Substrate-directed hierarchical assembly of 1,3,6,8-tetrabromopyrene: unraveling the interplay of halogen bonding and strain-mediated epitaxy

The self-assembly of 1,3,6,8-tetrabromopyrene (Br 4 Py) on Au(111) leads to two competing monolayer structures, M 1 and M 2, with near-identical formation energies. First-principles calculations reveal that this structural duality originates from distinct hierarchical pathways: three stable molecular chain intermediates ( C 1– C 3), identified via energy minimization, first form through a balance of directional Br⋯H hydrogen bonds and repulsive Br⋯Br interactions, with the former acting as the primary structural driver. These chains then laterally organize into the monolayers, where M 1 arises from complementary C 1/ C 2 chain packing and M 2 from homologous C 3 chain assembly. The simulated structural parameters (e.g., lattice constants b / c ≈ 21.70 Å, Br⋯H distances ≈ 3.23 Å) are in good agreement with scanning tunneling microscopy data, showing deviations below 6 %. Electron density analysis quantitatively corroborates the competitive interplay, showing charge accumulation at Br⋯H bonding sites and depletion in Br⋯Br repulsive zones. Substrate-mediated strain from Au(111) induces lattice distortions up to 5.8 %, highlighting the role of surface-molecule coupling. By integrating computational and experimental insights, this work establishes a mechanistic framework for understanding and designing halogen-mediated, surface-confined supramolecular assemblies with potential in molecular electronics. This framework highlights the exquisite structural control achievable through halogen bonding and substrate effects, and lays the groundwork for future explorations on alternative surfaces, molecular derivatives, and device integration.