DOI: 10.5281/zenodo.16801181
title: Metal-Organic Framework Xe@1bar Adsorbate Probability Distributions

description: Metal-organic framework adsorbate probability distributions (APDs) of xenon at conditions of 1 bar and 298 K. These APDs were used to train ML models in the paper <paper title>. The training set and development set come from the ARC-MOF database (primarily hypothetical MOFs), while the test set comes from the MOSAEC-DB (exclusively experimentally characterized MOFs from the CSD). All APDs were obtained using GCMC, with framework parameters taken from UFF. The tarballs in this repository contain the following information:



Xe_1bar_train.tar.gz -- APDs used in the training set in VASP CHGCAR format.

Xe_1bar_dev.tar.gz -- APDs used in the development set in VASP CHGCAR format.

Xe_1bar_test_MOSAECDB -- APDs of the MOSAEC-DB test set.

Xe_1bar_dev_binding_sites.tar.gz -- Binding sites extracted from the APDs in the Xe_1bar_dev.tar.gz set using our binding site extraction code (GALA).

Xe_1bar_test_binding_sites.tar.gz -- Binding sites extracted from the APDs in the Xe_1bar_test.tar.gz set using our binding site extraction code (GALA).


The binding_sites.tar.gz files contain one directory per MOF, with the following files/subdirectories in each directory: (Note that "Xe" represents the adsorbate "xenon". "Xex" is the atom type corresponding to the Xe adsorbate.)



Prob_Guest_Xe_Site_Xex_folded.cube -- the APD of the MOF in .cube format.

FIELD -- a file in DLPOLY FIELD format defining interaction parameters for guest-host binding energy calculations.

GALA.inp -- file containing GALA binding site extraction parameters.

gala.log -- GALA log file.

gala.out -- GALA output file.

slurm-* -- standard output.

DL_poly_BS -- a directory generated by GALA to compute the guest-host interaction energy of each binding site. Each subdirectory within DL_poly_BS contains DLPOLY input/output files for each configuration (i.e., the framework, and each binding site configuration). The <framework>_<guest> subdirectory contains the framework with a randomly placed guest configuration. This configuration is important to get the electrostatic energy of the framework, which is subtracted from the binding site configuration energies in GALA (the charges of the guest, if any, are zeroed out in this configuration). See the GALA documentation for more details on binding energy calculations.

GALA_Output -- a directory generated by GALA containing the following files:



Xe_binding_sites.cif -- all binding sites in .cif format, with the binding sites listed in the .cif file in order of decreasing occupancy.

Xe_binding_sites_fractional.xyz -- fractional coordinates of all binding sites in the MOF

Xe_binding_sites_optimized.cif -- all binding sites optimized using MD as implemented in DLPOLY. In this work, a time-step of 0 ps was used, so this is the same as O_binding_sites.cif.

Xe_gala_binding_sites.xyz -- the Cartesian xyz coordinates of each binding site, ordered in order of decreasing occupancy. This file also contains the guest-host interaction energy of each site (Ebind), the % of Ebind arising from electrostatics (esp%), the van der Waals interaction energy (Evdw), the electrostatic interaction energy (Eesp), and the relative occupancy in % (occ).  

Xe_guest_information.xyz -- a file containing adsorbate information, and binding sites listed in order of increasing occupancy, with the absolute occupancy values, fractional, and Cartesian coordinates of each binding site.