This thesis presents and develops the path integral simulation techniques in application to small quantum systems at finite temperatures. The first goal is to obtain exact thermodynamic expressions for systems of noninteracting The rest and the major part of the thesis is dedicated to the development and testing of Bead-Fourier path integral molecular dynamics. Although, path integral molecular dynamics as well as path integral Monte Carlo are well First, molecular dynamics under Bead-Fourier scheme was developed and tested on the examples of quantum harmonic oscillator and Hydrogen atom. The main attention was paid to ergodicity problems. Then we addressed the question, Later, the formalism for identical particles was developed. Finally, the question of molecular dynamics efficacy was raised. It was shown, that formalisms for identical and distinguishable particles, both, can be reformulated into a more efficient ones, providing all dynamical variables

This thesis describes the use of nuclear magnetic resonance (NMR) spectrometry as an analytical tool. The theory of NMR spectroscopy in general and quantitative NMR spectrometry (qNMR) in particular is described and the instrumental properties and parameter setups for qNMR measurements are discussed. Examples of qNMR are presented by impurity determination of pharmaceutical compounds and analysis of urine samples from rats fed with either water or a drug (metabolic profiling). The instrumental parameter setup of qNMR and traditional data pre-treatments are examined. Spectral smoothing by convolution with a triangular function, which is an unusual application in this context, was shown to be successful regarding the sensitivity and robustness of the method in paper II. In addition, papers III and IV comprise the field of peak alignment, especially designed for 1H-NMR spectra of urine samples. This is an important preprocessing tool when multivariate analysis is to be applied. A novel peak alignment method was developed and compared to the traditional bucketing approach and a conceptually different alignment method. Univariate, multivariate, linear and nonlinear data analyses were applied to qNMR data. In papers I–II, calibration models were created to examine the potential of qNMR for these applications. The data analysis in papers III–VI was mainly explorative. The potential of data fusion and data correlation was examined in order to increase the possibilities of analysing the highly complex samples from metabolic profiling (papers V–VI). Data from LC/MS analysis of the same samples were used with the 1H-NMR data in different ways. Correlation analyses between the 1H-NMR data and the drug metabolites identified from the LC/MS data were also performed. In this process, data fusion proved to be a valuable tool.

In this thesis, the chemistry of compounds containing P-Se bonds has been studied. As a new addition to this class of compounds, H-phosphonoselenoate monoesters, have been introduced and two synthetic pathways for their preparation have been developed. The reactivity of H-phosphonoselenoate monoesters towards a variety of condensing agents has been studied. From these, efficient conditions for the synthesis of H-phosphonoselenoate diesters have been developed. The produced diesters have subsequently been used in oxidative transformations, which gave access to the corresponding P(V) compounds, e.g. dinucleoside phosphoroselenoates or dinucleoside phosphoroselenothioates. Furthermore, a new selenizing agent, triphenyl phosphoroselenoate, has been developed for selenization of P(III) compounds. This reagent has high solubility in organic solvents and was found to convert phosphite triesters and H-phosphonate diesters efficiently into the corresponding phosphoroselenoate derivatives. The selenization of P(III) compounds with triphenyl phosphoroselenoate proceeds through a selenium transfer reaction. A computational study was performed to gain insight into a mechanism for this reaction. The results indicate that the transfer of selenium or sulfur from P(V) to P(III) compounds proceeds most likely via an X-philic attack of the P(III) nucleophile on the chalcogen of the P(V) species. For the transfer of oxygen, the reaction may also proceed via an edge attack on the P=O bond.

