Geometric constraints of molecular self-assembly of normal alkanes on graphite

An abrupt increase of CH3-groups brightness as well as CH2-groups modulation along alkyl skeleton were observed in scanning tunneling microscopy (STM) images of n-alkanes monolayers on graphite. Analysis of STM-patterns demonstrates that both effects strongly depend on deformations of molecules and scanning conditions. We have observed that due to deformations, the monolayer is going to be compressed, thus methylene units protrude away from the surface forming a corrugated structure. Moreover, the distance between adjacent lamellae narrows, leading to the absence of furrows and, in particular, to a significant increasing of tunneling current from peripheral groups. The whole monolayer has been conserving its anomalous brightness for a few hours. Moreover, when the scanning conditions are changed, the monolayer could undergo an instantaneous reordering from the structure with increased brightness to the uniform one.