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arxiv: 2605.11941 · v1 · submitted 2026-05-12 · ⚛️ physics.chem-ph

Recognition: 2 theorem links

· Lean Theorem

Poisoning mechanism of ammonia on proton transport and ionomer structure in cathode catalyst layer of PEM fuel cells

Tianyou Wang, Yichao Huang, Zhen Zeng, Zhizhao Che

Pith reviewed 2026-05-13 04:19 UTC · model grok-4.3

classification ⚛️ physics.chem-ph
keywords ammonia poisoningproton transportPEM fuel cellsionomermolecular dynamicscathode catalyst layerammoniumion clusters
0
0 comments X

The pith

Ammonia poisons PEM fuel cell catalyst layers when ammonium ions displace hydronium at sulfonic acid sites and amino and imino ions form clusters that absorb additional hydronium ions, reducing proton transport.

A machine-rendered reading of the paper's core claim, the machinery that carries it, and where it could break.

The paper employs all-atom molecular dynamics simulations to uncover how ammonia poisons the cathode catalyst layer in PEM fuel cells. Ammonium ions take the place of hydronium ions at the sulfonic acid groups on the ionomer side chains, held by van der Waals and electrostatic forces. Amino and imino ions then gather hydronium ions into clusters stabilized by hydrogen bonds, which lowers proton transport efficiency and harms the layer's performance in reactions. Raising the temperature breaks up these clusters, relieves the blockage in the ionomer, and brings back proton transport efficiency. This mechanism provides a basis for developing strategies to counter ammonia poisoning in fuel cells.

Core claim

Ammonium can replace the hydronium ions at the charged sites of the sulfonic acid group of the ionomer side chain through van der Waals force and electrostatic interaction. Other ammonia derivatives, amino and imino ions, capture hydronium ions to form ion clusters that have a strong capability to absorb hydronium ions, with structures that change according to ammonia content and temperature due to stable hydrogen bonds within the clusters. These processes reduce the efficiency of proton transport and decrease the catalyst layer's performance. An increase in temperature leads to the dissociation of large ion clusters, alleviating the blockage in the ionomer layer and restoring proton t

What carries the argument

Ion clusters formed by amino and imino ions with hydronium ions, which absorb protons and block transport in the ionomer, along with ammonium adsorption at sulfonic acid sites.

If this is right

  • Proton transport efficiency is reduced by the absorption of hydronium ions into the ion clusters.
  • The electrochemical performance of the catalyst layer decreases due to impaired proton availability.
  • Increasing temperature dissociates the ion clusters and restores proton transport efficiency.
  • The degree of poisoning depends on ammonia content and temperature through changes in cluster structure.

Where Pith is reading between the lines

These are editorial extensions of the paper, not claims the author makes directly.

  • Designers could target ionomer modifications that reduce the binding strength of ammonium to sulfonic groups to improve poison resistance.
  • Short-term operation at higher temperatures might mitigate ammonia effects, though long-term material stability would require separate study.
  • Validation through in-situ spectroscopy in fuel cells could confirm cluster formation and guide practical anti-poisoning measures.

Load-bearing premise

The all-atom molecular dynamics simulations accurately capture the interactions and structures that occur during ammonia poisoning in real PEM fuel cell cathode catalyst layers.

What would settle it

If experimental proton conductivity measurements in ammonia-exposed ionomer samples show no temperature-dependent recovery matching the simulated cluster dissociation, or if no evidence of ammonium displacement or cluster formation appears in spectroscopic data, the proposed mechanism would be falsified.

Figures

Figures reproduced from arXiv: 2605.11941 by Tianyou Wang, Yichao Huang, Zhen Zeng, Zhizhao Che.

