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Development of a synthetic methodology for the preparation of advanced cycloarenes and their analogues
Bambas, Daniel ; Stará, Irena (advisor) ; Míšek, Jiří (referee)
This Bachelor's Thesis deals with a design and preparation attempts leading to building blocks suitable for macrocycle construction with further utilization in cycloarene synthesis. In Theoretical Background methods for preparation of [n]circulenes and kekulene-like structures are summarized with focus on the final ring-closing steps. In Results and Discussion chapter efforts to prepare the selected advanced building block as a starting compound for macrocyle construction whose transformation using [2+2+2] cyclotrimerization as a ring-forming reaction might provide the selected cycloarene are described. Part Proposed alternatives of synthesis and discussion of further approach is about future possible development of this study. Experimental Part provides practical information about undertaken experiments and characterizations of the prepared compounds.
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Simulation of processes in cellular membranes
Melcr, Josef ; Jungwirth, Pavel (advisor)
Simulation of processes in cellular membranes Abstract Many important processes in cells involve ions, e.g., fusion of synaptic vesi- cles with neuronal cell membranes is controlled by a divalent cation Ca2+ ; and the exchange of Na+ and K+ drives the the fast electrical signal transmis- sion in neurons. We have investigated model phospholipid membranes and their interactions with these biologically relevant ions. Using state-of-the-art molecular dynamics simulations, we accurately quantified their respective affinites towards neutral and negatively charged phospholipid bilayers. In order to achieve that, we developed a new model of phospholipids termed ECC-lipids, which accounts for the electronic polarization via the electronic continuum correction implemented as charge rescaling. Our simulations with this new force field reach for the first time a quantitative agreement with the experimental lipid electrometer concept for POPC as well as for POPS with all the studied cations. We have also examined the effects of transmembrane voltage on phospholipid bilayers. The electric field induced by the voltage exists exclusively in the hydrophobic region of the membrane, where it has an almost constant strength. This field affects the structure of nearby water molecules highlighting its importance in electroporation. 1
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Synthesis of cyclodextrin derivatives for organocatalysis
Chena Tichá, Iveta
Synthesis of cyclodextrin derivatives for organocatalysis This doctoral thesis examines the preparation of new cyclodextrin (CD) derivatives suitable for organocatalysis. The aim of this work is to prepare monosubstituted and disubstituted CD derivatives as organocatalysts for different types of enantioselective reactions potentially performed in water. In addition, disubstituted CD derivatives require considering the potential mixture of regioisomers and pseudoenantiomers. Thus, this thesis is divided into several sections - preparation of CD precursors and derivatives for organocatalysis, preparation of pure regioisomers and pseudoenantiomers of disubstituted CDs and final application of CD derivatives in enantioselective reactions. Furthermore, this thesis also focuses on the molecular modeling of the prepared CD derivatives and on their catalytic activity in silico. The first section covers the preparation of new disubstituted CD precursors as pure regioisomers for organocatalysts, specifically to develop a new method for the preparation of heterodisubstituted AC regioisomers on the primary rim of α-CD. This section also includes the determination of the regioisomer ratios of common α-CD intermediates disubstituted on the primary rim to evaluate their potential as precursors in organocatalysis....
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Simulation of processes in cellular membranes
Melcr, Josef ; Jungwirth, Pavel (advisor)
Simulation of processes in cellular membranes Abstract Many important processes in cells involve ions, e.g., fusion of synaptic vesi- cles with neuronal cell membranes is controlled by a divalent cation Ca2+ ; and the exchange of Na+ and K+ drives the the fast electrical signal transmis- sion in neurons. We have investigated model phospholipid membranes and their interactions with these biologically relevant ions. Using state-of-the-art molecular dynamics simulations, we accurately quantified their respective affinites towards neutral and negatively charged phospholipid bilayers. In order to achieve that, we developed a new model of phospholipids termed ECC-lipids, which accounts for the electronic polarization via the electronic continuum correction implemented as charge rescaling. Our simulations with this new force field reach for the first time a quantitative agreement with the experimental lipid electrometer concept for POPC as well as for POPS with all the studied cations. We have also examined the effects of transmembrane voltage on phospholipid bilayers. The electric field induced by the voltage exists exclusively in the hydrophobic region of the membrane, where it has an almost constant strength. This field affects the structure of nearby water molecules highlighting its importance in electroporation. 1
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Modelling Binding of Insulin Variants toward Insulin Receptor Based on Recent Structural Breakthroughs
Černeková, Michaela ; Lepšík, Martin (advisor) ; Biedermannová, Lada (referee)
Insulin receptor is a multi-domain signalling protein acting as a dimer. It comprises an extracellular ectodomain, a transmembrane domain and intracellular tyrosine kinase domain. Upon insulin binding, conformational changes in insulin as well as in insulin receptor occur and trigger the signaling cascade via the kinase domain. Abnormalities in insulin and insulin receptor function cause diabetes mellitus, a widespread disorder which can be consequence of genetic factors as well as lifestyle and is manifested by increased level of blood glucose. A common treatment of diabetes mellitus is via insulin analogues with different molecular properties. Insulin/insulin receptor interactions in the binding pocket are divided into two groups, so-called "site1" and "site2". The molecular details of the interactions in site1 are well known, while site2 residues are still not completely elucidated. It is important to shed light on the binding properties of insulin and insulin receptor, especially site2 interactions, because it could contribute to improved design of new insulin analogues. In this work, we used the very recent breakthroughs in the structural biology of insulin receptor to study the interactions by computational chemistry methods. It was thus possible to assess the noncovalent interactions and...
