Annotation of PhD topics

Graphene and Graphene Derivatives (for Fischer stipend)

Supervisor: prof. RNDr. Michal Otyepka, Ph.D.

Graphene is without any doubt an extraordinary material. Some of its properties (hydrophobicity, zero band-gap, low chemical reactivity), however, limit its application potential, e.g., in electronics and biosensing. We seek for new preparation routes for tailored graphene modifications. The modification can be achieved via covalent as well as noncovalent approaches (Chem. Rev., 112(11), 6156-6214, 2012). The framework topic focuses on development of alternative routes for synthesis of graphene derivatives, on understanding of mechanism of chemistries of carbon 2D materials and understanding of physical-chemical properties of graphene derivatives. The aims will be fulfilled via experimental (synthesis, characterization via e.g., HRTEM, SEM, AFM, XPS, and sensing, and (electro)catalytic applications) or computational (DFT, advanced DFT and post-HF) methods and simulation (all-atom and coarse-grained molecular dynamics simulations) techniques. The particular topics will be focused on design, synthesis, and characterization of new graphene derivatives with tailored properties (e.g., magnetic, electronic, dispersability etc.), understanding on the strength and nature of noncovalnet interactions to graphene and graphene derivatives etc. The topic is supported by ERC grant.

Advanced nanomaterials for heterogeneous catalysis, photocatalysis and electrocatalysis (for Fischer stipend)

Supervisor: prof. RNDr. Radek Zbořil, Ph.D.

Nanomaterials offer a great application potential in catalytic reactions due to the small size and a high fraction of surface atoms enabling to achieve higher rate constants and better selectivity compared to microcrystalline counterparts. Their efficiency would be further enhanced by combination of various nano-species creating so called hybrid or integrated catalysts. The aim of this research topic is the development of such hybrid nanoarchitectures including core-shell nanostructures, magnetically separable catalysts, micro-mesoporous hybrids and N-doped carbon systems and their applications in selected organic, photocatalytic and electrocatalytic reactions.

Hybrid nanostructures for photoelectrochemical water splitting (for Fischer stipend)

Supervisor: prof. RNDr. Radek Zbořil, Ph.D.

Solar-powered water splitting is a central technology for the realization of a sustainable economy based on clean and renewable energy vectors such as hydrogen (H2). The overall reaction (2H2O → 2H2 + O2) is endothermic (E = 1.23 V vs RHE) and consists of two half reactions: 2H+ + 2e → H2 (HER, E°red = 0.0 V) and 2H2O + 4h → O2 + 4H+ (OER, E°ox = 1.23 V). Adopted semiconductors should ideally absorb photons with energies higher than 1.23 eV and feature conduction band (ECB) and valence band (EVB) edges that straddleE°red and E°ox, respectively. However, though CB and VB may have appropriate energies, unavoidable potential losses and kinetic overpotentials imply that 1.6–2.4 eV is the actual energy necessary to sustain the overall water splitting. Such a severe thermodynamic and kinetic restriction explains why a semiconductor able to efficiently drive the overall reaction has yet to be identified. Transition metal oxides rarely meet the criteria of an Eg suitable for sunlight activation, or of favorable band edges relative to E°red and E°ox. Thus, the well renowned earth abundant materials potentially stable in the long-term, such as TiO2, α-Fe2O3, WO3, BiVO4, etc. still represent the most viable option for PEC applications. However, the intrinsic limitations of these materials still have to be addressed. There are several viable options to increase the PEC water splitting efficiency including (i) 1D material nanostructuring, to overcome the short hole diffusion length and prevent the photogenerated charge recombination; (ii) engineering of multi-component hybrid nanostructures and (iii) the use of co-catalysts/sensitizers, to enhance structural stability and extend the spectral range of light absorption, pointing to improve the efficiencies in PEC processes. The framework of this PhD program is based on developing a new class of multicomponent hybrid systems composed of a central semiconductor (CS), most likely TiO2, α-Fe2O3, ZnO and WO3, with controlled shape and dimensionality (e.g., 1D-nanotubes, 2D-ultrathin films). The key-approach is represented by the simultaneous and synergistic combination of strategies (nanostructuring, co-catalyst deposition, surface sensitization) usually studied and developed independently. Therefore, the nanostructured CSs will be coupled to counterparts with specific functionalities (extended visible light absorption, remarkable efficiency in charge transfer, enhanced carrier mobility) and the effective interaction of the single components will significantly benefit the PEC efficiency of the composite system.

