Scanning Tunneling Microscopy Images of Alkane Derivatives on Graphite: Role of Electronic Effects

Abstract

Scanning tunneling microscopy (STM) images of self-assembled monolayers of close-packed alkane chains on highly oriented pyrolitic graphite often display an alternating bright and dark spot pattern. Classical simulations suggest that a tilt of the alkane backbone is unstable and, therefore, unlikely to account for the contrast variation. First principles calculations based on density functional theory show that an electronic effect can explain the observed alternation. Furthermore, the asymmetric spot pattern associated with the minimum energy alignment is modulated depending on the registry of the alkane adsorbate relative to the graphite surface, explaining the characteristic moiré pattern that is often observed in STM images with close packed alkyl assemblies.

A priori calculations of the free energy of formation from solution of polymorphic self-assembled monolayers

“…nearly parallel to the HOPG substrate h1120i lattice vector, as has been observed for the SAMs of pure alkanes (65)(66)(67)(68). These calculations and all measurements also indicate that the SAMs are incommensurate with the substrate lattice (49,51), and Table 1 shows good agreement between the observed and calculated SAM lattice parameters.…”

“…Naively, one hydrogen atom per methylene group is expected to be observed, and indeed sometimes is, but, more often, the images reveal only a hydrogen atom on every second group. This arises owing to the chains not sitting perfectly flat at room temperature and to consequences of the SAM lattice being incommensurate with that of HOPG (65). In all cases, the alkyl chains are calculated by QM/MM and observed to lie parallel or C 11 P M C 12 P C M 13 P M Fig.…”

“…Sometimes, atomically resolved tunneling is also seen among the long flat-lying chain regions, dominated by the chain hydrogen atoms (65,66). Naively, one hydrogen atom per methylene group is expected to be observed, and indeed sometimes is, but, more often, the images reveal only a hydrogen atom on every second group.…”

Problems, successes and challenges for the application of dispersion-corrected density-functional theory combined with dispersion-based implicit solvent models to large-scale hydrophobic self-assembly and polymorphism

“…[87,88,113,115,116,117,118,119] Relaxing this constraint allows much better fits to be made to the vector lengths, resulting in an overall lower energy penalty for commensurate-lattice production. Table 1 gives the QM/MM optimized lattice parameters defined in Fig.…”

“…[87,88,113,115,116,117,118,119] This poses a serious technical challenge as electronic-structure computational methods treat surfaces using periodic boundary conditions, therefore demanding that the two lattices (or multiples thereof) be commensurate. The QM/MM calculations overcome this problem as the MM force field only is used for the intermolecular interactions and these are so efficient that a large real-space sum can be performed, including interactions up to very large distances.…”