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Synthesis of cyclodextrin derivatives for organocatalysis
Chena Tichá, Iveta
Synthesis of cyclodextrin derivatives for organocatalysis This doctoral thesis examines the preparation of new cyclodextrin (CD) derivatives suitable for organocatalysis. The aim of this work is to prepare monosubstituted and disubstituted CD derivatives as organocatalysts for different types of enantioselective reactions potentially performed in water. In addition, disubstituted CD derivatives require considering the potential mixture of regioisomers and pseudoenantiomers. Thus, this thesis is divided into several sections - preparation of CD precursors and derivatives for organocatalysis, preparation of pure regioisomers and pseudoenantiomers of disubstituted CDs and final application of CD derivatives in enantioselective reactions. Furthermore, this thesis also focuses on the molecular modeling of the prepared CD derivatives and on their catalytic activity in silico. The first section covers the preparation of new disubstituted CD precursors as pure regioisomers for organocatalysts, specifically to develop a new method for the preparation of heterodisubstituted AC regioisomers on the primary rim of α-CD. This section also includes the determination of the regioisomer ratios of common α-CD intermediates disubstituted on the primary rim to evaluate their potential as precursors in organocatalysis....
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Synthesis of cyclodextrin derivatives for organocatalysis
Chena Tichá, Iveta ; Jindřich, Jindřich (advisor) ; Lhoták, Pavel (referee) ; Šindelář, Vladimír (referee)
Synthesis of cyclodextrin derivatives for organocatalysis This doctoral thesis examines the preparation of new cyclodextrin (CD) derivatives suitable for organocatalysis. The aim of this work is to prepare monosubstituted and disubstituted CD derivatives as organocatalysts for different types of enantioselective reactions potentially performed in water. In addition, disubstituted CD derivatives require considering the potential mixture of regioisomers and pseudoenantiomers. Thus, this thesis is divided into several sections - preparation of CD precursors and derivatives for organocatalysis, preparation of pure regioisomers and pseudoenantiomers of disubstituted CDs and final application of CD derivatives in enantioselective reactions. Furthermore, this thesis also focuses on the molecular modeling of the prepared CD derivatives and on their catalytic activity in silico. The first section covers the preparation of new disubstituted CD precursors as pure regioisomers for organocatalysts, specifically to develop a new method for the preparation of heterodisubstituted AC regioisomers on the primary rim of α-CD. This section also includes the determination of the regioisomer ratios of common α-CD intermediates disubstituted on the primary rim to evaluate their potential as precursors in organocatalysis....
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Simulation of processes in cellular membranes
Melcr, Josef ; Jungwirth, Pavel (advisor) ; Otyepka, Michal (referee) ; Tarek, Mounir (referee)
Simulation of processes in cellular membranes Abstract Many important processes in cells involve ions, e.g., fusion of synaptic vesi- cles with neuronal cell membranes is controlled by a divalent cation Ca2+ ; and the exchange of Na+ and K+ drives the the fast electrical signal transmis- sion in neurons. We have investigated model phospholipid membranes and their interactions with these biologically relevant ions. Using state-of-the-art molecular dynamics simulations, we accurately quantified their respective affinites towards neutral and negatively charged phospholipid bilayers. In order to achieve that, we developed a new model of phospholipids termed ECC-lipids, which accounts for the electronic polarization via the electronic continuum correction implemented as charge rescaling. Our simulations with this new force field reach for the first time a quantitative agreement with the experimental lipid electrometer concept for POPC as well as for POPS with all the studied cations. We have also examined the effects of transmembrane voltage on phospholipid bilayers. The electric field induced by the voltage exists exclusively in the hydrophobic region of the membrane, where it has an almost constant strength. This field affects the structure of nearby water molecules highlighting its importance in electroporation. 1
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Intramolecular and intermolecular interactions in proteins
Fačkovec, Boris ; Vondrášek, Jiří (advisor) ; Berka, Karel (referee)
Folding free energy of a protein is a delicate balance between stabilizing and destabilizing non-covalent itneractions. In this work, we decompose folding free energy into physically meaningful contributions, in which we aim to find general trends. Empirical potential is used to calculate interaction energy between all protein fragments, which are classified based on their dominant term in multipolar expansion. Calculations are done using 1200 non-redundant structures from PDB database. Based on the general trends found in interactions between these fragments, we attempt to better understand relationships between interaction energies calculated using computational chemistry methods and their corresponding free energy contributions on stabilization. 1
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