Mobile metal adatoms on single layer, bilayer and trilayer graphene: an ab initio study correlated with experimental electron microscopy data

The plane-wave density functional theory code CASTEP was used with the Tkatchenko-Scheffler van der Waals correction scheme and the generalized gradient approximation of Perdew, Burke, and Ernzerhof (GGA PBE) to calculate the binding energy of Au, Cr, and Al atoms on the armchair and zigzag edge binding sites of monolayer graphene, and at the high-symmetry adsorption sites of single layer, bilayer, and trilayer graphene. All edge site binding energies were found to be substantially higher than the adsorption energies for all metals. The adatom migration activation barriers for the lowest energy migration paths on pristine monolayer, bilayer, and trilayer graphene were then calculated and found to be smaller than or within an order of magnitude of kBT at room temperature, implying very high mobility for all adatoms studied. This suggests that metal atoms evaporated onto graphene samples quickly migrate across the lattice and bind to the energetically favorable edge sites before being characterized in the microscope. We then prove this notion for Al and Au on graphene with scanning transmission electron microscopy (STEM) images showing that these atoms are observed exclusively at edge sites, and also hydrocarbon-contaminated regions, where the pristine regions of the lattice are completely devoid of adatoms. Additionally, we review the issue of fixing selected atomic positions during geometry optimization calculations for graphene/adatom systems and suggest a guiding principle for future studies

EELS from organic crystalline materials

We report the use of the electron energy loss spectroscopy (EELS) for providing light element chemical composition information from organic, crystalline pharmaceutical materials including theophylline and paracetamol and discuss how this type of data can complement transmission electron microscopy (TEM) imaging and electron diffraction when investigating polymorphism. We also discuss the potential for the extraction of bonding information using electron loss near-edge structure (ELNES)

Incisive probing of intermolecular interactions in molecular crystals: core level spectroscopy combined with density functional theory

The α-form of crystalline para-aminobenzoic acid (PABA) has been examined as a model system for demonstrating how the core level spectroscopies X-ray photoelectron spectroscopy (XPS) and near-edge X-ray absorption fine-structure (NEXAFS) can be combined with CASTEP density functional theory (DFT) to provide reliable modeling of intermolecular bonding in organic molecular crystals. Through its dependence on unoccupied valence states NEXAFS is an extremely sensitive probe of variations in intermolecular bonding. Prediction of NEXAFS spectra by CASTEP, in combination with core level shifts predicted by WIEN2K, reproduced experimentally observed data very well when all significant intermolecular interactions were correctly taken into account. CASTEP-predicted NEXAFS spectra for the crystalline state were compared with those for an isolated PABA monomer to examine the impact of intermolecular interactions and local environment in the solid state. The effects of the loss of hydrogen-bonding in carboxylic acid dimers and intermolecular hydrogen bonding between amino and carboxylic acid moieties are evident, with energy shifts and intensity variations of NEXAFS features arising from the associated differences in electronic structure and bonding

Ab-initio modelling, polarity and energetics of clean rutile surfaces in vacuum and comparison with water environment

All terminations of the (1x1) rutile (110), (101), (001), (100) and (111) surfaces are classified according to their electrostatic polarity. Six are found to be non-polar. The plane-wave density functional theory code CASTEP is used with a GGA-PBE exchange-correlation functional and a vacuum/material slab supercell method to calculate the surface energy density of symmetric thin rutile films with the six non-polar terminations in vacuum. The ratio of the surface energy densities of a rutile crystal with {111} and {110} facets in water is deduced using Lagrange multipliers and found to be consistent with the DFT vacuum results

Electron microscopy of nuclear graphite: A modelling approach

Graphite acts as both a major structural component and moderator in nuclear reactors. Upon neutron irradiation, various structural and property changes occur. Property changes include; coefficient of thermal expansion (CTE), Young's modulus and thermal resistivity. This work focuses on the characterisation of irradiated graphite models using both electron energy-loss spectroscopy (EELS) and imaging techniques. A number of models of irradiated graphite have been found, whereby one or more interstitial atoms form between the hexagonal layers. In this work, density functional theory (DFT) modelling is used to predict EEL spectra (carbon K edges) at the spiro-interstitial position, and contrast those to bulk predictions. We observe that for a 'bulk-like' position in the spiro-interstitial model, the carbon K edge shape is similar to that of true bulk, thus confirming the validity of the model used. For the carbon K edge prediction at the spiro-interstitial position, although peaks in the π* region remain in approximately the same energy positions, there is considerable broadening suggesting the presence of strained sp2 bonding character. The σ* peak is significantly altered, both in energy position and intensity relative to the π* region. These observations are arguably consistent with a spiro-interstitial strained from the ideal bonding angles observed in spiro-pentane. Simulations of TEM and HAADF images of the spiro-interstitial model were also performed. These suggested that in a typical TEM, for the (100) orientation, even at a thickness of ~15Å the interstitial would be difficult to observe. In the case of (S)TEM, a similar situation exists

Probing the bonding and electronic structure of single atom dopants in graphene with electron energy loss spectroscopy

A combination of scanning transmission electron microscopy, electron energy loss spectroscopy, and ab initio calculations reveal striking electronic structure differences between two distinct single substitutional Si defect geometries in graphene. Optimised acquisition conditions allow for exceptional signal-to-noise levels in the spectroscopic data. The near-edge fine structure can be compared with great accuracy to simulations and reveal either an sp3-like configuration for a trivalent Si or a more complicated hybridized structure for a tetravalent Si impurity

Extended interplanar linking in graphite formed from vacancy aggregates

The mechanical and electrical properties of graphite and related materials such as multilayer graphene depend strongly on the presence of defects in the lattice structure, particularly those which create links between adjacent planes. We present findings which suggest the existence of a new type of defect in the graphite or graphene structure which connects adjacent planes through continuous hexagonal sp2 bonding alone and can form through the aggregation of individual vacancy defects. The energetics and kinetics of the formation of this type of defect are investigated with atomistic density functional theory calculations. The resultant structures are then employed to simulate high resolution transmission electron microscopy images, which are compared to recent experimental images of electron irradiation damaged graphite

Stacking variants and superconductivity in the Bi-O-S system.

High-temperature superconductivity has a range of applications from sensors to energy distribution. Recent reports of this phenomenon in compounds containing electronically active BiS2 layers have the potential to open a new chapter in the field of superconductivity. Here we report the identification and basic properties of two new ternary Bi-O-S compounds, Bi2OS2 and Bi3O2S3. The former is non-superconducting; the latter likely explains the superconductivity at T(c) = 4.5 K previously reported in "Bi4O4S3". The superconductivity of Bi3O2S3 is found to be sensitive to the number of Bi2OS2-like stacking faults; fewer faults correlate with increases in the Meissner shielding fractions and T(c). Elucidation of the electronic consequences of these stacking faults may be key to the understanding of electronic conductivity and superconductivity which occurs in a nominally valence-precise compound