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At the end of this thesis, selected 1H NMR spectra and crystallographic data are given as an Appendix. / Chapter 1 presents an overview of supramolecular chemistry and the general properties of phthalocyanines, focusing on the self-assembly of mixed porphyrin and phthalocyanine systems. / Chapter 2 describes the complexation of bis(pyridinolato) silicon(IV) phthalocyanines to several cobalt(II) porphyrins. As shown by absorption spectroscopy, both 1:1 and 1:2 molecular assemblies can be obtained depending on the relative amount of the two components and the position of the pyridyl ligand. The axially bound 1:1 phthalocyanine-porphyrin arrays have also been isolated and characterized spectroscopically. / Chapter 3 reports an extension of this work. Two novel phthalocyanines with 3 or 4 pyridyl axial substituents have been synthesized. These compounds bind to meso-tetraphenyl zinc porphyrin to form the corresponding tetrakis- and pentakis-mixed tetrapyrrole systems. / Chapter 4 discusses the preparation of several covalently-linked phthalocyanine-cyclodextrin conjugates. These compounds can form inclusion complexes with sulfonated porphyrin in water providing a new strategy to construct mixed phthalocyanine and porphyrin systems. / Chapter 5 reports the interactions of two octacarboxy phthalocyanines with beta-cyclodextrin. Through the formation of inclusion complexes, the latter serves as a disstacking agent reducing the aggregation tendency of these phthalocyanines. This supramolecular approach could be an effective way to generate hydrophilic and non-aggregated phthalocyanines, improving their photosensitising properties in aqueous media. / This thesis reports our investigation on the supramolecular chemistry of phthalocyanines. The first part of the thesis describes the self-assembly of mixed porphyrin and phthalocyanine systems through axial coordination. The second part complexes between phthalocyanines and reports the formation of some novel inclusion phthalocyanine-cyclodextrin conjugates and porphyrins, beta-cyclodextrin. / Leng, Xuebing. / "March 2007." / Adviser: Dennis K. P. Ng. / Source: Dissertation Abstracts International, Volume: 68-09, Section: B, page: 5946. / Thesis (Ph.D.)--Chinese University of Hong Kong, 2007. / Includes bibliographical references. / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Electronic reproduction. [Ann Arbor, MI] : ProQuest Information and Learning, [200-] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstract in English and Chinese. / School code: 1307.

The movement away from metals towards polymers for automobile bearing coatings opens a new area for the possible modification of these coatings. This project, done in collaboration with Castrol, was to understand adsorption of small molecules at the surface of these polymers and work towards engineering host-guest interactions at the surface to provide binding of specific molecules. Initially, the commercial polyamide-imide was characterised via Nuclear Magnetic Resonance (NMR), Infrared (IR) and Ultra-Violet/Visible (UV-Vis) spectroscopy to understand the nature of the functional groups and structures present. This revealed that the imidisation reaction was incomplete so the functionality within the polymer could change and thus alter how molecules interact with it. This reaction was then investigated via IR and NMR spectroscopy and it was shown that the degree of imidisation varied with temperature. Then the characterised polyamide-imide was used to study the adsorption of alkylphenols, a class of molecules that have structures and functionality like common additives used in engine oils. Additionally, the adsorption of water was studied as it is a common contaminant. These two systems were studied via solution depletion isotherms and neutron reflectivity measurements. The isotherms confirmed the adsorption of the molecules whilst neutron reflection was used to characterise the layers. For alkylphenol, a rather sparsely packed layer of the molecules and solvent existed at the surface with their alkyl tails extending into the solvent. For water; the molecules diffuse into the polyamide-imide. It can be partially removed by washing the surface with dry dodecane; however, some water remains in the polymer layer. A viologen-cucurbit[8]uril binding site was chosen as the supramolecular surface interaction. The binding unit was incorporated into the polyamide-imide. The synthesis of the binding site polymer was achieved in two stages; the reproduction of the commercial polymer and the synthesis of a polymer containing 100% viologen with and without threaded cucurbit[8]uril. Whilst the synthesis appeared successful, neutron reflectivity measurements showed that, when in