PolyPal: A Python Package for Molecular Dynamics Simulation of Amorphous Polymers

MC Warndorf and TM Swager and A Alexander-Katz, JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 21, 6151-6160 (2025).

DOI: 10.1021/acs.jctc.5c00254

Easily tunable and processable, porous organic polymers (POPs) have found increasing utility in various applications. Molecular modeling and simulations are invaluable tools in polymer science but remain under- reported in the POP literature. Accurate modeling and simulation of these materials could boost the discovery of high-performance POPs and allow for a more thorough contribution to big data. These polymers contain free volume-promoting structural units, such as iptycenes, and exhibit high glass-transition temperatures, excellent thermal stability, and tunable functionality. However, popular transferable force fields utilized in all-atomistic molecular dynamics (MD) simulations are not fully parametrized for intrinsically porous thermoplastic materials. We present a streamlined workflow for all-atomistic MD simulations of nonporous and porous amorphous polymer materials. In conjunction with the programs ORCA, Q-Force, Assemble!, and GROMACS, a highly accessible methodology is established for force field (FF) parametrization, creation of initial configurations, and simulation of various nonporous and porous polymers. This protocol can reproduce experimental bulk densities and fractional free volume values for amorphous polymeric materials with excellent accuracy and has been made available as a Python package, called PolyPal. As an example, we present our results using PolyPal on a series of nonporous and porous polymers that were previously synthesized and experimentally characterized. FF accuracy was also validated through solid-state NMR studies. These simulations will not only open new avenues for the rational design of high-performance POPs through the contribution of improved insight but also provide a streamlined pathway for simulating previously unexplored porous polymeric materials.

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