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Analysis of vibrational spectra of selected environmental contaminants
Valášková, Martina ; Profant, Václav (advisor) ; Procházka, Marek (referee)
This bachelor thesis deals with the study of the vibrational spectra of melamine and thiram molecules using methods of Raman spectroscopy. Quantum chemical simulations are then used for a detailed interpretation of the measured spectra. Melamine is used as an industrial chemical in plastics and adhesives. However, its ingestion can lead to urinary bladder or kidney stones and, in extreme cases, cause death. Thiram is used as a fungicide and animal repellent, but it is toxic. The investigations included the variability of the Raman spectra of both contaminants in the polycrystalline and liquid phase and the spectra obtained by using the drop coating deposition Raman spectroscopy at different concentrations. 1
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Characterisation of polyproline I secondary structure by means of vibrational and chiroptical spectroscopy methods and quantum mechanical simulations
Vančura, Martin ; Profant, Václav (advisor) ; Hudecová, Jana (referee)
Our investigation was focused on a secondary protein structure called polyproline I. This helical structure has been known for a long time, but its occurrence and significance in nature is not yet fully known. In this thesis, we use Raman spectroscopy and chiral sensitive Raman optical activity. These methods are sensitive to the structure of proteins but are more informative and sensitive to the local arrangement than the commonly used ECD and UV absorption. We were able to obtain polyproline I Raman and ROA spectra that have not yet been published. We have described important differences between the spectra of polyproline I and II and observed the process of mutarotation. The experimental part of the work is supplemented by quantum chemistry calculations of spectra using the transfer of molecular property tensor. The calculated spectra corresponded very well with the experimental spectra.
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The thermodynamics of DNA-hairpin formation
Sgallová, Ráchel ; Římal, Václav (advisor) ; Profant, Václav (referee)
Serum response factor (SRF) is a transcription factor which binds to a highly conserved DNA sequence called the CArG box. According to the nucleotide sequence of CArG box it could form a hairpin structure or a cruciform. In this master thesis, the structure of the CArG box in a human gene c-fos was studied by nuclear magnetic resonance. 1 H spectra at temperatures 274{356 K, two-dimensional 1 H{1 H NOESY spectra, and two-dimensional 1 H{13 C HMBC spectra for DNA sequences with lengths of 12, 14 and 16 nucleoti- des were acquired. The thermodynamic parameters of formation of the secondary structure in the samples were determined from the measured temperature depen- dencies. The hairpin formation in the samples was con rmed based on the NOESY spectra and the lack of dependency of the melting temperature on concentration. The observed difference of the secondary structure from B-DNA could serve as a possible explanation of the high a nity of SRF to CArG box. 1
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Conformational transitions and stability of quadruplex nucleic acids
Johanovská, Zuzana ; Mojzeš, Peter (advisor) ; Profant, Václav (referee)
The work deals with guanine quadruplexes, i.e., non-canonical four-stranded structures of nucleic acids rich in repetitive guanine sequences with potential biological and nanotechnological significance. The first part summarizes basic information about the structure and topology of quadruplexes, in the second part, the present knowledge about the quadruplexes in vivo are overviewed. The third part is devoted to experimental methods used in the present study, namely Raman spectroscopy, circular dichroism, and absorption spectroscopy. The next sections are devoted to the acquisition and treatment of your own experimental results. Five sequentially related oligonucleotides differing in the bases in a single-member loop were investigated. The effect of concentration of oligonucleotide and potassium ions K+ on the stability of these quadruplexes was investigated by Raman spectroscopy, and an unusually high thermal stability was observed. Other experiments included measurements of CDs and absorption spectra at lower oligonucleotide concentrations, two different potassium ion concentrations, and a comparison of the stability of individual modifications with the previously published results. Furthermore, the possible interaction with the cationic porphyrin CuTMPyP4, similar to the interaction with the antiparallel...
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Cluster studies in molecular beams
Profant, Václav ; Dian, Juraj (advisor) ; Kužel, Petr (referee)
In the present work we study properties of clusters of small heteroatomic molecules with biological relevance by several experimental methods based on molecular beams. In the rst experiment structure and dynamics of size-selected charged pyrrole clusters have been studied by means of molecular beam scattering experiment. Small neutral P yn clusters were produced in Py/He expansions and larger mixed P ynArm clusters in Py/Ar expansions, and the scattering experiment with a secondary beam of He atoms was used to select the neutral clusters of dierent sizes. The complete size-selected fragmentation patterns for the neutral dimer to tetramer after an electron impact ionization at 70 eV from the measurements of the angular and velocity distributions at dierent fragment masses. In second experiment photolysis of size selected pyrrole, imidazole and pyrazole clusters has been investigated. Comparison with the photolysis of an isolated molecules and between studied systems has been made. Clusters were photolyzed at 243 and 193 nm and the kinetic energy distributions of the H-photofragments have been measured and analyzed. Finally the mass spectra of the fragments after multiphoton ionization have been measured. The signicant inuence of the cluster environment to the photolytic behavior was observed and discussed.
