Dataset for: Aggregation of porous organic cryptophane cages and xenon-aggregate interactions in aqueous media: Implications for host-guest chemistry and hyperpolarised 129Xe NMR biosensing

Data archive Simulation input files supporting: Perttu Hilla, "Aggregation of porous organic cryptophane cages and xenon-aggregate interactions in aqueous media: Implications for host-guest chemistry and hyperpolarised 129Xe NMR biosensing", Physical Chemistry Chemical Physics. This archive covers the three cryptophane-A (CryA) cage derivatives studied in the paper: 1AC, 3AC and 6AC (one, three and six deprotonated acetic-acid arms, respectively; all fully deprotonated at physiological pH). The production simulations used the GAFF2 force field with RESP-derived atomic partial charges, as described in the manuscript's Computational Details section. The intermediate MD-preparation steps (the ORCA geometry-optimisation/RESP calculations themselves, the subsequent force-field parametrisation, and system packing) are not included here — only the resulting cage structures and the files needed to actually launch the reported simulations. Further details and the necessary scripts for the intermediate steps are available from the author on request. Contents - `01_cage_structures/` — the bare cage structure for each system (`1ac.xyz`, `3ac.xyz`, `6ac.xyz`), fully deprotonated, at the ORCA HF/6-31G* optimised geometry actually used for the RESP charge fit. Each file is ORCA's own RESP output format: element and xyz coordinates followed by a fourth column giving that atom's fitted RESP point charge.- `02_gromacs_md_input_files/{1ac,3ac,6ac}/` — everything needed to launch the production run with GROMACS: the force-field parameters as actually used (topology `.top` and atom-type/molecule `.itp` files for the cage, xenon, water and ions), the `.mdp` parameter files for each simulation stage (ion addition, energy minimisation, NVT, NPT, production), the HPC batch job script (for Finnish Mahti supercomputer at CSC), and the starting configuration (`md_init_*.pdb`, the solvated and ionised simulation box) for `gmx grompp`. Not included The MD-preparation pipeline that produced the files in `02_gromacs_md_input_files/` from the cage structures in `01_cage_structures/` is not included — this covers the ORCA geometry-optimisation and RESP calculation setup itself (only its resulting structure and charges are given, in `01_cage_structures/`), the subsequent GAFF2/antechamber parametrisation, and system packing with Packmol. The raw MD trajectories and the in-house trajectory-analysis scripts are likewise not included. All are available from the author on reasonable request. Software used GROMACS 2025.4 for the simulations reported here; xtb/GFN-FF, ORCA 6.1, antechamber/acpype and Packmol for system preparation. See the manuscript's Computational Details section for full method references.