This thesis presents theoretical studies of several x-ray spectroscopies - x-ray absorption, x-ray photoelectron emission, radiative and non-radiative resonant Raman scattering spectroscopy. The main focus point is investigating the influence of nuclear dynamics on these spectra for a variety of small molecules - naphthalene, biphenyl, ethylene, the water dimer, HCl, CO. The theoretical tools used consist of the basic equations of the relevant x-ray spectroscopy. Wave packet methods are also used. The molecular parameters needed for our simulations are obtained through suitable quantum chemical calculations, based on either wave function or density functional methods. Our simulations are compared to experimental data, where available. Simulations of x-ray absorption and x-ray photoionization spectra for naphthalene and biphenyl show that the spectral shapes are heavily influenced by the joint effect of two factors -- chemical shifts and excitations of vibrational progression. Comparison between the two molecules and also comparison to a reference case -- benzene, provides useful insight into the molecular behavior under core excitation. In a further step, we consider the O1s x-ray photoelectron spectrum of the water dimer. A substantial broadening of the two bands originating from the donor and the acceptor oxygen is found. It is caused by excitations of soft intermolecular vibrational modes, associated with the hydrogen bond. Another strong influence of the nuclear dynamics is clearly seen in the resonant x-ray Raman scattering of HCl. Vibrational collapse is observed experimentally and confirmed theoretically for distinctive situations. This effect allows to eliminate completely the vibrational broadening, and hence, considerably increase the spectral resolution. We considered also the vibrational dynamics in resonant soft x-ray Raman scattering from ethylene. The importance of vibronic coupling and symmetry effects is discussed and emphasized. We obtained excellent agreement with the experimental data. We predict an interference effect in the resonant Auger scattering from fixed-in-space molecules. By exciting a molecule to a dissociative state and measuring the angular distribution of the Auger electrons in coincidence with the molecular ion, one can observe this effect. The interference pattern can be used after Fourier transformation for extracting structural data about the studied system. We have found that two-center interference leads to an enhancement of the recoil effect. Finally, it is shown that core excitation to doubly-excited dissociative Pi state is accompanied by Doppler splitting of the atomic peak in resonant Auger scattering from carbon monoxide. / QC 20100910

In this thesis, the application of electrospray ionisation mass spectrometry (ESI-MS) to the analysis of intact proteins is demonstrated. In papers I and II, the use of ESI-MS for the analysis of noncovalent protein-ligand complexes were discussed. In addition, the interfacing of liquid chromatography (LC) with ESI-MS and the development of an LC-ESI-MS method were demonstrated in paper III for the quality control of recombinant proteins. Furthermore, this method was applied in paper IV for the analysis of covalent glycosyl-enzyme intermediates. The monitoring of noncovalent complexes by ESI-MS is well established. However, the varying characteristic of ESI-MS data, especially in the analysis of noncovalent complexes can make the quantification of such complexes troublesome. In paper I, it was demonstrated how the variation in the position of the ESI-emitter and the initial droplet size of the electrosprayed droplets, together with different partitioning of a protein and its ligand in these droplets, can be the cause of such varying characteristics. Furthermore, it was shown that the partitioning can be of electrostatic and/or hydrophobic/hydrophilic origin. Thus it was demonstrated that if the ligand is more hydrophobic and thereby more surface active relative to the protein, decreasing the droplet size or increasing the distance between the electrospray emitter and the sampling orifice will lead to more efficient sampling of the droplet bulk where the ligand concentration is low. This results in a favoured sampling of free protein relative to the protein ligand complex. The opposite was shown to occur if the ligand is more hydrophilic than the protein. In paper II, Ribonuclease A (RNAse) was used as a model for enzymes acting on polymeric substrates with different chain lengths. Nano-ESI-MS was applied to monitor the noncovalent interactions between RNAse and different target ligands. Among the single building blocks of RNA, including