contact with a solution containing a second guest, no adsorption was seen on the polymer containing cucurbit[8]uril. In order to study the supramolecular interaction in non-polar solvent, a series of rotaxanes were synthesised with viologen-cucurbit[8]uril cores and bulky stopper groups to prevent unthreading of the cucurbituril as well as enhancing the solubility of the system. The two components were linked via an amidisation reaction between an acid chloride and an amine. Due to the low solubility of the products confirmation of synthesis was only possible in one case. As well as using a viologen-cucurbit[8]uril binding site, binding in cucurbiturils via halogen bonding was investigated as common halogen bonding species show good solubility in non-polar solvents. Initially co-crystals of 2,5-diiodo-1,3,4,6-tetrafluorobenzene with tertiary amides were studied. With N,N-dimethylformamide, a 1:2 co-crystal was seen but the structure with N-methyl-2-pyrrolidone had a stoichiometry of 1:1. In both structures the oxygen of the amide is involved in a halogen bonding; however, for N-methyl-2-pyrrolidone it is bifurcated leading to the formation of chains. A 50-50 mixture of pyridine and formic acid was found to solubilize both halogen bond donors and cucurbit[n]uril. Over the course of these experiments the structure of the co-crystals of two halogen bond donors, 2,5-diiodo-1,3,4,6-tetrafluorobenzene and 2,4,6-triiodo-1,3,5-trifluorobenzene, with pyridine were determined. Crystals of the cucurbituril-adducts weren’t of sufficient quality to determine the structure. The presence of binding solution was confirmed by 1H and 19F NMR experiments on the methyliodide-cucurbit[6]uril and Trans-diiodooctrafluoroazobenzene-cucurbit[8]uril systems.

Resumo: Este trabalho contempla a preparação e a caracterização estrutural, térmica e morfológica de novas espécies de paládio (II), discretas e multidimensionais, usando o complexo [PdCl2(CH3CN)2] como material de partida. Visando obter sólidos de coordenação porosos, foram utilizados como ligantes os espaçadores lineares nitrogenados 4,4'-bipiridina (4,4'-bipy), trans-1,2-bis(4-piridil)etileno (bpe) e pirazina (pz), além dos grupos dicarboxilatos oxalato e fumarato. Foram obtidas duas séries de compostos, [Pd2(μ-ox)(ox)(L)]n (1-3) e [Pd(μ-fum)(μ-L)]n.nH2O (4-6) (ox = oxalato; fum = fumarato; L = 4,4'-bipy, bpe, pz). As hipóteses estruturais mais prováveis para essas metalosupramoléculas envolvem a formação de espécies octanucleares contendo cavidades quadradas e grades 2D retangulares, respectivamente. Curvas TG/DSC permitiram o estabelecimento da ordem de estabilidade térmica e a confirmação das estequiometrias propostas para os compostos obtidos. A microscopia eletrônica de varredura permitiu averiguar as características morfológicas das partículas dos compostos, bem como inferir a presença de poros nos mesmos. Foram realizados, então, ensaios de adsorção de nitrogênio e de porosimetria de mercúrio, onde pode ser observado que as dimensões das cavidades ou canais formados nas estruturas das supramoléculas podem ser manipuladas pela escolha adequada do tamanho ou funcionalidade do espaçador. / Abstract: This work deals with the synthesis and structural, thermal and morphological characterization of novel, discrete and multidimentional, palladium(II) species using the complex [PdCl2(CH3CN)2] as starting material. In order to obtain porous coordination solids, the linear N-based spacers, 4,4'-bipyridine (4,4'-bipy), trans-1,2-bis(4- pyridil)ethylene (bpe) and pyrazine (pz), as well the dicarboxylate groups, oxalate and fumarate, were utilized as ligands. Two series of compounds were obtained, [Pd2(μ- ox)(ox)(L)]n (1-3) and [Pd(μ-fum)(μ-L)]n.nH2O (4-6) (ox = oxalate; fum = fumarate; L = 4,4'- bipy, bpe, pz). The more probable structural hypothesis for these metallosupramolecules includes the formation of octanuclear species containing square cavities and 2D retangular grids, respectively. TG/DSC curves allowed the proposition of a thermal stability order and the confirmation of the proposed stoichiometric composition for the obtained compounds. MEV micrographies permitted to investigate the morphologic characteristics of the particles of the compounds, as well to infer about the presence of the porous in these systems. Mercury porosimetry and nitrogen adsorption experiments were then carried out, in which it was possible to observe that the dimentions of the cavities or canals of the supramolecules can be manipulated by the convenient choice of the size or the functionality of the spacer. / Orientador: Regina Célia Galvão Frem Di Nardo / Coorientador: Antonio Eduardo Mauro / Coorientador: Adelino Vieira de Godoy Netto / Banca: Luiz Antonio Andrade de Oliveira / Banca: Vera Regina Leopoldo Constantino / Mestre

