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Theoretical calculations
This protocol is extracted from research article:
Microscopy with a single-molecule scanning electrometer
Sci Adv, Jun 29, 2018; DOI: 10.1126/sciadv.aat5472

The geometry optimizations were performed using DFT at the Generalized Gradient Approximation (GGA)–Perdew-Burke-Ernzerhof (PBE) level, with the dispersion correction (DFT-D3) (42) on the ADF-BAND package (43, 44). The Slater-type orbitals represented by double zeta basis sets without polarization functions with small frozen cores were used. The relativistic effects were taken into account by means of the scalar zero-order regular approximation (4547). The spin-unrestricted approach was used for the open shell system of CoTPP adsorbed on the Au(111) surface. During the structural minimizations, the Au slab was constrained to the bulk with the experimental lattice parameter of 4.08 Å to be consistent with the experimental adsorbate ordering (34). The CoTPP was placed on the top side with the orientation of 39.5° between N-Co-N axis and (110) direction of the face-centered cubic (111) surface.

To reduce the interplay effects arising from the molecules on the adjacent unit cells, the size of the unit cell was extended to 28.8 × 29.9 × 22.7 Å in the electronic state calculations. The Au slab model consisted of 360 atoms in three layers. The plane-wave DFT calculations were carried out using the Quantum ESPRESSO package (48) to reduce the computational cost. The GGA-PBE functional incorporated with dispersion correction (DFT-D2) was used. We found that the combination of wave function cutoff of 80 rydberg (Ry) and charge density cutoff of 800 Ry, together with ultrasoft pseudopotentials, provided a reliable electron densities for the electrostatic field calculations. The spin-polarization calculations with the initial guess of 0.05 static magnetization were used for the CoTPP system.

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