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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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Novel Molecular Materials for Optics - Synthesis and Characterization of 5-aminotetrazole Salts
Pospíšil, Stanislav ; Zábranský, Martin (advisor) ; Tyrpekl, Václav (referee)
Title: Novel Molecular Materials for Optics - Synthesis and Characterization of 5-aminotetrazole Salts Author: Stanislav Pospíöil Department: Department of Inorganic Chemistry Supervisor: Mgr. Martin Zábransk˝, Ph.D., Department of Inorganic Chemistry Advisors: Prof. RNDr. Ivan N mec, Ph.D., RNDr. Irena Matulková, Ph.D., De- partment of Inorganic Chemistry Abstract: Nonlinear optics is currently an important field for the development of areas such as laser physics or telecommunications, and its understanding is essen- tial for development of new technologies. Its development can also be aided by the investigation of various crystalline materials, such as salts containing cations and anions derived from polarizable organic molecules, exhibiting essential properties for nonlinear optics. This bachelor thesis is focused on preparation of crystalline forms of these compounds. These are salts of simple, nitrogen-rich bases with 5- aminotetrazole. Bigunidium 5-aminotetrazolate, guanidinium 5-aminotetrazolate and aminoguanidium 5-aminotetrazolate were prepared and further characteri- zed. The structures of the latter salts were solved from X-ray di raction data. The methods of spectral vibrational analysis supplemented with nuclear magne- tic resonance and powder di raction were applied to these prepared compounds....
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Development of pharmacophore-guided molecular docking protocol for design of SARS-CoV-2 main protease inhibitors
Klenor, Mikuláš ; Lepšík, Martin (advisor) ; Riedlová, Kamila (referee)
Covid-19 is a highly contagious potentially life-threatening disease caused by the SARS-CoV-2 coronavirus. The virus is responsible for a global pandemic and has claimed over 6 million human lives between years 2020 and 2022. To limit the spread of SARS-CoV-2, numerous vaccines have been developed and applied. For already infected individuals, antiviral drugs are applied. An important validated target is the main protease of SARS-CoV-2 (Mpro ). Although thousands of inhibitors have been prepared and one is used in clinical practice (sold under the name of Paxlovid), improved computational protocols to design new active compounds are needed. The computational approach used here is based on pharmacophores. By curating and inspecting 298 structures of Mpro /inhibitors complexes retrieved from the Protein Data Bank (PDB), we have generated six distinct pharmacophores featuring different binding modes. With their aid, we have carried out molecular docking, whose effectiveness was evaluated by measuring root-mean-square deviation (RMSD) of the generated poses with respect to the native conformations. The routine captured 177 out of 213 ligands naturally binding to the active site of the protein with 127 (72% of the captured) generated with RMSD within 2 Å relative to the native conformation....
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Preparation and characterization of crystalline materials - salts of N-guanylglycinium and guanidinium
Skopalík, Jiří ; Matulková, Irena (advisor) ; Zákutná, Dominika (referee)
The scope of this bachelor thesis is the preparation and study of new salts, which can be obtained from systems N-guanylglycine - inorganic acid and guanidine - amidosulfuric acid, as new materials with potential for applications in nonlinear optics. Prepared crystalline salts of N-guanylglycinium - i.e. chloride, two hydrogenphosphites and sulfate dihydrate along with guanidinium amidosulfate were characterized by methods of vibrational spectroscopy (infrared and Raman) and X-ray diffraction (single crystal and powder methods). To estimate the nonlinear optical properties and for the interpretation of the vibrational manifestations of N-guanylglycinium cation, quantum-chemical calculations were performed. Finally, for two non-centrosymmetric N-guanylglycinium hydrogenphosphites, the efficiency of second harmonic generation was determined for powder samples.
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Molecular Crystals for Nonlinear Optics - Salts of Nitrogen-containing Bases with Selenious Acid and Hypophosphorous Acid
Němcová, Tereza ; Matulková, Irena (advisor) ; Tyrpekl, Václav (referee)
In this bachelor thesis, systems of selenious acid and hypophosphorous acid with six organic bases (2-aminopyrimidine, 3-amino-1,2,4-triazole, 4-amino-1,2,4-triazole, 3,5-diamino-1,2,4-triazole, 2-aminoguanidine and biguanide) were studied as the source of new materials for nonlinear optics. The six prepared crystalline compounds were identified and characterized by vibrational spectroscopy and X-ray diffraction. Unfortunately, all prepared salts contain a centre of symmetry in their structures, and therefore none of them are suitable for nonlinear optics especially the second harmonic generation.
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Parasite cystatins as inhibitors of cysteine proteases: structural aspects of functional specificity and their evolution
Buša, Michal ; Mareš, Michael (advisor) ; Hudeček, Jiří (referee) ; Kukačka, Zdeněk (referee)
Members of the cystatin family are important inhibitors of cathepsin-type cysteine proteases and are involved in a number of pathologies. Parasite cystatins are attractive target molecules for parasite control, but our knowledge about them is still limited. This work is focused on cystatins of two blood-feeding parasites: the common tick (Ixodes ricinus) as the main vector of Lyme disease and tick-borne encephalitis, and the liver fluke (Fasciola hepatica), the causative agent of fasciolosis. Four novel cystatins were functionally and structurally characterized to determine the structural determinants of their inhibitory specificity and describe them in the context of evolution and physiological role of cystatins. The cystatin FhCyLS-2 from F. hepatica has broad inhibitory specificity and is suggested to play a dual role in the regulation of proteolytic systems in host tissue and the parasite gut. FhCyLS-2 combines the characteristics of two cystatin subfamilies in a unique way and is a model representative of a novel evolutionary group of cystatins identified in several orders of parasitic flukes. Ricistatin and iristatin are salivary cystatins of I. ricinus with immunomodulatory effects on the host caused by an exceptionally narrow inhibitory specificity. It was explained by structural modifications of...
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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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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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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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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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