The work in this dissertation has two main focuses: (1) to develop sensors based on a quadruplex-forming oligonucleotide scaffold for the sensing of specific sequences, (2) to develop an indicator displacement assay for the high-throughput determination of host-guest binding capable of easy discrimination between strong and weak-binding species. Chapter 1 serves to provide a brief introduction to some shared background for both projects, through introducing basic tenants of aqueous supramolecular chemistry and nucleic acid chemistry, in addition to some general lessons in system design that can be learned from the study of biology. Chapter 2 describes the design of a sensor based on a naphthalene mono-imide (NMI) scaffold, which due to an intramolecular charge-transfer from the naphthalene to a conjugated bipyridine has a low native fluorescence emission. When exposed to curcubit[7]uril (CB[7]) a macromolecular host able to encapsulate the bipyridine unit, the intramolecular charge-transfer is interrupted, resulting in a significant increase in fluorescence quantum yield (by over an order of magnitude). This enhancement is reversible, with competing binders for CB[7] causing a return to the unbound state with quenched emission. Importantly, this sensor exhibits robust activity with no significant variance in properties throughout the range of 5-10 pH, and is amenable to secondary functionalization for surface attachment without loss of activity. A facile microplate assay was developed on the surface-bound sensor, and a proof of concept study was shown by testing for binding against a library of therapeutically relevant drug classes, resulting in the discovery of three novel guests for CB[7] possessing strong to moderate binding affinities. Chapter 3 discusses the development of an oligonucleotide sensor called a quadruplex molecular beacon (QMB) that is able to transition between a closed, intramolecular quadruplex state and an open, intermolecular duplex state on the sequential application of two stimuli in the form of specific oligonucleotide sequences. The chapter initially focuses on optimizing strand exchange mechanisms that allow for the sequential stimuli to open (and close) the system, finding that the combined use of a short toehold sequence with a targeted base-pair mismatch leads to efficient hybridization and displacement with sequential stimuli. The remaining part of the chapter examines the use of this strand exchange mechanism to drive a fully constituted QMB through sequential opening and closing in response to sequential stimuli, with a corresponding fluorescence signal. / Cooper Battle

acase@tulane.edu / Since the mid-20th century supramolecular chemistry has become a thriving field in synthetic chemistry. Supramolecular assemblies are assemblies of molecules formed and stabilized by non-covalent interactions. Deep-cavity cavitands, bowl-shaped molecules, are one such class of molecules that form assemblies using the hydrophobic effect when in the presence of suitable hydrophobic guests in an aqueous environment. Computer simulations allow us to study these assemblies at the molecular level and provide valuable insight into both the thermodynamics of assembly as well as provide information relevant to the design of the next generation of deep-cavity cavitands. This research begins by investigating dimeric capsules of a deep-cavity cavitand known as Octa-acid (OA). We use Molecular Dynamics to study a homologous series of n-alkane guests in order to learn some of the "rules" of guest packing. Additionally we use a machine learning technique to harvest a dominant conformation from each simulation and compare computed chemical shifts of that structure with experimental chemical shifts. The second part of this dissertation looks into multimeric systems formed by one of OA's derivatives known as Tetra-endomethyl Octa-acid (TEMOA). The entrance to the binding pocket of TEMOA is narrower than OA due to four methyls being added to its rim. TEMOA forms not only dimers, but also tetramers and hexamers, depending on the guest size. We use free energy techniques to show that guest packing primarily drives the transitions between each assembly state. Additionally we obtain the interior volumes of each multimer and demonstrate that they now approach that of structures formed by other means. We give insight into why TEMOA forms multimeric systems and OA does not. The last section of this dissertation compares the interior hydration characteristics of OA and TEMOA. We show that the small structural changes from OA to TEMOA promote a large change in wetting/dewetting behavior inside the binding pocket. Normally OA is full of water in its interior, but TEMOA exhibits a two-phase behavior. Here we also demonstrate a simple bridge between simulation and experiment to validate our findings by using partial molar volume calculations. / 1 / James Wesley Barnett

