CYP2C9 is one of our major drug metabolising enzymes and belongs to the cytochrome P450 (CYP) super family. The aim of this thesis was to gain an understanding of the quantitative structure–activity relationships (QSAR) of CYP2C9 substrates and inhibitors. This information will be useful in predicting drug metabolism and the potential for drug–drug interactions. To achieve this, a well characterised data set of structurally diverse, competitive CYP2C9 inhibitors was identified in our laboratory. Several computational methodologies, many based on GRID molecular interaction fields, were applied or developed in order to handle issues such as compound alignment and bioactive conformer selection. First, a traditional 3D QSAR was carried out in GOLPE, generating a predictive model. In this model the selection of a bioactive conformer and alignment was based on docking in a homology model of CYP2C9. Secondly, we introduced the concept of alignment independent descriptors from ALMOND. These descriptors were used to generate quantitatively and qualitatively predictive models. We subsequently derived conformation independent descriptors from molecular interaction fields calculated in FlexGRID. This enabled the derivation of 3D QSAR models without taking into account the selection of an alignment or a bioactive conformer. A subsequent programming effort enabled the conversion of this model back to 3D aligned pharmacophores. Similar alignment independent descriptors were also used in the development of the software MetaSite® that predicts the site of metabolism for CYP2C9 ligands. Finally, as crystal information on this isoform emerged, the performance of molecular dynamics simulations and homology models and the flexibility of the protein were evaluated using statistical analyses. These modelling efforts have resulted in detailed knowledge of the structural characteristics in ligand interactions with the cytochrome P450 2C9 isoform.

The Li-ion battery has, from its commercialisation in the early 1990's, now become the most widely used power source for portable low-power electronics: laptops, cellular phones and MP3-players are a few examples. To further develop existing and find new electrode materials for these batteries, it is vital to understand the lithium insertion/extraction mechanisms taking place during battery operation. In this thesis, single-crystal X-ray diffraction has been used to investigate lithium insertion/extraction mechanisms in the cathode materials V6O13 and LiFePO4. A novel single-crystal electrochemical cell for in situ single-crystal X-ray diffraction studies has also been developed. The phases Li3V6O13 and Li3+xV6O13, 0<x<1, both contain a disordered lithium ion. A low-temperature study of Li3.24V6O13 (at 95 K) shows that this disorder is static rather than dynamic; the lithium ion is equally distributed above and below an inversion centre in the centrosymmetric V6O13 host structure. Short-range-ordering between this disordered lithium ion and the lithium ion inserted into Li3V6O13 gives rise to solid-solution behaviour not observed earlier in the LixV6O13 system. A model is proposed for the lithium insertion mechanism up to the end-member composition Li6V6O13. Lithium has also been electrochemically extracted from LiFePO4 single crystals. On the basis of the shapes of the LiFePO4 and FePO4 reflections, it is concluded that FePO4 is formed at the crystal surface and that the LiFePO4/FePO4 interface propagates into the crystal. This is in agreement with an earlier proposed model for lithium extraction from LiFePO4 particles. Initial experiments with the newly developed single-crystal electrochemical cell for in situ single-crystal X-ray diffraction demonstrate that it is possible to insert lithium into a single crystal of V6O13 and then collect single-crystal X-ray diffraction data. The method needs further development but promises to become a powerful tool for studying lithium insertion/extraction mechanisms.

Amino acid radicals are key redox intermediates in several natural enzymes including Cytochrome c peroxidase, DNA photolyase, ribonucletide reductase, cytochrome c oxidase and photosystem II. Electron transfer from amino acids is often coupled to deprotonation and this thesis concerns the coupling of electron transfer from tyrosine and tryptophan to trisbipyridineruthenium(III) with deprotonation in model complexes. Specifically the mechanisms for these proton coupled electron transfer reactions have been studied and the controlling parameters have been identified, the possible mechanisms being stepwise electron transfer followed by deprotonation and deprotonation followed by electron transfer or concerted electron transfer/deprotonation. Proton coupled electron transfer reactions have been studied using nano-second flash photolysis in water solution and the effect of pH, temperature, reaction driving force, deuteration and nature of the amino acid has been determined. I have shown that the rate constant for the concerted reaction depends intrinsically on the mixing entropy of the released proton and that the pH-dependence can be used as an experimental tool for mechanistic discrimination. Moreover I have shown that the concerted reaction inherently has a high reorganisation energy due to the coupling of the electron motion with deprotonation. Hydrogen bonding to the transferring proton however significantly reduces this reorganisation energy. The concerted reaction also has a relatively high driving force counteracting the high reorganisation energy in the competition between the concerted reaction and the stepwise electron transfer first reaction. The relative importance of the high reorganisation energy and the high driving force for the concerted reaction determines the mechanistic outcome of the reaction, the stepwise reaction being favoured by high over-all driving forces and the concerted reaction by high pH. By comparing my results from model complexes with tyrosineZ oxidation in photosystem II, I give strong evidence for a concerted electron transfer/deprotonation mechanism.

