<p>This thesis presents the results of investigations on the application of modern spectroscopic techniques to the characterisation of secondary bonding interactions (SBIs) in selected organo-chalcogen compounds. Although the research was mostly focused on two families of compounds, ditellurides and chalcogen-substituted azodyes, the observations and conclusions are applicable to a wide variety of compounds. Because the effects of the SBIs are subtle, great care was taken to carefully distinguish contributions from other factors. DFT computational studies showed that the molecular conformation influences the electronic excitations observable in the UV-vis spectrum and the frequency of resonance in ¹²⁵Te NMR of organoditellurides. In the absence of protection to shield the chalcogen from intermolecular interactions, the ¹²⁵Te NMR chemical shift is dependent on the concentration of ditellurides; intramolecular SBIs attenuate the concentration dependency and steric protection cancels it entirely. The nature of the solvent impacts the results of both spectroscopic techniques through several mechanisms, including the solvatochromic effect, conformational changes due to the polarity of the medium and solvation. Solution ¹²⁵Te NMR spectroscopy is sensitive to all those contributions but, for the same reason, it cannot be applied in an unambiguous way to identify the presence of SBIs.</p> <p>Conversely, the use of intramolecular SBIs to modify the spectroscopic properties of a conjugated chromophore was investigated. Push-pull azobenzenes were derivatised with functional groups containing divalent chalcogen atoms through metathesis with a mercurated derivative of the azodye. The regiochemistry of formation of the intermediate was shown to be under kinetic control. In the chalcogen-substituted molecules, the efficiency of electron delocalisation through the SBIs was assessed by calculations of the nucleus independent chemical shift (NICS). The linear (UV-vis absorption) and nonlinear (second harmonic-generation) optical responses of the modified chromophore were investigated and interpreted in the context of the SBIs. Substitution with the chalcogen groups, and the consequent perturbation of the π-system, cause a blue shift in the first absorption maxima but little change was observed in the hyperpolarisability of the chromophore ortho-functionalised with the phenylselenenyl group. The sensitivity of the electronic spectrum to the SBI was applied to monitor the process of halide exchange in the halo-chalcogenyl derivatives of the push-pull azobenzene.</p> <p>Very strong SBIs can result in interatomic distances so short that they are difficult to distinguish from hypervalent covalent bonds. This is the situation observed in the structure of the first 2,5,8,11,1,4,7,10,3,6,9,12-tetraoxatetratelluratetrazacyclododecane. DFT calculations showed that this unusual macrocycle is stable with respect to dissociation into isotellurazole oxide and VT NOESY experiments indicate it remains intact in solution.</p> / Doctor of Philosophy (PhD)

<p> The properties of crystalline materials are controlled by their composition and by their structure, however, the structure of a crystal is only partly controlled by its composition. Development of specifically directed inorganic syntheses will require an understanding of the dynamics of crystal phase forming processes, especially those processes involved in generating specific symmetry features. One successful strategy, intended to exert synthetic control over the symmetry of crystal structures involves incorporating polar, anionic species, called basic building units (BBUs). Polar BBUs tend to adopt ordered configurations, increasing the probability that discovered structures will have polar symmetry. Discovery of eight new compounds with general formula K₁₀(M₂O_nF_11-n)X (M = V^V, Nb^V, n = 2, M = Mo^VI, n = 4; X^- = (F₂Cl)_1/3, Cl, ([Br][Br₃])_1/2, and ([I][I₃])_1/2) is reported. Post-synthetic structure analysis these compounds which crystallize in the space groups<i> P3&macr;m</i>1, <i> Pmn</i>2₁, and C2/<i>m,</i> is used to analyze and expand on the &Lambda;-shaped anionic unit strategy.</p><p> The atom scale processes involved in the phase transition are examined through computational Molecular Dynamics (MD) simulations. Atomistic MD simulations present the technical challenge of developing models for calculating interatomic interactions that can reliably reproduce experimental results. A strategy for improving the accuracy of empirical interatomic interaction models is outlined. Cryogenic temperature (~15K) and variable-pressure (1-10 GPa) diamond anvil cell single crystal diffraction experiments on the <i>Pna</i>2₁ phase of KNaNbOF₅ are used to develop a set of empirical pairwise interatomic interaction functions of the complex five element system. The atom scale dynamics of a temperature driven reconstructive phase transition in KNaNbOF₅ are examined, leading to the discovery of a dynamically disordered high temperature crystal structure, and the origin of the NCS phase stabilization upon cooling. The reconstructive transition going from the <i> P</i>4/<i>nmm</i> phase to the high temperature <i>Cmcm </i> phase is believed to result from a loss of O/F site ordering caused by rigid rotations of octahedral [NbOF₅]^2- BBUs. The high temperature phase is found to be a dynamically disordered state involving two locally stable phases in the potential energy landscape with <i> Pbcm</i> and <i>Pnma</i> space group symmetries. </p>

