Chapter 1. Introduction This chapter is an overview on the literature of self-association of small organic molecules. The chapter is presented in four parts. First, an introduction to aggregation of small molecules is given with the emphasis on micelles and gels(Parts 1 and 2) In part 3, a short overview is given on bile acid based aggregates and their applications. Lastly, the content of the thesis is outlined. Chapter 2. Solution properties of novel cationic bil salts: A structure-aggregation property study Scheme 1: Structures of Cationic bile salts(Refer PDF File) Bile Salts are biosurfactants and they are known to form micelles in aqueous medium. We studied the micellar properties of cationic bile salts(Scheme 1) and compared with their natural (anionic) counterparts. A serendipitous discovery of the gelation of a cationic bile salt(4) led us to investigate the aggregation properties of this new class of cationic hydrogelators. This chapter highlights the recent efforts on the study of side chain structure-aggregation property relationship of cationic bile salts. Bile acid analogues with a quaternary ammonium group(Scheme 1, compounds 2, 3, 4, 6, 8 and 12) on the side chain were found to efficiently gel aqueous salt solutions. Some of the cationic bile salts gelled water alone and many of them gelled aqueous salt solutions even in the presence of organic co-solvents(≤ 20%) such as ethanol, methanol, DMSO and DMF. A strong counter ion dependent gelation was observed. These gels showed interconnected fibrous networks. Unlike natural anionic bile salt gels(reported for NaDC, NaLC), the cationicgels reported here are pH independent. Cationic gels derived from DCA showed more solid-like rheological response compared to natural NaDC gels studied earlier by Tato et al. A strong structure(side-chain) andcounter-ion dependent flow of the cationic bile salt gels was seen. Chapter 3. Applications of cationic bile salts and their aggregates Cationic bile salts are useful in many ways. We have studied some of the applications of cationic bile salts(discussed in chapter 2) and their aggregates in this chapter. The chapter is presented in three parts. Part 1. Interaction of Cationic bile salts and DNA The bile acid amphiphilicity is believed to help the DNA binding process of polyamines. This has prompted us to study the DNA-bile salt binding interaction of bile salts. The binding of cationic bile salts has been expressed in terms of C50 values, which were determined from the plot of fluorescence of ethidium bromide bound DNA vs. bile salt concentration(Fig 1) The C50 values for cationic bile salts were estimated to be about 1.2 mM. Fig1: A plot of fluorescene of ethidium bromide bound DNA against bile salt concentration (Refer PDF File) Part 2. Cholesterol solubilization and crystallization studies in aqueous bile salt solutions. Dihydroxy bile salt micelles are well known for cholesterol dissolution(e.g. UDCA and CDCA). We studied the dissolution of cholesterol in the cationic bile salt micelles(of 21-25) and the results are discussed in this part. Scheme 2: Cationic bile salt chlorides studied for cholesterol dissolution (Refer PDF File) A powder dissolution method was used to study the solubility of anhydrous cholesterol in cationic bile salt solution. These cationic bile salt micelles can dissolve cholesterol to the same extent as the taurine conjugates of bile acids, but lesser than the natural anionic bile salts(Fig.2) Addition of PC(Phosphatidylcholine) to cationic bile salt micelles enhanced the micellar cholesterol solubilization. Fig 2:Cholesterol dissolution in cationic bile salt solutions(Refer PDF File) The crystal nucleation time of cholesterol did not change significantly by adding 5-30 mM of the cationic bile salts. The bile salt analogues did, however, attenuate cholesterol crystallization to a similar extent at all concentrations studied. All these effects wer comparable to those fo cholic acid. Part 3. Hydrogels as a reaction vessel for photodimerization Bile salt micelles have been shown to control the product selectivity in photochemical reactions. The dynamic nature of the bile salt micelles results in differential effects on reaction selectivity. The photodimerization of acenaphthylene(sheme 3) was studied in micellar and hydrogel medium(e.g. NaDC, 22, 28, etc.) The ratio of anti- to synphotodimer was found