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Chemie

Chemie

Doctoral programme, Faculty of Chemical Engineering
CHYBI CHARAKTERISTIKA PROGRAMU

Cílem doktorského studijního programu Chemie je vzdělávat vysoce kvalifikované odborníky s teoretickými znalostmi a praktickými dovednostmi z oblasti analytické a fyzikální chemie. Absolventi tohoto programu budou připraveni na samostatnou vědeckou práci ve výzkumných institucích, na univerzitách nebo v praxi v oblasti analytické chemie léčiv, forenzní analytické chemie, analytické chemie a jakostního inženýrství, technické fyzikální chemie, termodynamiky, kvantové chemie, chemické fyziky, membránového inženýrství atd.

Careers

Absolvent studijního programu Chemie získá hluboké interdisciplinární teoretické i praktické znalosti v oboru analytické a fyzikální chemie, bude zvládat a vyvíjet experimentální techniky a kvalifikovaně ovládat přístroje odpovídající jeho specializaci díky nabytým teoretickým a praktickým znalostem principů a možností jejich použití. Osvojená metodologie vědecké práce, moderní laboratorní a výpočetní techniky, pokročilé metody aplikované matematiky a statistiky spolu s jazykovými a softskills dovednostmi zajistí absolventovi odpovídající personální růst, zvýšenou prestiž ve společnosti a lepší postavení na trhu práce.

Programme Details

Language of instruction Czech
Standard length of study 4 years
Form of study Full time + Combined
Guarantor of study programme doc. Ing. Vladimír Setnička, Ph.D.
Programme Code D402
Place of study Praha
Capacity 25 students
Number of available PhD theses 41
Recommended Curriculum Apply

List of available PhD theses

Ab initio photodynamics in condensed phase: Method development and applications

Department: Department of Physical Chemistry, Faculty of Chemical Engineering
Also available in programme: Molekulární chemická fyzika a senzorika

Annotation

Computational photodynamics is a fast evolving field. At present, we are able to simulate ultrafast porcesses in medium-sized molecules. This Thesis focuses on developement and applications of photodynamical methods describing light-induced processes in condensed phase. For more information, see http://photox.vscht.cz/

Analysis of drugs and counterfeit pharmaceuticals using vibrational and chiroptical spectroscopy

Department: Department of Analytical Chemistry, Faculty of Chemical Engineering

Automated study of photochemical mechanisms

Department: Department of Physical Chemistry, Faculty of Chemical Engineering
Also available in programme: Molekulární chemická fyzika a senzorika

Annotation

The thesis will focus on mechanisms of organic reactions in both the ground and excited states. Ab initio techniques and methods of ab initio molecular dynamics will be used. It is anticipated that new computational techniques will be developed, in attempt to automatize the search for key aspects of reaction mechanisms.

Computer simulations of critical phenomena

Department: Department of Physical Chemistry, Faculty of Chemical Engineering

Annotation

This work addresses the problem of critical phenomena using computer simulations. The critical phenomena are ubiquitous in nature and are of great interest not only in natural sciences but also in everyday situations such as social networks. The characteristic features of the critical phenomena is a presence of strong fluctuations, long-ranged correlations and system self-similarity, which thus exhibits signs of deterministic chaos. All these features make any theoretical attempt for a description of such systems a daunting task. Computer simulations are thus a vital tool which can be used both for a description of critical systems or as a "referee" assessing predictive capability of approximative theories.

Degradation of organic compounds fixed in the cement matrix

Department: Department of Analytical Chemistry, Faculty of Chemical Engineering

Determining the human race and other specific attributes using a chemical analysis of human scent

Department: Department of Analytical Chemistry, Faculty of Chemical Engineering

Annotation

Basic patterns in molecular compositions of human scent samples determining the ethnical origins and other attributes (age, illnesses etc.) of people will be investigated.

