Thesis (MSc)--University of Stellenbosch, 2011. / Please refer to full text to view abstract.

Understanding how atoms interact is a fundamental aspect of chemistry, biology and materials science. There have been great advances in the knowledge of covalent and ionic bonding over the past twenty years but one of the major challenges for chemistry is to develop full understanding of weak interatomic/intermolecular forces. This thesis describes fundamental studies that develop the basic understanding of weak interactions between heavier polarisable elements. The chosen methodology is to constrain heavy atoms using a rigid naphthalene backbone. When substituents larger than hydrogen, are positioned at close proximity at the peri-positions of a naphthalene molecule they experience steric strain; the extent of which is dictated by intramolecular interactions. These interactions can be repulsive due to steric hindrance or attractive due to weak or strong bonding. In efforts to understand the factors which influence distortion in sterically crowded naphthalenes and study possible weak intramolecular interactions between peri-atoms, investigations focussed on previously unknown mixed 1,8-disubstituted naphthalene systems. Mixed phosphorus-chalcogenide species were initially studied; three mixed phosphine compounds of the type Nap[ER][PPh2] were prepared along with their chalcogenides and a series of metal complexes. The study of interactions between heavy atoms was progressed by investigations into a series of mixed chalcogenide compounds of the type Nap[EPh][E’Ph] (E = S, Se, Te). Subsequent reaction of the chalcogenide systems with the di-halogens, dibromine and diiodine, afforded a mixture of charge transfer and insertion adducts displaying an array of different geometries around the chalcogen atom. From molecular structural studies, a collection of intramolecular peri-interactions were found, extending from no interaction due to repulsive effects, weak attractive 3c-4e type interactions and one example containing a strong covalent peri-bond. Further weak intramolecular interactions observed include CH-π and E•••E’ type interactions plus π-π stacking between adjacent phenyl rings. It was discovered that the bulk of the peri-atoms is influential on the distance between them, but this is not the only factor determining the naphthalene geometry. Inter- and intramolecular interactions can also have an impact and furthermore the number, size and electronic properties of substituents attached to the peri-atoms can determine molecular distortion.

Inhibitors belonging to the serpin (serine protease inhibitor) family control proteases involved in various physiological processes. All serpins have a common tertiary structure based on the dominant b-sheet A, but they have different inhibitory specificity. The specificity of a serpin is determined by the Pl-Pl’ peptide bond acting as a bait for the target protease which is made up of an exposed reactive centre loop (RCL). The serpin plasminogen activator inhibitor type-1 (PAI-1) is the main physiological inhibitor of urokinase-type and tissue-type plasminogen activators (uPA and tPA, respectively). Elevated plasma levels of PAI-l have been correlated with a higher risk of deep venous thrombosis, and PAI-1 is a risk factor for recurrent myocardial infarction. Furthermore, PAI-1 has a role in cell migration and has been suggested to regulate tumor growth and angiogenesis. PAI-1 is unique among the serpins in that it can spontaneously and rapidly convert into its latent form. This involves full insertion of the RCL into b-sheet A. There were two partially overlapping goals for this thesis. The first was to use latent PAI-1 as model for development of a fluorescence-based method, Donor-Donor Energy Migration for intramolecular distance measurements. The second goal was to use DDEM, together with other biochemical methods, to reveal the structure of the PAI-1/uPA complex, the conformation of the RCL in active PAI-1, and molecular determinants responsible for the conversion of PAI-1 from the active to the latent form. The use of molecular genetics for introduction of fluorescent molecules enables the use of DDEM to determine intramolecular distances in a variety of proteins. This approach can be applied to examin the overall molecular dimensions of proteins and to investigate structural changes upon interactions with specific target molecules. In this work, the accuracy of the DDEM method has been evaluated by experiments with the latent PAI-1 for which X-ray structure is known. Our data show that distances approximating the Förster radius (57±1 Å) obtained by DDEM are in good agreement (within 5.5 Å) with the distances obtained by X-ray crystallography. The molecular details of the inhibitory mechanism of serpins and the structure of the serpin/protease complex have remained unclear. To obtain the structural insights required to discriminate between different models of serpin inhibition, we used fluorescence spectroscopy and cross-linking techniques to map sites of PAI-1/uPA interaction, and distance measurement by DDEM to triangulate the position of the uPA in the complex. The data have demonstrated clearly that in the covalent PAI-1/uPA complex, the uPA is located at the distal end of the PAI-1 molecule relative to the initial docking site. This indicates that serpin inhibition involves reactive center cleavage followed by full loop insertion, whereby the covalently linked protease is translocated from one pole of the inhibitor to the opposite one. To search for molecular determinants that could be responsible for conversion of PAI-1 to the latent form, we studied the conformation of the RCL in active PAI-1 in solution. Intramolecular distance measurements by DDEM, the newly a developed method based on probe quenching and biochemical methods revealed that the RCL in PAI-1 is located much closer to the core of PAI-1 than has been suggested by the recently resolved X-ray structures of stable PAI-1 mutants, and it can be partially inserted. This possibly explains for the ability of PAI-1 to convert spontaneously to its latent form.

