Smaller cellular telephones and more energy-efficient windows are just two examples of technological advances which call for new materials. Materials chemists seek to develop new materials, both out of pure curiosity to see which combination of elements and structures can be obtained and in efforts to produce materials, with specific properties. The starting materials (in solid, liquid or gaseous form) can then be combined and prepared in various ways. A chemical method that is gaining more attention for thin-film growth is Atomic Layer Deposition (ALD). This is a sophisticated type of vapor deposition in which the precursor gases are introduced separately into the reaction chamber. Silicon carbide (SiC) and cubic boron nitride (c-BN) are extremely hard diamond-like materials, both with a high potential for application within the modern microelectronics and tool industry. Hexagonal boron nitride (h-BN), with its graphite-like layered structure, is a promising ceramics material. Deposition of thin SiC and BN films from gaseous precursors has been studied by theoretical and experimental methods. The chemical composition and atomic arrangement of a growing surface is important for vapor growth. The surface may be terminated (e.g., by hydrogen atoms) and adopt various geometrical structures. Reconstruction of unterminated SiC(0001) surfaces, as well as H abstraction from the corresponding H-terminated surfaces, were studied using quantum mechanical calculations. Elementary reactions for vapor growth of SiC and BN, and in situ incorporation of dopant and contaminant species into these surfaces were also investigated theoretically. Moreover, thin films of BN were deposited by means of laser-assisted ALD. The general goal has been to predict and/or explain experimental results by investigating growth mechanisms.

Catalysis has a profound impact on all living species on the earth. Nature’s catalysts, the enzymes, have the ability to selectively promote a specific bio-chemical transformation, given the required substrate. As well as being highly selective, enzymes enhance the speed of these reactions, helping them to run at temperatures much lower than normally required, i.e. at body temperature. In comparison, reactions used in the production of new materials such as polymers, medicines, fragrances, petrochemicals, etc. are often catalyzed by transition metals. This thesis describes how the selectivity and activity of these catalysts can be influenced via two conceptually different methods: chelation control and microwave heating. The thesis primarily focuses on regio- and stereochemical aspects of the palladium-catalyzed arylation of olefins, i.e. the Heck reaction. Reaction rate enhancement of both palladium and enzyme (polymerase chain reaction [PCR]) catalysis by microwave heating is also discussed. Novel chelation-controlled palladium-catalyzed multi- and asymmetric arylations of vinyl ethers were performed, resulting in tetra-substituted olefins as well as chiral quaternary carbon centers with excellent optical purity. In addition, a new synthetic route to diarylated ethanals, relying on a double chelation-controlled regioselective arylation followed by hydrolysis, has been discovered. High temperature conditions, using microwave heating, substantially reduce the reaction time for ligand-controlled asymmetric Heck arylations, while retaining levels of enantioselectivity in most cases. In addition, a potentially useful fast synthetic protocol for the employment of aryl boronic acids in oxidative Heck arylation was developed. Finally, microwave-assisted PCR was described for the first time; this method allows reductions in the run time of 50%.

