Identifying On-Surface Site-Selective Chemical Conversions by Theory-Aided NEXAFS Spectroscopy: The Case of Free-Base Corroles on Ag(111).

We demonstrate here that theory-assisted near-edge X-ray absorption fine-structure (NEXAFS) spectroscopy enables the site-sensitive monitoring of on-surface chemical reactions, thus, providing information not accessible by other techniques. As a prototype example, we have used free-base 5,10,15-tris(pentafluorophenyl)corroles (3H-TpFPC) adsorbed on Ag(111) and present a detailed investigation of the angle-dependent NEXAFS of this molecular species as well as of their thermally induced derivatives. For this, we have recorded experimental C and N K-edge NEXAFS spectra and interpret them based on XAS cross-section calculations by using a continuous fraction approach and core-hole including multiprojector PAW pseudopotentials within DFT. We have characterized the as-deposited low temperature (200 K) phase and unraveled the subsequent changes induced by dehydrogenation (at 330 K) and ring-closure reactions (at 430 K). By exemplarily obtaining profound insight into the on-surface chemistry of free-base corrolic species adsorbed on a noble metal this work highlights how angle-dependent XAS combined with accurate theoretical modeling can serve for the investigation of on-surface reactions, whereby even highly similar molecular structures, such as tautomers and isomers, can be distinguished.

Surface induced vibrational modes in the fluorescence spectra of PTCDA adsorbed on the KCl(100) and NaCl(100) surfaces.

We report a combined experiment-theory study on low energy vibrational modes in fluorescence spectra of perylene-3,4,9,10-tetracarboxylic acid dianhydride (PTCDA) molecules. Using very low coverages, isolated molecules were adsorbed on terrace sites or at sites located at residual steps on (100) oriented alkali halide films (KCl and NaCl). The low energy modes couple to the optical transition only because the PTCDA molecule is geometrically distorted (C2v) upon adsorption on the surface; they would be absent for the parent planar (D2h) PTCDA molecule. The modes differ in number and energy for molecules adsorbed on regular terrace sites and molecules adsorbed at step edge sites. Modes appearing for step edge sites have the character of frustrated rotations. Their coupling to the optical transition is a consequence of the further reduced symmetry of the step edge sites. We find a larger number of vibrational modes on NaCl than on KCl. We explain this by the stronger electrostatic bonding of the PTCDA on NaCl compared to KCl. It causes the optical transition to induce stronger changes in the molecular coordinates, thus leading to larger Franck-Condon factors and thus stronger coupling. Our results demonstrate how optical spectroscopy can be used to gain information on adsorption sites of molecules at low surface concentrations.

Influence of structural defects and oxidation onto hole conductivity in P3HT.

The effect of structural imperfections as well as oxygen impurities on the quantum conductance of poly(3-hexylthiophene) is calculated from first-principles by solving the scattering problem for molecular structures obtained within density functional theory. It is shown that the conductivity of molecular crystals perpendicular to the polymer chains depends strongly on the stacking geometry and is roughly described within the Wentzel-Kramers-Brillouin approximation. Furthermore, it is found that local relaxation for twisted or bent polymer chains efficiently restores the conductance that drops substantially for sharp kinks with curvature radii smaller than 17 Å and rotations in excess of ∼60°. In contrast, isomer defects in the coupling along the chain direction are of minor importance for the intrachain transmission. Also, oxidation of the side chains as well as molecular sulfur barely changes the coherent transport properties, whereas oxidation of thiophene group carbon atoms drastically reduces the conductance.

Structure formation in diindenoperylene thin films on copper(111).

First-principles calculations were combined with scanning tunneling microscopy (STM) measurements to analyze the adsorption of diindenoperylene (DIP) molecules on Cu(111) surfaces. The influence of the substrate on the geometry of single adsorbed molecules, their diffusion barriers, as well as the role of step-edges and intermolecular interactions for molecular self-assembly and structure growth are studied. Long-range ordered arrangements of DIP molecules are found to be most favorable irrespective of the terrace width. Energetically less favored short-range order structures, however, are observed as well.

The atomic structure of ternary amorphous TixSi1-xO2 hybrid oxides.

Atomic length-scale order characteristics of binary and ternary amorphous oxides are presented within the framework of ab initio theory. A combined numerically efficient density functional based tight-binding molecular dynamics and density functional theory approach is applied to model the amorphous (a) phases of SiO2 and TiO2 as well as the amorphous phase of atomically mixed TixSi1-xO2 hybrid-oxide alloys over the entire composition range. Short and mid-range order in the disordered material phases are characterized by bond length and bond-angle statistics, pair distribution function analysis, coordination number and coordination polyhedra statistics, as well as ring statistics. The present study provides fundamental insights into the order characteristics of the amorphous hybrid-oxide frameworks formed by versatile types of TiOn and SiOm coordination polyhedra. In a-SiO2 the fourfold crystal coordination of Si ions is almost completely preserved and the atomic structure is widely dominated by ring-like mid-range order characteristics. In contrast, the structural disorder of a-TiO2 arises from short-range disorder in the local coordination environment of the Ti ion. The coordination number analysis indicates a large amount of over and under-coordinated Ti ions (coordination defects) in a-TiO2. Aside from the ubiquitous distortions of the crystal-like coordinated polyhedra, even the basic coordination-polyhedra geometry type changes for a significant fraction of TiO6 units (geometry defects). The combined effects of topological and chemical disorder in a-TixSi1-xO2 alloys lead to a continuos increase in both the Si as well as the Ti coordination number with the chemical composition x. The important roles of intermediate fivefold coordination states of Ti and Si cations are highlighted for ternary a-TixSi1-xO2 as well as for binary a-TiO2. The continuous decrease in ring size with increasing Ti content reflects the progressive loss of mid-range order structure characteristics and the competing roles of network forming and network modifying SiOm and TiOn units in the mixed hybrid oxides.

