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In part I of this thesis are described some studies toward the total synthesis of tetracycline. Attempts to transform the key aromatic compounds, terrarubein and 6-methylpretetramid into actual or hypothetical biosynthetic intermediates, failed to yield useful non-aromatic products. However, several of the transformations further along the route have been achieved. Thus, the conversion of 12a-deoxy-5a,6-anhydrotetracycline into 7-chloro-5a,6-anhydrotetracycline was successfully carried out. In a different approach it was attempted to convert the synthetic tetracycline derivative 7-chloro-4-dedimethylamino-5a,6-anhydrotetracycline to 7-chloro-5a,6-anhydrotetracycline via a series of bromination-aminatipn experiments. Chromatographic evidence is presented for the formation, in trace amounts, of 7-chloro-5a,6-anhydro-4-epi-tetracycline. Part II is concerned with the study of the possible precursor activity of triacetic acid lactone, a potential polyketomethylene chain intermediate in the biosynthesis of aromatic compounds. (3,5-¹⁴ C) Triacetic acid lactone was fed to P. patulum and labelled griseofulvin was isolated and degraded. It was found that radioactivity is incorporated into griseofulvin a non-specific way. In one strain of the mould used two new metabolites were found as a result of the addition of triacetic acid lactone. Addition of triacetic acid lactone to the mould also causes an unexplained enhancement of metabolite formation. / Science, Faculty of / Chemistry, Department of / Graduate

The work described in this thesis is divided into four sections: 1. The electrochemical reduction of fluorocarbon derivatives has been investigated. A number of systems have been studied analytically (using cyclic volt amine try) ; whilst preparatively a range of compounds have been synthesised, including semi-conducting polymers and four-membered perfluorocyclic products. 2. The use of sodium amalgam as an electromimetic medium to facilitate reduction of various fluorocarbon substrates has been studied. A series of volatile cyclic and acyclic F-dienes have been prepared from F-alkenes in good yield and conversion. The chemistry of these F-dienes is then described: 3. Both mono- and bi- functional nucleophiles have been reacted, giving a range of novel substitution products. 4. A number of free radical and cycloaddition reactions have been attempted without success. However, the complexation of decamethylferrocene as a metallocene one electron donor, with various F-alkenes of low reduction potential, has allowed a radical anion of a perfluorocyclic-diene to be stabilized and fully characterized for the first time.

My research involved in two different areas, development of novel glycosylation methodology and scope in oligosaccharide synthesis. A new scaffold for antibiotic development targeting the bacterial cell wall: Total synthesis of Albocycline and its analogs to see the mechanism of action in cell wall biosynthesis. Developed novel gem-dimethyl analogs of Fraser-Reid’s NPGs from 3,3-dimethyl 4-pentenol and 2,2-dimethyl 4-pentenol. These donors are stable toward acidic and basic conditions, which makes them step-efficient when compared to other glycosylating agents. The scope and reactivity of 3,3-dimethyl 4-pentenyl glycosides of glucose, mannose, galactose, and N-acetylglucosamine have been studied extensively for oligosaccharide synthesis. The donors are readily prepared from commercial starting materials and both glycosylation and hydrolysis yields are in the synthetically useful in oligosaccharide synthesis. NSMD methodology introduced a key step in albocycline synthesis, where (‒)-albocycline has great biological activity against “superbug” methicillin-resistant Staphylococcus aureus (MRSA). We hypothesize that albocycline inhibits the first committed step in bacterial cell wall biosynthesis. We have successfully completed two generation syntheses of albocycline. Vinylogous aldol on the left-handed fragment, aldehyde to get selectively up alcohol at the C-8 position using Davis-Ellman sulfinylimine chemistry and then oxidation with Davis oxaziridine to access requisite stereochemistry at C-4 alcohol followed by Horner-Wadsworth-Emmons to access seco-acid. Finally, a Keck macrolactonization reaction provided access to desired (‒)-Albocycline. / Chemistry

