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Studying the properties of molecular photoactive materials via the methods of computational chemistry
Truksa, Jan ; Rapta, Peter (referee) ; Toman, Petr (referee) ; Salyk, Ota (advisor)
V této práci jsou nejprve rychle nastíněny principy teorie funkcionálu elektronové hustoty (DFT), spolu s praktickými metodami hledání nejníže energeticky postavených struktur organických molekul a predikování jejich spektroskopických a elektronických vlastností. Poté jsou prezentovány výsledky teoretické analýzy geometrie a elektronové struktury dvou druhů molekul v kombinaci s experimentálními výsledky. Nejprve jsou diskutovány alloxazin, lumazin a jejich deriváty, souhrnně nazývané flaviny, které reprezentují molekulární materiály. Naproti tomu, struktury na bázi polythiofenu reprezentují polymerní materiály. V případě flavinů byla nejprve nalezena nejlepší možná korelace teoretických absorpčních spekter s experimentálními na základě výpočtů se třemi různými bázovými soustavami v kombinaci s funkcionálem B3LYP. Dobrá shoda byla nalezena pomocí metod B3LYP/6-31+G** a B3LYP/aug-cc-PVDZ, které dosáhly korelačních koeficientů 0.95 a 0.96. Naproti tomu soustava def2SVP dosáhla pouze 0.94. V tomto kontextu se tak metoda B3LYP/6-31+G** jeví jako nejefektivnější vzhledem k náročnosti na výpočetní kapacitu. Měřením absorpčních spekter vybraných flavinů ve směsi dimethylsulfoxidu (DMSO) a vody byla získána spektra jednotlivých izomerů – alloxazinové a isoalloxazinové formy. Reakce těchto molekul na změny koncentrace DMSO a vody bude předmětem dalšího studia. U polythiofenů byly studovány optické a elektrické vlastnosti na modelových oktamerech, zatímco geometrie a konformace adamantylovaných substitutentů byly z důvodu vysoké výpočetní náročnosti modelovány na trimerových molekulách. Bylo zjištěno, že thiofenový řetězec s postranními methyladamantylovými skupinami vykazuje vyšši rigiditu než řetězec substituovaný ethyladamantylem, což bylo později potvrzeno krystalografickou analýzou a skenováním povrchu pomocí mikroskopie atomárních sil. Byly nalezeny krystalické struktury s parametry srovnatelnými s poly(3-hexylthiofenem) (P3HT). Na základě tohoto výzkumu byly navržený nové páteřní řetězce pro možnou syntézu, jako hlavní doporučení se zde jeví snížení počtu substituentů, aby adamantylový postranní řetězec byl přítomen pouze na každém druhém či třetím thiofenu. Zde prezentované molekuly jsou zajímavými kandidáty pro využití v optoelektronice, a teoretické predikce dosahují dobrou shodu s experimentem, přestože jejich srovnání není vždy triviální, jako je tomu například u postranních řetězců polythiofenu.
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Theoretical Investigation of the Zeolite Hydrolysis under Realistic Conditions
Jin, Mengting ; Grajciar, Lukáš (advisor) ; Chizallet, Céline (referee) ; Piskorz, Witold (referee)
Zeolites are one of the most widely used and one of the most industrially important materials. They are utilized in a variety of commercial applications, particularly in heterogeneous catalysis, adsorption/separations applications and as ion exchangers. Zeolites are stable when exposed to water or water vapor at ambient conditions and exhibit high thermal stability. However, zeolites can be partially or even fully hydrolyzed under certain conditions. This hydrolytic instability of zeolites can be considered both a major problem in some applications and a useful means to tune catalyst properties in the others. However, the thorough studies of the hydrolytic mechanisms under realistic conditions (high water loading, alkaline conditions, high heteroatom concentrations, etc.) and employing realistic models (dynamical simulation of ab initio accuracy) is mostly lacking. This dissertation uses the ab initio calculations to systematically study the hydrolysis mechanism of zeolites under realistic conditions, including: (1) hydrolysis mechanism of germanosilicate zeolite UTL, (2) hydrolysis of siliceous zeolite CHA under alkaline conditions, and (3) identification of the nature of framework-associated Al(Oh) species in aluminosilicate zeolite CHA under wet conditions. The main results obtained are as...
