Chemistry

The acoustic signal associated with the plasma formation during the Laser-Induced Breakdown Spectroscopy (LIBS) will be studied. Investigation of the frequency spectrum of the acoustic signal during ablation of various materials as well as study concerning the shot-to-shot evolution of the laser-induced crater morphology and plasma emission lines will be the main topic of this work. The previous results confirm that the acoustic signal is well correlated with the target hardness/density and also can be used as an ablation rate indicator. Acoustic signal provides new information relative to the ablation process that is independent of the LIBS spectrum.

Supervisor

doc. Mgr. Karel Novotný, Ph.D.

OBJECTIVES: Use inorganic and organic nanoparticles as labels for sensitive mass spectrometry detection. The method allows detection of a single molecule on a tissue section or another suitable substrate.

EXAMPLES of doctoral projects:

- Development of sample preparation protocol for specific detection of selected markers on sections of 3D cell aggregates, other tissues and substrates.

- Optimization of specific labelling with nanoparticles. The specificity will be based on antibody-antigen and avidin-biotin interactions, aptamer bindings, nucleic acid pairing etc.

- Development of nanoparticle detection schemes using inductively coupled plasma (ICP) and laser desorption/ionization (LDI) techniques.

- Study of nanoparticle transport efficiency in ICP MS. Confocal fluorescence and electron microscopy will be used as reference methods.

MORE INFORMATION: bart.chemi.muni.cz

Supervisor

prof. Mgr. Jan Preisler, Ph.D.

Supervisor

Ing. František Foret, DSc.

During this thesis the research will be devoted the development of LA-ICP-MS for quantification of elemental maps. Emphasis will be placed in particular on biological samples. Different calibration procedures will be tested to select the most appropriate procedure for quantification. Moreover, improving of laser spot diameter will be optimized with respect to reach sufficient limit of detection and lateral resolution.

Supervisor

doc. Mgr. Tomáš Vaculovič, Ph.D.

1. Prepare a literature survey on charged molecular silicon phosphates and phosphonates.
2. Synthesize new charged compounds containing Si-O-P bonds.
3. Characterize the molecular compounds by appropriate methods.
4. Apply the prepared molecules in heterogeneous catalysis with a special focus on reaction between carbon dioxide and epoxides.

Supervisor

Mgr. Aleš Stýskalík, Ph.D.

1. Prepare a literature survey on molecular silicon phosphates and phosphonates.
2. Synthesize new molecular compounds containing Si-O-P bonds.
3. Characterize the prepared molecules with appropriate methods.
4. Apply the molecular compounds in the synthesis of porous silicophosphate and silicophosphonate materials.

Supervisor

Mgr. Aleš Stýskalík, Ph.D.

Many transition-metal complexes are known to be biologically active. This applies particularly to coordination compounds containing platinum represented by clinical drugs cisplatin, carboplatin, and oxaliplatin. Highly promising compounds with antimetastatic potential contain ruthenium active core. We are working on the development of novel ruthenium and platinum coordination compounds containing anchors designed for binding with macrocyclic carriers from the family of cyclodextrins, cucurbiturils or calixarenes.
This project includes the synthesis of a series of mono and multinuclear, homo and heteroleptic metallocomplexes containing mono or polydentate ligands possessing hard or soft donor atoms. The molecular and supramolecular structures of compounds are characterized by using modern methods of NMR spectroscopy, ESI-MS, and ITC. Automatic crystallization robotics together with advanced crystallization techniques are employed to grow monocrystals and to reveal further structural details of complexes in the solid state by X-ray diffraction.
References:
1) Sojka, M.; Fojtu, M.; Fialova, J.; Masarik, M.; Necas, M.; Marek, R. Locked and Loaded: Ruthenium(II)-Capped Cucurbit[n]Uril-Based Rotaxanes with Antimetastatic Properties. Inorg. Chem. 2019, 58 (16), 10861-10870. https://doi.org/10.1021/acs.inorgchem.9b01203.
2) Chyba, J.; Novák, M.; Munzarová, P.; Novotný, J.; Marek, R. Through-Space Paramagnetic NMR Effects in Host-Guest Complexes: Potential Ruthenium(III) Metallodrugs with Macrocyclic Carriers. Inorg. Chem. 2018, 57 (15), 8735-8747. https://doi.org/10.1021/acs.inorgchem.7b03233.
3) Szymański, M.; Wierzbicki, M.; Gilski, M.; Jędrzejewska, H.; Sztylko, M.; Cmoch, P.; Shkurenko, A.; Jaskólski, M.; Szumna, A. Mechanochemical Encapsulation of Fullerenes in Peptidic Containers Prepared by Dynamic Chiral Self-Sorting and Self-Assembly. Chemistry - A European Journal 2016, 22 (9), 3148-3155. https://doi.org/10.1002/chem.201504451.