ribose, the bases adenine, guanine, cytosine and uracil, and phosphate, only phosphate was observed to interact at multiple RNAse sites at a higher cone voltage. Furthermore, monobasic singlestranded deoxycytidylic acid oligomers (dCx) of different lengths (X=6, 9 and 12), and RNAse were analysed with nano-ESI-MS. The deoxycytidylic acid with 12 nucleotides was observed with the highest complex to free protein ratio, hence indicating the strongest interaction. Finally, collision induced dissociation of the noncovalent RNAseA-dC6 complex resulted in dissociation of covalently bound cytosine from the nucleotide backbone rather than break up of the noncovalent complex, illustrating the cooperative effect of multiple noncovalent interactions. In paper III an LC-ESI-MS method was presented capable of analysing proteins 10-100 kDa in size, from salt-containing liquid samples. The proteins included human protein fragments for the largescale production of antibodies and human protein targets for structural determination, expressed in E. coli. Also, glycosylated proteins expressed in Pichia pastoris were analysed. The method provides fast chromatography, is robust and makes use of cheap desalting/trap columns. In addition it was used with optimised reduction and alkylation protocols in order to minimize protein aggregation of denatured and incorrectly folded proteins containing cysteins, which otherwise form adducts by disulfide bond formation. Furthermore, the method was used in paper IV for the quantification of covalent proteinligand intermediates formed enzymatically between PttXET16-34, a xyloglucan endo-transglycosylase (XET) from hybrid aspen, and the synthetic substrates GalGXXXGGG and GalXXXGXXXG designed in order to function as donor substrates only. Thus covalent GalG-enzyme and GalGXXXG-enzyme complexes were detected. Moreover, establishing of a pseudo equilibrium for the formation of the covalent GalGXXXG-enzyme complex enabled quantification of the saccharide and enzyme constituents of this equilibrium and determination of the free energy of formation (∆G0). The high mass resolution of the TOF-MS allowed unambiguous assessment of the covalent nature of the glycosyl-enzyme complexes. Morover, the formation of noncovalent complexes between excess substrate and protein, which can deteriorate MS-signal and increase spectrum complexity, was efficiently avoided by the chromatographic step, which separated the saccharide content from the protein content. / QC 20100913

This thesis reports on synthesis, microstructure and properties of binary and ternary carbide thin films deposited by dc magnetron sputtering. These materials are interesting since they exhibit a wide range of useful properties, such as high hardness, resistance to wear and oxidation, and high electrical conductivity. Here, an early transition metal (M) and carbon (C) have been used as the basis, often with the addition of a second M-element or an A-group element (A). In these systems nanocomposites, metastable solid solutions, multilayers, or Mn+1AXn-phases have been deposited. The Mn+1AXn-phases are a group of nanolaminated compounds with a unique mixture of metallic and ceramic properties. In general X is carbon or nitrogen, although here only carbon has been used. Epitaxial MAX-phase thin films of Ti2AlC, Ti3AlC2 and V2GeC have been deposited for the first time. They have been studied with emphasis on phase stability, phase composition and nucleation characteristics to gain deeper insights into their growth. The microstructure of the films was characterized by electron microscopy and X-ray diffraction. In addition, bond strength characteristics have been studied by soft X-ray spectroscopy and complementary calculations within DFT. Their mechanical and electrical properties have been studied, and the results are discussed on the basis of their electronic structure. Furthermore, by interleaving the Ti3SiC2 MAX-phase with TiC0.67 a multilayer structure has been formed, for which a new intrusion-type deformation behaviour has been described. A new concept in the design of nanocomposite films has been developed, whereby a solid solution of a weak carbide-forming element in the carbide structure creates a driving force for surface segregation of C. This concept has been verified both theoretically and experimentally for the Ti-Al-C and Ti-Fe-C systems. It has been shown by pin-on-disc measurements that this surface segregation leads to graphitization and consequently a very low friction coefficient for these films. Finally, it has been demonstrated that low-friction films with tunable magnetic properties can be achieved in the Ti-Fe-C system.

