The use of theoretical and computational methods to understand molecular electronics experiments has been hindered by the fact that the geometric structure of the molecular junction is usually not very well understood. This problem can be overcome by using an STM tip to form one of the electrodes of the junction [1,2], and hence taking advantage of the STM\u2019s imaging capabilties to characterize the junction. Here we present the results of recent calculations related to a set of STM experiments studying PTCDA on metallic surfaces, using the non-equilibrium Green function formalism in combination with DFT [3, 4]. This comparison demonstrates that DFT based transport calculations are insufficient to accurately describe such systems, even when the geometric configuration is well-controlled. This is due to the failure of approximate exchange-correlations to describe phenomena such as the derivative discontinuity and the Kondo effect.
 F. Pump, R. Temirov, O. Neucheva, S. Soubatch, S. Tautz, M. Rohlfing, and G. Cuniberti, Appl. Phys. A 93, 335 (2008).
 R. Temirov, A. Lassise, F.B. Anders, and F.S. Tautz, Nanotechnology 19, 065401 (2008).
 J.M. Soler et. al., J. Phys. Cond. Matter 14, 2745 (2002).
 A.R. Rocha et. al., Phys. Rev. B 73, 085414 (2006).