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.
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