The electronic structures of perylene tetracarboxylic dianhydride on Sn/Si(111)-2 root 3 x 2 root 3 have been studied by scanning tunneling microscopy and spectroscopy. Individual molecules have been investigated at 0.15 ML, while at 0.3 ML molecules formed short rods. At 0.6 ML, the molecular rods interacted with each other, coupling with the substrate and forming a new 4 root 3 x 2 root 3 super structure. At 0.9 ML, the surface was further reconstructed and consisted of strips with two and three rods of molecules. We found that these surface structures are strongly modified by the molecule/substrate and the intermolecular interactions. As a result, the HOMO-LUMO gaps of these molecules change with respect to the phases and the thickness. For a single molecular layer of the 4 root 3 x 2 root 3 phase, the HOMO-LUMO levels were split with a gap of approximately 2.1 eV, which is caused by charge transfer from the substrate to the molecules. (C) 2016 AIP Publishing LLC.