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This dissertation presents the development of a synthetic strategy to produce various spiroligomer-based macrocycles that bridge the gap between organic molecules and small proteins. “Spiroligomers” (formerly known as “bis-peptides”) are a class of molecules produced by the assembly of “bis-amino acids”, molecules containing two amino acid regions on a single cyclic core. Each bis-amino acid is connected through pairs of amide bonds to form a diketopiperazine consequently eliminating single bond rotation and, therefore, avoids the complicated folding process common to the field of peptidomimetics. Spiroligomers are shape-programmable since the three-dimensional structure is controlled by the stereochemistry of the bis-amino acid monomers used in the synthesis, the connectivity of the monomers, and the number of monomers used. Furthermore, bis-amino acids can contain additional functional groups attached to multiple locations on the monomer which allows each spiroligomer, once synthesized, the ability to display these functional groups in predictable three-dimensional coordinates, with respect to each other. The synthesis of large spiroligomer-based structures requires the production of large amounts of bis-amino acid monomers. To this end, the scale of the synthesis of proline-based bis-amino acids from inexpensive trans-4-hydroxy-L-proline has been increased roughly 5-fold with respect to the previously published method. In addition to the time and solvent savings as a result of increasing the scale, the synthetic steps have been altered with considerations to ensure the production takes place in a convenient and environmentally friendly manner. Additionally, the desire to synthesize large spiroligomer-based structures means that the synthesis of each spiroligomer fragment must be as efficient and high-yielding as possible. To achieve this goal, a new synthetic approach to highly functionalized spiroligomers on solid support has been developed that results in increased yields relative to previously published methods. This new approach makes use of a protecting group, para-nitrobenzyl carbamate, which has not previously been incorporated in bis-amino acids as well as a pentafluorophenol ester activation strategy that also has not been in the synthesis of spiroligomers. Finally, an extendable synthetic route to spiroligomer-based macrocycles has been developed and representative macrocycles have been synthesized. This approach uses solid support to assemble multiple spiroligomers together through amino acids linkers before being cyclized in solution at dilute concentration to yield the desired macrocycles. Minimal functionality was included in the representative macrocycles to simplify structural information, confirmed by NMR and other means, and the macrocyclic structures were further investigated for host-guest activity using fluorescent, solvatochromic dyes. / Chemistry

This thesis research presents the synthesis and first application of bis-amino acid-based spiroligomers towards the development of organocatalysis, from small molecules to moderate size spiroligomers, and to macromolecules. By synthesizing a toolbox of cyclic monomers called "bis-amino acids", the Schafmeister group has developed an approach to construct both small and macromolecules named "Spiroligomers". These molecules arrange catalytic functional groups in a shape-persistent and programmable backbone. Unlike proteins and small peptides, spiroligomers do not fold; rather, their polycyclic backbone structures are controlled by the sequence and stereochemistry of the component monomers. Firstly, we demonstrated a structure/catalytic activity relationship together with computational modeling that suggests that a specific hydrophobic interaction between the modified pro4 catalyst and the aldehyde substrate is responsible for an observed rate enhancement in the aldol reaction. For the moderate size molecules, several spiroligomer libraries were prepared through solid phase or solution phase synthesis and screened for either the alcohol kinetic resolution reaction or the aldol reaction. The poor activity and selectivity suggest that the scaffolds involved cannot create the necessary chiral environment for asymmetric catalysis. Finally, a synthetic method of macromolecules using cross metathesis coupling was developed and a series of tetra-functionalized macrocyclic spiroligomers were synthesized. Three of these macromolecules were examined as asymmetric catalysts in the aldol reaction and gave moderate activity and selectivity. The NMR analysis of these macromolecules indicates their dynamic nature. As the first application of bis-amino acid based macromolecules in organocatalysis area, although these catalysts only generated moderate activity and selectivity, they provided evidence that changing the configuration of one stereocenter of the fourteen available within these macromolecules can alter the selectivity. This synthetic methodology also provides an effective way to create more complicated pocket like spiroligomer macromolecules for the future applications in catalysis and molecular recognition. / Chemistry

