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Crystallography has traditionally been studied by diffraction methods involving X ray or neutron radiation. These methods have some limitations, from requiring the substance under study to form single crystals to the limited ability of X rays to locate hydrogen atoms. While neutron radiation can characterize hydrogens, it is expensive, not readily available and has its own particular limits on resolution. It this dissertation, it is demonstrated that NMR is extraordinarily sensitive to atomic positions, with variations of mere tens of femtometers creating statistically distinguishable chemical shift changes. To date, no other means of measurement can detect structural changes at this scale. This thesis presents a NMR based refinement technique that refines existing X ray structures to an unprecedented resolution. The refinement uses computational methods to make theoretical models then fits these models to the experimental data. This refinement process can also be modified to generate positional uncertainties known as the anisotropic displacement parameters, or ADPs, to accompany the refined structure. This creation of ADPs fulfills requirements set by the international union of crystallography that all deposited crystal structures contain ADPs.

Proteins are the fundamental machinery that enables the functions of life. It is critical to understand them not just for basic biology, but also to enable medical advances. The field of protein structure prediction is concerned with developing computational techniques to predict protein structure and function from a protein’s amino acid sequence, encoded for directly in DNA, alone. Despite much progress since the first computational models in the late 1960’s, techniques for the prediction of protein structure still cannot reliably produce structures of high enough accuracy to enable desired applications such as rational drug design. Protein structure refinement is the process of modifying a predicted model of a protein to bring it closer to its native state. In this dissertation a protein structure refinement technique, that of potential energy minimization using hybrid molecular mechanics/knowledge based potential energy functions is examined in detail. The generation of the knowledge-based component is critically analyzed, and in the end, a potential that is a modest improvement over the original is presented. This dissertation also examines the task of protein structure comparison. In evaluating various protein structure prediction techniques, it is crucial to be able to compare produced models against known structures to understand how well the technique performs. A novel technique is proposed that allows an in-depth yet intuitive evaluation of the local similarities between protein structures. Based on a graph analysis of pairwise atomic distance similarities, multiple regions of structural similarity can be identified between structures independently of relative orientation. Multidomain structures can be evaluated and this technique can be combined with global measures of similarity such as the global distance test. This method of comparison is expected to have broad applications in rational drug design, the evolutionary study of protein structures, and in the analysis of the protein structure prediction effort.

Prussian blue (PB) and Prussian blue analogues (PBAs) are compounds with potential applications in a large variety of fields such as gas storage, poison antidotes, electrochromism, electrochemistry and molecular magnets. The compounds are easy to synthesize, cheap, environmentally friendly and have been pursued for both fundamental research and industrial purposes. Despite the multifunctionality of PB and PBAs, they have complicated compositions, which are largely dependent on the synthesis methods and storage conditions. Thus, performing investigations on such compounds with defined composition, stoichiometry and crystal structure is essential. This thesis has focused on synthesis and detailed structure characterization of copper hexacyanoferrate (CuHCF) via X-ray powder diffraction (XRPD), neutron powder diffraction (NPD), thermogravimetric analysis (TGA), differential scanning calorimetry (DSC), inductively coupled plasma-optical emission spectroscopy (ICP-OES), scanning electron microscopy-energy dispersive spectroscopy (SEM-EDS), Mössbauer spectroscopy, extended X-ray absorption fine structure (EXAFS), infrared (IR) and Raman techniques. In addition, kinetics of thermal dehydration process, CO2 adsorption and CO2 adsorption kinetics were investigated. Moreover, in operando synchrotron X-ray diffraction experiments were performed to gain insight into the structure-electrochemistry relationships in an aqueous CuHCF/Zn battery during operation. / <p>At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 4: Manuscript. Paper 5: Manuscript.</p>

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The use cases of Information Extraction (IE) are more or less endless, often consisting of a combination of Named Entity Recognition (NER) and Relation Extraction (RE). One use case of IE is the extraction of transaction information from Norwegian insider transaction Press Releases (PRs), where a transaction consists of at most four entities: the name of the owner performing the transaction, the number of shares transferred, the transaction date, and the price of the shares bought or sold. The relationships between the entities define which entity belongs to which transaction, and whether shares were bought or sold. This report has investigated how a pair of supervised NER and RE models extract this information. Since these Norwegian PRs were not labeled, two different approaches to annotating the transaction entities and their associated relations were investigated, and it was found that it is better to annotate only entities that occur in a relation than annotating all occurrences. Furthermore, the number of PRs needed to achieve a satisfactory result in the IE pipeline was investigated. The study shows that training with about 400 PRs is sufficient for the results to converge, at around 0.85 in F1-score. Finally, the report shows that there is not much difference between a complex RE model and a simple rule-based approach, when applied on the studied corpus.

