Study of transport properties of a molecular junction as a function of distance between the leads

We consider a model of a molecular junction made of BDT (benzene dithiol) molecule trapped between two Au(100) leads. Using the ab initio approach implemented in the SIESTA package we look for the optimal configuration of the molecule as a function of a distance between the leads. We find that for the distance long enough the energy of the system is minimized when the molecule is bonded asymmetricaly, i.e. chemisorbed to one of the leads, whereas for the distance shorter than 12 \AA the energy is minimized for the molecule sitting in the middle between the leads. We discuss possible consequences of the above findings for the transport properties of the junction.