The two projects described in this dissertation demonstrate the wide utility of noble metal N-heterocyclic carbene (NHC) complexes. The first project details the design of iridium NHC amino acid complexes for asymmetric transfer hydrogenation (ATH) of prochiral ketones. Iridium(I) bis-NHC complexes were found to undergo oxidative addition with a variety of alpha-amino acids, generating chiral iridium(III) complexes of the form Ir(NHC)2(aa)(H)(X) (aa = amino acid, X = halide). The complexes were screened for ATH of aryl and alkyl ketones, and optimization studies found enantioselectivity in this system was highly sensitive to the reaction temperature, NHC ligand, and amino acid. Incorporation of secondary amino acids was essential to enantioselectivity. Aryl ketones were reduced in high conversion and enantioselectivity when employing the Ir(IMe)2(L-Pro)(H)(I) catalyst in isopropyl alcohol, in some cases giving over 90% ee of the alcohol products. Density functional theory calculations were conducted in order to gain insight into the active catalytic species, and the results suggest that the high enantioselectivity of this system primarily arises from steric effects. The second project details the design of rhodium and iridium NHC piano-stool complexes featuring derivatized tetramethylcyclopentadienyl ligands (Cp*R, R = alkyl or aryl substituent) for antimicrobial applications. Complexes of the form (Cp*R)M(NHC)Cl2 (M = Rh or Ir) were synthesized by transmetallation of the NHC ligand using silver(I) oxide in the presence of the desired noble metal Cp*R dimer. The complexes were screened for biological activity against various bacteria, yeast, and fungi. Many of these compounds were highly active against Mycobacterium smegmatis, displaying minimum inhibitory concentrations (MICs) as low at 0.25 microgram per mL. Analysis of structure-activity relationships found that incorporation of the NHC ligand greatly enhances the antimicrobial properties of rhodium and iridium piano-stool complexes, more so than previously investigated diamine, amino acid, or beta-diketonato ligands. Cytotoxicity studies on one of the rhodium NHC complexes showed this compound was nontoxic towards mammalian cells at low concentrations, which strengthens the potential of these types of compounds as viable drug candidates. / Doctor of Philosophy / This dissertation describes two practical applications of a series of complexes featuring the noble metals rhodium and iridium. In all of these complexes, the metal center is bonded to one or two groups known as N-heterocyclic carbenes (NHCs). The most common structural variant of NHCs are five-membered rings. The metal is usually bonded to a carbon atom on these rings, which is flanked by two nitrogen atoms. Noble metal complexes containing NHCs are widely investigated in contemporary chemical literature for a variety of reactions, primarily because noble metals form exceptionally strong bonds with NHCs, making these complexes very stable. N-Heterocyclic carbene compounds are also fairly easy to synthesize and structurally modify, which allows fine-tuning for specific applications. The first project in this dissertation employed iridium NHC amino acid complexes for the selective production of alcohols, meaning only one structure of the alcohol product is favorably generated. This is an important transformation in the chemical and pharmaceutical industries, which often require the synthesis of highly pure products. These complexes were found to be quite successful for this application on a range of model substrates, in some cases generating as high as 95% of one alcohol product over the other. Product selectivity was found to depend on the specific structure of the NHC compound. The second project investigated the antimicrobial properties of rhodium and iridium NHC complexes. In recent years, the growing threat of antimicrobial resistance against traditional pharmaceuticals has led to an interest in the development of metal-based drugs, which may allow for metal-specific mechanisms of drug action that are not possible for commonly employed antimicrobial agents. These NHC complexes were screened for biological activity against various bacteria, yeast, and fungi. Many of the complexes displayed high activity against Mycobacterium smegmatis, comparable to those displayed by other clinical drugs such as ampicillin or streptomycin. These results were highly encouraging, as Mycobacterium smegmatis often serves as a model to study other mycobacteria.

