Effects of Molecular Geometry on the STM Image Contrast of Methyl- and Bromo-Substituted Alkanes and Alkanols on Graphite

Abstract

Scanning tunneling microscopy (STM) images have been collected for a series of substituted alkanes and alkanols that form ordered overlayers at room temperature on highly ordered pyrolytic graphite surfaces. Molecules that have been imaged possess an internal bromide, with or without terminal alcohol groups (HO(CH2)9CHBr(CH2)10OH and H3C(CH2)16CHBr(CH2)16CH3), an internal −OH group (H3C(CH2)16CHOH(CH2)16CH3), and an internal methyl group (H3C(CH2)16CHCH3(CH2)16CH3). These data allow comparison to the STM image contrast reported previously for molecules in which −OH, −Br, and −CH3 groups were located in terminal positions of alkane chains adsorbed onto graphite surfaces. When the functional groups were in gauche positions relative to the alkyl chain, and thus produced molecular features that protruded toward the tip, the functional groups were observed to produce bright regions in a constant current STM image, regardless of the STM contrast behavior observed for these same functional groups when they were in terminal positions of adsorbed alkyl chains. These observations are in excellent agreement with theoretical predictions of the STM behavior of such systems. Additionally, several interesting packing structures have been observed that have yielded insight into the intermolecular forces that control the packing displayed by these overlayers.

Electrical Conformational Bistability of Dimesogen Molecules with a Molecular Chord Structure

“…[9][10][11] These studies are complementary to our observations, which show little observable dependence on bias polarity of the mesogen unit in both specimens examined, while the contrast variation is solely associated with the methylene portion. It is therefore reasonable to conclude that the contrast of the mesogen unit does not contribute to the observed contrast reversal of the methylene units.…”

“…[9][10][11] The variation in vertical contrast of the functional groups of various alkane derivatives relative to the methylene units was affected by both topographic and electronic factors, with ionization potential (IP) accounting for the observed contrast. A lower IP leads to higher contrast in the STM images.…”

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.…”

Use of Specific Functionalised Tips with STM: A New Identification Method of Ester Groups and Their Molecular Structure in Self‐Assembled Overlayers

“…For example, alkanes and alkanols adsorbed on graphite tend to adopt in most cases an all-trans conformation with their molecular axes parallel to each other in order to optimise the intermolecular and molecule-substrate interactions. [15][16][17] Self-assembly was also studied with a number of substituted alkanes, [18][19] long-chain ethers, [20] fatty acids, [21] or benzene derivatives. [22][23][24] Moreover, the STM has a wider application field rather than just providing images of surface structures.…”