Bilirubin is a degradation product of haem, which is constantly formed in all mammals. Increased levels of bilirubin in humans lead to jaundice, a condition that is very common during the first days after birth. This neonatal jaundice can routinely be treated by phototherapy without any serious side effects. During this treatment, bilirubin undergoes a photoreaction to isomers that can be excreted. The most efficient photoreaction is the isomerisation around a double bond (Z-E-isomerisation), which results in more soluble photoproducts. The work presented in this thesis shows results of a femtosecond optical spectroscopy study, combined with quantum-mechanical investigations, of the mechanism of isomerisation of bilirubin. The spectroscopic research was conducted with bilirubin in organic solvents, and in buffer complexed by human serum albumin. This albumin complex is present in the blood, and has thus medical importance. Quantum-chemical calculations (CASSCF) on a bilirubin model were used to explain experimental results. The fluorescence decay observed with femtosecond spectroscopy shows an ultrafast component (~120 fs), which is explained by exciton localisation, followed by processes with a lifetime of about 1-3 ps. These are interpreted as the formation of a twisted intermediate, which decays with a lifetime of 10-15 ps back to the ground state, as observed by absorption spectroscopy. CASSCF calculations, in combination with the experimental results, suggest the ca. 1-3 ps components to be relaxation to the twisted S1 minimum, followed by the crossing of a barrier, from where further relaxation takes place through a conical intersection back to the ground state. Time-dependent DFT calculations were utilised to analyse the absorption spectrum of bilirubin. Good agreement with the measured spectrum was achieved, and low-lying states were observed, that need further investigation. The theoretically obtained CD spectrum provides direct evidence that bilirubin preferentially binds to human serum albumin in the enantiomeric P-form at neutral pH. / Bilirubin är en nedbrytningsprodukt av hem som ständigt bildas hos alla däggdjur. En förhöjd bilirubinkoncentration i den mänskliga kroppen kan leda till gulsot, något som är mycket vanligt under de första dagarna efter födelsen (neonatal gulsot). Fototerapi används rutinmässigt som säker behandlingsmetod, under vilken bilirubin genomgår en fotoreaktion till en isomer som kan utsöndras. Den mest effektiva fotoreaktionen är en Z-Eisomerisation, vilken leder till lösligare fotoprodukter. Arbetet som presenteras i denna avhandling visar resultaten av en kombinerad femtosekund optisk-spektroskopisk och kvantmekanisk undersökning av mekanismen bakom bilirubins isomerisation. Den spektroskopiska studien genomfördes med bilirubin, löst i organiska lösningsmedel och i buffert i komplex med humant serumalbumin. Detta albuminkomplex finns i blodet, och är därför av medicinskt intresse. Kvantmekanistiska CASSCFberäkningar på en bilirubinmodell användes för att förklara de experimentella resultaten. Det uppmätta fluorescence sönderfallet visar ultrasnabba komponenter (~120 fs). Dessa tolkas som excitonlokalisering, som följs av bildandet av ett vridet intermediat med en hastighetskonstant på ca. 1 ps-1(beroende på lösningsmedlet). Absorptionsmätningar visar att detta intermediat sönderfaller tillbaka till grundtillståndet med en livstid på 10-15 ps. CASSCF beräkningar, i kombination med de experimentella resultaten, tyder på att sönderfallet med livslängden på ca. 1 ps är en relaxation till det vridna S1-tillståndet. Reaktionsvägen därifrån antas passera en barriär till en konisk genomskärning, som möjliggör snabb relaxation till grundtillståndet. Tidsberoende DFT-beräkningar användes för att analysera bilirubins absorptionsspektrum, vilket gav bra överensstämmelse med uppmätta data. Dessutom hittades ett tillstånd med låg excitationsenergi, som kräver ytterligare studier. Med hjälp av det beräknade CD-spectret kunde det visas att bilirubin binder till albumin i P-formen vid neutralt pH.

Individual proteins, and small collections of proteins, have been extensively studied for at least two hundred years. Today, more than 350 genomes have been completely sequenced and the proteomes of these genomes have been at least partially mapped. The inventory of protein coding genes is the first step toward understanding the cellular machinery. Recent studies have generated a comprehensive data set for the physical interactions between the proteins of Saccharomyces cerevisiae, in addition to some less extensive proteome interaction maps of higher eukaryotes. Hence, it is now becoming feasible to investigate important questions regarding the evolution of protein-protein networks. For instance, what is the evolutionary relationship between proteins that interact, directly or indirectly? Do interacting proteins co-evolve? Are they often derived from each other? In order to perform such proteome-wide investigations, a top-down view is necessary. This is provided by network (or graph) theory. The proteins of the cell may be viewed as a community of individual molecules which together form a society of proteins (nodes), a network, where the proteins have various kinds of relationships (edges) to each other. There are several different types of protein networks, for instance the two networks studied here, namely metabolic networks and protein-protein interaction networks. The metabolic network is a representation of metabolism, which is defined as the sum of the reactions that take place inside the cell. These reactions often occur through the catalytic activity of enzymes, representing the nodes, connected to each other through substrate/product edges. The indirect interactions of metabolic enzymes are clearly different in nature from the direct physical interactions, which are fundamental to most biological processes, which constitute the edges in protein-protein interaction networks. This thesis describes three investigations into the evolution of metabolic and protein-protein interaction networks. We present a comparative study of the importance of retrograde evolution, the scenario that pathways assemble backward compared to the direction of the pathway, and patchwork evolution, where enzymes evolve from a broad to narrow substrate specificity. Shifting focus toward network topology, a suggested mechanism for the evolution of biological networks, preferential attachment, is investigated in the context of metabolism. Early in the investigation of biological networks it seemed clear that the networks often display a particular, 'scale-free', topology. This topology is characterized by many nodes with few interaction partners and a few nodes (hubs) with a large number of interaction partners. While the second paper describes the evidence for preferential attachment in metabolic networks, the final paper describes the characteristics of the hubs in the physical interaction network of S. cerevisiae.

