Title from title page of PDF (University of Missouri--St. Louis, viewed Mar. 3, 2010). Includes bibliographical references.

This thesis describes the synthesis of halogen bonding receptors for integration within interlocked anion host systems. Chapter 1 introduces the field of supramolecular chemistry, with a particular focus on anion recognition and sensing, halogen bonding, and the synthesis of mechanically interlocked structures. Chapter 2 describes the preparation and anion binding properties of carbazole-based receptor molecules. A systematic anion binding study on a series of halogen- and hydrogen-bonding 3,6-bis-triazolium carbazole acyclic receptors is described initially, followed by the development of a halogen bonding rotaxane. The anion and metal complexation properties of acyclic and macrocyclic systems incorporating the 1,8-bis-triazole carbazole motif are also presented. Chapter 3 details the synthesis and anion complexation investigations of halogen and hydrogen bonding naphthalene-based acyclic and interlocked rotaxane host molecules. Chapter 4 presents receptors based on the 4,4'-bis-triazole-2,2'-bipyridyl motif. A halogen bonding rhenium(I) bipyridyl complex is exploited in the development of a rotaxane host system which optically senses anions via luminescence purely through halogen bonding interactions. The anion recognition and sensing properties of diquat-based receptors are also investigated, and shown to exhibit optical and electrochemical responses to anions. Chapter 5 summarises the major conclusions from Chapters 2-4. Chapter 6 describes the experimental procedures used in the work, and includes characterisation data for the synthesised compounds. Supplementary information relating to crystallographic data, and absorption, luminescence and electrochemical studies, is provided in the Appendices.

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.

Understanding the supramolecular interactions governing the self-assembly of molecular building blocks upon surfaces is fundamental to the design of new devices such as sensors or catalysts. Successful heterogeneous enantioselective catalysts have relied upon the adsorption of ‘chiral modifiers’, usually chiral amino acids, onto reactive metal surfaces. One of the most researched examples is the hydrogenation of β-ketoesters using nickel-based catalysts. The stability of the chiral modifiers upon catalyst surfaces is a major obstacle to the industrial scale-up of this reaction. In this study, the replacement of conventional modifiers with porous, chiral and functionalised self-assembled networks is investigated. Perylene-3,4,9,10-tetracarboxylic diimide (PTCDI) and melamine (1,3,5-triazine,-2,4,6-triamine) have been shown to form hydrogen bonded networks on Ag-Si(111)√3x√3R30° in ultra-high vacuum (UHV) and Au(111) substrates in UHV and ambient conditions, these networks are capable of hosting guest molecules. These networks are investigated further in this study. In UHV, the behaviour of the components and network formation on Ni(111) is probed using scanning tunnelling microscopy (STM) and temperature-programmed desorption (TPD). The stability of the PTCDI-melamine network on Au(111) was analysed using TPD. Metal coordination interactions between each of the network components and nickel upon the Au(111) surface were examined by STM before testing the ability of the network to act as a template for metal growth. Finally, a number of polymerisation reactions are investigated with a view to replacing chiral modifiers with porous, chiral, functionalised covalent networks. Periodic covalent networks should possess the greater chemical and thermal stability required for more widespread use. In UHV and ambient conditions, STM is used to monitor the progress of surface-confined reactions on Au(111) and characterise the resultant covalent structures.

There is currently a need for vaccine adjuvants that are effective for eliciting Th1-type CD4 and CD8 T cell responses when formulated with protein and peptide-based subunit vaccines. Some of the most promising adjuvants in this regard are combined small molecule Toll-like receptor-7/8 agonists (TLR-7/8a). However, poor pharmacokinetic properties have precluded TLR-7/8a for use in vaccines. In this thesis, polymer carriers were used to control pharmacokinetics and to modulate activity of TLR-7/8a for use as vaccine adjuvants. Combinatorial synthesis and in vivo structure-activity studies were used to evaluate how properties of Polymer-TLR-7/8a conjugates (Poly-7/8a) influence innate immune activation in lymph nodes that drain the site of vaccine administration. The most striking finding was that particle formation by Poly-7/8a strongly enhances the magnitude and duration (>14 days) of innate immune activation in lymph nodes by restricting agonist biodistribution and promoting uptake by dendritic cells. Particle-forming Poly-7/8a optimized for activity were found to induce only local innate immune activation (not systemic) and were effective for eliciting Th1-type CD4 and CD8 T cells that mediated protection against infectious challenge. Based on the importance of particle formation for activity of Poly-7/8a, thermo-responsive Poly-7/8a were developed that exist as single water-soluble macromolecules in solution but undergo temperature-driven particle formation in vivo. In conclusion, polymer carriers of TLR-7/8a represent a versatile and effective platform for modulating innate immune activity and warrant further investigation as a class of adjuvants for vaccines.

