A combined theoretical and experimental study on the adsorption of an isolated benzonitrile molecule on the Si(001) surface, followed by the adsorption of Al (group III), Pb (carbon group) and Ag (transition metal) is presented. It is shown that two new adsorption sites with enhanced reactivity are formed on the surface in the vicinity of the pre-adsorbed molecule. This is evidenced by the increase of the calculated binding energy of the metallic ad-atoms adsorbed at these sites. Experimentally, this enhanced local reactivity of the modified surface is only partially retained when more metallic atoms are adsorbed on the modified surface at room temperature. This is evidenced by the formation of 1-dimensional atomic chains (Pb, Al) attached to one side of the pre-adsorbed molecule.