Chemie

Školitel: prof. Mgr. Jan Preisler, Ph.D.

OBJECTIVES: Use metal nanoparticles as labels for sensitive mass spectrometry imaging. The method allows detection of a single molecule on a tissue section.

EXAMPLES of doctoral projects:

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

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

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

- Study of nanoparticle transport efficiency in ICP MS. Confocal fluorescence or electron microscopy will be used as a reference method.

MORE INFORMATION: bart.chemi.muni.cz

Školitel: prof. Mgr. Jan Preisler, Ph.D.

OBJECTIVES: The dissertation projects focus on matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI MSI) for visualization of spatial distribution of biologically important compounds without chemical labelling.

EXAMPLES of doctoral projects:

- Development of sample preparation protocols for MALDI MSI. Samples may include 3D cell aggregates or other biological tissues.

- MALDI MSI of perifosine and other antitumor agents in 3D cell aggregates.

- Optimization of reactions on tissue sections. The aim will be, e.g., determination of double bond position in fatty acid chains in lipids.

MORE INFORMATION: bart.chemi.muni.cz

Školitel: Ing. František Foret, CSc.

Školitel: Mgr. Tomáš Vaculovič, Ph.D.

Development of methods based on:

a) labelling of antibodies by nanoparticles
b) preparation of molecularly imprinted polymers (MIP)

and their application for imaging of proteins in soft tissues.

Školitel: doc. Mgr. Karel Novotný, Ph.D.

Vývoj metod pro sledování prostorové distribuce prvků v různých materiálech na principu spektroskopie laserem buzeného plazmatu. Vývoj a optimalizace konfigurace a experimentálních parametrů sestavy na signál. Použití pokročilých chemmometrických postupů pro vyhodnocení naměřených dat.

Školitel: Mgr. Tomáš Vaculovič, Ph.D.

Development of conection of capillary electrophoresis with ICP. Application for analysis of nanoparticles.

Školitel: RNDr. Pavel Kubáň, DSc.

Experimentální část práce bude zahrnovat vývoj nových mikroextrakčních technik, které jsou založeny na selektivních přechodech analytů přes semi-permeabilní fázová rozhraní [1,2]. Při přechodu analytů bude využito difuze [1] nebo bude přechod urychlen účinkem elektrického pole [2]. Výsledné mikroextrakční techniky budou spojeny off-line nebo in-line s vhodnými analytickými metodami (primárně s kapilární elektroforézou) a adekvátnost takového spojení bude demonstrována analýzami biologicky, klinicky a toxikologicky významných analytů v reálných komplexních vzorcích jako je moč, krevní sérum/plasma a plná krev. [1] Kubáň, P., Boček, P., J. Chromatogr. A 1234 (2012) 2-8. [2] Kubáň, P., Šlampová, A., Boček, P., Electrophoresis 31 (2010) 768-785.

Školitel: doc. Mgr. Karel Novotný, Ph.D.

Vývoj technik umožňující selektivní detekci biomolekul značených kovovými nanočásticemi pomocí spektroskopie laserem buzeného plazmatu. Vývoj metod pro rychlou detekci biomolekul s vysokým prostorovým rozlišením a citlivostí.

Školitel: prof. RNDr. Radek Marek, 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.

Školitel: prof. RNDr. Jiří Pinkas, Ph.D.

OBJECTIVES: These dissertation projects will focus on the synthesis of new homometallic and heterometallic molecular and polymeric phosphonate complexes, their structural characterization, investigation of their magnetic properties, and reactivity. Also alumazene reactivity will be examined in addition and substitution reactions.

EXAMPLES of potential student doctoral projects:

- Synthesis of polynuclear molecular precursors of metal phosphates and silicates

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

- Studies of alumazene addition and substitution reactions

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.

Školitel: doc. Mgr. Jana Pavlů, Ph.D.

Jedním z možných předmětů práce je počítačové modelování elektronové struktury a stability vybraných fází pomocí metody FLAPW (Full-potential Linearized Augmented Plane Wave) nebo pseudopotenciálového kódu VASP (Vienna Ab initio Simulation Package). Získané informace o elektronové struktuře, energetických, magnetických a mechanických vlastnostech studovaného materiálu budou následně rozšířeny o studium poruch krystalové mříže a jejich vlivu na stabilitu a vlastnosti materiálů. Aktuálně řešené problémy se týkají stability nanokompozitů, hranic zrn a fázových rozhraní.

Kromě kvantově mechanického modelování je též možné se zabývat semiempirickým termodynamickým modelování fázových rovnovah a fázových diagramů pomocí metody CALPHAD (Computer Coupling of Phase Diagrams and Thermochemistry). Toto studium je zaměřeno na systémy obsahující intermetalické fáze, neboť tyto struktury vykazují specifické vlastnosti, které významným způsobem ovlivňují chování technologicky významných materiálů. Na základě znalosti stability intermetalických fází v závislosti na teplotě a složení bude možné předvídat chování studovaných systémů.