Structural and mechanistic complexities of copper-dioxygen systems have attracted much attention in the field of bioinorganic chemistry, both in model systems and trapped protein intermediates. The research presented herein is focused on model and naturally occurring metallopeptide systems, from its design to catalysis. Copper is used as the coordinating metal ion, with cobalt and zinc as probes for metal binding. The bioinorganic chemistry of copper proteins and its coordination and spectroscopic properties are briefly discussed in chapter 1. The next two chapters are centered on the de novo design of a minimalistic metallopeptide system with an amino acid sequence of RHHPPHHE. Structural characterization of the peptide by means of CD and NMR spectroscopy techniques are presented in chapter 2, suggesting a characteristic beta-turn structure in its apo and di-metal bound form. The designed metallopeptide exhibits catecholase activity, which is presented in chapter 3. The data suggest the presence of two mononuclear copper active sites, exhibiting specificity towards the oxidation of catecholamine substrates. Similarly, the catecholase activity has been previously observed in copper complexes of Alzheimer's disease related peptide beta-amyloid, exhibiting metal-centered redox chemistry. The metallo-(beta-amyloid); complexes are the hallmark Alzheimer's disease and have been attributed to the generation of reactive oxygen species causing oxidative stress. Thus, inhibition of the observed oxidative activities was investigated. Probing the role of phosphate moieties in various compounds as potential inhibitors against the induced oxidative stress is presented in chapter 4. The phosphate analogs of the studied compounds exhibit more pronounced potency, where mutation of the beta amyloid peptide at Arg-5 and Lys-16 give insight into the interactions of the side chains of Arg and Lys with the phosphate moiety. 31P NMR relaxation studies further support the binding/interaction of phosphate with the Cu(II)-(beta-amyloid); complexes. The correlation of phosphate moiety binding/activity will allow for the design of more potent inhibitors toward the Cu(II)-(beta-amyloid); induced oxidative stress.

The drive to find reliable sources of fuel that follow our green concerns and reduce our dependence on foreign sources of fossil fuels has pushed exploration and recovery of natural gas from within the United States to a top priority. Earthquakes generated from the use of hydraulic fracturing techniques and/or use of high pressure injection wells are occurring at an alarming rate due to increases in hydrocarbon exploration and recovery. While the link between earthquakes and hydrocarbon production is still uncertain, earthquake induced changes to groundwater chemistry are clear. Yet it has not been determined if repetitive, smaller earthquakes, i.e. earthquakes with magnitudes less than Mw<4.5, can result in similar disturbances to water chemistry as the more significant events have been proven to cause. Two known earthquake swarms, each having repetitive, small earthquake events, occurred in an intraplate setting in Faulkner County, Arkansas. Testing for groundwater chemical changes related to the timing of earthquake events and total energy released show that small earthquakes indeed create changes to groundwater chemistry most probably due to fluid intrusion from deep, chloride, calcium, and magnesium rich waters. The reduction of the United States dependence on foreign sources or finding green sources of fuel should not be the only mitigating factor for our decisions concerning our natural resources.