A novel target-promoted DNA alkylation system was designed, which consists of a DNA intercalating/alkylating quinone methide (QM) precursor, a removable amine linker, and a sequence-specific delivery. The QM in this system was regenerated by eliminating the amino linker promoted by the hydrophobic interaction between the target DNA and the intercalating QM precursor. Three alkylation model systems (methoxyl polycyclic system, intramolecular hydrogen bonding system and biaryl system) were proposed and synthesized. The potential DNA QM alkylation was investigated by deoxyadenosine (dA) and deoxyguanosine (dG) alkylation with the biaryl system. Only one deoxynucleoside adduct was observed when dA or dG reacted with quinoline or naphthalene QM precursor, in which both dA adducts degraded with time, while dG adducts remained unchanged after 72h at room temperature. The quinoline dG adduct was fully characterized as quinoline dG N1 adduct by NMR techniques. Naphthalene dG was found as a 1:1 mixture of diastereomers.

Organic frameworks with rigid backbones, such as acenaphthene, are highly suitable for the study of interatomic interactions. The short “natural” peri-distance (2.44 Å) and the rigidity of the aromatic system causes considerable steric strain between peri-substituted heteroatoms. As a consequence, substitution at both peri-positions leads to in- and out-of-plane distortions, which often result in buckling of the ring system. In order to relax this geometric strain, weak bonding interactions can also exist between the peri-substituents. This thesis focuses on the synthesis, structural characterisation and investigation of a range of sterically crowded peri-substituted acenaphthene compounds. This involves the study of the acenaphthene geometry, through X-ray crystallography when different peri-substituents occupy the close 5,6-positions; our main focus is to study weak non-bonded interactions that can occur across the peri-gap, for example weakly attractive three-centre four-electron (3c-4e) type interactions which are known to prevail in such compounds under the appropriate conditions. Repulsion within these systems, resulting from the steric crowding of the peri-space is also investigated, employing changes in bond lengths, bay-region angle splay, displacement of atoms from the mean plane and central acenaphthene torsion angles to help quantify the degree of acenaphthene distortion, which are all conveniently probed by the peri-distance. To this end we have synthesised a range of novel sterically crowded mixed bromo-tin acenaphthene derivatives (Chapter 3), chalcogen-tin acenaphthene molecules (Chapter 4), phosphorus–tin derivatives (Chapter 5) and a series of homologous tin-tin acenaphthenes (Chapter 6). All the compounds studied in this thesis were characterised by multinuclear NMR spectroscopy and X-ray crystallography in an effort to gain a greater understanding of the deformation that occurs when disparate functionalities are located in close proximity and explore the potential for weak non-covalent intramolecular interactions to occur.

Nanopartículas de prata foram preparadas pela redução química de íons prata (AgNO3) por borohidreto de sódio (NaBH4) na presença de poli-(N)-vinil-2-pirrolidona em solução de álcoois de cadeia curta. As nanopartículas de prata apresentaram maior estabilidade em 2- propanol, e o diâmetro aproximado das nanopartículas Ag0 obtidas neste solvente é de aproximadamente 6 nm. As propriedades fotofísicas dos corantes coumarinas e derivados de acridina, em 2-propanol, são afetados pela presença das nanopartículas de prata. A interação das nanopartículas de prata com os derivados de acridina leva a uma mudança espectral da banda de absorção de transferência de carga intramolecular ´ICT - intramolecular charge transfer´. Para dois dos derivados de acridina, há um aumento significativo de emissão com a adição inicial de nanopartículas de Ag0. Mas em altas concentrações de nanopartículas de prata, ocorre supressão estática de fluorescência, com uma progressiva diminuição da eficiência de fluorescência. A intensidade de fluorescência das amino coumarinas é somente suprimida pela presença de nanopartículas de prata em solução. / Silver nanoparticles were synthesized by chemical reduction of silver ions by sodium borohydride in the presence of poly-(N)-vinyl-2-pyrrolidone in solution of short chain alcohols. The nanoparticles are stable in 2-propanol, and the average diameter of the Ag colloid obtained in this solvent is about 6 nm. The photophysical properties of acridinium and coumarin dyes in 2-propanol are affected by the presence of silver nanoparticles. The interaction of silver nanoparticles with acridinium derivative leads to a spectral change of its intramolecular charge transfer (ICT) absorption band. The dye emission increases suddenly with the initial addition of the Ag metal nanoparticles, but at a high concentration of the colloid, static fluorescence quenching occurs with a progressive decrease of the fluorescence efficiency. Amino coumarin fluorescence is only quenched by the silver nanoparticles in solution in the concentration range used.