It is well known that folded proteins in water are destabilized by the addition of urea. When a protein loses its ability to perform its biological activity due to a change in its structure, it is said to denaturate. The mechanism by which urea denatures proteins has been thoroughly studied in the past but no proposed mechanism has yet been widely accepted. The topic of this thesis is the study of the mechanism of urea-induced protein denaturation, by means of Molecular Dynamics (MD) computer simulations and Nuclear Magnetic Resonance (NMR) spectroscopy. Paper I takes a thermodynamic approach to the analysis of protein – urea solution MD simulations. It is shown that the protein – solvent interaction energies decrease significantly upon the addition of urea. This is the result of a decrease in the Lennard-Jones energies, which is the MD simulation equivalent to van der Waals interactions. This effect will favor the unfolded protein state due to its higher number of protein - solvent contacts. In Paper II, we show that a combination of NMR spin relaxation experiments and MD simulations can successfully be used to study urea in the protein solvation shell. The urea molecule was found to be dynamic, which indicates that no specific binding sites exist. In contrast to the thermodynamic approach in Paper I, in Paper III we utilize MD simulations to analyze the affect of urea on the kinetics of local processes in proteins. Urea is found to passively unfold proteins by decreasing the refolding rate of local parts of the protein that have unfolded by thermal fluctuations. Based upon the results of Paper I – III and previous studies in the field, I propose a mechanism in which urea denatures proteins mainly by an enthalpic driving force due to attractive van der Waals interactions. Urea interacts favorably with all the different parts of the protein. The greater solvent accessibility of the unfolded protein is ultimately the factor that causes unfolded protein structures to be favored in concentrated urea solutions.

With the retreating sources of carbon based fuels, thermoelectric materials can play an important role in the future of environmentally friendly power generators. Sb based framework have in some cases shown some promising properties as thermoelectric materials. The physical properties may be modified with doping or incorporation of new elements. Zn4Sb3 and Cd4Sb3 are structurally related with a Sb-based network and Zn/Cd occupying the rest of the positions. Both structures undergo order-disorder α–β transition of the Zn/Cd positions, at 254 K and ~355 K respectively. The previously ordered interstitial atoms become distributed in the structure and the two high temperature phases are isostructural (R-3c). Cd4Sb3 was synthesized from melt-quench, flux synthesis with Sn, Bi and In. The syntheses made with In resulted in interstitial-free β-Cd4Sb3 with the composition Cd11.7In1.5Sb10. This compound exhibits no phase transitions until decomposition. ZnSnSb2 and InSb both exhibit the cubic sphalerite structure. ZnSnSb2 is metallic and InSb narrow band-gap semiconductor. Attempts were made to fine-tune the electrical properties by probing the mutual solid solubility range. The formula [ZnSnSb2]x[2(InSb)]1-xSn4 and 0<X<1 with 0.1 increments for the whole composition range was used. Resistivity changes from semiconducting to metallic conduction between x=0.9 and x=0.8. In the attempt to dope Zn4Sb3 by In a novel metastable compound with the composition Zn9Sb6In2 was found. Another novel phase was discovered with the composition Zn5Sb4In2-δ (δ=0.15).  The two phases have the same Sb-framework with a CuAl2 structure. Zn and In arrangements fill the square antiprisms formed by the stacking of 32434 nets in anti configuration. The filling of the antiprisms in the two phases are different, in Zn9Sb6In2 the antiprisms have two filling arrangements, an In or Zn3 triangles. In Zn5Sb4In2-δ the antiprisms are filled with an In and a Zn that occupies a split position to form a hetero-atomic dimers.