The thesis entitled ‘Studies on the Chemistry of Carbonates and Carbamates’ comprises of seven chapters. Chapter 1 The reactivity of propargyloxycarbonyl (Poc) derivatives of amines and alcohols with various sulphur nucleophiles is addressed in this chapter. The chapter is divided into three different parts. Part 1: The difference in reactivity of propargyloxycarbonyl (Poc) derivatives of amines and alcohols with benzyltriethylammonium tetrathiomolybdate [(PhCH2NEt3)2MoS4, 1] is studied in detail and the results are discussed. It has been shown that amino alcohols can be protected as their diPoc derivatives using 2 equiv of propargyloxycarbonyl chloride (2). The selective deprotection of the O-Poc group using 1 equiv of 1 without affecting the N-Poc group is achieved (Scheme 1). Scheme 1 Part 2: The reactivity of propargyloxycarbonyl derivatives of various alcohols, phenols and primary and secondary amines with benzyltriethylammonium tetrathiomolybdate (1) is compared with the reactivity of these Poc derivatives with other sulphur nucleophiles such as sodium thiophenoxide, lithium sulphide, hydrogen sulphide and ammonium sulphide. The study reveals that tetrathiomolybdate (1) is the best sulphur nucleophile for the deprotection of Poc group. Poc derivatives of primary amines cyclized to the corresponding 4-methylene-2-oxazolidinones when treated with other sulphur nucleophiles (Scheme 2). Scheme 2 Part 3: The reaction between different propargyloxycarbonyl derivatives of alcohols and benzyltriethylammonium tetrathiomolybdate (1) is studied. It is found that propargyloxycarbonyl derivatives can be made more reactive towards tetrathiomolybdate by substituting the propargyl system with electron withdrawing substituents. Chapter 2 The application of propargyloxycarbonyl group for the protection of the side chain hydroxyl groups of serine, threonine and tyrosine is discussed. The O-Poc derivatives are shown to be stable to a variety of acidic and basic conditions and the applications of these derivatives in solution phase peptide synthesis is addressed. The easy and effective deprotection of the O-Poc group provides a new strategy for the synthesis of peptides bearing the hydroxy amino acid residues: serine, threonine and tyrosine. Scheme 3 Chapter 3 Development of a novel C2-symmetric protecting group for amines and amino acids is described in this chapter. But-2-ynyl-1,4-bisoxycarbonyl chloride (BbcCl, 3) is synthesized from 1,4-dihydroxybut-2-yne and used as a reagent for protecting amines as biscarbamates (Scheme 4). These biscarbamates (Bbc derivatives) are deblocked using benzyltriethylammonium tetrathiomolybdate (1) to get the amines back. Scheme 4 The orthogonal stability of the Bbc group with Boc, Cbz and Fmoc groups is established. It is also shown that Bbc group can be deblocked to the corresponding amines using resin-bound tetrathiomolybdate. The application of Bbc protected amino acids in solution phase peptide synthesis is demonstrated (Scheme 5). Scheme 5 Chapter 4 The simultaneous protection and activation of amino acids using various pentafluorophenyl carbonates is described in two parts. Part 1: A very efficient and high yielding method for the simultaneous protection of the amino group and activation of carboxylic acid group using propargyl pentafluorophenyl carbonate (PocOPfp, 4) is discussed. Treating amino acids with 2 equiv of 4 protects the amino group as a propargyl carbamate and activates the carboxylic acid group as a pentafluorophenyl ester (Scheme 6). Scheme 6 Part 2: The generality of the methodology developed for the simultaneous protection and activation of amino acids using PocOPfp (4) is studied with five different pentafluorophenyl carbonates viz. AlocOPfp, CbzOPfp, BocOPfp, EocOPfp and TrocOPfp. The studies reveal that the effectiveness of the methodology depends on the nature of the pentafluorophenyl carbonates and on the nature of the amino acids. Sterically bulky pentafluorophenyl carbonates such as BocOPfp reacted slowly with amino acids while electron deficient pentafluorophenyl carbonates such as TrocOPfp reacted faster and gave the N-protected active esters in very good yields. Amino acids bearing longer aliphatic side chains reacted better than the other amino acids. Chapter 5 The chapter describes results of the detailed studies on the base catalyzed cyclization of N-alkyl and N-aryl-O-propargyl carbamates to the corresponding 4-alkylidene-2-oxazolidinones. The effect of various bases and solvents on these cyclization reactions is studied systematically to design the most suitable conditions. The best results were obtained using catalytic amount of LiOH in DMF. The cyclization reactions of N-aryl-O-propargyl carbamates were faster than the cyclization of N-alkyl-O-propargyl carbamates. The effect of substitutions on the propargyl group in these reactions is studied by preparing various substituted propargyl carbamate derivatives from the corresponding amines and propargyl chloroformates (Scheme 7). Scheme 7 Chapter 6 An efficient procedure for the synthesis of dehydroalanine and dehydroamino butyric acid derivatives from the preformed carbonate derivatives of serine and threonine respectively, by treating with K2CO3 in DMF is discussed in this chapter. The reaction proceeds stereoselectively through a trans E2-elimination pathway to give only the Z-isomer of dehydroamino butyric acid derivatives from the carbonate derivatives of threonine. The methodology offers an easy access to dehydropeptides and proceeds without racemization of other stereogenic centers present in the peptide (Scheme 8). Scheme 8 Chapter 7 This chapter describes the use of propargyloxycarbonyl derivatives of lysine as an efficient tool for the synthesis of peptide conjugates using a click chemistry approach. The Cu(I) catalyzed cycloaddition reaction between azides and alkynes is employed in the synthesis of conjugates of lysine. Peptides bearing an Nε-Poc Lysine residue can be synthesized using traditional strategies and these peptides can be easily conjugated with azide derivatives of sugars and amino acids (Scheme 9). Scheme 9 The efficiency of the method is demonstrated by carrying out more than one click reaction in one pot using di and tri-propargyl derivatives of lysine. A dendritic core (6) is prepared from a tri-propargyl derivative (5) of lysine and an azide derived from leucine (Scheme 10). Scheme 10 The abbreviations used in the thesis are consistent with those reported in J. Org. Chem. 2007, 71, 23A. Less common abbreviations are defined, the first time they are mentioned in the thesis.

