This thesis describes synthetic applications of α-keto carbocations, which represent potentially useful, but poorly studied, reversed polarity equivalents of enolates. In the first chapter, a Ag(I) – mediated method for the nucleophilic displacement of α-halocarbonyl compounds to construct carbon-carbon bonds is described. The highly electrophilic nature of the putative α-keto carbocation intermediates enables the use of relatively unreactive nucleophiles in both intra- and intermolecular contexts. Such intermediates also present interesting opportunities for stereocontrol: our efforts to carry out diastereoselective additions to chiral α-keto carbocations are described. Oxazoles are an important class of heterocycles, and several syntheses are addressed in Chapter 2. Our approach to this class of compounds employs a TMSOTf mediated Ritter reaction to construct the carbon-nitrogen bond. Cycloaddition of 2-alkoxyoxazoles with alkynes presents a facile route for furan synthesis. The final chapter describes our attempts to apply anion-π interaction in organocatalysis. These interactions between anions and electron-deficient arenes have been characterized in some detail and have recently been applied in ion transport. Applications of prolinol-based secondary amines incorporating electron-deficient aromatic groups are described.

Cyclodextrins (CDs) are macrocycles composed of several glucose units bound through α-1,4 glycosidic linkages. They can be chemically modified to display functional groups on their primary or secondary rim. CDs display these groups in defined geometries ideally suited to bind biomacromolecules. Moreover, CDs have a hydrophobic cavity that allows them to form stable host-guest complexes with lipophilic molecules. This combination of functionality and guest binding ability makes CDs important scaffolds for the design of functional supramolecular systems. This thesis explored the interaction of heptakis-[6-deoxy-6-(2-aminoethylsulfanyl)]-β-cyclodextrin (1) with many hydrophobic guest molecules. The binding constants of CD host-guest interactions were measured using ITC and fluorometry-based approaches. These studies revealed 1 to form the highest affinity 1:1 cyclodextrin-guest complexes reported to date. This thesis then explored the use of CD inclusion complexes as biomacromolecular sensors. CD 1 and its derivatives were used to develop self-assembling sensors. First, a library of polycationic CDs with differing charge distribution was synthesized. The sensing motif was synthesized by covalently linking a quinolinium fluorophore to lithocholic acid (LCA). The CD-based binding motifs and the LCA-based sensing motif self-assemble through host-guest interactions (i.e. 1 binding to LCA displays a Ka = 5.52 × 107 M-1). These inclusion complexes were then used as an array of self-assembling sensors capable of differentiating between pure and contaminated samples of heparin (anticoagulant). To capitalize on the promise of CD 1 a new technique was explored to functionalize a single amine of 1. The technique relies on an S to N acyl transfer from a guest molecule to a CD host resulting in the mono-acylation of the host. The importance of the linker between the guest and the reactive acylating agent was fully explored. Furthermore, two CD probes are synthesized and are shown to display differential fluorescent responses with a small series of proteins.

Synthesizing proteins containing unnatural amino acids inserted at specific positions within the protein sequence has been a longstanding goal of biological chemists. This poses unique challenges, as aminoacyl tRNA synthetases, the enzymes responsible for protein synthesis, are highly specific. To overcome this, a lanthanum-catalyzed, biomimetic tRNA aminoacylation method has been developed(1). However, due to unproductive lanthanum coordination of ethyl phosphate, a reaction byproduct, a full equivalent of lanthanum must be added to each reaction. This may threaten the integrity of tRNA, as lanthanides are known to catalyze the hydrolysis of RNA (2, 3). Using uridine as a simplified tRNA mimic, magnesium, which is known to coordinate strongly with phosphate ions, has been utilized to optimize this reaction and increase the selectivity of lanthanum towards esterification. In the presence of magnesium, ester yield is substantially increased. In addition to this, optimal pH and buffer reaction conditions were determined.

The conjugate acid of pyridine had been found to catalyze decarboxylation of alpha-mandelylthiamin (MTh). It was proposed this occurs by association between the substrate and pyridinium ion in a pi-stacked complex prior to cleavage of the C-C bond. Despite the evidence for selective acid catalyzed decarboxylation of MTh with pyridine and its derivatives, the nature of proton transfer occuring after the C-C bond breaks and before the final products form had not been investigated. General base catalyzed deprotonation of hydroxybenzylthiamin (HBnTh) has been applied as a model for the reverse reaction of acid-catalyzed decarboxylation. Kinetic analysis of this process suggests the acceleration by a preassociated pyridinium ion and the product-determining step in the decarboxylation of MTh are facilitated by independent sequential proton transfers.

