Disorder-order phase change of ω-(N-pyrrolyl) alkanethiol self-assembled monolayers on gold induced by STM scans and thermal activation

Molecular ordering of pyrrolyl-terminated alkanethiol self-assembled monolayers (PyCnSH SAMs) on Au(111) substrates (n = 11 or 12) was investigated by scanning tunneling microscopy (STM) and various spectroscopic methods. The SAMs, which were in a disordered state when formed at room temperature, could be ordered either globally by thermal annealing at 70 degrees C, or locally via stimulation with repetitive STM scans. The ordered phase was characterized by small domains of molecular rows formed along < 112 > directional set with an inter-row corrugation period close to 1.44 nm, in which defects were abundant. Based on the experimental results, the molecular arrangement in the ordered PyCnSH SAM was proposed to be a (5 x root 3)rect structure with a molecular deficiency >= 10%. While mechanical interactions between molecules and scanning probe tips had been pointed out as the major cause of scan-induced phase transformations in other SAM systems, electronic or electrostatic factors were thought to affect considerably the scan-induced ordering process in this SAM system. From comparison of surface molecular coverage between disordered and thermally ordered SAMs of PyC12SH, it was inferred that the disorder could be ascribed to both kinetic and thermodynamic factors. The kinetic barrier to the ordered phase was supposed to result from strong dipole-dipole interactions among the pyrrolyl endgroups.