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Understanding of the dynamics of the bonding states of molecules with electrodes while the molecular conformation is changed is particularly important for elucidating the details of electrochemical devices as well as molecular devices in which the reaction dynamics of the electrodes and molecules plays an important role, such as in fuel cells, catalysis and bioelectrochemical devices. However, it has been difficult to make measurements when the distance between counter electrodes is short, namely, the molecule is raised from a lying form, almost parallel and close to the electrodes, toward a standing form and vice versa. We previously have developed a method called the three-dimensional (3D) dynamic probe method, which enables conductance measurement while the conformation of a single-molecule junction is precisely controlled by scanning tunneling microscopy (STM) techniques. Here, by combining this method with density functional theory (DFT) calculations, it has become possible to simultaneously consider the effects of the dynamics of molecular structures and the bonding states at the electrodes on the local transmission pathways, local-bond contributions to conductance. Here, by performing an analysis on 1,4-benzenediamine (BDA) and 1,4-benzenedithiol (BDT) single molecule junctions, we have observed, for the first time, the effect of a change in the molecular conformations and bonding states on the local transmission pathways for a short Au electrode distance condition.

Evolution of local conductance pathways in a single-molecule junction studied using the three-dimensional dynamic probe method