Thesis (MSc (Chemistry and Polymer Science))--University of Stellenbosch, 2009. / ENGLISH ABSTRACT: This thesis reports an in-depth investigation of the intermolecular interaction motifs in secondary, primary and ammonium carboxylate salts. The investigation was conducted using the Cambridge Structural Database (CSD), together with a systematic steric-specific experimental study. The tendency in the literature has been to analyse organic salt crystal structures in terms of hydrogen bonding patterns, almost ignoring cation-anion interactions. This study focuses on the cation-anion interactions in secondary, primary and ammonium carboxylate salts, which have a direct effect on the formation of specific structural motifs. The ideas of ring-stacking and ring-laddering, which arise from the tendency of cations and anions to arrange themselves so as to maximise electrostatic interactions, have been applied to ammonium carboxylate salts. An extensive survey of organic ammonium carboxylate salt structures in the CSD has been carried out. The structural motifs in ammonium carboxylates were investigated, and a set of predictive rules for the pattern of intermolecular interactions in these salts was developed. Using these results, the formation of ring-stacking or ring-laddering in primary ammonium carboxylate salts can be predicted. The results from the CSD survey are discussed in Chapter 3. An experimental study has been carried out, which complements the results obtained from the CSD survey. The experimental study formed 19 novel ammonium carboxylate salts, of which 2 formed hydrates and 2 co-crystals of salts. The experimental results confirm what was found in the CSD survey, and this is discussed in Chapter 4. This study has found that the principle of ring-stacking and ring-laddering can be applied in a general form to the crystal structures of organic ammonium carboxylate salts. The size of the cation and the anion in these salts has a significant effect on the formation of structural motifs in the solid state. Interactions between cation and anion substituents also play an important role in the formation of particular structural motifs in ammonium carboxylate salts. / AFRIKAANSE OPSOMMING: In hierdie tesis word die intermolekulêre interaksie motiewe in die sekondêre, primêre en ammonium karbosilaat soute in-diepte ondersoek. Die studie is gedoen met behulp van die Cambridge Strukturele Databasis (CSD), saam met ‟n sistematiese steriesspesifieke eksperimentele studie. Die neiging in die literatuur is om organiese sout kristal strukture in terme van waterstofbindings patrone te analiseer sonder om katioon-anioon interaksies in ag te neem. Die studie fokus juis op hierdie katioon-anioon interaksies tussen sekondêre, primêre en ammonium karbosilaat soute wat ‟n direkte effek het op die vorming van spesifieke strukturele motiewe naamlik „ring-stacking‟ en „ring-laddering‟ wat hul oorsprong kry vanaf die neiging van katione en anione om hulself op so ‟n wyse te rangskik sodat die elektrostatiese interaksies ‟n maksimum kan bereik, op die ammonium karboksilaat soute. ‟n Volledige ondersoek van ammonium karboksilaat soute in die CSD is gedoen. Die strukturele motiewe in ammonium karboksilaat is ondersoek, en ‟n stel reels wat die patrone van intermolekulêre interaksies in hierdie soute voorspelis ontwikkel. Hierdie resultate kan gebruik word om die vorming van „ring-stacking‟ en „ring-laddering‟ in primêre ammonium karbosilaat soute te voorspel. Die resultate van die CSD ondersoek word bespreek in Hoofstuk 3. ‟n Eksperimentele studie is uitgevoer en die resultate hiervan komplimenteer die resultate van die CSD ondersoek. In die eksperimentele studie is 19 nuwe ammonium karboksilaat soute gekristaliseer, waarvan 2 hidraat-soute en 2 ko-kristal-van-soute is. Die eksperimentele resultate bevestig die bevindings van die CSD ondersoek, en dit word bespreek in Hoofstuk 4. Hierdie studie het gevind dat die beginsel van „ring-stacking‟ en „ring-laddering‟ kan in „n algemene vorm in die kristal strukture van organiese ammonium karboksilaat soute toegepas word. Die grootte van die katioon en anion in hierdie soute het ‟n beduidende effek op die vorming van strukturele motiewe in die vaste toestand. Interaksie tussen die katioon en anioon substituente speel „n belangrike rol in die vorming van spesifieke motiewe in ammonium karbosilaat soute.