Supervisor

prof. RNDr. Radek Marek, Ph.D.

OBJECTIVES: These dissertation projects will focus on one of several possible topics. All of them are aimed at the synthesis and complete chemical and structural characterization of new molecules. The characterization will be based on advanced techniques, such as single-crystal X-ray diffraction, liquid and solid state NMR spectroscopy, IR and Raman spectroscopy, thermal analysis, magnetic measurements, and UV-vis spectroscopy. The actual thesis direction will be decided based on student's interest and discussion with the supervisor.

EXAMPLES of potential student doctoral projects:

- Synthesis of polynuclear molecular precursors of metal phosphates and silicates

Molecular building blocks are polyhedral molecules that mimic structural units present in zeolites, MOFs and other 3D networks. The aim of this project is to synthesize and structurally characterize new types of polynuclear molecular precursors that could be used to directed synthesis of framework metal phosphates and silicates.

- Synthesis of metallophosphonate molecular and polymeric complexes of 3d and 4f metals

This project will be directed at the synthesis of new polynuclear homometallic and heterometallic molecular and polymeric phosphonate complexes, their structural characterization, investigation of their magnetic properties, and reactivity.

- Studies of alumazene addition and substitution reactions

Alumazene is a heavy analogue of benzene, however, its chemical reactivity is quite different. This project will examine various reaction modes with suitable reagents, such as addition and substitution reactions, with the aim to isolate and characterize the new types of products.

PLEASE NOTE: before initiating the formal application process to doctoral studies, all interested candidates are required to contact Prof. Jiri Pinkas (jpinkas@chemi.muni.cz) for informal discussion.

Supervisor

prof. RNDr. Jiří Pinkas, Ph.D.

Tato disertační práce se bude zabývat přípravou materiálů nesoucích makrocykly bambusurilu. Práce se bude skládat ze syntézy derivátů bambusurilu obsahujících funkční skupiny a jejich připojení k různým materiálům prostřednictvím kovalentních vazeb. Bude testována schopnost připravených materiálů odstraňovat anionty roztoků.

This doctoral thesis will deal with the preparation of materials bearing bambusuril macrocycles. This thesis will consist of the synthesis of bambusuril derivatives containing functional groups and their attachment to different materials through covalent bonds. The resulting materials will be tested for their potency to remove anions from their solutions.

Supervisor

prof. Ing. Vladimír Šindelář, Ph.D.

OBJECTIVES: These dissertation projects will explore new routes to porous materials based on metallosilicates. The synthetic procedures will be based on non-hydrolytic sol-gel reactions. Developed procedures will be optimized with respect to maximizing surface area and pore volume and controlling chemical composition and catalytic activity in topical catalytic reactions (e.g. ethanol dehydration, ethanol to butadiene conversion, etc.).
EXAMPLES of potential student doctoral projects:

• Synthesis of aluminosilicates for ethanol dehydration
• Synthesis of metallosilicates for conversion of ethanol to 1,3-butadiene
• Synthesis of metal nanoparticles deposited on porous supports for ethanol dehydrogenation
• Synthesis of silicophosphates for ethanol dehydration

Further information at:
https://matchem.sci.muni.cz/laboratore/laborator-syntezy-materialu-a-jejich-prekurzoru-lamps

Supervisor

Mgr. Aleš Stýskalík, Ph.D.

OBJECTIVES: These dissertation projects will explore new routes to porous materials based on metal oxides, silicates, phosphates and phosphonates, as well as hybrid inorganic-organic materials. The synthetic procedures will be based on non-hydrolytic sol-gel reactions. Developed procedures will be optimized with respect to maximizing surface area and pore volume and controlling chemical composition, surface functionalities, and pore size. The reactions will be also directed towards obtaining aerogels by specific drying techniques.

EXAMPLES of potential student doctoral projects:

- Synthesis of aluminophosphates and phosphonates by non-hydrolytic sol-gel methods

- Synthesis of inorganic porous matrices

- Synthesis of hybrid materials with high porosity

- Preparation of calcium phosphates by nonhydrolytic methods

- Synthesis of inorganic materials by electrospinning

Further information at:

https://matchem.sci.muni.cz/laboratore/laborator-syntezy-materialu-a-jejich-prekurzoru-lamps

PLEASE NOTE: before initiating the formal application process to doctoral studies, all interested candidates are required to contact Prof. Jiri Pinkas (jpinkas@chemi.muni.cz) for informal discussion.

Supervisor

prof. RNDr. Jiří Pinkas, Ph.D.

Low solubility, biostability, and inefficient targeting of otherwise highly promising active pharmaceutical ingredients are often the limiting factors for their final approval for clinical use. We are developing a methodology to suppress these deficiencies by introducing a novel family of biocompatible macrocyclic carriers. The work consists of three main tasks: 1) the synthesis of covalent molecular capsules, 2) using these in analytical studies of their supramolecular host-guest interactions with selected drug candidates, and 3) carrying out further synthetic modifications of the capsules in order to fine-tune their affinity, activity, targeting, and release of drugs, which are based on results of complementary biological studies.