This thesis is based on 9 papers dealing with the synthesis, physicochemical and biochemical properties of two types of chemically modified oligonucleotides which have the potential to down-regulate gene expression: (i) The first set is comprised of antisense oligonucleotides (AONs) conjugated with different chromophores of varying size, charge and π-electron density. Conjugation of the chromophores at the 3'- or 5'-end enhanced the target RNA binding affinity and RNase H recruitment capabilities compared to the native counterpart without changing the global helical conformation of their AON/RNA hybrid duplexes. The 3'-dipyridophenazine (DPPZ) has emerged as the most promising non-toxic chromophore in this series. (ii) The second set encompasses a new class of AONs containing North-East conformationally constrained 1',2'-oxetane-nucleosides. The introduction of oxetane-<b>T</b> and -<b>C</b> units imparts lowering of the Tm by ~ 6º and ~ 3 ºC/modification, respectively, of the AON/RNA hybrids, whereas the incorporation of the corresponding oxetane-<b>A</b> and-<b>G</b> units into AONs did not alter the thermostability in comparison with that of the native hybrid duplex. The oxetane-modified AONs have been found to possess enhanced serum stability compared to that of the native, whereas oxetane-<b>T</b> and -<b>C</b> containing AONs were more endonuclease-resistant than oxetane-<b>A</b> and-<b>G</b> modified AONs. All oxetane-modified mixmer AON/ RNA hybrid duplexes were, however, found to be excellent substrates for RNase H cleavage, which has been analyzed by Michaelis-Menten kinetics. The oxetane-modified mixmer AONs have shown effective down-regulation of the proto-oncogene c-myb mRNA in the K562 human leukemia cells, which was analyzed by QRT-PCR and Western Blot. Based on the amount of AON uptake after delivery, determined by slot blot, it was apparent that the oxetane-modified AONs are 5-6 times more effective antisense agents than the corresponding isosequential phosphorothioate analogues. The electrochemical assay based on sensitive nucleic acid mediated charge transport (CT) has revealed that the presence of oxetane-<b>T</b> unit causes more stacking perturbations in a DNA/DNA duplex than in a DNA/RNA duplex.

The elastic properties of oil/water/surfactant interfaces play an important role in the phase behaviour of microemulsions and for the stability of macroemulsions. The aim of this thesis is to obtain an understanding of the relationship between the structure of the surfactant molecules, the structure of the interface, and macroscopic interfacial properties. To achieve this aim, we performed molecular simulations of oil/water/surfactant systems. We made a quantitative comparison of various model surfactants to determine how structural changes affect interfacial properties and film rupture. The model consists of water, oil, head, and tail beads, and surfactants are constructed by coupling head and tail beads with harmonic springs. We used a hybrid dissipative particle dynamics-Monte Carlo scheme. The former was used to simulate particle trajectories and the Monte Carlo scheme was used to mimic experimental conditions: bulk-interface phase equilibrium, tensionless interfaces in microemulsions, and the surface force apparatus. A detailed comparison of various non-ionic model surfactants showed how structural changes affect interfacial properties: Comparison between linear and branched surfactants showed that the efficiency of adsorption is higher for linear surfactants, although branched surfactants are more efficient at a given surface density. Linear surfactants can be more efficient also at the same surface density if the head group is sufficiently soluble in oil, because low head-oil repulsion makes the branched isomers stagger at the interface. The bending rigidity is higher for linear surfactants. Furthermore, branched surfactants make oil droplets coalesce more easily than linear surfactants do, but linear and branched surfactants have roughly the same effect on water droplet coalescence. Comparison of linear surfactants with varying chain lengths showed that longer surfactants have a lower surface tension and higher bending rigidity. The increase in rigidity with chain length follows a power law, but the exponent is higher for surfactant monolayers at a fixed density than at a fixed tension. Longer tails and/or denser monolayers influence the stability of water droplets in a positive direction, and the stability of oil droplets in a negative direction. Addition of cosurfactant showed that mixed monolayers have a lower bending rigidity than pure monolayers at the same average chain length and tension. Cosurfactants have a negative effect on the stability of water droplets, and a positive effect on the stability of oil droplets. / Paper I reprinted with kind permission of EDP Sciences. Paper III reprinted with kind permission of the American Institute of Physics. Paper IV reprinted with kind permission of the American Physics Society.

