Coexisting Honeycomb and Kagome Characteristics in the Electronic Band Structure of Molecular Graphene.

We uncover the electronic structure of molecular graphene produced by adsorbed CO molecules on a copper (111) surface by means of first-principles calculations. Our results show that the band structure is fundamentally different from that of conventional graphene, and the unique features of the electronic states arise from coexisting honeycomb and Kagome symmetries. Furthermore, the Dirac cone does not appear at the K-point but at the Γ-point in the reciprocal space and is accompanied by a third, almost flat band. Calculations of the surface structure with Kekulé distortion show a gap opening at the Dirac point in agreement with experiments. Simple tight-binding models are used to support the first-principles results and to explain the physical characteristics behind the electronic band structures.

Exchange-Correlation Catastrophe in Cu-Au: A Challenge for Semilocal Density Functional Approximations.

Semilocal density functional approximations occupy the second rung of the Jacob's ladder model and are thus expected to have certain limits to their applicability. A recent study [Y. Zhang, G. Kresse, and C. Wolverton, Phys. Rev. Lett. 112, 075502 (2014)] hypothesizes that the formation energy, being one of the key quantities in alloy theory, would be beyond the grasp of semilocal density functional theory (DFT). Here, we explore the physics of semilocal DFT formation energies and shed light on the connection between the accuracy of the formation energy and the ability of a semilocal approximation to produce accurate lattice constants. We demonstrate that semilocal functionals designed to perform well for alloy constituents can concomitantly solve the problem of alloy formation energies.

Collective excitations and viscosity in liquid Bi.

The analysis of extensive density functional/molecular dynamics simulations (over 500 atoms, up to 100 ps) of liquid bismuth at four temperatures between 573 K and 1023 K has provided details of the dynamical structure factors, the dispersion of longitudinal and transverse collective modes, and related properties (power spectrum, viscosity, and sound velocity). Agreement with available inelastic x-ray and neutron scattering data and with previous simulations is generally very good. The results show that density functional/molecular dynamics simulations can give dynamical information of good quality without the use of fitting functions, even at long wavelengths.

Oxygen adsorption on (100) surfaces in Fe-Cr alloys.

The adsorption of oxygen on bcc Fe-Cr(100) surfaces with two different alloy concentrations is studied using ab initio density functional calculations. Atomic-scale analysis of oxygen-surface interactions is indispensable for obtaining a comprehensive understanding of macroscopic surface oxidation processes. Up to two chromium atoms are inserted into the first two surface layers. Atomic geometries, energies and electronic properties are investigated. A hollow site is found to be the preferred adsorption site over bridge and on-top sites. Chromium atoms in the surface and subsurface layers are found to significantly affect the adsorption properties of neighbouring iron atoms. Seventy-one different adsorption geometries are studied, and the corresponding adsorption energies are calculated. Estimates for the main diffusion barriers from the hollow adsorption site are given. Whether the change in the oxygen affinity of iron atoms can be related to the chromium-induced charge transfer between the surface atoms is discussed. The possibility to utilize the presented theoretical results in related experimental research and in developing semiclassical potentials for simulating the oxidation of Fe-Cr alloys is addressed.

First-principles data set of 45,892 isolated and cation-coordinated conformers of 20 proteinogenic amino acids.

We present a structural data set of the 20 proteinogenic amino acids and their amino-methylated and acetylated (capped) dipeptides. Different protonation states of the backbone (uncharged and zwitterionic) were considered for the amino acids as well as varied side chain protonation states. Furthermore, we studied amino acids and dipeptides in complex with divalent cations (Ca(2+), Ba(2+), Sr(2+), Cd(2+), Pb(2+), and Hg(2+)). The database covers the conformational hierarchies of 280 systems in a wide relative energy range of up to 4 eV (390 kJ/mol), summing up to a total of 45,892 stationary points on the respective potential-energy surfaces. All systems were calculated on equal first-principles footing, applying density-functional theory in the generalized gradient approximation corrected for long-range van der Waals interactions. We show good agreement to available experimental data for gas-phase ion affinities. Our curated data can be utilized, for example, for a wide comparison across chemical space of the building blocks of life, for the parametrization of protein force fields, and for the calculation of reference spectra for biophysical applications.

Atomic and electronic structures of an extremely fragile liquid.

The structure of high-temperature liquids is an important topic for understanding the fragility of liquids. Here we report the structure of a high-temperature non-glass-forming oxide liquid, ZrO2, at an atomistic and electronic level. The Bhatia-Thornton number-number structure factor of ZrO2 does not show a first sharp diffraction peak. The atomic structure comprises ZrO5, ZrO6 and ZrO7 polyhedra with a significant contribution of edge sharing of oxygen in addition to corner sharing. The variety of large oxygen coordination and polyhedral connections with short Zr-O bond lifetimes, induced by the relatively large ionic radius of zirconium, disturbs the evolution of intermediate-range ordering, which leads to a reduced electronic band gap and increased delocalization in the ionic Zr-O bonding. The details of the chemical bonding explain the extremely low viscosity of the liquid and the absence of a first sharp diffraction peak, and indicate that liquid ZrO2 is an extremely fragile liquid.