In gas chromatography, analytes are separated by differences in their partition between a mobile phase and a stationary phase. Temperature-program, column dimensions, stationary and mobile phases, and flow rate are all parameters that can affect the quality of the separation in gas chromatography. To achieve a good separation (in a short amount of time) it is necessary to optimize these parameters. This can often be quite a tedious task. Using computer simulations, it is possible to both gain a better understanding of how the different parameters govern retention and separation of a given set of analytes, and to optimize the parameters within minutes. In the research presented here, this was achieved by taking a thermodynamic approach that used the two parameters ΔH (enthalpy change) and ΔS (entropy change) to predict retention times for gas chromatography. By determining these compound partition parameters, it was possible to predict retention times for analytes in temperature-programmed runs. This was achieved through the measurement of the retention times of n-alkanes, PAHs, alcohols, amines and compounds in the Grob calibration mixture in isothermal runs. The isothermally obtained partition coefficients, together with the column dimensions and specifications, were then used for computer simulation using in-house software. The two-parameter model was found to be both robust and precise and could be a useful tool for the prediction of retention times. It was shown that it is possible to calculate retention times with good precision and accuracy using this model. The relative differences between the predicted and experimental retention times for different compound groups were generally less than 1%. The scientific studies (Papers I-IV) are summarized and discussed in the main text of this thesis. / At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 4: Submitted.

The development of ligands derived from natural amino acids for asymmetric transfer hydrogenation (ATH) of prochiral ketones is described herein. In the first part, reductions performed in alcoholic media are examined, where it is found that amino acid-derived hydroxamic acids and thioamides, respectively, are simple and versatile ligands that in combination with [RhCp*Cl2]2 efficiently catalyze this particular transformation. Selectivities up to 97% ee of the corresponding secondary alcohols are obtained, and it is furthermore observed that the two different ligand classes, albeit based on the same amino acid scaffold, give rise to products of opposite configuration. The highly interesting enantioswitchable nature of the two abovementioned catalysts is studied in detail by mechanistic investigations. A structure/activity correlation analysis is performed, which reveals that the diverse behavior of the catalysts arise from different interactions between the ligands and the metal. Kinetic studies furthermore stress the catalyst divergence, since a difference in the rate determining step is established from initial rate measurements. In addition, rate constants are determined for each step of the overall reduction process. In the last part, catalyst development for ATH executed in water is discussed. The applicability of hydroxamic acid ligands is further extended, and catalysts based on these compounds are found to be efficient and compatible with aqueous conditions. The structurally even simpler amino acid amide is also evaluated as a ligand, and selectivities up to 90% ee are obtained in the reduction of a number of aryl alkyl ketones. The very challenging reduction of dialkyl ketones is moreover examined in the Rh-catalyzed aqueous ATH, where a modified surfactant-resembling sulfonylated diamine is used as ligand, and the reaction is carried out in the presence of SDS-micelles. A positive effect is to some extent found on the catalyst performance upon addition of phase-transfer components, especially regarding the catalytic activity in the reduction of more hydrophobic substrates. / At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 4: In press.

The desire to use the tools and concepts of chemometrics when studying problems in the life sciences, especially biology and medicine, has prompted chemometricians to shift their focus away from their field‘s traditional emphasis on model predictivity and towards the more contemporary objective of optimizing information exchange via model interpretation. The complex data structures that are captured by modern advanced analytical instruments open up new possibilities for extracting information from complex data sets. This in turn imposes higher demands on the quality of data and the modeling techniques used. The introduction of the concept of orthogonal variation in the late 1990‘s led to a shift of focus within chemometrics; the information gained from analysis of orthogonal structures complements that obtained from the predictive structures that were the discipline‘s previous focus. OPLS, which was introduced in the beginning of 2000‘s, refined this view by formalizing the model structure and the separation of orthogonal variations. Orthogonal variation stems from experimental/analytical issues such as time trends, process drift, storage, sample handling, and instrumental differences, or from inherent properties of the sample such as age, gender, genetics, and environmental influence. The usefulness and versatility of OPLS has been demonstrated in over 500 citations, mainly in the fields of metabolomics and transcriptomics but also in NIR, UV and FTIR spectroscopy. In all cases, the predictive precision of OPLS is identical to that of PLS, but OPLS is superior when it comes to the interpretation of both predictive and orthogonal variation. Thus, OPLS models the same data structures but provides increased scope for interpretation, making it more suitable for contemporary applications in the life sciences. This thesis discusses four different research projects, including analyses of NIR, FTIR and NMR spectroscopic data. The discussion includes comparisons of OPLS and PLS models of complex datasets in which experimental variation conceals and confounds relevant information. The PLS and OPLS methods are discussed in detail. In addition, the thesis describes new OPLS-based methods developed to accommodate hyperspectral images for supervised modeling. Proper handling of orthogonal structures revealed the weaknesses in the analytical chains examined. In all of the studies described, the orthogonal structures were used to validate the quality of the generated models as well as gaining new knowledge. These aspects are crucial in order to enhance the information exchange from both past and future studies.

