The final geometry configuration and the barrier energy for the reaction in the gas phase were obtained at the MP2/6-311++G(d,p), DFT-B3LYP/6-31++G(d,p), and B3LYP/6-31G(d) theory level, respectively. These calculations have been carried out using the Quantum Chemistry package Gaussian (see the Supplementary Materials for more details). In the geometry optimization, a full relaxation of all the coordinates was carried out without imposing any condition on the symmetry of the molecule.

DFT-based adsorption studies of the TCNQ-CH2CN molecule on gr-Ru(0001) were carried out using the Projector Augmented Wave (PAW) method as implemented in the Vienna Ab initio Simulation Package code (37), and we applied the Perdew-Burke-Ernzerhof exchange correlation functional, whereas weak dispersion forces were taken into account using the Tkatchenko-Scheffler method (38). The gr-Ru(0001) interface was modeled by a (11 × 11) graphene unit cell adsorbed on a three-layer-thick (10 × 10) Ru unit cell. In all periodic calculations, the Brillouin zone sampling was limited to the Γ point, and a strict 10−5–eV convergence criterion was set for the self-consistent runs. The moiré pattern was obtained by a geometry optimization in which we optimized all the coordinates of the graphene atoms and of the topmost Ru layer until the maximum force acting on the active atoms was less than 0.01 eV/Å. The final adsorption configuration of the molecule was obtained by fully relaxing the coordinates of all the molecule and graphene atoms. The charge transfer from the substrate to the molecule was obtained by using the partitioning methods of atoms in molecules first introduced by Bader (39). The simulated STM images have been calculated using the Tersoff-Hamann approach (40), integrating the electron density in an energy window going from the Fermi energy to Eb = e*Vb and calculating the isosurface (Isov), which corresponds to a given value of the tunneling current (It) as given by the relation Isov (Å−3) = 2 × 10−4It (nA).

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