to be greater in gel bound state than in solution. Substitution on the CAN ring did not show larger variation on the product distribution from solution gel. Scheme 3: Photodimerization of acenaphthylene(Refer PDF File) Chapter 4. Bile acid derived sulfur analogues in designing novel materials. Part 1. A simple approach towards nanoparticle-gel hybrid material. Scheme 4: Scheme for the synthesis of thiols derived from bile acids (Refer PDF File) Our interest in bile acid based gelator molecules led us to explore the synthesis and properties of bile analogues with the side chain carboxylic acid replaced by a thiol(Scheme 4) to stabilize metal NPs. We reasoned that the specific self-aggregation modes of facially amphiphilic bile units would enable a metal NP capped by such a thiol to “lock” onto a gel fiber derived from a structurally related gelator molecule. AuNPs stabilized by 38-40 were obtained by the NaBH4 reduction of homogeneous methanolic solutions of the thiol and gold salt. These steroid capped nanoparticles were found to stay dispersed in a gel of 28, thus providing a simple approach to obtain gel-nanoparticle hybrid. A photograph of the hybrid material and their morphology are shown in Fig 3.(Refer PDF File) Chart 1: Structure of the gelator used for designing a hybrid material(Refer PDF File) Part 2. Gelation of aromatic solvents using sulfur analogues of bile acid A few of the sulfur derivatives were serendipitously fouond to gel organic solvents (Fig 4). Thiol 38 formed stable gels at room temperatures while the disulphide 36 formed stable gels below 5º C. The aggregation properties, morphology, and the melting profiles of gels of disulfides and thiols derived from bile acids have been highlighted in this part. Fig 4: A photograph of the gels derived from 38(Refer PDF File) (For Figures and Molecular Formula Pl refer the Original Thesis)

Functional Dendritic Structures from Bile Acids: Supramolelcular Hosts, Light Harvesters and Drug Carriers Chapter 1. An Overview of Functional Dendrimers. Dendrimers are welldefined, hyperbranched macromolecules that are prepared by highly controlled iterative methodologies. The ability to modulate the size, molecular weight, chemical functionalities and the position and number of functional groups in dendrimers make them promising candidates for a wide variety of applications. In this chapter, three areas 1) hostguest chemistry 2) light harvesting and 3) drug delivery, where dendrimers are increasingly finding applications, are discussed with selected examples. Chapter 2. Hydroxyl Terminated Dendritic Oligomers from Bile Acids: Synthesis and Properties. Bile acids are excellent building blocks for dendritic construction because of their many interesting features. They are readily available, chiral, facial amphiphiles with complementary functionalities. Moreover, due to the large size of the bile acid units, a dendritic structure consisting of only a few such repeat units can have an extended structure with multiple functionalizable groups. (figure 1) The high reactivity of the chloroacetyl group has been exploited for the synthesis of bile acid based first and second-generation dendrons with glycolate linkers and multiple hydroxyl groups. The synthesis involves only a few steps and avoids the use of protecting groups for the terminal hydroxyl groups. The synthesis of a bile acid tetramer is shown here as an example (Figure 1). Carboxyl protected cholic acid was reacted with chloroacetylchloride to generate the trischloroacetylated derivative. This compound on reaction with excess of sodium cholate generated the tetramer with nine hydroxyl groups via displacement of the chlorides. In order to synthesize higher generation dendritic structures, perchloroacetylated firstgeneration dendrons were first synthesized. These were subsequently reacted with excess of sodium deoxcholate to generated secondgeneration dendrons with multiple hydroxyl groups (Figure 2). All the compounds were characterized by H NMR, C NMR, IR, ESIMS/MALDI-TOF, HPLC and elemental analysis(wherever possible) Figure 2. Structure of tridecamer. These dendritic structures with facially amphiphilic bile acid backbones on the periphery were able to solubilize cresol red, a hydrophilic dye, in a nonpolar solvent, thus exhibiting reverse micellar characteristics. Chapter 3. Multiple Naproxen Appended Bile Acid