This thesis investigates the design and synthesis of macrocycles and examines their ion-pair recognition, anion recognition and interpenetrative assembly capabilities. Chapter One introduces the field of supramolecular chemistry. Key concepts in host–guest complexation and self-assembly are outlined, with particular emphasis on the design of host systems for anion and ion-pair recognition. Chapter Two details the synthesis and binding properties of a heteroditopic 1,2,3-triazole- containing macrocycle that exhibits cooperative ion-pair recognition. Solution and solid-state evidence shows that the triazole motif simultaneously binds anions and cations. The exten- sion of this work towards the formation of interlocked structures containing an expanded heteroditopic macrocycle and threading components is explored. Chapter Three discusses the design and syntheses of series of electron-deficient macrocycles based on imidazolium, pyridinium and triazole. These are investigated for anion binding ability and assembly of interpenetrative assemblies with electron-rich threading components. Chapter Four describes research into the formation of interpenetrative assemblies using neutral components. Their design is based around aromatic donor–acceptor interactions and halogen bonding. Chapter Five presents some conclusions from the research undertaken. Chapter Six provides titration protocols, Job plot approximations, experimental procedures and characterisation of the compounds described in this thesis. Appendix details additional X-ray crystallographic data.

The synthesis, characterisation and anion binding properties of a series of mono- and bifunctional Lewis acidic borylferrocene compounds are described within this thesis. The original parent compound FcBMes₂ (3.1), revealed a versatile route for the synthesis of such borylferrocenes and subsequently the analogous compound Fc*BMes₂ (3.2) was synthesised. The anion binding properties of (3.1) and (3.2) were investigated and both were shown to bind one equivalent of cyanide. The binding event was signalled by an electrochemical shift (ca. -560 mV) and a quenching of bands at 510 or 542 nm respectively in the UV/Vis spectrum, while the mode of anion binding in the solid state was established by X-ray crystallography for [ⁿBu₄N]⁺[(3.1)·CN]⁻. Incorporation of a suitable redox active dye (i.e. tetrazolium violet for 3.2) allowed conversion of the electrochemical response to a colorimetric change on cyanide binding. However, a competing response for fluoride is also seen for (3.1) and (3.2). Thus a two component system is reported involving (3.2) and the boronic ester FcB(OR)₂ (3.4), [where (OR)₂ = OCH(Ph)CH(Ph)O], which from previous research is known to selectively bind fluoride, and allows for selective colorimetric cyanide sensing by simple Boolean AND/NOT logic. 1,4-C₆H₄(BMes₂)[B(OR)₂] (3.5), 4,4-C₁₂H₈(BMes₂)[B(OR)₂] (3.6) and 1,1′-fc(BMes2)(B(OR)2) (3.7) were synthesised as possible single molecules for discrimination between cyanide and fluoride. (3.5) and (3.6) proved only capable of binding one equivalent of either anion, (3.7) showed some ability to bind two equivalents of fluoride however based on ESI-MS studies although only in the presence of a large excess of anion. Systematic variation of the para-boryl substituent was investigated by synthesis of compounds FcB(Xyl^F)₂ (4.1), FcB(Xyl)₂ (4.2) and FcB(Xyl^OMe)₂ (4.3). Anion binding studies reveal a linear increase in fluoride binding affinity consistent with that expected based on the para,/em>-Hammett parameters, however with only minor differences, while no pattern is observed with respect to their cyanide binding capabilities. The addition of neutral and cationic peripheral substituents has been investigated through synthesis of [1,2-fc(CH₂NMe₂)BMes₂] (4.6) and [1,2-fc(CH₂NMe₃)BMes₂]⁺ (4.7). Subsequent binding studies revealed (4.6) to be moisture sensitive, however reaction of (4.7) with fluoride and cyanide led to formation of the adducts [(4.7)·F]⁻ and [(4.7)·CN]⁻. The anion affinity of (4.7) exhibits a substantial increase when compared to the parent compound (3.1). Even when compared to the isomeric 1,1′ system an increase of approximately three orders of magnitude is seen attributed to the closer nature of the cationic charge and in the fluoride adduct the presence of a cooperative intramolecular hydrogen bond. The 1,1′-bifunctional analogues of the mono-substituted systems were synthesised [e.g. 1,2-fc(BMes₂)₂ (5.1)] and shown to complex two equivalents of fluoride or cyanide in acetonitrile. The 1:1 cyanide adduct of (5.1) was isolated in chloroform however, no evidence for chelation was observed. The analogous systems 1,2-fc(BMes₂)₂ (5.5), 1,2-fc(BXyl₂)2 (5.7), and 1,2-fc(BMes₂)(BXyl₂) (5.8) were also investigated. Reaction of (5.5) with fluoride and cyanide revealed it to bind only one equivalent of either anion, neither however was bound in a chelating fashion although X-ray crystallography revealed cyanide binds exo whilst fluoride binds endo to the B···B cavity. Finally the kinetics of fluoride binding were studied by UV/Vis spectroscopy and showed a systematic increase in rate constant upon reduction of steric bulk.

