The chemisorption of the allylamine molecule, which contains two functional groups (ethenyl and hydroxyl), on a Si(001) - (2 x 1) surface was studied using density functional theory (ab-initio DFT) based on the pseudopotential approach. In particular, we focused on the determination of the most stable position of the C=C double bond in the ethenyl group and observation of the passivation effect of allylamine on the electronic structure of the clean Si(001) - (2 x 1) phase. For this purpose, all of the possible interaction mechanisms occurring at the interface were considered: (i) dissociative bonding where the C=C bond is parallel to the silicon surface, (ii) dissociative bonding where the C=C bond is perpendicular to the silicon surface, and (iii) the [2 + 2] C=C cycloaddition reaction. From our total energy calculations, it was found that the bifunctional allylamine molecule attached to the Si(001) - (2 x 1) surface through the amino functional group, by breaking the N-H bond and forming a Si-H bond and Si-NHCH2CHCH2 surface fragments. During this process, the ethenyl functional group remains intact, and so can be potentially used as an extra reactive site for additional chemical interactions. In addition to these findings, the nudged elastic band method (NEB) calculations related with the reaction paths showed that the parallel position of the C=C bond with respect to the surface of the substrate is more favorable. In order to see the influence of the chemisorbed allylamine molecule on the surface states of the clean Si(001) - (2 x 1), we also plotted the density of states (DOS), in which it is seen that the clean Si(001) - (2 x 1) surface was passivated by the adsorption of allylamine. (C) 2011 Elsevier RV. All rights reserved.