Dendrimers as Light Harvesters and Drug Carriers. Part I. Synthesis and Characterization. Using the same synthetic strategy as in Chapter 2, bile acid based dendritic structures appended with multiple bioactive (S)naproxens were generated as potential drug carriers. The construction of these dendrimers was accomplished using per(chloroacetylated) bile acid dendrons and conveniently displacing all the chlorides with naproxen units. Since naproxen is photoactive with a high fluorescence quantum Figure 3. Structures of secondgeneration dendrimers and a monomer with multiple naproxens. yield, the photophysical properties of these multichromophoric dendrimers could be further explored (Figure 3). By functionalizing the carboxyl group on the side chain with an anthracenyl moiety the energy transfer properties of these dendrimers could be studied. In this section the synthesis of first and secondgeneration dendritic structures with multiple naproxen units at the periphery and benzyl/anthracenyl moiety on the side chain are described (Figure 3). Model compounds using monomeric bile acid units were synthesized for comparison with the dendritic structures. All the compounds were characterized by H NMR, C NMR, IR, ESIMS/MALDITOF, HPLC and elemental analysis (wherever possible). Part II: Absorption, Fluorescence and Intramolelcular Energy Tranfer Studies. Absorption studies showed that the molar extinction coefficients increase linearly with increasing number of naproxen units and the absorption spectra of anthracenyl moiety remain unchanged in all the dendritic systems. These indicated the absence of ground state interaction between the chromophores. In the 275-290 nm absorption region, the molar extinction coefficient of naproxen is much greater than that of the 9-anthracenylmethyl chromophore. Hence excitation in this region would mainly excite the naphthalene chromophore. Upon excitation at 275 nm, there was predominant emission from the anthracenyl moiety in the dendritic structures (containing both chromophores) and the fluorescence intensity increased with increasing number of naproxens(Figure4). This indicated that the dendrimers act as efficient light harvesters with energy transfer from naproxen to anthracene (intramolecular nature of the energy transfer was confirmed through control experiments). (Figure 4: Refer PDF File) The fluorescence and energy-transfer properties were further investigated by time-resolved fluorescence spectroscopy. The presence of fast decay component(s) in the naproxen decay in dendritic structures (containing both chromophores) indicates that its fluorescence is quenched in the presence of anthracene due to energy transfer ((λex 275 nm, λem 350 nm (Figure 5). This was further confirmed by monitoring the fluorescence of the sensitized anthracenyl chromophore (λex 275 nm, λem 436 nm) which exhibited a fast rise comparable to he quenched naproxen lifetime(s). The efficiency of energy transfer was estimated by donor quenching by both steadystate and timeresolved techniques. The dendritic structures exhibited high energy transfer efficiencies (~ 70 – 90 %) with the net efficiency decreasing from the first to second-generation. Part III. In vitro Study of Hydrolysis of Naproxen Appended Bile Acid Prodrugs by Chemical and Enzymatic Methods. The naproxen appended bile acid dendrimers consist of hydrolyzable ester and glycolate linkers. Hence the chemical stability and enzymatic degradation with possible release of naproxen was studied. Two compounds, monomer appended with two naproxens and trimer with four naproxens have been used for the initial investigations (Figure 6). The compounds were found to be highly stable towards chemical hydrolysis and did not show any hydrolysis in phosphate buffer, pH = 7.4 even after 7 days. Since the compounds were not soluble in water, Arabic gum and TritonX were used for emulsification. Figure 6. Structures of monomer and trimer. (Refer PDF File) The enzymatic hydrolysis of the compounds was then studied using Candida Rugosa Lipase. In both cases, there was slow hydrolysis of the substrate and intermediates were formed (with release of free naproxen) which were detected by HPLC (reverse phase column with a UV detector). The trimer underwent much slower hydrolysis compared to the monomer. The intermediates were characterized by absorption and mass (ESIMSQTOF) spectrometry.