Hemoglobin-based oxygen carriers (HBOCs) are of great interest for their potential as a safer alternative to blood transfusions. To overcome the vasoactivity associated with small HBOCs, our group is interested in connecting two hemoglobin tetramers together, forming “bis-tetramers”. Bis-tetramers have previously been synthesized by our group, but yield and purity of the resulting solutions have been low and hindered their usefulness for trials. A new cross-linker was designed in an attempt to improve yield. This thesis describes the synthesis of an acyl phosphate cross-linker N-[bis(sodium methyl phosphate)isophthalyl]-4-azidomethylbenzoate (5), its modification of hemoglobin and subsequent purification attempts of the resulting solution. Cross-linker 5 was found to be selective to β-β-crosslinking and produced singly modified subunits as byproducts. Attempts to purify the resulting reaction mixture by heating resulted in the decomposition of the azide group on the cross-linker, which was critical for the coupling step. Efforts to overcome this problem were unsuccessful.

Hemoglobin-based oxygen carriers (HBOCs) are of great interest for their potential as a safer alternative to blood transfusions. To overcome the vasoactivity associated with small HBOCs, our group is interested in connecting two hemoglobin tetramers together, forming “bis-tetramers”. Bis-tetramers have previously been synthesized by our group, but yield and purity of the resulting solutions have been low and hindered their usefulness for trials. A new cross-linker was designed in an attempt to improve yield. This thesis describes the synthesis of an acyl phosphate cross-linker N-[bis(sodium methyl phosphate)isophthalyl]-4-azidomethylbenzoate (5), its modification of hemoglobin and subsequent purification attempts of the resulting solution. Cross-linker 5 was found to be selective to β-β-crosslinking and produced singly modified subunits as byproducts. Attempts to purify the resulting reaction mixture by heating resulted in the decomposition of the azide group on the cross-linker, which was critical for the coupling step. Efforts to overcome this problem were unsuccessful.

Photoisomerization of azobenzene can be used to reversibly photo-control peptide and protein structure, thereby offering the potential to probe peptide and protein function directly in living systems. Most azobenzene photo-switches to date however require the use of UV light, which suffers from poor tissue penetration and can lead to cell damage. In addition, the unknown stability of azobenzene photo-switches within the reducing intracellular environment has limited these switches to extracellular applications. The ability to red-shift the photo-switching wavelength and tune the thermal cis-to-trans rate independently from one another has been a central challenge. Incorporating a piperazine-like moiety at the 4,4′-para positions red-shifts the π-π* band of an azobenzene-based cross-linker such that trans-to-cis photoisomerization can be triggered with blue light. Accompanying this red-shift was a faster cis-to-trans thermal rate, which allowed for fast secondary structural changes of the attached peptides (τ½ ~2s). Piperazine-like moieties at the 2,2′-ortho positions of an azobenzene-based cross-linker resulted in a similar red-shift in the π-π* band but a longer-lived cis isomer relative to its para-counterpart (τ½ ~minutes). These results suggest that the thermal rate could be tuned independently from the photo-switching wavelength by appropriate para or ortho substitution. The effect of 2,2′,6,6′-ortho-tetramethoxysubstitution provided an alternative approach to red-shifting the photo-switching wavelength. These groups caused an unconventional red-shift in the n-π* band of the trans isomer allowing for trans-to-cis and cis-to-trans photoisomerization to occur with green and blue light, respectively. In this case, the half-life of the cis isomer was not shortened, but rather extended relative to its parent compound (τ½ ~days versus minutes). These results provide progress in tuning the photo-switching wavelength independently from the thermal rate. A fluorescent reporter was developed to determine the stability of a commonly employed 4,4′-diamido derivative in vivo. Photoisomerization was found to cause time-dependent changes in fluorescein emission intensity. The reporter was microinjected in zebrafish embryos and photo-switching could be imaged for at least two days. This work provides the first direct evidence of azobenzene photo-switching in vivo, and indicates that it will be possible, in general, to photo-control peptide and protein function in living systems.