Noncovalent interactions at metallic and non-metallic surfaces: qauntum mechanical study (for Fischer stipend)

Supervisor: prof. Ing. Pavel Hobza, DrSc., FRSC

Noncovalent interactions of small and medium-sized molecules on metallic and non-metallic surfaces will be studied by using nonempirical and semiempirical quantum mechanical methods. Besides structure and geometry of complexes formed also total stabilization energy as well as its components will be investigated. Attention will be paid to eletric and magnetic properties of molecules adsorbed and thier complexes with the surfaces. The study will be based on cluster model as well as on infinitive surface model based on periodic boundary conditions.

Molecular Simulations of Biomembrane Systems

Supervisor: doc. RNDr. Karel Berka, Ph.D.

The aim of this research topic is to understand behavior and the nature of interaction of small molecules as well as biomacromolecules with biological membranes. A combination of simulation techniques (e.g. all atomic and coarse-grained molecular dynamics simulations or quantum chemical calculations) and bioinformatics and cheminformatics approaches will be used to understand and quantify interactions of molecules with biological membranes - e.g. penetration and partitioning of small molecules into the individual membranes (Pharmacol. Res., 111, 471–486, 2016; Langmuir, 30(46), 13942-13948, 2014) and storage of such information in publicly available database; mode of action of membrane-bound proteins - e.g. interplay between cytochromes P450 and other metabolic enzymes (Drug. Metab. Dispos., 44(4), 576-590, 2016) including studies of molecular pathways within structure of those membrane proteins (J. Chem. Theory Comput., 12(4), 2101–2109, 2016) together with development of necessary structural bioinformatics tools (e.g. - Nucleic Acids Res., 40(W1), W222-W227, 2012). We expect a tight cooperation with colleagues from European bioinformatics infrastructure ELIXIR, Masaryk University, Czech Republic, Procter & Gamble company, USA, Université de Limoges, France, and Friedrich-Alexander Universität Erlangen-Nürnberg, Germany.

Understanding biology at an atomic resolution

Supervisor: Dr. Patrick Trouillas

Interaction of new materials and new chemical derivatives with biological systems is of crucial importance in many research fields related to healthcare. The today and tomorrow’s challenges lie in rationalization of these interactions with an atomistic resolution. The gamut of theoretical chemistry methods allows achievement of that outcome, with increasingly precise accuracy. We propose a series of research topics focusing on noncovalent interaction between π-conjugated systems, interaction with lipid bilayers membranes and interactions with proteins

Theoretical study of charge transport in nanostructures

Supervisor: doc. Ing. Pavel Jelínek, Ph.D.

Possibility to actively control charge states on atomic scale in nanostructures opens new horizons in the field of nanoelectronics. To get more insight into processes of charge transfer on atomic scale requires new theoretical approaches. The aim of this work is to employ the density functional theory and its application on selected cases charge transport in nanostructures. Theoretical simulations will be performed in close collaboration with ongoing experimental measurements. Development of computational methods is expected.

Chemical and physical properties of molecular nanostructures on surfaces investigated by means of scanning probe microscopy

Supervisor: doc. Ing. Pavel Jelínek, Ph.D.

The current development of the scanning microscopes working in ultrahigh vacuum allows high-resolution measurements of atomic force and tunneling currents on individual atoms or molecules deposited on the surface of solids. Simultaneous measurement of the atomic force and tunneling current opens up completely new possibilities for the characterization of single molecules or molecular nanostructures on solid surfaces. The candidate will learn to work with atomic force microscope and scanning tunneling microscope in ultra-high vacuum. The aim of this work is carried out high-resolution measurements of the atomic and electronic structure of selected molecules deposited on solid surfaces. The main objective is to study chemical and physical properties of the molecular nanostructure by means of scanning probe microscopy.

Magnetism of 2D systems

Supervisor: doc. Mgr. Jiří Tuček, Ph.D.

The long-term challenge of the scientific community is to develop metal-free magnetic systems based on carbon. However, so far, magnetism self-sustainable at higher temperatures (up to room temperature) has not been reported for any sp-based material including all carbon allotropes. The most promising results have been achieved with 2D graphene and its derivatives, which would exhibit low-temperature magnetism after appropriate chemical treatment. Among carbon nanoallotropes, graphene has been identified as the most promising candidate to show interesting self-sustainable magnetic features once defects are introduced. The defects include local topology perturbations, vacancies, non-carbon atoms in the graphene lattice, adatoms (i.e., atoms added to the surface of the graphene sheet), mixed sp2/sp3 hybridization (i.e., suitable sp2/sp3 ratio), and zigzag-type edges (i.e., confinement-related phenomena). The imprinting of self-sustainable magnetism at room temperature to graphene and/or its derivatives is widely recognized as a key challenge for the further development of 2D carbon-based materials with a huge potential in spintronics devices, biomedicine, environmental technologies etc. The goal of this PhD topic is viewed in finding, both experimentally and theoretically, the optimal combination of defects of various natures towards generation of magnetic centers, promotion of their communication and, at the same time, preservation of the role of conduction electrons. The issue of imprinting self-sustainable magnetism will be also addressed for systems analogous to graphene such as MoS2, WS2, etc.