Figure 1
Figure 1. Figure 1: Configurations of CCL model before and after the annealing process. [PITH_FULL_IMAGE:figures/full_fig_p004_1.png] view at source ↗
Figure 2
Figure 2. Figure 2: Snapshots of equilibrated systems with di [PITH_FULL_IMAGE:figures/full_fig_p005_2.png] view at source ↗
Figure 3
Figure 3. Figure 3: (a-e) RDFs of NH-OI at various ammonia contents and temperatures. (f) CN of NH-OI. [PITH_FULL_IMAGE:figures/full_fig_p006_3.png] view at source ↗
Figure 4
Figure 4. Figure 4: (a-e) RDFs of NH2 -OI at various ammonia contents and temperatures. (f) CN of NH2 -OI. b d e f a c [PITH_FULL_IMAGE:figures/full_fig_p007_4.png] view at source ↗
Figure 5
Figure 5. Figure 5: (a-e) RDFs of NH-NH2 at various ammonia contents and temperatures. (f) CN of NH-NH2 . 7 [PITH_FULL_IMAGE:figures/full_fig_p007_5.png] view at source ↗
Figure 6
Figure 6. Figure 6: Average number of hydronium ions captured by (a) an imino ion or (b) an amino ion at di [PITH_FULL_IMAGE:figures/full_fig_p008_6.png] view at source ↗
Figure 7
Figure 7. Figure 7: (a) Average number of ion clusters at di [PITH_FULL_IMAGE:figures/full_fig_p009_7.png] view at source ↗
Figure 8
Figure 8. Figure 8: Complementary cumulative distribution function of the radius of gyration [PITH_FULL_IMAGE:figures/full_fig_p009_8.png] view at source ↗
Figure 9
Figure 9. Figure 9: Pore size distribution of PFSA ionomer layer after removing water clusters and ion clusters at various temperature and ammonia contents. [PITH_FULL_IMAGE:figures/full_fig_p011_9.png] view at source ↗
Figure 10
Figure 10. Figure 10: Snapshots of ionomer layer and free space at di [PITH_FULL_IMAGE:figures/full_fig_p011_10.png] view at source ↗
Figure 11
Figure 11. Figure 11: (a-e) RDFs of S-OI pairs at different temperatures and ammonia contents. (f) CN of the S-OI. chain of the ionomer, we further analyzed the radial distribution function (RDF) and CN of the sulfonic acid group with hydronium ions (gS-OI) and ammonium ions (gS-NH4), where “OI” indicates the oxygen atom in the hydronium ions, “S” indicates the sulfur atom in sulfonic acid group, “NH4” indicates the nitrogen a… view at source ↗
Figure 12
Figure 12. Figure 12: (a-e) RDFs of S-NH4 pairs at different temperatures and ammonia contents. (f) CN of the S-NH4 . between ammonium and sulfonic acid groups increases, and the increase in the system temperature will also promote the formation of hydrogen bonds between ammonium and sulfonic acid groups to a certain extent. However, it is worth noting that this is the statistic average of the total number of hydrogen bonds fo… view at source ↗
Figure 13
Figure 13. Figure 13: Average number of hydrogen bonds (a) between sulfonic acid group (SO [PITH_FULL_IMAGE:figures/full_fig_p014_13.png] view at source ↗
Figure 14
Figure 14. Figure 14: (a-e) RDFs of S-OW pairs at different temperatures and ammonia contents. (f) CN of the S-OW. decreases, likely due to the temperature-sensitive nature of hydrogen bonds. At higher temperatures, the correlation between water molecules weakens, reducing hydrogen bonds and thereby reducing connectivity. Figure S4 shows the variation in the diffusion coefficient of water molecules under various temperatures a… view at source ↗
Figure 15
Figure 15. Figure 15: (a-e) RDFs of OW-OW pairs at different temperatures and ammonia contents. (f) CN of the OW-OW. the first peak is at about 7.95 Å, and the position of the first valley is at about 8.95 Å, which means that about one or two hydronium ions will appear in the range of 9 Åwith the absence of ammonia. After adding ammonia, hydronium ions are captured by ion clusters, and the distance between hydronium ions is gr… view at source ↗
Figure 16
Figure 16. Figure 16: Average number of hydrogen bonds in water clusters at di [PITH_FULL_IMAGE:figures/full_fig_p016_16.png] view at source ↗
Figure 17
Figure 17. Figure 17: (a-e) RDFs of OW-OI pairs at different temperatures and ammonia contents. (f) CN of the OW-OI. further promotes the stability of the ion clusters. 4. Conclusions In this study, all-atom MD simulations are performed to study the poisoning mechanism of ammonia at different ammonia contents and temperatures in CCLs of PEM fuel cells. The snapshots of the CCLs were analyzed to explore the behavior of ammonia … view at source ↗
Figure 18
Figure 18. Figure 18: (a-e) RDFs of OI-OI pairs at different temperatures and ammonia contents. (f) CN of the OI-OI. Acknowledgements This work was financially supported by the Department of Science and Technology of Inner Mongolia Autonomous Region (Grant No. 2022JBGS0027) and the National Natural Science Foundation of China (Grant Nos. 51920105010 and 51921004). References [1] W. R. W. Daud, R. E. Rosli, E. H. Majlan, S. A. … view at source ↗
read the original abstract

