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Development and applications of molecular dynamics for molecular spectroscopy
Kessler, Jiří
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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The synthesis of π-electron systems suitable for transfer and retention of charges
Nejedlý, Jindřich
The aim of my Thesis was to develop a general synthetic methodology for the preparation of long helicenes equipped with suitable functional groups that control their solubility or serve as anchoring groups for attachment to metallic surfaces, especially gold. The well-established transition metal catalyzed [2+2+2] cyclotrimerization of triynes was selected as the key scaffold-forming transformation in the synthesis of long helicenes because of its high regioselectivity, atom efficiency, functional group tolerance and general robustness. A modular approach was used for the preparation of the starting oligoynes, thus enabling a high level of their structural diversity. Individual resorcinol- based aromatic building blocks were interconnected by Sonogashira cross-coupling reactions, providing complex cyclization precursors encompassing up to twelve alkyne units pre-arranged for the multiple [2+2+2] cycloisomerization to produce three six- membered rings from each set of three neighboring alkyne units. Thus, a small series of long helicenes with up to 19 rings constituting the helical scaffold was synthesized. The quadruple cyclization leading to the longest oxahelicene prepared to date was performed in a high-temperature-high-pressure flow reactor at 250 řC in the presence of CpCo(CO)2. The set of...
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The synthesis of π-electron systems suitable for transfer and retention of charges
Nejedlý, Jindřich ; Starý, Ivo (advisor) ; Tobrman, Tomáš (referee) ; Storch, Jan (referee)
The aim of my Thesis was to develop a general synthetic methodology for the preparation of long helicenes equipped with suitable functional groups that control their solubility or serve as anchoring groups for attachment to metallic surfaces, especially gold. The well-established transition metal catalyzed [2+2+2] cyclotrimerization of triynes was selected as the key scaffold-forming transformation in the synthesis of long helicenes because of its high regioselectivity, atom efficiency, functional group tolerance and general robustness. A modular approach was used for the preparation of the starting oligoynes, thus enabling a high level of their structural diversity. Individual resorcinol- based aromatic building blocks were interconnected by Sonogashira cross-coupling reactions, providing complex cyclization precursors encompassing up to twelve alkyne units pre-arranged for the multiple [2+2+2] cycloisomerization to produce three six- membered rings from each set of three neighboring alkyne units. Thus, a small series of long helicenes with up to 19 rings constituting the helical scaffold was synthesized. The quadruple cyclization leading to the longest oxahelicene prepared to date was performed in a high-temperature-high-pressure flow reactor at 250 řC in the presence of CpCo(CO)2. The set of...
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Synthesis and application of helicene-based N-heterocyclic carbene ligands
Gay Sánchez, Isabel ; Starý, Ivo (advisor) ; Veselý, Jan (referee) ; Pour, Milan (referee)
The aim of my PhD Thesis was to explore the potential of helically chiral N-heterocyclic carbene (NHC) ligands in asymmetric catalysis. Helicenes and helicene-like molecules are inherently chiral. Their application in this field has been rather limited. To date, only a few examples of enantiopure helically chiral NHCs have been described in the literature. Using a well-established method based on the diastereoselective metal catalysed [2+2+2] cycloisomerisation of centrally chiral triynes as the key step, I have synthesised a series of optically pure 2H-pyran based penta- and hexahelicenes bearing an amino group on the terminal benzene ring. The triynes were prepared by a sequence of Sonogashira and Mitsunobu coupling reactions using the commercially available (S)-but-3-yn-2-ol as the source of chirality. The resulting aminooxa[5]- and aminooxa[6]helicenes were then converted into the corresponding 1,3-disubstituted imidazolium salts, from which, upon deprotonation, the helically chiral N- heterocyclic carbenes were generated. To evaluate the performance of the new helically chiral ligands, the enantioselective Ni0 - catalysed [2+2+2] intramolecular cycloisomerisation of prochiral triynes to nonracemic dibenzohelicenes was chosen as a model reaction. All the synthesised imidazolium salts provided,...
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Algebraic approaches to elementary excitations in media with broken spatial or time-reversal symmetry
Erb, Kay Condie ; Hlinka, Jiří (advisor) ; Mokrý, Pavel (referee) ; Schranz, Wilfried (referee)
Title: Algebraic Approaches to Elementary Excitations in Media with Broken Spatial or Time-reversal Symmetry Author: Kay Condie Erb Institute: Institute of Physics of the Czech Academy of Sciences Supervisor: Ing. Jiří Hlinka, Ph.D., Institute of Physics of the Czech Academy of Sciences Abstract: Structural phase transitions with macroscopic symmetry breaking can be divided into 212 non-magnetic species according to the mutual spatial orien- tation of the point groups of both phases. Classification into the given species implies a set of universal transition properties such as the number of macroscopic domain states of the low-symmetry phase and their distinguishability by order parameter. In this work, the distinguishability of macroscopic domain states by all order pa- rameters which transform as vectors or vectorlike quantities (called bidirectors) was studied. For solving this task, a computer algorithm was designed which enabled an explicit listing of all vector and vectorlike order parameters, not only for the 212 non-magnetic species, but even for all 1602 magnetic species which includes transitions between crystallographic gray and bicolor point groups. In addition, irreducible representations of the 122 magnetic crystallographic point groups which transform as vectors or vectorlike quantities are...
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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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Photochemical Derivatization of Helicenes.
Jakubec, Martin
Helicenes are a class of polyaromatic compounds that have been increasingly studied over the past years. Their chirality, extended π-system and other intriguing characteristics make them worth exploiting in various fields of chemistry and material science.
Fulltext: content.csg -  PDF
Plný tet: SKMBT_C22019053108330 - PDF
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Development and applications of molecular dynamics for molecular spectroscopy
Kessler, Jiří
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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