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DFT simulations of interaction of organic molecules with oriented surfaces
 Krejčí, Ondřej ; Kocán, Pavel (advisor) ; Lazar, Petr (referee) ; Palotás, Krisztián (referee)
This thesis concerns my theoretical calculations and simulations in comparison with experimental measurements acquired by means of surface science techniques on bare surfaces and molecules adsorbed on surfaces. In the beginning of the thesis I briefly describe the density functional theory (DFT) method, which is used for calculations of geometric and electronic structure of surfaces and absorbed molecules. It is followed by a quick overview of the scanning probe microscopy (SPM) and X-ray spectroscopy techniques that provided experimental context for my calculations. In the later part of my thesis I introduce publications on which I participated. In these works, direct results of my DFT calculations or simulations based on DFT outputs helped to reveal geometric and electronic structure of acetophenone adsorbed on Si(111) surface, on-surface oligomerized organic molecules and boron atoms used for substitational doping of graphene. The simulations also enable us to probe a laser initiated CO hydrogenation in real time. A big part of my work was the development of some simulation methods for SPM imaging of molecules on surfaces with flexible tip apexes. These simulation methods helped to create a comprehensive overview of SPM techniques performed with flexible tip apexes. 1
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