addco2substrate

Fortran tool that adds a CO2 adsorbate to a metalloporphyrin (M-POR) structure at a consistent starting geometry, for high-throughput DFT screening of CO2 adsorption and activation.

What it does

1. Reads an M-POR structure in XYZ format.
2. Translates the structure so the metal centre sits at the origin.
3. Defines the porphyrin plane from the metal and two adjacent coordinating N atoms, and computes its normal (cross product).
4. Places the CO2 carbon 2.0 Å above the metal along that normal.
5. Adds the two O atoms 1.16 Å either side of the carbon (linear CO2), parallel to the porphyrin plane.
6. Writes the combined structure (M-POR + CO2) in XYZ format.

Every system therefore starts from the same, well-defined geometry, so results after optimisation are directly comparable across the screening set.

Input

A file named CONFIG in XYZ format (coordinates in Å):

• Atom 1: the metal centre
• Atoms 2 and 3: two adjacent (cis) N atoms coordinated to the metal

If atoms 2 and 3 are opposite (trans) N atoms, the plane normal is undefined.

Build and run

./compile.sh
./co2_adsorption_generator.x > OUTPUT.xyz

Used in

A. T. Uddin, Q. Zhao, D. Toroz, R. Crespo-Otero, D. Di Tommaso, "Computational screening of metalloporphyrin catalysts for the activation of carbon dioxide", Molecular Catalysis 565 (2024) 114386. https://doi.org/10.1016/j.mcat.2024.114386

Author

Amira T. Uddin