Esta tese tem como objetivo contribuir para o conhecimento e desenvolvimento das células solares sensibilizadas por corantes, através da elaboração de novas espécies supramoleculares e de estudos fundamentais de caracterização do filme de TiO2-P25 e da interface TiO2-Corante pela técnica de microscopia Raman confocal. Os estudos de microcopia Raman confocal da distribuição das fases cristalinas rutilo e anatase em filmes de TiO2-P25 (Degussa) mostraram que a fase rutilo está presente em agregados de diferentes tamanhos (de 250 nm a 3 µm) distribuídos na fase anatase e que estes agregados permaneceram mesmo após os processos de preparação da suspensão coloidal. Na presença do corante N3, verificou-se que a irradiação com laser em 532 nm, usando potência acima de 25 mW cm-2, provoca a absorção e posterior combustão do filme interfacial, com drásticas mudanças na morfologia visualizadas por microscopia Raman confocal, revelando a ocorrência da transformação de anatase em rutilo na região de incidência do feixe de laser. Outro ponto investigado nesta tese, foi a síntese e aplicação de novos sensibilizadores supramoleculares em células solares sensibilizadas por corante (DSC), visando diminuir os processos de recombinação e melhor aproveitamento do espectro solar através da estabilização do corante foto-oxidado e da transferência vetorial de elétron/energia. Além dos trabalhos com novas porfirinas supramoleculares, reproduzidas no apêndice, esta tese apresenta um estudo detalhado de uma série, formada por três espécies diméricas, constituídas pelas unidades [Ru(dcbH2)Cl]+ e [Ru(dmb)2Cl]+, unidas por ligantes ponte com dimensões lineares crescentes, isto é: bpy, bpe e bpeb (dcbH2= ácido-2,2\'-bipiridina-4,4\'-dicarboxílico, dmb= 4,4\'-dimetil-2,2\'- bipiridina, bpy= 4,4\'-bipiridina, bpe= trans-1,2-bis(4-piridil)-etileno e bpeb= trans-1,4- bis[2-(piridil)etenil]-benzeno). O rendimento global das DSCs correspondentes cresceram com o aumento do tamanho da ponte, passando de 2,78 % para o corante dim-Ru-bpy, para 2,89 e 3,25 % nos corantes dim-Ru-bpe e dim-Rbpeb, respectivamente. Foi observado que os valores de Jsc e η têm correlação linear com a distância de separação do buraco e da superfície do eletrodo de TiO2, ratificando que o processo de retardação da recombinação de carga, causado pelo aumento da ponte, é um fator muito importante para esta classe de compostos. Os resultados de IPCE mostraram que a unidade [Ru(dmb)2Cl(P)]+ também é responsável pela fotoinjeção de elétrons no TiO2. Assim, a excitação de qualquer uma das unidades, sempre acaba formando a espécie TiO2(e-)-Ru-Ru(h+) no filme interfacial. Os resultados confirmam as expectativas esperadas no planejamento energético vetorial, no qual o HOMO foi centrado na unidade distante da superfície e o LUMO ficou sobre a dcbH2 diretamente ancorada no superfície do TiO2. / This thesis encompasses our efforts to improve the knowledge and contribute to the development of dye-sensitized solar cells, by focusing on supramolecular design of new dyes and on critical aspects of the morphology of the TiO2-P25 and TiO2-Dye interfaces, as probed by confocal Raman microscopy. According to Raman imaging of the crystalline phase distribution of TiO2-P25 (Degussa) rutile was present as aggregates of different sizes (from 250 nm to 3 µm) dispersed in the 25 nm anatase powder, persisting even after applying criterious procedures for generating uniform colloidal suspensions. In addition, the irradiation of TiO2-P25 films containing adsorbed N3 dye, using a 532 nm laser (power over to 25 mW cm-2) led to the absorption and instantaneous combustion of the dye, promoting drastic local changes associated with the anatase to rutile conversion. The design and application of new supramolecular sensitizers in DSC has also been pursued, aiming an improvement of efficiency by slowing down the electron-hole recombination process, while enhancing the light harvesting effects in the visible range by means of vectorial electron/energy transfer. Studies concerning another efficient supramolecular porphyrin dye, have also been performed and published (Appendix). As the main subject, a series of dimeric species have been reported. They were based on the [Ru(dcbH2)Cl]+ and [Ru(dmb)2Cl]+ units connected by linear bridging ligands of increasing lengths, such as: bpy, bpe and bpeb (dcbH2= 2,2\'-bipyridine-4,4\'-dicarboxylic acid, dmb= 4,4\'-dimethyl-2,2\'-bipyridine, bpy= 4,4\'-bipyridine, bpe= trans-1,2-bis(4- pyridyl)-ethylene e bpeb= trans-1,4-bis[2-(4-pyridyl)ethenyl]-benzene). The overall yield of the corresponding DSCs increased with the bridging ligand length, from 2.78 % for dim-Ru-bpy, to 2.89 % and 3.25 % for dim-Ru-bpe and dim-Ru-bpeb, respectively. The electrochemical parameters associated with the short circuit current exhibited a linear correlation with the hole separation distance between the TiO2 electrode and the binuclear dye terminal, confirming that the retardation of charge recombination through the increasing distance is indeed a relevant factor for this series of compounds. The IPCE results indicated that the [Ru(dmb)2Cl(P)]+ unit is also involved in electron transfer, such that the dye excitation always leads the TiO2(e-)-Ru-Ru(h+) species. This conclusion confirmed the success of the supramolecular design and vectorial transfer strategy, in which the HOMO center was placed far away from the surface, but in communication with the LUMO center located at the dcbH2 group anchored on TiO2.

