Interaction of an adenine molecule with a Ag-terminated Si(111) surface

The adsorption of an adenine molecule, one of four DNA bases, on a Ag/Si(111) √3 × √3 surface is investigated using a first-principles total-energy calculation. Extensive search of the adsorption structures reveals that two structures are energetically competing. One is a structure with a hexagonal ring of adenine on a large Ag triangle (LT) of the substrate. The molecular plane is inclined at a tilt angle of 10.2° with respect to the surface plane due to weak bonds between N and substrate Ag atoms. The other is a structure with N just above a Ag atom (T) with the molecular plane vertical to the surface. The N ... Ag bond energy in the LT structure is of similar magnitude to the N ...H hydrogen bonds of an adenine dimer. The local-density approximation (LDA) and the generalized-gradient approximation (GGA) produce different energy orders between the LT and the T structures. An incorrect treatment of the van der Waals interaction in the density-functional theory could be the origin of the difference.