Supporting Information: Simulation of Gold Functionalization with Cysteine (J. Phys. Chem. Lett.)
Summary¶
This corpus entry stores the Supporting Information PDF for the Journal of Physical Chemistry Letter on gold functionalization with cysteine, paired with the main letter paper:2016susanna-monti-j-phys-chem-jz5b02769. The SI documents how density functional theory optimizations build training data for Au–cysteine interactions used in a modified ReaxFF parametrization, compares ab initio molecular dynamics–sampled configurations against ReaxFF single-point energies, and provides auxiliary trajectory analyses referenced by figure labels such as Figures 1S–5S in the SI text. It is a companion artifact for parameter validation rather than a standalone experimental report. Treat it as the engineering appendix for reproducing the reactive model: training geometries, error plots, and optional parameter file dumps.
Methods¶
1 — MD application (AIMD / RC-MD as cited). The SI documents training-set construction, lists of DFT-optimized geometries, and diagnostic trajectory analyses (distance traces, minimum-distance distributions for cysteine and water relative to Au, energy versus time curves) referenced by Figure 1S–5S labels in the SI text. Production RC-MD in the parent letter uses ReaxFF within ADF, NVT at 300 K and ambient pressure as stated there, timestep 0.25 fs, Berendsen thermostat (0.1 ps coupling), 25 ps equilibration, and ~100 ps production with saves every 0.025 ps on a cysteine + 303 H\(_2\)O + Au(111) slab model (PBC); see [[2016susanna-monti-j-phys-chem-jz5b02769]]. Electric field driving and umbrella/metadynamics/replica-exchange sampling are N/A — unless the SI explicitly adds them.
2 — Force-field training. DFT/QM reference energies and structures train patched ReaxFF parameters for Au–S/O/H chemistry; some SI revisions include an ffield listing for the modified ReaxFF—match the PDF revision to your bibliography.
3 — Static QM / DFT. DFT settings for optimizations and NEB/AIMD benchmarks are tabulated in the SI (N/A — not duplicated on this page).
Findings¶
The SI substantiates that the ReaxFF extension reproduces key quantum energy ordering and structural motifs for cysteine on gold in explicit water within the stated validation windows. It does not replace the main letter for interpreting the full binding pathway, kinetics, or spectroscopic predictions. Practically, readers use the SI to audit whether the classical model is faithful on the sampled trajectories before trusting longer reactive runs. Any discrepancy between SI tables and main-text claims should be resolved against the published letter and, if needed, publisher corrections. This wiki entry is an archival pointer to the SI PDF bytes in pdf_path.
Limitations¶
extraction_quality: partial in normalized metadata; rely on the full SI PDF for complete figures and any parameter tables. No DOI is assigned to the SI file alone.
Relevance to group¶
Documents quantum-chemistry training and validation for ReaxFF extensions on Au–thiol chemistry in aqueous environments.
Citations and evidence anchors¶
- Primary PDF:
papers/ReaxFF_others/Monti_Cystein_Gold_JPC_Letter_SI_2016.pdf - Main article:
[[2016susanna-monti-j-phys-chem-jz5b02769]]