The work in this thesis demonstrates how to obtain an atomic-scale picture of a diverse set of complex surface structures observed using STM, under disparate conditions. Chapters 4−6 each represent... Show moreThe work in this thesis demonstrates how to obtain an atomic-scale picture of a diverse set of complex surface structures observed using STM, under disparate conditions. Chapters 4−6 each represent a different approach to answer the same question: How can we find out what a surface looks like at the atomic scale? By employing appropriate theoretical tools that complement the experimental conditions and measurement techniques, it is possible to compare the results from theory and experiment in an intuitive manner to obtain additional insights. Additionally, Chapter 4 shows that theoretical studies, which do not take experimental conditions into account appropriately, can lead to wrong conclusions. Show less
Ice, the solid state of water, plays an important role on our planet as well as the entire universe.Despite the fact that an individual water molecule has a very simple structure, its chemical... Show moreIce, the solid state of water, plays an important role on our planet as well as the entire universe.Despite the fact that an individual water molecule has a very simple structure, its chemical bonding in the solid phase can be surprisingly complex.Nowadays, atomistic computational models allow to describing and understanding these properties in a way that has not been possible for a long time.Chemical interactional potentials are at the heart of these atomistic models.In increasing order of complexity, these potentials range from simple pair potentials over polarizable force fields up to density functional theory (DFT).It is an ongoing scientific challenge is to improve and test these potentials.This thesis attempts to provide some answers to the following research questions:(i) How important is the contribution of zero-point energy to thermodynamical properties of ice phases?(ii) How accurately do available interaction potentials allow to model (small) differences between H2O and D2O ices related to nuclear quantum effects?(iii) Do interaction potentials need to be improved when nuclear quantum effects in ice are taken into account? Show less
This dissertation focused on computational methods based on first principles calculations using the Density Functional Theory (DFT) framework. Emphasis was laid on affordable methods that can... Show moreThis dissertation focused on computational methods based on first principles calculations using the Density Functional Theory (DFT) framework. Emphasis was laid on affordable methods that can provide a tradeoff between computational expense and accuracy. Specifically, we investigated solvation effects near the surface of the electrode, used thermodynamic cycles to compute solution-phase energies and also proposed a workflow to detect gas-phase errors on the free energies of target molecules. We used these simple methods to study complex adsorption processes at the PdMLPt(111) electrode surface. DFT and experimental studies (performed by Dr. Chen from our group) were crucial to guide the investigation forward. Show less
Fundamental understanding of molecular reactions on metal surfaces is important for improving heterogeneous catalysis. Therefore, the reaction of small molecules on well-defined metal surfaces is... Show moreFundamental understanding of molecular reactions on metal surfaces is important for improving heterogeneous catalysis. Therefore, the reaction of small molecules on well-defined metal surfaces is investigated with state-of-the-art DFT calculations. Efforts are made to improve the agreement between experiment and theory by employing density functionals belonging to a higher level of theory than typically used. Furthermore, molecular dynamics are performed both with ab initio calculations and precomputed potential energy surfaces to investigate reaction mechanisms. This way dynamical aspects of reaction mechanisms can be investigated, e.g., the effect of rovibrational excitation of a molecule on the reaction probability and mechanism. Show less
Organic molecules in interstellar space are important as they influence the structure of galaxies and star formations. Studying catalytic processes in space allows us to understand how molecular... Show moreOrganic molecules in interstellar space are important as they influence the structure of galaxies and star formations. Studying catalytic processes in space allows us to understand how molecular species are formed and chemically evolved in the interstellar medium and solar system objects. Quantum chemical methods, such as “Density Functional Theory” (DFT), can be employed to study the chemical pathways for the formation of molecular species, which is challenging with only observations and experiments. This thesis studies, with DFT methods, how polycyclic aromatic hydrocarbons (PAHs), the most abundant organic species in space, catalyze the formation of molecular hydrogen in the interstellar medium. Specifically, how linear PAHs become superhydrogenated and how the presence of Stone Wales defect in PAHs contributes to their catalytic activity for molecular hydrogen formation. In addition, this thesis reports the study of the catalytic activity of forsterite, a silicate mineral abundant in grains, asteroids, and meteorites. Specifically, the presence of Schottky MgO vacancy in forsterite can catalyze the C-H activation of PAHs as the first step to study the breakdown reaction of PAHs in asteroidal settings. The latter is indispensable to understand the formation of the so-called organic inventory of solar system objects. Show less
The thesis is focused on the DNA-cleaving antibiotic bleomycin that is successfully used in the chemotherapy against several types of cancer like head and neck cancer or certain lymphomas and... Show moreThe thesis is focused on the DNA-cleaving antibiotic bleomycin that is successfully used in the chemotherapy against several types of cancer like head and neck cancer or certain lymphomas and testicular cancer. Although it has been in use for more than two decades, the mechanism of its action is not known. Thus the harmful side effects are difficult to eliminate. On the other hand the process of design or improvement of pharmaceuticals is extremely complex and expensive. Therefore a new trend within drug discovery is emerging with the application of clean chemistry, by performing molecular modeling of new compounds and by running virtual tests to assess their suitability before an expensive synthesis attempt is made. In the thesis, the contribution of different computational methods into this field is discussed, emphasizing the growing role played by quantum mechanical methods. Using state-of-the-art methods, an insight into the mechanism of bleomycin action was gained. The possible reaction pathways of the active bleomycin-Fe(III)-OOH complex with the deoxyribose sugar of DNA were investigated. The simulations show that a facile decaying process involves a homolytic O-O bond cleavage with an almost simultaneous hydrogen atom abstraction. The formation of a hydrogen bond appears to be crucial for the O-O bond cleavage in the Fe(III)-OOH species. The highly selective reaction between the bleomycin drug and the genetic material comes from the selectivity of the created hydrogen bond Show less
