The magnitude of an electric field possible to apply in a capillary separation system is limited, because a high electric field causes a too high current through the capillary. Application of the electric field in-line will give an increased conductivity in the column, further increasing the risk of too high currents. The conductivity changes were found to result from an overall increase in ionic strength within the electric field. The increase in ionic strength is caused by the increase in mobile phase ions with electrophoretic velocity against the flow, together with OH- or H3O+ ions (depending on polarity) formed at the inlet electrode. Further it was found that the use of a pressurized reservoir or splitting of the flow at the inlet electrode could significantly limit the conductivity changes and thereby the maximum applicable electric field strengths could be increased.

This thesis is based on six research publications concerned with (i) study of the molecular structures and dynamics of modified nucleosides; (ii) investigation of the effect of incorporation of modified nucleosides on the structure of DNA; (iii) examination of the effect of the sugar modifications on the pseudo-aromatic properties (pKa) of the nucleobases; (iv) analysis of the effect of the CH-π interactions on the relative stability of the DNA-RNA hybrid duplexes. The structural stability of the nucleic acids as well as their behavior in molecular recognition is dominated by hydrogen bonding and stacking interactions beside other non-covalent interactions. Naturally occurring nucleosides are found to have some specific functions. Modifications of nucleic acids, followed by studies of the resulting structural, chemical and functional changes, contribute to an understanding of their role in various biochemical processes, such as catalysis or gene silencing. In papers I-III, analysis of the structures of modified thymidine nucleosides with 1′,2′-(oxetane or azetidine) and 2′,4′-(LNA, 2′-amino LNA, ENA, and Aza-ENA) conformationally constrained sugar moieties, and dynamics of the modified nucleosides by NMR, ab initio, and molecular dynamics simulations are discussed. Based on whether the modification leads to 1′,2′- or 2′,4′- constrained sugar moieties, it is found that they fall into two distinct categories characterized by their respective internal dynamics of the glycosidic and backbone torsions as well as by their characteristic NE-type (P = 37° ± 27°, Φm = 25° ± 18°) for 1′,2′-constrained nucleosides, and N-type (P = 19° ± 8°, Φm = 48° ± 4°) for 2′,4′-constrained systems, respectively. Moreover, each group has different conformational hyperspace accessible. The effect of the incorporation of 1′,2′-oxetane locked thymidine nucleoside on the structure and dynamics of the Dickerson-Drew dodecamer, d(CGCGAATTCGCG)2, determined by NMR, is discussed in the paper IV. It shows that the incorporation of oxetane locked T into the dodecamer has made local structural deformations and perturbation in base pairing, where the modification is included. The modulations of physico-chemical properties of the nucleobases in nucleotides by the C2′-modification of the sugar (paper V), 5′-phosphate group, and the effect of constrained pentofuranosyl moiety (sugar, paper III) have been studied. CH-π interactions between the methyl group of thymidine and the neighboring aromatic nucleobase are shown to increase the relative stability of the DNA-RNA hybrid duplexes over the isosequential RNA-DNA duplexes or vice versa (paper VI).

Nanoparticles of iron, cobalt and tungsten oxide were synthesised by photolytic laser assisted chemical vapour deposition (LCVD). An excimer laser (operating at 193 nm) was used as an excitation source. The LCVD process, was monitored in situ by optical emission spectroscopy (OES). The synthesised particles were further analysed using transmission electron spectroscopy (TEM), X-ray diffraction (XRD), high resolution scanning electron microscopy (HRSEM), X-ray fluorescence spectroscopy (XRF), X-ray photoelectron spectroscopy (XPS) and Raman spectroscopy. Iron and cobalt single crystalline nanoparticles were synthesized using ferrocene and cobaltocene precursors. The diameter of the particles could be tailored by the experimental parameters (e.g., partial pressure and laser power) and were in the range 1 - 50 nm in diameter. In both cases, the particles were covered by a carbon shell, typically 7 nm thick. A thin graphitic layer was observed at the interface metal-carbon. Amorphous carbon was deposited on top of the graphitic carbon. Particle temperature, reaching the boiling point of the respective metal, was observed by OES of the thermal emission during the laser-induced particle formation process (and subsequent heating). Both bcc and fcc Fe phases were formed, both hcp and fcc for the Co phases. Size dependent magnetic properties were observed using superconducting quantum interference device (SQUID) measurements, where super-paramagnetic magnetic domains dominated for d < 10 nm. The iron particles were further processed, whereby the amorphous shell was removed by refluxing in nitric acid. In a subsequent step, the graphitic surface was functionalized by attaching an octyl ester, rendering the particles hydrophobic. Tungsten oxides were synthesized from combinations of WF6/H2/O2 as precursors. No particles could be deposited if H2 was removed from the gas-mixture. The as-deposited oxide nanoparticle film was amorphous. A monoclinic WO3 particle film could be achieved by annealing the amorphous oxide. Above 400°C, the oxide particles increased in size from ca. 20 nm to 60 nm through coalescence. The gas-sensing properties of the tungsten oxide were tested by conductance measurements using H2S as analyte. The sensitivity of the amorphous oxide nanoparticle film was found to be superior to that of a crystalline oxide nanoparticle film.