The work described in this thesis demonstrates the use of supramolecular chemistry in the template-directed synthesis of porphyrin nanorings and as a tool to control conformation and topology of π-conjugated porphyrin oligomers. Particular emphasis is placed on changes to the electronic structure of these oligomers depending on their conformation. Chapter 1 gives an overview of π-conjugated porphyrin oligomers and conjugated macrocycles in general, followed by an introduction into supramolecular cooperativity and small angle X-ray scattering in solution. Chapter 2 describes advances in the synthesis, solution structure elucidation and optoelectronic properties of a fully conjugated cyclic porphyrin hexamer. The high rigidity and symmetry of this nanoring as well as its bent π-system lead to a significant decrease in its HOMO-LUMO gap. The resulting near-infrared emission was exploited in the fabrication of light emitting diodes, demonstrating the use of a bent topology for minimizing aggregation in thin films. The synthesis of a [12]porphyrin nanoring using a hexadentate template is presented in Chapter 3. The concept of Vernier templating is introduced as a general strategy for the synthesis of large monodisperse macrocycles. The nanoring is characterized and its cooperative binding to two template molecules is studied. In Chapter 4 a bidentate ligand is used in the cooperative formation of a sandwich complex beween two nanorings. Chapter 5 provides an analysis of the rigidity of the butadiyne linked porphyrin oligomers used throughout this thesis. A linear chain is significantly more flexible in solution than on a surface where it is confined within two dimensions. Analysis of the persistence length indicates that a porphyrin nanoring with more than around 20 units would not be significantly strained. The supramolecular binding of linear porphyrin oligomers to carbon nanotubes is analyzed in Chapter 6. The binding strength increases sharply with oligomer length and binding is strongest with (8,6) and (7,5) tubes. The energy level alignment in these porphyrin CNT complexes appears to be favorable for an application in photovoltaics. In Chapter 7 bisamidine-carboxylate salt bridges together with zinc-nitrogen coordination chemistry are used to access a variety of topologies in assemblies based on carboxylic acid functionalized porphyrin dimers.

This thesis describes the synthesis and investigation of novel anion templated interlocked structures which incorporate the positively charged imidazolium and triazolium binding motifs for applications in anion recognition and sensing. Chapter One introduces the fields of anion supramolecular chemistry and mechanically interlocked structures, focusing on topics of particular relevance to this thesis, including anion recognition, anion sensing and the templated synthesis of interlocked architectures. Chapter Two details the incorporation of the imidazolium motif into the axle components of anion templated rotaxane hosts to achieve selective anion recognition by virtue of their interlocked binding cavities. The effects of exploiting imidazolium motifs with contrasting hydrogen bond donor arrangements and reducing the macrocycle size on the anion recognition properties of such systems were investigated using 1H NMR spectroscopy. Chapter Three reports the work undertaken to utilise fluorescent reporter groups as stoppers in the synthesis of anion sensing rotaxanes. Imidazolium- and triazolium based systems containing either luminescent ruthenium(II) bipyridyl complexes or the organic fluorophore anthracene were prepared and their anion sensing behaviours explored using fluorescence spectroscopy. Synthetic efforts to construct suitable photo-active rotaxanes are detailed. Chapter Four describes investigations of the novel naphthalimide triazolium motif both for use in interlocked molecular motion systems, and for fluorescence sensing applications. The preparation of a naphthalimide triazolium rotaxane, capable of selective, anion-induced, uni-directional shuttling which was investigated extensively using 1H NMR spectroscopy and optically signalled by perturbations in the UV/Vis spectrum, is detailed. Preliminary research studies into the potential to exploit this motif for surface based fluorescence sensing devices are also included. Chapter Five presents research into the utilisation of acyclic receptors displaying considerable binding induced conformational changes for fluorescence anion sensing. The recognition properties of a series of imidazolium-based receptors were studied, whilst the ability of a pyrene appended analogue to signal anion complexation via changes in excimer emission is reported. The control of interpenetrated assembly formation using anion-induced conformational changes within the threading component of a pseudorotaxane is also discussed. Chapter Six provides the experimental procedures and characterisation details for the compounds synthesised in this thesis. Chapter Seven is a summary of conclusions from Chapters Two, Three, Four and Five. Supplementary information relating to titration protocols, crystallographic data and surface studies is provided in the Appendices.