Esta tese tem como objetivo contribuir para o conhecimento e desenvolvimento das células solares sensibilizadas por corantes, através da elaboração de novas espécies supramoleculares e de estudos fundamentais de caracterização do filme de TiO2-P25 e da interface TiO2-Corante pela técnica de microscopia Raman confocal. Os estudos de microcopia Raman confocal da distribuição das fases cristalinas rutilo e anatase em filmes de TiO2-P25 (Degussa) mostraram que a fase rutilo está presente em agregados de diferentes tamanhos (de 250 nm a 3 µm) distribuídos na fase anatase e que estes agregados permaneceram mesmo após os processos de preparação da suspensão coloidal. Na presença do corante N3, verificou-se que a irradiação com laser em 532 nm, usando potência acima de 25 mW cm-2, provoca a absorção e posterior combustão do filme interfacial, com drásticas mudanças na morfologia visualizadas por microscopia Raman confocal, revelando a ocorrência da transformação de anatase em rutilo na região de incidência do feixe de laser. Outro ponto investigado nesta tese, foi a síntese e aplicação de novos sensibilizadores supramoleculares em células solares sensibilizadas por corante (DSC), visando diminuir os processos de recombinação e melhor aproveitamento do espectro solar através da estabilização do corante foto-oxidado e da transferência vetorial de elétron/energia. Além dos trabalhos com novas porfirinas supramoleculares, reproduzidas no apêndice, esta tese apresenta um estudo detalhado de uma série, formada por três espécies diméricas, constituídas pelas unidades [Ru(dcbH2)Cl]+ e [Ru(dmb)2Cl]+, unidas por ligantes ponte com dimensões lineares crescentes, isto é: bpy, bpe e bpeb (dcbH2= ácido-2,2\'-bipiridina-4,4\'-dicarboxílico, dmb= 4,4\'-dimetil-2,2\'- bipiridina, bpy= 4,4\'-bipiridina, bpe= trans-1,2-bis(4-piridil)-etileno e bpeb= trans-1,4- bis[2-(piridil)etenil]-benzeno). O rendimento global das DSCs correspondentes cresceram com o aumento do tamanho da ponte, passando de 2,78 % para o corante dim-Ru-bpy, para 2,89 e 3,25 % nos corantes dim-Ru-bpe e dim-Rbpeb, respectivamente. Foi observado que os valores de Jsc e η têm correlação linear com a distância de separação do buraco e da superfície do eletrodo de TiO2, ratificando que o processo de retardação da recombinação de carga, causado pelo aumento da ponte, é um fator muito importante para esta classe de compostos. Os resultados de IPCE mostraram que a unidade [Ru(dmb)2Cl(P)]+ também é responsável pela fotoinjeção de elétrons no TiO2. Assim, a excitação de qualquer uma das unidades, sempre acaba formando a espécie TiO2(e-)-Ru-Ru(h+) no filme interfacial. Os resultados confirmam as expectativas esperadas no planejamento energético vetorial, no qual o HOMO foi centrado na unidade distante da superfície e o LUMO ficou sobre a dcbH2 diretamente ancorada no superfície do TiO2. / This thesis encompasses our efforts to improve the knowledge and contribute to the development of dye-sensitized solar cells, by focusing on supramolecular design of new dyes and on critical aspects of the morphology of the TiO2-P25 and TiO2-Dye interfaces, as probed by confocal Raman microscopy. According to Raman imaging of the crystalline phase distribution of TiO2-P25 (Degussa) rutile was present as aggregates of different sizes (from 250 nm to 3 µm) dispersed in the 25 nm anatase powder, persisting even after applying criterious procedures for generating uniform colloidal suspensions. In addition, the irradiation of TiO2-P25 films containing adsorbed N3 dye, using a 532 nm laser (power over to 25 mW cm-2) led to the absorption and instantaneous combustion of the dye, promoting drastic local changes associated with the anatase to rutile conversion. The design and application of new supramolecular sensitizers in DSC has also been pursued, aiming an improvement of efficiency by slowing down the electron-hole recombination process, while enhancing the light harvesting effects in the visible range by means of vectorial electron/energy transfer. Studies concerning another efficient supramolecular porphyrin dye, have also been performed and published (Appendix). As the main subject, a series of dimeric species have been reported. They were based on the [Ru(dcbH2)Cl]+ and [Ru(dmb)2Cl]+ units connected by linear bridging ligands of increasing lengths, such as: bpy, bpe and bpeb (dcbH2= 2,2\'-bipyridine-4,4\'-dicarboxylic acid, dmb= 4,4\'-dimethyl-2,2\'-bipyridine, bpy= 4,4\'-bipyridine, bpe= trans-1,2-bis(4- pyridyl)-ethylene e bpeb= trans-1,4-bis[2-(4-pyridyl)ethenyl]-benzene). The overall yield of the corresponding DSCs increased with the bridging ligand length, from 2.78 % for dim-Ru-bpy, to 2.89 % and 3.25 % for dim-Ru-bpe and dim-Ru-bpeb, respectively. The electrochemical parameters associated with the short circuit current exhibited a linear correlation with the hole separation distance between the TiO2 electrode and the binuclear dye terminal, confirming that the retardation of charge recombination through the increasing distance is indeed a relevant factor for this series of compounds. The IPCE results indicated that the [Ru(dmb)2Cl(P)]+ unit is also involved in electron transfer, such that the dye excitation always leads the TiO2(e-)-Ru-Ru(h+) species. This conclusion confirmed the success of the supramolecular design and vectorial transfer strategy, in which the HOMO center was placed far away from the surface, but in communication with the LUMO center located at the dcbH2 group anchored on TiO2.

