Data and notebooks for Quantitative Single-molecule Spatial Site Reactivity Analysis by Atomic-resolution Chemical Interaction Microscopy

This is the data and notebooks needed to reproduces the figures in Quantitative Single-molecule Spatial Site Reactivity Analysis by Atomic-resolution Chemical Interaction Microscopy 

CONTENT:

Theoretical calculations: The following files are a notebook to reproduce the force curves and frequency shift images present in the paper, as well as the necessary data to do so. Additionally, we include the coordinates files for the relaxed structures of both molecules on the substrate.

figures.ipynb: Jupyter notebook that reproduces the figures in the main and supplementary sections of the article.

CoPc_experimental_pN_A.csv and NH2_experimental_pN_A.csv: experimental F(z) for the sites in the curves before the Lennard Jones correction (Fig 3).

CoPc_experimental_LJcorrect_pN_A.csv and NH2_experimental_LJcorrect_pN_A.csv: experimental F(z) for the sites in the curves after the Lennard Jones correction (Fig 4).

fs_copc_nh2_bridge_beta_k0.2000_a1.08_V42.91_r3.27_amp0.67.npz and fs_copc_bridge_beta_k0.2000_a1.08_V42.91_r3.27_amp0.67.npz: frequency shift data (needed to reproduce the images)

CoPc_theory_nosub_pNA.csv and NH2_theory_nosub_pNA.csv: theoretical F(z) for the sites in the curves after substrate removal, theoretical curves in Figs 3 and 4.

CoPc_static_forces.csv, NH2_static_forces.csv, CoPc_relax_forces.csv and NH2_relax_forces.csv: theoretical relaxed and static F(z) curves for Supplementary Figure 4. (before substrate removal)

relax_copc_bridge_beta_k0.2000_a1.08_V42.91_rpivot3.27.npz and relax_copc_bridge_beta_conf2_k0.2000_a1.08_V42.91_rpivot3.27.npz: CO relaxation data. Contains the tip relaxed positions needed for Supplementary Figures 5 and 6.

Cext_different_functionals.csv, Next_different_functionals.csv, Cint_different_functionals.csv: theoretical F(z) curves with different DFT functionals for the CoPc in gas phase used in Supplementary Figure 9.

fdbm_static_molecule.csv: static F(z) calculated with FDBM for the CoPc molecule in gas phase  used in Supplementary Figure 9.

CoPc_dft_forces.csv: DFT (PBE-D3) F(z) computed on the CoPc molecule on Ag(111)  for the sites in Supplementary Figures 10 and 11.

CoPc_static_a1.19_V91.7_forces.csv:  static FDBM F(z) computed with the fitted α and V0 parameters on the CoPc molecule on Ag(111)  for the sites in Supplementary Figure 11.

POSCAR_CoPc, POSCAR_NH2, copc.xyz and nh2.xyz: structures of the molecules on the Ag(111) substrate in VASP and xyz formats.

Experimental data: The following compressed folders include the experimental data from the STM and AFM measurements.

Main_paper_Fig1.zip: STM images of the main text figure 1.

Original_data_for_CoPc_3D_AFM.zip and Original_data_for_CoPcNH2_3D_AFM.zip: AFM frequency shift images of CoPc and CoPcNH2 molecules to construct 3DAFM set

Point_Spectroscopy_data.zip: Freq shit vs. z data at specific sites of the molecule to verify the correctness of interpretation. (Extend Fig.2)

The theoretical calculations have been obtained using the DBSPM method at https://github.com/SPMTH/DBSPM/

NOTEBOOK DEPENDANCIES:Language:-python 3Python Libraries:-scipy-numpy-pandas-matplotlib-ase-argparse