Development of methods for examination of heavy metals in microplastics

Department: Department of Physical Chemistry, Faculty of Chemical Engineering
Theses supervisor: prof. Dr. RNDr. Pavel Matějka

Annotation

The subject of this thesis will be the study and development of the methodology for monitoring sorption processes between heavy metals and microplastics, which are increasingly present in water, even drinking and packaged. In general, plastics contain heavy metals from technological processes. Moreover, they are also able to bind these metals from the environment and serve as their vectors. Hence, the ability to describe adsorption and desorption appears to be crucial in studying the toxic potential of microplastics in the environment and human health. The following analytical methods will be used for the study of sorption processes: optical microscopy, infrared and Raman spectroscopy, tip-enhanced Raman spectroscopy, scanning electron microscopy, inductively coupled plasma mass spectrometry and secondary ion mass spectrometry to monitor both organic and toxic heavy metals ions.

Development of new composite materials for efficient adsorption and gas separation

Department: Department of Analytical Chemistry, Faculty of Chemical Engineering
Also available in programme: Chemistry

Annotation

High greenhouse gas production has a negative impact on the environment. Therefore, the development of new separation technologies with enhanced efficiency and low capital cost is an emerging demand in the near future. Separation, adsorption and storage of greenhouse gases, in particular CO2 and the recovery of H2 or CH4 as energy sources are of paramount importance for the further development of society. The project is focused on the preparation, characterization and use of advanced materials for the capture and separation of gases, mainly CO2. One possibility is to use dendrimers, a class of synthetic macromolecules with a regular and highly branched structure, characterized by a large interior space and a large number of functional groups on the surface. These properties of dendrimer can lead to an increase in the adsorption capacity and selectivity of the new material. The work includes experimental determination of adsorption capacity and separation efficiency of newly prepared materials for selected gases.

Exploring the fundamental molecular interactions modulating glycocalyx bioactivity

Department: Department of Analytical Chemistry, Faculty of Chemical Engineering

Annotation

Glycocalyx or extracellular matrix is a charged thick layer of biomacromolecules, which is bound to the membrane at the cell surface. It is constituted fundamentally of polymeric-sugars, proteins, and the underlying membrane. Although the molecular structure of glycocalyx is directly responsible for many functions and pathologies, it is far from being understood. In this project, we have the ambitious goal of getting a more in-depth insight into the molecular interactions between fundamental components of the glycocalyx, e.i., sugar–sugar, sugar–protein, sugar–membrane. This project mainly focuses on computational methods(Molecular and Quantum mechanics). The students are also expected to do complementary experimental work, primarily spectroscopic methods (e.g., Raman, Fluorescence, and NMR) but also other physical chemistry technics (e.g., measurements of osmotic coefficients).

Gas transport study in graphene oxide and carbon nanotubes based membranes

Department: Department of Physical Chemistry, Faculty of Chemical Engineering
Also available in programme: Chemistry
Theses supervisor: doc. Ing. Karel Friess, Ph.D.

Annotation

Membrane separation processes (MSP) belong to the modern technologically significant separation methods. Furthermore, MSP are less economical demanding and more eco-friendly industrial processes compared to the conventional separation techniques used in chemical, petrochemical, pharmaceutical and food industries. The most significant industrial applications of MSP for gas separation are focused on separation of helium from natural gas, separation of hydrogen from hydrocarbons, carbon monoxide or nitrogen and also for removing carbon dioxide from biogas or organic vapors from air. Generally, graphene oxide (GO) based membrane materials belong to the modern and dynamically growing group of materials that have many interesting properties. Especially, this work will be targeted on GO based separation of hydrogen from carbon dioxide. Our laboratory is focused on the topic of membrane separation for more than 15 years. Currently, we participate in two grant projects of the GA CR aimed at increasing the efficiency of membrane separation processes. This doctoral thesis is thematically linked to these projects. The thesis will be focused on the study of theoretical and experimental aspects of the transport of gases and their mixtures in GO and polymer based membranes.

High resolution microwave spectroscopy of complex organic molecules

Department: Department of Analytical Chemistry, Faculty of Chemical Engineering

Annotation

Subject of this thesis is focused on measurements of the advanced high-resolution rotation spectra of complex organic molecules and subsequently on quantum mechanics interpretation of experimental data in terms of the Hamiltonian matrix elements.

How does the presence of water influence the properties of functionalized ionic liquids

Department: Department of Analytical Chemistry, Faculty of Chemical Engineering
Also available in programme: Chemistry
Theses supervisor: Ing. Magdalena Bendová, Ph.D.

