STM images and tunneling channels of substituted benzene molecules

We analyze STM images of phenyl rings and substitutional nitrobenzene in terms of molecular symmetry, local electronic structure and tunneling channels. In experimental STM images, the phenyl ring of a benzene or a substituted nitrobenzene is seen as a dark depression. In a free phenyl, the nonresonant tunneling channels through the frontier orbitals interfere in a way that makes the molecule rather transparent. In adsorption, the mixing of molecular orbitals and the surface wave functions decrease the LDOS of the system with respect to a clean surface, and this leads to low current at the molecule. Substituting one hydrogen by a nitro group leaves the STM image of the phenyl dark, but makes the substitutional group appear bright. According to our calculations the molecular orbitals of a free nitrobenzene would be also quite transparent. However, the nitro group reconstructs upon adsorption, as seen in molecular dynamics simulations. This reconstruction almost closes the energy gap between the frontier orbitals localized at the nitro group. Thus, the tunneling through the group is almost resonant and a large tunneling amplitude is obtained.