Computer simulations can be useful aids for both developing new analytical methods and enhancing the performance of existing techniques. This thesis is based on studies in which computer simulations were key elements in the development of several new tools for use in gas chromatography and dielectrophoresis. In gas chromatography, gaseous analytes are separated by exploiting differences in their partitioning between different phases, and after their partitioning parameters have been determined the separations can be computationally predicted, and optimized, for a wide range of operating conditions. Similarly, in dielectrophoresis, particles with differing polarizability or size can be separated, and since particle trajectories within a separation device can be predicted using computations, the suitability of new designs, applications of forces and combinations of operational parameters can be assessed without necessarily making or empirically testing all of the variants. Using two existing numerical methods combined with semi-empirical determinations of retention behavior, temperature-programmed gas chromatograms were predicted with less than one percent deviations from experimental data, and a new method for improving the capacity of a gas-trapping device was predicted and experimentally verified. In addition, two new concepts with potential capacity to enhance dielectrophoretic separations were developed and tested in simulations. The first provides a promising way to improve the trapping of bacteria in media with elevated conductivity by using super-positioned electric fields, and the second a way to increase selectivity in the separation of bio-particles by using multiple dielectrophoretic cycles. The studies also introduced a more accurate method for determining the conductivity of suspensions of bacteria, and a new computational method for determining the dielectrophoretic behavior of particles in concentrated suspensions. The scientific studies are summarized and discussed in the main text of this thesis, and presented in detail in seven appended papers.

This thesis describes the synthesis of structures related to the capsular polysaccharide of Neisseria meningitidis serogroup A and the synthesis of analogues of mycothiol, a compound produced by Mycobacterium tuberculosis. The first part of the thesis describes the synthesis of structural elements present in the native capsular polysaccharide of Neisseria meningitidis serogroup A. In this part, an improved synthesis of 2-azido-2-deoxy-D-mannopyranose is included. The second part of the thesis describes the formation of stable C-phosphonate analogues related to the capsular polysaccharide. The last part outlines the formation of analogues of mycothiol, where the syntheses of a bicyclic analogue and a thioglycosidic analogue are described.

In order to understand biological processes, to treat and diagnose diseases, find appropriate vaccines and to prevent the outbreak of epidemics, it is essential to obtain more knowledge about carbohydrate structures. This thesis deals with structure and conformation of carbohydrates, analysed by NMR spectroscopy and MD simulations.In the first two papers, the structures of O-antigen polysaccharides (PS) from two different E. coli bacteria were determined using NMR spectroscopy. The O-antigenic PS from E. coli O152 (paper I) consists of branched pentasaccharide repeating units, built up of three different carbohydrate residues and a phosphodiester, whilst the repeating unit of the O-antigen from E. coli O176 (paper II) is built up of a linear tetrasaccharide consisting of two different monosaccharides. In papers III and IV, the conformational analysis of different disaccharides is described. Conformational analysis was performed using NMR spectroscopy and MD simulations (paper IV). In paper III four different glucobiosides were studied using coupling constants and Karplus-type relationships. By use of specific 13C isotopically labelled derivatives, additional coupling constants were obtained and the number of possible torsion angles was reduced by half. In paper IV, we examine the conformations of two disaccharides that are part of an epitope of malignant cells. From NOE and T-ROE experiments, short proton-proton distances around the glycosidic linkage were estimated. Furthermore, interpretation of the extracted coupling constants using Kaplus relationships gave the values of the torsion angles. As in paper III, isotopically labelled compounds were synthesised in order to enhance the sensitivity of the analysis. Finally, MD simulations were performed and the results were compared with results from NMR data.

Complex transition metals oxyhalides containing a lone pair element, such as tellurium (IV), form an attractive research field because there is a high probability of finding new low-dimensionally arranged compounds and, particularly, a low-dimensionally arranged transition metals substructures, leading to interesting physical properties. Tellurium (IV) can drive the formation of many unusual structures because of its stereochemically active lone pair electrons, E. It commonly takes a coordination of three or four oxygen atoms to form either a TeO3E square pyramid or a TeO3+1E trigonal bipyramid. These lone pairs are very important players involved in lowering the dimensionality of crystal structures. Previous studies in transition metal tellurium (IV) oxohalide quarternary systems revealed a family of compounds, many of which exhibit interesting properties e.g. magnetic frustration. The unique point of this thesis is to employ alkaline earth elements (AE) to augment this ability of lone pair elements to lower the dimensionality of the transition metal arrangements. By this double usage of “chemical scissors” (a lone pair element used in conjunction with alkaline earth elements) we obtained new types of low-dimensionally arranged compounds. This thesis is focused on the syntheses and characterization of a series of compounds in the pentanary (five components) system AE-TeIV-TM-O-X (AE=alkaline earth metal, TM=transition metal and X=halogen), in which nine new compounds were found. The crystal structures of each of these compounds were determined by the single crystal X-ray diffraction data.

