STM Investigation of the Y[C₆S-Pc]₂ and Y[C₄O-Pc]₂Complex at the Solution–Solid Interface: Substrate Effects, Submolecular Resolution, and Vacancies

Abstract

Substituents present on a molecule are known to significantly control the assembly, adsorption, and orientation behavior on solid surfaces. Using scanning tunneling microscopy (STM), self-assembly of the Y[C 6 S-Pc] 2 and Y[C 4 O-Pc] 2 double-decker complexes was investigated at a solution−solid interface. At concentrations above 1 μM, Y[C 6 S-Pc] 2 formed well-defined monolayers with low defect density on highly oriented pyrolytic graphite (HOPG). On Au(111), on the other hand, it formed dense groups of small islands with some isolated molecules. There was a clear preference for multiples of 15°between the orientations of the islands. A clear visualization of the Y[C 6 S-Pc] 2 inner molecular structure, including all eight of the sulfur atoms linked to the top phthalocyanine ring, was achieved. At concentrations below 1 μM, stable isolated single molecules of Y[C 6 S-Pc] 2 were observed only on Au(111), not on HOPG. The thiol-linked side chains favor strong adsorption on the Au(111) surface, with isolated single molecules being easily visualized and stable over several image scans. At concentrations where well-defined monolayers form, we observe defects in the form of molecular vacancies whose number can be controlled by bias voltage. The enhanced stability of the S-linked system over an O-linked system is demonstrated by comparison with Y[C 4 O-Pc] 2 and discussed in terms of the organic sulfide−gold interaction. On both HOPG and Au(111), isolated molecules of Y[C 4 O-Pc] 2 are never observed. Even at very low solution concentrations, small rafts of molecules on an otherwise open substrate surface are observed. On HOPG, the structure of the Y[C 4 O-Pc] 2 monolayer is complex with both an open and filled cubic structure occurring as a mixed structure. The surface structures seen with either double-decker on HOPG are probably controlled by equilibrium thermodynamics. The structure of the Y[C 6 S-Pc] 2 complex on Au( 111) is determined by the kinetic barrier to diffusion across the gold surface and is therefore kinetically trapped. We suggest that core moieties with peripheral S-linked alkanes may generally be particularly strong adsorbates on gold. Density functional calculations suggest that the S-linked alkane substituent system may be as much as 1 eV more stable on Au than a similar O-linked system. We have also observed that the Y[C 6 S-Pc] 2 monolayer on HOPG has bias and setpoint current dependent defects. At constant tunneling current, less negative bias generates a greater number of vacancies as compared to high negative bias. Consecutive STM scanning shows the diffusion, disappearance, and appearance of new vacancies which are induced both thermally and by the STM tip. This work demonstrates the important role of molecule−substrate interactions, bias voltage, tunneling current, and the STM tip in controlling and stabilizing molecular assembly.

Scanning Tunneling Microscopy Reveals Surface Diffusion of Single Double-Decker Phthalocyanine Molecules at the Solution/Solid Interface

“…STM has also been used to study the diffusion of molecular vacancies within an organized adlayer; in this case, intermolecular interactions become highly important and complicate the analysis. , Takami and Weiss observed tip and thermally induced sliding (hopping) motion of double-decker phthalocyanine that results in vacancy motion at the solution/highly ordered pyrolytic graphite (HOPG) interface . We have also reported tip and thermally induced vacancy hopping of double-decker phthalocyanines on both HOPG and on Au(111) . We note here that vacancy motion which has been considered in several studies is far different from the motion of isolated molecules because of the absence of intermolecular interactions.…”

“…The Y­[C 6 S-Pc] 2 , 2,3,9,10,16,17,23,24-octakis­(hexylthio)-phthalocyaninato complex was synthesized as described previously. , …”

Characterizing the CH3SSCH3–Au(111) System From Single Molecules To Full Surface Coverage: A Scanning Tunneling Microscopy Study

“…The choice of our DFT methodology and plane wave cutoff energies was based on previous periodic DFT simulations of systems of similar types 37−41 and sizes. 42 Additional computational details are presented in the Supporting Information. VASP calculations for species on Au were performed (1) on a supercell composed of three layers of 4 × 10 Au(111) with the bottom two layers frozen at the experimental crystal structure and a 1.6 nm vacuum space, (2) upon the same supercell having molecules on the above Au, and (3) upon a single S 2 (CH 3 ) 2 molecule (without Au) all in the same size supercell.…”

“…All the geometries were fully optimized up to 0.001 eV energy and less than 0.01 eV/Angstrom forces. The choice of our DFT methodology and plane wave cutoff energies was based on previous periodic DFT simulations of systems of similar types − and sizes . Additional computational details are presented in the Supporting Information.…”

Solvent Co-adsorption Changing the Type of Halogen-Based Bonds Associated with the Position of Bromine Substituents Revealed by Scanning Tunneling Microscopy

“…Two-dimensional (2D) molecular self-assembly is of great significance for building preprogrammed structures and patterns on such a scale using the bottom–top approach . The formation of 2D self-assembled nanostructures is a result of thermodynamic equilibrium, affected by temperature, − molecular chemical structure, − solvent, − solution concentration, − substrate, , and so on. These factors essentially change the intermolecular interaction and/or molecule–substrate interaction of self-assembly adlayers.…”