DOI: 10.5281/zenodo.17303560
title: Supporting data for "Molecular insights into the dynamic evolution of ketene conversion in MAPO-18 (M = Si and Mg) molecular sieves from ab initio molecular dynamics simulations"

description: This dataset provides the supporting data for the research article titled "Dynamic Evolution and Stability of Ketenes in MAPO-18 (M = Si or Mg): Molecular Insights into the Reaction Mechanism for CO2-to-Hydrocarbons" It contains all input files, optimized structures, and simulation results related to both static and dynamic studies of ketene conversion in SAPO-18 and MgAPO-18 molecular sieves.

The dataset is organized into two main subfolders: Static-Calculations and Dynamic-Simulations, each containing relevant data and scripts used in the corresponding computational studies.

Static-Calculations

This folder contains all necessary files and results associated with static ab initio calculations.





Input-files:Includes example CP2K input files for geometry optimization, transition state searches, and vibrational frequency analyses. A Python script for generating CP2K input files for relaxed scans is also provided.




Structures:Contains all optimized structures in .xyz format. The cell parameters of SAPO-18 and MgAPO-18 are included within the input files.




Frequency:Provides vibrational frequency results in .mol format. These can be visualized using the free Jmol software (https://jmol.sourceforge.net/).




Energies:Contains CP2K input and output files for single-point energy calculations performed using various methods, including revPBE-D3, PBE0, M06, M06-2X, wB97XD, wB97X-V, and RPA.



Dynamic-Simulations

This folder includes all data and scripts related to umbrella sampling molecular dynamics simulations used to investigate the interconversion of neutral species, cationic intermediates, and surface-bound species for ketene, methyl ketene, and dimethyl ketene in both SAPO-18 and MgAPO-18 frameworks.

The results are organized into six subfolders, each corresponding to one of the studied reactions. Additionally, two Python scripts for launching analyses with Thermolib are provided.



CP2K.inp – CP2K input file to launch AIMD simulation with umbrella sampling.

plumed_US.dat – PLUMED input file defining the umbrella sampling parameters.



match_cv1_xx_cv2_xx.xyz – Initial structure extract from the metadynamic simulation used for the umbrella sampling simulation.




colvar_xx_xx.dat – Records the evolution of collective variables (CV1 and CV2) during umbrella sampling.




wham_input.txt – Thermolib input file for generating the 2D free energy surface.




2D-FES-with-error-estimation.py – Generates 2D free energy surfaces (FES) and 1D projected free energy profiles with error estimation along selected collective variables.




2D-FES-xxxxxxx.dat – Original 2D free energy surface file generated by Thermolib.




1D-FES-xxxx-with-error.dat – 1D free energy profile derived from projection of the 2D surface with error estimates.




plumed_CV.dat – PLUMED input file used to extract CV1 and additional parameters from umbrella sampling trajectories.




2D-FES-CV1-sin_beta-from-deprojection.py – Produces deprojected 2D FES along CV1 and sin(β) using extracted data files.