Chemistry

The project will focus on the development of novel approaches for the sensitive detection of low-molecular-weight biomarkers in non-invasive biofluids such as sweat, saliva, and exhaled breath condensate (EBC). It will address the optimization of sampling and sample-preparation protocols to preserve analyte stability, minimize matrix interferences, and achieve sufficient sensitivity through effective preconcentration. Several preconcentration strategies will be explored, including isotachophoresis, solid-phase extraction, and transient isotachophoresis. The work will target multiple classes of clinically relevant analytes. For example, neurotransmitters are key chemical messengers of the nervous system, and their reliable quantification in biological samples is essential for improving neurological diagnostics. Although non-invasive matrices such as saliva and sweat offer clear advantages over blood or urine, they remain underexplored due to extremely low analyte concentrations. New analytical methods will therefore be developed for the determination of norepinephrine, epinephrine, and selected metabolites in saliva and sweat, with a particular focus on early-stage diagnosis of Parkinson s disease. Another application area will involve the selective preconcentration of biological thiols using gold nanoparticle-modified solid-phase extraction materials. The resulting data will be used to evaluate biologically and clinically relevant changes in analyte profiles. An integral part of the project will be the implementation of advanced data-analysis strategies for interpreting complex chemical information. The expected outcome is the development of sensitive, selective, and potentially miniaturizable analytical platforms suitable for non-invasive diagnostics. 

Literatura:

Itterheimová, P., et al. Use of metal nanoparticles for preconcentration and analysis of biological thiols. Electrophoresis 44 (2023) 135-157. 

Volánek et al. Capillary electrophoresis with laser induced fluorescence for the analysis of biological thiols in exhaled breath condensate after preconcentration using gold and gold-grafted magnetic nanoparticles. Talanta 297 (2026) 128550. 

Kubáň et al. Capillary electrophoresis with amperometric detection for neurotransmitter analysis: Principles, electrode materials, methodologies, and applications. Electrophoresis 2026, in press. 

Malá et al. 3D Printed Skin-Wash Sampler for Sweat Sampling in Cystic Fibrosis Diagnosis Using Capillary Electrophoretic Ion Ratio Analysis. Separations 5 (2021) 234. 

Dosedělová et al. A novel temperature-controlled open source microcontroller based sampler for collection of exhaled breath condensate in point-of-care diagnostics. Talanta 237 (2022) 122984.

Supervisor

doc. RNDr. Petr Kubáň, Ph.D.

The objective of this dissertation is to investigate the uptake, intracellular distribution, and accumulation of selected elements in biological cells at the single-cell level using advanced analytical techniques with high sensitivity and spatial resolution. The work will focus on characterizing heterogeneity between individual cells, understanding interactions of elements with cellular structures, and optimizing methodologies for reliable quantification.
Examples of doctoral projects:

• Optimization of an experimental model for investigating the cellular uptake of selected metals (Ni, Mn, Ti, Mo, Cr), including the establishment of suitable exposure conditions and analytical workflows.
• Quantification of the uptake of individual metals and comparison of their accumulation and intracellular distribution within cells.
• Investigation of the uptake of metal mixtures and evaluation of potential competitive, synergistic, or antagonistic interactions during their transport into cells.
• Assessment of the time-dependent behavior of metal uptake and description of the kinetics of intracellular accumulation under varying exposure durations.
• Identification and evaluation of compounds capable of inhibiting or reducing metal uptake into cells, both for individual metals and their mixtures.
• Examination of the influence of experimental conditions on metal uptake and determination of the key factors affecting this process.
• Contribution to the understanding of mechanisms governing metal transport into cells based on experimental observations, and proposal of possible mechanistic interpretations.

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 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 and cucurbiturils.
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 and biological activity is tested.
References:
1) S. S. Paul et al.  Revealing the effect of host–guest complementarity in supramolecular monofunctional platinum(ii) drugs. Inorg. Chem. Front. 2024, 11, 8510-8525.
https://doi.org/10.1039/D4QI02012J
2) M. Sojka et al.  Supramolecular Coronation of Platinum(II) Complexes by Macrocycles: Structure, Relativistic DFT Calculations, and Biological Effects. Inorg. Chem. 2021, 60, 17911-17925.
https://doi.org/10.1021/acs.inorgchem.1c02467
3) M. Sojka et al. Locked and Loaded: Ruthenium(II)-Capped Cucurbit[n]Uril-Based Rotaxanes with Antimetastatic Properties. Inorg. Chem. 2019, 58, 10861-10870. https://doi.org/10.1021/acs.inorgchem.9b01203.

