Oligomeric Gold−Thiolate Units Define the Properties of the Molecular Junction between Gold and Benzene Dithiols

Understanding the structure and conductance of the molecular junction between benzene dithiolates (BDT) and gold electrodes has posed a classic unsolved problem for high-level theoretical work for over a decade. Recent breakthroughs for the gold−thiolate interface in thiolate-passivated gold clusters and in Au(111)/self-assembled monolayers (SAMs) motivated us to reanalyze the properties of Au−BDT−Au junctions. We show that distinct molecular Au(SR) 2 and Au 2 (SR) 3 units, which are known to exist at the nanoparticle−thiolate and Au−SAM interfaces, define the properties of the electrode−molecule junction. These units can form multiple contacts. The junction can be stretched by more than 1 nm whereby alternating gold−thiolate chains are spontaneously formed in ab initio molecular dynamics simulations. The calculated conductance values for the BDT junctions agree with a wide range of reported experimental data. Our results give a solid ground for further theoretical studies of molecular junctions between gold and a wide variety of organic molecules containing dithiols.