The Role of Hydrogen Bonding and Proton Transfer in the Formation of Uracil Networks on the Gold (100) Surface: A Density Functional Theory Approach

Abstract

We have used density functional theory calculations, including a correction for the dispersive forces (DFT-D), to investigate the formation of a monolayer superstructure of uracil molecules adsorbed on the Au(100) surface. Our calculations provide insight into the interplay between lateral adsorbate adsorbate and vertical adsorbate substrate interactions, where we found that uracil adsorption to the surface is strongly dependent on the lateral interactions, particularly hydrogen bonding, although the first adsorbed molecule, before the formation of a uracil network, is covalently bonded to the surface. The self-assembly of the uracil network on the surface is mediated by proton transfer, and the ensuing charge separation stabilizes the geometry. Dispersive forces also play a role, and in particular, the introduction of a correction leads to flatter geometries with molecules lying parallel to the surface, thereby enhancing pi-pi stacking and hydrogen-bonding

Periodic DFT+U investigation of the bulk and surface properties of marcasite (FeS2)

“…More details about the method can be found elsewhere. 99 Due to the difficulty associated with obtaining single crystals with welldefined surfaces experimentally, our simulated STM images provide insight into the structures and compositions of the marcasite surfaces, which may otherwise be hard to resolve experimentally, thus explaining why at present no experimental STM images are available for comparison with our results. However, we consider that the simulated STM images may become useful in clarifying future experiments, for instance to distinguish between the {101} and {010} facets, which are the most likely facets to be observed under experimental conditions.…”

Hydrogen Generation from Additive-Free Formic Acid Decomposition Under Mild Conditions by Pd/C: Experimental and DFT Studies

“…The inner electrons were represented by the projector-augmented wave (PAW) pseudopotentials considering also non-spherical contributions from the gradient corrections [55]. All the calculations include the long-range dispersion correction approach by Grimme [56,57], which is an improvement on pure DFT when considering large polarizable atoms [58][59][60][61][62][63]. We included a self-consistent aqueous implicit solvation model [64,65].…”

A Density Functional Theory Study of the Adsorption of Benzene on Hematite (α-Fe2O3) Surfaces

“…The reader is referred to Reference [119] for the implementation within VASP and a more detailed description of the GGA+U method. Dispersion forces were accounted for in our calculations using the DFT-D2 method of Grimme [120], which accurately describes the interaction between organic molecules and solid surfaces [121,122]. The Brillouin zone was sampled using 11 × 11 × 7 and 5 × 5 × 1 Monkhorst-Pack [123] mesh k-points for bulk and surface calculations, respectively.…”