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

Abstract

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.

Figure 1

Illustration of “parallel” and “perpendicular” configurations of benzene molecules between two gold electrodes. The blue rectangle next to it shows the initial structures of the benzene, cyclohexane, and toluene junctions for one of the two configurations studied in this work. The starting distance between the two gold apex atoms of the tips in the “parallel” configuration is depicted with dashed lines and is 3.27 Å. Three of the “perpendicular” configurations have a starting distance between the gold tip apex atoms, indicated by dashed lines, of 6.96 Å. In the fourth “perpendicular” configuration, the toluene molecule with the methyl group attached to the upper electrode has gold tip atoms that start apart 9.06 Å. The “perpendicular” configuration of the toluene is labeled as L.R. and U.D., which indicates if the methyl group is located left–right or up–down.

Figure 2

Calculated electronic transport vs relative displacement of the initial structures of benzene, cyclohexane, and toluene, labeled as a, b, and c. Colored markers represent the calculated values of benzene (black), cyclohexane (pink), and toluene (green).

Figure 3

Snapshots of the simulation during the rupture and formation cycles. Each row corresponds to a different molecule: benzene (top), cyclohexane (middle), and toluene (bottom).

Figure 4

Panel (a) classification hierarchy of molecular contacts used in this work. To the left and right, we show example structures that illustrate each type of last contact. Panel (b) shows the percentage calculated from Table 1 for the different types of last rupture with benzene, cyclohexane, and toluene.

Figure 5

In panels (a–c), we show rupture traces for benzene, cyclohexane, and toluene, respectively. Gray- and blue-shaded areas represent the range of values of the theoretical traces calculated via DFT based on the different geometric configurations tested. Bottom panels (d–f) show one-dimensional experimental histograms of conductance for benzene, cyclohexane, and toluene. These histograms have been normalized with respect to the number of traces that contributed to each histogram bin, i.e., each bin count is divided by the total number of traces.

Figure 6

Experimental conductance–displacement density plots for benzene, cyclohexane, and toluene are shown in panels (a–c), respectively. The points connected by lines within these density plots represent ab initio transport values calculated for molecular junctions simulated through molecular dynamics. Additionally, the panels labeled as (a1,a2), (b1,b2), and (c1,c2) correspond to benzene, cyclohexane, and toluene. In each panel, the calculated conductance versus relative displacements are displayed, overlaid on the density plots, along with illustrations corresponding to each point, allowing for a reference of the molecular contact geometry. The color code for the theoretical data and overlaid on the experimental data corresponds to that used in the side panels, where the colors of the box and the trace are the same.