Ammonia has strong poisoning effects on cathode catalyst layers of proton exchange membrane (PEM) fuel cells, but the poisoning mechanism is still unclear. In this study, all-atom molecular dynamics simulations are employed to investigate the poisoning mechanisms of ammonia. The results show that ammonium can replace the hydronium ions at the charged sites of sulfonic acid group of the ionomer side chain, and the adsorption of ammonium to sulfonic acid group can be attributed to van der Waals force and electrostatic interaction. Furthermore, other ammonia derivatives, amino and imino ions, can capture hydronium ions to form ion clusters. These ion clusters have strong capability to absorb hydronium ions, and their structures change with ammonia content and temperature. The main mechanism of formation of these clusters is due to the formation of relatively stable hydrogen bonds between ions within the clusters. These mechanisms significantly reduce the efficiency of proton transport, thereby decreasing the catalyst layer's performance in electrochemical reactions. We also discover that the increase in temperature leads to the dissociation of large ion clusters, the blockage in the ionomer layer can be alleviated, and the proton transport efficiency can be restored. The understanding of the poisoning mechanisms obtained in this study is helpful for subsequent research aimed at resolving ammonia poisoning and enhancing the anti-poisoning performance of catalyst layers.

Editorial analysis

A structured set of objections, weighed in public.

Desk editor's note, referee report, simulated authors' rebuttal, and a circularity audit. Tearing a paper down is the easy half of reading it; the pith above is the substance, this is the friction.

Referee Report

3 major / 2 minor

Summary. The manuscript employs all-atom molecular dynamics simulations to probe the poisoning mechanism of ammonia in the cathode catalyst layer of PEM fuel cells. It reports that ammonium ions displace hydronium at sulfonic acid sites through combined van der Waals and electrostatic interactions, while amino and imino ions form hydrogen-bonded clusters that sequester hydronium, thereby lowering proton transport efficiency. The study further claims that elevated temperature dissociates these clusters, relieving ionomer blockage and restoring transport.

Significance. If the simulated structures and dynamics prove robust, the work supplies atomistic detail on a practically relevant degradation mode in PEM fuel cells and identifies temperature as a potential operational lever for mitigation. The emphasis on competitive ion adsorption and cluster formation aligns with known ionomer chemistry, but the absence of any experimental anchoring or force-field validation keeps the significance provisional rather than definitive.

major comments (3)
  1. [Methods] Methods section: the force fields employed for NH4+, amino/imino ions, and their interactions with SO3− and H3O+ at λ ≈ 5–10 are not benchmarked against DFT binding energies, experimental diffusion coefficients, or spectroscopic cluster lifetimes. Because the central claims of site replacement and cluster-mediated hydronium sequestration rest directly on these interaction strengths, the lack of validation constitutes a load-bearing uncertainty.
  2. [Results] Results on proton transport: the efficiency metric is derived solely from vehicular diffusion of intact H3O+ ions. The simulations omit Grotthuss hopping, which dominates proton conduction in hydrated Nafion; consequently the reported reduction in transport cannot be taken as quantitative without additional analysis or justification.
  3. [Discussion] Discussion of temperature effect: the observed dissociation of large clusters upon heating is presented without sensitivity checks to force-field parameters, cutoff distances, or system size. If these structural changes are force-field artifacts, the claim that temperature restores proton transport efficiency would not hold.
minor comments (2)
  1. [Abstract] Abstract and introduction: the term “amino and imino ions” is used without explicit structural formulas or pKa context; a brief clarification of the species considered would aid readability.
  2. Figure captions: several panels lack scale bars or explicit labeling of ion types, making it difficult to correlate visual clusters with the quantitative metrics reported in the text.

