Combining high-resolution scanning tunnelling microscopy and first-principles simulations to identify halogen bonding

Scanning tunnelling microscopy (STM) is commonly used to identify on-surface molecular self-assembled structures. However, its limited ability to reveal only the overall shape of molecules and their relative positions is not always enough to fully solve a supramolecular structure. Here, we analyse the assembly of a brominated polycyclic aromatic molecule on Au(111) and demonstrate that standard STM measurements cannot conclusively establish the nature of the intermolecular interactions. By performing high-resolution STM with a CO-functionalised tip, we clearly identify the location of rings and halogen atoms, determining that halogen bonding governs the assemblies. This is supported by density functional theory calculations that predict a stronger interaction energy for halogen rather than hydrogen bonding and by an electron density topology analysis that identifies characteristic features of halogen bonding. A similar approach should be able to solve many complex 2D supramolecular structures, and we predict its increasing use in molecular nanoscience at surfaces. Scanning tunnelling microscopy (STM) is commonly used to study 2D molecular self-assembly but is not always enough to fully solve a supramolecular structure. Here, the authors combine a high-resolution version of STM with first-principles simulations to precisely identify halogen bonding in polycyclic aromatic molecules.