid mass loss and denaturation. Attaching the enzyme covalently reduces the mass loss caused by potential cycling but does not mitigate activity loss. Covalent attachment also changes the orientation of the surface bound enzyme as verified by the position of the catalytic wave (related to the overpotential for catalysis) and reactive labelling followed by mass spectrometry analysis. The E–QCM–D was used to show how electrostatic interactions affect enzyme conformation where high pH causes a reduction in both mass loading at the electrode and a reduction in activity. At pH lower than the enzyme isoelectric point, there is a build up of multilayers in a clustered adsorption. When enzyme adsorbs to hydrophobic surfaces there is a rapid denaturation which completely inactivates the enzyme. Changing the surface chemistry from carboxyl groups to hydroxyl and acetamido groups shows that catalysis is shifted to more negative potentials as a result of an enzyme misorientation. Further to this, increasing the chain length of the thiol modifier indicates that an increased distance between surface and enzyme reduces activity, enzyme loading and results in a conformational rearrangement that permits electron transfer over longer distances.