Atomic structure of interface states in silicon heterojunction solar cells.

Combining orientation dependent electrically detected magnetic resonance and g tensor calculations based on density functional theory we assign microscopic structures to paramagnetic states involved in spin-dependent recombination at the interface of hydrogenated amorphous silicon crystalline silicon (a-Si:H/c-Si) heterojunction solar cells. We find that (i) the interface exhibits microscopic roughness, (ii) the electronic structure of the interface defects is mainly determined by c-Si, (iii) we identify the microscopic origin of the conduction band tail state in the a-Si:H layer, and (iv) present a detailed recombination mechanism.

Identification of the nitrogen split interstitial (N-N)(N) in GaN.

Combining electron paramagnetic resonance, density functional theory, and positron annihilation spectroscopy (PAS), we identify the nitrogen interstitial defect in GaN. The isolated interstitial is unstable and transforms into a split interstitial configuration (N-N)(N). It is generated by particle irradiation with an introduction rate of a primary defect, pins the Fermi level at E(C)-1.0 eV for high fluences, and anneals out at 400 °C. The associated defect, the nitrogen vacancy, is observed by PAS only in the initial stage of irradiation.

The electronic structure and optical response of rutile, anatase and brookite TiO2.

In this study, we present a combined density functional theory and many-body perturbation theory study on the electronic and optical properties of TiO(2) brookite as well as the tetragonal phases rutile and anatase. The electronic structure and linear optical response have been calculated from the Kohn-Sham band structure applying (semi)local as well as nonlocal screened hybrid exchange-correlation density functionals. Single-particle excitations are treated within the GW approximation for independent quasiparticles. For optical response calculations, two-particle excitations have been included by solving the Bethe-Salpeter equation for Coulomb correlated electron-hole pairs. On this methodological basis, gap data and optical spectra for the three major phases of TiO(2) are provided. The common characteristics of brookite with the rutile and anatase phases, which have been discussed more comprehensively in the literature, are highlighted. Furthermore, the comparison of the present calculations with measured optical response data of rutile indicate that discrepancies discussed in numerous earlier studies are due to the measurements rather than related to an insufficient theoretical description.

Extended atomic hydrogen dimer configurations on the graphite(0001) surface.

We present density functional theory calculations and scanning tunneling microscopy experiments investigating the structures and kinetics of extended hydrogen dimer configurations on the graphite (0001) surface. We identify several hydrogen dimer structures where surface mediated interactions between the two hydrogen atoms lead to increased binding energy even at interatom separations as large as 7 A. By modeling the formation of dimers as sequential adsorption of hydrogen atoms, we find that these dimer configurations exhibit decreased barriers to sticking for the second H atom, compared to the sticking barrier of an H atom on the clean surface. According to our calculations, the activation energies for desorption of a single H atom from any of the experimentally observed extended dimers are higher than the barriers for diffusion to the paradimer configuration. Consequently, molecular hydrogen formation out of the extended dimer structures takes place via diffusion over the paradimer configuration.

Extended one-dimensional supramolecular assembly on a stepped surface.

2,6-naphthalene-dicarboxylic acid was adsorbed on a Ag110 surface with an average terrace width of only some tens of a nm. Scanning tunneling microscopy shows that the adsorbates self-assemble into one-dimensional mesoscale length chains. These extend over several hundred nanometers and thus the structure exhibits an unprecedented tolerance to monatomic surface steps. Density functional theory and x-ray photoelectron spectroscopy explain the behavior by a strong intermolecular hydrogen bond plus a distinct template-mediated directionality and a high degree of molecular backbone flexibility.

Clustering of chemisorbed H(D) atoms on the graphite (0001) surface due to preferential sticking.

We present scanning tunneling microscopy experiments and density functional theory calculations which reveal a unique mechanism for the formation of hydrogen adsorbate clusters on graphite surfaces. Our results show that diffusion of hydrogen atoms is largely inactive and that clustering is a consequence of preferential sticking into specific adsorbate structures. These surprising findings are caused by reduced or even vanishing adsorption barriers for hydrogen in the vicinity of already adsorbed H atoms on the surface and point to a possible novel route to interstellar H2 formation.

Metastable structures and recombination pathways for atomic hydrogen on the graphite (0001) surface.

We present scanning tunneling microscopy results which reveal the existence of two distinct hydrogen dimer states on graphite basal planes. Density functional theory calculations allow us to identify the atomic structure of these states and to determine their recombination and desorption pathways. Direct recombination is only possible from one of the two dimer states. This results in increased stability of one dimer species and explains the puzzling double peak structure observed in temperature programmed desorption spectra for hydrogen on graphite.