This thesis explores the surface assembly of mechanically interlocked molecular architectures at gold surfaces for potential applications in molecular switches, anion sensing and stimuli (redox and optical) responsive molecular films. <b>Chapter One</b> introduces the field of mechanically interlocked molecules focusing on rotaxane and catenane surface assemblies in the form of single molecule thick self-assembled monolayers. A review of the surface-attached characteristics of mechanically interlocked molecules is given before exploring specific anion template directed strategies for their construction. The potential to incorporate both redox-active and optically-active functional groups within these mechanically interlocked molecules is also discussed. <b>Chapter Two</b> provides the experimental details and procedures employed in this thesis to characterise the molecular systems under investigation. <b>Chapter Three</b> introduces several surface characterisation techniques such as; ellipsometry, contact angle, X-ray reflectivity and X-ray photoelectron spectroscopy, with a particular focus of applying these tools to probe the surface co-conformation of switchable and interlocked molecules at surfaces. Electroanalytical techniques such as cyclic voltammetry, chronoamperometry and electrical impedance spectroscopy are also introduced. <b>Chapter Four</b> details the surface assembly of a series of ferrocene containing anion templated catenane self-assembled monolayers on gold. Detailed electrochemical and angle resolved X- ray photoelectron spectroscopy characterisation elucidates the co-conformation upon surface attachment. <b>Chapter Five</b> details the anion templated surface assembly of a redox-active rotaxane self- assembled monolayer on gold. Subsequent electroanalysis and X-ray photoelectron spectroscopy characterisation confirms the structural integrity of the film and a possible co- conformation at the surface is discussed. <b>Chapter Six</b> describes efforts towards constructing optically responsive hybrid d-f lanthanide containing mechanically interlocked molecules. Initial work focuses on switching characteristics of a redox switchable antennae and its ability to modulate the luminescence of a series of lanthanide complexes in solution. Subsequent surface attachment of the lanthanide complexes in the form of emissive self-assembled monolayers is also investigated.

Thesis submitted in fulfilment of the requirements for the degree Magister Technologiae: Chemistry in the Faculty of Applied Science at the CAPE PENINSULA UNIVERSITY OF TECHNOLOGY 2012 / Chirality is very important to the pharmaceutical industry as enantiomers have the same macroproperties except for their optical and pharmacological activity. Industrial research has thus focused to find the most effective resolution technique. However, our aim was to obtain more information regarding the discrimination process. In this project the structures of the hydrates of di-quininium L-malate, (2QUIN+)(L-MA2-)•2H2O and the di-quininium D-malate, (2QUIN+)(D-MA2-)•2H2O have been investigated. (-)-Quinine (QUIN) did not show selectivity between the D and L malic acid and the structure of (2QUIN+)(DL-MA2-)•2H2O was obtained. Effect of solvents was demonstrated in the study and the structure of (QUIN+)(D-MA-)•H2O) was reported. The relationship between C-O bonds of the carboxylate and carboxylic moieties and ÄpKa was explored in salt and co-crystal formation. Kinetics of absorption was conducted for the reaction of (+)-deoxycholic acid (DCA) with n-propylamine and DCA with racemic sec-butylamine. The rate constants of the reactions were determined. Kinetics of desolvation was performed on the powder samples of mixtures of DCA and sec-butylamine and DCA with di-n-butylamine. Non-isothermal methods were used where a series of TG analyses was carried out at different heating rates (2, 4, 10, 32 K min-1). The structures of DCA with n-propylamine and di-n-butylamine were elucidated. The selectivity of DCA was investigated. The host compound was found to be able to successfully resolve racemic sec-butylamine (2-BUAM) and 2-amino-3-methylbutane (MeBUAM). The structures of DCA with enantiomers of these guests are reported in the study. The structures of R-BUAM and S-BUAM were solved in different space groups while R-MeBUAM and S-MeBUAM crystallized in the same space group.

