National Repository of Grey Literature 39 records found  1 - 10nextend  jump to record: Search took 0.00 seconds. 
Quantum mechanical study of the electron hoping processes of conjugated systems.
Tichý, Ondřej ; Burda, Jaroslav (advisor) ; Pittner, Jiří (referee)
In this thesis the electron hopping of selected heterocyclic compounds and selected carotenoids was studied using QM/MM simulations of excited states dynamics. Tully electron hopping and semiempirical methods OMx in combination with MRCI method was used in the simulations. Calculations were performed using Newton-X, MNDO99, MNDO2020 and Gromacs. The lifetimes of the excited states were estimated based on the simulations. The results showed that used methods correctly describes the time evolution of excited states of heterocyclic compounds. In case of carotenoids only deexcitation from first excited state was described correctly.
Violation and Conservation of Symmetries in Atomic Systems
Uhlířová, Tereza ; Zamastil, Jaroslav (advisor) ; Čížek, Martin (referee) ; Pittner, Jiří (referee)
This thesis focuses on the three pillars of any high-precision ab initio calculation: on the Hartree-Fock (HF) model, on the choice of a suitable basis set, and on the inclusion of electron correlation. We start with a study of singular properties of the HF model. Specifically, we sys- tematically investigate the stability of all atomic closed-shell systems up to xenon using a symmetry-adapted Thouless stability matrix. To obtain a global view on the stability of a particular isoelectronic sequence, we employ high-order perturbative method and then analyze the obtained series. This allows us to determine onsets of spin and orbital symmetry breaking. In addition, we also propose a physical meaning of the instabilities. In the next part of this thesis, we focus on the use of the Sturmian basis set for relativistic calculations. We propose a numerically stable algorithm for the evaluation of one- and two-electron matrix elements. Thus we defeat the major impediment of a wider use of this basis set in precise atomic structure calculations. The use of the proposed method and its significance is illustrated on a series of calculations. For instance, we evaluate the so-called parity non-conserving amplitude for cesium; this is a second-order property and thus greatly depends on the accuracy of the used wave...
Non-adiabatic molecular dynamics of photochemical processes accelerated by machine learning
Martinka, Jakub ; Pittner, Jiří (advisor) ; Sršeň, Štěpán (referee)
Nonadiabatic molecular dynamics is an important approach for the study of photochemical phenomena. Using a stochastic algorithm and a set of trajectories, it is possible to study phenomena where the Born-Oppenheimer approximation breaks down. This approach is limited by the size of the molecule and the length of time intervals that can be studied. Machine learning techniques, which have proven themselves in many different fields, can be a helpful tool. In this thesis, I focus on the applicability of a kernel ridge regression technique as a potential tool for accelerating nonadiabatic molecular dynamics simulations. Vinyl bromide is a small molecule with a heavy bromine atom, which from a computational point of view represents a suitable test system for nonadiabatic molecular dynamics with the inclusion of non-adiabatic and spinorbital couplings.
Aplication of explicitly correlated multi-reference coupled cluster methods
Lang, Jakub ; Pittner, Jiří (advisor) ; Fišer, Jiří (referee)
Nowdays, coupled cluster method belongs to one of the most used quantum chemical methods. However, the single-reference coupled cluster methods are not able to describe systems where the static correlation have an important role. Multireference coupled cluster methods developed in our group can describe both static and dy- namic correlation and can be used for problematic systems. Together with explicitly correlated wavefunction, which can properly describe the electronic cusp and speed up the convergence to the complete ba- sis set limit, they are able to calculate computationally demanding diradicals. Multireference CC calculations of tetramethylenethane have been perforemd and the performance of explicitly correlated version is discussed. Calculations of the isomerization of bicyclobu- tane using the multireference approach are presented as well. 1
Structure and dynamics of electronic defects in liquid water
Maršálek, Ondřej ; Jungwirth, Pavel (advisor) ; Horáček, Jiří (referee) ; Pittner, Jiří (referee)
Title: Structure and dynamics of electronic defects in liquid water Author: Ondřej Maršálek Institute: Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic Supervisor: prof. Mgr. Pavel Jungwirth, DSc. Supervisor's e-mail address: Abstract: In this thesis we present ab inito molecular dynamics simulations of two different electronic defects in water. Photoionization of liquid water produces a cationic hole, which undergoes ultrafast dynamics and forms the hydrated proton and the hydroxyl radical as its products. We study both the dynamics and spectroscopy of this process. The hydrated electron is a key intermediate in radiation chemistry of aqueous systems. We simulate its equilibrium properties in anionic water clusters as well as the dynamics of vertical electron attachment to cold and warm clusters. The hydrated electron reacts with a hydrated proton to form a hydrogen atom. We examine this reaction at a finite temperature in a larger cluster as well as in more detail in a smaller cluster. Because both of the electronic defects studied here are challenging open-shell species, we put emphasis on benchmarking and testing our computational setup. Six published articles are attached to the thesis. Keywords: density functional theory,...
