Department of Physical Chemistry

Granting Departments:	Department of Physical Chemistry
Study Programme/Specialization:	Molecular chemical physics and sensorics ( in Czech language )
Supervisor:	Ing. Ctirad Červinka, Ph.D.

Annotation

Large structural and chemical variability of organic semiconductors raises the need for computational screening of the electronic structure of the bulk phase and related material properties, such as the band gap or the charge-carrier mobility. The latter property remains rather low for most existing organic semi-conductive materials when compared to the traditional inorganic crystalline platforms of the optoelectronic devices. Understanding relationships among the bulk structure, non-covalent interactions therein, electronic properties, conductivity, and the response of all such properties to temperature and pressure variation will greatly fasten the material research in the field of organic semiconductors. This thesis will employ the established electronic structure methods with periodic boundary conditions, as well as fragment-based ab initio methods to map the cohesion of bulk organic semiconductors with the charge-carrier mobility is both crystalline and amorphous structures of these materials. Ab initio calculations and the Marcus theory will be used as the starting point for a detailed investigation of the impact of local structure variations, due to chemical substitution, thermal motion, or polymorphism on the conductivity of target materials.

Granting Departments:	Department of Physical Chemistry
Study Programme/Specialization:	Chemistry ( in Czech language )
Supervisor:	doc. RNDr. Mgr. Jan Heyda, Ph.D.

Annotation

Thanks to the increasing computational power, the results of computer simulations are practically limited only by the quality of input parameters of the used model. In the case of molecular simulations, it is about the used "empirical" force fields, which traditionally rely on available experimental thermodynamic data and simple information from quantum-chemical calculations. These traditional approaches can be replaced by using precise ab-initio calculations, which are computationally extremely demanding. These demanding calculations can be used for training neural networks. With the help of machine learning, the computational demands of these approximate ab-initio simulations can be brought closer to the demands of simulations with force fields [1], and as a result, obtain numerically precise solutions to the studied models. This modern approach has the potential to significantly limit the influence of the choice of force field on the obtained results and thus receive correct answers to fundamental scientific questions for the right reasons. In this work, we focus on the application of this method to the study of aqueous solutions of salts and solutes dissolved in them.

Granting Departments:	Department of Physical Chemistry
Study Programme/Specialization:	Molecular chemical physics and sensorics ( in Czech language )
Supervisor:	Ing. Ctirad Červinka, Ph.D.

Annotation

Organic semiconductors represent a broad material class offering interesting properties such as potential biocompatibility, large structural variability, mechanical flexibility, or transparency. These promising properties, however, cannot outweigh insufficient conductivity of the organic matter when compared to crystalline silicon, which impedes wider spread of alternatives to the traditional inorganic platforms for optoelectronic devices. This work will concern development and applicability testing of quantum-chemical methods for modelling polymorphism of molecular crystals similar to relevant organic semiconductive materials. Larger molecular size, high degree of conjugation and frequent heterocyclic nature of the target molecules represent the challenges that the computational chemistry has to face in order to provide accurate decription of molecular interactions in this field. Accurate quantum-chemical treatment of the non-covalent interactions, their relationship to the bulk structure, and the stability of individual polymorphs at various conditions will be targeted within this thesis. Finally, an interpretation of the impact of subtle variations of bulk structure on the charge-carrier mobility in organic semiconductors will be searched for.

Granting Departments:	Department of Physical Chemistry
Study Programme/Specialization:	Molecular chemical physics and sensorics ( in Czech language )
Supervisor:	Ing. Ctirad Červinka, Ph.D.

Annotation

Modern formulations of drugs often rely on cocrystalline forms the crystal lattice of which is built from multiple chemical species, mainly an active pharmaceutical ingredient and another biocompatible compound being called a coformer in this context. These cocrystalline drug forms often exhibit higher solubility, stability or other beneficial properties when compared to crystals of pure active pharmaceutical ingredients. Since molecular materials tend to crystallize in single-component crystals rather than in cocrystals, the task of finding a suitable coformer for a given active pharmaceutical ingredient may be very tedious and labor demaning. To circumvent the costly experimental trial-and-error attempts, in silico methods can help to preselect a list of possible coformers offering a high probability of forming the cocrystal. Currently available methods focus on screening the electrostatic potential around the assessed molecules and empiric pairing of its maxima and minima for the individual molecules, which enables coformer screening with a fair accuracy for predominantly hydrogen-bonded molecules. This thesis will aim at incorporation of ab initio calculations of molecular interactions that will bring further improvements also for cocrystal screening of larger molecules with prevailing dispersion components of their interactions. Also the impacts of stechiometry variations and of the spatial packing of the molecules in the cocrystal lattice will be newly considered, greatly enlarging the applicability range of the current cocrystal screening procedures.