Structure and Dynamics of RNA (for Fischer stipend)

Supervisor: prof. RNDr. Jiří Šponer, DrSc.

The topic of the thesis will be studies of selected RNA molecules (ribosomal RNA motifs, protein-RNA complexes, ribozymes, riboswitches, selected from systems presently studied in our laboratory as well as in collaborating laboratories) using methods of classical molecular dynamics simulations, bioinformatics and quantum-chemistry. RNA presently belongs to the most widely studied biomolecules. Functional RNA molecules are fascinating 3D architectures and computational chemistry is one of the basic tools in their characterization, as can be documented also by number of our preceding studies in the field (see, e.g., the WOS database). Computer simulations can obtain new information for example about the role of noncanonical base pairs in RNA structure and evolution, and can substantially complement information obtained by X-ray crystallography, NMR and bioinformatics. The work may include either studies of specific systems or tasks oriented more towards method testing and development. We collaborate with a number of experienced laboratories across the world, including F.H.T. Allain, G. Bussi, N.B. Leontis, N.G. Walter, M. Nowotny, and others.

Origin of Life Theory – Studies of Prebiotic Chemical Reactions (for Fischer stipend)

Supervisor: prof. RNDr. Jiří Šponer, DrSc.

The topic of the thesis will be origin of life theory, which is a complex research area ranging from the evolution of planetary systems through prebiotic synthesis of basic components of the living materials up to simple protocells. Theoretical quantum-chemical (QM) methods can be efficiently applied to studies of prebiotic chemical reactions. The main advantage of QM methods is their capability to describe processes which in some cases cannot be fully satisfactorily understood by means of experiments. Presently, we are involved in studies related for example to the formamide pathway to the origin of life, non-templated synthesis of the first RNAs from the cyclic nucleotides, role of photochemical processes in prebiotic chemistry, QM molecular dynamics simulations, high energy impact chemistry and some other topics. The dissertation is suitable for students who are interested in application of modern QM methods and have a feeling for chemical reactions. Because it is a very difficult topic, specific research goal can be proposed only after careful assessment of the capabilities of the applicant. We closely collaborate with other experimental and theoretical laboratories, e.g. E. Di Mauro, R. Salladino, M. Ferus, M. Saitta, J.D. Sutherland and some others.

Multiscale Modeling of Nucleic Acids

Supervisor: prof. RNDr. Jiří Šponer, DrSc.

Nucleic acids (RNA and DNA) belong to the most important biomacromolecules. Studies of structure and dynamics of nucleic acids represent an important task of modern life sciences. Due to fast development of hardware and software, computational and theoretical approaches are frequently used in nucleic acids studies and represent a respected counterpart of experimental techniques. This PhD project will be based on integrated interdisciplinary utilization of a broad spectrum of computational methods (multi-scale modelling) ranging from state-of-the-art quantum-chemical (QM) approaches through modern explicit solvent molecular dynamics (MD) simulation methods up to bioinformatics. Cooperation with established experimental laboratories will provide necessary experimental feedback. State-of-the-art computational facilities are available not only in our laboratory but also in cooperating laboratories abroad. The exact topic will be specified based on the discussion with the applicant and her/his scientific interests and capabilities. Currently available specific themes include for example multiscale studies of protein-RNA complexes, RNA catalysis, structural dynamics and folding of quadruplex DNA and large-scale QM studies of complete nucleic acids building blocks.

Advanced Nanomaterials: Synthesis and Applications in Catalysis, Organic Transformations, Photo (electro) catalysis

Supervisor: doc. Manoj B. Gawande, Ph.D.

Nanoparticles are regarded as attractive candidates for heterogeneous catalysis in various imperative catalytic processes as they are now easy to synthesize with a desired size, structure, morphology and composition. Keeping in mind the current environmental sustainability concerns, it is important to design inexpensive and benign nanocatalysts for organic transformations/catalytic processess. Over the last decade, a variety of new types of nanocatalysts have been investigated, including well-defined Morphology Depdendent Catalysts, Single-atom catalysts, Core–shell and yolk–shell nanocatalysts, Silica-based hybrid catalysts, 2 D graphene-based materials and 2D single metal or mixed metal ionic nanocatalysts. The ascent of these complex nanomaterials over the last few years has enabled chemists to understand traditional catalysts from a new perspective. The aim of these hot research areas is to desinged the materials based on highly important targated catalytic, organic transformations and Photo (electro) catalysis applications.