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Theoretical Investigation of Low-dimensional Magnetic Materials
Li, Shuo ; Grajciar, Lukáš (advisor) ; Frauenheim, Thomas (referee) ; Jelínek, Pavel (referee)
Low-dimensional (D) materials, such as graphene, transition metal dichalcogenides and chalcogenide nanowires, are attractive for spintronics and valleytronics due to their unique physical and chemical properties resulting from low dimensionality. Emerging concepts of spintronics devices will greatly benefit from using 1D and 2D materials, which opens up new ways to manipulate spin. A majority of 1D and 2D materials is non-magnetic, thus their applications in spintronics are limited. The exploration, design and synthesis of new 1D and 2D materials with intrinsic magnetism and high spin-polarization remains a challenge. In addition, the valley polarization and spin-valley coupling properties of 2D materials have attracted great attention for valleytronics, which not only manipulates the extra degree of freedom of electrons in the momentum space of crystals but also proposes a new way to store the information. The computational investigation of magnetic and electronic properties of low-dimensional materials is the subject of this thesis. We have systematically investigated geometric, electronic, magnetic and valleytronic properties of several 2D and 1D materials by using the density functional theory. These investigations not only theoretically show rich and adjustable magnetic properties of...
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Optimization of Semiempirical Quantum Mechanical Methods for in Silico Drug Design
Kříž, Kristian ; Řezáč, Jan (advisor) ; Klimeš, Jiří (referee) ; Kolář, Michal (referee)
Optimization of Semiempirical Quantum Mechanical Methods for in Silico Drug Design Doctoral thesis Kristian Kříž The subject of this thesis is the optimization of semiempirical quantum mechanical methods (SQM) for their use in in silico drug design. The thesis covers two topics - COSMO2 solvation model optimization part and PLF547, PLA15 dataset development part. The first part is devoted to the optimization of COSMO solvation model by addition of a nonpolar term and reparametrization of the model for SQM methods PM6 and PM7. We have shown that the accuracy of the resulting "COSMO2" optimized model improved on all the tested datasets and we have compared it to other selected SQM solvation models. The method has also been tested on the protein ligand complexes as a part of a scoring function, where it provides better preditction of binding affinity of drug candidates for their target protein. The second part of the thesis describes the construction of datasets for noncovalent interactions aimed speicificly to represent an environment of an enyzme active site complexed with a ligand with reliable benchmark values of interaction energies in vacuum and solvent (water). The developed PLF547 and PLA15 datasets are suitable for testing and development of methods for the use in drug design. We have...
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Theoretical Investigation of Mechanisms of Chemical Reactions Taking Place in Microporous Materials
Položij, Miroslav
Mechanisms of three reactions catalyzed by microporous materials were investigated computationally; the reactions investigated include Friedländer and Knoevenagel reactions catalyzed by Cu3BTC2 metal organic framework (MOF) and an intramolecular cyclisation of unsaturated alcohols catalyzed by zeolite H-ZSM-5. It was found that the reaction mechanisms of all three reactions are controlled by a high concentration of active sites in materials. Reaction intermediates interact with more than one active site simultaneously. This novel concept of "multiple-site" interactions is described. The concerted effect of two catalytic sites leads to a decrease of activation barriers on reaction paths of Friedländer and Knoevenagel reactions. On the contrary, a simultaneous interaction of reactants with two active sites has a negative effect on reaction rate in case of alcohol cyclization catalyzed by H-ZSM-5; it was found that the interaction with dual sites results in the increase of activation barriers and diffusion limitations. In case of Knoevenagel reaction catalyzed by CuBTC, the adsorption of reaction precursor to the reaction site allows the creation of a dynamic defect in the MOF framework that subsequently catalyses the reaction. Both, the multiple sites effect and the dynamical defect formation effect...
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Study of derivatization reactions for ESI-MS analysis of hardly ionizable rhenium aryl chlorocomplexes
Vlk, Mikuláš ; Štícha, Martin (advisor) ; Kozlík, Petr (referee)
Mass spectrometry with electrospray ionization is an excellent method for structural analysis of coordination compounds with outstanding sensitivity and selectivity. However, it fails to detect some low-polar rhenium complexes. This master thesis describes derivatization method of non-ionizable rhenium complexes with 1,2-dihydroxybenzene and 2,3- dihydroxytoluenene. Fragmentation mechanisms and structure of prepared complexes was studied using high resolution mass spectrometry and collision-induced dissociation (CID). Furthermore, density functional theory (DFT) computational method was used for prediction of bond cleavage based on bond lengthening.