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The current energy crisis is becoming more and more serious due to the industrial development and increasing population. Mimicking photosynthesis in plants provides a new way to solve this crisis. The goal is to harness solar energy and convert it into energy stored in chemical bonds such as methanol or hydrogen gas. Currently, most catalysts for proton reduction contain precious metals, such as palladium, platinum and ruthenium. The main goal of our research is to develop catalysts made of earth abundant metals. By incorporating organic ligands in our complexes, we can make catalysts that have similar catalytic activity as those made of rare metals. Herein, I report an iron and a nickel catalysts that can generate hydrogen from water.

Research on substituted polypyrazolylborate ligands could potentially lead to the development of useful compounds in the material sciences such as catalysis and metal ion extraction. A wide variety of substituents can be introduced to the pyrazole rings that modify the properties and reactivity of the complexes. Synthesis of 4-cyano-3-tolylpyrazole followed by the formation of a corresponding thallium(I) complex could allow one to examine the Tl-N bond length. When compared with other related complexes such as TlBpt-Bu, 4CN and TlBpPh, 4CN, the Tl-N bond length in the synthesized complex will help determine the effect of the new substituent.

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Metal tetrapyrroles represent a large class of earth-abundant catalysts but are limited to naturally-occurring combinations. Chelatase enzymes are responsible for the catalyzed metal insertion into a specific tetrapyrrole. CfbA is a class II chelatase from Archaeaglobis fulgidus that catalyzes the insertion of nickel into sirohydrochlorin to give rise to Coenzyme F430 required for methanogensis. This archaeal chelatase was used to study the substrate scope of divalent metals and tetrapyrroles to probe various metal tetrapyrrole combinations. A spectroscopic study established that the CfbA is capable of binding to cobalt and nickel, in addition to various tetrapyrroles. Magnetic circular dichroism (MCD) established that the metal binding site of CfbA contains a labile high spin 6-coordinate cobalt species that is ligated to nitrogen- or oxygen- atoms. The two residues involved in metal binding is likely His10 and His74. Tetrapyrrole binding resulted in a shift in energy. Computational studies have shown that resultant red-shift in energy is due to slight ruffling upon binding to CfbA. The enzymatic capabilities of CfbA was probed with various metal and tetrapyrrole combinations. The rate of insertion was significantly impacted by identity of the metal and the position of the propionate and acetate side chains on the rings of the tetrapyrrole as compared to sirohydrochlorin. Modifications to these side chains resulted in changes in ruffling. An increase in the ruffling resulted in a decrease in the rate of the reaction. These results have shown a significant expansion of the tetrapyrrole substrate scope. Additionally, detailed insights into the proposed chelatase mechanism have been established. IsdG serves as the primary enzyme involved in iron acquisition from heme in Staphylococcus aureus. The active site contains a tryptophan residue at 67 that is expected to be involved in heme ruffling. Trp67 was substituted with a smaller amino acid, phenylalanine to determine the role it plays in heme ruffling and degradation. The optical spectroscopic characterization of W67F IsdG resulted in changes to the geometric and electronic structure. The absorbance spectrum of W67F blue-shifted in the Q- and Soret bands indicating a change in the heme ruffling. MCD, VTVH and 1H NMR spectroscopy have shown that the electronic ground state is indicative of a 2Eg state, consistent with reduced heme ruffling. The degradation of heme by W67F IsdG resulted in the formation of biliverdin, a product seen in canonical HOs. These data suggest that Trp67 significantly influences heme ruffling and degradation. Additionally, W67F IsdG follows a unique reaction mechanism compared to IsdG. These data provide information on the development of a selective inhibitor of IsdG to prevent pathogenesis.

