Supporting information: Improved ReaxFF force field parameters for Au–S–C–H systems
Summary¶
This Supporting Information PDF is a second corpus path (papers/ReaxFF_others/Bae_Aikens_AuSCH_supplement.pdf) for the same supplementary bundle as 2013aikens-venue-si8, tied to the parent article DOI 10.1021/jp405992m (“Improved ReaxFF Force Field Parameters for Au–S–C–H Systems”). The extract (normalized/extracts/2013aikens-venue-si8-2_p1-2.txt) lists Tables 1S–6S and Figures 1S–3S, including explicit comparisons of old versus NP-specific parameters and PBE versus ReaxFF bond lengths/angles for Au₂₅(SCH₃)₁₈⁻, Au₃₈(SCH₃)₂₄, and Au₁₄₄(SCH₃)₆₀ clusters, plus PES scans for S–Au–S bending in CH₃–S–Au–S–CH₃. The opening table fragment in the extract records representative parameter shifts (for example Au–S (rσ) from 2.1505 to 1.9000 and S–Au–S (Θ₀,₀) from 20.0000 to 5.0000 in the displayed columns), illustrating how the reparameterization tightens staple bending relative to the legacy set.
Methods¶
Corpus role (duplicate SI path)¶
Second corpus filename (papers/ReaxFF_others/Bae_Aikens_AuSCH_supplement.pdf) for the same supplementary bundle as [[2013aikens-venue-si8]], parent DOI 10.1021/jp405992m.
Force-field training (SI)¶
Parent FF / elements: ReaxFF Au–S–C–H updates relative to Järvi et al.; Tables 1S–6S list parameter deltas and cluster benchmarks vs PBE for thiolate-protected gold motifs containing hundreds of atoms per particle (extract 2013aikens-venue-si8-2_p1-2.txt).
QM reference / training / optimization / benchmarks: ADF PBE/TZP/ZORA and the parameter optimization narrative are in the main article; the SI supplies LAMMPS-ready numeric tables.
MD application¶
Engine / code: LAMMPS is referenced in the SI bundle for downstream molecular dynamics users (wiki cross-link to parent article).
N/A — ensemble (NVE/NVT/NPT), timestep (fs), ps/ns trajectory schedule, thermostat, barostat, temperature, and PBC details for validation molecular dynamics are not taken from this duplicate SI stub—use [[2013bae-venue-jp405992m]].
Findings¶
Outcomes / comparisons: Figures/tables document improved S–Au–S bending PES behavior and cluster geometries vs DFT for the Au–thiolate benchmarks highlighted in the parent abstract.
Corpus honesty / limitations: Treat as a manifest alias for [[2013aikens-venue-si8]]; byte-compare PDFs before retiring either path. PDF copy/paste can corrupt exponent fields in wide tables—verify against the typeset SI when importing into LAMMPS data files.
Limitations¶
Maintaining two filenames for one SI package can confuse manifests; prefer a single canonical path when cleaning the corpus.
Relevance to group¶
Auxiliary gold–thiolate ReaxFF data used across nanoparticle and interface simulations in the knowledge base.
When parameter tables span multiple pages, optical character recognition errors occasionally corrupt exponent formatting; always cross-check critical exponents against the main article’s Typeset values or the LaTeX-style tables in the primary JPCA PDF before importing into LAMMPS data files.
If two SI filenames differ only by “_SI” versus “supplement,” prefer whichever file hash matches the publisher’s current download bundle before regenerating MANIFEST.jsonl rows.
Theme hubs that mention gold–thiolate parameterization should link this SI stub only as a reproducibility appendix, not as a substitute for the peer-reviewed parameter rationale in the JPCA article body.