Observation of 1-dodecanethiol molecules on graphite by scanning tunneling microscopy

Molecular-resolution images of 1-dodecanethiol on the graphite substrate are successfully observed with a scanning tunneling microscope in air. The image reveals a two-dimensional ordering with the molecules lying down and arranged in rows on the graphite surface. A 5.5 nm periodicity observed suggests that there are three molecules arranged in series along the molecular axis. Two kinds of molecular arrangements exist within a single row, with one subrow about 1.5 nm wide with one 1-dodecanethiol and the other subrow about 3.5 nm in width approximately double the length of the molecule. The periodicity vertical to the molecular axis is about 0.55 nm, comparable with the Van der Waals diameter of the molecule. A model for the possible arrangement of the molecules on graphite surface is proposed.