Lev Kantorovich

The energetics and electronic structure of defective and irregular surfaces on MgO

Ab initio calculations based on the density-functional pseudopotential approach have been used to study the fully relaxed structure, the electron distribution and the electronic density of states of (001) terraces, steps, corners and reverse corners, and of F-centers at these surface features on MgO. The calculations confirm earlier predictions of the relaxed structures of surface irregularities based on simple interaction models. A substantial narrowing of the band-gap is found at the surface, which for terraces and steps is due to surface states at the bottom of the conduction band, but for the corner and reverse corner is also due to surface states at the top of the valence band. The F-center formation energy decreases steadily as the coordination of the oxygen site is reduced. The energy of the F-center level shows a tendency to approach the top of the valence band as the coordination of its site decreases.

The Structure of the Stoichiometric and Reduced SnO2 (110) Surface

First-principles calculations based on density functional theory (DFT) and the pseudopotential method have been used to study the stoichiometric and reduced SnO2(110) surface. The ionic relaxations are found to be moderate for both the stoichiometric and reduced surfaces, and are very similar to those found in recent DFT-pseudopotential work on TiO2. Removal of neutral oxygen leaves two electrons per oxygen on the surface, which are distributed in channels passing through bridging oxygen sites. The associated electron density can be attributed to reduction of tin from Sn4+ to Sn2+, but only if the charge distribution on Sn2+ is recognized to be highly asymmetric. Reduction of the surface gives rise to a broad distribution of gap states, in qualitative agreement with spectroscopic measurements.

Study of the surface electronic structure of MgO bulk crystals and thin films

The electronic structures of the surfaces of MgO single crystals, oxidized Mg polycrystals and oxidized Mg films grown by molecular beam epitaxy on Si(100) surfaces were studied using several techniques. These include metastable impact electron spectroscopy (MIES), ultraviolet photoelectron spectroscopy (UPS (He I)), and X-ray photoelectron spectroscopy (XPS). Spectra of oxidized Mg layers on Si(100) show additional features to those obtained for cleaved MgO crystals. These spectral features are attributed to dissociative adsorption of oxygen at bulk oxygen sites. Weak heating of the oxidized Mg layers removes these features and the electronic spectra for all three studied systems become similar. However, the experimental MIES and UPS spectra, both arising mainly from the ionization of the O 2p orbitals, have different structures. They are interpreted on the basis of ab initio Hartree-Fock and density functional calculations of the electronic structures of the ideal MgO(100) surface. It is shown, that the differences in the spectra can be understood by taking into account that UPS spectra reflect the density of electronic states within several surface layers, whereas MIES probes the surface states which are the most extended into the vacuum.

Growth of epitaxial graphene: Theory and experiment

A detailed review of the literature for the last 5-10 years on epitaxial growth of graphene is presented. Both experimental and theoretical aspects related to growth on transition metals and on silicon carbide are thoroughly reviewed. Thermodynamic and kinetic aspects of growth on all these materials, where possible, are discussed. To make this text useful for a wider audience, a range of important experimental techniques that have been used over the last decade to grow (e.g. CVD, TPG and segregation) and characterize (STM, LEEM, etc.) graphene are reviewed, and a critical survey of the most important theoretical techniques is given. Finally, we critically discuss various unsolved problems related to growth and its mechanism which we believe require proper attention in future research.

Role of van der Waals interaction in forming molecule-metal junctions: flat organic molecules on the Au(111) surface.

The self-assembly of flat organic molecules on metal surfaces is controlled, apart from the kinetic factors, by the interplay between the molecule-molecule and molecule-surface interactions. These are typically calculated using standard density functional theory within the generalized gradient approximation, which significantly underestimates nonlocal correlations, i.e. van der Waals (vdW) contributions, and thus affects interactions between molecules and the metal surface in the junction. In this paper we address this question systematically for the Au(111) surface and a number of popular flat organic molecules which form directional hydrogen bonds with each other. This is done using the recently developed first-principles vdW-DF method which takes into account the nonlocal nature of electron correlation [M. Dion et al., Phys. Rev. Lett. 2004, 92, 246401]. We report here a systematic study of such systems involving completely self-consistent vdW-DF calculations with full geometry relaxation. We find that the hydrogen bonding between the molecules is only insignificantly affected by the vdW contribution, both in the gas phase and on the gold surface. However, the adsorption energies of these molecules on the surface increase dramatically as compared with the ordinary density functional (within the generalized gradient approximation, GGA) calculations, in agreement with available experimental data and previous calculations performed within approximate or semiempirical models, and this is entirely due to the vdW contribution which provides the main binding mechanism. We also stress the importance of self-consistency in calculating the binding energy by the vdW-DF method since the results of non-self-consistent calculations in some cases may be off by up to 20%. Our calculations still support the usually made assumption of the molecule-surface interaction changing little laterally suggesting that single molecules and their small clusters should be quite mobile at room temperature on the surface. These findings support a gas-phase modeling for some flat metal surfaces, such as Au(111), and flat molecules, at least as a first approximation.

