PTCDA molecules were evaporated onto the AG/Si(1 1 1)-root 3 x root 3 surface. Simple HOMO and LUMO models have been made to explain the STM images of the square and herringbone phases. The charge transfer from the substrate and the H-bonding between the molecules play crucial roles for the formation of these phases. We found that their electronic structures are strongly modified by the molecule-substrate and intermolecular interactions. As a result, the HOMO-LUMO gaps of the PTCDA films are different for different phases and thicknesses. The increase in the HOMO-LUMO gaps with film thicknesses is discussed based on the surface and the interface polarization effect. (C) 2009 Elsevier B. V. All rights reserved.