A Computational Study of Interfacial and Dynamical Effects in Thiol-Contacted Single-Molecule Junctions

The metal-molecule interface plays a critical role in charge transport in single-molecule junctions. Even the prototypical alkanedithiol (HS-C_nH_2n-SH) junction in which an alkane is contacted to metal electrodes via sulfur atoms exhibits large variations in electrical and mechanical properties depending on the length of the alkyl chain, the nature of the metal, and the thiol-metal interactions at the interface. Further, the conductance and current vs voltage (I-V) characteristics of the junction are very sensitive to the molecular geometry and, consequently, to dynamics of the alkane backbone and the thiol-metal interface. In particular, motions involving the S-metal bonding motif or torsional strain in the saturated alkane chain could lead to broad conductance distributions and multiple I-V regimes. Here we study coherent transport in alkanedithiol junctions containing gold, silver, or copper electrodes using a voltage-dependent, ab initio tunneling model. This theoretical approach offers the dual benefit of accurately reproducing experimentally observed conductance properties and efficiently integrating with our home-built ab initio molecular dynamics simulation program. We found that the conductance in alkanedithiol aromatic and aliphatic based junctions is impacted by the nature of the metal-S bond. Namely, a thiol (HS-Au) bond yields greater conductance and weaker binding, whereas a thiyl (Au-S) bond has a greater binding and lower conductance with a tunneling -decay constant of 0.79 Å^-1 matching experimental findings of 0.84 Å^-1. Investigating these effects in a dynamic way along with known conformational strain in alkane chains offers an avenue to understand the broad conductance peaks and varied I-V curves seen in alkanedithiol based junctions. Understanding the impact of chemical bonding, molecular strain and metal-molecule interactions will advance the understanding of how molecules behave as quantum circuitry.