This thesis has been divided into five sections. The first chapter introduces the main themes of this thesis, including the description of the concepts of supramolecular chemistry, crystal engineering, hydrogen bonding and graph set analysis. The final section of chapter one describes a typical X-ray experiment used to determine the structures of the compounds presented in this thesis. Chapter two describes the synthesis and single crystal structures of copper(I) complexes with pyridine- and pyrazine-carboxylic acids. A series of novel solvent inclusion compounds of copper(I) complexes with pyridine- and pyrazine-carboxylic acids and the hydrogen bonding patterns adopted are also discussed. Chapter three reports the potential uses of boronic acids as building blocks for the design of novel solid-state architectures utilising hydrogen bonds. Novel copper(I) pyridine-/pyrazine-carboxylate complexes with boronic acid co-crystals are presented in which the heterodimeric boronic carboxylate R22(8) ring motif is present in all cases. Chapter four discusses the synthesis of novel ditertiary phosphines bearing functional groups with hydrogen bonding potential either via a three-step or single step synthetic route which involves a well known method of reductive amination followed by an efficient Mannich-based condensation. Complexation studies of these P,P-bidentate ligands with various transition metal centres such as Pt(II), Mo(0), Ru(II) and Au(I) are also presented. The effect on the structural motifs observed in these series of compounds by the regioselective incorporation of functional groups with potential hydrogen bonding capability such as hydroxyl and amide is also given. Finally, chapter five contains the synthesis and coordination studies of new phosphorus donor ligands leading to ideas for further work.

L'organocatalyse asymétrique est un domaine en plein développement. L'immobilisation de ce type de catalyseurs pourrait présenter de multiples avantages. Ces travaux de thèse s'intéressent à la préparation de silices hybrides organiques/inorganiques par voie sol-gel et aux applications de ces matériaux en organocatalyse asymétrique. La première partie du manuscrit est consacrée à une présentation bibliographique du sujet. Dans la deuxième partie, l'utilisation de la L-proline comme modèle est décrite. Des matériaux contenant un fragment L-proline ont été préparés et leurs performances catalytiques évaluées pour une réaction d'aldolisation asymétrique. Les processus à l'origine des propriétés catalytiques modérées de ces catalyseurs supportés sont discutés. La troisième partie porte sur le catalyseur de Takemoto, organocatalyseur bifonctionnel contenant un groupement donneur de liaisons hydrogène et une fonction amine tertiaire. Les différentes stratégies envisagées pour préparer des dérivés silylés de ce catalyseur sont exposées. Enfin, la nanostructuration de silsesquioxanes par le biais de liaisons hydrogène entre fonctions thiourée est présentée. / Asymmetric organocatalysis is a blossoming area of research. Immobilisation of this kind of catalysts could present numerous advantages. This thesis deals with the sol-gel synthesis of organic/inorganic hybrid silicas and their applications in asymmetric organocatalysis. The first part of this work is dedicated to a bibliographic presentation of this area of research. In the second part, the use of L-proline as a model is described. Hybrid materials containing a L-proline component were prepared and their catalytic performances were evaluated in an asymmetric aldolisation reaction. The processes accounting for the moderate performances of these materials are discussed. The third part relates the synthetic strategies used to prepare silylated derivatives of the Takemoto catalyst, a bifunctional catalyst containig a H-bond donnor and a tertiary amine. Finally the nanostructuring of bridged silsesquioxanes through H-bonding interactions between thiourea cross-linkers is presented.

Na última década sistemas supramoleculares vêm atraindo a atenção de muitos pesquisadores na área da química. Este interesse é devido a capacidade dos sistemas supramoleculares mimetizarem sistemas biológicos e pelo seu importante papel na construção de novos materiais com interesse tecnológico. No contexto de interações supramoleculares as espécies oxocarbônicas têm se mostrado como excelentes sondas para o estudo dessas interações devido às características sui generis dos seus espectros eletrônicos e vibracionais, o que por sua vez decorre da presença do efeito Jahn-Teller. Neste trabalho foram investigados os sistemas supramoleculares: mordenita/ácido esquárico, tiouréia/ácido esquárico e agregação de esquaraínas em solução. Nessa investigação foram utilizadas técnicas de espectroscopia eletrônica e vibracional. As espectroscopias Raman e Raman ressonante se mostraram eficientes para o estudo dos sistemas supramoleculares acima. Através do uso das espectroscopias eletrônica e vibracional foi possível caracterizar interações do tipo \"transferência de carga\" em mordenitas incluídas, caracterizar clatratos formados por tiouréia e espécies oxocarbônicas, e determinar os modos vibracionais envolvidos no processo de agregação em solução de esquaraínas e, conseqüentemente, sua geometria de agregação. / Over the last decade supramolecular systems have received the attention of many researchers. Such interest can be explained by the ability of supramolecular systems to mimic biological systems, as well as by their important role in the design of new materials with technological relevance. In the context of supramolecular interactions oxocarbon species have proved to be excellent probes for the study of such interactions thanks to the unique features of their vibrational and electronic spectra, a consequence of the Jahn-Teller effect. In the present work the following systems were investigated: Mordenite/squaric acid, thioureia/squaric acid and aggregated squaraines in solution. Electronic and vibrational spectroscopies were the techniques of choice. Raman and resonance Raman spectroscopies showed to be convenient techniques for the study of the forementioned systems. It was possible to characterize the charge-transfer interaction induced by the restrict geometry in mordenite, the clathrate-like host formed by thioureia squaric acid, as well as to determine the nature of the squaraines aggregates formed in solutions.

