TAFEIP (Topological Aromaticity For Estimating Interface Properties)

Python Scripts for estimating the interface properties on a Cu(111) surface solely from the molecular structure using topological aromaticity (conjugated-circuit resonance energy & topological resonance energy) as a descriptor. It is the result of two publications. If you use any of the scripts, please cite our work.

Dependencies

• argparse
• ase
• ast
• itertools
• numpy
• pandas
• rdkit
• sympy

Individual Scripts

• Estimate_Interface_Properties.py: Main script for estimating interface properties from molecular structure. Can be used directly from command line. Uses Generate_Connectivity.py, CCRE.py, and TRE.py.

• Generate_Connectivity.py: Script for generating connectivity (topological) matrix from .xyz-file, SMILES string, or matrix.

• Find_Rings.py: Script for finding all possible rings (circuits) in a structure (graph).

• Kekule.py: Script for generating all possible Kekule structures (chemical structure with explicit single and double bonds) for given connectivity (topological) matrix.

• CCRE.py: Script for calculating the conjugated-circuit resonance energy (CCRE). Uses Kekule.py and Find_Rings.py.

• TRE.py: Script for calculating the topological resonance energy (TRE). Uses Find_Rings.py.

References

• J. Schramm, R. Tonner-Zech, Unveiling Correlations in Metal-Organic Interface Properties: A Computational Exploration of Alternant and Non-Alternant π-Electron Systems, ChemPlusChem 2025, 90 (6), e202400771, https://doi.org/10.1002/cplu.202400771.
• J. Schramm, R. Tonner-Zech, Molecular Aromaticity Determines Metal-Organic Interface Properties: Alternant and Non-Alternant π-Electron Systems on Cu(111), J. Phys. Chem. C 2026, 130 (1), 546-559, https://doi.org/10.1021/acs.jpcc.5c05720.