Modelling of interactions of polar and nonpolar pollutants with soil minerals and soil organic matter

Environmental pollution of soils by organic contaminants such as pesticides is one of the serious problems of our civilization. Contaminants can undergo various physical, chemical and biological transformation processes in soils governing behaviour, distribution, and fate of organic species in environment and subsequent environmental risks. Mechanistic understanding of molecular interactions of organic pollutants with main soil components represents a key factor for estimating the behaviour of contaminants in soils. Molecular modelling offers an opportunity to investigate and characterize various details of these interactions at molecular level providing specifications, which are difficult to obtain at the experimental level. This work represents a comprehensive overview of our investigations of the molecular interactions of organic contaminants with selected soil components. Particularly, we focused on the characterization of the structure and the surface complexation of the phenoxyacetic acid derivatives (herbicides MCPA and 2,4-D) and typical soil minerals such as clay minerals (kaolinite and montmorillonite) and iron oxyhydroxides (goethite and lepidocrocite). Further, interactions of several representative nonpolar polycyclic aromatic hydrocarbons (e.g. naphthalene, anthracene, pyrene, and phenanthrene) with iron oxyhydroxides were modelled, as well. It was found that in case of polar species, hydrogen bonds and electrostatic interactions play an important role in the formation of the surface complexes. In case of nonpolar PAHs, dispersion forces dominate in the planar stacking of the PAHs molecules on mineral surfaces. Another study focused at a complex 3D model representing humic substances firstly, featuring polar hydrophilic and nonpolar hydrophobic domains and also a nanopore SOM structure. This model was taken to simulate trapping and interactions of MCPA (polar) and naphthalene (nonpolar) species inside of the nanopore. It was found that MCPA is preferentially stabilized close to polar functional groups (carboxyl) whereas naphthalene interacts mostly with nonpolar aliphatic chains through dispersion interactions

Structures and properties of bioorgano-clays

Interactions between microbial matter and clays are a common interfacial phenomenon in soil and sediment environments. However, fundamental mechanisms governing the formation and interactions of clay minerals with microbial-derived organic substances are still poorly understood. Therefore, our central aim was to study the formation of bioorgano-clay composites and their specific material properties and compare these properties with those of well-studied organo-clays. Pure organic cations (e.g., alkylammonium homologues) and complex microbial biomass (e.g., fungal biomass from Aphanocladium sp.) were used to prepare organo- and bioorgano-clays by varying the amount of clay (montmorillonite) and organic materials used. Interaction mechanisms between organic materials and clay and the resulting structure and physicochemical properties were explored by multiple experimental methods (e.g. IR spectroscopy, contact angle, zeta potential, X-ray photoelectron spectroscopy, transmission electron microscopy) in a combination with molecular modelling to determine the structure, composition, and properties of the prepared bioorgano-clays. Depending on origin, type, and size of the organic material and the clay, two basic types of bioorgano-clays were found: (i) bioorgano-clays having their clay particles coated by bioorganic matter with only limited or no penetration into interlayer galleries and (ii) bioorgano-clays having bioorganic matter distributed in the interlayer galleries and/or on the external surfaces of clay particles. Both types show heterogeneous arrangements of the amended organic matter inducing differences in shape and size of organo-clay particles. Consequently, changes in pore volumes, stability, and elemental interface properties can be verified. Compared to organo-clays, bioorgano-clays provided e.g. a higher adsorption capacity for uranyl, suggesting that modification of clays by rather unspecific microbial compounds significantly enhanced the number of exchange sites. Bioorganic-clays, although being less specific in nature, might therefore be applied more broadly in situations where a high sorption capacity, e.g., for contaminants, is required

Structure of hydrated calcium carbonates: A first-principles study

The structures of both ikaite (CaCO3·6H2O) and monohydrocalcite (CaCO3·H2O) were computed at the PBE0 level of theory, using all electron Gaussian type basis sets. Correction for the long-range dispersion contribution was included for the oxygen–oxygen interactions by using an additive pairwise term with the atomic coefficients fitted against the calcite vs aragonite enthalpy difference. The potential chirality of monohydrocalcite is discussed, as well as the helical motifs created by the three-fold rototranslational axes parallel to the [001] direction. These elements represent a significant link between monohydrocalcite and vaterite, both appearing as intermediate species during CaCO3 crystallization from amorphous calcium carbonate. The hydrogen bond pattern, never fully discussed for monohydrocalcite, is here described and compared to the available experimental data. Both phases are characterized by the presence of hydrogen bonds of moderate to high strength. Water molecules in monohydrocalcite interact quite strongly with 2 View the MathML source units through such hydrogen bonds, whereas their interaction with each other is minor. On the contrary, water molecules in ikaite create a complex network of hydrogen bonds, where each water molecule is strongly hydrogen bonded to one View the MathML source anion and to one or two other water molecules

