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This thesis describes the study of the three-dimensional structure and dynamics of the hepatitis B virus (HBV) encapsidation signal, epsilon, by means of nuclear magnetic resonance (NMR) and mutational data. HBV replicates by reverse transcription of an RNA pregenome into the viral DNA genome, which becomes enclosed in viral particles (encapsidation). Epsilon is a stem-loop structure within the RNA pregenome and both the primary sequence and secondary structure of epsilon are strongly conserved, in agreement with its essential function of propagating HBV. Epsilon is therefore a potential target for drug design. Studying the structure of epsilon requires development of new methods in the field of structural biology, as it is such a large RNA. Knowing the structure of epsilon will help to better understand the encapsidation mechanism and priming step of reverse transcription. This will help us in the search for antiviral drugs that block epsilon and prevent the viral reverse transcriptase from binding. NMR spectroscopy is a method that provides detailed structural and dynamical data in solution under natural conditions. However, the size of the molecules that can be studied with NMR is limited. NMR spectra become more and more difficult to interpret as the size of the molecule increases. To circumvent this problem, large RNA molecules can be divided into smaller parts and only the parts essential for NMR studies are selected. The information obtained from these smaller fragments can then be used to determine the structure of the larger molecule. Furthermore, a new method of enzymatically synthesizing nucleoside triphosphates with isotopes suitable for NMR has made it possible to specifically label the RNA molecules. Using this method it is possible to derive highly detailed molecular structures of RNA up to a size of 150 nucleotides. The method of selective isotope labelling was applied to different parts of HBV epsilon. Three RNA fragments of 27 (apical loop), 36 (internal bulge) and 61 (whole epsilon) nucleotides (nt) were synthesized in the unlabelled form. The 27-nt and 36-nt RNAs were also synthesized with (13C, 15N, 1', 3', 4', 5', 5"-2H5)-labelled uridines. The 61-nt sequence was (13C, 15N)-guanidine labelled. This labelling allowed unambiguous assignment of otherwise inaccessible parameters. The unlabelled and labelled RNA sequences provided the necessary data for structure derivation of the whole epsilon. The apical loop of epsilon forms a pseudo-triloop motif. There is only one conformation of the loop that fulfils all the restraints, including experimental chemical shifts. However, the loop adopts several structures that fulfil the experimental distance, torsion angle and residual dipolar coupling restraints. This may reflect true flexibility. Indeed, relaxation studies on the unlabelled and labelled 27-nt sequences show that the residues that show multiple conformations are flexible. This can be an important feature for the recognition and subsequent binding of epsilon to the viral polymerase. The information gained on the HBV encapsidation signal is useful in our understanding of the initiation of replication of the virus. This can in turn contribute to the search for drugs against HBV.

The results of three very different studies are presented. X-ray diffraction has been utilized for single-crystal structure determinations, fiber diffraction analyses, and in conjunction with molecular modeling of Cellulose IIII. Although each technique is different in its sampling, data acquisition, data treatment, and identification, the common denominator has been the use of x-rays. The single-crystal structure determination of ethylene glycol bis(tropane-3-carboxylate) is presented as an example of the use of modern single-crystal x-ray instrumentation including the use of coupled charged devices (CCDs) as detectors for accurate data collection and rapid elucidation of crystal structures. The structure determination of Cellulose IIII by x-ray diffraction and computer modeling is presented to show how the use of x-rays in weakly diffracting materials can generate a reliable structure and be a key component in model building. Finally, a study is presented in which x-ray fiber diffraction data is utilized to investigate possible correlations between the crystallite orientation, crystallinity, crystallize size and the strength properties of cotton fibers collected from various countries.

The three-dimensional structure of a protein molecule is the key to understanding its biological and physiological properties. A major problem in bioinformatics is to efficiently determine the three-dimensional structures of query proteins. Protein NMR structure de- termination is one of the main experimental methods and is comprised of: (i) protein sample production and isotope labelling, (ii) collecting NMR spectra, and (iii) analysis of the spectra to produce the protein structure. In protein NMR, the three-dimensional struc- ture is determined by exploiting a set of distance restraints between spatially proximate atoms. Currently, no practical automated protein NMR method exists that is without human intervention. We first propose a complete automated protein NMR pipeline, which can efficiently be used to determine the structures of moderate sized proteins. Second, we propose a novel and efficient semidefinite programming-based (SDP) protein structure determination method. The proposed automated protein NMR pipeline consists of three modules: (i) an automated peak picking method, called PICKY, (ii) a backbone chemical shift assign- ment method, called IPASS, and (iii) a protein structure determination method, called FALCON-NMR. When tested on four real protein data sets, this pipeline can produce structures with reasonable accuracies, starting from NMR spectra. This general method can be applied to other macromolecule structure determination methods. For example, a promising application is RNA NMR-assisted secondary structure determination. In the second part of this thesis, due to the shortcomings of FALCON-NMR, we propose a novel SDP-based protein structure determination method from NMR data, called SPROS. Most of the existing prominent protein NMR structure determination methods are based on molecular dynamics coupled with a simulated annealing schedule. In these methods, an objective function representing the error between observed and given distance restraints is minimized; these objective functions are highly non-convex and difficult to optimize. Euclidean distance geometry methods based on SDP provide a natural formulation for realizing a three-dimensional structure from a set of given distance constraints. However, the complexity of the SDP solvers increases cubically with the input matrix size, i.e., the number of atoms in the protein, and the number of constraints. In fact, the complexity of SDP solvers is a major obstacle in their applicability to the protein NMR problem. To overcome these limitations, the SPROS method models the protein molecule as a set of intersecting two- and three-dimensional cliques. We adapt and extend a technique called semidefinite facial reduction for the SDP matrix size reduction, which makes the SDP problem size approximately one quarter of the original problem. The reduced problem is solved nearly one hundred times faster and is more robust against numerical problems. Reasonably accurate results were obtained when SPROS was applied to a set of 20 real protein data sets.