Mixing excipients is a common way to produce pharmaceutical materials with suitable properties for drug formulation. An understanding of the basic mechanisms involved in the formation and transformation of the structures of solid state mixtures is crucial if one is to be able to produce materials with the desired properties in a reliable way. In the first part of the thesis, the atomic force microscopy (AFM) technique was used to visualise the re-crystallisation of spray-dried amorphous particles comprised of lactose and PVP. The transformation was quantified on a single particle level and analysed with a common kinetic model, the JMAK-equation. The way in which the PVP was incorporated into the particles and the impact this had on their physical stability on exposure to increasing levels of humidity was investigated. The amount and, to a certain extent, the molecular weight of the PVP affected the moisture induced crystallisation of the particles. The inhibition was further discussed in terms of nucleation and growth. In the second part of the thesis, the formation of phases in solid dispersions of monoolein (MO) in PEGs was studied by the use of SAXS and DSC. Upon solidification of a melt, the components phase separated, resulting in a PEG-rich phase and an MO phase. MO was intercalated into the amorphous domains of the lamellar structure of PEG. A second MO phase appeared in the mixtures where the average molecular weight of PEG was 1500 and 4000 g/mol. It was hypothesised that this second phase was formed in conjunction with the expulsion of MO as the PEG unfolded. This thesis describes the application of two relatively unexplored solid state techniques on two different solid mixtures of pharmaceutical interest and, in so doing, contributes to the knowledge of phase formation and transformations in the solid state.

In this thesis, the structure and stability of globular proteins adsorbed onto nanometer-sized hydrophilic silica particles were investigated using differential scanning calorimetry (DSC), hydrogen/deuterium exchange (HDX), and mass spectrometry (MS). The adsorption process itself was characterized with fluorescence and absorption spectroscopy and surface plasmon resonance (SPR). The combination of these methods offered a unique insight into adsorption-induced changes within proteins related to their adsorption characteristics. DSC contributed with thermodynamic information on the overall structural stability within the protein population. HDX in combination with MS contributed information on the structure and stability of adsorbed proteins with focus on changes within the secondary structure elements. In order to increase the structural resolution in this part of the investigation, proteolysis was performed prior to the MS analyzing step. Knowledge on the protein adsorption process was utilized in a practical approach called ligand fishing. In this approach, SPR was used to monitor the chip-based affinity purification of a protein with MS used for protein identification. Adsorption isotherms revealed that electrostatic interactions play an important role in the adsorption of proteins to hydrophilic surfaces. DSC investigation revealed that the thermal stability of proteins reduces with increasing electrostatic attraction between the protein and the surface and that this effect diminishes at higher surface coverage. The mass-increase due to exchange between protein hydrogen atoms and deuterium atoms in solution was investigated as a function of time. This gave insight into adsorption-induced changes in the structural stability of proteins. By combining DSC and HDX-MS, it was possible to differentiate between adsorption-induced changes in the secondary and tertiary structure. Additionally, if limited proteolysis was performed, the investigations gave insight into the orientation and protein segment specific changes in the stability of proteins adsorbed to silica surfaces. The adsorption of proteins to silica particles also provided the basis for a new experimental design that allows handling of minute amounts of proteins in a ligand fishing application, as used in the field of functional proteomics.

Liquid chromatography – mass spectrometry (LC-MS) methods were developed for the analysis of positron emission tomography (PET) radiotracers in biological matrices. Additionally, radiotracer chemistry was explored as an analytical tool for supporting LC-MS method development and imaging molecular interactions in miniaturised chemical analysis systems. Conventional radiodetection methods can offer high sensitivity in the analysis of radiotracers in biological matrices, although with the short half-life of PET tracers, this mass sensitivity decreases rapidly with time. This limits the time frame for analysis, and may compromise the precision and accuracy of the later measurements. Performing LC-MS analysis of the dominant stable isotope form of the tracer removes such time restrictions. An LC-MS/MS method was developed for determination of the tracer flumazenil in human plasma, with high inter-assay precision (RSD &lt; 7%) and accuracy (95 – 104%). The method was applied in a multiple scan PET study where the plasma concentration spanned from 0.07 to 0.21 nM. The method removed the time restrictions associated with radiodetection methods and thus provided the opportunity of analysing a greater number of samples than would have been possible with radioanalysis. Furthermore, an LC-MS/MS method was developed that provided an efficient metabolic screening tool of potential PET tracers, whereby the substrates could be collected directly from 11C-labelling batches. This permitted repeated incubation experiments without the need of repeated labelling syntheses. A para-methoxy-benzamide analogue of the radiotracer WAY-100635 was thus identified as a potential tracer with improved metabolic stability. Additionally, a capillary LC-MS method was developed with rapid (0.75 min) and efficient (&gt; 99%) on-line high flow-rate extraction for determination of metabolic stability of PET radiotracers. Finally, the concept of radionuclide imaging of miniaturised chemical analysis systems was demonstrated with the direct study of interactions within capillary extraction columns and microchannels moulded in a plastic CD and poly(dimethylsiloxane).

