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Development and applications of molecular dynamics for molecular spectroscopy
Kessler, Jiří ; Bouř, Petr (advisor) ; Bludský, Ota (referee) ; Setnička, Vladimír (referee)
This Thesis deals with simulations of chiroptical spectra using a combination of molecular dynamics and quantum chemistry. Molecular dynamics was used to explore conformational behaviour of studied systems (proteins), quantum chemistry for calculation of spectral prop- erties. The Quantum chemical methods are limited to relatively small systems. We overcome this problem mostly by a fragmentation of studied systems, when smaller, computationally feasible, fragments are created and used for the quantum chemical calculations. Calculated properties were then transferred to the big molecule. Vibrational Optical Activity (VOA) spectra of poly-L-glutamic acid fibrils (PLGA), insulin prefibrillar form and native globular proteins were studied. The simulated spectra provided satisfactory agreement with the experiment and were used for its interpretation. Experimental Vibrational Circular Dichroism (VCD) spectra of poly-L-glutamic acid fibrils were only qualitatively reproduced by the simulation. We could reproduce the major amide I band and a smaller negative band associated with the side chain carboxyl group. Our simulation procedure was then extended to a set of globular proteins and their Raman Optical Activity (ROA) spectra. Here we achieved an exceptional precision. For example, we were able to reproduce...
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Enantioselective separation of certain analytes using supercritical fluid chromatography and high performance liquid chromatography
Martínková, Monika ; Tesařová, Eva (advisor) ; Čabala, Radomír (referee)
(EN) Cellulose tris-(3,5-dimethylphenylcarbamate) chiral stationary phase was used for separation of selected 24 analytes. Enantioseparations were realized using two systems, high performance liquid chromatography and supercritical fluid chromatography. Effect of mobile phase composition was studied. Five different aditives (isopropylamine, diethylamine, triethylamine, trifluoroacetic acid, isopropylamine combined with trifluoroacetic acid) and their influence on enantioseparation were tested. Influence of two different modifiers (methanol, propan-2-ol) combined with all aditives was also tested in supercritical fluid chromatography system. The aim of this work was to find optimized composition of mobile phase which was suitable for separation of the analytes studied and to compare separation potential among all mobile phases and also between used separations systems. The supercritical fluid chromatography was shown to yield better results, i.e. better resolution in shorter analysis time. However examples of analytes better resolved under optimized conditions in high performance liquid chromatography system have also been found. Keywords (EN) Chirality, enantiomers, enantioselective separation, chiral stationary phase, high performance liquid chromatography, supercritical fluid chromatography.
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Studies of Lanthanide Complexes by a Combination of Spectroscopic Methods
Krupová, Monika ; Bouř, Petr (advisor) ; Kapitán, Josef (referee)
Studies of Lanthanide Complexes by a Combination of Spectroscopic Methods Monika Krupová (Department of Physical and Macromoecular Chemistry, Faculty of Science, Charles University in Prague) Since conventional structural analysis offers rather limited means for the chirality detection, a series of lanthanide tris-(β-diketonates) are investigated as effective receptors for a better chirality sensing in biomolecular substrates. These lanthanide complexes containing β-diketonate ligands are electrically neutral; they can further coordinate with various small organic molecules such as chiral alcohols, amino alcohols or amino acids in organic solvents and produce a strong chiral signal. Previously, a resonance in Raman scattering was observed in the studied systems due to the correspondence of europium electronic transition energy to the laser excitation wavelength, about a 100-fold signal enhancement if compared to non-resonant vibrational ROA was observed. This enabled shorter detection times as well as lower sample concentrations. In the current work, interaction of the Eu(FOD) complex with (R)- and (S)- enantiomer of 1-phenylethanol in n-hexane was studied using IR spectroscopy, Raman spectroscopy and Raman optical activity (ROA), UV-Vis spectroscopy and ultraviolet circular dichroism (UVCD). Only...