The self-assembly of structured particles into monodisperse clusters is a challenge on the nano-, micro- and even macro-scale. While biological systems are able to self-assemble with comparative ease, many aspects of this self-assembly are not fully understood. In this thesis, we look at the strategies and rules that can be applied to encourage the formation of monodisperse clusters. Though much of the inspiration is biological in nature, the simulations use a simple minimal patchy particle model and are thus applicable to a wide range of systems. The topics that this thesis addresses include: Encapsulation: We show how clusters can be used to encapsulate objects and demonstrate that such `templates' can be used to control the assembly mechanisms and enhance the formation of more complex objects. Hierarchical self-assembly: We investigate the use of hierarchical mechanisms in enhancing the formation of clusters. We find that, while we are able to extend the ranges where we see successful assembly by using a hierarchical assembly pathway, it does not straightforwardly provide a route to enhance the complexity of structures that can be formed. Pore formation: We use our simple model to investigate a particular biological example, namely the self-assembly and formation of heptameric alpha-haemolysin pores, and show that pore insertion is key to rationalising experimental results on this system. Phase re-entrance: We look at the computation of equilibrium phase diagrams for self-assembling systems, particularly focusing on the possible presence of an unusual liquid-vapour phase re-entrance that has been suggested by dynamical simulations, using a variety of techniques.