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Preparation and study of novel crystalline materials for nonlinear optics based on nitrogen-containing heterocycles
Kloda, Matouš ; Němec, Ivan (advisor) ; Schwendt, Peter (referee) ; Holubová, Jana (referee)
The presented Ph.D. thesis is aimed at the preparation and characterisation of novel crystalline materials with application potential in nonlinear optics (NLO). The main goal was preparation of crystalline salts and adducts (cocrystals) of selected nitrogen-containing heterocycles with a range of organic and inorganic acids. Based on previous study and quantum- chemical calculations, the following starting heterocycles were selected: 2-aminopyrimidine, 4-aminopyrimidine, 5-aminopyrimidine, 3-amino-1,2,4-triazine and 3-amino-5,6-dimethyl- 1,2,4-triazine. The prepared materials were characterised mainly by X-ray diffraction and vibrational spectroscopy and the interpretation of the vibrational spectra was based on quantum-chemical calculations. The systems based on aminopyrimidines were the first field of study in presented thesis. The thesis represents a finalisation of our previous study focused on inorganic salts and cocrystal in the case of 2-aminopyrimidine. The characterisation of a pair of cocrystals with boric acid was accomplished. The 12 new salts and adducts were prepared and characterised in the case of 4-aminopyrimidine and only one crystalline product - adduct with succinic acid - was obtained in the case of 5-aminopyrimidine. The systems based on 3-amino-1,2,4-triazine and its...
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Crystal and molecular structure study of garnets from selected localities of the České středohoří Mts.
Píšová, Barbora ; Skála, Roman (advisor) ; Laufek, František (referee)
Major and minor element contents of garnets from mantle peridotites and eclogites brought to the surface by volcanic rocks of the České středohoří Mts. were determined by an electron probe microanalyzer. Garnets are homogenous and their chemical composition corresponds to solid solution containing 65-71 % pyrope, other end members significantly present are almandine, uvarovite and grosulare. This method also help to discover polyphase inclusions chemically corresponding to amphiboles (pargasite, cummingtonite, magnesio-hornblende and katophorite). Next to amphiboles following minerals were found in inclusions: omphacite, carbonates, phlogopite, clinochlore, olivine, apatite, spinel group minerals, and sulfidic phases potentially close to pentlandite. Samples were also analyzed by powder X-ray diffraction. Qualitative phase analysis confirmed pyrope homogeneity. The refinement of crystal structure parameters was performed by the Rietveld method. Raman microspectroscopy showed shifts of individual bands in the Raman spectra compared to those of pure pyrope. Position of bands in spectra differs due to the substitution of Ca for Mg at the dodecahedral sites of the structure. Mutual positive correlations among elements Cr, Ca, Mg, Al, Si, Mn, Ti and Na were observed. Correlations were found also between...
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Molecular crystals for NLO applications - compounds of 1H-pyrazole-carboxamidine
Kohúteková, Soňa ; Němec, Ivan (advisor) ; Šloufová, Ivana (referee)
Title: Molecular crystals for NLO applications - compounds of 1H-pyrazole-carboxamidine Author: Bc. Soňa Kohúteková Department: Department of Inorganic Chemistry Supervisor: prof. RNDr. Ivan Němec, Ph.D. Abstract: The aim of this diploma thesis is preparation and characterisation of novel compounds of 1H-pyrazole-carboxamidine in consideration of their potential application in the field of nonlinear optics. This thesis is focused on preparation of crystalline salts or adducts combining 1H-pyrazole-carboxamidine with selected inorganic and organic acids. Prepared materials were characterised mainly by the means of vibrational spectroscopy and X-ray diffraction analysis. Quantum-chemical calculations were used for a prediction of nonlinear optical properties as well as for interpretation of measured vibrational spectra. Four different approaches of calculations were used for an optimisation of computing time together with accuracy of the fit of calculated and measured spectra. Finally, measurements of second harmonic generation efficiency of two powder samples with non-centrosymmetric crystal structures were performed. Key words: NLO, vibrational spectroscopy, crystal structure, quantum-chemical calculations
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Novel materials for nonlinear optics - salts and cocrystals of heteroaromatic bases
Kloda, Matouš ; Němec, Ivan (advisor) ; Gyepes, Róbert (referee)
The main issue of this master thesis is investigation of new compounds of aminopyrazine and 3-amino-1,2,4-triazine in consideration of their potential usage in the field of nonlinear optics. The focus of this thesis was finishing of characterisation of an adduct of aminopyrazine and boric acid prepared as a part of previous bachelor thesis, as well as preparation of salts and cocrystals combining 3-amino-1,2,4-triazine with selected acids. Prepared materials were characterised mainly by the means of vibrational spectroscopy and x-ray diffraction analysis. Prediction of nonlinear optical properties of selected molecules and interpretation of recorded vibrational spectra was based on quantum chemical calculations. Finally, measurements of second harmonic generation efficiency of selected powder samples were performed.