Gas phase molecular clusters present an ideal medium for observing factors that drive chemical reactions without outside interferences from excessive solvent molecules. Introducing an ion into the cluster promotes ion-molecule interactions that may manifest in a variety of non-covalent or even covalent binding motifs and are of significant importance in many fields including atmospheric and astronomical sciences. For instance, in outer space, molecules are subject to ionizing radiation where ion-molecule reactions become increasingly competitive to molecule-molecule interactions. To elucidate individual ion-molecule interaction information, mass spectrometry was used in conjunction with appropriate theoretical calculations. Three main categories of experiment were conducted in this dissertation. The first of which were thermochemical equilibrium measurements where an ion was introduced to an ion mobility drift cell wherein thermalizing collisions occur with helium buffer gas facilitating a reversible reaction with a neutral molecule allowing the standard changes in enthalpy and entropy to be determined. The second type of experiment was an ion mobility experiment where an ionized homo- or hetero-cluster was injected into the drift cell at specific conditions allowing the reduced mobility and collisional cross-section to be evaluated. Thirdly, kinetics measurements were taken following injection of an ion into the drift cell were an irreversible reaction ensued with the neutral species hindering equilibrium, but prompting rate constant assessment. Previous research has laid the groundwork for this dissertation as the results and discussion contained herein will build upon existing data while maintaining originality. For example, past work has given support for ion-molecule reactions involving precursor species such as acetylene and hydrogen cyanide to form more complex organics, perhaps leading to biologically relevant species. The chemical systems studied for this research are either ionized substituted benzenes like phenylacetylene and benzonitrile or polycyclic aromatic nitrogen-containing hydrocarbons like quinoline and quinoxaline interacting with a variety of neutral species. Hydrogen bonding and its many sub-sections are of the utmost importance to the kinds of reactions studied here. Past work has shown the tendency of organic radical cations to form conventional and unconventional ionic hydrogen bonds with gas phase solvents. Other non-covalent modes of interaction have also been detected in addition to the formation of covalently bound species. Gas phase reactions studied here will explore, via mass-selected ion mobility, reversible and irreversible reactions leading to binding enthalpy and entropy and rate constant determination, respectively, in addition to collisional cross-section determination.

Nous visons dans ce travail de thèse à développer une méthodologie de fonctionnalisation par chimie click des silices hybrides synthétisées par voie sol-gel. La réaction click de cycloaddition azoture-alcyne catalysée au cuivre (CuAAC) offre une tolérance exceptionnelle pour les fonctions organiques en plus de conversions très élevées. Dans cette optique, nous avons mis en œuvre en premier lieu des matériaux clickables à base d'organosilice pure (organosilice à mésoporosité périodique (PMO) et silsesquioxanes pontés (BS)) qui ont permis une conversion quasi-quantitative de greffage par CuAAC. Nous avons ensuite utilisé cette particularité pour contrôler les propriétés de surface des BS en modifiant leur caractère hydrophile/lipophile. Dans le second axe de travail, nous nous sommes intéressés à l'apport de la chimie click pour la préparation de nanoparticules mésoporeuses de silice multifonctionnelles, dites mécanisées, pour des systèmes à délivrance contrôlée de principes actifs. / The present work aims to develop a trustful methodology of functionalization for hybrid silica materials made by the sol-gel process using the copper-catalyzed alkyne-azide cycloaddition (CuAAC)Click reaction. This transformation can be highly useful in materials science thanks to its high conversions and the excellent functional group tolerance. In this prospect, we have synthesized fully clickable bridged silisesquioxanes and periodic mesoporous organosilica that show high extents of click grafting. CuAAC was then used for tailoring the surface of bridged silsesquioxane and fine-tuning the hydrophilic/lipophilic balance. Finally, the click reaction was used as an efficient way to obtain multiply functionalized mesoporous silica nanoparticles in order to make nanomachines for controlled delivery of cargo molecules.

<p dir="ltr">Mass spectrometry (MS) is a powerful and versatile technique that is useful for addressing a wide range of complex analytical challenges. In this work, mass spectrometry-based assays were developed to address issues relating to environmental contamination and for detecting analytes of interest to the defense industry. Chapter one is an overview of the history of mass spectrometry, the fundamental operation of a mass spectrometer, as well as, advancements in chromatographic separation and ionization methods. Chapter two focuses on the development of an assay that uses blow flies as environmental sensors of chemical weapon release. In that work, a liquid chromatography – tandem mass spectrometry (LC-MS/MS) method was developed to detect chemical warfare agent simulants and chemical warfare agent hydrolysis products in flies exposed to the chemicals in controlled feeding experiments. The work in chapter three describes the development of a surface enhanced Raman spectroscopy assay coupled to paper spray mass spectrometry for a more fieldable and environmentally friendly approach to detect organophosphorus compounds. Chapter four describes the development of a paper spray mass spectrometry assay for the detection and semi-quantitation of per- and polyfluoroalkyl substances in whole blood without sample cleanup or chromatographic separations. This method would be useful in detecting high levels of these carcinogenic compounds in individuals highly exposed via their occupations. The final chapter (chapter five) returns to using blow flies as environmental sensors, but this time to detect insensitive munitions in the environment. The work focuses on the development of two different liquid chromatography mass spectrometry methods for the detection of insensitive munitions, which are less shock sensitive explosives, and their transformation products in the environment. Controlled feeding experiments were also performed where flies were exposed to contaminated soil and water sources to show the feasibility of this method in a more realistic scenario. The projects detailed herein show the extensive range with which mass spectrometry can be used for the detection of harmful chemistries of environmental concern.</p>