Adsorption structure and reaction mechanism of purine on Ge(100) studied by scanning tunneling microscopy and theoretical calculations

The adsorption of purine on Ge(100) has been investigated using scanning tunneling microscopy (STM) supported by ab initio theoretical calculations. Purine molecules were found to spontaneously adsorb via double dative bonding with both ring nitrogen atoms (N(1) and N(7)) donating charge to the two neighboring Ge down atoms across the dimer row trench at room temperature. The additional surface Ge atom reacts with C(8) or N(9) to stabilize the positive charge of the datively bonded N(7) atom. The reaction with N(9) atom induces N(9)H bond dissociation. This reaction mechanism is different from the "isotope exchange reaction" observed in solution chemistry, which results in α-CH dissociation. Under vacuum conditions, the CH dissociation is unfavorable without a stabilizing agent to stabilize the zwitterions. In the absence of water, we find the surface Ge atom contributes to stabilization by donating an electron of its dangling bond. The electron donated from the surface Ge atom is transferred into the resonance structure of the purine and stabilizes the system.