Supervisor

prof. RNDr. Radek Marek, Ph.D.

For highlights of our current research, please visit http://orgsyn.sci.muni.cz/

Supervisor

doc. Mgr. Jakub Švenda, PhD.

Student navrhne a provede syntézu nových organických sloučenin - potenciálních inhibitorů vybraných proteinových kináz. Nově připravené sloučeniny budou následně testovány ve spolupráci s interními a externími biologickými pracovišti.

Supervisor

doc. Mgr. Kamil Paruch, Ph.D.

Our group focuses on the development and photophysical studies of novel photochemically active compounds and fluorophores, emphasizing the use of photochemistry to solve some interdisciplinary problems in chemistry, biology, physics, and environmental sciences. The prospective student will use organic synthesis and physico-chemical tools in the course of his/her studies. The (photo)reaction mechanisms will be investigated using state-of-the-art techniques, such as nanosecond laser flash or femtosecond pump-and-probe spectroscopies. Web page: https://photochem.sci.muni.cz/

Supervisor

prof. RNDr. Petr Klán, Ph.D.

In 2010, our group discovered a new family of macrocyclic receptors, bambusurils. These macrocycles are priced for their ability to bind inorganic and organic anions in water and organic solvents. The PhD topic are aimed to develop synthesis of more complex bambusuril derivatives which can be used for applications including anion sensing, anion transmembrane transport, and development of molecular machine. More about research of our group can be found on the group website: Supramolecular chemistry group

Supervisor

prof. Ing. Vladimír Šindelář, Ph.D.

Student připraví pomocí organické syntézy (sestávající z více než 15 lineárních kroků) nové syntetické analogy přírodní sloučeniny forskolinu. Tyto nově připravené sloučeniny budou následně testovány - zejména na jejich schopnost (selektivně) aktivovat jednotlivé isoformy adenylylcykláz.

Supervisor

doc. Mgr. Kamil Paruch, Ph.D.

Development of novel coordination compounds of transition metals is stimulated by their broad applications in chemical catalysis, material science, and medical treatment or diagnosis. Understanding their chemical properties (stability, reactivity, formation of host-guest complexes) requires their molecular and electronic structure to be known. We use modern methods of NMR spectroscopy to investigate the above-mentioned systems in detail.
The presence of heavy metal atoms, open-shell character, conformational flexibility, and supramolecular interactions with binding partner must be carefully considered. Thus, the interpretation of NMR experiments requires synergy with various computational tools of quantum chemistry and molecular modelling. The general goal of this study is to apply developed methodology for the structure characterization of new metallocomplexes associated with various cavitands.
Selected references:
1) Novotny, J; Sojka, M; Komorovsky, S; Necas, M; Marek, R, 2016: Interpreting the Paramagnetic NMR Spectra of Potential Ru(III) Metallodrugs: Synergy between Experiment and Relativistic DFT Calculations. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 138(27), p. 8432-8445, DOI: 10.1021/jacs.6b02749.
2) Chyba, J; Novak, M; Munzarova, P; Novotny, J; Marek, R, 2018: Through-Space Paramagnetic NMR Effects in Host-Guest Complexes: Potential Ruthenium(III) Metallodrugs with Macrocyclic Carriers. INORGANIC CHEMISTRY 57(15), p. 8735-8747, DOI: 10.1021/acs.inorgchem.7b03233.
3) Novotny, J; Prichystal, D; Sojka, M; Komorovsky, S; Necas, M; Marek, R, 2018: Hyperfine Effects in Ligand NMR: Paramagnetic Ru(III) Complexes with 3-Substituted Pyridines. INORGANIC CHEMISTRY 57(2), p. 641-652, DOI: 10.1021/acs.inorgchem.7b02440.
4) Jeremias, L; Novotny, J; Repisky, M; Komorovsky, S; Marek, R, 2018: Interplay of Through-Bond Hyperfine and Substituent Effects on the NMR Chemical Shifts in Ru(III) Complexes. INORGANIC CHEMISTRY 57(15), p. 8748-8759, DOI: 10.1021/acs.inorgchem.8b00073.
5) Bora, PL; Novotny, J; Ruud, K; Komorovsky, S; Marek, R, 2019: Electron-Spin Structure and Metal-Ligand Bonding in Open-Shell Systems from Relativistic EPR and NMR: A Case Study of Square-Planar Iridium Catalysts. JOURNAL OF CHEMICAL THEORY AND COMPUTATION 15(1), p. 201-214, DOI: 10.1021/acs.jctc.8b00914.

Supervisor

prof. RNDr. Radek Marek, Ph.D.