The results of an ab initio calculation, based on pseudopotentials and the density functional theory, for the atomic and electronic structures of the chemisorption of 3-aminopropyltrimethoxysilane (APTS) on the Si(001)-(2 × 2) surface are presented. Two possible models for the chemisorption location of the APTS molecule are considered on the hydroxylated Si(001)-(2 × 2) surface: (i) an above-pedestal position (intra-row) between adjacent Si dimers and (ii) an above-hollow position. The first case is found to be energetically more favorable than the latter by 1.04 eV. The electronic band structure of this site has been compared with that of the bare Si(001)-(2 × 2) surface. It is observed that the chemisorption of APTS has considerably changed the electronic structure of the Si(001)-(2 × 2) surface. © 2007 American Chemical Society.