This thesis is based on ten publications (Papers I-X). The phosphodiester backbone makes DNA or RNA to behave as polyelectrolyte, the pentose sugar gives the flexibility, and the aglycones promote the self-assembly or the ligand-binding process. The hydrogen bonding, stacking, stereoelectronics and hydration are few of the important non-covalent forces dictating the self-assembly of DNA/RNA. The pH-dependent thermodynamics clearly show (Papers I and II) that a change of the electronic character of aglycone modulates the conformation of the sugar moiety by the tunable interplay of stereoelectronic anomeric and gauche effects, which are further transmitted to steer the sugar-phosphate backbone conformation in a cooperative manner. 3'-anthraniloyl<b> </b>adenosine<b> </b>(a mimic of 3'-teminal CC<u>A</u>OH of the aminoacyl-tRNAPhe) binds to EF-Tu*GTP in preference over 2'-anthraniloyl<b> </b>adenosine<b>, </b>thereby showing (Paper III) that the 2’-endo sugar conformation is a more suitable mimic of the transition state geometry than the 3’-endo conformation in discriminating between correctly and incorrectly charged aminoacyl-tRNAPhe by EF-Tu during protein synthesis. The presence of 2'-OH in RNA distinguishes it from DNA both functionally as well as structurally. This work (Paper IV) provides straightforward NMR evidence to show that the 2'-OH is intramolecularly hydrogen bonded with the vicinal 3'-oxygen, and the exposure of the 3'-phosphate of the ribonucleotides to the bulk water determines the availability of the bound water around the vicinal 2'-OH, which then can play various functional role through inter- or intramolecular interactions. The pH-dependent 1H NMR study with nicotinamide derivatives demonstrates (Paper V) that the cascade of intramolecular cation (pyridinium)-π(phenyl)-CH(methyl) interaction in edge-to-face geometry is responsible for perturbing the pKa of the pyridine-nitrogen as well as for the modulation of the aromatic character of the neighboring phenyl moiety, which is also supported by the T1 relaxation studies and ab initio calculations. It has been found (Papers VI-IX) that the variable intramolecular electrostatic interaction between electronically coupled nearest neighbor nucleobases (steered by their respective microenvironments) can modulate their respective pseudoaromatic characters. The net result of this pseudoaromatic cross-modulation is the creation of a unique set of aglycones in an oligo or polynucleotide, whose physico-chemical properties are completely dependent upon the propensity and geometry of the nearest neighbor interactions (extended genetic code). The propagation of the interplay of these electrostatic interactions across the hexameric ssDNA chain is considerably less favoured (effectively up to the fourth nucleobase) compared to that of the isosequential ssRNA (up to the sixth nucleobase). The dissection of the relative strength of basepairing and stacking in a duplex shows that stability of DNA-DNA duplex weakens over the corresponding RNA-RNA duplexes with the increasing content of A-T/U base pairs, while the strength of stacking of A-T rich DNA-DNA duplex increases in comparison with A-U rich sequence in RNA-RNA duplexes (Paper X).

The usefulness of low concentrations (typically 10 to 100 µM) of [11C]carbon monoxide and aryl triflates as substrates in 11C-carbonylation using different nucleophiles in the presence of lithium bromide was investigated. The reactions were performed in a micro autoclave of 200 µL volume and catalysed (mediated) by palladium(0). A peripheral type benzodiazepine receptor (PBR) ligand, 1-(2-chlorophenyl)-N-methyl-N-(1-methylpropyl)isoquinoline-3-carboxamide (PK11195) and its structural analogues including an irreversible ligand for PBR, some other amides, ketones and carboxylic acids, were all labelled with 11C using this approach. The [carbonyl-11C]PK11195, analogues and other amides were prepared from aryl triflates and amines, and the [carbonyl-11C]ketones were prepared from aryl triflates and organoboranes. In the synthesis of [carboxyl-11C]carboxylic acids, water was utilised as nucleophile. The decay-corrected radiochemical yields were 10 to 55% for [11C]PK11195 and analogues, 2 to 63% for other [11C]amides, 10 to 75% for [11C]ketones and 25 to 65% for [11C]carboxylic acids. The specific radioactivity of the labelled compounds was in the range of 150 to 900 GBq/µmol. Some [11C]amines were prepared by a reductive amination of the corresponding [carbonyl-11C]ketones. These reactions were performed using different amines in the presence of TiCl4 and NaBH3CN. The radiochemical yields of the [11C]amines varied from 2 to 78% (determined by analytical HPLC). In order to confirm the labelling position, synthesis of selected 13C-substituted compounds were performed. For each substance group/ synthesis method, a selected compound was synthesised using (13C)carbon monoxide and the 13C-substituted compound was then analysed by 13C NMR. A synthetic route was developed for the preparation of 1-(2-chloro-phenyl)-isoquinolin-3-yl trifluoromethanesulfonate used as the precursor in the synthesis of [carbonyl-11C]PK11195 and analogues.

In this thesis oxidative coupling of H-phosphonate and H phosphonothioate diesters with different alcohols and amines are presented. Since the reactions with alcohols previously have been particularly unfavourable due to competing side reactions, a modified protocol leading to high coupling yields of structurally diverse hydroxylic components was developed. The phosphorylation reaction was studied using 31P NMR spectroscopy and for the first time the previously only postulated reactive intermediate involved in these reactions was observed. The use of iodine in combination with a bulky chlorosilane in pyridine was found to have a profound effect on both the suppression of side reactions and the rate of the oxidative couplings, and led to a clean formation of phosphorylated products in high yields. This synthetic protocol was then extended to include coupling reactions with bis-functional reagents containing hexamethylene linkers to provide handles for derivatisations of oligonucleotides. A synthetic protocol consisting of the stereospecific oxidative coupling of amines with H-phosphonate diesters to produce phosphoroamidates was designed in such a way that it permitted control of the stereochemical outcome of the reactions. Based on a silylation-mediated reaction utilising phenyl H phosphonothioate monoester as a thiophosphonyl transferring agent, a method was developed and used for the preparation of H-phosphonothioate building blocks for the synthesis of DNA analogues.