This thesis contains seven papers dealing with iridium and ruthenium based catalytic asymmetric reductions, either of ketones into chiral alcohols, or olefins into chiral alkanes. The first part of the thesis describes how we have designed and evaluated new bicyclic ligands containing either N,S or N,N chelating atoms. The ligands have been evaluated in the asymmetric Ir-catalyzed transfer hydrogenation of acetophenone. The complexes evaluated induced good enentioselectivity of the product. Moreover we have also utilized a commercially available chiral diamine (QCD-amine) as a ligand in the Ru-catalyzed hydrogenation of prochiral ketones, with excellent enantioselectivity for some of the substrates used. As part of this work we investigated, both theoretically and experimentally, the mechanism of this hydrogenation. Based on these results we have proposed a new reaction mechanism for this type of hydrogenations which involves active participation of the solvent in the catalytic cycle. The last part of the thesis describes the design, synthesis and evaluation of N,P and N2C-carbene,N ligands for the Ir-catalyzed hydrogenation of carbon-carbon double bonds. The selectivities obtained in these investigations are among the best reported so far for a broad variation of substrates. A selectivity model for this hydrogenation has been derived and used in the rationalization of the results. As a part of this work we have synthesized and evaluated a new class of substrates, vinyl silanes, and showed that the scope of the hydrogenation reaction can be expanded to this new substrate class.

This thesis is based upon synthesis and structure determination of new transition metal oxo-halide compounds, which includes p-element cations that have a stereochemically active lone pair. A synthesis concept has been developed, which uses several different structural features to increase the possibility to yield a low-dimensional arrangement of transition metal cations. A total of 17 new compounds has been synthesised and their structures have been determined via single-crystal X-ray diffraction. The halides and the stereochemically active lone-pairs will typically act as terminating species segregating into regions of non-bonding volumes, which may take the form of 2D layers, 1D channels or Euclidean spheres. The transition metals that have been used for this work are copper, cobalt and iron. The Hard-Soft-Acid-Base principle has been utilized to match strong Lewis acids to strong Lewis bases and weak acids to weak bases. All compounds show tendencies towards low-dimensionality; they all have sheets of transition metal cations arranged into layers, where the layers most often are connected via weak dispersion forces.

An intrinsic mathematical model for simulation of fixed bed chromatography was demonstrated and compared to more simplified models. The former model was shown to describe variations in the physical, kinetic, and operating parameters better than the latter ones. This resulted in a more reliable prediction of the chromatography process as well as a better understanding of the underlying mechanisms responsible for the separation. A procedure based on frontal liquid chromatography and a detailed mathematical model was developed to determine effective diffusion coefficients of proteins in chromatographic gels. The procedure was applied to lysozyme, bovine serum albumin, and immunoglobulin γ in Sepharose™ CL-4B. The effective diffusion coefficients were comparable to those determined by other methods. Molecularly imprinted polymers (MIPs) are traditionally prepared as irregular particles by grinding monoliths. In this thesis, a suspension polymerization providing spherical MIP beads is presented. Droplets of pre-polymerization solution were formed in mineral oil with no need of stabilizers by vigorous stirring. The droplets were transformed into solid spherical beads by free-radical polymerization. The method is fast and the performance of the beads comparable to that of irregular particles. Optimizing a MIP formulation requires a large number of experiments since the possible combinations of the components are huge. To facilitate the optimization, chemometrics was applied. The amounts of monomer, cross-linker, and porogen were chosen as the factors in the model. Multivariate data analysis indicated the influence of the factors on the binding and an optimized MIP composition was identified. The combined use of the suspension polymerization method to produce spherical beads with the application of chemometrics was shown in this thesis to drastically reduce the number of experiments and the time needed to design and optimize a new MIP.