Os corantes benzazólicos fluorescentes por ESIPT são conhecidos pela sua grande estabilidade e variabilidade no comprimento de onda da sua emissão de fluorescência. Novos derivados, nomeados HBs, foram estudados como corantes para sangue por possuírem grupos sulfônicos na sua estrutura molecular, o que é característico dos corantes proteicos utilizados para a análise de sangue. Estudos sobre essa aplicação foram desenvolvidos nesse trabalho, visando estabelecer vantagens e desvantagens em comparação aos reagentes mais utilizados. Os resultados foram satisfatórios para essa utilização, sendo tão sensível quanto o Amido Black e permitindo a combinação de técnicas com diferentes reveladores, sendo eles: Amido Black, Cianoacrilato e Luminol. Este trabalho também estudou a síntese do Luminol reproduzindo metodologias descritas na literatura, além da síntese do isômero Isoluminol. A obtenção de um produto com alto grau de pureza é difícil. Como são necessárias várias etapas, o rendimento do produto não é alto. / The benzazole fluorescent dyes by ESIPT are known for their high stability and fluorescence emission wavelength variability. New derivatives, appointed HBs, were studied as blood enhancement dyes once they have sulfonic groups in its molecular structure, which is characteristic of protein dyes used for blood analysis. Studies about this application were developed in this work, in order to establish its advantages and disadvantages compared to commonly used reagents. The results were satisfactory for the referred use, being as sensitive as Amido Black and allowing for techniques combination with different developers: Amido Black, Cyanoacrylate and Luminol. This work also studied the Luminol synthesis by reproducing methodologies described in the literature, as well as the isomer Isoluminol synthesis. The obtaining of a product with high purity is difficult. As several steps are required, the product yield is not high.

Further investigations intending illucidate the mechanism of a newly discovered redox-alkylation reaction of azo dyes are presented. Preliminary results indicate that this reaction most probably proceeds via initial N-alkylation of the anion derived from an alpha-ketohydrazone. An investigation is continued to study the synthesis of macrocycle-carbohydrate-dye hybrids. The development of a modular approach to macrocycle assembly has enabled the synthesis of a library of pyridine-based macrocycles possessing multiple donor sites. A central dye scaffold, prepared from the SNAr reaction between halo-substituted azo dye and a disubstituted phenol, was decorated with a representative carbohydrate or macrocycle using Sharpless click chemistry. Also an "S3N-ligand azo-dye" conjugate has been synthesised with a view to the development of a sensor for heavy metal ions. Complexation of this system with Ag(I), Hg(II) and Cu(II) salts has been investigated. Complexation of the dye to metals results in a bathochromic shift in the absorption maximum of the azo dye, an effect which is most pronounced for Cu(II).The Kobayashi fragmentation has transformed the area of benzyne chemistry as it enables its generation from readily available precursors under mild reaction conditions. The controlled generation of benzyne in this manner has been utilised by many groups, allowing readily access to a variety of functionalised aromatic and heteroaromatic from simple precursors. During the course of a synthetic project, which was to utilise the Kobayashi fragmentation in a key intramolecular Diels-Alder reaction, we noticed that alternate modes of fragmentation/rearrangement accompanied the desired elimination reaction leading to benzyne generation. In particular, competing Fries or Smiles rearrangements became the major routes of fragmentation in appropriately functionalised substrates. The results of an investigation into the factors affecting the course of the Kobayashi fragmentation, together with the development of a novel bi-aryl synthesis are presented in this thesis.