Ab initio molecular dynamics with non-adiabatic and spin-orbit effects applied to time-dependent fluorescence
Pederzoli, Marek ; Pittner, Jiří (advisor) ; Mitric, Roland (referee) ; Gonzáles, Leticia (referee)
Ab initio molecular dynamics with non-adiabatic and spin-orbit effects applied to time-dependent fluorescence Marek Pederzoli1,2 1Charles University in Prague, Faculty of Science, Department of Physical and Macromolecular Chemistry, Hlavova 8, 12840 Prague 2, Czech Republic 2J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, 18223 Prague 8, Czech Republic Fluorescent probes are essential for many experimental techniques in biochemistry and microbiology. Accurate simulations of these molecules are theoretically challenging as they can involve conical intersections and intersystem crossings as well as interactions with the environment. This thesis is a compilation of papers dealing with development, implementation, and application of ab initio molecular dynamics techniques with non-adiabatic and spin-orbit interactions that can be used to model fluorescent probes not only in the gas phase but also in the complex molecular environment of biomembranes. Initial work involves a study of 9H-adenine using ab initio MD with non-adiabatic ef- fect using time-dependent density functional theory and two single reference methods CC2 and ADC(2). The central part of the thesis discusses the implementation of spin-orbit coupling into surface hopping dynamics with application to...
Multireference State-Specific Mukherjee's Coupled Cluster Method with Non-iterative Triexcitations.
Bhaskaran Nair, Kiran ; Pittner, Jiří (advisor) ; Noga, Jozef (referee) ; Fišer, Jiří (referee)
The multireference (MR) generalization of coupled cluster (CC) theory aims to describe both the static and the dynamic correlation accurately, as the standard CC method (at lower truncation levels) generally does not perform well when quasidegenerate boundary orbitals are encountered. The most promising among the MR Hilbert-space methods seems to be the state-specific MR Mukherjee's CC (MkCC) method, formulated by Mukherjee et al. [J. Chem. Phys. 110, 6171 (1999)], due to its rigorous size-extensivity and insensitivity to the intruder state problem. The main goal of this work was to include connected triples in the MkCC method. As the cost of the iterative triples limits its application, the main focus was on including triples non-iteratively. Two perturbative triples methods, namely MkCCSD(Tn) and MkCCSD(Tu) have thus been developed. For studying their accuracy, iterative triples methods (MkCCSDT and MkCCSDT-n) were also developed using the "linked" formulation. All these methods and an uncoupled version of MkCC (uMkCC) were implemented in the ACES II program. The assessment of these methods was performed on the O2, cyclobutadiene, methylene diradical, twisted ethylene, F2, BeH2 and tetramethyleneethane (TME) molecules. All these studies show that the inclusion of triexcitations improves the...
Structure, dynamics and reactivity of the hydrated electron
Uhlig, Frank ; Jungwirth, Pavel (advisor) ; Pittner, Jiří (referee) ; Sebastiani, Daniel (referee)
Structure, dynamics and reactivity of the hydrated electron Frank Uhlig In this work, one of the products of ionization of water, namely the hydrated electron, has been investigated. The hydrated electron is a key-intermediate in aqueous radiation chemistry. Although known to exist for over 50 years, its structure remained elusive and under discussion up to the present day. We show in this work, that we can obtain a faithful picture of the hydrated electron, its equilibrium structure, dynamics after attachment to water, and its reactivity, using ab initio methods. To this end, small cluster models and extended bulk and slab geometries of water including an excess electron have been investigated.

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