Two-Dimensional Self-Assemblies of Thiophene-Fluorenone Conjugated Oligomers on Graphite: A Joint STM and Molecular Modeling Study

The formation of self-assembled monolayers of bithiophene-fluorenone conjugated oligomers, 2,7-bis-(4-octyl-thien-2-yl)-fluoren-9-one (B4OTF) and 2,7-bis-(5-octyl-thien-2-yl)-fluoren-9-one (B5OTF), has been studied on highly oriented pyrolitic graphite (HOPG) by scanning tunneling microscopy (STM), with the aim of determining the influence of the molecular structure and conformation on the supramolecular organization. The experimental data are discussed in light of a modeling study of the molecular conformation and the adsorption on graphite using molecular mechanics and molecular dynamics simulations. It is shown that molecules with alkyl groups grafted in the C4 position (B4OTF) self-assemble into an anti-anti chiral lattice which is favored both by dipole-dipole and Van der Waals interactions. The short-range organization appears more complex for molecules with alkyl groups grafted in the C5 position (B5OTF). Due to a competition between dipole-dipole and Van der Waals interactions, the modeled assemblies based on syn-syn, syn-anti, and anti-anti B5OTF conformers are all stable and very close in energy, but do not explain the feature of a long-range periodicity evidenced from large-scale STM images. On the basis of the comparative analysis between the experimental data and the modeling, it is then suggested that the supramolecular self-assembly of B5OTF on HOPG implies the presence of several conformers in the monolayer.