The effect of the molecular structure on the self-assembly of specially designed two-core 1,3,2-dioxaborines has been studied with various techniques. It was found that the molecules spontaneously adsorbed on HOPG surfaces and self-organized into well-ordered two-dimensional (2D) monolayers. The structural details of the 2D assemblies were investigated by scanning tunneling microscopy (STM). From X-ray analysis of the corresponding three-dimensional (3D) crystal and from theoretical calculation, we were able to reveal the driving force behind the specific self-assembly. The C-H center dot center dot center dot F hydrogen bonding between the ortho carbon of the phenyl ring and the fluorine of the BF2 group plays an important role in the formation of the adlayers. The different electron affinities and geometries of the molecules affect the intermolecular interactions which further lead to different properties in the bulk materials.