The ground-state Hamiltonian and optimized geometry of each molecule was obtained using the density functional theory code SIESTA (Spanish Initiative for Electronic Simulations with Thousands of Atoms) (32). The local density approximation exchange correlation functional was used along with double zeta-polarized (DZP) basis sets and norm-conserving pseudo-potentials. The real space grid is defined by a plane-wave cutoff of 185 rydberg. The geometry optimization was carried out to a force tolerance of 0.01 eV/Å. This process was repeated for a unit cell with the molecule between gold and graphene electrodes, where the optimized distance between graphene and the thiol anchor group was found to be 2.9 Å.

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