Simulated Author's Rebuttal

3 responses · 0 unresolved

We thank the referee for the thorough and constructive review of our manuscript on the ammonia poisoning mechanism in PEM fuel cell cathodes. We address each major comment point by point below, providing clarifications and noting revisions made to the manuscript where appropriate.

read point-by-point responses

  1. Referee: [Methods] Methods section: the force fields employed for NH4+, amino/imino ions, and their interactions with SO3− and H3O+ at λ ≈ 5–10 are not benchmarked against DFT binding energies, experimental diffusion coefficients, or spectroscopic cluster lifetimes. Because the central claims of site replacement and cluster-mediated hydronium sequestration rest directly on these interaction strengths, the lack of validation constitutes a load-bearing uncertainty.

    Authors: We acknowledge the referee's concern regarding force-field validation. The simulations employed standard OPLS-AA parameters for the ions and the Nafion ionomer model, which have been used and partially validated in prior literature for hydrated ionomer systems involving ammonium and hydronium ions. In the revised manuscript, we have expanded the Methods section with additional references to these prior validations and added a dedicated paragraph in the Discussion explicitly acknowledging the absence of new DFT or experimental benchmarks for the specific ion clusters at λ ≈ 5–10. We agree this is a limitation and note that future ab initio work would be valuable, but the current choice is consistent with established practices in the field. revision: partial

  2. Referee: [Results] Results on proton transport: the efficiency metric is derived solely from vehicular diffusion of intact H3O+ ions. The simulations omit Grotthuss hopping, which dominates proton conduction in hydrated Nafion; consequently the reported reduction in transport cannot be taken as quantitative without additional analysis or justification.

    Authors: We agree that classical all-atom MD captures only vehicular diffusion of intact H3O+ and cannot simulate Grotthuss hopping. Our reported efficiency metric therefore quantifies changes in vehicular transport due to ammonium displacement and cluster sequestration of hydronium. We have revised the Results and Discussion sections to state this limitation explicitly and to note that the observed ion clustering reduces the availability of free hydronium ions, which would impair both vehicular and Grotthuss contributions to conductivity. The qualitative finding that ammonia poisoning lowers proton transport efficiency is retained, with the clarification that the numerical reductions apply specifically to the vehicular component. revision: yes

  3. Referee: [Discussion] Discussion of temperature effect: the observed dissociation of large clusters upon heating is presented without sensitivity checks to force-field parameters, cutoff distances, or system size. If these structural changes are force-field artifacts, the claim that temperature restores proton transport efficiency would not hold.

    Authors: We concur that additional sensitivity tests on force-field parameters, cutoffs, and system size would strengthen the temperature-dissociation claim. Our original simulations showed consistent cluster breakup across independent trajectories at elevated temperatures. In the revised manuscript, we have added a sentence in the Discussion acknowledging the lack of explicit sensitivity analysis and noting that the observed trend is consistent with experimental reports of partial performance recovery in ammonia-exposed PEM fuel cells at higher operating temperatures. We maintain that the hydrogen-bond-driven cluster mechanism provides a physically plausible explanation, while recognizing this as a computational limitation. revision: partial

Circularity Check

0 steps flagged

No circularity: results follow directly from MD simulation outputs

full rationale

The paper's central claims rest on all-atom MD trajectories that compute ion positions, hydrogen bonds, and cluster statistics under explicit force fields. No parameter is fitted to the target poisoning metrics and then relabeled as a prediction; no equation defines a quantity in terms of itself; no uniqueness theorem or ansatz is imported via self-citation to close the argument. The observed replacement of H3O+ by NH4+ and temperature-dependent cluster dissociation are direct consequences of the chosen potentials and initial conditions, making the derivation self-contained rather than circular.

Axiom & Free-Parameter Ledger

0 free parameters · 1 axioms · 0 invented entities

The paper uses established MD techniques without introducing new free parameters or entities beyond standard physical interactions.

axioms (1)
  • domain assumption Molecular dynamics simulations with standard force fields can model ionomer-ammonia interactions accurately.
    Common assumption in computational studies of fuel cell materials.

pith-pipeline@v0.9.0 · 5543 in / 1214 out tokens · 110187 ms · 2026-05-13T04:19:40.531161+00:00 · methodology

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Reference graph

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