Thesis advisor: Jianmin Gao / My graduate research career has focused on studying the principles that underlie molecular recognition, which include protein folding, protein-membrane interactions, structural preoranization for target binding and non-covalent interactions. This thesis will present an overview of this work through three different projects. I) Synthetic receptors for target binding in water. Molecular interactions in water provide the foundation for life. More specifically, the interactions between one or more molecules, through hydrogen bonding, π-effects, hydrophobic interactions and electrostatic interactions, all play a significant role essential to biological processes. This chapter will present an overview of supramolecular chemistry in water, with a focus on small molecule receptor “warheads” that target biomolecules of interest. The discussion will then move towards the ability to preorganize these “warheads” on a scaffold to improve their potency towards a target. The fundamental principles discussed in this section will provide a foundation for the following chapter in this thesis.II) Understanding Phosphatidylserine Recognition Using the Model cLac Peptide. The plasma membrane serves as a defining feature of the cell membrane, acting as a barrier for material exchange between a cell and its local environment. More importantly, membrane lipids are involved in mediating numerous cell-signaling events and acting as receptors to recruit proteins that carry out a specific function. Due to the important role that lipids play, it is highly desirable to develop affinity ligands for the diverse range of lipid headgroup structures on a cell membrane. Although prevalent, proteins have intrinsic limitations due to their size, low stabilities and slow clearance rates. This chapter will focus on the model peptide, cLac, which was previously developed as an affinity ligand for phosphatidylserine recognition. We will focus on understanding the key properties that contribute to PS selectivity and affinity, then attempt to improve this scaffold through structural preorganization. III) A prolinomycin-based scaffold for developing functional peptides. Nature has evolved proteins to bind cell-signaling molecules with exquisite affinity and specificity, making molecular recognition an essential part of biology. It has been a highly sought after goal within the chemistry field to be able to mimic the structure and function of certain proteins with smaller molecules, such as peptides. Specifically, cyclic peptides are showing promise as therapeutic agents due to their high proteolytic stabilities, faster clearance rates and ease of synthesis compared to proteins. One challenge, however, is that peptides generally do not possess the ability to properly fold and display their side chains for target binding, as proteins do. In this chapter, I will present a prolinomycin-based scaffold, which can fold in the presence of K+ ions to preorganize its side chains for target binding. Moreover, the focus will be on the structural aspects of this cyclic peptide, along with proof-of-concept studies demonstrating its ability to recognize a target under physiological conditions. The findings in this study will be useful in developing peptide-based tools that recognize various targets. IV) Dissecting the energetic consequences of fluorinating a protein core. Proteins have emerged as a powerful class of therapeutic agents due to their superior properties over small molecules in the clinic. Some of the key advantages include their large surface areas and highly defined structures, which allow them to perform very specific functions that are generally not reproducible with traditional small molecule scaffolds. In addition, proteins possess the ability to properly fold under physiological conditions through precise, noncovalent interactions between their side chain residues. Perhaps the most relevant interactions arise from aromatic side chains, which can interact in a variety of ways to help proteins fold. In this chapter, we will focus on the model protein, VHP35, which contains a hydrophobic core of three interacting Phe residues, to study the effects of fluorination on an edge-face interaction. / Thesis (PhD) — Boston College, 2016. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Chemistry.

Thesis advisor: Jianmin Gao / The oligomerization of membrane proteins has been shown to play a critical role in a myriad of cellular processes, some of which include signal propagation, cell-to-cell communication, and a cell's ability to interact with its surroundings. Diseases that are associated with disruption of protein-protein interactions in the membrane include cystic fibrosis, certain cancers, and bone growth disorders. Although significant progress has been made in our mechanistic understanding of protein-protein interactions in membranes, it remains difficult to predict the oligomerization state of transmembrane domains and explain the physiological consequences of a point mutation within a membrane embedded protein. The development of novel classes of chemical tools will allow us to better understand the energetics of transmembrane domain association at the molecular level. Herein, we demonstrate that fluorinated aromatic amino acids offer intriguing potential as chemical mediators of transmembrane protein association. We have systematically examined the effects of fluorination on the physical properties of aromatic systems in the context of a soluble protein model system. Our results illustrate the ability of fluorinated aromatic amino acids to simultaneously stabilize protein structure and facilitate highly specific protein self-assembly. An improved understanding of the fundamental energetics of aromatic interactions should allow for their more efficient incorporation into designed inhibitors of transmembrane protein association. In addition to chemical tools, the development of simple methods for directly monitoring transmembrane domain association in vitro and in vivo is necessary to advance our understanding of these interactions. Towards this goal, we have established FlAsH-tetracysteine display as an effective approach to quantifying the association propensities of transmembrane α-helices (TMHs) in vitro. Our assay is compatible with two of the most commonly utilized model membrane systems, detergent micelles and vesicles. The high spatial resolution of FlAsH binding (˂ 10 Å) allows for the differentiation of parallel and antiparallel oligomerization events. Importantly, preliminary studies suggest the assay's ability to detect inhibition from exogenous TMHs. Encouraged by our understanding of aromatic interactions and the success of our assay, we are beginning to incorporate fluorinated aromatics in the model TMHs and monitoring their ability to associate. The ultimate goal is to modulate the association of endogenous TMHs such as ErbB2. Research in this direction is ongoing. / Thesis (PhD) — Boston College, 2013. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Chemistry.