The human brain (lat. cerebrum) is the most complex and heterogeneous organ in the human body. It is involved in a great number of body functions like movement, touch sensing, vision, hearing, smelling, hormone regulation and many more. In no other organ, the molecular communication mechanisms between different cells are so poorly understood. Due to the extensive diversity of processes that are controlled by the brain, diseases and injuries of the nervous system affect the human body significantly. Because of the immense complexity of the brain, the molecular mechanisms underlying the pathology of the diseases remain largely unknown. Hence, there is an urgent need for the development of new analytical strategies in order to investigate these conditions on a molecular level. Here, a central focus lies in the study of protein and peptide expression profiles, which can provide an insight in ongoing molecular mechanisms underlying the pathophysiology of the diseases. A powerful approach for studying proteins and peptide dynamics is mass spectrometry based proteomics, which is defined as the comprehensive study of all proteins expressed in a biological matrix at a certain point of time. The central objective of this thesis was to develop and employ different mass spectrometric techniques to study protein and peptide dynamics in the central nervous system in different neurological diseases. The individual studies comprise different aspects of proteome research. The first two studies included clinical proteomic applications for investigating protein dynamics in traumatic brain injury and amyotrophic lateral sclerosis. A further study was focused on method development for MS analysis of intact neural cells. The final three projects described in this thesis comprised MS based protein and peptide imaging in brain and spinal cord tissue samples. Here, the aim was to elucidate topological changes in protein expression in ALS as well as neuropeptide alterations in distinct brain structures in L-DOPA induced dyskinesia (LID) in Parkinson’s disease. / Felaktigt tryckt som Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 713

Interactions between carbohydrates and proteins are increasingly being recognized as crucial in many biological processes, such as cellular adhesion and communication. In order to investigate the interactions of carbohydrates and proteins, the development of efficient analytic technologies, as well as novel strategies for the synthesis of carbohydrates, have to be explored. To date, several methods have been exploited to analyze interactions of carbohydrates and proteins, for example, biosensors, nuclear magnetic resonance (NMR); enzyme-linked immunosorbent assays (ELISA), X-ray crystallography and array technologies. This thesis describes the development of novel strategies for the synthesis of carbohydrates, as well as new efficient strategies to Quartz Crystal Microbalance- (QCM-) biosensors and carbohydrate microarrays technologies. These methodologies have been used to probe carbohydrate-lectin-interactions for a range of plant and animal lectins. / QC 20100915

Liquid chromatography is an important separation technique for a vast number of analytes. This thesis mainly focuses on the development of stationary phases for liquid chromatography based on zwitterionic sulfobetaine polymers. In the thesis, various ways to prepare zwitterionic polymers in an aqueous environment using reversible addition fragmentation chain transfer (RAFT) polymerization are described. Both telomers, i.e. short soluble polymer chains containing a functional terminal group, as well as graft polymers on various supports have been synthesized. The RAFT polymerization technique provides an increased degree of control of the final polymers, which may aid in the preparation of more specifically tailored separation materials. Sulfobetaine polymers carry both a positive and a negative charge within a single entity, which results in interesting solution properties as well as highly biocompatible features. These unique features make them especially suited for separation of highly polar and/or charged compounds. An example of the successful separation of short peptides using a stationary phase synthesized with the RAFT technique is given. The unusual properties of sulfobetaine-type polymers are believed to be associated with the structure of water close to the polymer. A study of water structure in some silica based stationary phase grafted with zwitterionic sulfobetaine polymers was conducted. The impact of water structure on retention characteristics was investigated.

The recent determination of several crystal structures of voltage-gated ion channels has catalyzed computational efforts of studying these remarkable molecular machines that are able to conduct ions across biological membranes at extremely high rates without compromising the ion selectivity. Starting from the open crystal structures, we have studied the gating mechanism of these channels by molecular modeling techniques. Firstly, by applying a membrane potential, initial stages of the closing of the channel were captured, manifested in a secondary-structure change in the voltage-sensor. In a follow-up study, we found that the energetic cost of translocating this 310-helix conformation was significantly lower than in the original conformation. Thirdly, collaborators of ours identified new molecular constraints for different states along the gating pathway. We used those to build new protein models that were evaluated by simulations. All these results point to a gating mechanism where the S4 helix undergoes a secondary structure transformation during gating. These simulations also provide information about how the protein interacts with the surrounding membrane. In particular, we found that lipid molecules close to the protein diffuse together with it, forming a large dynamic lipid-protein cluster. This has important consequences for the understanding of protein-membrane interactions and for the theories of lateral diffusion of membrane proteins. Further, simulations of the simple ion channel antiamoebin were performed where different molecular models of the channel were evaluated by calculating ion conduction rates, which were compared to experimentally measured values. One of the models had a conductance consistent with the experimental data and was proposed to represent the biological active state of the channel. Finally, the underlying methods for simulating molecular systems were probed by implementing the CHARMM force field into the GROMACS simulation package. The implementation was verified and specific GROMACS-features were combined with CHARMM and evaluated on long timescales. The CHARMM interaction potential was found to sample relevant protein conformations indifferently of the model of solvent used. / At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 3: Manuscript.

