Are STAM MOFs overlooked as promising water-stable adsorbents? Elucidating their physical and hydrolytic properties using Machine-Learned Potentials.
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2024
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| _version_ | 1866901822731452416 |
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| author | Yifei, Yue Athulya, S. Palakkal Loh, Duane Jiang, Jianwen |
| author_facet | Yifei, Yue Athulya, S. Palakkal Loh, Duane Jiang, Jianwen |
| contents | <div>This repository contains data for QHA calcations/MLP-MD simulations of STAM MOFs. </div> <div> </div> <div>1. The 'QHA-Calculations' folder contains the scripts/results obtained from QHA calculations. The subfolders within are organized as follows:</div> <div>- 'CIF-structures' contain the optimized geometries of STAMs that were then used for DFTPT calculations</div> <div>- 'INCAR_Configurations' contain the input parameters for VASP; including the ones used for geometry optimized (INCAR.OPT) and DFTPT (INCAR.DFTPT). The KPOINTS contains the kpoint-mesh (just the gamma point)</div> <div>- 'QHA_results' contains the raw outputs from QHA calculations using phonopy (see subfolder CpData, BulkModulusData), the processed data for reference is provided in the csv files (Cp.csv, BulkModulus.csv)</div> <div> </div> <div>2. The 'StructureSnapshots' folder contains the contain the structures used in illustrations:</div> <div>- 'WaterClusters' contains the geometry of water clusters taken from 1ns MLP-MD simulation of water-sovlated STAM (Figure 4)</div> <div>- 'STAM1-paddlewheels' contains the .VESTA files of the defective and stable paddlewheel obtained from the final snapshot of water-solvated STAM-1 (Figure 4) from 1 ns MLP-MD simulations</div> <div>- 'DFT-Optimized' contains the optimized geometeries (without water) of the STAMs (shown in Figure S1)</div> <div> </div> <div>3. The 'EnergyAndAngularData' folder contains a compressed csv-file "Ewc_Angle_inTriangular_HexagonalPores.csv";</div> <div> - This file contains raw data used to analyze distribution of relative water energy (e.g. Figure 5b) and angular information (Figure 5a):</div> <div>- The relative potential energy of water clusters at each position in STAMs (denoted DeltaEwc, the column name in file is 'PotEner_Norm'). This is the data used to plot the 2D-histogram distributions of Delta_Ewc in the STAMs in (e.g. Figure 3b and 5b) . </div> <div>- Also the deviation in ange (denoted Delta_theta, referred to as 'stdAngle') is also used to plot the 2D-histogram distribution of Delta_Angle plots (e.g. Figure 4c and 5a). </div> <div> </div> <div>4. The 'WaterDiffusivity' folder contains 'water-diffusivity.csv', which has the raw data collected from diffusion studies in STAM, namely</div> <div>- Water MSD (Ang^2) curves obtained from the mean MSD values over five 200 ps trajectories (200,000 points, sampled every 1fs).</div> <div>- The MSD curves are shown separately for water in the hexagonal/triangular channels.</div> <div>- The calculated diffusion coefficients (Dc in 10^-10 m^2/s) and the R-square of linear fit is also provided. </div> <p> </p> |
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| publishDate | 2024 |
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| spellingShingle | Are STAM MOFs overlooked as promising water-stable adsorbents? Elucidating their physical and hydrolytic properties using Machine-Learned Potentials. Yifei, Yue Athulya, S. Palakkal Loh, Duane Jiang, Jianwen <div>This repository contains data for QHA calcations/MLP-MD simulations of STAM MOFs. </div> <div> </div> <div>1. The 'QHA-Calculations' folder contains the scripts/results obtained from QHA calculations. The subfolders within are organized as follows:</div> <div>- 'CIF-structures' contain the optimized geometries of STAMs that were then used for DFTPT calculations</div> <div>- 'INCAR_Configurations' contain the input parameters for VASP; including the ones used for geometry optimized (INCAR.OPT) and DFTPT (INCAR.DFTPT). The KPOINTS contains the kpoint-mesh (just the gamma point)</div> <div>- 'QHA_results' contains the raw outputs from QHA calculations using phonopy (see subfolder CpData, BulkModulusData), the processed data for reference is provided in the csv files (Cp.csv, BulkModulus.csv)</div> <div> </div> <div>2. The 'StructureSnapshots' folder contains the contain the structures used in illustrations:</div> <div>- 'WaterClusters' contains the geometry of water clusters taken from 1ns MLP-MD simulation of water-sovlated STAM (Figure 4)</div> <div>- 'STAM1-paddlewheels' contains the .VESTA files of the defective and stable paddlewheel obtained from the final snapshot of water-solvated STAM-1 (Figure 4) from 1 ns MLP-MD simulations</div> <div>- 'DFT-Optimized' contains the optimized geometeries (without water) of the STAMs (shown in Figure S1)</div> <div> </div> <div>3. The 'EnergyAndAngularData' folder contains a compressed csv-file "Ewc_Angle_inTriangular_HexagonalPores.csv";</div> <div> - This file contains raw data used to analyze distribution of relative water energy (e.g. Figure 5b) and angular information (Figure 5a):</div> <div>- The relative potential energy of water clusters at each position in STAMs (denoted DeltaEwc, the column name in file is 'PotEner_Norm'). This is the data used to plot the 2D-histogram distributions of Delta_Ewc in the STAMs in (e.g. Figure 3b and 5b) . </div> <div>- Also the deviation in ange (denoted Delta_theta, referred to as 'stdAngle') is also used to plot the 2D-histogram distribution of Delta_Angle plots (e.g. Figure 4c and 5a). </div> <div> </div> <div>4. The 'WaterDiffusivity' folder contains 'water-diffusivity.csv', which has the raw data collected from diffusion studies in STAM, namely</div> <div>- Water MSD (Ang^2) curves obtained from the mean MSD values over five 200 ps trajectories (200,000 points, sampled every 1fs).</div> <div>- The MSD curves are shown separately for water in the hexagonal/triangular channels.</div> <div>- The calculated diffusion coefficients (Dc in 10^-10 m^2/s) and the R-square of linear fit is also provided. </div> <p> </p> |
| title | Are STAM MOFs overlooked as promising water-stable adsorbents? Elucidating their physical and hydrolytic properties using Machine-Learned Potentials. |
| url | https://doi.org/10.5281/zenodo.14287106 |