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Investigation of photodissociation dynamics implementing the velocity map imaging technique
Moriová, Kamila ; Fárník, Michal (advisor) ; Profant, Václav (referee)
The aim of this thesis is to investigate the effects of change in the chain length and chlorine group position on C-Cl bond photodissociation dynamics of chloroalkanes using the velocity map imaging (VMI) method. Three different chloroalkanes are studied (1-chloropropane, 2-chloropropane, 1-chloropentane) and compared with previously investigated chloromethane. Regardless of the parent chloroalkane, measured kinetic energy distributions (KEDs) of chlorine photofragments exhibit a single peak at energy around 0.8 eV. Photodissociation of higher chloroalkanes involves a recoil of a semi-rigid alkyl fragment, whose internal energy absorbs 40-60% of the total available energy. For chloromethane, however, only less than 10% of the available energy goes into the alkyl fragment excitation. Measured results of the energy partitioning are compared with cal- culations based on classical impulsive models. VMI experiment in combination with theory also yields information about the nature of electronic transition and probability of the intersystem crossing. Analysis indicates that the direct absorp- tion into the triplet state is more probable for the chloroalkanes with longer chain length, especially for the branched one. 1
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Vibrational optical activity of nucleotides and shorter nucleic acid segments
Jílek, Štěpán ; Profant, Václav (advisor) ; Kaminský, Jakub (referee)
1 Nucleotides are organic molecules that have a wide range of functions in living organisms. They participate in cell signaling, serve as cofactors of enzymatic reactions, play a central role in cellular metabolism, and are the basic monomeric units of nucleic acid polymers. Nucleotides consist of three subunit molecules - nitrogen nucleobase, a five-carbon sugar (ribose or 2'-deoxyribose), and a phosphate group containing one to three phosphates. The subject of this master thesis is the study of various nucleotides and their self-assemblies in water by means of vibrational spectroscopy - Raman scattering and its chirally sensitive variant Raman optical activity (ROA). ROA has the potential to provide new information about the structural arrangement, dynamics, and interactions of nucleotides, as it supposes to be much more sensitive to vibrations of its sugar part containing three to four chiral carbons, compared to Raman scattering. We study spectral manifestations associated with chemical modifications (difference between ribo- and deoxyribonucleotides, the influence of different phosphate positions) and the change of physical conditions (various charge states according to the set pH, effect of concentration, influence of ions). A substantial amount of work is devoted to studying the self-association of...
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Cluster studies in molecular beams
Profant, Václav ; Dian, Juraj (advisor)
In the present work we study properties of clusters of small heteroatomic molecules with biological relevance by several experimental methods based on molecular beams. In the first experiment structure and dynamics of size-selected charged pyrrole clusters have been studied by means of molecular beam scattering experiment. Small neutral Pyn clusters were produced in Py/He expansions and larger mixed PynArm clusters in Py/Ar expansions, and the scattering experiment with a secondary beam of He atoms was used to select the neutral clusters of dierent sizes. The complete size-selected fragmentation patterns for the neutral dimer to tetramer after an electron impact ionization at 70 eV from the measurements of the angular and velocity distributions at dierent fragment masses. In second experiment photolysis of size selected pyrrole, imidazole and pyrazole clusters has been investigated. Comparison with the photolysis of an isolated molecules and between studied systems has been made. Clusters were photolyzed at 243 and 193 nm and the kinetic energy distributions of the H-photofragments have been measured and analyzed. Finally the mass spectra of the fragments after multiphoton ionization have been measured. The significant inuence of the cluster environment to the photolytic behavior was observed and discussed.
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Characterisation of polyproline I secondary structure by means of vibrational and chiroptical spectroscopy methods and quantum mechanical simulations
Vančura, Martin ; Profant, Václav (advisor) ; Hudecová, Jana (referee)
Our investigation was focused on a secondary protein structure called polyproline I. This helical structure has been known for a long time, but its occurrence and significance in nature is not yet fully known. In this thesis, we use Raman spectroscopy and chiral sensitive Raman optical activity. These methods are sensitive to the structure of proteins but are more informative and sensitive to the local arrangement than the commonly used ECD and UV absorption. We were able to obtain polyproline I Raman and ROA spectra that have not yet been published. We have described important differences between the spectra of polyproline I and II and observed the process of mutarotation. The experimental part of the work is supplemented by quantum chemistry calculations of spectra using the transfer of molecular property tensor. The calculated spectra corresponded very well with the experimental spectra.
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