Annotation

Functionalization of ionic liquids has extensively been studied over the past two decades because of their application potential in various fields of chemistry. However, unequivocal knowledge of structure-property relationships for ionic liquids and a good understanding of their interactions with molecular solvents are still far from being established. In this work, mixtures of various functionalized ionic liquids with water will thus be studied in terms of their phase equilibria and intermolecular interactions. Phase equilibria will be studied both by synthetic and dynamic methods, whereas the molecular structure at ambient temperature will be investigated by a range of diffraction and spectroscopic methods.

Identification and quantification of various drug forms using THz spectroscopy

Department: Department of Analytical Chemistry, Faculty of Chemical Engineering

Annotation

Advanced Terahertz Spectroscopy which is able to measure special vibrational transitions reflecting the weak inter- and intra-molecular interactions, makes also possible to recognize various polymorphic forms of pharmaceuticals. By this technique, the different procedures of the drug fabrications (counterfeits), ageing etc. can be examined.

Identification of biomarkers of cancer and degenerative diseases via molecular spectroscopy of biofluids

Department: Department of Analytical Chemistry, Faculty of Chemical Engineering

Individual and class identifications of persons based on digitally encoded human scent signatures

Department: Department of Analytical Chemistry, Faculty of Chemical Engineering

Annotation

Subject of this thesis is focussed on detailed analyses of human scent samples using GCxGC-TOF, on their digitizing and, above all, on the development of advanced olfactronic methods of individual as well as class identifications of persons.

Interaction of selected tracers with cementitious materials

Department: Department of Analytical Chemistry, Faculty of Chemical Engineering

Investigation of the relationship between amorphous solid dispersion physical stability and polymer functionality: experimental and theoretical predictions

Department: Department of Physical Chemistry, Faculty of Chemical Engineering
Also available in programme: Chemistry
Theses supervisor: prof. Ing. Michal Fulem, Ph.D.

Isolation of biologically active compounds from Sutherlandia and identification of their molecular structure

Department: Department of Analytical Chemistry, Faculty of Chemical Engineering
Also available in programme: Chemistry

Annotation

Sutherlandia plants have been identified as being useful in the treatment of various diseases. The aim of this work is to isolate new biologically active substances, to identify their molecular structure using high-resolution NMR and MS, and to describe their biological activity in cooperation with screening centres.

Machine Learning in Computational Spectroscopy

Department: Department of Physical Chemistry, Faculty of Chemical Engineering
Also available in programme: Molekulární chemická fyzika a senzorika

Annotation

Artificial intelligence and machine learning approaches have recently witnessed a massive development in various fields of science and technology. In the suggested thesis, the candidate will apply these techniques into the field of computational spectrsocopy with a focus on electronic spectroscopies. For more information, see http://photox.vscht.cz

Mass spectrometry imaging of bioactive compounds

Department: Department of Analytical Chemistry, Faculty of Chemical Engineering
Theses supervisor: doc. Dr. RNDr. David Sýkora

Annotation

The work will be directed to the development and optimization of MALDI mass spectrometry imaging (MSI) methods for visualization of drugs and lipids in tissue slices of laboratory mice and rats. Various methods of sample preparation procedures will be evaluated and compared. The optimized methods will be used to characterize changes in lipid composition in mouse models of neurodegeneration. The influence of potential novel neuroprotective drugs on the lipid content and composition versus controls will be also evaluated.

Microscopic description of interfacial phenomena

Department: Department of Physical Chemistry, Faculty of Chemical Engineering

Annotation

The work is of a computational nature and its purpose is to study interfacial phenomena from the microscopic perspective, i.e. from the knowledge of inter-molecular interactions in the given system. The main task is to study conditions under which a thick liquid film nucleates at a surface of a solid substrate and how its width grows (and eventually diverges) depending on external parameters. In particular, one of the crucial targets to be addressed is the dependence of the film growth on the surface geometry and details of the microscopic interactions. These predictions are not only of high fundamental interest but are also relevant in modern technologies, such as micro- and nanofluidics.