In this thesis, we focus on theoretical study of adsorbates on metal and oxide surfaces that are important for surface chemistry and catalysis. Based on first principles calculations, the adsorption ofCO, NO, NO2, C4H6S2, C22H27SH and other molecules or radicals on nobel metal surfaces (gold and silver) are investigated. Also, NO oxidation on oxygen pre-covered Au(111)surface and CO oxidation on water-oxygen covered Au(111)surface aretheoretically studied. A new mechanism of water-enhanced COoxidation is proposed. As for oxide surfaces, we first investigatethe geometric, electronic and magnetic structures of FeO ultrathin film on Pt(111) surface. The experimentally observed scanning tunneling microscopy images are well reproduced for the first timewith our model. The adsorption and dissociation of water on rutileTiO2(110) surface are investigated by quantum molecular dynamics.By theoretical X-ray photoemission spectroscopy (XPS) calculations,the surface species are properly assigned. The same strategy has applied to the study of the phase transition of water covered reconstructed anatase TiO2(001) surface, from which two different phases are theoretically identified. The structure of graphene oxideis also studied by comparing experimental and theoretical XPS spectra. Based on the novel structures identified, a new cutmechanism of graphene oxide is proposed. / QC 20100819

The present thesis is devoted to theoretical studies of pulse propagation of light through linear and nonlinear media, and of light-induced nuclear dynamics. The first part of the thesis addresses propagation of light pulses in linear periodical media - photonic crystals. The main accent was put on studies of the angular properties of two qualitatively different types of photonic crystals: holographic photonic crystals, and impurity band based photonic crystals. The anisotropy of band structure, group velocity and pulse delay with respect to the light polarization are analyzed. In the second part of the thesis a strict theory of nonlinear propagation of a few strong interacting light beams is presented. The key idea of this approach is a self-consistent solution of the nonlinear wave equation and the density matrix equations of the material. This technique is applied to studies of dynamics of cavityless lasing generated by ultra-fast multi-photon excitation. It is shown that interaction of co- and counter-propagating pulses of amplified spontaneous emission (ASE) affects the dynamics and efficiency of nonlinear conversion. Our dynamical theory allows to explain the asymmetric spectral properties of the forward and backward ASE pulses, which were observed in recent experiment with different dye molecules. It is shown that the ASE spectral profile changes drastically when the pump intensity approaches the threshold level. The effect of the temporal self-pulsation of ASE is studied in detail. The third part of the thesis is devoted to light-induced nuclear dynamics. Time- and frequency-resolved X-ray spectroscopy of molecules driven by strong and coherent infrared (IR) pulses shows that the phase of the IR field strongly influences the trajectory of the nuclear wave packet, and hence, the X-ray spectrum. Such a dependence arises due to the interference of one (X-ray) and two-photon (X-ray + IR) excitation channels. The phase of the light influences the dynamics also when the Rabi frequency approaches the vibrational frequency, breaking down the rotating-wave approximation. The probe X-ray spectra are also sensitive to the delay time, the duration, and the shape of the pulses. The evolution of the nuclear wave packets in the dissociative core-excited state affects the dynamics of resonant Auger scattering from fixed-in-space molecules. One of the important dynamical effects is the atomic-like resonance which experiences electronic Doppler shift. We predict that the scattering of the Auger electrons by nearby atoms leads to new Doppler shifted resonances. These extra resonances show sharp maxima in the bond directions, which makes them very promising as probes for local molecular structure using energy and angular resolved electron-ion coincidence techniques. Our theory provides prediction of several new effects, but also results that are in good agreement with the available experimental data. / QC 20100906

This thesis deals mainly with two oxidation reactions: water oxidation and aerobic oxidation, both of which have been applied in a biomimetic fashion. In the former reaction molecular oxygen is generated whereas in the latter it was used as terminal oxidant in oxidation reactions. The first part of this thesis describes the synthesis of different ruthenium and manganese complexes that could potentially act as catalysts for water oxidation. This part includes a discussion of the stability and reactivity of a new manganese(III) amide-type complex, that has been used as a catalyst for both epoxidation of stilbene and alcohol oxidation. The second part of this thesis discusses the synthesis of two new hybrid catalysts consisting of hydroquinone linked cobalt(II) salophen and cobalt(II) salmdpt, which have been used as oxygen-activating catalysts in aerobic oxidation reactions. The former catalyst was applied to the Pd-catalyzed reactions such as 1,4-diacetoxylation of cyclohexadiene whereas the latter was applied to the Ru-catalyzed oxidation of secondary alcohols to ketones. Moreover, these two hybrid catalysts could be used in the Pd-catalyzed carbocyclization of enallenes. In all cases molecular oxygen was used as the stoichiometric oxidant.