The stability and electronic properties of highly packed 1-hexyl-naphthalene (HNap) molecular wire on Si(001) have been studied with first principles DFT method. HNap assembles into a 1D arrangement on the Si(001)[2 x 1] surface on which molcules adopt a commensurate structure along a dimer row with an intermolecular distance of 3.8 Angstrom. HNap is attached to the surface through the hexyl chain, and stands normal to the surface. This highly packed structure leads to the formation of delocalized pi-orbitals over the entire wire but essentially localized on the naphthalene counterpart, and well separated from the Si surface states. Cohesion energy within the wire arises from a significant attraction between hexyl chains, and to a weaker stabilizing pi-pi interaction between naphthalenes. (C) 2004 Elsevier B.V. All rights reserved.