The chemisorption of pyrimidine and s-triazine, two aromatic molecules with N atoms in the aromatic ring, is studied by first principles calculations to examine not only the chemisorption energy, but also the reaction barriers and the cooperative effects. Among the reaction paths at low coverage, the formation of a cross-bridge structure with two N-Si dative bonds is almost barrierless and should be dominant at low temperature. At higher coverage and low temperature, these cross-row structures should produce an ordered zig-zag pattern, even though it is not the energetically most stable arrangement. Upon heating, the zig-zag pattern could be transformed into lines along dimer rows. These two molecules also provide structural motifs that could facilitate the formation of ordered adsorption structures on Si(100). By symmetry, the complexity of tight-bridge structures could be greatly reduced, while the X-C-X motif, with X being an electronegative atom, could provide the building blocks for cross-row bridges.