Increasing drug resistance towards the front line influenza neUraminidase inhibitor Oseltamivir (Tamiflu®, Roche) has recently been reported, emphasising the need to perform further studies to gain insight into receptor ligand interactions. Recently, influenza neuraminidase activity has been tackled using a novel class of mechanism-based inactivator, which incorporates fluorine atoms at positions C-2 and C-3 of sialic acid. These inactivators are anticipated to be less susceptible to drug induced resistance as they target essential catalytic amino acids. However, individual hydrogen-bonding interactions formed between these inactivators and the neuraminidase in both the Michaelis complex and at the transition-state remain unclear. The syntheses of the four novel monodeoxygenated 2,3-difluorosialic acid inactivators at position C-4,C-7, C-8 and C-9 deploying a Barton-McCombie protocol were accomplished. The time-dependant inactivation of wild type influenza neuraminidase N9 G70C by these monodeoxygenated 2,3-difluorosialic acid inactivators was tested in a fluorescent kinetic assay. Further biochemical evaluation (performed by our collaborators) in ICso measurements against a panel of influenza viruses including wild types (wt.) and Oseltamivir resistant mutants showed potent inhibition of influenza Band H1 N1 strains. We also wished to develop a further understanding of the effects of the monodeoxygenated 2,3-difluorosialic acid inactivators upon inactivation on a physical basis. Hence, we will discuss X-ray crystallographic structures, (obtained by our collaborators) of influenza neuraminidase N9 in complex with the monodeoxygenated 2,3-difluoro-sialic acid inactivators. 11

Thesis. 1978. Ph.D.--Massachusetts Institute of Technology. Dept. of Chemistry. / MICROFICHE COPY AVAILABLE IN ARCHIVES AND SCIENCE. / Includes bibliographical references. / Ph.D.

Thesis (M.S.)--Oregon State University, 2007. / Printout. Includes bibliographical references (leaves 89-93). Also available on the World Wide Web.

Thesis (Ph. D.)--University of North Texas, May, 2008. / Title from title page display. Includes bibliographical references.

A new approach in the syntheses of 3-bromo-2-butanone and 2-bromo-3-fluorobutane has been developed. All attempts to alkylate the sodium salt of diethyl malonate, ethyl acetoacetate, or diethyl acetamidomalonate with 2-bromo-3-fluorobutane failed. New phosphonoacetates, tert-butyl and benzyl diethylphosphono-acetates were prepared as very versatile intermediates in the syntheses of carboxylic acids. Methyl-, ethyl-, tert-butyl-, and benzyl 4-fluoro-3-methyl-2-pentenoates were synthesized in high yields by the Horner-Emmons reaction. The reaction is stereoselective and gave E and Z form in 75:25 ratio as determined from proton and fluorine nmr spectra. A long-range coupling was observed in fluorine nmr spectrum of 3-fluoro-2-butanone. From the ethyl 4-fluoro-3-methyl-2-pentenoate, ethyl 2-bromo-4-fluoro-3-methyl-2-pentenoate was prepared, but the latter could not be reduced under the conditions of catalytic hydrogenation. Ethyl 2-chloro-4-fluoro-3-methyl-2-pentenoate was prepared from 3-fluoro-2-butanone and ethyl diethylphosphonochloroacetate, but could not be reduced. Catalytic hydrogenation of alky 4-fluoro-3-methyl-2-pentenoates gave the corresponding saturated esters in high yields. Treatment of alkyl 4-fluoro-3-methylpentanoates with lithium diisopropylamide and bromine at -78° yielded the corresponding 2-bromoderivatives. Methyl-, ethyl-, and tert-butyl 2-bromo-4-fluoro-3-methyl-pentanoates were treated with sodium azide to give the corresponding 2-azido derivatives which were further reduced into methyl-, ethyl-, and tert-butyl 2-amino-4-fluoro-3-methylpentanoates. / Ph. D.

A method for the preparation of air stable difluoroboryl acrylamides is reported. In contrast to the ubiquitous organotrifluoroborate salts, difluoroboryl acrylamides are relatively nonpolar and are readily purified by silica gel chromatography. Difluoroboryl acrylamides serve as efficient substrates in cross-coupling reactions to afford the corresponding trisubstituted acrylamides in good to excellent yields. The utility of the difluoroboryl group in various chemical transformations is presented. / A new method for the formation of a unique difluorinated boron-based functional group is reported. In contrast to the commonly observed trifluoronated boron species, the difluoroboryl species is relatively nonpolar, which allows for these compounds to be purified by silica gel chromatography, a convenient method for purification of compounds. Similarly to trifluoroborate salts, difluoroboryl species are capable of undergoing cross-coupling reactions, which form carbon-carbon bonds, in good to excellent yields. Additional examples of chemical reactions using difluoroboryl acrylamides are also presented.