This thesis describes the synthesis and X-ray crystallographic analysis of a series of supramolecular architectures prepared using seven flexible multimodal ligands with Ag(I), Cu(I), Cd(II), Co(II), Ni(II) and Pd(II) metal salts. Chapter one introduces some examples of fundamental supramolecular systems with particular focus on metallo-supramolecular motifs, specifically coordination polymers. Topological analysis is discussed as a method for the simplified description and comparison of network structures. Chapter two describes the design, synthesis and characterisation of the symmetrical ligands bis(2-pyrazylmethyl)sulfide (psp), bis(4-pyrimidylmethyl)sulfide (msm) and 5,5�-(thiodimethylene)di-pyrazine-2-carboxylic acid methyl ester (csc) as well as the asymmetrical ligands 2-benzylsulfanylmethyl-pyrazine (psb), 2-pyridylsulfanylmethyl-pyrazine (psd), 3-pyridylsulfanylmethyl-pyrazine (psn) and 4-pyridylsulfanylmethyl-pyrazine (psy). Chapter three presents a literature review of ligands related to psp, msm and csc, followed by the synthesis and characterization of thirteen Ag(I), Cd(II), Co(II), Ni(II) and Pd(II) complexes. The X-ray crystal structures of nine of these complexes are reported and compared. The structures were present as either one- or two-dimensional coordination polymers. The {[Ag(psp)](PF₆)}[infinity] and {[Ag₂(psp)(C₆H₆)(CH₃CN)₂](PF₆)₂�CH₃CN}[infinity] structures demonstrated a solvent dependence by forming a 1-D twisted ladder with a [eta]�-bound benzene and a 2-D undulating sheet with a 4.8� topology respectively. Six of the structures {[Cd₂(psp)(CH₃CN)(H₂O)(NO₃)₄]�H₂O}[infinity], {[Co(psp)(CH₃CN)₂](ClO₄)₂}[infinity], {[Ni(psp)(NO₃)₂]}[infinity] and {[Ag(msm)](X)}[infinity] (X = BF₄⁻, ClO₄⁻, PF₆⁻) displayed anion-[pi] interactions between multi-atomic anions and [pi]-acidic ring centres. A novel N[pz]���cent[pz] T-shaped [pi]-[pi] interaction was also identified in the {[Ni(psp)(NO₃)₂]}[infinity] structure. A 2-D sheet with 6� topology was observed in the X-ray structure of {[Ag₂(csc)](NO₃)₂}[infinity]. Following a review of related ligands, chapter four focuses on seven Ag(I), Cd(II), Co(II) and Cu(I) complexes formed using the asymmetric pyrazine-benzene ligand psb. In total six 1-D coordination polymer chains are reported. Two structurally disparate supramolecular isomers were formed in [Ag(psb)NO₃][infinity] and {[Ag₂(psb)₂NO₃]NO₃�H₂O}[infinity]. The compound {[Ag(psb)](BF₄)}[infinity] was similar to the former isomer [Ag(psb)NO₃][infinity]. The structurally similar coordination polymers {[Cd(psb)(H₂O)(NO₃)₂]}[infinity] and {[Co(psb)(H₂O)₃](ClO₄)₂�H₂O}[infinity] formed structures that showed anion-[pi] interactions using coordinated and non-coordinated anions respectively. The [Cu₂(psb)I₂][infinity] chain consisted of ligands linked together by a Cu₄I₄ stepped cubane tetramer. Chapter five presents seventeen Ag(I) and Cu(I) complexes prepared using three asymmetric pyrazine-pyridine ligands psd, psn and psy. A review of asymmetric pyrazine-pyridine ligands is provided. Seventeen X-ray crystal structures are described. Four psd complexes using AgBF₄, AgClO₄, AgNO₃ and AgPF₆ crystallised as discrete dimers with three types of crystal packing and ligand-supported Ag���Ag interactions. The complexes {[Ag₂(psd)₂CF₃SO₃]CF₃SO₃}[infinity] and {Cu₂(psd)I₂}[infinity] were a 1-D X-shaped chain and a 2-D 6� net respectively. The isostructural 2-D sheets in {[Ag(psn)]ClO₄}[infinity] and {[Ag(psn)]PF₆�CH₃CN}[infinity], had 4.8� topologies whereas a thicker sheet was formed in {[Ag₂(psn)₂](BF₄)₂}[infinity] with a complicated (4�.6�.8�)₂(4.6.8)₂ topology. The {[Ag₃(psn)₂](CF₃SO₃)₃�CH₃CN}[infinity] chain polymer displayed three different coordination geometries around the three Ag(I) centres with two ligand-unsupported Ag���Ag interactions. The complex [Cu₂(psn)₂I₂] crystallised as a discrete dimer with a different ligand arrangement than those found in the psd dimers. Six Ag(I) 3-D networks were formed using psy. The complexes {[Ag(psy)]X}[infinity] (X = BF₄, ClO₄, PF₆) formed as isostructural non-interpenetrated (10,3)-d networks. An unprecedented tri-nodal (4.6.8)₂(6.8�)₂(4.6.8�.10)₂ topology was observed in the {[Ag₂(psy)₂](CF₃SO₃)₂}[infinity] structure. The suprarmolecular isomers {[Ag₃(psy)₂(NO₃)₂]NO₃]}[infinity] and {[Ag₃(psy)₂(NO₃)₃]�H₂O}[infinity] formed inclined interpenetrated 6� sheets and a (4�.6)₂(4⁴.6�.8⁸.10) 3-D network respectively. The structures in this chapter showed a general trend of increasing dimensionality when progressing from psd to psn to psy. Chapter six presents a summary of the more significant results and concluding remarks.