Através da abordagem bottom-up, foram desenvolvidos novos sistemas supramoleculares baseados em complexos metálicos ligados por meio do ligante conjugado, trans-1,4-bis[2-(4-piridil)etenil]benzeno (BPEB). A combinação adequada de várias espécies selecionadas, conduziu a compostos bastante interessantes que foram caracterizados por meio 1H-RNM, voltametria cíclica e de espectrometria de massa, espectroscopia eletrônica, espectroeletroquímica. Seus correspondentes filmes moleculares também foram investigados por meio de microscopia de força atômica. Um desses sistemas foi constituído por clusters triangulares de acetato de rutênio com pontes &#181;-oxo e BPEB. Nesses casos, a espectrometria de massa acoplada à técnica de dissociação induzida por colisão, foi uma ferramenta poderosa para a investigação do processo de fragmentação em fase gasosa, permitindo a caracterização de novos intermediários, bem como a avaliação das energias de ligação envolvidas nos sistemas. Uma correlação linear das energias de ligação e parâmetros eletroquímicos foi demonstrada neste trabalho. Além disso, o comportamento eletrocrômico dos clusters de BPEB suportados sobre dióxido de titânio nanocristalino, também foi explorado na elaboração de dispositivos eletrocrômicos, com ótimo desempenho em termos de mudanças ópticas, reversibilidade e reprodutibilidade. Outro tipo de sistema foi baseado em complexos de rutênio-bipiridina e BPEB. Esses complexos foram empregados com bons resultados como sensibilizadores em células fotoeletroquímicas baseadas em dióxido de titânio nanocristalino, bem como em dispositivos eletrocrômicos de mesma natureza. Finalmente, as características estruturais do BPEB mostraram ser adequadas para exploração do reconhecimento molecular dos complexos na presença de &#946;-ciclodextrina (&#946;-CD). Neste estudo, foram gerados rotaxanos por meio da automontagem coordenativa do complexo binuclear &#181;-BPEB- bis[pentacianoferrato(II)] na presença de &#946;-CD. Também foi demonstrado por meio de 1H-NMR, que a agregação do complexo de BPEB é bastante pronunciada em espectros de solução aquosa, sendo porém inibida na presença de &#946;-CD. / The bottom up approach has been applied for the development of new supramolecular systems based on metal complexes connected by the linear, conjugated bridging ligand trans-1,4-bis[2-(4-pyridyl)ethenyl]benzene (BPEB). The combination of the many selected species led to very interesting compounds, which have been extensively characterized by means of ESI-MS, electronic spectroscopy, 1H-NMR, cyclic voltammetry and spectroelectrochemistry. Their molecular films have also been investigated by means of atomic force microscopy. One of such systems was constituted by triangular µ-oxo bridged ruthenium acetate clusters containing BPEB. In particular, mass spectrometry coupled with a collision induced dissociation technique provided a versatile tool for the investigation of their fragmentation process, allowing the characterization of novel intermediates, as well as, the evaluation of the binding energies involved in the systems. A linear correlation of the binding energies and electrochemical parameters has also been demonstrated in this work. In addition, the electrochromic behavior of the cluster-BPEB complexes supported on nanocrystalline titanium dioxide has also been exploited for the design of novel electrochromic devices, exhibiting sharp optical changes, high reversibility and great reproducibility. Another interesting type of system was based on polypyridine ruthenium(II) complexes and BPEB. Such species have been successfully employed as sensitizers in nanocrystalline titanium dioxide photoelectrochemical cells, and in photoelectrochromic devices. Finally, the suitable structural characteristics of BPEB have been explored in molecular recognition processes involving the corresponding complexes in the presence of ß-cyclodextrin (ß-CD). In this study, rotaxanes have been generated by coordination self-assembly of the binuclear µ-BPEB- bis[pentacyanoferrate(II)] complex and ß-CD. It has also been shown that the aggregation of the BPEB complexes, which proceeds to a high extent in aqueous solution, can be inhibited by adding ß-CD, as deduced by means of 1H-NMR spectroscopy

