Data for: Understanding diffusion and exchange of amino acids into montmorillonite interlayer space: Insights from molecular dynamics simulations based on machine learning analysis

This dataset contains the raw numerical data underlying the figures presented in the accompanying manuscript entitled "Understanding diffusion and exchange of amino acids into montmorillonite interlayer space: Insights from machine learning-based molecular dynamics simulations". All data files are provided in plain text format (.dat) and can be used to reproduce the figures in the manuscript. File descriptions: ADPS.dat — Atomic density profiles (ADPs) of amino acids and water oxygen atoms along the c-axis of MMT, corresponding to Fig. 3 (Na⁺ and Ca²⁺ systems) Columns include position along the c-axis and density values. Exchange_ratios.dat — Interlayer occupancy data showing the proportion of amino acids (Lys⁺, Gly, Asp⁻) entering the interlayer over simulation time, corresponding to Fig. 2 (Na⁺ vs. Ca²⁺ systems) . Columns include time and occupancy fractions. Interaction_energy.dat — Interaction energy between amino acids and MMT surfaces over simulation time, corresponding to Fig. 6. Columns include time and total Coulombic and van der Waals interaction energies for each amino acid-cation system. MSD.dat — Mean square displacement (MSD) curves and fitted diffusion coefficients for amino acids in bulk aqueous solution and MMT systems, corresponding to Fig. 7. Columns include time, MSD values. PMF.dat — Potential of mean force (PMF) profiles for amino acid exchange from bulk solution into the MMT interlayer, corresponding to Fig. 8. Columns include reaction coordinate (distance from interlayer center) and free energy values. Additional notes: All data were generated from classical molecular dynamics simulations using GROMACS 2018.4 with the CLAYFF-MOH force field. Detailed simulation protocols and analysis methods are described in the Methods section of the manuscript. The data are provided in a text-based numerical format to facilitate reproducibility and reuse.