Mode-Selective CuI Anchoring on Lignin-Inspired Fiber Interfaces: A DFT Cluster-Model Study

This dataset is the complete computational audit pipeline for the manuscript
"Mode-Selective CuI Anchoring on Lignin-Inspired Fiber Interfaces: A DFT
Cluster-Model Study" by Andrei Ursachi (Independent Researcher, Diepholz,
Germany; ORCID 0009-0002-6114-5011).

SCOPE

The pipeline computes copper-lignin coordination chemistry using DFT cluster
models across four copper environments — naked Cu+, the CuI monomer, the
neutral Cu2I2 rhombic cluster, and the iodide-saturated [CuI2]- anion — paired
with monomeric lignin proxies (guaiacol, phenol, anisole, catechol, methanol,
water, galacturonic acid, substituted methoxyphenols) and an etherified
guaiacyl proxy (1,2-dimethoxybenzene = veratrole) on Cu2I2 and on [CuI2]-
with paired starting geometries.

COMPUTATIONAL BASIS

ORCA 6.1.1 official binary; B3LYP-D3(BJ); def2-TZVP all-electron Cu;
def2/J auxiliary basis for RIJCOSX; SMD(water) single points at gas-phase
optimized geometry; TightSCF, TightOpt; DefGrid3 (Lebedev 302/m4) for both
geometry and analytic Hessian/frequencies. Reference monomer cross-checks
at Grid5/FinalGrid6 converged within 0.05 mEh of the DefGrid3 baseline.
A def2-TZVPP basis-sensitivity check on the central CuI methanol /
guaiacol-phenolic-O comparison preserved the qualitative ordering: the
relative gap remained approximately 0.5 kcal/mol while absolute binding
energies shifted by a few kcal/mol.

WHAT THE DATASET CONTAINS

audit_final/
  - BINDING_SURVIVAL_TABLE.csv: 39-row canonical table of every productive,
    metastable, detached, or fragmented Cu-ligand combination with binding
    energies (gas, SMD water, water-exchange), geometric distances, mode
    survival status, vibrational frequency analysis, and conservative
    binding-class verdict.
  - RAW_FILE_INDEX.csv: SHA-256 indexed manifest of source ORCA output
    files for the Tier A (naked Cu+), Tier B (CuI monomer), control set,
    and def2-TZVPP basis-sensitivity production runs.
  - Per-cluster binding, mode, exchange, and water-competition tables
    (CU2I2_*.csv, CUI2_*.csv, CUI_CLUSTER_*.csv, CONTROL_*.csv).
  - ORCA_GEOMETRY_AUDIT.csv, ORCA_FREQUENCY_AUDIT.csv, ORCA_SMD_AUDIT.csv,
    ORCA_VIBRATIONAL_MODES.csv, ORCA_DISCREPANCY_TABLE.csv.
  - Per-claim verdict tables: BELEGEN_EVIDENCE_MATRIX.csv,
    CLAIM_SUPPORT_STATUS.csv, MECHANISM_VERDICT_TABLE.csv,
    SITE_OCCUPANCY_TABLE.csv, RANK_REVERSAL_TABLE.csv.
  - RECLASSIFICATION_NOTES.md: documentation of the conservative classifier
    rules used to derive Class A/B/D/E verdicts.
  - V9_GUAIACOL_BIDENTATE_RESOLUTION.md: Category C resolution explaining
    the dual-basin behavior of free guaiacol on Cu2I2.
  - V9_CASE_DECISION.md: case-determination decision document.
  - MANUSCRIPT_IMPACT_v8_to_v9.md: sentence-level analysis of how the audit
    findings reframed the v8 manuscript into the v9 mode-selective framing.
  - OXIDE_AGING_REGIME_NOTE.md: scope statement for the literature-only
    oxide/hydroxide aging extension.
  - grid_test_v9_results/: ORCA inputs and outputs for the Grid5/FinalGrid6
    sensitivity check.

audit_final_setD_alt_diag/
  - setD_alt_v2_analysis.json: distilled geometry, energy, frequency, and
    classifier data for the four Set D V2 veratrole rotamer scan species
    (cu2i2_veratrole_methoxyO_startA, cu2i2_veratrole_methoxyO_startB,
    cui2_veratrole_methoxyO_anion_startA, cui2_veratrole_methoxyO_anion_startB)
    including initial XYZ coordinates, ORCA method line, charge,
    multiplicity, and final-geometry analysis.
  - build_v9_closeout.py: authoritative build script that regenerates all
    v9 closeout tables from canonical inputs.
  - grid_test/: input templates and queue scripts for high-grid
    sensitivity testing.