Granting Departments:	Department of Physical Chemistry
Study Programme/Specialization:	Chemistry ( in Czech language )
Supervisor:	doc. RNDr. Mgr. Jan Heyda, Ph.D.

Annotation

Smart materials are rapidly growing field, due to wide spectrum of potential aplications and tunable properties. Such materials typically possess at least one property, which can be reversibly changed in a controlable way by an external stimuli. One group of such materials are thermoresponsive polymers. They undergo collapse transition at the critical temperature. Moreover, near to this temperature their properties are extremally sensitive to changes in the solution environment, such as pH, salt concentration, polymer concentration. In terms of molecular dynamics simulations student will investigate thermoresponsive polymer PNIPAM, and/or its copolymers with ionic liquid. The effect of ionic strengt, as well as of pH on the thermodynamics of collapse transition will be studied. At the second step, besides the atomistic simulations, student will develop a coarse-grained model (with T-dependent effective potentials) that allows to study large scale systems, and thus answer the role of polymer concentration, or of polymer chain length. Flory-like mean-field models will be constructed, and their applicability discussed. This work is motivated by already published experimental work, and connects to the recent thermodynamic modelling of thermoresponsive polymers. If time permits, the salt and cosolvent specific effects will be also addressed. An intensive collaboration with the group of Prof. Joachim Dzubiella at Freiburg University is expected.

Granting Departments:	Department of Physical Chemistry
Study Programme/Specialization:	Drugs and Biomaterials ( in Czech language )
Supervisor:	Ing. Marcela Dendisová, Ph.D.

Annotation

V přírodě, a hlavně v odpadních vodách, se vyskytuje čím dál větší množství residuí farmakologických přípravků, jako jsou hormonální přípravky, antibiotika, výživové doplňky a jiné. Jejich rostoucí množství má neblahý vliv na životní prostředí a je tudíž zapotřebí najít spolehlivý nástroj pro jejich detekci a analýzu. K tomu mohou sloužit metody povrchem zesílené vibrační spektroskopie, které jsou využívány pro detekci látek o nízkých koncentracích. Před využitím těchto metod v praxi je zapotřebí studovat adsorpční procesy daných farmakologických látek s využitím technik povrchem-zesílené vibrační spektroskopie, zahrnující Ramanův rozptyl a infračervenou absorpci. Dalším krokem je využití technik blízkého pole založených na mikroskopii skenující sondou. Tyto techniky umožňují sledovat optickou odezvu v závislosti na experimentálních podmínkách (materiál substrátu, energie budícího záření, morfologie povrchu, …) a nalézt optimální podmínky pro jejich detekci.

Granting Departments:	Department of Physical Chemistry
Study Programme/Specialization:	Chemistry ( in Czech language )
Supervisor:	prof. Ing. Karel Friess, Ph.D.

Annotation

Membrane separation processes belong to modern, technologically important separation methods, which are less demanding (economically and ecologically) in comparison with classical separation methods. For gas separation applications, polymer membranes are mainly used. Their performance (permeability or separation effect) can be additionally adjusted by the targeted embedding of liquid or solid additives into the polymer matrix. The dissertation thesis will focus on the preparation of 2D/3D membranes via the electrospinning method, characterization, and testing of the composite membranes for the separation of gases based on polymers and functional nano-additives with a purposefully prepared structure. In addition, the modeling of the separation process will be part of the work. The result of this work will be the preparation and testing of membrane material for effective gas separations.

Granting Departments:	Department of Physical Chemistry
Study Programme/Specialization:	Chemistry ( in Czech language )
Supervisor:	doc. RNDr. Mgr. Jan Heyda, Ph.D. Prof. Werner Kunz

