Studentská vědecká konference

Dentistry is not everyone’s cup of tea, but tooth decays and dental fillings are part of our life. Nowadays plenty of materials are used as dental fillings. One of them are resin-based composites, which benefits from the white colour, absence of mercury and electric nonconductivity. In contrast, the composites are more expensive and have worse mechanical properties. Tooth reparation is not only a subject of interest of dentists but also theoretical photochemists because of the chemical reaction - photoinduced polymerisation. Photoinitiators are crucial substances for photoinduced polymerisation as they absorb the UV/VIS light and decompose themselves forming reactive species to start polymerisation. In this work we took a look into novel potential photoinitiators: germanium based compounds. Using the techniques of computational chemistry we examined and compared the properties of acetophenone and its germanium derivate benzoyl germane.  We modelled electron absorption spectra using the nuclear ensemble method with and without spin orbital couplings. Next step was to run dynamical simulations using Landau Zener Hopping scheme, which allows theoretical investigation of the processes following the irradiation of the molecule and possible formation of reactive forms.  

Lipases are enzymes that catalyze hydrolysis of the ester bonds in fats. They are an essential part of lipid metabolism of the living organisms, but they also have industrial applications. They can be utilized for synthesis such as transesterification or aminolysis, due to their ability to function in both polar and organic solvents. Our research focuses on the modeling of transesterification catalyzed by Candida Antarctica lipase B, which contains the Asp-His-Ser catalytic triad. Transesterification is a transformation, where the alcohol group of an ester is exchanged by another, usually more complex, group. The rate-limiting step of the reaction is the formation of the second tetrahedral intermediate, which we investigated in detail in different solvents. At first, we studied whether this step is sequential or concerted. For that, we investigated the nucleophilic attack of the alcohol and the proton transfer from alcohol to the histidine by QM/MM. Classical molecular dynamics was also used to sample the interactions of the substrate with its environment – the solvent and the protein. The results of this work are the potential energy surfaces of the formation of the second tetrahedral intermediate and the quantification of its interactions with its surroundings.  

Polymorfismus organických sloučenin je častým jevem a jednotlivé polymorfy dané látky se mnohdy zásadně liší svými fyzikálně-chemickými vlastnostmi, na kterých závisí možné využití těchto polymorfů v nejrůznějších oborech. Zároveň bývá velmi pracné experimentálně nalézt jak všechny polymorfy, které sloučenina může tvořit, tak jejich termodynamické vlastnosti a stabilitu (určenou Gibbsovou energií). Proto je snaha najít dostatečně přesné a zároveň efektivní výpočetní cesty pro predikci polymorfismu a souvisejících termodynamických vlastností. V této práci byly metodou založenou na teorii funkcionálu hustoty (DFT) optimalizované geometrie tří polymorfů modelové sloučeniny, sulfathiazolu. Stejné výpočty byly pro srovnání provedeny také semiempirickou metodou DFTB3. Těmito teoretickými postupy byla vypočtena závislost elektronové energie na objemu a pomocí kvazi-harmonické aproximace byly modelovány vibrační stupně volnosti krystalů. Na základě těchto mikroskopických charakteristik krystalů jsou predikovány jejich makroskopické vlastnosti jako např. rovnovážný objem, tepelná kapacita či Gibbsova energie jako funkce teploty a tlaku. Z porovnání Gibbsových energií je predikována relativní stabilita tří polymorfů sulfathiazolu za různých podmínek.  

Density profiles of liquid-vapor interfaces far from their critical points are readily measured by X-ray scattering experiments. The results are commonly interpreted in the context of capillary wave theory (CWT). CWT describes the interface in terms of thermally activated capillary waves which corrugate an otherwise sharp surface. However, as one approaches the critical point of the liquid-vapor coexistence, the characteristic width of the interface increases along with a decrease in the surface tension until it goes to zero. This behavior suggests the breakdown of CWT close to the critical point. Here, we investigate the behavior of liquid-vapor interfaces close to their critical points, and the validity of CWT at high temperatures. To test the physical quality of the interface, we compare density profiles obtained from MD simulations of argon close its critical point to two reference systems. The first model is the CWT predicted sharp surfaces, while the second one assumes an essentially flat region that continuously transitions between the liquid and vapor densities. According to our results, the surfaces 1-T/T_c = 0.013 can still well be represented by a sharp, undulating surface, beyond which the distinction between the models becomes increasingly meaningless.

Ribosomes are essential organelles for every living organism. Their significance lies in their ability to perform translation, a process where information encoded in mRNA is transformed into proteins, the most versatile biomolecules found in organisms.  They consist of ribosomal RNA (rRNA) and ribosomal proteins. One of these proteins, uL22, is the subject of our research. It consists of 4 main parts: 3 alpha helices incorporated in the rRNA and one beta sheet, which reaches into a narrow space through which nascent proteins leave the organelle – the exit tunnel. It has been determined that the protruding parts are essential for formation and fuctionality of ribosomes and that they are evolutionarily very old. Our aim was to assess the isolated protruding part‘s propensity for secondary structures. To this aim, we have performed unbiased MD simulations and also Hamiltonian Replica Exchange simulations, both in 3 different force fields. The obtained propensity qualitatively agrees with estimates obtained from NMR chemical shifts.   We have determined that the protruding protein sequence, when isolated and dissolved in water, has only a little secondary structure preference. Its beta sheet conformation, observed in the ribosome, is probably induced by interactions with the organelle.  

This work explores the possibilities and limitations of various computational techniques to simulate photoemission spectra. Nimorazole (nitroimidazolic compound) was chosen as a testing system since it plays an important role in radiotherapy as a radiosensitizer. Moreover, new experimental data are available for this molecule in a cooperating laboratory. Here, we provide the performance of several approaches of simulating valence and core ionizations of nimorazole in both the gas and the liquid phase. We involve the commonly used methods of modeling ionizations such as the time-dependent density functional theory, but also the less conventional approaches like the maximum overlap method and the ionization as an excitation to a distant center with optimally tuned range separated functionals. Furthermore, we investigate different models of solvation such as the polarizable continuum model with variant cavity radii specifications. We also examined the cluster-continuum model of solvation, particularly the effect on solvating different parts of the molecule. Our results show the comparison of tested techniques and provide the guide to efficiently simulate the whole photoemission spectrum of molecules in both the gas and the liquid phase.  

Water is the primary solvent of most biological processes and as such it permanently receives widespread research attention.  In a recent systematic study of the volumetric properties of hydroxy- substituted neopentanes in water (C(CH₃)_4-n(CH₂OH)_n) , it was shown that introduction of polar hydroxy- groups has a significant impact on the temperature dependence of partial molar volumes at elevated temperatures and pressures.  In order to interpret the experimental results on theoretical grounds, we have performed molecular dynamics simulations of hydroxy- substituted neopentanes in TIP4P-2005 water over a broad range of temperatures and pressures. Solutes partial molar volumes have been calculated from the water structure in the solute vicinity employing the Kirkwood–Buff theory and from system volumes via finite differences. Both approaches agree well with the experimental data.  Furthermore, we have investigated the water structure in the proximity of methyl- and hydroxymethyl- groups. Namely, we have calculated directional radial distribution functions and tetrahedral order parameter of water in the solvation shell. Lastly, we have qualitatively compared solvation properties of the studied solutes by means of spatially resolved density distributions of water.