This dissertation investigates the synthesis, characterization and electrochemical properties of viologen-containing dendrimers. Additionally, the self-assembled system of resorcinarenes was investigated with paramagnetic guests using EPR and 1H NMR techniques. Chapter one is a brief introduction to the dendrimers and describes its evolution, structural features, synthetic methods and emerging applications to various fields of research such as catalysis, material science, drug delivery and medicine. Chapter two describes the synthesis, characterization and electrochemical properties of a new series of dendrimers. These dendrimers have a viologen unit at the core surrounded by Newkome and Fr¨¦chet dendrons. The potentials of two consecutive one-electron reductions of the viologen core were determined by cyclic voltammetry. The electrochemistry of viologen unit showed a distinct and obvious trend. Newkome and Frechet dendrons having different functional groups as repeating units has opposite effect on the half-wave potentials. The overall effect of these two dendrons is reflected by the corresponding reduction potentials. The redox site encapsulation by the Frechet and Newkome dendrons is indicated by the attenuation in heterogeneous electron transfer rate constants. Chapter three describes the probing of self-assembled capsule of resorcinarenes with 4-amino tempo and 4-trimethyl-ammonium tempo derivative. EPR spectroscopy and 1H NMR spectroscopy were used to investigate the nature of complexations involved in these systems. We observed a subsequent change in their spectroscopic parameters. Careful investigation of rotational correlation times and NMR line-widths at half height revealed that 4-trimethyl-ammonium tempo has stronger binding affinity with these capsules compared to 4-amino tempo due to favorable cation -pi interactions.

The research work presented in this thesis is a consolidated report of experiments aimed at controlling the product selectivity in photochemical reactions. Water soluble hosts such as p-sulfonato calix[n]arenes (n= 6 or 8) and cyclodextrins have been used to solubilize organic molecules in water and to control the product selectivity. These host molecules control the product selectivity by their ability to encapsulate and interact with guest molecules. Furthermore, carrying out reactions in water as solvent is important from green chemistry point of view.

In this study, a synthetic, water soluble cavitand octa acid (OA) is used as medium for conducting photochemical reactions. The cavitand octa acid is soluble in water in slightly basic conditions. OA forms different types of complexes with variety of organic guest molecules. Remarkably, in presence of a hydrophobic guest, two of these OA molecules self assemble to form a capsular complex (guest@(OA)2). The confined inner phase of the cavitand can be utilized to control both photochemistry and photophysics of organic guest molecules. Stilbene derivatives undergo cis/trans (Z/E) photoisomerization in organic solvents. The results of our studies with stilbenes@(OA)2 suggest that the available free volume for encapsulated guest stilbenes could be manipulated by changing the number and position of the substituent methyl groups which has a significant influence on the photoisomerization process. Further, energy transfer from caged donor ((fluorenone)2@(OA)2) to caged acceptor ((stilbene)@(OA)2) was explored. It is also demonstrated that photoinduced electron transfer (PET) between acceptor (cationic) present outside the OA capsule to donor (a stilbene) present within the capsule is feasible and occurs at a higher than diffusion controlled rate. The PET in the above supramolecular system could be controlled by employing another cavitand, cucurbit[7]uril (CB7) to complex with cationic acceptor. Also, studies with carefully chosen guest molecules suggest that selective photocyclodimerization can be carried out within the inner phase of OA.