An investigation into the interactions between self-assembled adenine molecules and a Au(111) surface

Two molecular phases of the DNA base adenine (A) on a Au(111) surface are observed by using STM under ultrahigh-vacuum conditions. One of these phases is reported for the first time. A systematic approach that considers all possible gas-phase two-dimensional arrangements of A molecules connected by double hydrogen bonds with each other and subsequent ab initio DFT calculations are used to characterize and identify the two phases. The influence of the gold surface on the structure of A assemblies is also discussed. DFT is found to predict a smooth corrugation potential of the gold surface that will enable A molecules to move freely across the surface at room temperature. This conclusion remains unchanged if van der Waals interaction between A and gold is also approximately taken into account. DFT calculations of the A pairs on the Au(111) surface show its negligible effect on the hydrogen bonding between the molecules. These results justify the gas-phase analysis of possible assemblies on flat metal surfaces. Nevertheless, the fact that it is not the most stable gas-phase monolayer that is actually observed on the gold surface indicates that the surface still plays a subtle role, which needs to be properly addressed.

Mapping the force field of a hydrogen-bonded assembly

Hydrogen bonding underpins the properties of a vast array of systems spanning a wide variety of scientific fields. From the elegance of base pair interactions in DNA to the symmetry of extended supramolecular assemblies, hydrogen bonds play an essential role in directing intermolecular forces. Yet fundamental aspects of the hydrogen bond continue to be vigorously debated. Here we use dynamic force microscopy (DFM) to quantitatively map the tip-sample force field for naphthalene tetracarboxylic diimide molecules hydrogen-bonded in two-dimensional assemblies. A comparison of experimental images and force spectra with their simulated counterparts shows that intermolecular contrast arises from repulsive tip-sample interactions whose interpretation can be aided via an examination of charge density depletion across the molecular system. Interpreting DFM images of hydrogen-bonded systems therefore necessitates detailed consideration of the coupled tip-molecule system: analyses based on intermolecular charge density in the absence of the tip fail to capture the essential physical chemistry underpinning the imaging mechanism.

Adsorption of atomic and molecular oxygen on the MgO (001) surface

Abstract Ab initio calculations based on density functional theory and the pseudopotential method have been used to study the energetics, fully relaxed structure, charge and spin densities, and electronic density of states of adsorbed atomic and molecular oxygen on terraces, steps, corners and reverse corners on the MgO (001) surface. The calculations include spin polarization and gradient corrections, and are performed on periodically repeated systems large enough for the adsorbed species and surface features like steps, corners and reverse corners to be regarded as isolated in most cases. We find substantial binding energies of up to 2.0 eV for atomic oxygen adsorption at oxygen terrace sites and of over 2.5 eV at the surface irregularities. On the terrace, step and corner, the most favorable adsorption mode is for atomic oxygen to bind to a lattice oxygen ion to form a peroxide ion (O 2− 2 ), and the geometry and electronic structure of the ion depend very little on the surface environment. A range of different adsorption sites and orientations for molecular oxygen have been studied but in no case does the adsorption energy exceed 0.2 eV, in agreement with experimental indications. The relevance of our findings to an understanding of oxygen gas-surface exchange is discussed.

Adenine monolayers on the Au(111) surface: Structure identification by scanning tunneling microscopy experiment and ab initio calculations

From an interplay between scanning tunneling microscopy (STM) and ab initio density functional theory (DFT) we have identified and characterized two different self-assembled adenine (A) structures formed on the Au(111) surface. The STM observations reveal that both structures have a hexagonal geometry in which each molecule forms double hydrogen bonds with three nearest neighbors. One of the A structures, with four molecules in the primitive cell, has p2gg space group symmetry, while the other one, with two molecules in the cell, has p2 symmetry. The first structure is observed more frequently and is found to be the dominating structure after annealing. Experimental as well as theoretical findings indicate that the interaction of A molecules with the gold surface is rather weak and smooth across the surface. This enabled us to unequivocally characterize the observed structures, systematically predict all structural possibilities, based on all known A-A dimers, and provisionally optimize positions of the A molecules in the cell prior to full-scale DFT calculations. The theoretical method is a considerable improvement compared to the approach suggested previously by Kelly and Kantorovich [Surf. Sci. 589, 139 (2005)]. We propose that the less ordered p2gg symmetry structure is observed more frequently due to kinetic effects during island formation upon deposition at room temperature.

Specificity of Watson–Crick Base Pairing on a Solid Surface Studied at the Atomic Scale

by hydrogen bonds is thought to be the crucial factor for the recognition of nucleobases, and base pairing probably also played an important role in the polymerization of the first oligonucleotide. It has been shown that short RNA strands can act as templates that catalyze the polymerization of complementary RNA strands from activated nucleotides in