Modeling of ultrafast processes in radiation chemistry

Department: Department of Physical Chemistry, Faculty of Chemical Engineering
Also available in programme: Molekulární chemická fyzika a senzorika

Annotation

The enormous experimental development allows for a direct study of electron photoemission from water and solutions. New, hithertho unknown phenomena have emerged. The Intermolecular Coulomb Decay represents one example. The new phenomena can give rise to novel spectroscopies or to application in radiooncology. The proposed Thesis will focus on the exploration of these phenomena, using the methods of quantum theory of molecules and molecular simulations. For more information, see http://photox.vscht.cz/

Modelling of solvated electrons properties in polar solvents

Department: Department of Analytical Chemistry, Faculty of Chemical Engineering

Molecular Simulations of Atmospheric Aerosols

Department: Department of Physical Chemistry, Faculty of Chemical Engineering
Also available in programme: Molekulární chemická fyzika a senzorika

Annotation

Atmosphere of Earth is a unique chemical reactor. Light induced reactions play a prominent role in the intiation of many important chemical reactions. Many of the atmospheric processes also take place within heterogeneous processes, e.g. on the surface of aerosols or dust particles. The project focuses on theoretical modeling of chemical and photochemical processes in the stratosphere and in the troposhere. The whole toolbox of theoretical methods will be used within the project. For more information, see http://photox.vscht.cz/

Molecular modeling of PETase – a unique plastic-degrading enzyme

Department: Department of Physical Chemistry, Faculty of Chemical Engineering

Annotation

PETase is an interesting enzyme with a unique plastic-degrading ability. It was discovered in 2016, but since then more than ten crystal structures have been published and its potential applications under different reaction conditions are extensively studied. PETase mainly degrades polyethylene terephthalate (PET), the efficiency of such process depends on the solvent which surrounds the enzyme and the plastic particles. In addition, it is possible to enhance the PETase activity by mutations. It has been also shown, that thanks to mutations, it can gain ability to degrade other plastics. By means of classical molecular dynamics simulations we will study the structure and flexibility of PETase and its selected mutants under different reaction conditions. The QM/MM methods will be used to describe the reaction mechanism in details. The project will be realized in collaboration with Center for Nanobiology and Structural Biology in Nové Hrady. The results of the study will provide deeper understanding of the PETase function and they could lead to the design of better reaction conditions or mutants with higher catalytic efficiency.

Molecular modeling of proteins in crowded environment

Department: Department of Physical Chemistry, Faculty of Chemical Engineering

Annotation

Cellular environment contains large amounts of macromolecules, none of them is present in high concentration, but overall, we call the environment crowded, because macromolecules occupy about 40 % of the volume of the cells. Proteins are frequently studied only in aqueous solutions with presence of other macromolecules both in vitro and in in silico. However, including these crowding agents is required for realistic description, because they influence the overall stability of proteins, preference of more compact conformations, association constants and rates of diffusion. By means of classical molecular dynamics simulations we will study citrate synthase, which possesses open and closed conformation, in aqueous solutions of dextrane, polyethyleneglycole and other crowding agents. The project will be realized in collaboration with Center for Nanobiology and Structural Biology in Nové Hrady. The results of the study will provide deeper understanding of the effects of crowding agents on the structure and stability of this enzyme.

Molecular simulations of electrode-electrolyte interface

Department: Department of Physical Chemistry, Faculty of Chemical Engineering
Also available in programme: Molekulární chemická fyzika a senzorika

Annotation

The thesis will focus on theoretical study of the interfaces between the electrode material and electrolytes. Extremely concentrated electrolytes will be studied as well, especially in the context of novel energy sources. The work will include techniques of quantum chemistry and statistical mechanics. For more information, see http://photox.vscht.cz/

New nanostructured composite membranes for selective gas separation

Department: Department of Physical Chemistry, Faculty of Chemical Engineering
Also available in programme: Chemistry
Theses supervisor: doc. Ing. Karel Friess, Ph.D.

