Structural and electronic properties of self-assembled monolayer with 4-(4-amino-phenylazo) benzoic acid (APABA) on the Si(001)(4 x 2) surface are investigated by ab initio calculation based on density functional theory. For the APABA chemisorption on the silicon surface, we have assumed two different binding sites: (i) amino group of molecule and (ii) carboxyl group of molecule. Considering amino-site, we have assumed two possible models for the chemisorption of molecules on the Si(001)-(4 x 2) surface: (i) an intrarow position between two neighboring Si dimers in the same dimer row (Model 1), (ii) on-dimer position (Model 11). We have found that Model 11 is 1.10 eV energetically more favorable than Model I. The Si-N bond length was calculated as 1.85 angstrom which is in excellent agreement with the sum of the corresponding covalent radii of 1.87 angstrom. Considering carboxyl-site, we have assumed exactly the same model as mentioned above. Again we have found that Model 11 is energetically favorable than Model I. The calculated bond lengths for Si-O and O-C are 1.76 and 1.35 angstrom, respectively. (c) 2007 Elsevier B.V. All rights reserved.