Chapter 1. Supramolecular Gels and their Applications Supramolecular gels are viscoelastic materials composed of a solid like three dimensional fibrillary network that is embedded in a liquid. Supramolecular gels are derived from low molecular weight compounds (typically MW < 3000). In the 1990s, the investigations on gels were mainly focused on designing new gelator molecules. However, during the last decade, research focus shifted towards designing functional gels and their applications. As a result of extensive work in this area, gels have been found to have varied applications in the templated synthesis of inorganic nanomaterials, hybrid materials, light harvesting systems, as responsive system and sensors, and also in drug delivery, tissue engineering etc. This chapter gives an introduction to supramolecular hydrogels/organogels and relevant bile acid chemistry touching upon the gelation properties of the bile acid derivatives. Diverse applications of the supramolecular gels are also illustrated with several examples. Scheme 1. Various applications of functional supramolecular gels Chapter 2. Bile Acid derived novel Hydrogelators Part 1. Hydrogelation of Bile acid protected Amino acids and Hybrid Materials Hydrogels from low molecular weight molecules have significant importance in biomedical applications. In this chapter, we report injectable hydrogel formation from bile acid conjugates of various amino acids. Hydrogel formation was found to be dependent on multiple factors such as bile acid backbone structure, linkage between the bile acid and the amino acid, pH etc. Single crystal structures of lithocholyl phenylalanine, lithocholyl-glycine, lithocholyl-L valine and lithocholyl-L alanine were also determined. Finally, the hydrogel frameworks were utilized to produce hybrid materials with Gold and ZnO nanoparticles. Scheme 2. (a) Crystal structure of LC-LF-OH gelator molecule, (b) photograph of gel, (c) SEM and (d) AFM image of LC-LF-OH xerogel Part 2. Hydrogelation of bile acid-dipeptide conjugates and in situ synthesis of silver and gold nanoparticles in the hydrogel matrix Fabricating supramolecular hydrogels with embedded metal nanostructures are important for the design of novel hybrid nanocomposite materials for diverse applications such as bio sensing and chemo sensing platforms, catalytic and antibacterial functional materials etc. Supramolecular self-assembly of bile acid-dipeptide conjugates have led to the formation of new supramolecular hydrogels. Gelation of these molecules depends strongly on the hydrophobic character of the bile acids. Ag+ and Au3+ salts were incorporated in the hydrogels, and photo reduction and chemical reduction led to the in situ generation of Ag and Au NPs in these supramolecular hydrogels without the addition of any external stabilizing agent. The color, size and shape of silver nanoparticles formed by photo reduction depended on the amino acid residue on the side chain. Furthermore, the hydrogel-Ag nanocomposite was tested for its antimicrobial activity. Scheme 3. Bile acid based dipeptide hydrogelators and soft hybrid materials Chapter 3. Sonogels of bile salts of In(III): use in the formation of self-templated indium sulfide nanostructures In this chapter, facile hydrogel formation by Indium(III) cholate and deoxy cholate are reported. When In(III) solution was added to aqueous solutions of sodium cholate and sodium deoxy cholate and sonicated, the mixtures formed gels. The gels thus obtained were translucent/turbid and thermos irreversible. Rheological measurements showed that all of them could be classified as viscoelastic soft solids. Scanning electron microscopy and atomic force microscopy showed typical entangled three dimensional fibrous networks. The In-Ch hydrogel were further used to prepare nanostructured In2S3 in which the cholate units possibly acted as a surfactant to confine the growth of the Nano flakes. Scheme 4. In-Ch hydrogel (Photograph and SEM image of In-Ch gel) Chapter 4. Palladium-Hydrogel Nanocomposite for C-C Coupling Reactions Supported metallic nanoparticles are important composite materials owing to their enormous potential for applications in various fields. This chapter describes the in situ formation of palladium nanoparticles in a calcium-cholate (Ca-Ch) hydrogel by reduction with sodium cyan borohydride. The hydrogel matrix appeared to assist the controlled growth as well as stabilization of palladium nanoparticles. The