Quantifying the effect of molecular geometry on the conductance of single molecule junctions

Abstract: 

In single molecule circuits, conductance (the inverse of resistance) depends critically on the geometry at the junction. Simulations based on DFT-NEGF are ideally suited to address the effect on conductance of these changes in molecular conformation. However, their computational cost restricts them to only a few junction geometries, and the challenge remains to quantify the influence on conductance of molecular structural changes within DFT. At the same time, STM break-junction experiments are often carried out at room temperature and molecular geometry is believed to change significantly during the measurements.

To address this outstanding problem, we use a recently developed computationally efficient method to calculate molecular conductance within DFT for thousands of geometries, based on small Au-molecule-Au clusters [1,2]. We perform MD simulations of the junction at room temperature, which allow us to sample the thermally-accessible geometries adopted by the molecule. We then calculate the junction conductance of these thousands of geometries. This way, we can compute the variation in conductance arising from thermally-induced conformational changes.

We interpret these datasets with machine-learning methods including regression models and SHAP analysis. We identify which of the bond lengths, angles, or dihedral angles in the molecule, all of which are changing continuously and simultaneously during the simulations, have a greater impact on conductance. We apply these techniques to study a series of amine-bonded oligophenyls of different lengths. Our work identifies how each of the different molecular conformational changes contribute to the width of the conductance signal in single molecule junctions.

[1] H. Vázquez, J. Phys. Chem. Lett. 13, 9326 (2022).
[2] E. Montes, W.Y. Rojas and H. Vázquez, J. Phys. Chem. C 129, 9947 (2025).

Short biography:

I did my PhD on energy level alignment at metal/organic and organic/organic interfaces at the Universidad Autónoma de Madrid with Fernando Flores. I then moved to the field of single molecule transport theory, in postdoctoral stays with Antti-Pekka Jauho and Mads Brandbyge at DTU-Nanotech, and Latha Venkataraman and Mark Hybertsen at Columbia University and Brookhaven National Lab. On my way back to Europe, I worked on exciton dissociation and organic photovoltaics as a postdoc with Alessandro Troisi at the University of Warwick. I arrived to Prague on a tenure-track J.E. Purkyně fellowship and started the Molecular Transport Group. I am now senior scientist at the Institute of Physics, Czech Academy of Sciences.