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Electron-phonon Coupling in Finite Multi-chromophoric Systems
Herman, Daniel ; Mančal, Tomáš (advisor) ; Profant, Václav (referee)
Quantum systems in nature interact with other quantum systems, and these are examples of open quantum systems. In this work, we provide an introduction to the theory of open quantum system with a particular focus on the dynamics of molecular systems embedded in the protein environment, such as those found in photosynthetic antennas. We devote some time to the techniques of constructing equations of motion for the dynamics of a selected quantum system under the interaction with the bath, where we restrict ourselves to a finite number of degrees of freedom. We compare the exact calculation of the whole finite system with the results of approximate equations derived from an ansatz for the time evolution for the degrees of freedom of the bath part. We also reformulate the exact equations into a time non-local master equation using projection operator techniques, and we study the quality of results obtained with the modified quantum master equation. The time evolution of studied systems is also compared to the time evolution obtained by Schrödiger and Liouville-von Neumann equations. 1
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Quantum mechanical study of the electron hopingp rocesses of heterocyclic molecules.Simulation of absorption and emission spectra.
Tichý, Ondřej ; Burda, Jaroslav (advisor) ; Profant, Václav (referee)
This thesis is about computing lifetimes of excited states of molecules by using semiempirical methods in simulations of molecular dynamics. Pyrimidine nucleobases and three aza- derivatives were chosen as reference molecules. Simulations of molecular dynamics by program MNDO99 were performed with these molecules and static spectra were computed by programs Gaussian and Orca. All the examined molecules have femtosecond lifetimes of second excited states, pyrimidine nucleobases have also short lifetimes of first excited states in hundreds of femtoseconds. The computed first excited states of aza-derivatives have lifetimes in tens or hundreds of picoseconds and suggest that the higher stability of the states is related to the smaller number of amino groups attached to the ring.
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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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Vibrational optical activity of 3-aminoquinuclidine
Jílek, Štěpán ; Profant, Václav (advisor) ; Kaminský, Jakub (referee)
1 The bachelor thesis deals with the study of the chiral molecule 3-aminoquinuclidine (AQN), which is an important pharmacophore. The derivates of this molecule form a basis for several biologically important molecules and drugs: serotonin receptors activity modulators, agents displaying neuronal activity and medicaments supressing side effects of chemotherapy administration (antiemetics). AQN is a chiral molecule and information on its absolute configuration and enantiomeric purity is crucial to the use of AQN in drug synthesis. AQN contains both primary and tertiary amine group and depending on pH value it can be found in three differently charged forms. This thesis presents characterization of AQN utilizing methods of vibrational spectroscopy - infrared absorption and Raman scattering, together with their variants - vibrational circular dichroism (VCD) and Raman optical activity (ROA), all these in combination with quantum chemical simulations. The attention was paid to a choice of the suitable solvents and settings of experimental conditions. Based on pH dependent Raman spectral series we determined pKA dissociation constants associated with transitions between AQN's protonated states, which were further characterized by ROA and VCD. The properties of AQN in various phases (aqueous solution, crystalline...
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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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Structure and dynamics of peptides and proteins in solution: application of Raman optical activity
Profant, Václav ; Baumruk, Vladimír (advisor) ; Kapitán, Josef (referee) ; Setnička, Vladimír (referee)
The thesis inquires the specific and advantageous applications of Raman optical activity (ROA) in wide range of diverse structural and conformational studies of biomolecules and other biologically important molecules. Our investigation was focused on several interconnected topics covering the fields of methodology, basic and applied research. The combination of experimental and theoretical approaches facilitated deeper understanding of studied phenomena, and allowed for the effects of solute-solvent interactions. High-quality spectra of model molecules in the C-H stretching region, acquired as a result of successful extension of ROA measurements to the whole region of fundamental molecular vibrations, enabled verification and further development of methods for ROA spectra simulations encompassing anharmonic corrections. Utilizing spirodilactams with highly nonplanar amide groups, we have traced the specific ROA spectral manifestations of amide nonplanarity. In case of antimicrobial peptide lasiocepsine, we have successfully simulated ROA signals of S-S stretching vibrations which contrary to current belief do not seem to reflect sense of the S-S group torsion. In larger molecular systems, we have better understood the process of the formation of stable polyproline II conformation and proved that ROA may...
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Emergencies related with using narcotic and psychotropic substances in South Bohemian Region
PROFANT, Václav
I chose the topic "Emergencies related with using narcotic and psychotropic substances in South Bohemian Region" for my bachelor thesis. These events are extraordinarily dangerous and overall abuse drugs threatens the healthy development of the whole society. The main objective of empirical quantitative research was descriptively chart development trend of emergencies related with using narcotic and psychotropic substances in South Bohemian Region. Availability of literature to the topic was considerably limited. In the theoretical part I focused on theoretical background, basic concepts regarding with emergencies related with using narcotic and psychotropic substances. Further I wrote overview about the most famous abused drugs and their classification. At the end of this part I mention laws and regulations regarding drugs. The practical part consists of empirical quantitative research whose the main objective was descriptively chart development trend of emergencies related with using narcotic and psychotropic substances in South Bohemian Region. For the method I chose content analysis of the text which I made in a quantitative way. By determining statistical population of texts I analyzed official documents - public available official statistical data of criminality of Police of the Czech Republic and data provided of Police Presidium of the Czech Republic, Department of Computer Science and Information Technology Operation. The research survey in the term of 5 years - 2010 - 2015 I answered on a research problem, defined by using research questions. I concluded that some emergencies are trully committed under the influence of narcotics and psychotropic substances. The research demonstrated upward developmental trend of emergencies committed under the influence of narcotics and psychotropic substances. Finally I summarize the results of bachelor thesis and I recommend its use in practice.
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Cluster studies in molecular beams
Profant, Václav ; Kužel, Petr (referee) ; 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 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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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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