The medicinal uses of gold date as far back as 2500 B.C. in China. In modern times, gold has been used in the treatment of a number of different human diseases including rheumatoid arthritis, cancer, and viral infections. This dissertation will focus on the development of gold complexes for the purpose of selective inhibition of HIV NCp7, a 55 amino acid zinc finger protein with two Cys3His zinc binding domains. NCp7 is involved in a number of viral life cycle processes including activation of reverse transcription, integration, DNA recognition, RNA packaging, and formation of the viral envelope. The diversity in the roles of NCp7 across the viral life cycle make it a highly attractive target for chemical intervention. Ejection of the tetrahedrally coordinated zinc atoms, modification or deletion of the zinc coordinating amino acids, or modification or deletion of the “essential” tryptophan residue can result in the loss of viral infectivity. This is due to the inability of NCp7 to recognize its “natural” substrate – polynucleic acids. Previous studies have investigated the differences in the manner in which platinum(II), gold(I), and gold(III) complexes interact with NCp7. The platinum(II) complex [Pt(dien)(9-EtGua)]2+ interacts with the C-terminal zinc finger of NCp7 in a non-covalent manner, through a π-π stacking interaction between the platinated 9-EtGua and the “essential” tryptophan residue. The isostructural and isoelectronic complex [Au(dien)(9-EtGua)]3+ ejects the tetrahedrally coordinated zinc atom and replaces it with a gold atom, forming “gold fingers”. This result is consistent with the interactions of the gold(I) complex [(PPh3)Au(9-EtGua)]+. In order to complete the series of isoelectronic and isostructural platinum(II), palladium(II), and gold(III) complexes with N-heterocyclic ligands and diethylenetriamine chelates, the complexes [Au(dien)(1-MeCyt)]3+ and [Au(N-Medien)(1-MeCyt)]3+ were synthesized. These complexes were found to dimerize the C-terminal zinc finger once the central zinc atom is ejected. This is likely the result of a charge transfer from the 1-methylcytosine ligand to the tryptophan residue, and is a product that was not seen as a result of interaction with the previously published 4-dimethylaminopyridine and 9-ethylguanine analogs. The 1-methylcytosine complexes also stabilize the gold(III) oxidation state and associate with N-acetyltryptophan in a manner consistent with the previously studied gold(III) analogs. Finally, in order to address concerns arising from the inner filter effect, a proof of concept study using 1H-NMR spectroscopy was utilized to show that the complex [Au(dien)(1-MeCyt)]3+ likely has a lower association constant with N-acetyltryptophan than the value determined by fluorescence quenching. The impact of the incorporation of additional steric hindrance on the gold(III) chelate was studied using the di-(2-picolyl)amine ligand. The gold(III) chlorides incorporating this ligand and the centrally methylated analog were found to eject zinc from the C-terminal zinc finger of NCp7, and the electronegativity differences between the gold(III) and platinum(II) metal centers were highlighted. The attempts to incorporate an N-heterocyclic ligand into these complexes were unsuccessful due to the steric and electronic demands of the chelate. The use of an organometallic chelating ligand led to the investigation of the ability of gold(III) complexes to catalyze the arylation of zinc-coordinating cysteine residues. The complex [AuCl2(dampa)], which had been formerly investigated as a chemotherapeutic agent due to its structural similarities to cisplatin, was found to arylate N-acetylcysteine, glutathione, and NCp7. The arylation was not found to be dependent on the cis- chloride ligand, as blocking that site with the ligand triphenylphosphine did not prevent the arylation of NCp7. The X-Ray crystal structure of the complex [AuCl(dampa)(PPh3)](PF6) was also solved. Using the advancement of the knowledge of how the electronic and structural properties of gold(III) complexes described herein impact interactions with NCp7, it is possible that a coordination complex that is a selective inhibitor of NCp7 may eventually be developed.

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