Interplay of molecule–substrate and intermolecular interactions in 5thiaheterohelicene assembly on Ag(111)

The adsorption and self-assembly of racemic 5thiaheterohelicene (rac-5TH) adsorbed on Ag(111) were investigated using molecular dynamics (MD) simulations and density functional theory (DFT) calculations and compared with scanning tunneling microscopy (STM) results. While the molecule is physisorbed on Ag(111), the results of DFT calculations also exhibit pronounced site and orientation dependence with respect to the substrate lattice. Displacements from preferred adsorption sites and orientations on Ag(111) result in an energy cost nearly an order of magnitude larger than that associated with deviations from the optimal intermolecular distances favoured by simple intermolecular interactions. This indicates that self-assembly is governed primarily by substrate registry, while intermolecular interactions act as secondary constraints. Consequently, the ordered structures observed experimentally can be understood as a balance in which molecules anchor at their preferred adsorption sites and orientations on the substrate, while locally adopting dimer motifs favoured by intermolecular interactions. These findings provide insight into how helical length controls the balance between intermolecular and molecule-substrate interactions in chiral self-assembly on the Ag(111) surfaces.