In this thesis, the preparation of new photoactive substances containing mono- and bipyridines coordinated to ruthenium is presented together with initial evaluations of their photoelectrochemical and photophysical properties. Complexes of the type Ru(bpy)2(4-X-py)2 (X = SH, COOH) were prepared and used in Grätzel-type solar cells based on ZnO. The results show that the thiol complex binds to the surface but give rather low solar cell efficiencies. Different routes to obtain Ru(bpy)2(4,4´-dithio-2,2´-bipyridine) were evaluated, among them substitution reactions on 4,4´-dichloro-2,2´-bipyridine coordinated to ruthenium. Due to reactivity issues, the target sulphur-containing complex has not yet been obtained. The synthesis of methanofullerenes, fulleropyrrolidines and –pyrazolines are presented, among them dyads containing Ru(bpy)n-units. A common feature for the dyads is the unusually short linkers between the fullerene and the ruthenium complex. Dyad preparations were in some cases simplified by carrying out the reactions in the presence of silver salts. A preliminary evaluation of the emission of the dyads showed almost complete quenching of the excited state of a pyrrolidine-based dyad, whereas emission remained from the pyrazoline-based ones. Whether this was due to incomplete quenching of the excited states of the ruthenium complex, or induced by the presence of hydrazones has yet to be revealed. The use of fullerene-substituted malonic acid and its ethyl ester as dyes in Grätzel-type solar cells resulted in even lower efficiencies (IPCE) than for bare TiO2. This could be due to electron transfer in the reverse direction compared to what is observed for ruthenium complexes. Thus, these fullerene derivatives are not suitable as sensitisers for Grätzel-type solar cells.

In this thesis, the improved synthesis and investigations into the properties of some 3,7-diazabicyclo[3.3.1]nonane (bispidine) derivatives are described. These compounds are structurally related to the naturally occurring lupanine alkaloids, they are of interest because of their cardiac antiarrhythmic function as well as their use as bases or ligands in organic chemical reactions. Their chemical properties are related to the presence of a rigid molecular scaffold with two nitrogen atoms that can be utilized for binding interactions with a variety of Lewis acids. An improved synthesis has been developed, providing access to bispidines via bispidinones while avoiding the use of highly toxic hydrazine, which is required as reducing agent in alternative methods. A series of bispidine derivatives with a variety of substituents were characterized regarding their basicity, which spans thirteen orders of magnitude. Correlations between structure and basicity are discussed and computational methods have been used to propose further derivatives with even higher basicity. The structures of several bispidine derivatives and their protonated forms have been characterized in the solid state by X-ray crystallography and in solution using NMR spectroscopy. Structure and solution dynamics in a sterically congested (π-allyl)palladium complex with a bispidine ligand have been investigated, revealing mechanistic insight into the dynamic process. Using a bulky bispidine as a temporary ligand for a (η3-propenyl) palladium complex, the novel adamantanoid [{(η3-propenyl)Pd}6(μ3-OH)4] cluster was prepared.

