Scanning tunneling microscopy and spectroscopy reveal that the energy of orbitals of individual perylenetetracarboxylic-dianhydride molecules depends on their adsorption geometry. Internal molecular structure appears at characteristic energies for each of the coexisting adsorption domains on Au(788) and Au(111). Tunneling spectroscopy on single molecules belonging to different adsorption domains exhibits an energy shift of the lowest and second-to-lowest unoccupied molecular orbital of approximate to 0.35 eV. On the basis of density functional theory calculations a possible contribution to this shift can be traced back to hydrogen bond-mediated intermolecular interaction. Hence, tunneling spectroscopy can be used as an efficient tool to discriminate between phases of organic molecular layers. (c) 2007 Elsevier B.V. All rights reserved.