  Using an updated simulation tool, we examine molecular junctions comprised of
benzene-1,4-dithiolate bonded between gold nanotips, focusing on the importance
of environmental factors and inter-electrode distance on the formation and
structure of bridged molecules. We investigate the complex relationship between
monolayer density and tip separation, finding that the formation of
multi-molecule junctions is favored at low monolayer density, while
single-molecule junctions are favored at high density. We demonstrate that tip
geometry and monolayer interactions, two factors that are often neglected in
simulation, affect the bonding geometry and tilt angle of bridged molecules. We
further show that the structures of bridged molecules at 298 and 77 K are
similar.
