Hydration-Dependent Nanostructure and Proton Transport in Nafion: A Molecular Dynamics Study

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Proton exchange membrane fuel cells (PEMFCs) require polymer electrolytes that combine high proton conductivity with mechanical robustness. Although Nafion remains the industry standard, the mechanisms linking its performance to hydration and nanoscale structural organization remain unclear. In this work, we employ molecular dynamics simulations to elucidate how these factors control membrane properties at the molecular level, with particular emphasis on backbone ordering in both amorphous and crystalline Nafion configurations. A central contribution of this study is the development and validation of a highly accurate force field for the hydronium ion (H₃O⁺) based on density functional theory calculations. This model enables detailed characterization of proton–water interactions, hydrogen-bonding statistics, and the energetic landscape governing charge transport within the membrane. Using this new potential, we systematically investigate how structural ordering affects density, hydration, and water-channel formation. Water-clustering analysis reveals distinct hydration-dependent regimes: at low water content, isolated clusters dominate; at intermediate hydration, larger clusters form and percolate preferentially in crystalline systems; and at high hydration, continuous water networks span the simulation domain. Such well-connected pathways are crucial for facilitating efficient proton transport via the Grotthuss mechanism. Complementary Voronoi tessellation analysis demonstrates that highly ordered (crystalline) backbones consistently exhibit higher densities than disordered (amorphous) counterparts across all hydration levels, as spatial ordering enables more efficient packing of the hydrophobic polymer matrix. 1 Overall, our results establish a direct link between membrane nanostructure, hydration dynamics, and transport properties. By integrating force-field development with detailed structural and energetic analyses, this work provides a robust framework for the rational design of next-generation polymer electrolyte membranes with enhanced performance for fuel cells and related electrochemical technologies. Acknowledgments The authors acknowledge funding from the European Union’s Horizon Europe research and innovation program under the Marie Sklodowska-Curie project BLESSED grant agreement No - 101072578. References: [1] Jovanović, M.; Bernhard, N.; Baldofski, M.; Rybicki, M.; Dašić, M.; Stanković, I., Linking Density and Nanoscale Crystallinity to Hydration in Nafion PEMFC Membranes: Insights From Experiment and Molecular Dynamics Simulations, Small Structures, , DOI: 10.1002/sstr.202500573 Figure 1: Comparison between experimental data, the analytic model (bold line) and densities obtained in simulations in hydrated Nafion. The various structural configurations obtained via MD simulations within the scope of this study: amorphous (blue shaded region), semi-crystalline (green shaded region), and crystalline (orange shaded region). Figure 1

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