Atoms construct the molecules and molecules construct the material substances (with the exceptions as well, e.g.., metals, where atoms directly construct the material substances). Intermolecular interactions play an important role in most of the branches of sciences, ranging from material sciences to biological sciences. Van der Waals interactions are weak intermolecular interactions while hydrogen bonding varies in strength from weak to strong (1 to 40 kcal/mol). The present work focuses on applying some theoretical methods (ab initio and Atoms in Molecules theory) on these interactions to differentiate them with physically meaningful parameters such as hydrogen bond radii and atoms in molecules theory parameters. 1)Defining and calculating H-bond radii have been done using atoms in molecules theory approach which can explain ruling out the presence or absence of an H-bond in an intermolecular interaction. 2) A blue-shift of 200 cm-1 for a weakly bound complex is unprecedented. Our studies on weakly bound complexes showed the blue-shift of 200 cm-1 for H3C•••CIF and shift has been found to be purely from the mixing of normal modes and not because of an interaction. 3)Methane, a symmetric top molecule can act both as H-bond acceptor and donor. The present work shows that methane is rather a better H-bond acceptor than a donor and all the calculated parameters are in favor of this description. 4) Microwave spectrometer is an ultimate tool (at least at present) for structural characterization of the weakly bound complexes accurately. The rotational spectrum of the weakly bound isotopomer weakly bound complexes accurately. The rotational spectrum of the weakly bound isotopomer 13CC5H6•••Ar, which is a symmetric top and gives only “B” rotational constant. Moreover, the A rotational constant of the complex is the same as the rotational constant for 13CC5H6, which has no dipole moment. C2H2 molecule is an astrophysically important molecule as it is present in asymptotic giant branch and T-type stars (Teff<3000K). Due to its various infrared active vibrational modes, C2H2 is one of the most important sources in cool stars. The production of C2H2 infrared spectroscopic data at high temperature is therefore essential to trace back physical characteristics of these objects and to model the radiative transfer in their envelope. The databases such as “HITRAN”, do not have enough data available for stimulating high temperature spectra. Keeping all these objectives in mind, high temperature emission spectrum of acetylene has been recorded around 3µm region of acetylene.

The polyamines spermine and spermidine play important roles in many cellular processes, and unusual levels of these polyamines have been associated with numerous human diseases. Spermidine/spermine N¹-acetyltransferase (SSAT) is an enzyme involved in polyamine regulation, where acetylation of polyamines by SSAT ultimately leads to their degradation or export from the cell. In this dissertation, x-ray crystallography and nuclear magnetic resonance (NMR) are used to provide insights into the structure and function of this important enzyme. X-ray crystallography provided two distinct views of SSAT: one of the enzyme in complex with coenzyme A (CoA), and another of the enzyme in complex with CoA and the polyamine spermine. Together, the two structures reveal structural plasticity in the active site of the enzyme. The complex with spermine provides a direct view of polyamine binding by SSAT, and shows that the enzyme relies heavily on associated water molecules to bind spermine; these water molecules also appear to form a "proton relay" between the primary amine of spermine and the side-chain of a conserved glutamate residue. Guided by the structural results, NMR methods were used to test hypotheses regarding the enzyme mechanism of SSAT. The activity of the enzyme over a range of solution conditions, and towards different polyamine substrates, was determined; the effects of mutating single amino acids in the enzyme were also evaluated. The enzyme appeared to be most active between pH 8.5 and 9.5, and mutation of the aforementioned glutamate significantly altered this behavior. This suggests the glutamate is directly involved in the acetyltransfer reaction, where it likely functions as a catalytic base though the proton relay in the enzyme active site. These studies advance our general understanding of how polyamines are regulated in mammalian cells, and have the potential to assist in developing new therapeutic options for human diseases involving polyamines. / text

It has long been observed that salts affect proteins in a variety of ways, yet comprehensive explanations for different salt effects are still lacking. In the work presented here, the effect of salts on proteins has been investigated through three different effects: the hydrophobic effect; their conformational stability; the hydrogen bonding network of water in a protein’s hydration shell. UV-vis absorbance and fluorescence spectroscopy were used to monitor changes in two model systems, the phenol-acetate contact pair and the model enzyme ribonuclease t1. It was shown that salts affect the hydrophobicity of the contact pair according to their charge density, induced image charges play an important role in the observed salt-induced increase of ribonuclease t1 stability, and that salts affect ribonuclease t1 activity through modulation of the hydrogen bonds of water in the enzyme’s hydration shell. This work contributes a greater understanding of the effect of salts on proteins.

