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Studium biologicky relevantních systémů v elektronicky excitovaných stavech
Zámečníková, Martina ; Soldán, Pavel (advisor) ; Bludský, Ota (referee) ; Nachtigallová, Dana (referee)
Very short lifetimes of excited states of isolated bases in nucleic acids, on the picosec- ond order, are believed to contribute to photostability of the genetic code. When embedded in DNA this behavior becomes more complex, mainly due to their inter- actions via stacking and hydrogen bonding. The DNA photophysiscs is not fully understood yet. It depends e.g. on the conformation and the character of excited states. The studies on smaller systems can help to improve the understanding of these phenomena. The aim of this work was to examine the dynamics of the excited states of the n → π∗ character of the complex of N-methylformamide dimer and two waters. The study was performed using non-adiabatic dynamics simulations with on-the-fly Surface Hopping algorithm based on the potential energy surfaces and non-adiabatic couplings obtained with multi-reference approach. The results show that after the vertical excitation into delocalized S2 state the system relaxes into S1 state within several tens femtoseconds. For majority of the population, the charac- ter of the state then oscillates between localized and delocalized during the whole course of the dynamics. Comparison with calculations with the waters removed in- dicates that the delocalization is caused by waters serving as a bridge between the two chromophores. 1
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Studium biologicky relevantních systémů v elektronicky excitovaných stavech
Zámečníková, Martina ; Soldán, Pavel (advisor) ; Bludský, Ota (referee) ; Nachtigallová, Dana (referee)
Very short lifetimes of excited states of isolated bases in nucleic acids, on the picosec- ond order, are believed to contribute to photostability of the genetic code. When embedded in DNA this behavior becomes more complex, mainly due to their inter- actions via stacking and hydrogen bonding. The DNA photophysiscs is not fully understood yet. It depends e.g. on the conformation and the character of excited states. The studies on smaller systems can help to improve the understanding of these phenomena. The aim of this work was to examine the dynamics of the excited states of the n → π∗ character of the complex of N-methylformamide dimer and two waters. The study was performed using non-adiabatic dynamics simulations with on-the-fly Surface Hopping algorithm based on the potential energy surfaces and non-adiabatic couplings obtained with multi-reference approach. The results show that after the vertical excitation into delocalized S2 state the system relaxes into S1 state within several tens femtoseconds. For majority of the population, the charac- ter of the state then oscillates between localized and delocalized during the whole course of the dynamics. Comparison with calculations with the waters removed in- dicates that the delocalization is caused by waters serving as a bridge between the two chromophores. 1
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Assessment of dispersion corrected density functional methods.
Hermann, Jan ; Bludský, Ota (advisor) ; Nachtigallová, Dana (referee)
The problem of dispersion interaction in the DFT is reviewed, followed by a systematic study of the behaviour, in particular the transferability, of the LAP method. Dispersion is a kind of van der Waals forces, dominant in important molecular systems such as biomolecules or adsorption systems. The DFT is an ever increasingly used method for modelling chemical sys- tems. However, dispersion is rendered rather poorly in the DFT. We give an illustration of the problem and present some known correction methods. One of them is the local atomic potential (LAP) approach which we develop further from its original formulation, and this enables us to exactly match the benchmark interaction curves. We apply this development on systems consisting of benzene and a noble gas. We construct the LAPs for noble gas atoms and for carbon. It is shown that the LAP approach is poorly transfer- able based on our calculations. The investigation reported in this bachelor's thesis represents the rst attempt for an detailed study of the behaviour of the LAP method.
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Accurate multireference calculations of electronic states and their selected properties for organic and bioinorganic molecules.
Chalupský, Jakub ; Havlas, Zdeněk (advisor) ; Straka, Michal (referee) ; Nachtigallová, Dana (referee)
Presented thesis is focused on the investigation of the lowest electronic states and some of their properties in the molecules lacking in closed-shell configuration. Thesis is divided into two parts - first part deals with biradicals, second with transition-metal compounds. In the first part, we show that the so far rarely observed inverse heavy-atom effect could be in methylcarbenes achieved by changing the substituent. While bromo substitu- tion of methylcarbene strengthens the spin-orbit coupling between S0 and T1 states, the presence of germyl group decreases SOC. According to our results, a decrease in SOC caused by the germyl group should reduce the probability of both radiationless and ra- diative S0/T1 transitions. We ascribe the qualitatively different effect of the substituents to absence of the lone pairs of GeH3 group and we show that the contributions of heavy atoms are mainly caused by interactions of their p orbitals. Moreover, inverse heavy-atom effect seems to be additive and multiple substitutions may lead to its strong enhance- ment. We further suggest new approach to possible measurement of the parity-violation effects in chiral molecules based on the electronic-energy shifts of the components of the lowest triplet of a biradical. It seems that the best candidates among systems studied...
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