Annotation

Membrane separation processes (MSP) belong to the modern technologically significant separation methods. Furthermore, MSP are less economical demanding and more eco-friendly industrial processes compared to the conventional separation techniques used in chemical, petrochemical, pharmaceutical and food industries. The most significant industrial applications of MSP for gas separation are focused on the separation of helium from natural gas, separation of hydrogen from hydrocarbons, carbon monoxide or nitrogen and also for removing carbon dioxide from biogas or organic vapours from the air. Generally, single-wall carbon nanotubes (SWCNT) and graphene oxide (GO) based membrane materials belong to the modern and dynamically growing group of materials that have many interesting properties. Especially, this work will be targeted on SWCNT-GO-based separation of hydrogen from carbon dioxide or from other gases. Our laboratory is focused on the topic of membrane separation for more than 15 years. Currently, we participate in two grant projects of the GA CR aimed at increasing the efficiency of membrane separation processes. This doctoral thesis is thematically linked to these projects. The thesis will be focused on the study of theoretical and experimental aspects of the transport of gases and their mixtures in GO and polymer-based membranes.

Physico-chemical properties of model electrolytes for next-generation energy storage devices

Department: Department of Physical Chemistry, Faculty of Chemical Engineering

Annotation

Following current trends in electrochemical technology research, this PhD project will deal with systematic investigations towards safe, sustainable and high-performance electrolyte media for next generation rechargeable batteries and supercapacitors. It will focus on experimental determination of essential physico-chemical properties for some prospective water-in-salt electrolyte (WiSE) mixtures and elucidation of the behavior observed. Solubility and phase transitions of selected lithium and sodium salts in water and model water/cosolvent mixtures will be examined, to delimit the homogenous liquid domains. Chemical, electrochemical and thermal stability of the WiSE formulations will be explored and their water activity, density, viscosity, and ion conductivity measured as functions of composition and temperature, these properties being then correlated and analyzed in terms of suitable models. Computation chemistry methods will also be employed, to get insight into molecular background of the observed behavior.

Preparation of solid surfaces with a molecular receptor covalently anchored, and studies of their usability in sensors construction

Department: Department of Analytical Chemistry, Faculty of Chemical Engineering
Also available in programme: Chemistry

Annotation

The aim of this work is to modify the chemical structure of molecular receptors functional in solution so that they can be covalently attached to a solid surface or prepare a polymer. Study the functionality and usability of such materials for sensor construction.

Solubility of gases in non-volatile liquid media

Department: Department of Physical Chemistry, Faculty of Chemical Engineering
Theses supervisor: doc. Ing. Karel Řehák, CSc.

Annotation

Knowledge of the gas solubility in non-volatile liquid media is important in various application spheres. These may be the solubility of carbon dioxide or methane in aqueous salt solutions, which are important for geological storage of carbon, oil extraction or desalination of seawater. It may also be the solubility of nitrogen and air in the electrolyte solutions that are considered in the construction of batteries. Experimental determination of gas solubility usually does not cover a wide range of possible conditions - temperatures, pressures and composition, so it is advisable to have suitable calculation tools to predict or extrapolate data with reasonable accuracy. The subject of this work is experimental determination of solubility of gases in non-volatile solvents (e.g. in ionic liquids) or in electrolyte solutions and study of possibilities of relevant thermodynamic description and prediction.

Speciation analysis of selenium in microorganisms used in food industry

Department: Department of Analytical Chemistry, Faculty of Chemical Engineering
Theses supervisor: prof. Ing. Oto Mestek, CSc.

Spectroscopic Studies of Protein Fibrils

Department: Department of Analytical Chemistry, Faculty of Chemical Engineering
Also available in programme: Chemistry
Theses supervisor: prof. RNDr. Petr Bouř, CSc.

Annotation

Many biological processes involve aggregation of proteins into insoluble aggregates, "fibrils". Their properties are studied, for example, to prevent neurodegenerative diseases limiting human live time. We use optical spectroscopic, computational and other methods to understand basic principles of fibril behavior and structure. Particular aim of the thesis is to develop measurement and interpretation procedures for the modern spectroscopy of Raman optical activity, the topic involves spectroscopic experiments as well as computational modeling.

Spectroscopic studies of sugar-lectin interactions

Department: Department of Analytical Chemistry, Faculty of Chemical Engineering
Theses supervisor: prof. RNDr. Petr Bouř, CSc.