I den här avhandlingen har vi studerat hur man kan göra nya tensider. En tensid är en speciell molekyl som har förmågan att lösa sig i både vatten och olja. Man kan göra följande experiment hemma: Fyll en glasburk till hälften med vatten och tillsätt en droppe matolja. Oljan bildar en droppe ovanpå vattnet, därför att vatten och olja inte är blandbara. Vatten är polärt och olja är opolärt. Om man rör om med en sked kommer oljedroppen förvisso att dela upp sig i mindre droppar, men så snart man slutar att röra kommer dessa att lägga sig på vattenytan igen. Sätt nu en droppe diskmedel till blandningen och rör om. Nu sprider sig oljedropparna mycket bättre i vattnet, och de lägger sig heller inte på vattenytan lika fort när man slutar att röra. Det här beror på att diskmedel innehåller en tensid, som har en polär och en opolär del. Den polära delen passar ihop med det polära vattnet, medan den opolära delen passar ihop med den opolära oljan. På så vis kan tensiden hjälpa till att lösa upp opolära ämnen i polära vätskor. Den aktiva delen av ett läkemedel består ofta av opolära ämnen, vilka inte löser sig i polära vätskor såsom vatten. Eftersom kroppen består till stor del av vatten måste man ändå försöka få läkemedlet vattenlösligt, för att möjliggöra transport via blodet till problemområdet. Det kan man uppnå genom att tillsätta tensider. Om läkemedel-tensidblandningen ska ges till djur eller människor får inte tensiden orsaka någon skada i kroppen. Vi har försökt framställa tensider som ska kunna användas för att just lösa läkemedel i vatten. För att kunna framställa nya tensider måste man ha kunskap i organisk syntes. Det betyder att man måste veta hur man från små intermediat (”byggstenar”) successivt kan bygga upp nya molekyler som har de önskvärda egenskaperna. Genom olika typer av organisk syntes har vi byggt upp tre nya tensidtyper, vars egenskaper vi studerat med olika mätningar. Ingen av dessa tensider lämpade sig som tillsats till läkemedel, men vårt arbete har givit mycket ny kunskap om hur framtida tensidmolkyler kan tillverkas och vilka egenskaper de får. / This thesis deals with the synthesis and characterization of new polyhydroxy surfactants. The first part describes the synthesis of three new surfactant classes, and the second part concerns the surface chemical characterization of the synthesized surfactants. A stereodivergent route for preparation of hydrophilic head groups was developed, that featured consecutive stereoselective dihydroxylations of a diene. This method provided in total four different polyhydroxylated head groups. These surfactant head groups were natural and unnatural sugar analogues, and were used for the coupling with two different hydrophobic tail groups. Another approach took advantage of a metathesis reaction and provided a polyhydroxylated compound that was coupled to 12-hydroxy stearic acid The third class of surfactants contained an amide linkage between the hydrophilic and the hydrophobic parts. The hydrophilic part consisted of two glucose units, and 12-hydroxy stearic acid was used as the hydrophobic part. The hydroxy moiety in the tail group was further functionalized as aliphatic esters, which provided in total four different surfactants. A selection of the surfactants was used to investigate the chiral discrimination in Langmuir monolayers at an air-water interface. The isotherms showed a remarkable difference in compressibility between diastereomeric surfactants and also a pronounced chiral discrimination between racemic and enantiomerically pure surfactants, favoring heterochiral discrimination. The monolayers were also investigated with Brewster angle microscopy (BAM) and grazing incidence X-ray diffraction (GIXD). It was not possible to observe any chirality dependent features from the BAM images, but the GIXD measurement supported the conclusion that heterochiral discrimination governed the intermolecular forces within the racemic monolayer. The third class of surfactants, containing an amide linkage between the glucose units and 12-hydroxy stearic acid was evaluated with respect to the CMC and the haemolytic activity. These surfactants were all haemolytic close to their respective CMC. / QC 20101015

