  A detailed computational analysis has been performed, considering copper
atomic contacts that are exposed directly to water molecules, hydroxyl groups,
and monatomic as well as molecular hydrogen and oxygen species. The optimized
physical bonding structure, electrical conductance and inelastic tunneling
spectra (IETS) have been determined theoretically for moderately large
structures by performing appropriate ab-initio and semi-empirical calculations.
By considering the aforementioned properties, it has been possible to determine
that some of the molecular bridging structures may be regarded as being
highly-probable outcomes, resulting from the exposure of copper electrodes to
the atomic/molecular contaminants. We specifically identify the conductance
properties of a variety of configurations including examples with very high and
very low conductance values. This is done in order to identify junction
geometries that may be realized experimentally and their conductance and IETS
signatures. By reporting geometries with very high and very low conductance
values here, we intend to provide a wider perspective view than previous
studies of copper-molecular junctions that have focused on high conductance
structures. In addition, we explore the properties of metal junctions with
multiple molecules, a class of systems for which little theoretical work has
been available in the molecular electronics literature. We find that water
molecules surrounding the junction can influence the bonding geometry of the
molecules within the junction and consequently can affect strongly the
calculated conductances of such junctions.