palladium nanoparticle/Ca-Ch hydrogel hybrid was characterized by scanning and transmission electron microscopy, atomic force microscopy, X-ray diffraction, and energy-dispersive X-ray spectroscopy. Furthermore, PdNP/Ca-Ch hybrid xerogel was shown to act as an active catalyst for Suzuki reaction under aqueous aerobic conditions, up to 4 cycles. This PdNP/Ca-Ch xerogel retained its catalytic activities on storage for several months. Scheme 5. Palladium-hydrogel nanocomposite for C-C coupling reactions in water Chapter 5. Sensitization of Terbium/Europium in self-assembled cholate hydrogel: An approach towards the detection of amine vapours "Luminescent" lanthanides have intrinsic low molar absorptivity, although this problem can be addressed by complexing the lanthanide ion with suitable chelating ligands which improve the luminescence properties drastically. However the design of such systems often involves careful planning and laborious synthetic steps. It is therefore desirable to have a simpler way to sensitize lanthanides with high efficiency. It was observed in our group that trivalent lanthanides formed hydrogels on the addition of sodium cholate. This chapter describes the discovery of the several biphenyl derivatives (such as 4-biphenylcarbaxaldehyde, 4-acetylbiphenyl) for sensitization of Tb(III) and Eu(III) in lanthanide hydrogels. Sensitization of Tb(III) and Eu(III) were observed by doping was characterized by scanning and transmission electron microscopy, atomic force microscopy, X-ray diffraction, and energy-dispersive X-ray spectroscopy. Furthermore, PdNP/Ca-Ch hybrid xerogel was shown to act as an active catalyst for Suzuki reaction under aqueous aerobic conditions, up to 4 cycles. This PdNP/Ca-Ch xerogel retained its catalytic activities on storage for several months. Scheme 6. Schematic representation of the sensitization process (the arrangement of themolecules in the gel fiber is arbitrary)(For figures pl refer the abstract pdf file)

Doctor of Philosophy / Department of Diagnostic Medicine and Pathobiology / Kyeong-Ok Chang / Caliciviruses are important pathogens of humans and animals. Noroviruses are major causes of foodborne gastroenteritis cases, but their research is hindered due to the inability to grow human noroviruses in cell culture. Detailed studies on entry events of caliciviruses are lacking and may be crucial for development of cell culture models. We examined the entry events of caliciviruses using porcine enteric calicivirus (PEC), feline calicivirus (FCV) and murine norovirus-1 (MNV-1). PEC replication in LLC-PK cells requires bile acid in the medium, but the mechanism is not well understood. Our studies showed that bile acids are required in the early stage of virus replication, and while internalization of PEC is not dependent of them, they are required for endosomal escape and successful replication. Further examination on virus entry, we demonstrated that endosomal acidification and cathepsin L activity are essential in the replication of PEC, FCV and MNV-1. The results showed that inhibition of endosomal acidification or cathepsin L activity led to retention of viruses in the endosomes. Also we demonstrated that recombinant cathepsin L cleaved structural protein of PEC, FCV or MNV-1, which suggests that the enzyme may facilitate uncoating viruses in endosomes. In addition to bile acids, we found that a cold shock treatment during virus entry supported PEC replication by facilitating the endosomal escape. While PEC alone did not induce ceramide formation, bile acids or cold shock treatment induce ceramide formation on endosomes through activation acid sphingomyelinase (ASM), and this event was crucial for virus replication because inhibition of ASM blocked ceramide formation and significantly reduced PEC replication. Incubation of FCV or MNV-1 with cells led to ceramide formation during virus entry, and inhibition of ASM also significantly reduced their replication. Inhibition of ASM led to endosomal retention of PEC, FCV or MNV-1 during virus entry, which may be the reason for the reduction of viral replication. These studies revealed the important and common events during calicivirus entry for successful replication, including virus endosomal escape, cathepsin L activity and ASM/ceramide formation. This detailed information may provide clues for understanding the replication of fastidious caliciviruses and for potential therapeutic targets.