Annotation

Traditional ionic liquids are based on functionalized imidazolium cations, alkyl ammonium cations, etc. in which the delocaliazed charge and hydrophobic groups play dominant role. As a consequence, these compound, which are too different from the natural materials, are toxic for the environment. This contrasts with the recent ionic liquids, in which softer motifs, such as short alkyl chains alternating with hydrophilic ethoxy groups take place, and carboxyl groups carry the charge. These compounds are nontoxic, usually easy to degradate by natural processes. In this thesis, we will investigate the family of Akypo LF2 ionic liquids. Akypo LF2 is a carboxylic acid with a hydrocarbon chain containing 8 ethylene glycol blocks and an octyl chain. Due to presence of a hydrophilic and hydrophobic part it behaves in aqueous solutions as a surfactant. Since it is an acid, various salts can be formed. Significantly, most of the metallic salts are liquid, which means these structures are room temperature ionic liquids with lots of possible uses. In this PhD project we focus on the molecular and structural determination of metallic Akypo LF2 ionic liquids, measuring physicochemical properties with the aim for industrial use. These findings will be used in the development of an atomistic model of Akypo LF2-based ionic liquids. Its application in molecular dynamics simulations should validate the thermodynamic, kinetic, and structureal experimental findings on strict theoretical grounds. Last, the simulation should contribute to microscopic explanations of unique properties of Akypo LF2.

Granting Departments:	Department of Physical Chemistry
Study Programme/Specialization:	Molecular chemical physics and sensorics ( in Czech language )
Supervisor:	prof. RNDr. Bc. Petr Slavíček, Ph.D.

Annotation

Granting Departments:	Department of Physical Chemistry
Study Programme/Specialization:	Chemistry ( in Czech language )
Supervisor:	prof. RNDr. Bc. Petr Slavíček, Ph.D.

Annotation

Charge transfer processes are fundamental to understanding chemical reactions. Traditional electrochemical techniques often struggle to fully characterize these processes. However, recent advancements in liquid phase photoemission spectroscopy offer promising avenues for integrating spectroscopy with electrochemistry. In this thesis, the applicant will employ innovative methods from quantum chemistry, statistical mechanics, and molecular modeling to elucidate the connection between these fields.

Granting Departments:	Department of Physical Chemistry
Study Programme/Specialization:	Molecular chemical physics and sensorics ( in Czech language )
Supervisor:	prof. RNDr. Bc. Petr Slavíček, Ph.D.

Annotation

Processes that involve the simultaneous transfer of electrons or energy along with atoms, typically hydrogen or protons, are widely recognized for their significant involvement in biophysical phenomena. This thesis will center on the emerging field of proton-coupled energy transfer (PCEnT) from a theoretical chemistry standpoint. The research will integrate quantum dynamics, molecular simulations, and modern quantum chemistry methodologies. Collaboration with experimentalists is envisioned.

Granting Departments:	Department of Physical Chemistry
Study Programme/Specialization:	Chemistry ( in English language )
Supervisor:	prof. Ing. Michal Fulem, Ph.D.

Annotation

The objective of the thesis is to explore the current possibilities of in silico approaches as tools for the rational design of drug delivery systems. The project will consist of interconnected research activities involving both experimental and theoretical undertakings, which will lead to the development of an optimized computational tool for the selection of polymeric carriers for given drugs and subsequent optimization of the performance-related characteristics of the resultant drug delivery systems.

Granting Departments:	Department of Physical Chemistry
Study Programme/Specialization:	Molecular chemical physics and sensorics ( in Czech language )
Supervisor:	Ing. Martin Klajmon, Ph.D.

Annotation

Knowledge of the phase behavior of substances is a key factor for the design of amorphous molecular materials, such as organic semiconductors or pharmaceutical formulations. Large structural and chemical variability of these materials require the application of computational screening methods that would enable fast and as-accurate-as-possible estimation of their bulk thermodynamic properties. Common molecular mechanics methods (e.g., grand-canonical Monte Carlo simulations) with classical force field models for predicting the phase behavior are notoriously challenging and give results that are far from acceptable numerical accuracy. Therefore, this thesis aims at developing a novel computational methodology based on a unique synergy of established first-principles electronic structure methods and efficient Monte Carlo simulations to map the thermodynamic properties (e.g., densities, enthalpies, and Gibbs energies) of different phases at a wide range of temperatures and pressures to construct global phase diagrams. Furthermore, this approach will enable a better understanding of the relationship between the molecular properties and interactions and the macroscopic phase transformations of bulk materials. At each stage, the developed methodology and its features will be compared with the available experimental data and results from existing computational approaches. Since it is expected that the methodology will exploit various different computational frameworks, the project will also include the creation of program tools for the required interfaces and processing of the simulated data in a form that would allow automation of the calculations, making the developed methodology available to a broader community.

Granting Departments:	Department of Physical Chemistry
Study Programme/Specialization:	Molecular chemical physics and sensorics ( in Czech language )
Supervisor:	prof. RNDr. Bc. Petr Slavíček, Ph.D.

Annotation