This thesis presents a study on two types of X-ray diffraction methodologies applied to the characterization of amorphous materials. The purpose of this study was to assess the feasibility of measuring the diffractive spectrum of amorphous materials by Energy-Dispersive X-ray Diffraction (EDXRD) utilizing Cadmium Zinc Telluride detectors. The total scattering intensity (coherent plus incoherent scatter) spectra precisely measured by high-energy Wide-Angle X-ray Scattering (WAXS) were compared to the EDXRD spectra to determine the level of agreement between the two techniques. The EDXRD spectra were constructed by applying a spectra fusing technique which combined the EDXRD spectra collected at different scattering angles rendering a continuous total scattering spectrum. The spectra fusing technique extended the momentum transfer range of the observed scattered spectrum beyond the limitations of the X-ray source and CZT detection efficiencies. Agreement between the WAXS and fused EDXRD spectra was achieved. In addition, this thesis presents the atomic pair correlation functions and coordination numbers of the first coordination shell for four hydrogen peroxide solutions of varying mass concentrations using Empirical Potential Structural Refinement (EPSR). The results are compared to the state-of-the art ad initio quantum mechanical charge field molecular dynamics (QMCF MD) model of the hydrogen peroxide in solution to support the model's predictions on why hydrogen peroxide is stable in water. The EPSR results using the coherent scattering intensity calculated from the WAXS data set predicts a hydration shell of 6.4 molecules of water surrounding hydrogen peroxide. The results also indicate that hydrogen peroxide is more likely to behave as a proton donor than acceptor. These findings are in agreement with QMCF MD model of aqueous hydrogen peroxide. / Physics