This thesis describes the design of polypeptides, unordered in the monomeric state but capable of folding into helix-loop-helix motifs and dimerise to form four-helix bundles. The goal of the design was to encode them with the capacity to form dimers highly selectively and the ability to carry out molecular functions in the folded state but not in the unordered state, and thus to establish a molecular link between recognition and function. The 42-residue sequences JR2E and JR2K were both shown by CD spectroscopy to adopt unordered conformations under single solute conditions at pH 7 but to form helical conformations in a 1:1 mixture. Analytical ultracentrifugation showed that JR2E and JR2K formed a clean heterodimer and the dissociation constant Kd, measured by CD spectroscopy, was found to be 5 ± 1 μM. Discrimination was enabled by the incorporation of charged residues at the dimer interface in the helical segments of the helix-loop-helix motif. Glutamic acids were incorporated in JR2E and lysines in JR2K, and charge repulsion prevented the monomeric subunits from forming homodimers. In mixtures, however, highly helical heterodimers were formed. The cooperative transition from unordered conformation to heterodimeric four-helix bundle was exploited in the design of a signal response system by incorporating a reactive site, capable of catalysing the hydrolysis of a m-nitrophenyl ester, into the negatively charged polypeptide. In the unfolded state the functionalised polypeptide was virtually inactive but in the folded state, induced by the interaction with JR2K, the substrate was hydrolysed approximately an order of magnitude more efficiently. Interactions between the designed polypeptides and a functionalised polythiophene polymer were studied and it was found that the conformation of the polymer was controlled by the polypeptides, largely by electrostatic interactions. The negatively charged JR2E forced the polymer to adopt a planar conformation while the positively charged JR2K induced a more twisted conformation of the polymer. The spectral changes coupled to the conformational transitions of the polymer were used to measure the binding of human Carbonic anhydrase II by JR2E functionalised with a benzenesulphonamide ligand, in demonstration of its use as a tool for high-throughput screening. JR2E immobilised on gold nanoparticles was shown to form homodimers reversibly under pH control, with affinities large enough to determine the state of aggregation of the gold nanoparticles.

Malaria is one of the major public health problems in the world. Approximately 500 million people are afflicted and almost 3 million people die from the disease each year. Of the four causative species Plasmodium falciparum is the most lethal. Due to the rapid spread of parasite resistance there is an urgent need for new antimalarial drugs with novel mechanisms of action. Several promising targets for drug intervention have been revealed. This thesis addresses the parasitic aspartic proteases termed plasmepsins (Plm), which are considered crucial to the hemoglobin catabolism essential for parasite survival. The overall aim was to identify inhibitors of the P. falciparum Plm I, II, and IV. More specific objectives were to attain activity against P. falciparum in infected erythrocytes and selectivity versus the most homologous human aspartic protease cathepsin D (Cat D). To guide the design process the linear interaction energy (LIE) method was employed in combination with molecular dynamics. Initial investigations of the stereochemical requirements for inhibition resulted in identification of an L-mannitol derived scaffold encompassing a 1,2-dihydroxyethylene transition state isostere with affinity for Plm II. Further modifications of this scaffold provided inhibitors of all three target plasmepsins (Plm I, II, and IV). Apart from the stereochemical analysis three major kinds of manipulation were explored: a) P1/P1′ and P2/P2′ side chain alterations, b) replacement of amide bonds by diacylhydrazine, 1,3,4-oxadiazole, and 1,2,4-triazole, and c) macrocyclization. Several inhibitors of Plm I and II with Ki values below 10 nM were discovered and one Plm IV selective inhibitor comprising two oxadiazole rings was found which represents the most potent non-peptide Plm IV inhibitor (Ki = 35 nM) reported to date. Some of the identified plasmepsin inhibitors demonstrated significant activity against P. falciparum in infected erythrocytes and all inhibitors showed a considerable selectivity for the plasmepsins over the human Cat D.

The voltammetric properties of Olsalazine sodium, seven other azosalicylic acids and the azoxy analogue of Olsalazine sodium have been studied in aqueous solutions mainly by cyclic voltammetry and constant potential coulometry. It was found that these compounds can all be both reduced and oxidised at a glassy carbon electrode. The reduction and oxidation potentials of the compounds were dependent on the pH and the structure of the compounds. All compounds, except 4,4'-azobis-(2-hydroxybenzoic acid), were reduced to the corresponding amino salicylic acids in a 4 e-, 4 H+ reaction, as shown by spectrophotometric and voltammetric investigations of the reduced solutions. A further electrochemical characterisation of the formed reduction products 3-, 4- and 5-aminosalicylic acid was also carried out. It was found that the oxidation of the investigated azo compounds occurs according to two different pathways. Compounds with, at the most one hydroxyl group in the 2- or 4- position were shown to be irreversibly oxidised while Olsalazine sodium, its azoxy analogue and 2-hydroxy-5-[(3'-carboxy-2'-hydroxyphenyl)azo]benzoic acid disodium salt were oxidised in a reversible 2e-, 2H+ reaction. The oxidation product of Olsalazine sodium was characterised by UV/VIS and NMR spectroscopic methods and a structure for the oxidation product was proposed. The oxidative properties of Olsalazine sodium were also utilised to determine nM concentrations of this compound by liquid chromatography with electrochemical detection (LCEC).