This thesis focuses on synthetic and mechanistic aspects of palladium-catalyzed C(sp2)-P bond-forming reactions, with the aim to develop mild and efficient methods for the synthesis of biologically active phosphorus compounds, e.g. DNA analogs. The first part of the thesis is devoted to detailed mechanistic investigations of the palladium-catalyzed C-P cross-coupling reaction, in order to fully understand the underlying chemistry and by rational design of the reaction conditions, improve the overall efficiency of the process and broaden its applicability. In particular influence of palladium coordination by different anions on the rate of ligand substitution and reductive elimination steps of the reaction was studied. It was found that coordination of acetate ion results in unprecedented acceleration of both of the mechanistic steps, what leads to remarkable shortening of the overall reaction times. In-depth kinetic investigations enabled to ascribe the observed effects to ability of the acetate ion to act as a bidentate ligand for palladium. This causes considerable alternation of the reaction mechanism, comparing to the reaction involving halide-containing complexes, and results in significant rate increase. Based on the above mechanistic studies an efficient method for the synthesis of arylphosphonates, using substoichiometric amounts of inorganic acetate additive and reduced amount of catalyst, was developed. In the next part of the thesis, efforts to further enhance the palladium-catalyzed cross-coupling efficiency by using a microwave-assisted synthesis are described. These explorations resulted in a successful development of two protocols, one for a cross-coupling of H-phosphonates and the other for H,H-phosphinates, under the microwave heating conditions. Application of this energy source resulted in extremely short reaction times, measured in minutes. The final chapter of this thesis deals with studies on palladium-catalyzed SN2’ propargylic substitution reaction with phosphorus nucleophiles, which leads to allene products. Efficient procedure for the synthesis of allenylphosphonates and related compounds was developed. The method enables full control of stereochemistry in the allene moiety and at the asymmetric phosphorus center. Some conclusions on the mechanism of the reaction were also drawn. / At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 7: In press.

This thesis is devoted to the development of new organophosphorus compounds for potential uses in material science and as reagents in Organic Chemistry. Organophosphorus compounds in a single molecule or organic electronics context are appealing as the phosphorous centers perturb the electronic properties of the π-conjugated systems while at the same time provide synthetic handles for subsequent synthetic modifications. As such, new synthetic methodology to such compounds and the exploration of new building blocks is of considerable interest. In a different study, novel organophosphorus compounds are synthesized and shown to promote a reaction in Organic Chemistry that has previously not been possible, i.e. the stereoselective reductive coupling of aldehydes to alkenes. Such developments enlarge the toolkit of reactions that are available to Organic Chemists, and may impact the synthetic routes to pharmaceuticals and other important commodity chemicals. A general introduction of the key structural unit of this thesis, phosphaalkenes, is given in the first chapter. The synthesis, reactivity, properties and applications of these P=C double bond containing compounds are highlighted. The Wittig reaction and its variations as well as the phosphorus analogues that produce phosphaalkenes are outlined in detail. The second chapter is dedicated to the synthesis of a precursor that is used for the preparation of novel π-conjugated, organophosphorus compounds. C,C-Dibromophosphaalkenes are prepared and the halide substituents are used for the selective introduction of acetylene units. Besides the phosphaalkenes, the successful syntheses of two new diphosphenes is presented, indicating a broad applicability of the precursors. The third chapter is dedicated to the isolation of a metal-free phosphanylphosphonate that transforms aldehydes quantitatively to their corresponding E-phosphaalkenes in a transition metal-free phospha-HWE (Horner-Wadsworth-Emmons) reaction. The reaction benefits from mild conditions, high E-stereoselectivity, and a broad substrate scope. In the last chapter, a novel method for the reductive coupling of aldehydes to olefins is introduced. The reaction, which is a vast improvement over the McMurry coupling, allows for the selective synthesis of symmetrical and most importantly unsymmetrical E-alkenes. The phosphanylphosphonate mentioned above is the reagent that facilitates the coupling of the aldehydes via a phosphaalkene intermediate. This one-pot reaction benefits from mild conditions, good conversions, and high E-stereoselectivity. In summary, the thesis presents novel aspects of organophosphorus chemistry. These include the preparations and exploration of interesting precursors for the construction of π-conjugated organophosphorus compounds, and the use of organophosphorus reagents for unprecedented transformations in Organic Chemistry.

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Biocatalytic methods of synthesis are becoming increasingly important in industry. Using enzymes as catalysts allows highly selective reactions to be performed under milder physical conditions and in a more environmentally benign fashion than most corresponding chemical catalysts. Enzymes have in general evolved to perform one type of reaction on a limited set of molecules, and hence there is often a need to alter the specificity of an enzyme to suit a desired process. Understanding the details of enzymatic catalysis at a quantum mechanical level enables the intelligent redesign of these macromolecules. For this purpose, density functional theory (DFT) has been shown to epitomise a suitable balance of accuracy and computational cost. Thus, this thesis describes the quantum chemical rationalisation of the reaction mechanism and sources of selectivity of the bacterial alcohol dehydrogenase TbSADH – an enzyme highly suited to modification for industrial processes. ADHs catalyse reversibly the interconversion of alcohols and ketones or aldehydes. Herein, the general ADH reaction mechanism was shown to be viable for this enzyme. In addition, the experimental enantiopreference of the enzyme was reproduced, and thus the reversal of selectivity seen with the slight increase in substrate size was captured. The main determinant of selectivity was found to be a fine balance of repulsive steric interactions and attractive dispersion effects between the substrate and the hydrophobic binding pockets. The ability of the modelling methodology to capture effects such as these represents further evidence of its usefulness as a complement to experimental work in designing the biocatalysts of the future. The development of protocols to allow quantum mechanical investigation of the production of large and industrially interesting axially chiral alcohols is also presented. The work described has showed that quantum chemical models of many hundreds of atoms are now within our grasp, and although they were unable to correctly describe the selectivity for the large 4-(bromomethylene)cyclohexan-1-one in TbSADH, the protocols devised can be very useful for future investigations of enzymatic catalysis.

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L-type voltage gated calcium channels are membrane bound ion channels that regulate the intracellular concentration of calcium ions as a response to changes in the membrane potential. They exist in four isoforms and recent studies have brought extra attention to the Cav1.2 isoform as it has been shown to be critical for the maturation of oligodendrocyte progenitor cells in the brain. These cells are involved in neural myelination and if they do not mature properly, it can lead to abnormal neural myelination. This is a condition that is strongly correlated with neurodegenerative diseases such as Multiple Sclerosis and has been associated with psychiatric diseases such as schizophrenia. The number of tools for studying these proteins are few, and therefore this thesis aimed to expand the toolbox by developing an analogue (FluoBar2) to an existing probe (FluoBar1). The analogous probe could resolve some of the issues currently associated with labeling using FluoBar1 as well as open up the possibility of conducting pulse-chase experiments when used with FluoBar1. The short absorption and emission wavelengths of FluoBar1 causes large amounts of autofluorescence in cellular imaging, making the images hard to interpret. In FluoBar2, the Pacific Blue fluorophore used in FluoBar1 is exchanged for 5-carboxyfluorescein, causing the absorption and emission to be redshifted which theoretically should decrease the cellular autofluoresence. The project begun with the synthesis of FluoBar1 which was isolated in a 0.19% overall yield. During this, the synthetic route towards the linker used in FluoBar1 and FluoBar2 was developed as well, increasing the yield with respect to the most expensive reagent from 41.5% to 61%. An attempt at synthesizing FluoBar2 was made and its presence was supported by 1H NMR as well as UPLC-MS, but it was not fully isolated and characterized.