A química supramolecular de porfirinas e clusters trinucleares de rutênio foi investigada sob o ponto de vista teórico-experimental. Através do desenvolvimento de uma nova metodologia baseada em ferramentas teóricas, as propriedades desses sistemas puderam ser explicadas à luz da mecânica quântica, revelando os mecanismos eletrônicos envolvidos na modificação das propriedades dos anéis porfirínicos pelos compostos de coordenação. As geometrias, a dinâmica e as estruturas eletrônicas desses sistemas foram obtidas através do desenvolvimento de novos parâmetros para campos de força empíricos, e da utilização de métodos semi-empíricos e ab initio. Essas foram utilizadas para interpretar as propriedades físico-químicas dos mesmos, como por exemplo a associação intermolecular em solução e na forma de filmes finos obtidos sobre superfícies não rugosas. O estudo teórico detalhado das estruturas eletrônicas dessas espécies comprovou que a influência supramolecular dos compostos de coordenação se dá através de orbitais de simetria &#960;, representando o principal mecanismo de ativação de anéis porfirínicos por compostos de coordenação. Essa ativação diferenciada pôde ser evidenciada experimentalmente pela aplicação dessas espécies em células fotoeletroquímicas e em sistemas de catálise com atividade citocromo P-450. / The supramolecular chemistry of porphyrins and trinuclear ruthenium clusters has been investigated by a theoretical-experimental approach. Through the development of a new methodology based on theoretical tools, their relevant properties were explained using quantum mechanics, disclosing the electronic mechanisms by which coordination compounds modify the properties of porphyrin rings. Geometries, dynamics and electronic structures of these systems have been obtained by the development of new parameters for empirical force fields, and through semiempirical and ab initio methods. They have been used to explain the physical-chemical properties as, for example, the intermolecular association in solution, and thin film formation over flat surfaces. According to the detailed theoretical study coordination compounds increase the catalytic activity of porphyrin rings via &#960;-orbital coupling, and this is the main mechanism of porphyrin activation. Such enhanced activity has been experimentally observed in photoelectrochemical devices and in the oxidation catalysis of organic substrates, providing synthetic models of cytochrome P-450 systems.

Através da abordagem bottom-up, foram desenvolvidos novos sistemas supramoleculares baseados em complexos metálicos ligados por meio do ligante conjugado, trans-1,4-bis[2-(4-piridil)etenil]benzeno (BPEB). A combinação adequada de várias espécies selecionadas, conduziu a compostos bastante interessantes que foram caracterizados por meio 1H-RNM, voltametria cíclica e de espectrometria de massa, espectroscopia eletrônica, espectroeletroquímica. Seus correspondentes filmes moleculares também foram investigados por meio de microscopia de força atômica. Um desses sistemas foi constituído por clusters triangulares de acetato de rutênio com pontes &#181;-oxo e BPEB. Nesses casos, a espectrometria de massa acoplada à técnica de dissociação induzida por colisão, foi uma ferramenta poderosa para a investigação do processo de fragmentação em fase gasosa, permitindo a caracterização de novos intermediários, bem como a avaliação das energias de ligação envolvidas nos sistemas. Uma correlação linear das energias de ligação e parâmetros eletroquímicos foi demonstrada neste trabalho. Além disso, o comportamento eletrocrômico dos clusters de BPEB suportados sobre dióxido de titânio nanocristalino, também foi explorado na elaboração de dispositivos eletrocrômicos, com ótimo desempenho em termos de mudanças ópticas, reversibilidade e reprodutibilidade. Outro tipo de sistema foi baseado em complexos de rutênio-bipiridina e BPEB. Esses complexos foram empregados com bons resultados como sensibilizadores em células fotoeletroquímicas baseadas em dióxido de titânio nanocristalino, bem como em dispositivos eletrocrômicos de mesma natureza. Finalmente, as características estruturais do BPEB mostraram ser adequadas para exploração do reconhecimento molecular dos complexos na presença de &#946;-ciclodextrina (&#946;-CD). Neste estudo, foram gerados rotaxanos por meio da automontagem coordenativa do complexo binuclear &#181;-BPEB- bis[pentacianoferrato(II)] na presença de &#946;-CD. Também foi demonstrado por meio de 1H-NMR, que a agregação do complexo de BPEB é bastante pronunciada em espectros de solução aquosa, sendo porém inibida na presença de &#946;-CD. / The bottom up approach has been applied for the development of new supramolecular