Informace o tvorných teplech vybraných fází vzhledem k standardním stavům čistých složek potřebné pro modelování pomocí metody CALPHAD je možné získat z kvantově-mechanických výpočtů, a proto je možné se v disertační práci věnovat oběma typům výpočtů.

Pro studium bude vybrána modelová kovová soustava.

Školitel: prof. RNDr. Libuše Trnková, CSc.

Understanding the chemistry of nitrogen bases, nucleosides and their phosphates, oligo- and polynucleotides (or even nucleic acids or regions thereof) is crucial for a number of important applications ranging from diagnostics to targeted drug development. Within the scope of the presented topic, systematic research of structural series of these compounds will be performed by electrochemical methods (voltammetry, RDE,EIS) in combination with independent approaches - spectrometric (UV-VIS, EPR, NMR, spectro-electrochemistry) and theoretical methods (quantum mechanical calculations – cooperation with Prague, JH Institute of Physical Chemistry). In particular, the aim is to understand (and model) the reaction mechanisms of the compounds and to determine the relationship between structure, redox properties and biological effect.

EXAMPLES of possible research student projects:

development of cheap unmodified and modified sensors (pencil graphite leads, compact disc - trodes, screen printed electrodes);

development of perspective electroanalytical methods, e.g., elimination voltammetry;

determination of proteins (e.g., insulin, trombin) by electro-catalyzing metal nanoparticles;

study of the structure-electrochemical activity of biomolecules (effect of methylation).

OTHER useful information: LABIFEL - Laboratoře biofyzikální chemie a elektrochemie - https://www.sci.muni.cz/labifel/

Školitel: prof. RNDr. Radek Marek, 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.

Školitel: doc. Mgr. Dominik Heger, Ph.D.

Compounds on ice: Ice and snow, the solid forms of water, are very interesting reaction media. Organic compounds are mostly expelled from the inside to the surface of ice and to the veins between ice crystals. We study the compounds in these compartments by absorption, emission, microscopy, and reactivity. These compartments differ from the original solution: the concentration of impurities increases, and the amount of available protons changes. Electrical potential is created on the interface between ice and the solution during freezing. The above facts strongly affect the frozen compounds, whether in natural or human-induced freezing. We investigate the spectroscopy, speciation and compartmentation of compounds on ice to describe ice - compounds interactions.

Školitel: doc. RNDr. Pavel Brož, Ph.D.

OBJECTIVES: The work will be aimed at research in the field of solid matters, such as e.g. metals, alloys, nanoparticles, nanostructured materials and others via combination of thermal analysis and Knudsen effusion mass spectrometry. The research will include study of thermodynamic properties and study of phase equilibria, such as phase transformation temperatures, heats of sublimation, thermal stability etc. As the properties are closely related to a phase structure of a given system under study, a complementary experimental and theoretical study of phase properties and phase equilibria via methods of electron microscopy and CALPHAD approach for phase equilibria and phase diagram calculations will be conducted.

EXAMPLES of possible research student projects:

Study of thermodynamic properties of selected solid systems

Study of heat of sublimation of selected solid systems

Study of thermal stability and surface effects on nanoparticles

Study of catalytic properties of selected nanoparticles

OTHER useful information:

Laboratory of thermal analysis and KEMS

Laboratory of nanoparticle synthesis

Research group of thermodynamic modelling of materials

PLEASE NOTE: before initiating the formal application process to doctoral studies, all interested candidates are required to contact doc. Pavel Broz (broz@chemi.muni.cz) for informal discussion.

Školitel: doc. Mgr. Markéta Munzarová, Dr. rer. nat.

Úkolem doktoranda bude prozkoumat povrch potenciální energie vybraných organických elektrocyklizačních reakcí metodou funkcionálu hustoty. Konečným cílem tohoto tématu je - na základě strutur a energií nalezených lokálních minim a tranzitních stavů - pochopit vlivy substituentů na stereochemické chování Diels-Alderových reakcí, vedoucích ke vzniku vybraných enedionů. Téma bude vedeno ve spolupráci s experimentální skupinou organické syntézy na Ústavu chemie PřF (Doc. Kamil Paruch, Dr. Jakub Švenda a Dr. Lukáš Maier).

Školitel: doc. RNDr. Pavel Brož, Ph.D.

