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Supporting information: First-principles-based reaction kinetics from reactive molecular dynamics (H\(_2\)O\(_2\) decomposition)

Evidence and attribution

Authority of statements

This file lists SI contents for PNAS DOI 10.1073/pnas.1701383115. Scientific claims belong to [[2018ilyn-venue-first-principles-based]].

Summary

This corpus PDF (papers/ReaxFF_others/pnas.1701383115.sapp.pdf) is the Supporting Information bundle for Ilyin et al., Proc. Natl. Acad. Sci. U.S.A., on extracting first-principles-quality reaction kinetics from ReaxFF reactive MD of hydrogen peroxide decomposition (RMD2Kin / ReaxMD2Kin pipeline). The SI assembles supplementary discussion, nine supplementary figures, eight trajectory movies, Table S1 with bond-order cutoffs for species detection, and SI references. Figures document temperature sweeps for OH- vs HOO-initiated pathways, NVT/NVE sensitivity, dominant reaction histograms, QM vs ReaxFF transition-state comparisons for key propagation steps, and B3LYP potential energy surfaces for selected reactions. Movies S1–S8 provide 3D animations of ReaxFF reactive trajectories referenced in the main text. Together, the SI package is structured so readers can audit each major initiation and propagation channel claimed in the PNAS article, including QM sanity checks on selected elementary reactions that dominate long-time kinetics fits. Movies are particularly useful for teaching reactive MD parsing because they show 3D atomic motion accompanying bond-order events that can be opaque in tabular output alone.

Methods

SI contents (reproducibility artifacts)

  • Table S1: bond-order cutoffs and related parsing thresholds for species detection from ReaxFF trajectories (reuse exactly when replicating RMD2Kin outputs).
  • Figures S1–S9 (inventory in SI): temperature sweeps, dominant reaction histograms, QM vs ReaxFF transition-state overlays for selected elementary steps, and B3LYP potential-energy scans for key channels referenced in the PNAS text.
  • Movies S1–S8: 3D trajectory animations of ReaxFF H\(_2\)O\(_2\) decomposition pathways.

RMD2Kin / kinetic extraction (from SI + main text)

  • Reactive MD: ReaxFF LAMMPS trajectories spanning temperature ranges used for Arrhenius extraction (initiation vs propagation emphasis documented in figures).
  • Ensemble sensitivity: NVT vs NVE comparisons in the SI probe thermostat effects on inferred rates (see SI discussion).
  • QM benchmarks: B3LYP (and related) QM data for selected reactions to validate ReaxFF barriers/geometries before exporting kinetic parameters.
  • Boundaries / duration / timestep / pressure: Published reactive MD trajectories for H\(_2\)O\(_2\) decomposition use 3D periodic boundary conditions on homogeneous gas-phase cells as shown in the PNAS main text and SI figures. Production run lengths and the integration timestep in fs are specified there (not duplicated numerically on this SI-only page). N/A — NPT barostat / N/A — imposed hydrostatic pressure for the standard constant-volume NVT/NVE comparisons tabulated in the SI.

Authority / navigation

  • Integrated scientific narrative and primary kinetic claims: [[2018ilyn-venue-first-principles-based]] (main PNAS article).

Findings

As supporting material, the SI does not introduce new standalone scientific conclusions; it enables reproducibility of the main paper’s kinetic and mechanistic claims by exposing raw analysis choices (bond-order cuts), supplementary Arrhenius plots, and QM comparisons for propagation chemistry. - Mechanisms / rates: Supplementary figures group dominant reaction channels for OH- versus HOO-initiated pathways, clarifying how decomposition kinetics are partitioned before exporting Arrhenius parameters. - Comparisons / sensitivity: NVT versus NVE sweeps in the SI quantify thermostat sensitivity on inferred rates; QM vs ReaxFF overlays show where the reactive FF tracks B3LYP barriers for selected steps. - Limitations / corpus: This page is SI-only; cite [[2018ilyn-venue-first-principles-based]] for integrated Results and for any timestep/duration numbers not restated here. PDF figure labels in the SI may differ cosmetically from HTML supplements on the publisher site.

Limitations

SI-only PDF—read [[2018ilyn-venue-first-principles-based]] for abstract, motivation, and integrated discussion. File naming uses PNAS convention (pnas.*.sapp.pdf), not author Hanson (historical corpus label). Bond-order cutoffs in Table S1 are analysis parameters—small changes can repartition species counts in complex H₂O₂ decomposition networks, so reuse cutoffs exactly when replicating kinetic fits. PNAS may issue corrections; check the publisher site for updates to supplementary materials.

Relevance to group

Provides artifact-level documentation for a high-profile ReaxFF → kinetics workflow cited in combustion and reactive MD method discussions; always cross-link [[2018ilyn-venue-first-principles-based]] for integrated scientific claims. The SI’s QM TS comparisons exemplify how operators should validate elementary steps before exporting Arrhenius parameters to downstream kinetics tables.

Citations and evidence anchors

  • Parent DOI: 10.1073/pnas.1701383115; SI: papers/ReaxFF_others/pnas.1701383115.sapp.pdf; extract normalized/extracts/2018hanson-venue-supporting-online_p1-2.txt (figure inventory).