Hyaloperonospora arabidopsidis (Hpa) is a naturally occurring oomycete pathogen on Arabidopsis thaliana. It is related to downy mildews of economically important crops such as cabbage, kale and broccoli, belonging to the Brassicaceae family. Downy mildew pathogens are obligate biotrophs that extract nutrients exclusively from living plant cells. As a part of its obligate biotrophy lifestyle, Hpa has lost the ability to assimilate inorganic nitrogen and sulfur. It thus has to acquire these nutrients from the host in an organic form; possibly amino acids. Using a reverse genetic approach, I was able to identify two host amino acid transporters that are up-regulated during Hpa infection: AAP3 and AAP6. Both of these transporters are localized in the vasculature of the plant, AAP3 mostly in the root, and AAP6 in the roots and shoots. Using transgenic lines of Arabidopsis containing transcriptional and translational reporter fusion constructs for these genes, I found that AAP3 displays increased mRNA accumulation which is attributable to an increased promoter activity in regions of shoot tissue colonized by Hpa. On the other hand, AAP6 displays a mild increase in mRNA accumulation under Hpa infection, but the induction becomes more prominent at the protein level as seen by fluorescence from GFP fused to AAP6. Surprisingly, null mutants of AAP3 did not impact Hpa growth whereas null mutants of AAP6 made the plant more susceptible to Hpa. Furthermore, aap6 mutants accumulate fewer free amino acids in the phloem compared to wild-type plants when infected with Hpa. Together, these results suggest that AAP6 acts a nutritional starvation gene for the pathogen and hence aids the plant during infection. While we now know more about AAP3's regulation during infection, its function remains to be elucidated. To successfully colonize a plant, a pathogen must be able to achieve both suppression of plant immunity and acquisition of nutrients from the plant host. While the former has been well studied, research on the latter is sparse. This work was a step in the direction to increase our understanding of potential players in nutrient acquisition by pathogens. / Doctor of Philosophy / A key aspect of achieving and maintaining food security is sustainable agricultural production. This is endangered by plant diseases that lead to large losses in crop production. All plant pathogens have to acquire food and nutrients from the plants they infect. Understanding how they acquire nutrients from the plant at a molecular level can give us insight into potential methods to prevent this and hence reduce the impact of plant diseases. One such nutrient is nitrogen. Nitrogen is essential to all of an organism’s cellular and metabolic processes. Organisms utilize nitrogen by converting it from inorganic forms such as nitrates to organic forms such as amino acids. Some plant pathogens, such as Hyaloperonospora arabidopsidis (Hpa), which causes downy mildew disease on the model plant Arabidopsis, complete their entire life cycle on a living plant. They are also unable to convert the inorganic nitrogen to organic forms and hence depend on acquiring organic forms of nitrogen from the plant. Thus, it is important to understand how they acquire amino acids from the plant. Plants use amino acid transporters that serve as a siphon or a pump in moving amino acids from one region of the plant to another. It is possible that pathogens manipulate plant’s amino acid transporters to move amino acids towards the infection site while, at the same time, plants might use another set of transporters to move amino acids away from the pathogen. This work was an attempt at understanding this potential role of plant amino acid transporters in plant-pathogen interactions using the model system of Hpa and Arabidopsis.

The FeMo cofactor is one of two types of prosthetic group found in the larger of the two nitrogenase component proteins, called the MoFe protein, and it is strongly implicated as the substrate binding and reduction site. The glutamine-191 residue in the Alpha-subunit of the MoFe protein of A. vinelandii nitrogenase was targeted for substitution because its side chain is involved in a hydrogen-bond network from one of the terminal carboxylates of the homocitrate component of FeMo cofactor through to the backbone NH of Alpha Gly-61, which is adjacent to Alpha Cys-62, which ligates to the P cluster (the second type of prosthetic group in the MoFe protein). A variety of altered MoFe proteins produced by the A. vinelandii mutant strains, namely the Alpha Pro-191, Alpha Ser-191, Alpha Thr-191, Alpha His-191, Alpha Glu-191, and Alpha Arg-191 altered MoFe proteins, have been purified to homogeneity and the catalytic properties of these altered MoFe proteins have been compared to those of wild type MoFe protein. Unlike wild type, the six altered MoFe proteins have decreased catalytic activity on substrate reduction and exhibited H2 evolution that was partially inhibited by added CO. Moreover, some of altered MoFe proteins with lower specific activity for the C2H4 production can produce C2H6 from C2H2. The results from the pH and activity studies indicate that the substitutions on the MoFe protein have an effect on the contribution of the responsible acid-base group(s) involved in proton transfer for H+- and C2H2-reduction. Furthermore, the inhibition by CO of hydrogen evolution by these altered MoFe proteins is likely from a lowering of the rate of both electron and proton transfer to the H+- reduction site(s). Some altered MoFe proteins but not wild type MoFe protein can produce C2H6 from C2H2. This observation suggested a lower apparent binding affinity for C2H2 and a slower proton transfer to C2H2 reduction with these altered MoFe proteins, which allow the intermediate to stay at the site longer and be further reduced by two electrons and two protons to give C2H6. These changes in the biochemical properties of these altered MoFe proteins indicate that the Alpha Gln-191 residue is intimately involved in substrate binding and reduction including proton delivery to substrate. / Ph. D.