A novel strategy for synthesising segmented poly(urethane urea) (PUU) without using a chain extender but nevertheless with the opportunity to vary the hard segment content has been developed. The strategy is based on amine formation from isocyanate upon reaction with water. By adding a dissolved soft segment to an excess of diisocyanate followed by the addition of water in the gas phase, amines are formed in situ. Urea linkages are then formed when these amines react with the excess of isocyanate groups. The gas phase addition facilitates addition in a slow and continuous manner. The hard segment content can easily altered by varying the diisocyanate/soft segment ratio. Even though the strategy is shown to be applicable to different diisocyanates, the focus has been on the potentially biodegradable methyl-2,6-diisocyanatehexanoate (LDI) and 1.4-butanediisocyanate (BDI) and various well known biodegradable polyesters and polycarbonates. All the synthesised materials exhibited pronounced phase separation and hydrogen bonding within the hard domains. However, a major increase in hydrogen bonding strength was seen when a symmetric diisocyanate was used instead of an asymmetric. Based on FTIR measurements, PUUs with BDI and a polydisperse hard segment can exhibit the same degree of phase separation and hydrogen bonding as the monodisperse product. The elastic properties of this new group of PUUs were exceptional with an elongation at break from 1600% to almost 5000% and the elastic modulus could be varied from a few MPa up to a couple of hundreds. Hydrolytic degradation was greater in the polyester-based than in the polycarbonate-based PUUs due to the more reactive ester bonds. Low mass loss but a considerable loss in molecular weight was seen in the polyester PUUs. The tensile strength decreased dramatically due to the loss of strain hardening. An MTT seeding assay using human fibroblasts and an in vivo biocompatibility study were performed and no signs of cytotoxicity were seen and the inflammatory response was comparable to other inert polymers. A biodegradable PUU with properties that can be tailored through an easy synthesis is here presented.

Nano-powders of BaTiO3, SrTiO3, Ba0.6Sr0.4TiO3, a mixture of the composition (BaTiO3)0.6(SrTiO3)0.4 with particle sizes in the range of 60 to 80 nm, and Bi4Ti3O12 with an average particle size of 100 nm were consolidated by spark plasma sintering (SPS). The kinetics of reaction, densification and grain growth were studied. An experimental procedure is outlined that allows the determination of a “kinetic window” within which dense nano-sized compacts can be prepared. It is shown that the sintering behaviour of the five powders varies somewhat, but is generally speaking fairly similar. However, the types of grain growth behaviour of these powders are quite different, exemplified by the observation that the kinetic window for the (BaTiO3)0.6(SrTiO3)0.4 mixture is 125 oC, ~75 oC for Bi4Ti3O12, ~25oC for BaTiO3 and SrTiO3, while it is hard to observe an apparent kinetic window for obtaining nano-sized compacts of Ba0.6Sr0.4TiO3. During the densification of the (BaTiO3)0.6(SrTiO3)0.4 mixture the reaction 0.6BaTiO3+0.4SrTiO3 → Ba0.6Sr0.4TiO3 takes place, and this reaction is suggested to have a self-pinning effect on the grain growth, which in turn explains why this powder has a large kinetic window. Notably, SPS offers a unique opportunity to more preciously investigate and monitor the sintering kinetics of nano-powders, and it allows preparation of ceramics with tailored microstructures. The dielectric properties of selected samples of (Ba, Sr)TiO3 ceramics have been studied. The results are correlated with the microstructural features of these samples, e.g. to the grain sizes present in the compacts. The ceramic with nano-sized microstructure exhibits a diffuse transition in permittivity and reduced dielectric losses in the vicinity of the Curie temperature, whereas the more coarse-grained compacts exhibit normal dielectric properties in the ferroelectric region. The morphology evolution, with increasing sintering temperature, of bismuth layer-structured ferroelectric ceramics such as Bi4Ti3O12 (BIT) and CaBi2Nb2O9 (CBNO) was investigated. The subsequent isothermal sintering experiments revealed that the nano-sized particles of the BIT precursor powder grew into elongated plate-like grains within a few minutes, via a dynamic ripening mechanism. A new processing strategy for obtaining highly textured ceramics is described. It is based on a directional dynamic ripening mechanism induced by superplastic deformation. The new strategy makes it possible to produce a textured microstructure within minutes, and it allows production of textured ferroelectric ceramics with tailored morphology and improved physical properties. The ferroelectric, dielectric, and piezoelectric properties of the textured bismuth layer-structured ferroelectric ceramics have been studied, and it was revealed that all textured samples exhibited anisotropic properties and improved performance. The highly textured Bi4Ti3O12 ceramic exhibited ferroelectric properties equal to or better than those of corresponding single crystals, and much better than those previously reported for grain-orientated Bi4Ti3O12 ceramics. Textured CaBi2Nb2O9 ceramics exhibited a very high Curie temperature, d33-values nearly three times larger than those of conventionally sintered materials, and a high thermal depoling temperature indicating that it is a very promising material for high-temperature piezoelectric applications.