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PhD topics for academic year 2021/2022

Department of Organic Chemistry

Faculty of Chemical Technology

Calixarene analogues containing pyridine rings

Lhoták Pavel, prof. Ing. CSc. ( lho...@vscht.cz)
Design and synthesis of novel macrocyclic systems based on calixarene analogues, containing pyridine moieties within the skeleton. The study of their chemical behaviour, basic chemical transformations, and conformational preferences. The application of these novel macrocyclic systems in the design of novel receptors for the recognition of anions and/or neutral molecules (e.g. fullerenes).
Faculty of Chemical Technology

Calixarene analogues containing pyridine rings

Lhoták Pavel, prof. Ing. CSc. ( lho...@vscht.cz)
Design and synthesis of novel macrocyclic systems based on calixarene analogues, containing pyridine moieties within the skeleton. The study of their chemical behaviour, basic chemical transformations, and conformational preferences. The application of these novel macrocyclic systems in the design of novel receptors for the recognition of anions and/or neutral molecules (e.g. fullerenes).
Faculty of Chemical Technology

Carbohydrate-based ligands for lectin targeting

Ménová Petra, Ing. Ph.D. ( pet...@vscht.cz)
Mammalian carbohydrate receptors (lectins) are involved in a number of vital processes, including pathogen recognition, uptake and processing, cell communication and cell migration.
Targeted delivery of therapeutic nucleic acids to hepatocytes is an attractive strategy for the treatment of hepatitis B and prevention of hepatocellular carcinoma. The almost exclusive presence of the lectin asialoglycoprotein receptor (ASGPR) makes it an ideal gateway for hepatocyte-targeted therapy.
DC-SIGN is a lectin receptor found on the surface of immune cells, mainly dendritic cells and macrophages. It recognizes pathogens through the interaction with mannose-rich carbohydrates present in their glycocalyx. This interaction triggers the immune response, but is sometimes taken advantage of by certain pathogens to facilitate their spread in the host organism. Blocking this interaction has a high potential in the prevention of a number of diseases, including HIV or hepatitis C.
The aim of this thesis is to synthetize carbohydrate-based ligands specific for ASGPR and DC-SIGN. The ASGPR ligands will be attached to lipid nanoparticles and used for the delivery of CRISPR/Cas9 system into hepatocytes. The DC-SIGN ligands will be used to study ligand-protein interactions in order to get better understanding of these complex processes.
Faculty of Chemical Technology

Covalent catalysis with flavins

Cibulka Radek, prof. Ing. Ph.D. ( cib...@vscht.cz)
Flavins are natural compounds acting as cofactors in redox enzymes. The mechanism of transformations provided by flavoenzymes are known for several decades. Nevertheless, very recently, new principles of a substrate activation have been described. They are mainly based on covalent bonding of the substrate to the flavin moiety. Being inspired by these newly discovered enzymatic processes, new flavin artificial catalytic systems for application in organic synthesis will be designed. Main application will be in-situ umpolung of enolates.
Faculty of Chemical Technology

Covalent catalysis with flavins

Cibulka Radek, prof. Ing. Ph.D. ( cib...@vscht.cz)
Flavins are natural compounds acting as cofactors in redox enzymes. The mechanism of transformations provided by flavoenzymes are known for several decades. Nevertheless, very recently, new principles of a substrate activation have been described. They are mainly based on covalent bonding of the substrate to the flavin moiety. Being inspired by these newly discovered enzymatic processes, new flavin artificial catalytic systems for application in organic synthesis will be designed. Main application will be in-situ umpolung of enolates.
Faculty of Chemical Technology

Equilibrium and kinetics in mechanochemical processes

Krupička Martin, Ing. Ph.D. ( mkz...@gmail.com)
Synthetic organic mechanochemistry studies reactions induced by mechanical force, most importantly in ball mills. The experimental conditions are substantially different from the usual chemistry in solution. This allows studying the chemical processes equilibria and kinetics also under extreme conditions. The goal of the work is the application of mechanochemical procedures on organic transformations and reaction condition optimization.
Faculty of Chemical Technology

