Calculation of Single Molecule Conductance from Molecular Dynamics Simulations: Implementation in the SIESTA Code

The high computational cost of computing the conductance of single molecule junctions with standard methods based on Density-Functional Theory and Non-Equilibrium Green’s Functions (DFT-NEGF) limits its application to only a few junction geometries. Thus, calculations probing the variability of conductance using geometries from Molecular Dynamics simulations must often resort to approximate descriptions of the electronic structure. We describe the implementation in the SIESTA code of a method that allows for the fast computation of junction conductance from Molecular Dynamics geometries without a simplified description of the electronic structure. Its efficiency comes from considering small Au-molecule-Au clusters, which properly capture variations in conductance arising from changes in molecular conformation. After scaling with a few DFT-NEGF calculations, the conductance of tens of thousands of junction geometries can be accurately computed at the DFT level more than 2 orders of magnitude faster than with DFT-NEGF. Coupled with MD simulations at room temperature, it is used here to quantify the role of benzene ring rotations in conductance using the ensemble of geometries from the junction dynamics in paradigmatic single molecule junctions.