  Herein, we invesgate the consequence of local voltage pulses on the
adsorption state of single indigo molecules on the Cu(111) surface as well as
on the atomic structure underneath the molecule. With a scanning tunneling
microscope, at 5 K, intact molecules are imaged as two lobes corresponding to
the electron density of each indoxyl moiety of the molecule which are connected
by a carbon double bond. Then, two short successive voltage pulses with the tip
placed above the molecule generate irreversible modifications, as revealed by
consecutive scanning tunneling microscopy (STM) imaging. Density-functional
theory calculations coupled to STM image calculations indicate the creation of
a double surface vacancy of copper surface atoms below the oxygen atom of the
indigo molecule as the most plausible scenario. These extracted copper atoms
are stabilized as adatoms by the indigo oxygens, oxidizing each copper adatom
to 0.32 electron.