Electron crystallography has evolved as a powerful method for structural characterization of a wide range of materials. It has two significant advantages over other methods for structure determination, e.g. X-ray diffraction. Electrons interact much more strongly with matter compared to X-rays and they can be focused by electromagnetic lenses to form images with atomic resolution. These advantages make electron crystallography a unique tool for characterization of crystalline materials suffering from small crystal size and complex or disordered structures.      Zeolites are a class of microporous materials with significance in several applications. They often possess complex and disordered structures, which demand large efforts in the structure determination.      Over the last years, two new electron crystallographic methods have been developed; the rotation electron diffraction (RED) and the structure projection reconstruction from a through-focus series of high resolution transmission electron microscopy (HRTEM) images. In this thesis, they will be applied for structure determination of four new zeolite structures, including EMM-25 and EMM-23 with two ordered structures, and ITQ-39 and ITQ-38 with disordered structures. Each of the structure solutions have different challenges to overcome. The high silica borosilicate EMM-25 was solved by the RED method. The aluminosilicate EMM-23 was solved by a combination of HRTEM and RED. The structure solution of two materials with disordered structures, ITQ-39 and ITQ-38, will be described. For materials containing disorders, structure projection images are of utmost importance.      Furthermore, the mesoporosity inside hierarchically porous ZSM-5 crystals was studied by a combination of focused ion beam (FIB) and HRTEM imaging. The last part of this thesis explores STEM imaging for use in structure determination from 3D reconstruction. / <p>At the time of the doctoral defence the following papers were unpublished and had a status as follows: Papers 4 and 5: Manuscipts; Paper 10: Manuscript</p>

The three-dimensional structure of a protein molecule is the key to understanding its biological and physiological properties. A major problem in bioinformatics is to efficiently determine the three-dimensional structures of query proteins. Protein NMR structure de- termination is one of the main experimental methods and is comprised of: (i) protein sample production and isotope labelling, (ii) collecting NMR spectra, and (iii) analysis of the spectra to produce the protein structure. In protein NMR, the three-dimensional struc- ture is determined by exploiting a set of distance restraints between spatially proximate atoms. Currently, no practical automated protein NMR method exists that is without human intervention. We first propose a complete automated protein NMR pipeline, which can efficiently be used to determine the structures of moderate sized proteins. Second, we propose a novel and efficient semidefinite programming-based (SDP) protein structure determination method. The proposed automated protein NMR pipeline consists of three modules: (i) an automated peak picking method, called PICKY, (ii) a backbone chemical shift assign- ment method, called IPASS, and (iii) a protein structure determination method, called FALCON-NMR. When tested on four real protein data sets, this pipeline can produce structures with reasonable accuracies, starting from NMR spectra. This general method can be applied to other macromolecule structure determination methods. For example, a promising application is RNA NMR-assisted secondary structure determination. In the second part of this thesis, due to the shortcomings of FALCON-NMR, we propose a novel SDP-based protein structure determination method from NMR data, called SPROS. Most of the existing prominent protein NMR structure determination methods are based on molecular dynamics coupled with a simulated annealing schedule. In these methods, an objective function representing the error between observed and given distance restraints is minimized; these objective functions are highly non-convex and difficult to optimize. Euclidean distance geometry methods based on SDP provide a natural formulation for realizing a three-dimensional structure from a set of given distance constraints. However, the complexity of the SDP solvers increases cubically with the input matrix size, i.e., the number of atoms in the protein, and the number of constraints. In fact, the complexity of SDP solvers is a major obstacle in their applicability to the protein NMR problem. To overcome these limitations, the SPROS method models the protein molecule as a set of intersecting two- and three-dimensional cliques. We adapt and extend a technique called semidefinite facial reduction for the SDP matrix size reduction, which makes the SDP problem size approximately one quarter of the original problem. The reduced problem is solved nearly one hundred times faster and is more robust against numerical problems. Reasonably accurate results were obtained when SPROS was applied to a set of 20 real protein data sets.

