Unraveling the Interplay between Quantum Transport and Geometrical Conformations in Monocyclic Hydrocarbons’ Molecular Junctions

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.