On the suppression and significance of ghost transmission in electron transport modeling of single molecule junctions

The difficulty in achieving experimental control over a metal-molecule-metal junction formation hinders the understanding of the relationship between the contact geometry and electron transmittance. Computational studies on the other hand have the potential to resolve structural effects on the transport in molecular junctions. In a recent computational effort substantial transport was indicated even in the case where all the junction atoms were removed, while their corresponding atomic basis functions were included in the basis set (i.e., ghost atoms). In this report we explain the origin of the artifact termed as "ghost transmission." We provide a systematic analysis of the factors that enhance or suppress the artifact. We find that symmetric electronic densities at the two metal-molecule interfaces can lead to an amplification of the artificial transmission. In addition, interaction between an unpaired electron of the left electrode with one in the right electrode results with a substantial increase in "ghost transmission." Finally we find that a self-consistent single particle Green's function formalism that solves the junction electronic structure self-consistently with respect to the electrodes self-energies, reduces the artifact substantially. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.4767344]