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<p>In this work we have investigated the intercalation of electron-donors between NbS₂ slabs in Nb-based layer sulfides.</p><p>Two series of Sr substituted Nb-based misfit sulfides belonging to the 1.5Q/1H and 1Q/1H series of misfit layer compounds have been synthesised. For large lanthanides (Ln=La, Ce), only the 1Q/1H compounds formed whereas for smaller lanthanides and yttrium, both types of phases can be obtained. The crystal structure of misfit sulfide (Pr_0.55Sr_0.45S)_1.15NbS₂ has been refined using the composite approach. In the Q-slab, Pr-atoms are partly replaced by Sr with a random distribution over one cation position. The crystal structure of misfit sulfide [(Sm_1/3Sr_2/3S)_1.5]_1.15NbS₂ belonging to the 1.5Q/1H series have also been determined. The obtained results suggest a preferred occupancy of the cation positions in the slab where Sr atoms mainly occupy positions on the exterior of the slab while Sm atoms are in the center of the slab. The (La_1-xSr_xS)_1.15NbS₂ solid solution (0.1<x<0.9) has also been studied. It was found that the maximum value of Sr substitution is 40-50% and therefore, the minimal value of charge transfer to stabilize this structure type is about 0.6ē per Nb atom. </p><p>An attempt to synthesize Sr_xNbS₂ (0.1≤x≤0.5) intercalates was made but single phases were not obtained and increasing the temperature from 1000^оС to 1100^оС leads to the decomposition of these intercalates. Single crystals of Sr_0.22Nb_1.05S₂ and Sr_0.23NbS₂ were found and their structures were determined. The structures belong to two different types of packings with statistical distribution of Sr between layers.</p><p>A new superconducting sulfide, "EuNb₂S₅", was investigated by ED and HREM and its structure model consisting of Nb₇S₁₄ and (Eu₃S₄)₂ slabs alternating along the c-axis is suggested. An attempt to suggest a model for the structure of "SrNb₂S₅" by means of X-ray single crystal diffraction was made. The proposed structure consists of two types of slabs: a Nb₇S₁₄ and a [Sr₆(NbS₄)₂S] slab with niobium in tetrahedral coordination. It is shown that "SrNb₂S₅" and "EuNb₂S₅" are have similar structures.</p><p>For the first time, single crystals of the complex sulfide BaNb_0.9S₃ have also been studied by means of X-ray single crystal diffraction. The single crystal refinement and EDX analysis showed the existence of cation vacancies at the niobium position. BaNb_0.9S₃ has also been studied by ED and no superstructure was found which implies that and the vacancies are statistically distributed.</p><p>No improvement of the magnetic properties of the studied compounds was observed in comparison to NbS₂.</p>

<p>This thesis is focused on studies of substituted Hg-based superconducting copper oxides ((Hg_1-x<i>M</i>_x)Ba₂Ca_n-1Cu_nO2_n+2+δ). These compounds are promising objects of investigation, not only from a fundamental point of view but also because of their high values of superconducting transition temperature (<i>T</i>_c) and irreversibility field (<i>H</i>_irr).</p><p>The first part of the thesis is devoted to optimization of the synthesis procedure for Hg-based cuprates. The influence of different parameters (<i>T</i>,<i> t</i>, <i>p</i>(Hg),<i> p</i>(O₂)) on the synthesis of these compounds in sealed silica tubes was studied. Optimal conditions yielded samples containing up to 95% of HgBa₂Ca₂Cu₃O_8+δ (Hg-1223). The formation of solid solutions with the formula (Hg_1-xCu_x)Ba₂Ca₂Cu₃O_8+δ (where x <= 0.5) was also established. Another technique was developed, using LiF as a flux, for synthesis of samples containing up to 90% of the HgBa₂CaCu₂O_6+δ (Hg-1212) phase.</p><p>The second part concerns synthesis and studies of oxyfluorides using Hg-1212 and Hg-1223 as starting materials together with XeF₂ as a fluorinating agent. It was found that oxyfluorides of both phases have a parabolic dependence of T_c vs. <i>a</i> parameter as well as enhanced <i>T</i>_c values (Δ<i>T</i> ≈ 3-4 K) in comparison with optimally doped non-fluorinated analogues. The crystal structure of Hg-1223 oxyfluoride was studied by X-ray powder and neutron diffraction methods. It is suggested that chemical modification of the crystal structure leads to a decrease in Cu-O distance without noticeable change in Cu-O-Cu angle (in the (CuO₂) layers), which may be the significant factors influencing this <i>T</i>_c increase. Hg-1223 oxyfluoride was also studied under high pressure for first time. It was found that this compound has a record-high <i>T</i>_c value (≈ 166 K) at <i>P</i> ≈ 23 GPa.</p><p>The last part describes the investigation of substituted Hg-based superconductors in the series (Hg_0.9M_0.1)Ba₂CuO_4+δ {(Hg,<i>M</i>)-1201}, where <i>M</i> = Tl, Pb, W, Mo, Nb and V. A comprehensive study of these compounds by various methods (X-ray powder diffraction, EDX, IR-, EXAFS- and XANES -spectroscopy) indicated that the change of charge carrier doping level is a crucial factor determining the irreversibility line. (Hg_0.9Mo_0.1)Ba₂CuO_4+δ showed the most improved irreversibility line position among the (Hg,<i>M</i>)-1201 compounds studied in this series.</p>