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Spektroskopické a teoretické studium supramolekulárních komplexů symetrických porfyrinů s chirálními guesty
Březina, Václav ; Hanyková, Lenka (advisor) ; Šoltésová, Mária (referee)
Certain types of porphyrins can be used as achiral agent for determination of enantiomeric excess (ee) of chiral molecules. Particular organic chiral molecule (guest) and porphyrin (host) form host-guest complex while inducing nonequiv- alency of particular proton resonances in symmetrical host. It causes splitting of NMR signals linearly dependent on ee of guest. In this work we investigated com- plexation of di-brombenzylated oxoporphyrin with chiral camphorsulfonic acid. NMR titration revealed that they form complex with 1:1 stoichiometry with as- sociation constant K ≈ 5 × 104 l/mol. We confirmed linear dependence of split- ting of host β-protons on ee of guest. Low temperature measurements revealed two conformations of host-guest complex with population around 0.7:0.3 (at −60 ◦ C). DFT quantum mechanical computations at BLYP/3-21G* level revealed also two conformations with population 0.79:0.21. NMR shifts were computed on this geometries with method GIAO/PBE1PBE/6-31G(2df,2pd) and compared to experimental values. 1
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Chiral recognition by mass spectrometry
Kosíková, Lenka ; Roithová, Jana (advisor) ; Bednář, Petr (referee)
Title: Chiral recognition by mass spectrometry Author: Bc. Lenka Kosíková Department: Department of Organic Chemistry Supervisor: doc. Mgr. Jana Roithová, Ph.D. This work is focused on the use of mass spectrometry as the analytical method for chiral recognition in the gas phase. We have examined formation of complexes (S and R) isomers [dimethyl-2,2'-dihydroxy-1,1'binaphthalene-3,3'-dicarboxylate] with sodium. Chiral effect for the fomation of sodium dimers is 1,34±0,06 and that for formation of trimers 2,38±0,22 in favor of the formation of homochiral complexes. Part of the work is devoted to the preparation of isotopically labeled ester [(R)-(−)- di(D3-methyl)-2,2'-dihydroxy-1,1'binaphthalene-3,3'-dicarboxylate]. Mixing of equimolar amounts of D3-(R) and unlabeled (S) isomers leads to the artificial racemate, while we can still distinguish the enantiomers using mass spectrometry. Another part represents the study of the complex formation between (S and R) isomers of [dimethyl-2,2'-dihydroxy-1,1'binaphthalene-3,3'-dicarboxylate] with the metal complex [(S,S)-1,5-diaza-cis-decalin]Cu(OH)I depending on the molar ratios in the solution. I have showed that the molar concetration of the catalyst in the solution plays an important role in the complex formation and that the ESI source spectra of...
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Determination of enantiomers of amino acids by HPLC
Michalčíková, Regina ; Janečková, Lucie (referee) ; Tesařová, Eva (advisor)
This Bachelor's thesis deals with determination of amino acids enantiomers, namely alanine in the experimental part, by high performance liquid chromatography using chiral stationary phases based on teicoplanin. The theoretical part is focused on summarizing the fundamental issue of chirality and chiral amino acids in foods, the characteristics of high-performance liquid chromatography, as one of the most appropriate methods to enantioseparation amino acids, and description of the methods of derivatization, which are used in determination of enantiomers of amino acids. The experimental part deals with the separation of alanine enantiomers, with the choice of the best separation system for the separation and determination of D-and L-alanine in fruit juice.
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Switching of spin vortices in magnetic nanodiscs
Hladík, Lukáš ; Pekárková, Jana (referee) ; Urbánek, Michal (advisor)
The diploma thesis deals with the switching of spin vortices in magnetic nanodisks. First, the basic concepts of (micro)magnetism are defined and existing theoretical and experimental achievements in the field of switching of the two basic characteristics (chirality and polarity) of magnetic vortex are summarized. Then the principle of dynamic switching of magnetic vortex chirality using in-plane magnetic field pulse with a well defined amplitude and duration is presented. There is no need to use a certain shape of nanodisks or asymmetry in magnetic field distribution. Nanostructures were prepared by the multi-step electron beam lithography and ion beam sputtering. Individual steps of sample preparation and optimization for the magnetization dynamics measurements are described. Finally, the experimental measurements of the dynamic switching of chirality on prepared samples obtained by transmission x-ray microscopy at the synchrotron Advanced Light Source at Berkeley, USA are presented and discussed.
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Chiral analysis of drug residuals in waste waters
Svobodová, Dagmar ; Opatřilová, Radka (referee) ; Čáslavský, Josef (advisor)
The theoretical part shortly describes chirality with focus on chiral pharmaceuticals. The processes of their absorption, distribution, metabolism and elimination in human body are discussed. These points are very important to understand possible fate of chiral drugs in the environment as there is only little data concerning their environmental behaviour. The occurrence and enantioselective toxicity of chiral drugs is also discussed here. One of the chapters describes non-steroidal anti-inflammatory drugs, as they are analyzed in the wastewater in the experimental part, and their occurrence in the environment. The experimental part describes optimization of the enantioselective HPLC method using Chiralpak AD as column for ibuprofen and ketoprofen. Reproducible separation of enantiomers wasn’t achieved for naproxen. Optimized methods were then applied for analysis of samples from municipal wastewater treatment plant in Brno-Modřice.
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Chirality and its importance in environmental organic analysis
Svobodová, Dagmar ; Friedl, Zdeněk (referee) ; Čáslavský, Josef (advisor)
This bachelor thesis is elaborated as literature search focused on the characterization of chirality and its importance for the environment. This work also gives review of the analytical methods and procedures aplicable for the chiral analysis of the organic pollutants. Obtained information showed that the importance of the chirality in the environmental chemistry is great. Individual enantiomers exhibit different toxicity and biological activity in the environment and therefore their monitoring by chiral analytical methods is essential.
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