Enzymes are extraordinary molecules that can accelerate chemical reactions by several orders of magnitude. With recent advancements in structural biology together with classical enzymology the mechanism of many enzymes has become understood at the molecular level. During the last ten years significant efforts have been invested to understand the structure and dynamics of the actual catalyst (i. e. the enzyme). There has been a tremendous development in NMR spectroscopy (both hardware and pulse programs) that have enabled detailed studies of protein dynamics. In many cases there exists a strong coupling between enzyme dynamics and function. Here I have studied the conformational dynamics and thermodynamics of three model systems: adenylate kinase (Adk), Peroxiredoxin Q (PrxQ) and the structural protein S16. By developing a novel chemical shift-based method we show that Adk binds its two substrates AMP and ATP with an extraordinarily dynamic mechanism. For both substrate-saturated states the nucleotide-binding subdomains exchange between open and closed states, with the populations of these states being approximately equal. This finding contrasts with the traditional view of enzyme-substrate complexes as static low entropy states. We are also able to show that the individual subdomains in Adk fold and unfold in a non-cooperative manner. This finding is relevant from a functional perspective, since it allows a change in hydrogen bonding pattern upon substrate-binding without provoking global unfolding of the entire enzyme (as would be expected from a two-state folding mechanism). We also studied the structure and dynamics of the plant enzyme PrxQ in both reduced and oxidized states. Experimentally validated structural models were generated for both oxidation states. The reduced state displays unprecedented μs-ms conformational dynamics and we propose that this dynamics reflects local and functional unfolding of an α-helix in the active site. Finally, we solved the structure of S16 from Aquifex aeolicus and propose a model suggesting a link between thermostability and structure for a mesophilic and hyperthermophilic protein pair. A connection between the increased thermostability in the thermophilic S16 and residual structure in its unfolded state was discovered, persistent at high denaturant concentrations, thereby affecting the difference in heat capacity difference between the folded and unfolded state. In summary, we have contributed to the understanding of protein dynamics and to the coupling between dynamics and catalytic activity in enzymes.

Enzymes as tools in organic synthesis have provided enormous advantages. This thesis deals with the applications of enzymes in the kinetic resolutions of racemic compounds. The stereochemistry of chiral compounds and the kinetics of α/β hydrolase lipases are presented. From a practical point of view, the handling of a large number of parameters that influences the kinetic resolutions, especially enantioselectivity (E-value) are systematically described. A variety of approaches employed for raising the yields to over 50% are additionally discussed. Methods for the preparation of synthetically useful chiral building blocks were developed in this thesis. Thus, resolution of secondary alcohols bearing two vicinal stereocentres are studied. These building blocks can serve as starting materials for the synthesis of various enantiomerically pure compounds for agrochemistry, pharmaceuticals, chemical industry, and particularly for the total synthesis of pheromones. Racemic 3-substitued 2-hydroxybutane derivatives were produced in fairly high diastereomeric purities by a variety of chemical approaches, such as epimerization, metal-catalysed asymmetric addition etc. Kinetic resolution of these racemates was achieved by enzyme-catalysed reactions. Two lipases, Candida antarctica lipase B and Pseudomonas cepacia lipase were found to be useful in acylations as well as hydrolyses. In the biotransformations studied, the presence and nature of the second vicinal stereocentre in the chiral secondary alcohols investigated seemed to be important, e.g. in terms of the efficiencies of sequential kinetic resolutions, and altering the selectivities as well. / QC 20101020

This thesis deals with instrumental and methodological developments for speciation analysis of gaseous mercury (Hg(g)), based on isotope dilution analysis (IDA). The studied species include Hg0, (CH3)2Hg, CH3HgX and HgX2 (where X symbolises a negatively charged counter ion in the form of a halide or hydroxyl ion). Gas chromatography hyphenated with inductively coupled plasma mass spectrometry (GC-ICPMS) was used for separation and detection of Hg(g) species. Permeation tubes were used for the generation of gaseous isotopically enriched Hg standards (tracers). These tracers were continuously added to the sample gas stream during sampling of Hg(g). A mobile prototype apparatus incorporating both