Amino acids are necessary for protein synthesis and specialized metabolism in plants. Yet very little is known about how plants sense and regulate when and where to allocate amino acids to meet the demand for nitrogen in growing tissues. In particular, while characterized in yeast and mammals, no amino acid sensor has been identified in plants. Amino Acid Permease 1 (AAP1) has been previously characterized and was shown to mediate amino acid uptake from the soil. aap1 knockout plants and several EMS mutants affected in AAP1 sequence display enhanced tolerance to toxic concentrations of amino acids. Yet, two of the corresponding variant proteins appear to be functional transporters, effectively dissociating amino acid transport and phenotype. To understand this apparent discrepancy, I precisely studied AAP1 localization of expression at the plant and cellular level, and in specific tissue types of the root where AAP1 function is required for the tolerance phenotype and the amino acid uptake activity. I showed that AAP1 protein is present in the endoplasmic reticulum of the cortex in wild type plants Yet, its ectopic expression in root tip and phloem increased amino acid uptake, while expression in cortex could not. This and other of my results do not support the current model of AAP1 functioning in amino acid uptake by the root. I propose that the main effect of mutations in AAP1 is a disturbance in amino acid metabolism, possibly triggered by altered amino acid sensing. In this new model, AAP1 would be necessary for sensing amino acid status of cortex cells, possibly in the endoplasmic reticulum, and adjust amino acid metabolic activity and uptake to current availability. In effect, disruption of the sensing function, either by complete loss of AAP1 function (knockout) or by uncoupling the transport and sensing function (EMS mutants), would lead to the various characteristics of the phenotype of the aap1 mutants I observed. My main hypothesis is that AAP1 is a transporter endowed with sensing function, i.e., an amino acid transceptor. / Doctor of Philosophy / Changing environments create challenges for plants to grow under harsher, nutrient limiting conditions. Nitrogen is an essential nutrient for plant growth, used for the synthesis of amino acids and other nitrogen-containing metabolites. Amino acids are necessary for protein synthesis and other specialized metabolism – being targets for manipulation for improving agronomic traits. Protein content is a complex trait that involves many genes, possibly including amino acid transporters. In addition, the amount of nitrogen needed by and available to the plant increases or decreases depending on the environment conditions. How plants control nitrogen need and use at the molecular level is not well understood. The data presented here challenge a current model and I report how a protein (AAP1) involved in the acquisition of amino acids from the soil provides regulatory control over these processes. . This valuable information is useful for better understanding how plants use nitrogen and more precise breeding methods can be used to improve traits, such as protein content in agronomically important crops.

