Modelling the onset of oxide formation on metal surfaces from first principles

The formation of ultrathin oxide layers on metal surfaces is a non-thermally-activated process which takes place spontaneously at very low temperatures within nanoseconds. This paper reports mechanistic details of the initial oxidation of bare metal surfaces, in particular Al(111) and TiN(001), as obtained by means of first-principles molecular dynamics modelling within the Density-Functional Theory. It is shown that the reactions of bare metal surfaces with O2 molecules take place according to a 'hot-atom' dissociative mechanism which is triggered by the filling of the sigma-star antibonding molecular orbital and is characterised by a sudden release of a large amount of kinetic energy. This released energy provides a driving force for metal/oxygen place-exchange processes which are responsible for the onset of oxide formation at virtually 0 K and at oxygen coverages well below 1 monolayer (ML). Further simulations of the oxidation reactions reveal that a disordered ultrathin oxide forms on Al(111), whereas a rather ordered structure develops on TiN(001) following a selective oxidation process which leaves clusters of Ti vacancies in the TiN lattice underneath the oxide layer

Growth of Platinum Clusters in Solution and on Biopolymers: The Microscopic Mechanisms

Thema der vorgelegten Dissertation ist der Mechanismus der Keimbildung und des Wachstums von Platinclustern in Lösung und auf Biopolymeren nach der Reduktion von Platin-Salzen. Die Untersuchung wird auf atomarer Skala durch ab-initio Molekulardynamik mit der Methode von Car und Parrinello durchgeführt. In einem klassischen, generell akzeptierten Mechanismus erfolgt die Aggregation von Pt-Atomen nur nach kompletter Reduktion der Pt(II)-Komplexen zum metallischen Pt(0)-Zustand. Im Gegensatz dazu, in der hier beobachteten Reaktionsablauf entstehen stabile Pt-Pt-Bindungen schon nach einem einzigen Reduktionsschritt. Darüber hinaus wird es gefunden, dass kleine Pt-Cluster durch Addition von unreduzierten PtCl2(H2O)2-Komplexen wachsen können. Das stimmt mit einem experimentell beocbachteten autokatalytischen Clusterwachstumsmechanismus überein. Es wird weiterhin gefunden, dass Pt(II)-Komplexe, die kovalent an DNA oder an Proteine gebunden sind, als sehr effiziente Nukleationszentren für das weitere Metallclusterwachstum wirken können. Das ist eine Konsequenz des starken Donor-Charakters der organischen Liganden, in derer Anwesenheit stärkere Metall-Metall-Bindungen als frei in der Lösung gebildet werden können. In der Tat, in Metallisierungsexperimenten können 5 Nanometer dünne, mehrere Mikrometer lange, regelmässige Clusterkette erzeugt werden, die rein heterogen auf das Biomolekulare Templat gewachsen sind.In this thesis we investigate the molecular mechanisms of platinum cluster nucleation and growth in solution and on biopolymers by means of first-principles molecular dynamics. In contrast with a classical picture where clusters nucleate by aggregation of metallic Pt(0) atoms, we find that Pt--Pt bonds can form between dissolved Pt(II) complexes already after a single reduction step. Furthermore, we observe that small clusters grow by addition of unreduced PtCl2(H2O)2 complexes, consistently with an autocatalytic growth mechanism. Moreover Pt(II) ions covalently bound to biopolymers are found to act as preferred nucleation sites for the formation of clusters. This is a consequence of the strong donor character of the organic ligands which induce the formation of stronger metal-metal bonds than those obtained in solution. In fact, in metallization experiments we obtain a clean and purely heterogeneous metallization of single DNA molecules leading to thin and uniform Pt cluster chains extended over several microns

Density functional theory study of Fe(II) adsorption and oxidation on goethite surfaces

We study the interactions between Fe(II) aqua complexes and surfaces of goethite (alpha-FeOOH) by means of density functional theory calculations including the so-called Hubbard U correction to the exchange-correlation functional. Using a thermodynamic approach, we find that (110) and (021) surfaces in contact with aqueous solutions are almost equally stable, despite the evident needlelike shape of goethite crystals indicating substantially different reactivity of the two faces. We thus suggest that crystal anisotropy may result from different growth rates due to virtually barrierless adsorption of hydrated ions on the (021) but not on the (110) surface. No clear evidence is found for spontaneous electron transfer from an adsorbed Fe(II) hex-aqua complex to a defect-free goethite substrate. Crystal defects are thus inferred to play an important role in assisting such electron transfer processes observed in a recent experimental study. Finally, goethite surfaces are observed to enhance the partial oxidation of adsorbed aqueous Fe(II) upon reaction with molecular oxygen. We propose that this catalytic oxidation effect arises from donation of electronic charge from the bulk oxide to the oxidizing agent through shared hydroxyl ligands anchoring the Fe(II) complexes on the surface

Exploration, Representation, and Rationalization of the Conformational Phase Space of N-Glycans