OBJECTIVES: The work will be aimed at research in the field of advanced metal materials in various key areas such as thermoelectrics, hard and heat resistant alloys, lead free solders, nanoparticles, nanostructures and others. Experimental work will include preparation, characterisation and investigation of the materials properties as e.g. structure, thermal and phase properties, phase transformations etc. As the main methods, thermal analysis and Knudsen effusion mass spectrometry will be used. As complementary tools, methods of optical and electron microscopy will be utilized. Theoretical work will concern phase equilibria and phase diagram calculations based on semiempirical CALPHAD method, connected closely with the use of available ab-initio calculated energies of formation of phases.

EXAMPLES of possible research student projects:

Experimental and theoretical study of systems for perspective thermoelectric materials

Study of model systems for hard and heat resistant materials and thermodynamic description of phase equilibria

Study of thermodynamic behaviour and thermal stability of metal nanoparticles

Experimental and theoretical study of lead free-solder systems for high temperature application

OTHER useful information:

Laboratory of thermal analysis and KEMS

Research group of thermodynamic modelling of materials

PLEASE NOTE: before initiating the formal application process to doctoral studies, all interested candidates are required to contact doc. Pavel Broz (broz@chemi.muni.cz) for informal discussion.

Školitel: doc. Mgr. Jana Pavlů, Ph.D.

Jedním z možných předmětů práce je počítačové modelování elektronové struktury a stability vybraných fází pomocí metody FLAPW (Full-potential Linearized Augmented Plane Wave) nebo pseudopotenciálového kódu VASP (Vienna Ab initio Simulation Package). Získané informace o elektronové struktuře, energetických, magnetických a mechanických vlastnostech studovaného materiálu budou následně rozšířeny o studium poruch krystalové mříže a jejich vlivu na stabilitu a vlastnosti materiálů. Aktuálně řešené problémy se týkají stability nanokompozitů, hranic zrn a fázových rozhraní.

Kromě kvantově mechanického modelování je též možné se zabývat semiempirickým termodynamickým modelování fázových rovnovah a fázových diagramů pomocí metody CALPHAD (Computer Coupling of Phase Diagrams and Thermochemistry). Toto studium je zaměřeno na systémy obsahující intermetalické fáze, neboť tyto struktury vykazují specifické vlastnosti, které významným způsobem ovlivňují chování technologicky významných materiálů. Na základě znalosti stability intermetalických fází v závislosti na teplotě a složení bude možné předvídat chování studovaných systémů.

Informace o tvorných teplech vybraných fází vzhledem k standardním stavům čistých složek potřebné pro modelování pomocí metody CALPHAD je možné získat z kvantově-mechanických výpočtů, a proto je možné se v disertační práci věnovat oběma typům výpočtů.

Pro studium bude vybrána modelová kovová soustava.

Školitel: Mgr. Aleš Stýskalík, 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

Školitel: prof. RNDr. Jiří Pinkas, 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.

Školitel: prof. RNDr. Jiří Sopoušek, CSc.

OBJECTIVES: The aim of the research is to investigate the behaviour of advanced and newly prepared materials in the form of macro polycrystallic materials, nanoparticles, and nanocomposites. Research is mainly focused on the preparation of promising materials, their characterization and experimental study of phase diagrams and phase transformations. The experiment can be connected with thermodynamic modelling of equilibrium states (CALPHAD method) and simulation of diffusion-controlled processes in materials. Materials are prepared in the laboratories by methods of chemical synthesis. The aim is to synthesize new materials with high utility properties, functionalised nanostructures, and nanoparticles with properties enabling the introducing of new technologies (thermoelectrics, catalysis, sensors, diagnostics, ...).

EXAMPLES of student doctoral projects:

Thermodynamic assessment of the M-X-… chalcogenide system suitable for thermoelectric applications

Diffusion controlled phase transformations occurred in bimetallic M-N core-shell nanoparticles and their use in catalysis

The study of phase transformations of Me-X NPs by simultaneous thermal analysis.

Phase diagram calculations of M-X nanoparticles applied for hydrogen evolution.

Solvothermal synthesis of M-N Janus alloy nanoparticles

Microemulsion synthesis of sulphides of transition metals

The selection of materials to explore depends on the current grant support. However, a doctoral candidate proposal may be taken into account if the proposal is of significant scientific or application benefit and its realization is ensured.

More about research can be found on the websites:

Laboratory of nanoparticle synthesis

Laboratory of thermal analysis and KEMS

Research group of thermodynamic modelling of materials

PLEASE NOTE: before initiating the formal application process to doctoral studies, all interested candidates are required to contact prof. Jiri Sopousek (sopousek@mail.muni.cz) for informal discussion.

Školitel: prof. RNDr. Radek Marek, 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.

Školitel: Mgr. Jakub Švenda, PhD.

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

Školitel: doc. Mgr. Kamil Paruch, Ph.D.

Školitel: prof. Ing. Vladimír Šindelář, 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