the permeation source and a sampling unit for collection of Hg(g) was developed and used for this purpose. Hg(g) species were pre-concentrated on Tenax TA and / or Carbotrap solid adsorbents. Au-Pt was used for pre-concentration of total Hg(g), either as the primary medium, or as backup. Collected species were eluted from these media and introduced to the instrument by thermal desorption. Various degrees of species transformations, as well as losses of analyte during pre-concentration and elution, were found to occur for both Tenax TA and Carbotrap. The performance characteristics of these media were shown to be species specific, as well as matrix dependent. The development of an on-line derivatisation procedure allowed for minimised species transformations, as well as reduced adsorption and memory effects of ionic Hg(g) species within the analytical system. In conclusion, IDA provides an important tool for identification, minimisation and correction of the above mentioned analytical problems. Furthermore, it offers significant advantages with respect to quality assurance, compared to conventional techniques, both when it comes to rational development of new methodology, as well as for continuous validation of existing procedures. The developed methodology for speciation analysis of Hg(g) has been tested in various applications, including the determination of Hg(g) species concentrations in ambient air (both in and outdoor) and in the head space of sediment microcosms. Hg(g) species were formed in the sediments as a result of naturally occurring redox and methylation processes, after addition of an isotope enriched aqueous Hg(II) precursor. The methodology has also been used for assessing the risk of occupational exposure to Hg(g) species during remediation of a Hg contaminated soil and for studying Hg0(g) transport and Au-Pt pre-concentration characteristics in natural gases. Hg0 was used as the model species in the latter experiments, since it is believed to be the dominating form of Hg(g) in natural gas. The results indicate that the occurrence of H2S can cause temperature dependent adsorption and memory effects of Hg0(g) in the presence of stainless steel, thereby providing a plausible explanation to the variability of results for sour gases occasionally observed in the field. Hg0(g) has demonstrated overall high recovery during collection on Au-Pt tubes for all gases tested in this thesis. Recent (unpublished) results however indicate that there are potential species specific and matrix dependent effects associated with the Au-Pt based pre-concentration of Hg(g) in natural gases.

Synchrotron-based sulfur spectroscopy reveals a common concern for marine archaeological wood from seawater: accumulation of reduced sulfur compounds in two pathways. The distribution of sulfur species in the oak wood cell structure was mapped by scanning x-ray spectro-microscopy (SXM). Organically bound sulfur was found within lignin-rich parts, identified mainly as thiols and disulfides by sulfur K-edge x-ray absorption near edge structure (XANES) spectroscopy. Particles of iron sulfides, which may form in the presence of corroding iron, appeared in wood cavities. Cores scanned by x-ray fluorescence (XRF) show that high sulfur accumulation is restricted to the surface layers for the Swedish shipwreck Vasa, while the distribution is rather uniform throughout the hull timbers of the Mary Rose, U.K. Laboratory experiments, exposing fresh pine to simulated seabed conditions, show that the organically bound sulfur develop in reactions between lignin, exposed by cellulose-degrading erosion bacteria, and hydrogen sulfide produced in situ by scavenging sulfate reducing bacteria. With bacteria inoculated from shipwreck samples also iron sulfides formed. The iron sulfides oxidise in high humidity, and are the probable main cause of the numerous outbreaks on the Vasa’s hull of acidic sulfate salts, which were identified by x-ray powder diffraction (XRD). The iron ions catalyse several wood-degrading oxidative processes. Multi-elemental analyses were performed by scanning electron microscopy (SEM) and x-ray photoelectron spectroscopy (ESCA). The present amounts of total S remaining in the Vasa and the Mary Rose are estimated to at least 2 tonnes. After the Vasa´s spray treatment with polyethylene glycol solutions ceased in 1979, the continuing oxidation processes are estimated to have produced 2 tonnes of sulfuric acid in the wood. Laboratory experiments to gently neutralize acidic Vasa wood by ammonia gas have been conducted with promising results.