Time-averaging, the mixing of fossils of different ages within a single bed, defines the limit of temporal resolution of the fossil record. Quantitative estimates of this resolution threshold have not been acquired for any group other than mollusks. This study provides the first quantitative estimates of time-averaging for brachiopods, extending our understanding of intrinsic, or group specific controls on this process. Estimates were obtained by direct dating of individual terebratulid brachiopod shells Bouchardia rosea (Mawe) collected from modern surficial shelly accumulations in the Southeast Brazilian Bight (SW Atlantic). Using amino acid racemization dating calibrated with radiocarbon, 82 individual brachiopod shells, collected from four nearshore localities, were dated. The shells vary in age from modern to 3000 years, standard deviation = 680 years. The age distribution is significantly right-skewed (K3=2.48). At 50-year resolution, the temporal completeness is 75% for the last 1000 years and declines to 20% completeness for 1000-2000 yr. BP. Preservational quality (taphonomy) of modern (<50 yr.) shells is statistically indistinguishable from that of older shells, demonstrating that shell taphonomy is not a good predictor of within-assemblage relative age. These results conform to previously published results for mollusks. Therefore, brachiopods can show considerable time-averaging and this time-averaging can be on a scale similar to aragonitic mollusks despite the apparent lack of robustness of calcitic brachiopod shells. This suggests that the brachiopod fossil record can be notably time-averaged, but estimates of this mixing cannot be reliably deciphered from the taphonomic condition of shells. / Master of Science

This dissertation describes the design and synthesis of a series of half-sandwich amino acid complexes of the form), (aa = α-amino carboxylate), and their utility as asymmetric transfer hydrogenation catalysts of ketones. Variation of the metal center, the n-ring, and the aa was used to tune these systems for specific sets of ketones. Upon reaction with homochiral]s, the ligand environment in all of these complexes is pseudotetrahedral, leading to stereogenic metal ions (SM, RM). The addition of another stereogenic center from the amino acid ligand (the carbon, RC or SC;glycine) gives rise to two pairs of diastereomeric complexes. / Ph. D.

This dissertation describes the synthesis and antimicrobial use of a series of half-sandwich Ir(III), Rh(III), Co(III) amino acid and ethylenediamine complexes. This investigation focuses on the formulation (ηn-arene)M(L)X, (L = ethylenediamine or α-amino carboxylate), (M= Ir, Rh, Ru, Co). Arene, Ligand and metal center variations were designed to tailor antimicrobial activity specific for each organism studied (Staphylococcus aureus or Mycobacteria). Each of the D/L-amino acids formed a diasteromeric complex with chiral centers on both the metal center and amino acid ligand. The unique chirality of each center elicits different antimicrobial activity against the Mycobacteria studied. The metal center (M), arene ligand (ηn-arene), and amino acid (aa), were changed independently and studied for the antimicrobial activity. In a similar fashion, each of the complexes modified with ethylenediamine and diamine derivatives were studied for their antimicrobial activity against S.aureus. All complexes were synthesized,characterized by nuclear magnetic resonance (NMR), high-resolution mass spectroscopy (HRMS), single-crystal X-ray diffraction, and elemental analysis. During the course of this work it was found that the amino acid complexes with all metal centers were specific for antimicrobial activity against all types of Mycobacteria, while the diamine derivatives were active against different strains of S.aureus. Acitvity was measured to be as low as 2 ug/mL respectively depending on the complex used. A structure activity relationship was developed to determine what combinations of ligand, metal and arene were necessary to achieve the highest antimicrobial activity. The optimal arene R-chain length for CpR was determined to be R=hexyl for all complexes studied. The most active amino acidcomplex was determined to be that of L-phenylglycine for Mycobacteria, the cis-1,2-diaminocyclohexane complex is the most active ligand against S.aureus. Each metal center had similar activity levels. Toxicological studies were performed to test their viablity to be used in mammalian systems. The complexes with the highest activity were studied against several mammailan cell lines and revealed that mammailan cells were undergoing normal cellular processes at up to 40 times the minimal inhibitory concentration (MIC). A study of the MOA or mechanism of action revealed the ability of the amino acid complexes to affect the peptidyl transferase region on the 23s ribosomal subunit of M.smegmatis. This was accomplished by isolating resistant strains of M.smegmatis towards the most effective complex (Cp*hexyl)Ir(L-phenylglycine)-Cl. Cross drug resistance of these mutants was shown with clarithromycin. The DNA of the 23s ribosomal subunit was sequenced revealing a deletion/insertion mutation within domain V (bases 2057-2058). / Ph. D.