Thesis (Ph. D.)--University of Hong Kong, 2010. / Includes bibliographical references (leaves 270-292). Also available in print.

Thesis (Ph. D.)--Chemistry and Biochemistry, Georgia Institute of Technology, 2009. / Committee Chair: Hud, Nicholas; Committee Member: Doyle, Donald; Committee Member: Lobachev, Kirill; Committee Member: Oyelere, Adegboyega; Committee Member: Wartell, Roger. Part of the SMARTech Electronic Thesis and Dissertation Collection.

Thesis (M.S.)--Chemistry and Biochemistry, Georgia Institute of Technology, 2009. / Committee Chair: Weck, Marcus; Committee Member: Collard, David; Committee Member: Kubanek, Julia. Part of the SMARTech Electronic Thesis and Dissertation Collection.

Molecular recognition exploiting non-covalent interactions mediates the structure and function of many critical biological and synthetic molecules. There has thus been continuing and intense efforts in the design and synthesis of supramolecular systems with the capability of recognizing specific chemical species. Among various guest species, Prof. Sessler's group has been focused on the study of artificial anion receptors. Calix[4]pyrrole is a tetrapyrrolic macrocycle that is capable of binding anions via concerted and directional hydrogen bonding. Recently, a tetrathiafulvalene (TTF) functionalized calix[4]pyrrole (TTF-C4P) was synthesized and studied as a receptor for various guest species such as anions, electron deficient guest species, and C₆₀. This dissertation focuses on the recent discovery in supramolecular chemistry of TTF-calix[4]pyrrole derivatives. Chapter 1 provides a brief overview of the historical perspective, redox properties, and uses of TTF derivatives as functional building blocks for supramolecular assemblies, as well as previous findings involving the supramolecular chemistry of TTF-C4P. Chapter 2, as the major focus of this dissertation, describes ion mediated supramolecular and reversible electron transfer processes between TTF-C4P and bisimidazolium salts (BIQ²⁺2X⁻). We discovered that the electron transfer processes between these redox couples could be controlled reversibly by ion binding. Specifically, we found that anion binding to the TTF-C4P receptor promotes the forward ET processes. In contrast, cation complexation to the cavity of TTF-C4P causes the reverse ET processes. Such ion mediated ET processes play an essential role in biological ET systems including photosynthesis and respirations. These reversible ET processes were mapped out by spectroscopic (¹H-NMR, UV-Vis NIR titrations, and EPR analysis) and X-ray single crystallographic analyses of both the intermediate and products. Chapter 3 describes the synthesis of aromatic (thiophene and benzene) annulated TTF-calix[4]pyrroles as new and significantly improved receptors for poly-nitroexplosives. The resulting electronic modulations of the parent TTF-pyrrole structure result in significantly enhanced binding affinities for the corresponding TTF-C4Ps toward polynitro-explosives. This is reflected in a high level of positive homotropic allosterism. The degree of the cooperative effect was found to vary depending on the nature of both the receptors and guest species. The origin of the cooperative binding can be explained by conformational locking and an inductive effect of binding the first nitroaromatic guest. / text

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Photochromism is a phenomenon where two isomers with markedly different absorption spectra are interconverted by a reversible photochemical reaction. The photochromism of 1’,3’,3’-trimethyl-6-nitrospiro[2H-1]-benzopyran-2,2’-indoline (NSP) and 1,2-bis(2,4-dimethyl-5-phenyl-3-thienyl)-3,3,4,4,5,5-hexafluoro-1-cyclopentene) (DAE) was studied in aqueous solutions containing NaCl and the bile salts sodium cholate (NaC), sodium deoxycholate (NaDC) or sodium taurocholate (NaTC). Bile salts are amphiphilic compounds that aggregate in water. These aggregates can solubilize hydrophobic organic compounds in water and affect the reactivity of the bound compounds. NSP and DAE are photochromic compounds that can be switched between a colored and a colorless isomer. The colored isomer of DAE can only be transformed into the colorless form by irradiation of light, while the colored isomer of NSP is also converted into the colorless form by a dark reaction. The dark reaction rate constant of NSP increases at high concentrations of bile salt and NaCl. The bile salt structure also affects the dark reaction rate constant, which is smaller in NaTC and approximately the same in NaC and NaDC. The activation energy for the reaction in all conditions studied is similar to the value reported for polar organic solvents. A method that employs HPLC was developed to determine the molar absorptivity coefficients of photochromic compounds. The values obtained were important to determine the quantum yields for photocoloration (ΦAB) and photodecoloration (ΦBA). Quantum yield values were determined by a photokinetic method that employs irradiation at a single wavelength and numerical analysis. The values of ΦAB and ΦBA for DAE in bile salts are the same as the values in cyclohexane. For NSP, ΦAB is dependent on the structure of the bile salt and increases in the order NaTC < NaC < NaDC. / Graduate

