We report on a joint experimental and theoretical study of the ordered structures of melamine molecules formed on the Au( 111)-( 22× 3) surface. Scanning tunneling microscopy (STM) images taken under UHV conditions reveal two distinct monolayers one of which has never been reported before on gold. We also find that one of the structures may serve as a transition region ("domain wall") between islands formed by the other arrangement. Using state-of-the-art density functional calculations in conjunction with a systematic gas-phase analysis based on considering all planar structures melamine molecules can form with each other, we propose atomistic models for both structures and the transition region.

Nonsymmetrical organic molecules adsorbed on solid surfaces may assemble into random networks, thereby providing model systems for organic glasses that can be directly observed by scanning tunneling microscopy (STM). We investigated the structure of a disordered cytosine network on a gold(111) surface created by thermal quenching, to temperatures below 150 K, of the two-dimensional fluid present on the surface at room temperature. Comparison of STM images to density functional theory calculations allowed us to identify three elementary structural motifs (zigzag filaments and five- and six-membered rings) that underlie the whole supramolecular random network. The identification of elementary structural motifs may provide a new framework for understanding medium-range order in amorphous and glassy systems.

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.

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.

Using calculations based on the ab initio density functional theory, we for the first time report all possible planar DNA base adenine homodimers. Two density functionals and both localized and plane wave basis sets were used, and the results are compared with previous quantum chemical and semiempirical calculations available for a few pairs. We find that there are 21 possible planar adenine pairs with variable binding energies ranging from -0.03 to -0.86 eV. More stable pairs are associated with two strong hydrogen bonds formed between the monomers, while the least stable pairs are characterized by two or one relatively weak bonds. We find that stable hydrogen bonds can be characterized by the difference charge density that shows well-developed regions of alternating excess and depletion of the electron charge similar to a "kebab" structure. The presented detailed information on all planar adenine pairs can be utilized, for example, in considering possible adenine monolayers seen on various surfaces.

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.

We apply the nonequilibrium Green's function formalism to the problem of a multiterminal nanojunction subject to an arbitrary time-dependent bias. In particular, we show that taking a generic one-particle system Hamiltonian within the wide-band-limit approximation, it is possible to obtain a closed analytical expression for the current in each lead. Our formula reduces to the well-known result of Jauho et al. [Phys. Rev. B 50, 5528 (1994)] in the limit where the switch-on time is taken to the remote past, and to the result of Tuovinen et al. [Phys. Rev. B 89, 085131 (2014)] when the bias is maintained at a constant value after the switch-on. As we use a partition-free approach, our formula contains both the long-time current and transient effects due to the sudden switch-on of the bias. Numerical calculations performed for the simple case of a single-level quantum dot coupled to two leads are performed for a sinusoidally varying bias. At certain frequencies of the driving bias, we observe "ringing" oscillations of the current, whose dependence on the dot level, level width, oscillation amplitude, and temperature is also investigated.

We demonstrate explicitly that the derivation by Adelman and Doll ͑AD͒ ͓J. Chem. Phys. 64, 2375 ͑1976͔͒ of the generalized Langevin equation ͑GLE͒ to describe dynamics of an extended solid system by considering its finite subsystem is inconsistent because it relies on performing statistical averages over the entire system when establishing properties of the random force. This results in the random force representing a nonstationary process opposite to one of the main assumptions made in AD that the random force corresponds to a stationary stochastic process. This invalidates the derivation of the Brownian ͑or Langevin͒ form of the GLE in AD. Here we present a different and more general approach in deriving the GLE. Our method generalizes that of AD in two main aspects: ͑i͒ the structure of the finite region can be arbitrary ͑e.g., anharmonic͒, and ͑ii͒ ways are indicated in which the method can be implemented exactly if the phonon Green's function of the harmonic environment region surrounding the anharmonic region is known, which is, e.g., the case when the environment region represents a part of a periodic solid ͑the bulk or a surface͒. We also show that in general after the local perturbation has ceased, the system returns to thermodynamic equilibrium with the distribution function for region 1 being canonical with respect to an effective interaction between atoms, which includes instantaneous response of the surrounding region. Note that our method does not rely on the assumption made in AD that the stochastic force correlation function depends on the times difference only ͑i.e., the random force corresponds to a stationary random process͒. In fact, we demonstrate explicitly that generally this is not the case. Still, the correct GLE can be obtained, which satisfies exactly the fluctuation-dissipation theorem.