Periodic Density Functional Theory Investigation of the Uranyl Ion Sorption on Three Mineral Surfaces: A Comparative Study

Canister integrity and radionuclides retention is of prime importance for assessing the long term safety of nuclear waste stored in engineered geologic depositories. A comparative investigation of the interaction of uranyl ion with three different mineral surfaces has thus been undertaken in order to point out the influence of surface composition on the adsorption mechanism(s). Periodic DFT calculations using plane waves basis sets with the GGA formalism were performed on the TiO2(110), Al(OH)3(001) and Ni(111) surfaces. This study has clearly shown that three parameters play an important role in the uranyl adsorption mechanism: the solvent (H2O) distribution at the interface, the nature of the adsorption site and finally, the surface atoms’ protonation state

Optimization of the axle of an agricultural machine

Práce se zabývá optimalizací konstrukce nápravy zemědělského stroje Triton Heavy 490 s cílem zvýšit pevnost a životnost klíčových částí. Pomocí metody konečných prvků byla identifikována kritická místa, na která byly navrženy konstrukční úpravy vedoucí ke zlepšení pevnostních vlastností a provozní spolehlivosti. Výpočty byly provedeny s ohledem na platné normy a využití moderních výpočtových metod.The thesis focuses on optimizing the axle design of the agricultural machine Triton Heavy 490 with the aim of improving strength and durability of key components. Finite Element Method (FEM) was used to identify critical areas, where design modifications were proposed to enhance structural properties and operational reliability. Calculations were performed in accordance with applicable standards and employing modern computational methods.Dopravní fakulta Jana PerneraStudent přednesl obhajobu své závěrečné práce, zodpověděl všechny otázky oponentního posudku a také doplňující otázky členů zasedající komise.Dokončená práce s úspěšnou obhajobo

Dataset for article: Adsorption of the hydrophobic organic pollutant hexachlorobenzene to phyllosilicate minerals

<p>This repository contains data obtained from first principle DFT calculations at the PBE-D3 DFT level<br>by the program VASP  for the research article </p> <p><br>Title: "Adsorption of the hydrophobic organic pollutant hexachlorobenzene to phyllosilicate minerals"<br>published in Environmental Science and Pollution Research (2023) 30:36824–36837.</p> <p>Authors: Leonard Böhm, Peter Grančič, Eva Scholtzová, Benjamin Justus Heyde, Rolf-Alexander Düring, Jan Siemens, Martin H. Gerzabek & Daniel Tunega.</p> <p>Please cite that article when using this dataset.</p> <p>The systems in the dataset are models of Me-montmorillonite layers (Me = Li, Na, K, Rb, Cs, Mg, Ca, Sr, Ba)<br>interacting with hexachlorobenzene (HCB) molecule. Calculated are interaction energies of optimized geometries of HCB...Me-Mnt complexes. Dateset contains tables with collected calculated adsorption energies and main geometrical paramters.<br>The structure of dataset is following:<br>Rep_Ads_I directory contains directories for HCB molecule, and for complexes of HCB with Li-Mnt to Rb-Mnt. Each directory of complexes contains corresponding directory of isolated Me-Mnt layer. The second directory, Rep_ads_II has the same structure as Rep_Ads_I directory for Me=Mg, Ca, Sr, and Ba.<br>In each directory are the main files for VASP calculations:<br>input geometry data (POSCAR.norm file)<br>optimized geometry  (CONTCAR.norm file)<br>input parameters for VASP (INCAR file)<br>k-points (KPOINT file)<br>complete output files (OUTCAR.norm and vasprun.xml.norm files)<br>POTCAR file with pseudopotentials are not provided due to copyright restrictions. Their type can be found in OUTCAR file or vasprun.xml file.</p> <p>Funding: This work has been supported by German Research Foundation (Deutsche Forschungsgemeinschaft, DFG), grant number 443637168, BO5388/1–1 and Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung, FWF), grant number I 4876–N in the bilateral project ”Clay minerals as sorbents for hydrophobic organic chemicals – ClayHOC”.  The results<br>presented have been achieved using the Vienna Scientific Cluster (VSC), project number 70544.</p> <p>Terms of use: These data are provided "as is", without any warranty. This dataset is provided under the Creative Commons Attribution 4.0 International license.</p&gt