p-Sulfonatocalix[X]arene (X = 4 and 6) was explored as a host for trimethyllyated lysine. We found by 1H NMR and ITC titrations that p-sulfonatocalix[4]arene (PSC) bound the trimethyllysine amino acid with high affinity and good selectivity over dimethyllysine and similar dimethylated arginines. When trimethyllysine was in the context of a peptide of the histone 3 tail, affinities increased and PSC was up to 20 -fold selective over identical unmethylated peptides. Multiple scaffolds were synthetically explored as derivatives of PSC. I created five different scaffolds and synthesized a small library of compounds derived from these scaffolds as hosts for a variety of histone 3 peptides containing biologically important post-translationally modified amino acids. This library was tested using a high-throughput indicator displacement assay and I found three hosts that displayed tuned affinities and selectivities for post-translationally modified amino acids we had not previously targeted. I studied the ability of these synthetically elaborated calix[4]arenes to identify histone PTMs and monitor an enzymatic reaction. I found covalently linked fluorescent calixarenes were able to accomplish this goal. Furthermore, we studied the ability of these calix[4]arenes to disrupt protein-protein interactions that occur between the trimethyllyated lysine on histone tails and proteins that read these sites. I found that these calixarenes could disrupt these interactions between a variety of proteins and trimethyllyated lysine sites. These calix[4]arenes show promise as chemical tools that could be used to further probe epigenetic pathways in vitro and further work is needed to explore their utility in cellular assays and in vivo. / Graduate / 0490 / 0487 / kddaze@gmail.com

Photochromism is a phenomenon where two isomers with markedly different absorption spectra are interconverted by a reversible photochemical reaction. The photochromism of 1,3,3-trimethyl-6-nitrospiro[2H-1]-benzopyran-2,2-indoline (NSP) and 1,2-bis(2,4-dimethyl-5-phenyl-3-thienyl)-3,3,4,4,5,5-hexafluoro-1-cyclopentene) (DAE) was studied in aqueous solutions containing NaCl and the bile salts sodium cholate (NaC), sodium deoxycholate (NaDC) or sodium taurocholate (NaTC). Bile salts are amphiphilic compounds that aggregate in water. These aggregates can solubilize hydrophobic organic compounds in water and affect the reactivity of the bound compounds. NSP and DAE are photochromic compounds that can be switched between a colored and a colorless isomer. The colored isomer of DAE can only be transformed into the colorless form by irradiation of light, while the colored isomer of NSP is also converted into the colorless form by a dark reaction. The dark reaction rate constant of NSP increases at high concentrations of bile salt and NaCl. The bile salt structure also affects the dark reaction rate constant, which is smaller in NaTC and approximately the same in NaC and NaDC. The activation energy for the reaction in all conditions studied is similar to the value reported for polar organic solvents. A method that employs HPLC was developed to determine the molar absorptivity coefficients of photochromic compounds. The values obtained were important to determine the quantum yields for photocoloration (AB) and photodecoloration (BA). Quantum yield values were determined by a photokinetic method that employs irradiation at a single wavelength and numerical analysis. The values of AB and BA for DAE in bile salts are the same as the values in cyclohexane. For NSP, AB is dependent on the structure of the bile salt and increases in the order NaTC < NaC < NaDC. / Graduate / 2015-03-31

The set of molecules cucurbit[n]uril (Qn) are macrocycles composed of n glycoluril monomers linked by methylene groups. These molecules have two oxygen-ringed portals of a diameter slightly smaller than their internal cavity diameter. This thesis describes syntheses, crystallisations, crystal structure determinations, crystal packing analyses and force field calculations exploring the supramolecular chemistry of Qn molecules and their derivatives. Qn acts as a host for guest molecules and at the outset of this project no metal containing molecule had been encapsulated in a Qn molecule. One aim of this project was to prepare such complexes. This was achieved with the synthesis and characterisation of crystalline {[cis-SnCl4(H2O)2]@Q7}2(SnCl6)3(H3O)6(H2O)23. Other compounds prepared and characterised crystallographically in the course of this project are: [(Q6)(Na3(H2O)8)]2[CoCl4]4[Co(H2O)6]2[CoCl(H2O)5]2(Cl)4, (Q5@Q10)(CH3COOH)(Cl)2(H3O)2(H2O)26, (Cl@Q5)4Q6(SnCl6)8(H3O)20(H2O)24, (Q8)3(PtCl6)4(H3O)8(H2O)x, (Q8)2(PtCl6)3(H3O)6(H2O)18, (Q7)(Cr3O10)(H3O)2(H2O)x and (Q6)(SnCl6)(H3O)2(H2O)x. While the smaller Qn (n = 5?) retain their circular forms, the larger Qn (n &gt 8) are less rigid and distort to accommodate larger guests. After analysis of the crystal structures of these Qn compounds and those listed in the Cambridge Structural Database, the principal packing motifs of the Qn molecules were elucidated. The most common is the portal-to-side interaction in which the portal oxygen atoms of one Qn approach the hydrogen atoms around the equator of another Qn. Force-field calculations on guest@Qn complexes were conducted to determine the mechanism for the formation of these complexes. A comparison of the intermolecular interactions of phenylated systems and comparable fluorinated phenyl systems was made using both crystal packing analyses and forcefield energy calculations. Intermolecular energy parameters for these calculations were derived and validated in this work. The principal fluorinated species studied was the [B(C6F5)4]?anion. Examination of its crystal structures found that the substitution of the hydrogen atoms by fluorine atoms is influential enough to alter the predominant intramolecular conformation. It is the ???flipper?conformer, between pairs of perfluorophenyl groups, that is overwhelmingly the favoured conformation and this has a strong effect on the types of phenyl embraces that a [B(C6F5)4]?anion will form. While the parallel 4PFE, the offset parallel 4PFE and the orthogonal 4PFE are all observed the 6PFE is not.