In the field of molecular electronics, especially in
quantum transport
experiments, determining the geometrical configurations of a single
molecule trapped between two electrodes can be challenging. To address
this challenge, we employed a combination of molecular dynamics (MD)
simulations and electronic transport calculations based on density
functional theory to determine the molecular orientation in our break-junction
experiments under ambient conditions. The molecules used in this study
are common solvents used in molecular electronics, such as benzene,
toluene (aromatic), and cyclohexane (aliphatic). Furthermore, we introduced
a novel criterion based on the normal vector of the surface formed
by the cavity of these ring-shaped monocyclic hydrocarbon molecules
to clearly define the orientation of the molecules with respect to
the electrodes. By comparing the results obtained through MD simulations
and density functional theory with experimental data, we observed
that both are in good agreement. This agreement helps us to uncover
the different geometrical configurations that these molecules adopt
in break-junction experiments. This approach can significantly improve
our understanding of molecular electronics, especially when using
more complex cyclic hydrocarbons.