This thesis describes the synthesis and application of new chiral bicyclic ligands and their application in asymmetric catalysis. The studies involved: [i] The development of novel chiral bicyclic amino sulfur ligands and their use in transfer hydrogenation. [ii] The development of the kinetic resolution of racemic epoxide through the use of chiral lithium amides. [iii] The synthesis and application of chiral bicyclic amine in the organocatalysed epoxidation of alkenes. [iv] Development and application of new chiral diamine ligands in the rearrangement of epoxides into allylic alcohols. [i] The preparation of two-series of amino thiol ligands based on the structure of camphor is described, together with their application in the iridium-catalysed asymmetric transfer hydrogenation of acetophenone using isopropanol as the hydrogen source. Excellent activity and good enantioselectivity have been achieved using 2 mol% of chiral ligand in combination with [IrCl(COD)]2. [ii] The chiral diamines (1S,3R,4R)-3-(pyrrolidine-1-ylmethyl)-2-aza-bicyclo[2.2.1]heptane and its (2R,5R)-dimethylpyrrolidine derivative were applied to the kinetic resolution of a variety of racemic 5-7 membered cycloalkene oxides with lithium diisopropylamide (LDA) as the bulk base. Using 5 mol% of the chiral diamines, both unreacted epoxides and allylic alcohols could be produced in enantiomeric excess up to 99%. [iii] The synthesis of chiral bicyclic amines and their use in the organocatalysed epoxidation of alkene has been described. Using a substoichiometric amount of the chiral amines and aldehydes as ligands precursors, with Oxone® as oxidant, a good activity but moderate enantioselectivity was observed for the epoxidation of trans-stilbene. [iv] The preparation of 6-substituted-7-bromo-aza-bicyclo[2.2.1]heptanes via nucleophilic addition of organocopper reagents to 3-bromo-1-azoniatricyclo[2.2.1.0]heptyle bromide has been described. These compounds have been utilised as chiral building blocks in the preparation of novel chiral diamine ligands, which have been successfully applied to the catalysed asymmetric rearrangement of epoxide into the corresponding allylic alcohol.

The aqueous solvation of metal ions is one of the long-standing and complex problems in chemistry, with implications for and applications in a broad range of biochemical and electrochemical systems, where water is the all-pervasive medium. This thesis describes computer simulations of Al3+(aq), Fe2+(aq), Fe3+(aq) and Cu2+(aq). Various aspects of the solvation of these polyvalent metal ions in water are addressed, at different levels of theory, using Car-Parrinello molecular dynamics, classical molecular dynamics and quantum-mechanical cluster calculations. Polyvalent metal ions are particularly interesting because of their large influence on the solvent structure, dynamics and thermodynamics, as well as on the properties of the individual solvent molecules. Polyvalent metal ions in aqueous solution also constitute a challenging subject for computer simulations since a sophisticated interaction model is needed to incorporate the large many-body effects. All the ion-water coordination figures in this thesis are octahedral, except in the Cu2+(aq) solution, where the ion is penta-coordinated with four equatorial neighbours in a plane and one axial neighbour located ~0.45 Å further out from the ion. The equatorial ion-water bonds have covalent character, while the axial water molecule is only electrostatically bound. For all the ions, the OD stretching frequencies of the first-shell water molecules are much more downshifted than in liquid water. In the case of Cu2+(aq), however, only the OD frequencies of the equatorial water molecules are downshifted with respect to bulk water whereas the OD frequencies of the axial water molecule are slightly upshifted. Various limitations of the Car-Parrinello molecular dynamics simulations have been explored and compared, such as finite system-size effects and shortcomings in the electronic structure calculations. The Car-Parrinello simulations are found to give reasonable descriptions of the polyvalent metal ions in aqueous solution.