Les nouveaux matériaux carbonés modifiés par des films organiques constituent un domaine de recherche très actif depuis plusieurs décennies. Ces matériaux suscitent un intérêt grandissant dans les secteurs de l’énergie, de la santé et de l’environnement. Afin d’améliorer les performances de ces matériaux, les innovations reposent notamment sur la maîtrise de la fonctionnalisation des surfaces, le contrôle de la stabilité de la couche immobilisée ou encore sur les nouvelles propriétés liées à la modification. Selon les fonctions chimiques greffées, les applications sont multiples : détection et/ou la capture d’éléments chimiques, hydrophobicité, stockage d’énergie électrique ou de gaz ou encore biocompatibilité. Dans ce contexte, les travaux de cette thèse portent sur la modification de surfaces carbonées par différents composés organiques, dans le but d’une part de déterminer les relations structurepropriétés du film déposé et d’autre part d’améliorer les performances de supercondensateurs carbonés. Nos investigations reposent sur la synthèse d’un ensemble de composés conjugués ou non, suivi d’un greffage indirect passant par une construction sur surface ou par greffage direct via l’oxydation d’amine. Ces greffages ont été explorés méthodologiquement afin de déterminer l’impact de la conjugaison au sein du film organique déposé et l’influence de la structure du matériau carboné. Nous montrons également qu’une fonctionnalisation contrôlée sur carbone activé permet d’avoir une meilleure intégration des molécules dans des supercondensateurs carbonés. L’enjeu consiste à mieux comprendre les interactions molécules-substrat au cours de la modification de matériaux. / The new carbon materials modified with organic films has been a very active field of research for several decades. These materials are attracting increasing interest in the fields of energy, health and environmental. In order to improve the performance of these materials, the innovations are based in particular on the control of the functionalization of the surfaces, the control of the stability of the immobilized layer or on the new properties related to the modification. According to the chemical units grafted, the applications are numerous: detection and/or capture of chemical elements, hydrophobicity, storage of electrical energy or gas or also biocompatibility. In this context, the work of this thesis deals with the modification of carbon surfaces by various organic compounds firstly to determine the structureproperties relationships of the deposited film and secondly to improve the performance of carbon supercapacitors. Our investigations are based on the synthesis of conjugated or unconjugated compounds, followed by indirect grafting by build steps or direct grafting via amine oxidation. These grafts were explored methodologically to determine the impact of the conjugation within the deposited organic film and the influence of the structure of carbon material. We also show that controlled activated carbon functionalization allows for better integration of molecules into carbon supercapacitors. The challenge is to understand molecule-substrate interactions during the modification of materials.

Doctor of Philosophy(PhD), / This thesis describes the synthesis of terminal and internal amino and amidoalkynes and their hydroamination (cyclisation) catalysed by the complex (bis(N-methylimidazol-2-yl)methane)dicarbonylrhodium(I) tetraphenylborate (1). A series of analogous palladium complexes were also prepared and investigated for catalytic hydroamination. The scope of the rhodium(I) complex (1) for the intramolecular hydroamination of more complex amino and amidoalkyne substrates was investigated. This was made possible with the synthesis of aliphatic substrates, namely, 4 pentyn 1 amide (3) and 5 hexyn 1 amide (4) and a number of aromatic substrates, namely, 1, 4 diamino-2, 5 diethynylbenzene (5), 1, 4-diamino-2, 5 bis(phenylethynyl)benzene (6), 2, 3-diamino-1, 4-diethynylbenzene (7), 2, 3-diamino-1, 4-bis(phenylethynyl)benzene (8), 1, 5-bis(acetamido)-2, 4-diethynylbenzene (9), N-(acetyl)-2-ethynylbenzylamine (10) and N-(acetyl)-2-(phenylethynyl)benzylamine (11). The rhodium(I) complex (1) catalytically cyclised the aliphatic 4 pentyn 1 amide (3) regioselectively to the 6 membered ring, 3, 4 dihydro 2 pyridone (64) as the sole product. Attempts to cyclise 5 hexyn 1 amide (4) to produce either the 6 or 7 membered ring were unsuccessful. Compounds 5, 6, 7 and 8 were doubly cyclised to 1, 5 dihydro pyrrolo[2, 3 f]indole (71), 1, 5-dihydro-2, 6-diphenyl-pyrrolo[2, 3 f]indole (73), 1, 8-dihydro-pyrrolo[2, 3 g]indole (74) and 1, 8-dihydro-2, 7-diphenyl-pyrrolo[2, 3 g]indole (75) respectively. The aromatic amides with terminal acetylenes 9 and 10 cyclised to give 1, 7 diacetyl pyrrolo[3, 2 f]indole (76) and N (acetyl) 1, 2 dihydroisoquinoline (77) respectively. However, attempts to cyclise 11 were unsuccessful. Thus the rhodium(I) complex (1) successfully catalysed via hydroamination both terminal and internal acetylenic amine and amide substrates, to give pyridones, indoles and isoquinolines. Cationic and neutral palladium complexes incorporating the bidentate heterocyclic nitrogen donor ligand bis(N-methylimidazol-2-yl)methane (bim; 2) were synthesised: [Pd(bim)Cl2] (15), [Pd(bim)2][BF4]2 (17) [Pd(bim)(Cl)(CH3)] (14), [Pd(bim)(CH3)(NCCH3)][BF4] (16). All of the complexes were active as catalysts for the intramolecular hydroamination reaction, using the cyclisation of 4 pentyn 1 amine (21) to 2 methyl 1 pyrroline (22) as the model test reaction. Percentage conversions, turnover numbers and reaction profiles for each complex were compared to the rhodium(I) complex (1). These studies have shown that the catalytic activity was not significantly dependent on the bim donor ligand or the choice of metal. Substitution of the bim (2) ligand with the COD ligand and the use of methanol as the solvent did impact significantly on the efficiency of the hydroamination reactions.