Supervisor

prof. RNDr. Radek Marek, Ph.D.

V disertační práci budou studovány fyzikálně-chemické vlastnosti kovových komplexů vybraných ligandů ve vodných roztocích pomocí spektroskopických (UV/VIS/NIR/NMR), potenciometrických a jiných experimentálních metod. Také budou připraveny a izolovány koordinační sloučeniny v pevném stavu, které budou charakterizovány dostupnými experimentálními technikami a budou testovány na biologickou aktivitu. Molekulová struktura kovových komplexů budou teoreticky modelována s potenciálním využitím pro LFER korelaci fyzikálně-chemických parametrů za účelem vylepšení jejich biologické aktivity. Také budou studovány možností využití studovaných komplexů pro detekci a analýzu vybraných analytů. Disertační práce bude vypracována ve spolupráci s výzkumným týmem prof. Zuzany Vargové (Katedra anorganické chemie, Ústav chemických věd, Přírodovědecká fakulta, Univerzita Pavola Josefa Šafárika, Košice, Slovensko.

Supervisor

prof. RNDr. Přemysl Lubal, 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.

Collagen is the principal structural protein in the human body with a characteristic triple-helical tertiary structure. The prospective student will synthesize peptides that self-assemble into a collagen-like triple helix. The synthetic triple helices will be used to understand the properties of native collagen and/or will serve as artificial trimerization domains for a wide range of applications. For more details, see: https://fialalab.com/research/.

Supervisor

Mgr. Tomáš Fiala, Ph.D.

Within this research direction, our group develops methods for selective modification of proteins using purely synthetic probes. The prospective student will synthesize probes that recognize target proteins and introduce desired chemical modifications at specific amino acid residues. The probes are then used to address biological questions intractable with traditional biochemical approaches. For more details, see: https://fialalab.com/research/.

Supervisor

Mgr. Tomáš Fiala, Ph.D.

The development of high-performance electrochemical sensors is driven by the increasing demand for sensitive and selective detection in environmental monitoring, clinical diagnostics, and food safety. The performance of these devices is critically dependent on the architecture and composition of the functional sensing layers. This study focuses on the design and characterization of novel interfacial materials, such as nanomaterials, conducting polymers, or metal-organic frameworks to enhance electron transfer kinetics, molecular recognition and selectivity. We develop new methods of electrode modification, such as direct nanomaterial deposition using spark discharges, electropolymerization of novel monomers, the sensors are tested using a combination of voltammetric techniques, electrochemical impedance spectroscopy, and surface characterization methods.

1. Hernandez-Rodriguez, J; Trachioti, M; Hrbac, J; Rojas, D; Escarpa, A; Prodromidis, M, 2024: Spark-Discharge-Activated 3D-Printed Electrochemical Sensors. ANALYTICAL CHEMISTRY 96(25), p. 10177-10185, DOI: 10.1021/acs.analchem.4c01249.
2. Papavasileiou, A; Hoder, T; Medek, T; Prodromidis, MI; Hrbac, J, 2023: Sensitive riboflavin sensing using silver nanoparticles deposited onto screen-printed electrodes via controlled-energy spark discharges. TALANTA 258, 124409, DOI: 10.1016/j.talanta.2023.124409.
3. Novosad, D; Hrenakova, M; Vacek, J; Storch, J; Styskala, J; Hrbac, J, 2022: Cyclopentenedione-based ascorbate-rejecting permselective layers prepared by electropolymerization. JOURNAL OF ELECTROANALYTICAL CHEMISTRY 912, 116261, DOI: 10.1016/j.jelechem.2022.116261.
4. Riman, D; Prodromidis, MI; Jirovsky, D; Hrbac, J, 2019: Low-cost pencil graphite-based electrochemical detector for HPLC with near-coulometric efficiency. SENSORS AND ACTUATORS B: CHEMICAL 296, 126618, DOI: 10.1016/j.snb.2019.05.095.
5. Rozsypal, J; Riman, D; Halouzka, V; Opletal, T; Jirovsky, D; Prodromidis, M; Hrbac, J 2018: Use of interelectrode material transfer of nickel and copper-nickel alloy to carbon fibers to assemble miniature glucose sensors. JOURNAL OF ELECTROANALYTICAL CHEMISTRY 816, p. 45-53, DOI: 10.1016/j.jelechem.2018.03.039.

Supervisor

prof. RNDr. Jan Hrbáč, 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.