systems based on metal complexes connected by the linear, conjugated bridging ligand trans-1,4-bis[2-(4-pyridyl)ethenyl]benzene (BPEB). The combination of the many selected species led to very interesting compounds, which have been extensively characterized by means of ESI-MS, electronic spectroscopy, 1H-NMR, cyclic voltammetry and spectroelectrochemistry. Their molecular films have also been investigated by means of atomic force microscopy. One of such systems was constituted by triangular µ-oxo bridged ruthenium acetate clusters containing BPEB. In particular, mass spectrometry coupled with a collision induced dissociation technique provided a versatile tool for the investigation of their fragmentation process, allowing the characterization of novel intermediates, as well as, the evaluation of the binding energies involved in the systems. A linear correlation of the binding energies and electrochemical parameters has also been demonstrated in this work. In addition, the electrochromic behavior of the cluster-BPEB complexes supported on nanocrystalline titanium dioxide has also been exploited for the design of novel electrochromic devices, exhibiting sharp optical changes, high reversibility and great reproducibility. Another interesting type of system was based on polypyridine ruthenium(II) complexes and BPEB. Such species have been successfully employed as sensitizers in nanocrystalline titanium dioxide photoelectrochemical cells, and in photoelectrochromic devices. Finally, the suitable structural characteristics of BPEB have been explored in molecular recognition processes involving the corresponding complexes in the presence of ß-cyclodextrin (ß-CD). In this study, rotaxanes have been generated by coordination self-assembly of the binuclear µ-BPEB- bis[pentacyanoferrate(II)] complex and ß-CD. It has also been shown that the aggregation of the BPEB complexes, which proceeds to a high extent in aqueous solution, can be inhibited by adding ß-CD, as deduced by means of 1H-NMR spectroscopy

A química supramolecular de porfirinas e clusters trinucleares de rutênio foi investigada sob o ponto de vista teórico-experimental. Através do desenvolvimento de uma nova metodologia baseada em ferramentas teóricas, as propriedades desses sistemas puderam ser explicadas à luz da mecânica quântica, revelando os mecanismos eletrônicos envolvidos na modificação das propriedades dos anéis porfirínicos pelos compostos de coordenação. As geometrias, a dinâmica e as estruturas eletrônicas desses sistemas foram obtidas através do desenvolvimento de novos parâmetros para campos de força empíricos, e da utilização de métodos semi-empíricos e ab initio. Essas foram utilizadas para interpretar as propriedades físico-químicas dos mesmos, como por exemplo a associação intermolecular em solução e na forma de filmes finos obtidos sobre superfícies não rugosas. O estudo teórico detalhado das estruturas eletrônicas dessas espécies comprovou que a influência supramolecular dos compostos de coordenação se dá através de orbitais de simetria &#960;, representando o principal mecanismo de ativação de anéis porfirínicos por compostos de coordenação. Essa ativação diferenciada pôde ser evidenciada experimentalmente pela aplicação dessas espécies em células fotoeletroquímicas e em sistemas de catálise com atividade citocromo P-450. / The supramolecular chemistry of porphyrins and trinuclear ruthenium clusters has been investigated by a theoretical-experimental approach. Through the development of a new methodology based on theoretical tools, their relevant properties were explained using quantum mechanics, disclosing the electronic mechanisms by which coordination compounds modify the properties of porphyrin rings. Geometries, dynamics and electronic structures of these systems have been obtained by the development of new parameters for empirical force fields, and through semiempirical and ab initio methods. They have been used to explain the physical-chemical properties as, for example, the intermolecular association in solution, and thin film formation over flat surfaces. According to the detailed theoretical study coordination compounds increase the catalytic activity of porphyrin rings via &#960;-orbital coupling, and this is the main mechanism of porphyrin activation. Such enhanced activity has been experimentally observed in photoelectrochemical devices and in the oxidation catalysis of organic substrates, providing synthetic models of cytochrome P-450 systems.