Emergence and visualization of an interface state during contact formation with a single molecule

Contact formation dynamics and electronic perturbations arising from the interaction of a metallic probe and a single molecule (1,3 cyclohexadiene) bound on the Si (100) surface are examined using a series of plane wave, density functional theory calculations. The approach of the probe induces a relaxation of the molecule that ultimately leads to the formation of an interface state due to a specific interaction between the probe apex atom and the C=C bond of the molecule. The calculated interface state is located 0.2 eV above the Fermi energy, in agreement with low temperature scanning tunneling spectroscopy local density of states data (0.35 eV), and is responsible for the contrast observed in low bias empty-state STM images.