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Theoretical Investigation of Mechanisms of Chemical Reactions Taking Place in Microporous Materials
Položij, Miroslav
Mechanisms of three reactions catalyzed by microporous materials were investigated computationally; the reactions investigated include Friedländer and Knoevenagel reactions catalyzed by Cu3BTC2 metal organic framework (MOF) and an intramolecular cyclisation of unsaturated alcohols catalyzed by zeolite H-ZSM-5. It was found that the reaction mechanisms of all three reactions are controlled by a high concentration of active sites in materials. Reaction intermediates interact with more than one active site simultaneously. This novel concept of "multiple-site" interactions is described. The concerted effect of two catalytic sites leads to a decrease of activation barriers on reaction paths of Friedländer and Knoevenagel reactions. On the contrary, a simultaneous interaction of reactants with two active sites has a negative effect on reaction rate in case of alcohol cyclization catalyzed by H-ZSM-5; it was found that the interaction with dual sites results in the increase of activation barriers and diffusion limitations. In case of Knoevenagel reaction catalyzed by CuBTC, the adsorption of reaction precursor to the reaction site allows the creation of a dynamic defect in the MOF framework that subsequently catalyses the reaction. Both, the multiple sites effect and the dynamical defect formation effect...
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Computational investigation of adsorption of saturated and unsaturated hydrocarbons in CPO-27 Metal-Organic Framework
Smetanová, Tereza ; Nachtigall, Petr (advisor) ; Bludský, Ota (referee)
Title: Computational investigation of adsorption of saturated and unsaturated hydrocarbons in CPO-27 Metal-Organic Framework Abstract: The adsorption of hydrocarbons on coordinatively unsaturated sites (cus) in CPO-27 Metal-Organic Framework (MOF) was investigated computationally. Different levels of density functional theory (DFT), including vdW-DF2, PBE, DFT-D2 functionals, were used and their performance was compared to a reference method DFT/CC and available experimental data. The adsorption properties of Cu and Mg containing CPO-27 for ethane, ethylene, propane and propylene separations were investigated and discussed. Keywords: adsorption, metal-organic frameworks, density functional theory, coordinatively unsaturated sites, open metal sites
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Nové molekulární materiály pro nelineární optiku - příprava a detailní charakterizace
Mathauserová, Jana ; Němec, Ivan (advisor) ; Gyepes, Róbert (referee)
In this thesis both an experimental and computational study of selected prospective materials for nonlinear optics is presented. The main focus was put on 2-aminopyrimidinium hydrogen- phosphite (AMPPO3), a salt with high SHG efficiency and Type I. phase matching properties. AMPPO3 had been studied by our research group and its favourable qualities such as easy preparation, colourlessness, great water solubility and good crystallinity motivated further in- terest and the attempts for the growth of bulk single crystals from thermostated aqueous solu- tions as presented here. The products are meant to be probed by laser in a specific direction to determine the maximum SHG efficiency, so far the polarized microscopy study revealing the extreme dispersion effects is provided. AMPPO3 is an example of H-bond stabilized framework with both organic and inorganic building blocks. The computational study was led as to understand the structure which is typical for one of the classes of compounds exhibiting nonlinear optical properties. DFT implemented in parallel CP2K was used and for the comparison three other optically active materials of sim- ilar composition were studied - urea, guanylurea hydrogenphosphite and 2-aminopyrimidine- boric acid 3/2 cocrystal. After the constrained geometry optimization and cell...
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Theoretical Investigation of Mechanisms of Chemical Reactions Taking Place in Microporous Materials
Položij, Miroslav ; Nachtigall, Petr (advisor) ; Pulido Junquera, María Ángeles (referee)
Mechanisms of three reactions catalyzed by microporous materials were investigated computationally; the reactions investigated include Friedländer and Knoevenagel reactions catalyzed by Cu3BTC2 metal organic framework (MOF) and an intramolecular cyclisation of unsaturated alcohols catalyzed by zeolite H-ZSM-5. It was found that the reaction mechanisms of all three reactions are controlled by a high concentration of active sites in materials. Reaction intermediates interact with more than one active site simultaneously. This novel concept of "multiple-site" interactions is described. The concerted effect of two catalytic sites leads to a decrease of activation barriers on reaction paths of Friedländer and Knoevenagel reactions. On the contrary, a simultaneous interaction of reactants with two active sites has a negative effect on reaction rate in case of alcohol cyclization catalyzed by H-ZSM-5; it was found that the interaction with dual sites results in the increase of activation barriers and diffusion limitations. In case of Knoevenagel reaction catalyzed by CuBTC, the adsorption of reaction precursor to the reaction site allows the creation of a dynamic defect in the MOF framework that subsequently catalyses the reaction. Both, the multiple sites effect and the dynamical defect formation effect...
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