Fullerene complexation using higher calixarenes/thiacalixarenes

Lhoták Pavel, prof. Ing. CSc. ( lho...@vscht.cz)
The aim of this work is the design and synthesis of higher calixarenes (calix[5]arene and higher) that could be applied as receptors for the fullerene recognition. The aim of this work is to achieve selective complexation of C60 or C70 using suitably chemically modified calixarene skeletons and concave/convex principle of the interactions. Novel compounds will be used as receptors for the complexation of fullerenes and as the building blocks for construction of supramolecular self-assembly systems.
Faculty of Chemical Technology

Fullerene complexation using higher calixarenes/thiacalixarenes

Lhoták Pavel, prof. Ing. CSc. ( lho...@vscht.cz)
The aim of this work is the design and synthesis of higher calixarenes (calix[5]arene and higher) that could be applied as receptors for the fullerene recognition. The aim of this work is to achieve selective complexation of C60 or C70 using suitably chemically modified calixarene skeletons and concave/convex principle of the interactions. Novel compounds will be used as receptors for the complexation of fullerenes and as the building blocks for construction of supramolecular self-assembly systems.
Faculty of Chemical Technology

Heterogeneous catalysis on self-assembled organic semiconductors

Kovaříček Petr, Ing. Ph.D. ( kov...@vscht.cz)
Catalysis enable production of multitude of daily use products by lowering the energy barrier towards the formation of the desired product. In a particular subfield of catalysis on semiconductors, light as the cleanest energy source is converted into individual charge carriers, which then consequently trigger the catalytic transformation. The aim of this work is achieve photocatalysis on self-assembled organic semiconductors. Designing de novo a catalyst is a tedious task which tackles the challenges in order as they appear during the development process. Instead, in this work, the principles of combinatorial/dynamic chemistry and guided evolution of complex systems will be exploited to let the systems solve these issues on its own by several self-processes (assembly, sorting, organization). The performance of the developed systems will be tested on a few selected model reactions and potential leading structures will be a subject of dedicated studies.
Faculty of Chemical Technology

Heterogeneous catalysis on self-assembled organic semiconductors

Kovaříček Petr, Ing. Ph.D. ( kov...@vscht.cz)
Catalysis enable production of multitude of daily use products by lowering the energy barrier towards the formation of the desired product. In a particular subfield of catalysis on semiconductors, light as the cleanest energy source is converted into individual charge carriers, which then consequently trigger the catalytic transformation. The aim of this work is achieve photocatalysis on self-assembled organic semiconductors. Designing de novo a catalyst is a tedious task which tackles the challenges in order as they appear during the development process. Instead, in this work, the principles of combinatorial/dynamic chemistry and guided evolution of complex systems will be exploited to let the systems solve these issues on its own by several self-processes (assembly, sorting, organization). The performance of the developed systems will be tested on a few selected model reactions and potential leading structures will be a subject of dedicated studies.
Faculty of Chemical Technology

Chiral Triptycene- or [2.2]Paracyclophane-Based Fluorination Reagents

Rybáčková Markéta, Ing. Ph.D. ( ryb...@vscht.cz)
Kvíčala Jaroslav, prof. Ing. CSc. ( kvi...@vscht.cz)
Iptycenes and cyclophanes have found applications as molecular machines, in polymer chemistry, materials chemistry or catalysis. Triptycene is characterized by an unusual D3h symmetry and its derivatives can be chiral. Similarly, [2.2]paracyclophane derivatives are intriguing due to their planar chirality. This work aims at incorporating chiral triptycenes or [2.2]paracyclophanes into fluorination reagents (imidazole derivatives or hypervalent silicon compounds). The prepared compounds will be used to study chemo-, regio- and stereoselectivity in nucleophilic fluorinations.
Faculty of Chemical Technology

