Ab initio density functional theory has been used to analyze flexural modes, elastic constants, and atomic corrugations on single and bi-layer graphene. Frequencies of flexural modes are sensitive to compressive stress; its variation under stress can be related to the anomalous thermal expansion via a simple model based in classical Elasticity Theory. 1 Under compression, flexural modes are responsible for a long wavelength rippling with a large amplitude and a marked anharmonic behavior. This is compared with corrugations created by thermal fluctuations and the adsorption of a light impurity (hydrogen). Typical values for the later are in the sub-Angstrom regime, while maximum corrugations associated to bending modes quickly increase up to a few Angstroms under a compressive stress, due to the intrinsic instability of flexural modes PACS numbers: 63.22.Rc,65.80.Ck,61.48.Gh
We have studied the first stages leading to the formation of self-assembled monolayers of S-cysteine molecules adsorbed on a Au(111) surface. Density functional theory (DFT) calculations for the adsorption of individual cysteine molecules on Au(111) at room temperature show low-energy barriers all over the 2D Au(111) unit cell. As a consequence, cysteine molecules diffuse freely on the Au(111) surface and they can be regarded as a 2D molecular gas. The balance between molecule-molecule and molecule-substrate interactions induces molecular condensation and evaporation from the morphological surface structures (steps, reconstruction edges, etc.) as revealed by scanning tunnelling microscopy (STM) images. These processes lead progressively to the formation of a number of stable arrangements, not previously reported, such as single-molecular rows, trimers, and 2D islands. The condensation of these structures is driven by the aggregation of new molecules, stabilized by the formation of electrostatic interactions between adjacent NH(3)(+) and COO(-) groups, together with adsorption at a slightly more favorable quasi-top site of the herringbone Au reconstruction.
A combination of variable temperature scanning tunneling microscopy, near edge X-ray adsorption fine structure and density functional theory has been used to investigate the chemisorption and self-assembly of metal-free protoporphyrin IX molecules on Cu(110) surface. The molecules in contact with the substrate suffer irreversible molecular transformations, mainly deprotonation of the carboxylic groups and metalation of the pyrroline subunits. The carboxylate group has been revealed as the anchored group versus the tetrapyrrole ring. We study the role played by the carboxylic acid groups in the surface-molecular bonding and how its presence affects the supramolecular structure.
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