Diamond and cubic boron nitride surfaces have extreme properties that can be exploited in novel tribological, electrochemical and electronic applications. Normally insulating diamond surfaces can exhibit high surface conductivities due to hydrogen termination and the nature of the surrounding atmosphere. Successful growth of cubic boron nitride thin films is hindered when harsh synthesis methods are used. Three significant surface-related properties are addressed in this thesis using computational methods: (1) the structure, energy stability and reactivity of clean and differently terminated diamond surfaces, (2) the high surface conductivity of diamond, and (3) the adsorption-induced stability, reactivity and reconstruction of the cubic boron nitride (100) surface. Density Functional Theory (DFT) has been used at the GGA level under periodic boundary conditions to simulate the diamond and cubic boron nitride surfaces. The diamond surface structures are shown to be insensitive to hydrogen desorption. Oxygen atoms bind in different positions and with different bond strengths. Hydroxyl groups experience both attractive hydrogen bonding and steric repulsions within the adsorbed species. The reconstruction of diamond (111)-1x1 is strongly dependent on the species adsorbed onto the surface. Electron transfer was observed from a diamond surface into a water-based adlayer, yielding a p-type doped surface, depending on the nature of the surface and the adlayer. The cubic boron nitride (100)-1x1 surface was shown to reconstruct into a 2x1 configuration on both the boron- and nitrogen-rich side through the formation of B-B bonds, as well as N–N dimer-induced surface relaxation. Hydrogen stabilized the (100)-1x1 surface, but the partial removal of hydrogen yielded non-reactive dimer formation on the surface.

Thin films of cobalt oxide, iron oxide and niobium oxide, and nanostructured thin films of iron oxide, titanium oxide and multilayered iron oxide/titanium oxide have been deposited by Atomic Layer Deposition (ALD). The metal oxides were grown using the precursor combinations CoI2/O2, Fe(Cp)2/O2, NbI5/O2 and TiI4/H2O. The samples were analysed primarily with respect to phase content, morphology and growth characteristics. Thin films deposited on Si (100) were found to be amorphous or polycrystalline, depending on deposition temperature and the oxide deposited; cobalt oxide was also deposited on MgO (100), where it was found to grow epitaxially with orientation (001)[100]Co3O4||(001)[100]MgO. As expected, the polycrystalline films were rougher than the amorphous or the epitaxial films. The deposition processes showed properties characteristic of self-limiting ALD growth; all processes were found to have a deposition temperature independent growth region. The deposited films contained zero or only small amounts of precursor residues. The nanostructured films were grown using anodic aluminium oxide (AAO) or carbon nanosheets as templates. Nanotubes could be manufactured by depositing a thin film which covers the pore walls of the AAO template uniformly; free-standing nanotubes retaining the structure of the template could be fabricated by removing the template. Multilayered nanotubes could be obtained by depositing multiple layers of titanium dioxide and iron oxide in the pores of the AAO template. Carbon nanosheets were used to make titanium dioxide nanosheets with a conducting graphite backbone. The nucleation of the deposited titanium dioxide could be controlled by acid treatment of the carbon nanosheets.

This thesis presents the application of some of the NMR methods in studying host-guest complexes, mainly in solution. The general focus of the work is on investigating the reorientational dynamics of some small molecules that are bound inside cavities of larger moieties. In the current work, these moieties belong to two groups: cryptophanes and cyclodextrins. Depending on the structure of the cavities, properties of the guest molecules and the formed complexes vary. Chloroform and dichloromethane are in slow exchange between the cage-like cavity of the cryptophanes and the solvent, on the chemical shift time scale, whereas adamantanecarboxylic acid, quinuclidine and 1,7-heptanediol in complex with cyclodextrins are examples of fast exchange. Kinetics and thermodynamics of complexation are studied by measuring exchange rates and translational self-diffusion coefficients by means of 1-dimenssional exchange spectroscopy and pulsed-field gradient (PFG) NMR methods, respectively. The association constants, calculated using the above information give estimates of the thermodynamic stability of the complexes. Carbon-13 spin relaxation data were obtained using conventional relaxation experiments, such as inversion recovery and dynamic NOE, and in some cases HSQC-type (Hetereonuclear Single Quantum Correlation Spectroscopy) experiments. Motional parameters for the free and bound guest, and the host molecules were extracted using different motional models, such as Lipari-Szabo, axially symmetric rigid body, and Clore models. Comparing the overall correlation times and the order parameters of the free and bound guest with the overall correlation time of the host molecule one can estimate the degree of the motional restriction, brought by the complexation, and the coupling between the motion of the bound guest and the reorientation of the host molecule. In one case, the guest motions were also investigated inside the cavities of a solid host material.