Chiral Triptycene- or [2.2]Paracyclophane-Based Fluorination Reagents

Rybáčková Markéta, Ing. Ph.D. ( ryb...@vscht.cz)
Kvíčala Jaroslav, prof. Ing. CSc. ( kvi...@vscht.cz)
Iptycenes and cyclophanes have found applications as molecular machines, in polymer chemistry, materials chemistry or catalysis. Triptycene is characterized by an unusual D3h symmetry and its derivatives can be chiral. Similarly, [2.2]paracyclophane derivatives are intriguing due to their planar chirality. This work aims at incorporating chiral triptycenes or [2.2]paracyclophanes into fluorination reagents (imidazole derivatives or hypervalent silicon compounds). The prepared compounds will be used to study chemo-, regio- and stereoselectivity in nucleophilic fluorinations.
Faculty of Chemical Technology

Mechanochemical indicators for optical spectroscopy

Krupička Martin, Ing. Ph.D. ( mkz...@gmail.com)
Mechanochemical indicators change its spectroscopic properties as a function of applied mechanical force. The goal of the thesis is to synthesize and study such indicators. Suitable molecules will be proposed, based on known chromophores and mechanophores and studied using quantum chemical methods. Selected molecules will be synthesized and studied with spectroscopic techniques with and without presence of mechanical force. Molecules allowing for measuring and quantification of mechanical force should be result of this work, together with theoretical model of its action.
Faculty of Chemical Technology

New methods of C-O bond activation for advanced cross-coupling reactions

Tobrman Tomáš, doc. Ing. Ph.D. ( tom...@vscht.cz)
Cross-coupling reactions are part of modern chemistry. During cross-coupling reactions, the starting material, which contains a reaction center (e.g., an activated C-O bond), is modified to the reaction product by the action of a suitable reagent in the presence of a catalyst. The aim of this work is to increase the atomic economy by cross-coupling reactions of substances with activated C-O bond. During the project, new types of reaction centers represented by activated C-O bonding will be designed. For these substances, the cross-coupling reaction will be conducted so as to selectively form two easily separable products.
Faculty of Chemical Technology

Nucleophilic Fluorination Reagents Based on Hypervalent Silicon Compounds

Kvíčala Jaroslav, prof. Ing. CSc. ( kvi...@vscht.cz)
Rybáčková Markéta, Ing. Ph.D. ( ryb...@vscht.cz)
Fluorinated compounds play irreplaceable role in pharmaceutical chemistry and agrochemistry, whereas still higher emphasize is given to enantiomerically pure compounds. While nucleophilic fluorination belongs to basic methods of the synthesis of fluorinated compounds, asymmetric fluorination of sp3 centres and fluorination of aromatic ring still remain a challenge regarding chemo-, regio- and stereoselectivity. As a part of joint bilateral project, the work is aimed in the synthesis and applications of new more efficient and selective reagents based on hypervalent silicon compounds or fluoroimidazolidines. Asymmetric modifications of the reagents will use with advantage new chiral [2.2]paracyclophanes and triptycenes. Apart of experimental organic chemistry, 19F and 29Si NMR spectroscopy, as well as computational chemistry will be applied for the study of the synthesized compounds.
Faculty of Chemical Technology

Nucleophilic Fluorination Reagents Based on Hypervalent Silicon Compounds

Kvíčala Jaroslav, prof. Ing. CSc. ( kvi...@vscht.cz)
Rybáčková Markéta, Ing. Ph.D. ( ryb...@vscht.cz)
Fluorinated compounds play irreplaceable role in pharmaceutical chemistry and agrochemistry, whereas still higher emphasize is given to enantiomerically pure compounds. While nucleophilic fluorination belongs to basic methods of the synthesis of fluorinated compounds, asymmetric fluorination of sp3 centres and fluorination of aromatic ring still remain a challenge regarding chemo-, regio- and stereoselectivity. As a part of joint bilateral project, the work is aimed in the synthesis and applications of new more efficient and selective reagents based on hypervalent silicon compounds or fluoroimidazolidines. Asymmetric modifications of the reagents will use with advantage new chiral [2.2]paracyclophanes and triptycenes. Apart of experimental organic chemistry, 19F and 29Si NMR spectroscopy, as well as computational chemistry will be applied for the study of the synthesized compounds.
Faculty of Chemical Technology