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Salts of 2-aminoethanol and ferrocene-based acids
Zábranský, Martin ; Štěpnička, Petr (advisor) ; Němec, Ivan (referee)
Combination of the compact but sterically flexible ferrocene scaffold with intermolecular binding potential and conformational variability of (2-hydroxyethyl)ammonium structural motif was utilised in the construction of solid crystalline materials. Crystallisation in systems containing ferrocenecarboxylic, 2-ferrocenylacetic, 3-ferrocenylpropionic, 3-ferrocenyl- acrylic, 3-ferrocenylacrylic, 3-ferrocenylpropiolic, ferrocene-1,1'-dicarboxylic or ferrocene- sulfonic acid with 2-aminoethanol afforded crystals of the corresponding salts. The resulting crystalline products were characterised with the usual methods (proton nuclear magnetic resonance, infrared spectroscopy, elemental analysis) and their crystal structures were determined by means of single-crystal X-ray diffraction analysis. The crystal structures of the salts mentioned above usually contain rather complicated two dimensional networks of charge-assisted hydrogen bonds. With the aim of studying potentially more simple hydrogen-bonded structures, additional crystallisation experiments were conducted in systems of ferrocenecarboxylic acid and 2-(methylamino)ethanol or 2-(dimethylamino)ethanol. These experiments yielded simple salt of the former amine and adducts of salts of both bases with ferrocenecarboxylic acid in the ratio of 1:1. The...
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Structural and functional analysis of cathepsin B1 from the blood fluke, Schistosoma mansoni
Jílková, Adéla ; Mareš, Michael (advisor) ; Obšil, Tomáš (referee) ; Mikeš, Libor (referee)
Schistosomiasis is a serious infectious disease that afflicts over 200 million people in tropical and subtropical regions. It is caused by Schistosoma blood flukes that live in human blood vessels and obtain nutrients from host hemoglobin, which is degraded by digestive proteases. Current therapy relies on a single drug and concern over resistance necessitates new drug development. In Schistosoma mansoni, cathepsin B1 (SmCB1) is a critical digestive protease that is a target molecule for therapeutic interventions. This thesis provides a comprehensive characterization of SmCB1 focused on structure-activity relationships and inhibitory regulation based on six crystal structures solved for SmCB1 molecular forms and complexes. SmCB1 is biosynthesized as an inactive zymogen in which the N-terminal propeptide operates as a natural intra-molecular inhibitor by blocking the active site. Detailed biochemical and structural analyses have identified a new and, so far, unique mechanism of SmCB1 zymogen activation through which the propeptide is proteolytically removed and the regulatory role of glycosaminoglycans in this process has been described. A study of SmCB1 proteolytic activity has revealed that the enzyme acts in two modes, as endopeptidase and exopeptidase, which makes it an efficient tool for host...
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Structure and magnetic properties of f-electron compounds and their hydrides
Mašková, Silvie ; Havela, Ladislav (advisor) ; Kamarád, Jiří (referee) ; Reiffers, Marián (referee)
Title: Structure and magnetic properties of f-electron compounds and their hydrides Author: Silvie Mašková Department: Deparment of Condensed Matter Physics Supervisor: Doc. RNDr. Ladislav Havela, CSc., Deparment of Condensed Matter Physics, Faculty of Mathematics and Physics, Charles University, Prague, The Czech Republic Abstract: Magnetic properties were studied in several types of actinide- and lanthanide-based ternary compounds. We have shown indirect that anisotropy of compressibility and thermal expansion can be related to the direction of magnetic moments at U-compounds with "soft" directions (where the closest U-U links are) perpendicular to the moments direction. Comparison of U and RE compounds of the 2-2-1 type indicates that contrary to U compounds, RE compounds can absorb much more hydrogen. The involvement of the f-states in metallic bond, which takes place at actinides and not in lanthanides, makes the U-based compounds apparently more stable against hydrogenation. Basic electronic properties were established for ζ -Pu19Os, which is a close analogy to β-Pu, and for its low-temperature variety η -Pu19Os. The results confirm that the volume is not the main parameter driving Pu properties, as β-Pu with intermediate volume is the most strongly correlated Pu phase. Keywords: uranium compounds,...
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The secreted aspartic proteases of Candida parapsilosis.
Marečková, Lucie ; Dostál, Jiří (advisor) ; Novotný, Marian (referee)
Candida parapsilosis is an opportunistic fungal pathogen of humans causing a variety of infections. Immunocompromised individuals represent the most threatened group of patients. The increasing frequency of infections and occurrence of drug resistant strains are the main reasons for research focused on novel antimycotic compounds. Inhibition of secreted aspartic proteases (Sap) of pathogenic Candida spp. appears to be a potential target of therapeutic intervention. The genome of C. parapsilosis contains at least three genes coding for secreted aspartic proteases, denominated SAPP1-3. Protease Sapp1p has been well biochemically and structurally characterized, whereas Sapp2p and Sapp3p have been given less attention. The first part of the thesis is focused on structural analysis of Sapp1p complexes with selected peptidomimetic inhibitors binding to the active site of the enzyme. In addition, complex of the isoenzyme Sapp2p with the well-known secreted aspartate inhibitor Pepstatin A has been analyzed. The second part is related to the fact that C. parapsilosis belongs to the Candida spp. with the unique ability to translate standard leucine CUG codon mostly as serine. Even though it is a non-conservative substitution of hydrophobic amino acids for a hydrophilic one, this unique ability is maintained for more...
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Study of organic molecular compound by x-ray radiation
Stejkora, Jakub ; Richtera, Lukáš (referee) ; Salyk, Ota (advisor)
Derivates of diketopyrrolopyrrole are coloured pigments with potential use in field of organic semiconductor structures. Their electrical attributes such as conductivity, photocon- ductivity and electroluminescence relate to their crystal structures, that determine charge transport path through the compound. The work deals with determination of these structures by using x-ray diffractometry. The diffractogram based on known crystalografic structure of diketo-dipyridyl-pyrrolo-pyrrole is modeled by available software and measured diffractogram is used for structure re-modeling. This method is used for other related derivates with unknown crystal structure.
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