Electron transport through conjugated molecules: when the pi system only tells part of the story

In molecular transport junctions, current is monitored as a function of the applied voltage for a single molecule assembled between two leads. The transport is modulated by the electronic states of the molecule. For the prototypical delocalized systems, namely, pi-conjugated aromatics, the pi system usually dominates the transport. Herein, we investigate situations where model calculations including only the pi system do not capture all of the subtleties of the transport properties. Including both the sigma and pi contributions to charge transport allows us to demonstrate that while there is generally good agreement, there are discrepancies between the methods. We find that model calculations with only the pi system are insufficient where the transport is dominated by quantum interference and cases where geometric changes modulate the coupling between different regions of the pi system. We examine two specific molecular test cases to model these geometric changes: the angle dependence of coupling in (firstly) a biphenyl and (secondly) a nitro substituent of a cross-conjugated unit.