This thesis describes synthetic applications of α-keto carbocations, which represent potentially useful, but poorly studied, reversed polarity equivalents of enolates. In the first chapter, a Ag(I) – mediated method for the nucleophilic displacement of α-halocarbonyl compounds to construct carbon-carbon bonds is described. The highly electrophilic nature of the putative α-keto carbocation intermediates enables the use of relatively unreactive nucleophiles in both intra- and intermolecular contexts. Such intermediates also present interesting opportunities for stereocontrol: our efforts to carry out diastereoselective additions to chiral α-keto carbocations are described. Oxazoles are an important class of heterocycles, and several syntheses are addressed in Chapter 2. Our approach to this class of compounds employs a TMSOTf mediated Ritter reaction to construct the carbon-nitrogen bond. Cycloaddition of 2-alkoxyoxazoles with alkynes presents a facile route for furan synthesis. The final chapter describes our attempts to apply anion-π interaction in organocatalysis. These interactions between anions and electron-deficient arenes have been characterized in some detail and have recently been applied in ion transport. Applications of prolinol-based secondary amines incorporating electron-deficient aromatic groups are described.

The structural complexity of glycosaminoglycans (GAGs) such as heparin and heparan sulfate (HS) and their numerous biological roles, brings forth the need to develop new methods, capable of studying GAGs and their interactions with peptides and proteins under native settings. This thesis explores the development of chemical tools to study heparin/HS binding interactions under physiologically relevant conditions using fluorescence. In chapter 2, we designed peptide-based quinolinium probes to study the structural requirements of cationic peptides required for high affinity peptide-heparin interactions. These fluorescent probes enabled the study of peptide-heparin interactions at nM concentrations allowing the calculation of peptide-heparin binding constants. It was observed that peptides with positive charge displayed on one face of an α-helix in a continuous arrangement bound to heparin with the highest affinity and that heparin likely prefers to bind to these peptides while remaining in an extended conformation. In chapter 3, we set out to study an important biological role of HS which involves the binding and sequestering of proteins at the cell surface, facilitating endocytosis. HS has been implicated in the mechanism of cell penetrating peptide (CPP) cell uptake, with different CPPs showing different degrees of HS dependence on uptake as well as different mechanisms of entry. The role of HS in the mechanism of CPP uptake was investigated in chapter 3 using fluorescent peptide-based probes incorporating fluorophore/quencher pairs. These were used to identify and characterize the ability of heparin/HS to bind and cluster with CPPs to form colloidally stable aggregates. It was shown that the CPP Antp formed much more stable clusters with heparin than the TAT peptide despite both peptides having similar binding affinity for a single heparin chain. These findings were used to explain the cell surface HS dependence of Antp on cell uptake via endocytosis in contrast to the low dependance of TAT on HS and its uptake via translocation. A general model relating the ability of a CPP to cluster surface HS to its preferred mechanism of cell entry was proposed. In chapter 4, a strategy to selectively, and site specifically acylate carbohydrate binding proteins was developed using thioester-based affinity conjugates. It was possible to label maltose binding protein, a periplasmic protein, with high yield and selectivity at a single lysine residue proximal to the maltose binding site. Selective protein labeling could be carried out in bacterial cell extracts and in live bacterial cells. This strategy can potentially be applied to develop protein-based carbohydrate biosensors as well as profile carbohydrate binding proteins in biological samples.

Synthesizing proteins containing unnatural amino acids inserted at specific positions within the protein sequence has been a longstanding goal of biological chemists. This poses unique challenges, as aminoacyl tRNA synthetases, the enzymes responsible for protein synthesis, are highly specific. To overcome this, a lanthanum-catalyzed, biomimetic tRNA aminoacylation method has been developed(1). However, due to unproductive lanthanum coordination of ethyl phosphate, a reaction byproduct, a full equivalent of lanthanum must be added to each reaction. This may threaten the integrity of tRNA, as lanthanides are known to catalyze the hydrolysis of RNA (2, 3). Using uridine as a simplified tRNA mimic, magnesium, which is known to coordinate strongly with phosphate ions, has been utilized to optimize this reaction and increase the selectivity of lanthanum towards esterification. In the presence of magnesium, ester yield is substantially increased. In addition to this, optimal pH and buffer reaction conditions were determined.