The atomic structure and electronic transport properties of Au-mesitylene-Au molecular junctions formed from a mesitylene monolayer without any anchoring groups are investigated by employing the non-equilibrium Green's function formalism combined with density functional theory. The intermolecular and adsorbate-substrate interactions are described by the non-local optB88 van der Waals functional. Two types of Au-mesitylene-Au molecular junctions are constructed, in which either an isolated mesitylene molecule or a mesitylene molecule embedded into a monolayer lying flat on one electrode surface is in contact with an atomic protrusion of the other electrode surface. The calculated low-bias conductance values of these two junctions are both in quantitative agreement with the reported experimental values [S. Afsari, Z. Li, and E. Borguet, Angew. Chem. Int. Ed. 2014, 53, 9771; Angew. Chem. 2014, 126, 9929]. This indicates that the measured conductance is intrinsic at the single-molecule Au-mesitylene-Au junction and that the intermolecular interactions in the mesitylene monolayer have little effect.
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