Tesis por compendio / [ES] El Proyecto de investigación aquí descrito se estructura en dos partes. La primera parte se centra en la investigación fundamental con el objetivo de crear un protocolo para la síntesis de zeolitas. La segunda parte se refiere al diseño, síntesis y caracterización de nuevas zeolitas, particularmente utiles para aplicaciones DeNOx,, pero también podría ser útil para aplicaciones MTO. La investigación fundamental sugiere un Nuevo modelo de preparación de zeolitas utilizando otras zeolitas como simiente. Este proceso se llama transformación zeolita-zeolita o también conversión interzeolita. El alto rendimiento obtenido, la rápida cristalización y la mejor utilización y rendimiento de los materiales de partida se han tenido en cuenta para mejorar el proceso en base a un proyecto de doctorado financiado por una empresa. Este método se ha ilustrado utilizando varias zeolitas como semilla, entre otras FAU y CHA, para la preparación de las dos zeolitas objetivo: AEI y AFX. En la segunda parte, la investigación se centra en el diseño de nuevas zeolitas de poro medio. Se han seleccionado tres zeolitas hipotéticas de una base de datos de 933611 estructuras. Esta selección se ha realizado utilizando descriptores específicamente diseñados en base a la aplicabilidad de estas zeolitas en procesos DeNOx zeolitas. A continuación se han buscado los agentes directores de estructura (ADE) más apropiados, con la ayuda de métodos computacionales, algunos de los cuales se han sintetizado posteriormente. El uso de dichos ADE en el gel de síntesis ha permitido la obtención de una zeolita cuya topología (ERI) ha sido identificada mediante análisis por PXRD, y cuya morfología y tamaño de cristal (particularmente pequeño) la hacen muy adecuada para su uso como catalizador en algunos procesos. El trabajo de síntesis también reveló la aparición de una nueva zeolita de alta densidad, llamada 'paracelsio-K'. Este nuevo material se ha obtenido al explorar el espacio de fases que cristalizan al utilizar 1-methyl-DABCO como ADE. La síntesis de esta zeolita tiene un especial interés porque el ADE no se incorpora en los canales de la zeolita, pero más bien influyendo en la nucleación y cristalización. La caracterización reveló que la composición del material es próxima al mineral microcline, estructuralmente cercano al paracelsio, ambos feldespatos. A diferencia de los feldespatos el paracelsio-K contiene moléculas de agua en su interior (1 molécula por cavidad) y puede describirse como el material más simple de la familia de las zeolitas que contiene cadenas del tipo 'doble-cigüeñal'. Utilizando los elementos topológicos correspondientes a esta estructura es posible generar estructuras zeolíticas ya conocidas, como GIS, APC, MER, PHI, SIV y algunas otras zeolitas hipotéticas. / [CA] El Projecte d'investigació aquí descrit s'estructura en dos parts. La primera part se centra en la investigació fonamental amb l'objectiu de crear un protocol per a la síntesis de zeolites. La segona part es refereix al disseny, síntesis i caracterització de noves zeolites, particularment útils per a aplicacions DeNOx , però també podria ser útil per a aplicacions MTO. La investigació fonamental suggereix un nou model de preparació de zeolites utilitzant altres zeolites com a llavor. Aquest procés s'anomena transformació zeolita-zeolita o també conversió interzeolita. L'alt rendiment obtingut, la ràpida cristal·lització i la millor utilització i rendiment dels materials de partida s'han tingut en compte per millorar el procés en base a un projecte de doctorat finançat per una empresa. Aquest mètode s'ha il·lustrat utilitzant diverses zeolites com a llavor, entre altres FAU i CHA, per a la preparació de les dues zeolites objectiu: AEI i AFX. A la segona part, la investigació se centra en el disseny de noves zeolites de porus mitjà. S'han seleccionat tres zeolites hipotètiques d'una base de dades de 933.611 estructures. Aquesta selecció s'ha realitzat utilitzant descriptors específicament dissenyats sobre la base de l'aplicabilitat d'aquestes zeolites en processos DeNOx zeolites. A continuació s'han buscat els agents directors d'estructura (ADE) més apropiats, amb l'ajuda de mètodes computacionals, alguns dels quals s'han sintetitzat posteriorment. L'ús d'aquests ADE al gel de síntesi ha permès l'obtenció d'una zeolita la topologia (ERI) ha estat identificada mitjançant anàlisi per PXRD, i la morfologia i mida de vidre (particularment petit) la fan molt adequada per al seu ús com a catalitzador en alguns processos. El treball de síntesi també va revelar l'aparició d'una nova zeolita d'alta densitat, anomenada 'paracelsio-K'. Aquest nou material s'ha obtingut a explorar l'espai de fases que cristal·litzen en utilitzar 1-methyl-DABCO com ADE. La síntesi d'aquesta zeolita té un especial interès perquè el ADE no s'incorpora en els canals de la zeolita, però més aviat influint en la nucleació i cristal·lització. La caracterització va revelar que la composició del material és propera al mineral microcline, estructuralment proper al paracelsio, tots dos feldspats. A diferència dels feldspats el paracelsio-K conté molècules d'aigua al seu interior (1 molècula per cavitat) i pot descriure com el material més simple de la família de les zeolites que conté cadenes del tipus 'doble-cigonyal'. Utilitzant els elements topològics corresponents a aquesta estructura és possible generar estructures zeolítiques ja conegudes, com GIS, APC, MER, PHI, SIV i algunes altres zeolites hipotètiques. / [EN] The research project described herein is structured in two parts. The first part is focused on the fundamental research with the aim of creating a toolbox for zeolite preparation. The second part deal with the design, synthesis and characterization of novel zeolites particular useful for DeNOx applications, but could be also useful for MTO applications. The fundamental research is addressing a novel approach of preparing zeolites by using other zeolites as raw materials. This process is known as zeolite-to-zeolite transformation or interzeolite conversion. The high yield obtained, fast crystallization time and the better utilization of the raw materials (e.g. parent zeolite, organic structure directing agent (OSDA)), are important benefits of interzeolite conversion technic, which answer the objectives formulated for an industrial PhD project. The method has been exemplified by using various raw materials as parent zeolites, such as FAU and CHA for the preparation of two target small pore zeolites AEI and AFX. In the second part the focus has been on the design of novel small pore zeolites. Three hypothetical frameworks have been selected by narrowing down a database containing 933611 structures. The selection has been performed by using the general descriptors for the state-of-the-art DeNOx zeolites (e.g. CHA). This was followed by finding suitable OSDAs for the selected frameworks, by using computational methods. The usage of the theoretically predicted OSDAs in synthesis gels made possible the synthesis of a novel high-silica zeolite. PXRD analysis, revealed that the zeolite has the ERI framework topology. The obtained material has a distinct particle morphology and smaller crystallites, which are key parameters for various catalytic processes. The synthesis work revealed also a novel dense zeolite, named K-paracelsian. The new material has been obtained while exploring the phase space using 1-methyl-DABCO as OSDA. The synthesis of this zeolite is especially interesting in the sense that the OSDA is not being incorporated into the zeolite channels, but rather influencing the nucleation and crystallization. Further characterization revealed a material compositionally closely related to the mineral microcline and structurally closely related to the mineral paracelsian, both of which are feldspars. In contrast to the feldspars, K-paracelsian contains intrazeolitic water corresponding to one molecule per cage and can be described as the simplest endmember of a family of dense double-crankshaft zeolite topologies. By applying the identified building principle, a number of known zeolite frameworks (e.g. GIS, APC, MER, PHI, SIV) and hypothetical zeolite topologies can be constructed. / The authors thank Haldor Topsoe A/S and Innovation Fund Denmark for financial support under the Industrial PhD programme (Case no. 1355-0174B). We thank MINECO of Spain for funding (SEV-2016- 0683 and RTI2018-101033-B-100) and ASIC-UPV for the use of computational facilities. We also thank Prof. M. M. J. Treacy for assistance with the Database of Prospective Zeolite Structures. / Boruntea, C. (2020). Design, synthesis and characterization of small-pore zeolites for industrial environmental applications [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/141094 / TESIS / Compendio