Rational design of flavin photocatalysts

Cibulka Radek, prof. Ing. Ph.D. ( cib...@vscht.cz)
Visible-light photocatalysis is in the forefront of interest as it allows new chemical transformations not accessible by conventional methodologies. One of the most promising classes of organic photocatalysts are flavins derived from prominent natural chromophores like FMN and FAD. General trends in photophysical and electrochemical properties will be studied in series of flavin derivatives with the aim to establish general approaches to design efficient, sustainable and stable flavin catalysts for applications in photoredox chemistry like C-H activations and photoreductions.
Faculty of Chemical Technology

Rational design of flavin photocatalysts

Cibulka Radek, prof. Ing. Ph.D. ( cib...@vscht.cz)
Visible-light photocatalysis is in the forefront of interest as it allows new chemical transformations not accessible by conventional methodologies. One of the most promising classes of organic photocatalysts are flavins derived from prominent natural chromophores like FMN and FAD. General trends in photophysical and electrochemical properties will be studied in series of flavin derivatives with the aim to establish general approaches to design efficient, sustainable and stable flavin catalysts for applications in photoredox chemistry like C-H activations and photoreductions.
Faculty of Chemical Technology

Synthesis of cytochalasan analogues with antimetastatic activity

Perlíková Pavla, Mgr. et Mgr. Ph.D. ( per...@vscht.cz)
Cytochalasans are natural compounds with interesting biological activities. Binding to a barbed ends of actin microfilaments is typical for all cytochalasans. Thanks to their interference with microfilament dynamics, some of natural cytochalasans showed antimetastatic activities. Antimetastatic activity is a key feature of so called "migrastatics", a new class of potential cancer therapeutics. In this PhD thesis, new analogues of cytochalasans will be designed and synthesized based on rational drug design and structure-activity relationship study will be performed. Then, the thesis will be focused on design and synthesis of cytochalasan prodrugs with improved water solubility.

Synthesis and Production of Drugs - Drugs and Biomaterials

Faculty of Chemical Technology

Synthesis of cytochalasan analogues with antimetastatic activity

Perlíková Pavla, Mgr. et Mgr. Ph.D. ( per...@vscht.cz)
Cytochalasans are natural compounds with interesting biological activities. Binding to a barbed ends of actin microfilaments is typical for all cytochalasans. Thanks to their interference with microfilament dynamics, some of natural cytochalasans showed antimetastatic activities. Antimetastatic activity is a key feature of so called "migrastatics", a new class of potential cancer therapeutics. In this PhD thesis, new analogues of cytochalasans will be designed and synthesized based on rational drug design and structure-activity relationship study will be performed. Then, the thesis will be focused on design and synthesis of cytochalasan prodrugs with improved water solubility.

Faculty of Chemical Technology

Synthesis of ligands for C-type lectin receptors

Ménová Petra, Ing. Ph.D. ( pet...@vscht.cz)
Mammalian carbohydrate receptors (lectins) are involved in a number of vital processes, including pathogen recognition, uptake and processing, cell communication and cell migration.
DC-SIGN is a C-type lectin receptor found on the surface of immune cells, mainly dendritic cells and macrophages. It recognizes pathogens through the interaction with mannose-rich carbohydrates present in their glycocalyx. This interaction triggers the immune response, but is sometimes taken advantage of by certain pathogens to facilitate their spread in the host organism. Blocking this interaction has a high potential in the prevention of a number of diseases, including HIV or hepatitis C.
The aim of this thesis is to synthetize D-mannose- and L-fucose-based ligands specific for DC-SIGN receptor. The synthesized ligands will be studied for their selectivity for different C-type lectin receptors. The ligands will be used to study ligand-protein interactions in order to get better understanding of these complex processes.
Updated: 29.11.2019 12:30, Author: Jan Kříž

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