Theoretical Description of the STM Images of Alkanes and Substituted Alkanes Adsorbed on Graphite

Abstract

A theoretical model based on perturbation theory has been developed to predict the scanning tunneling microscopy (STM) images of molecules adsorbed on graphite. The model is applicable to a variety of different molecules with reasonable computational effort and provides images that are in qualitative agreement with experimental results. The model predicts that topographic effects will dominate the STM images of alkanes on graphite surfaces. The computations correlate well with the STM data of functionalized alkanes and allow assessment of the structure and orientation of most of the functionalized alkanes that have been studied experimentally. In addition, the computations suggest that the highly diffuse virtual orbitals of the adsorbed molecules, despite being much farther in energy from the Fermi level of the graphite than the occupied orbitals, may play an important role in determining the STM image contrast of such systems.

Amyloid β (1–42) Folding Multiplicity and Single-Molecule Binding Behavior Studied with STM

“…In the case of alkane derivatives, the vertical contrast in the STM image of methylene regions is dominated by H-atom positions as predicted by perturbation theory and extended Hükel calculations and is therefore dominated by topography effect. [36][37][38][39] On the other hand, the fine features in STM images for the functional groups other than methylenes were shown to be affected by both topographic and electronic factors, involving ionization potential to account for the observed contrast. The correlation could have originated from the contribution of highest occupied molecular orbital to the tunneling current in STM.…”

Chain‐length‐adjusted assembly of substituted porphyrins on graphite

“…15 The calculation indicates that an additional desorption energy from two-dimensional crystallization will be required to remove a single alkane molecule from an alkane self-assembly on a graphite substrate. A densely packed system that includes ten tetradecane molecules but with two possible orientations of a carbon skeleton 17,18 was modeled in our calculation. In the flat orientation, additional desorption energies of 1.77 and 3.90 kJ mol 1 are needed for the side and inner molecules in the alkane array, respectively.…”

Probing of the Voltammetric Features of Graphite Electrodes Modified with Mercaptoundecanoic Acid Stabilized Gold Nanoparticles

“…In principle, the adsorption of the Au-MUA NPs at the lipophilic surface of the graphite will take place via the lipophilic alkyl chain of the ligand (mercaptoundecanoic acid). [23][24][25][26] In this way, the hydrophilic gold sites of the Au-MUA NPs will be oriented toward the water solution. Very likely, this specific orientation of the Au-MUA NPs contributes to better electron conductivity with respect to the bare graphite.…”

“…Moreover, it is well-known that the long-chain alkanes and alkylated moieties self-assemble very strongly in lamellar monolayers on a crystalline substrate like the basal plane of graphite. [23][24][25][26] Rows of head groups, which may be positively or negatively charged, are separated by rows of hydrophobic alkyl chains. The chemical nature of the head groups and the length of alkyl chains define a surface potential ripple.…”

“…23,24 Therefore, our finding about the stability of the long chain MUA capped Au NPs on the graphite electrode is in agreement with the literature reports. [23][24][25][26] Very recently, work published by Salvarezza et al 12 has appeared, where the authors used gold nanoparticles stabilized by short and moderate alkyl chain thiols. After the spontaneous adsorption of thiol-capped Au nanoparticles on bare graphite, the authors of ref 12 observed that the thiol was released into the solution, once a potential difference was applied.…”