It has long been observed that salts affect proteins in a variety of ways, yet comprehensive explanations for different salt effects are still lacking. In the work presented here, the effect of salts on proteins has been investigated through three different effects: the hydrophobic effect; their conformational stability; the hydrogen bonding network of water in a protein’s hydration shell. UV-vis absorbance and fluorescence spectroscopy were used to monitor changes in two model systems, the phenol-acetate contact pair and the model enzyme ribonuclease t1. It was shown that salts affect the hydrophobicity of the contact pair according to their charge density, induced image charges play an important role in the observed salt-induced increase of ribonuclease t1 stability, and that salts affect ribonuclease t1 activity through modulation of the hydrogen bonds of water in the enzyme’s hydration shell. This work contributes a greater understanding of the effect of salts on proteins.

This thesis begins with a brief overview of supramolecular chemistry and selfassembly and simple examples derived from Nature that provide the motivation for the work presented here. The concept of a synthetic noncovalent toolbox is then introduced. The discussion then focuses more explicitly on side-chain and main-chain functionalized motifs and the methodologies employed in supramolecular polymer functionalization. The primary hypothesis of the thesis is that the combination of supramolecular strategies, ring-opening metathesis polymerization, and a well-understood toolbox of functionalities capable of noncovalent interactions, comprises a method for generating bioinspired materials. This hypothesis was tested by synthesizing unique functionalized supramolecular polymers that allowed for a detailed understanding of the orthogonality of noncovalent interactions and how such interactions can begin to mimic the complexity of functional biomaterials. The strategies and methods discussed in the synthesis of these bioinspired materials are divided into three chapters: (1) an exploration of the self-sorting phenomena between two non-complementary pairs of hydrogen bonds along polymer side-chains, (2) the extension of the self-sorting concept to include a metal coordination moiety, and (3) the side-chain functionalization strategies of chapters 2 and 3 in combination with the main-chain ROMP methodologies discussed in chapter 1 to form orthogonally self-assembled multifunctional block copolymers. The main results of this thesis include the results that multifunctional block copolymers can be fashioned via ROMP, functionalized in both the main- and side-chains, and self-assembled in an orthogonal fashion. In addition, these studies have found that self-sorting between pairs of non-complementary hydrogen bonding motifs can occur in supramolecular synthetic systems, that the interactions are extremely solvent dependent and that these interactions can result in unexpected phenomena. These results demonstrate the importance of a fully understood toolbox for the rapid development of supramolecular materials. The knowledge derived from this toolbox and presented in chapters 2, 3, and 4, allows for the careful selection of compounds for cleverly designed self-assembly materials inspired by Nature. Finally, conclusions are drawn to the success of the synthetic toolbox and the various strategies presented herein, and potential future directions are discussed.

[Truncated abstract] This work was concerned with investigations into the synthesis of Ce(OH)4, Sm(OH)3 and hydrated Ce-Sm mixed oxide nanoparticles with anisotropic morphologies via a chemical precipitation technique. The effect of various experimental parameters including temperature, aging time, ionic environment and thermal treatment on the morphology, structure of nanoparticles as well as elemental homogeneity of the mixed oxide nanoparticles was emphasised. It was shown that different experimental conditions resulted in different particle morphologies. This suggested that by tuning experimental parameters an ultimate goal of nanotechnology, the formation of nanoparticles with desired morphologies and sizes, may be achieved. It was found that by modifying experimental parameters it was possible to influence the development of various morphological and structural characteristics of Ce(OH)4 nanoparticles. The resulting morphologies were fibrous needle-like, rod-like and nanowire particles of various sizes. Characterisation of the nanoparticles was conducted through analysis by X-ray diffraction, surface area analysis and transmission electron microscopy techniques. Investigations into the structure of the hydrated CeO2 nanoparticles were undertaken since it is considered to be a key to the relevant properties of the material. The structure was found to exhibit multiple twinning phenomenon with 5-fold symmetry, with a consequence that atomic planes formed the particle surface. However, upon thermal treatment of needle-like particles, structural transformation was observed that possibly led to the development of more reactive and particle circumferential facets. A structural model and formation mechanism of such structures was proposed. ... A preliminary study into suitability of particle anisotropic morphology for compaction and densification processes was undertaken. Investigations into the sintering behaviour of the particles with anisotropic morphology were conducted on ceria nanoneedles. It was found that these particles displayed favourable sintering characteristics. The final densities of the hydrated ceria needle-like particle samples were achieved as high as 94.1% of the theoretical density after sintering at 1100°C for 5 hours.