Study of the effect of engine oil wear and operational load on the load-bearing capacity of the lubricating film

Pro správnou funkci motoru je důležité vytvoření olejového filmu mezi pohyblivými částmi motoru. Stárnutí motorového oleje ovlivňuje jeho schopnosti tento film vytvořit a udržovat. Tato schopnost je hlavně ovlivněna změnou viskozity, a to degradací a kontaminací nečistostmi, což vede k snížení únosnosti mazacího filmu. Tato bakalářská práce se zabývá vlivem opotřebení a zatížení na únosnost olejového filmu. Tyto vlastnosti jsou hodnoceny na výsledkách získaných pomocí Stabingerova viskozimetru, FTIR spektrometru a Reichertova testu.For proper engine function, it is important to create an oil film between the moving parts of the engine. The aging of the engine oil affects its ability to create and maintain this film. This ability is mainly influenced by changes in viscosity due to degradation and contamination with impurities, which leads to a decrease in the load-bearing capacity of the lubricating film. This bachelor's thesis deals with the impact of wear and load on the load-bearing capacity of the oil film. These properties are evaluated based on the results obtained using a Stabinger viscometer, FTIR spectrometer, and Reichert test.Dopravní fakulta Jana PerneraStudent přednesl obhajobu své bakalářské práce a s pouze malými zaváháními reagoval na otázky členů komise.Dokončená práce s úspěšnou obhajobo

Break & enter - a silo renewal

Abweichender Titel laut Übersetzung der Verfasserin/des VerfassersEin nicht mehr gebrauchter Zementsilo in Stupava (Slowakei) wird in ein Hotel umgewandelt. Das Konzept der Silo-Umnutzung geht von dem Gedanken aus, dass das ursprüngliche Objekt mit neuen Formen befallen wird, die ihn sich als Basis ihrer Existenz aneignen. Dieser fiktive Parasit sind gerade die Hotelzimmer, das Grundelement des neuen Raumprogrammes. In einem bespielten Raster sind sie an der äußeren Schale angesaugt, durchdringen Sie um sich Zugriff zum inneren Klima zu verschaffen. Es erfolgt das Durchbrechen der Schale "Break" gefolgt von dem Eindringen "Enter". Die Konzeption des Hotels könnte man in diese grundsätzlichen Einheiten enteilen: * Die Basis * Die Türme mit den Hotelzimmern * Aussichtskubus auf dem Dach Die Basis versucht formal den anderen Teilen unterlegen zu sein, sie versucht mit den umliegenden Grünflächen zu verschmelzen. Es findet hier die erste Verbindung mit der Umwelt statt, deshalb soll mit ihr eine ausreichende visuelle wie auch formale Verknüpfung gewährleistet werden.Die Basis bildet eine Art Hinterland des ganzen Projektes, von dem die Türme alles nötige in die parasitierenden Organismen also die Hotelzimmer übertragen. Das Innere des Silos bleibt als ungeteilter Freiraum erhalten, der nur von den nach Innen überragenden Kuben der Hotelzimmer, und den Überbrückungen der Erschließung gegliedert wird. So entsteht ein unerkannter Raumeindruck. Die Überbrückungen durchqueren in einer freien Anordnung den Raum wodurch eine fast abstrakte Komposition geschaffen wird. Der vertikale Eindruck des Raumes wird durch verglaste Oberseiten der Zylinder unterstützt, die den benötigten Anteil an Tageslicht in den Raum hineinlassen. Die Kuben der Hotelzimmer bilden eine Art Membrane zwischen der Panorama im Exterieur und dieser beeindruckenden Innenraumatmosphäre. Die Beendigung des ganzen Objektes ist der große Aussichtskubus, der über dem Silo "schwebt". Das Konzept geht im Allgemeinen davon aus, das der äußere Ausdruck des Silos nicht unbedingt erhalten bleiben muss. Es werden nur seine hauptsächlichen Qualitäten extrahiert und in einem neuen Gewand wieder zum Leben erweckt. Der "Befall" des Alten mit Neuem führt zur Entstehung einen neuen Organismus.6