Research into the gut microbiome has revealed the widespread influence that microbial species have on their host. Host genetics and environmental factors influence the abundance and diversity of the bacterial species living within the gastrointestinal tract. When the normal composition of the gut microbiota is altered, a dysbiotic state incurs. Inflammatory bowel disease (IBD) is a chronic/relapsing inflammatory disorder of the intestinal mucosa, which is characterized by a state of dysbiosis. Despite the large amount of information studying the role dysbiosis has in the pathogenesis of IBD, it is not clear how the altered microbial composition of the gut in IBD patients leads to susceptibility to enteric pathogens such as Clostridium difficile. This study aims to highlight the features of the gastrointestinal tract that are modified as a result of dysbiosis in the IBD population, and how these features facilitate colonization by C. difficile and symptom development. Review of the available literature demonstrated that the depletion of Clostridial cluster XIVa in IBD-associated dysbiosis alters bile acid metabolism and butyrate fermentation in the colon, ultimately promoting germination of C. difficile spores and weakening the gut's immune response against toxin-mediated inflammation. From continued research into the gut microbiota, more will be understood of how these microbial organisms influence human health and disease.

A better understanding of how dietary fibres impact the bioavailability of fat-soluble nutrients and nutraceuticals is required. The purpose of this research was to determine the influence of guar gum (GG) on the transfer processes impacting beta-carotene (BC) bioaccessibility (transfer to the aqueous phase) from an oil-in-water emulsion using an in vitro model simulating gastric and duodenal digestion. Canola oil emulsions (1.5 % soy protein isolate, 10 % canola oil and 0.1 % all trans BC, D4,3~160 nm) were prepared by microfluidization (40 MPa, 4 passes) and exposed, in the presence of 0.0, 1.0, 1.5, 2.0, or 4.0 % GG, to conditions representative of the stomach and duodenum in the fed state. Lipolysis, BC bioaccessibility, digestate apparent viscosities, droplet size, and bile acid (BA) binding were studied. With increasing concentration of GG, digestate viscosity was increased and lipolysis and bioaccessibility were decreased (P<0.05). Peak lipolysis was 56.2% vs. 21.6% for emulsions containing 0.0 % vs. 4.0 % GG, respectively. BC bioaccessibility was also lower in the presence of GG (i.e. 29.7 vs. 6.98 % for 0.0 vs. 4.0 % GG respectively). Thus, the presence of GG impacted digestive processes central to BC absorption. The impact of GG may be related to increased digestate viscosity entrapping mixed micelles or BAs and decreasing diffusion leading to decreased lipolysis and BC bioaccessibility. / NSERC, CFI

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Liquid crystalline materials (LCMs) have gained much popularity over the past century. The thermotropic forms of these materials have been extensively studied and employed in a range of innovative applications. The lyotropic liquid crystal systems that have been studied in the past have often been formed by the organization of natural and synthetic small molecules in solutions. In this study, we use self-assembled supramolecular structures as building blocks to fabricate lyotropic liquid crystals. We investigate the self-assembly of a naturally occurring bile acid called lithocholic acid (LCA), to form supramolecular fibrous and tubular structures in basic aqueous solutions. We control the morphology of the self-assembled structures by manipulating experimental parameters in order to gain comprehensive knowledge regarding the self-assembly process. We characterize these structures with respect to their morphology i.e. their length, diameter, flexibility and shape using atomic force microscopy, optical microscopy and infrared spectroscopy. We produce lyotropic liquid crystal phases using self-assembled LCA structures through modification of physical parameters such as concentration, temperature, shear and pH. The nature of the lyotropic liquid crystal phases depends upon the morphology of the fibers and tubes. We observe that the short, rigid fibers and tubes form nematic phases while long, flexible fibers and tubes form cholesteric phases. We also study the phase transitions of the liquid crystal (LC) phases by observing their patterns using a polarizing microscope. Observations show that LC phases form in samples with LCA concentration above 0.75%w/w. Since the process of self-assembly is time-dependent, so is the formation of liquid crystal phases. We note that the optimum LCA concentration for LC phase formation is 2%-4%w/w and that the liquid crystal transition temperature is about 70[degrees]C.