Anchoring sites to the STM tip can explain multiple peaks in single molecule conductance histograms

Abstract

Accelerated molecular dynamics and quantum conductance calculations are employed to shed light onto the electrochemical properties of the Au|1,8-octanedithiol|Au junction. Widely different contact geometries with varying degrees of roughness are examined. Strikingly, the two extreme situations considered in this work, tip-tip and tip-perfect surface junctions, give almost indistinguishable conductances. This result contrasts the usual notion that different S-Au bonding geometries combined with molecular torsions provide the explanation for the experimentally observed sets (low, medium, high) of conductance peaks. In this work, we provide an alternative explanation for the occurrence of these sets in terms of the specific anchoring sites of the molecule to the tip, which in turn determines the interaction of a portion of the carbon chain with the tip.

Molecular Electronics: Toward the Atomistic Modeling of Conductance Histograms

“…This suggests that the conductance histogram in simulations for elongated junctions is dominated by thermal fluctuations and is insensitive to the precise geometry of the electrodes. This result is consistent with simulations in ref that showed that the electrode shape plays a minor role in determining the conductance distribution of alkane dithiols. As shown in Figure b, the standard deviation of the conductance histogram in this case decreases with increasing Δ L for |Δ L | < 1.5 Å.…”

“…The observed gauche defects with low conductance are in agreement with the DFT-MD simulations of an alkane dithiol molecular junction in ref . However, both studies contrast with the results in refs and that suggest that when enhanced sampling is considered the formation of gauche defects for alkane dithiols becomes less favorable due to migration of the anchor group to a side of the tip. Further, we note that the bond that breaks during the pulling using the ReaxFF is the S–Au bond.…”

“…In break-junction experiments, reproducible histograms are formed by collecting conductances from hundreds of thousands of realizations on freshly formed molecular junctions with different and uncontrolled configurations. ,, By contrast, most computational simulations are limited to a few representative molecular and junction configurations because modeling real-time experiments and statistically sampling all experimentally relevant configurations is computationally challenging. Even approaches based on molecular dynamics (MD) that can capture some of the conformational variability inherent to the experiments have not attempted to capture the full complexity inherent to the experiments. − This is because these approaches often invoke fixed or implicit electrodes and do not typically capture bond-breaking and bond-making processes. In addition, approaches that have included explicit electrodes and bond-making/breaking using first-principle simulations are not able to sample all possible conformational events because of their computational cost. ,− There have also been advances in capturing structural complexity in these experiments by sampling conformations using Monte Carlo methods. − However, a direct comparison with experiment remains outstanding.…”

Nanomechanics of Bidentate Thiolate Ligands on Gold Surfaces

“…The pronounced inter est in these particular hybrid molecule-metal junctions and interfaces is due to a multitude of potential applications such as tailoring the properties of surfaces [3][4][5][6][7], chemical anchors for molecular electronics applications [8][9][10], or coating agents for the stabilization of gold nanoparticles [11,12]. Only lately, it has been realized that the consid eration of the mechanical properties of these moleculemetal hybrids becomes a crucial design factor [13][14][15][16][17][18][19][20][21][22][23][24] for nanoscale devices.…”

Structural versus Electrical Functionalization of Oligo(phenylene ethynylene) Diamine Molecular Junctions

“…The observation of more than one conductance peak has been previously related to possible different configurations and binding geometries on the electrodes. 21,28,39,47,48 It is reasonable that when the number of molecules in the junctions is reduced, and therefore there are fewer constrains due to the interaction with other molecules, a larger number of configurations can occur. In addition, the relative rotation of the benzene rings can be blocked for closely-packed molecules, but can become more important when the molecules are dispersed.…”