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Deposition of large organic molecules under UHV
Krajňák, Tomáš ; Novák,, Jiří (referee) ; Čechal, Jan (advisor)
In this thesis, large organic molecules (DM15N, DM18N, Cu(dbm)2) were deposited. These molecules are cannot be deposited by thermal sublimation due the fact that they decompose at lower temperature than they sublime. The employed molecules to single molecular magnets, which can be potentially used as quantum bites (qubit). The new method of deposition atomic layer injection made by Bihur Crystal company was introduced and tested. The method uses liquid solution with molecules which is driven by argon gas through pulse valve to the sample placed in ultra-high vacuum chamber. During the deposition, droplets of solution are formed on the sample surface. The solvent can be removed by light annealing or by keeping the sample in the vacuum for couple of days. The molecules were investigated by x-ray photoelectron spectroscopy and by scanning electron microscopy to determine fragmentation of the molecules, to study topography of the resultant surface and homogeneity of the deposited layer. We found conditions at which the intact molecules are deposited on the sample surfaces and form molecular nano- and micro- crystals.
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Deposition of large organic molecules under UHV
Krajňák, Tomáš ; Novák,, Jiří (referee) ; Čechal, Jan (advisor)
In this thesis, large organic molecules (DM15N, DM18N, Cu(dbm)2) were deposited. These molecules are cannot be deposited by thermal sublimation due the fact that they decompose at lower temperature than they sublime. The employed molecules to single molecular magnets, which can be potentially used as quantum bites (qubit). The new method of deposition atomic layer injection made by Bihur Crystal company was introduced and tested. The method uses liquid solution with molecules which is driven by argon gas through pulse valve to the sample placed in ultra-high vacuum chamber. During the deposition, droplets of solution are formed on the sample surface. The solvent can be removed by light annealing or by keeping the sample in the vacuum for couple of days. The molecules were investigated by x-ray photoelectron spectroscopy and by scanning electron microscopy to determine fragmentation of the molecules, to study topography of the resultant surface and homogeneity of the deposited layer. We found conditions at which the intact molecules are deposited on the sample surfaces and form molecular nano- and micro- crystals.
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Study of interactions of organic matter and its components via molecular dynamics
BARVÍKOVÁ, Hana
Humic acids and humates are principal components of humic substances major organic constituents of soil, peat, coal and water around the world. I was involved in research into molecular dynamics simulations of interactions of quartz surfaces with aqueous solutions of ions and small organic molecules representing basic building blocks of larger biomolecules and functional groups of organic matter. We studied interactions of molecules with surfaces for a set of surface charge densities corresponding to the experimentally or environmentally relevant ranges of pH values employing molecular mechanics, molecular dynamics and ab initio techniques. Simulated quartz surfaces covered the range of surface charge densities 0.00, -0.03, -0.06 and -0.12 C-m-2, approximately corresponding to pH values 4.5, 7.5, 9.5 and 11. As model molecules, benzoic acid, phenol, o-salicylic acid and their conjugated bases were chosen. My task was to prepare topologies and parametric models of selected organic matter basic building blocks organic molecules. I focused on studying interactions of these molecules in an aqueous environment with mineral surface quartz. The aim was to process simulation results and analyse conformations of the adsorption complexes and their thermodynamic properties such as interaction energies, free energies and adsorption geometries.
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Computer simulation of interactions of molecules with mineral surfaces
BARVÍKOVÁ, Hana
This thesis is focused on molecular dynamics, modelling interactions and their simulation. One of the tasks was to familiarize with GROMACS, a molecular dynamics simulation software. This work also introduces the basics of molecular dynamics and modelling interactions of organic molecules with mineral surfaces. The aim of the thesis was to solve model tasks in GROMACS and analyze the output results. The thesis describes some of the most important file formats and utilities that are needed for working with GROMACS and the use of both the formats and the utilities. In this program, I built up several systems consisting of combinations of organic molecules such as benzoic acid, phenol, salicylic acid and their conjugate bases with mineral surfaces (quartz crystal) of different surface charge density. Furthermore I analyzed the results of these simulations, behaviour of the structures and adsorption geometries and interaction energies within these systems. The thesis might also serve as a quick introduction and familiarization with GROMACS with emphasis on simulations and analysis of systems with planar interfaces. Within the MetaCentrum Project I worked on the Hermes Computer Cluster belonging to the Faculty of Science at the University of South Bohemia.
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