Date: 18 November, 2024

Dataset Title: Semifluorinated Polymer Membranes by Ring-Opening Metathesis Polymerization during Spin Coating

Dataset Creators: Arun Srikanth Sridhar

Dataset Contact: Arun Srikanth Sridhar: [email protected], Prof. Clare McCabe: [email protected]

Funding: Division of Materials Research (Award #2119575) , Graduate Research Fellowship Program, HWU high performance computing facility (DMOG)

Key Points:

• Molecular simulations and experiments agree that fluorocarbon side chains align parallel to the surface in the bulk but normal to the surface at the interface.
• Molecular simulations show preferential segregations of CF3 groups over CF2 and CH2 groups.
• Fractional free volume increases upon flourination

Research Overview:

Molecular dynamics (MD) simulations were utilised to validate the theoretical and semi-empirical approaches and provide insight in to the experientially observed behavior.

Methodology: All simulations were conducted in NPT, NVT ensembles using GROMACS 2023.2. MDanalysis, mdtraj, and gromacs utility functions were used for postprocessing atomic trajectories.

Files contained here:

The PNBFN_SI folder (the folder can be downloaded from here https://doi.org/10.5281/zenodo.14205213) contains two subfolders, PNBFN_signac and thickfilm_signac, a python file, analysis.py and a Jupyter notebook file, final_results.ipynb.

Inside the PNBFN_signac folder you will find workspace folder. Each folder inside workspace folder corresponds to a specific polymer system. The information regarding the system is contained in signac_statepoint.json file.

Inside any folder within the workspace folder of PNBFN_signac you will find

1. all the necessary GROMACS files to reproduce the simulations of bulk polymer systems.
2. The bash scripts used to run the simulations (for example 21stepbulk.sh is the script used to create bulk polymer systems ) in the cluster.
3. The free volume folders, freevol_300_0_2.8, freevol_300_500000_2.8, freevol_300_100000_2.8 contain the necessary files to reproduce the calculations carried out using pore blazer. Here, 300 refers to the temperature, the second item (0,500000,100000) refers to the time stamp (in ps), the third item 2.8 refers to the probe diameter.
4. log files and xvg files generated from GROMACS

Inside the thickfilm_signac folder you will find workspace folder. Each folder inside workspace folder corresponds to a specific polymer film system.

Inside any folder within the workspace of thickfilm_signac folder you will find

1. all the necessary GROMACS files to reproduce the simulations of polymer film systems.
2. The bash scripts used to run the simulations (for example 21stepfilm.sh is the script used to create polymer film systems) in the cluster.
3. log files and xvg files generated from GROMACS

analysis.py in PNBFN_signac contains the python codes for running the simulations (generating the bashscripts) and the codes used in post processing.

The final_results.ipynb calls the functions in analysis.py and contains the codes for generating the figures in the manuscript. Each code block in final_results.ipynb corresponds to a figure in the manuscript. The code blocks are commented for clarity. Use and Access: To use the signac framework of this project, MOSDEF suite (https://mosdef.org), SIGNAC (https://signac.io) and other python packages need to be installed. These python packages can be found in analysis.py and final_results.ipynb. The trajectories require large disk space and are not provided but the simulations can be easily extended/reproduced using the following commands. Execute these commands within any folder inside workspace to extend the simulations by 1000 ps.

gmx convert-tpr -s X.tpr -extend 1000 -o next.tpr

gmx mdrun -s next.tpr -cpi X.cpt -noappend

where X.tpr is the tpr file (topology file) and X.cpt is the check point file

The full signac framework and the data set will be made available upon request.