The importance of fluorinated organic molecules has grown over the last 50 years, particularly in the pharmaceutical and agrochemical industries. Therefore the development of new methods for fluorination is a very attractive research area. In Chapter 1, the properties and impact of the fluorine atom on organic molecules are overviewed. Existing electrophilic and nucleophilic fluorination methods are reviewed, and new developments in asymmetric fluorination are discussed. The emergence of the Prins fluorination reaction as a side product in BF₃.OEt₂ catalysed processes has been investigated as a synthesis method in Chapter 2. Indeed, it is possible to form 4-fluorotetrahydropyrans with some diastereoselectivity from an allylic alcohol and an aldehyde with a stoichiometric amount of BF₃.OEt₂. During this study, formation of 4-fluoropiperidines from N-tosyl-4-butenylamine was achieved. Optimisation of reaction conditions was investigated such as the solvent, the reaction temperature and the influence of substituents on the alcohol and the aldehyde reagents. A ring-opening reaction of 4-fluoro-2-phenyltetrahydropyran was successfully performed. Both oxa-Prins and aza-Prins fluorination reactions were investigated under microwave conditions, allowing reduced reaction times, a process that had a minimum impact on the diastereoselectivity. Attempt to form γ-hydroxy-α-vinylfluorides by the reduction-fluorination of propargylic alcohols with aluminium hydride, or by Horner-Emmons reaction with diethyl (fluoromethyl)phosphonate are reported in Chapter 3. Unfortunately these approaches were unsuccessful in the preparation of γ-hydroxy-α-vinylfluorides. Attempts to fluorinate epoxides by α-lithiation and then treatment with electrophilic fluorination reagents gave encouraging results, but the products could not be purified and characterised due to an apparent instability.

After a general introduction about the properties and preparation of organofluorine compounds (Chapter 1), this thesis is divided into two parts focussing on the development of new methods for C-F bond formation (Part A) as well as studies towards the development of novel fluorinating reagents (Part B). Part A: New Methods for Carbon-Fluorine Bond Formation Part A consists of two chapters outlining the development of a Pd-catalysed hydrofluorination of alkenylarenes (Chapter 2) as well as a halofluorination of alkynes (Chapter 3). Chapter 2 This chapter describes the development of a novel, regioselective, syn-specific hydrofluorination of alkenylarenes under Pd-catalysis leading to the formation of benzylic fluorides. An extensive substrate scope is presented together with a model of the catalytic cycle, based on observations during the development of this reaction, deuterium labelling experiments as well as mechanistic control experiments starting from isolated palladacycles. Chapter 3 In this chapter the development of a novel iodo- as well as bromofluorination of internal and terminal alkynes, leading to the formation of (E)-halofluoroalkenes, is presented. For the former substrate class, the effects of steric as well as electronic bias on regioselectivity are discussed. For the latter substrate class, this methodology could be extended to the corresponding double iodofluorination, and for both transformations it was found to exclusively lead to the fluorination of the internal carbon. An extensive substrate scope as well as different iodofluorination-cross-coupling sequences including Suzuki, Sonogashira and Ullmann couplings, are illustrated. A representative reaction was successfully carried out on gram-scale and an iodofluorination-Suzuki-coupling sequence was used to prepare a fluorinated tamoxifen derivative. Part B: Hydrogen-Bonded Fluoride Complexes as Novel Reagents for Carbon-Fluorine Bond Formation Part B consists of two chapters describing structural as well as reactivity studies of fluoride-alcohol (Chapter 4) and fluoride-urea complexes (Chapter 5). Chapter 4 In this chapter the synthesis of 19 novel hydrogen-bonded tetraalkylammonium fluoride-alcohol complexes is described. For a subset of 15, the solid-state structures as determined by single-crystal X-ray diffraction experiments are presented. Trends of reactivity and selectivity were determined using these complexes as sources of fluoride anion in a model SN2 reaction. Preliminary results from in silico modelling of the fluoride-alcohol system provide a basis for explaining the results. Chapter 5 This chapter summarises the synthesis and solid-state structures of 20 hydrogen-bonded fluoride complexes using the urea and related squaramide and amide motifs. Also, the size of the tetraalkylammonium counter-cation was varied to study the influence on the solid-state structure. The reactivity and selectivity of a series of complexes was studied using the same model SN2 reaction as in Chapter 4 and results were compared accordingly. Different UV-vis and NMR spectroscopic techniques were used to study the behaviour of the fluoride-urea system in solution. Preliminary results demonstrate the use of 1,3-diarylureas as organocatalysts for nucleophilic fluorination.