Despite their fundamental biological relevance, structure- property relationships in N-glycans are fundamentally lacking, and their highly multidimensional compositional and conformational phase spaces remain largely unexplored. The torsional flexibility of the glycosidic linkages and the ring dynamics result in wide, rugged free-energy landscapes that are difficult to sample in molecular dynamics simulations. We show that a novel enhanced-sampling scheme combining replica exchange with solute and collective-variable tempering, enabling transitions over all relevant energy barriers, delivers converged distributions of solvated N-glycan conformers. Several dimensionality reduction algorithms are compared and employed to generate conformational free-energy maps in two dimensions. Together with an originally developed conformation-based nomenclature scheme that uniquely identifies glycan conformers, our modeling procedure is applied to reveal the effect of chemical substitutions on the conformational ensemble of selected high-mannose-type and complex glycans. Moreover, the structure-prediction capabilities of two commonly used glycan force fields are assessed via the theoretical prediction of experimentally available nuclear magnetic resonance J-coupling constants. The results especially confirm the key role of w and yi torsion angles in discriminating between different conformational states and suggest an intriguing correlation between the torsional and ring-puckering degrees of freedom that may be biologically relevant

Dissociative adsorption of methane on surface oxide structures of Pd-Pt alloys

The dissociative adsorption of methane on variously oxidized Pd, Pt and Pd-Pt surfaces is investigated using density-functional theory, as a step towards understanding the combustion of methane on these materials. For Pd-Pt alloys, models of surface oxide structures are built on the basis of known oxides on Pd and Pt. The methane adsorption energy presents large variations depending on the oxide structure and composition. Adsorption is endothermic on the bare Pd(111) metal surface as well as on stable thin layer oxide structures such as the ($\sqrt{5}\times\sqrt{5}$) surface oxide on Pd(100) and the PtO$_2$-like oxide on Pt(111). Instead, large adsorption energies are obtained for the (100) surface of bulk PdO, for metastable mixed Pd$_{1-x}$Pt$_x$O$_{4/3}$ oxide layers on Pt(100), and for Pd-Pt(111) surfaces covered with one oxygen monolayer. In the latter case, we find a net thermodynamic preference for a direct conversion of methane to methanol, which remains adsorbed on the oxidized metal substrates via weak hydrogen-bond interactions

Stress Development and Impurity Segregation during Oxidation of the Si(100) Surface

We have studied the segregation of P and B impurities during oxidation of the Si(100) surface by means of combined static and dynamical first-principles simulations based on density functional theory. In the bare surface, dopants segregate to chemically stable surface sites or to locally compressed subsurface sites. Surface oxidation is accompanied by development of tensile surface stress up to 2.9 N/m at a coverage of 1.5 monolayers of oxygen and by formation of oxidised Si species with charges increasing approximately linearly with the number of neighbouring oxygen atoms. Substitutional P and B defects are energetically unstable within the native oxide layer, and are preferentially located at or beneath the Si/SiOx interface. Consistently, first-principles molecular dynamics simulations of native oxide formation on doped surfaces reveal that dopants avoid the formation of P-O and B-O bonds, suggesting a surface oxidation mechanism whereby impurities remain trapped at the Si/SiOx interface. This seems to preclude a direct influence of impurities on the surface electrostatics and, hence, on the interactions with an external environment

Development of a Classical Force Field for the Oxidised Si Surface: Application to Hydrophilic Wafer Bonding

We have developed a classical two- and three-body interaction potential to simulate the hydroxylated, natively oxidised Si surface in contact with water solutions, based on the combination and extension of the Stillinger-Weber potential and of a potential originally developed to simulate SiO2 polymorphs. The potential parameters are chosen to reproduce the structure, charge distribution, tensile surface stress and interactions with single water molecules of a natively oxidised Si surface model previously obtained by means of accurate density functional theory simulations. We have applied the potential to the case of hydrophilic silicon wafer bonding at room temperature, revealing maximum room temperature work of adhesion values for natively oxidised and amorphous silica surfaces of 97 mJ/m2 and 90mJ/m2, respectively, at a water adsorption coverage of approximately 1 monolayer. The difference arises from the stronger interaction of the natively oxidised surface with liquid water, resulting in a higher heat of immersion (203 mJ/m2 vs. 166 mJ/m2), and may be explained in terms of the more pronounced water structuring close to the surface in alternating layers of larger and smaller density with respect to the liquid bulk. The computed force-displacement bonding curves may be a useful input for cohesive zone models where both the topographic details of the surfaces and the dependence of the attractive force on the initial surface separation and wetting can be taken into account

Water structuring and collagen adsorption at hydrophilic and hydrophobic silicon surfaces

The adsorption of a collagen fragment on both a hydrophobic, hydrogen-terminated and a hydrophilic, natively oxidised Si surface is investigated using all-atom molecular dynamics. While favourable direct protein-surface interactions via localised contact points characterise adhesion to the hydrophilic surface, evenly spread surface/molecule contacts and stabilisation of the helical structure occurs upon adsorption on the hydrophobic surface. In the latter case, we find that adhesion is accompanied by a mutual fit between the hydrophilic/hydrophobic pattern within the protein and the layered water structure at the solid/liquid interface, which may provide an additional driving force to the classic hydrophobic effect

Anti-Staphylococcal Calopins from Fruiting Bodies of Caloboletus radicans

Three new and seven known calopins were isolated from Caloboletus radicans. The structures of the new cyclocalopins, 8-deacetylcyclocalopin B (1), cyclocalopin A-15-ol (2), and 12,15-dimethoxycyclocalopin A (3), were mainly elucidated by NMR and MS data analysis. The stereochemistry of 1–3 was assigned based on ROE correlations, coupling constants and by comparison of their CD spectra with those of similar known calopins. While 1–10 were inactive against two cancer cell lines, they displayed antistaphylococcal activity against methicillin-resistant Staphylococcus aureus strains (MRSA) with MIC values of 16−256 μg/mL. Moreover, some calopins were active against the fish pathogen Enterococcus faecalis F1B1