Role of Electronic Structures and Dispersion Interactions in Adsorption Selectivity of Pyrimidine Molecules with a Si(5 5 12) Surface

We show that the resonance energy and dispersion interactions (DIs) are critical factors in determining the selectivity and configuration in the reaction of pyrimidine molecules with a silicon surface. The atomic structures of the pyrimidine molecules after they reacted with a Si(5 5 12)–2 × 1 surface were studied. Binding configurations of the pyrimidines were distinct from those of other molecules with N lone-pair electrons and aromaticity. The pyrimidine molecules were adsorbed to produce two σ bonds to silicon with N2 and C5 on the adatom row (Adr) and honeycomb chain (Hnc) sites and with C1 and C4 on the dimer row (Dmr) and the tetramer row (Ttr) sites. The reactions occurred via a [4 + 2]-type cycloaddition to produce planar-type configurations with loss of aromaticity. That is, the atoms of the aromatic ring of pyrimidine form chemical bonds with silicon atoms, which is in contrast to the adsorption behaviors reported for other N-containing aromatic molecules. When pyrimidine is adsorbed, its molecular orbitals are distorted because the N–Si bond axis does not coincide with the molecular orbital symmetric axis. Therefore, the vertical geometry is relatively unstable. DIs contribute a range of 0.4–0.6 eV for all stable adsorption structures and are essential for producing planar-type configurations on the Dmr and Ttr sites. In the absence of DIs, the vertical structure is stable; however, when DIs are included, the planar-type configuration becomes more stable. Moreover, even though the aromaticity is stabilized in the vertical structure, the greater adsorption energy for the flat structure of pyrimidine is mainly attributed to the lower energy cost involved in breaking the aromaticity.