Annotation

Lectins are carbohydrate-binding proteins that control various functions in living organisms including the cell-cell interaction, inflammatory and immune response, fertilization, adhesion and virulence of pathogens. Particularly galectins (defined by their binding specificity for galactosides) are in the center of many research studies as immune checkpoints in pathogenesis, or tumor progression and metastasis. The ability to design new galectin inhibitors that would suppress these negative processes envisages not only understanding the carbohydrate-lectin structure but also requires knowing the conformational behavior of the inhibitor in an unbound state. In the thesis, we propose to prepare carbohydrate conjugates bearing metal tags that allow us to measure paramagnetic NMR pseudo-contact shifts (PCS) and circularly polarized luminescence (CPL) sensitive to the conformation and to close environment. The interpretation of the experiment is not straightforward and theoretically based predictions will be developed, to understand the spectral parameters.

Structure and reactions of solvated electron

Department: Department of Physical Chemistry, Faculty of Chemical Engineering
Also available in programme: Molekulární chemická fyzika a senzorika

Annotation

Solvated electron is an interesting redox species. Hydrated electron, i.e. the electron solvated in water, is a short living transient species (picosecond lifetime). It turns out that the solvated and presolvated electron play a major role in radiation damage of biomolecules and in atmospheric chemistry. The subject of the proposed Thesis is the interaction of high energy radiation and the research of solvated electron fomration and reactivity. For more information, see http://photox.vscht.cz/

Studies of new forms of vibrational optical activity

Department: Department of Analytical Chemistry, Faculty of Chemical Engineering
Theses supervisor: prof. RNDr. Petr Bouř, CSc.

Annotation

Analytical methods of molecular optical activity provide unique information about molecules in solution. However, interpretation of some experiments is a challenging process involving many aspects of molecular dynamics, physics and quantum chemistry. We will focus on new phenomena, such as enhanced vibrational circular dichroism, Resonance Raman optical activity and anharmonic vibrational bands.

Study of changes in material on the clay cement interface

Department: Department of Analytical Chemistry, Faculty of Chemical Engineering

Study of porphyrin derivatives of Tröger and spiro-Tröger bases enabling recognition of cancer cells and photodynamic therapy

Department: Department of Analytical Chemistry, Faculty of Chemical Engineering
Also available in programme: Chemistry

Annotation

A major problem in the treatment of cancer is the recognition of healthy cells from cancer and the selective removal or killing of cancer cells. Several substances that are used for visual diagnosis and photodynamic treatment are from the group of porhyrin and chlorine derivatives. The aim of this work is to prepare porphyrin, chlorine and bacteriochlorin derivatives of Tröger and spiro-Tröger bases and to study their usefulness for selective recognition of cancer cells and subsequent photodynamic therapy.

Surface enhanced fluorescence as a tool for nanotransporter localization in a cell

Department: Department of Analytical Chemistry, Faculty of Chemical Engineering
Also available in programmes: Chemistry, Molekulární chemická fyzika a senzorika
Theses supervisor: doc. Ing. Kamil Záruba, Ph.D.

Annotation

The project will deal with the development of fluorescence analysis methods for reliable detection of the localization of drug nanocarrires in a living cell. Although fluorescence methods show favorable detection limits in many cases, many organic fluorescent substances exhibit toxicity even at very low concentrations. Current methods of fluorescence microscopy make it possible to monitor the localization of practically individual nanoparticles that have penetrated the cell membrane into the cell. Surface-enhanced fluorescence that occurs near metallic nanoparticles may allow the detection of fluorescent substances at such low concentrations that allow the application of completely non-toxic (low) doses of the preparations to study the chemical behavior of living cells in the presence of these transporters.

The application of microspectroscopic and near-field techniques for drug development

Department: Department of Physical Chemistry, Faculty of Chemical Engineering
Theses supervisor: prof. Dr. RNDr. Pavel Matějka

Usage of lanthanide complexes for spectroscopic studies of DNA structure

Department: Department of Analytical Chemistry, Faculty of Chemical Engineering
Theses supervisor: prof. RNDr. Petr Bouř, CSc.

Annotation

Circularly polarized luminescence (CPL) of lanthanides is sensitive to the local molecular environment, which can be used in biomolecular science. So far, however, only a few CPL applications in DNA studies have been reported. We will try to overcome some restraints of the methodology, such as by using a Raman optical activity (ROA) spectrometer to measure CPL spectra. This will make it possible to use lanthanide aqua-ions as non-invasive DNA probes in concentrations not distorting DNA structure. We expect to establish a connection between CPL and ROA spectral features and specifics of DNA structures.


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