We study the interaction of H-2 , O-2 , CO, H-2 O and OH molecules with the vacancy defects of graphene and silicene. Atoms around the bare vacancy reconstruct and specific chemically active sites are created. While H-2 , O-2 and CO remain intact on both pristine graphene and silicene, these molecules can dissociate when they are placed at the close proximity of these chemically active sites and nucleate centers for the hydrogenation and oxygenation. Saturation of the dangling bonds at the defect sites by constituent atoms of dissociated molecules gives rise to significant modification of electronic and magnetic properties. We analyzed the mechanism of the dissociation and revealed a concerted action of surrounding host atoms together with dissociated molecules to lower the energy barrier needed for dissociation. The dissociations of H-2 O and OH are hindered by high energy barriers. Our study suggests that graphene and silicene can be functionalized by creating meshes of single vacancy, where specific molecules can dissociate, while some other molecules can be pinned.