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Plane-wave DFT calculations were conducted using the Vienna Ab initio Simulation Package (VASP 5.4.1) (29, 30) at SciNet supercomputer (31). The calculations used the projector augmented wave method (32, 33), Perdew-Burke-Ernzerhof functional (34), and Grimme’s semiempirical dispersion correction (DFT-D3) (35). The energy cutoff for the plane-wave basis set was 400 eV. The surface was modeled by a slab consisting of five layers of Cu atoms separated by 17 Å of vacuum layer. All atoms were allowed to move, except the bottom two layers of Cu atoms. The relaxation, projected density of state (pDOS), and climbing image nudged elastic band (CI-NEB) calculations were conducted on a (4 × 6) slab, whereas the MD calculations were conducted on a (3 × 8) slab. The relaxation, pDOS, CI-NEB, and MD calculations used a single Γ-point k-mesh sampling. In the relaxation calculation, the system was relaxed until the force on each atom was less than 0.01 eV/Å. In the pDOS calculation, Gaussian smearing (σ = 0.25 eV) was used. In the MD calculations, a time step of 0.5 fs was used under the microcanonical condition. At the start of the MD, the initial state was initialized by random velocities sampled from the Boltzmann distribution at 4.7 K. Molecular structures presented were visualized using the VESTA software (36).

STM simulations were used to identify the species observed on the surface (see fig. S3); the calculation was performed using the Tersoff-Hamann approximation (37) and visualized using the Hive software (38, 39).

CI-NEB (40) was used to obtain the diffusion barrier of chemisorbed CF2 and I atom along the Cu row direction. Five images were used in both cases. The calculations were conducted until the forces orthogonal to the band were less than 0.02 eV/Å.

The electron-induced dissociation of CF3 was simulated using the I2S model (1820) implemented in the MD calculations. The C–F repulsion caused by electron attachment to the CF3 molecule was modeled by the anionic pseudopotential method (41, 42). The anionic potential energy surface (pes*) for CF3 was constructed by exciting one 1s electron of the F atom in the C–F bond directed along the Cu row to its valence 2p orbital, giving a pseudo-ionic configuration [He] 2s2 2p6. The reaction trajectory was obtained by evolving the system on the pes* for a short period of time (t*) and, afterward, with a retention of positions and momenta, on the ground pes until the system settled in a potential well.

The MD trajectories for association reactions were obtained by introducing a relaxed, stationary CF2 target into the path of CF2 projectile obtained from the CF3 I2S dynamics at 179 fs. The direct MD trajectory was obtained by placing the CF2 target on a short-bridge site 3.5 unit cells (8.93 Å) away from the CF3 position. The indirect MD trajectory was obtained by placing the CF2 target on a short-bridge site 4.5 unit cells (11.47 Å) away from the CF3 position. The collision energy of 1.5 eV in the forward trajectory and 1.2 eV in the backward trajectory is the sum of rotational and translational energies of the CF2 projectile when both CF2 are at their closest-approach distances of 2.55 Å (1 unit cell).

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