manuscript/
  - V9_HANDOVER_PACKAGE.md and V9_HANDOVER_PACKAGE_v2.md: handover documents
    used by the manuscript writer.
  - V9_REFERENCE_AUDIT_FIXES.md: per-reference Crossref audit log.

reproducibility/
  - REPRODUCE.md: step-by-step instructions for reconstructing any ORCA
    input from the canonical CSVs and re-executing the calculation.
  - orca_input_templates/: example ORCA inputs (DefGrid3 and Grid5) for the
    Cu2I2 rhombic reference and the cu2i2_veratrole_methoxyO_startA
    productive site, plus the free veratrole reference monomer.

KEY FINDINGS SUPPORTED BY THIS DATASET

(1) On the CuI monomer, guaiacol phenolic-O and methanol O binding differ
by only 0.46 kcal/mol — within DFT error. The single-site affinity framing
that motivated prior substrate-selection arguments fails at the CuI cluster
level.

(2) The neutral Cu2I2 cluster supports two productive anchoring channels for
an etherified guaiacyl analog (veratrole): a kappa2-O,O bidentate chelate
(BE_smd = -26.24 kcal/mol) and an eta2-arene pi contact (BE_smd = -23.11
kcal/mol). Both are true minima with the rhombic cluster topology preserved,
and the two channels are competitive within approximately 3 kcal/mol.

(3) The iodide-saturated [CuI2]- anion behaves as a ligand-rejecting
saturation limit: the same veratrole motif is rejected with positive
binding energies (+47.93 to +53.60 kcal/mol).

(4) Free phenolic-OH guaiacol on Cu2I2 samples two distinct potential energy
basins — one cluster-cracking, one a weaker intact-cluster bidentate
(approximately 9 kcal/mol weaker than the etherified veratrole bidentate)
— rather than a single clean coordination mode.

PROVENANCE NOTE

The cu2i2_veratrole_pi result was originally computed in the Set D
production run. The raw output file was temporarily inaccessible after a
transient compute-platform storage event on 2026-04-30T11:02Z and was
subsequently recovered from a migrated compute node on 2026-04-30T15:19Z.
SHA-256:
f2a9007b88dc7098f266224b8715c741653e75e1d547dafd4236b8b2584a8ff2.
An independent confirmation rerun on the original platform (prior to the
storage event) gave binding energies of -22.99 kcal/mol (gas) and -23.12
kcal/mol (SMD water), in agreement with the recovered production result
(-22.98 / -23.11) within rounding.

REPRODUCING A CALCULATION

Every result in BINDING_SURVIVAL_TABLE.csv can be reproduced by:
(1) looking up the species in RAW_FILE_INDEX.csv to obtain the ORCA
method line; (2) looking up the species in ORCA_GEOMETRY_AUDIT.csv to
obtain charge, multiplicity, and final XYZ coordinates; (3) building the
ORCA input as <method_line> + * xyz <charge> <mult> + <XYZ block> + *;
(4) running with `orca input.inp > output.out`. For the original
optimization trajectory rather than the final-minimum re-converged
single point, use the archived starting geometries in
setD_alt_v2_analysis.json (Set D V2) or EXPERIMENT_RAW_PROVENANCE.csv
(Sets A/B/C). Full procedure in reproducibility/REPRODUCE.md.

VERSION

v9.0 — first public release of the audit pipeline supporting the v9
manuscript revision (mode-selective reframing of the v8 preprint).

CITATION

If you use this dataset, please cite both the dataset (this Zenodo record)
and the associated manuscript. See CITATION.cff in the repository.

LICENSE

Creative Commons Attribution 4.0 International (CC-BY-4.0). You may share
and adapt the material for any purpose, including commercially, provided
you give appropriate credit, provide a link to the license, and indicate
if changes were made.

ASSOCIATED MANUSCRIPT

Mode-Selective CuI Anchoring on Lignin-Inspired Fiber Interfaces: A DFT
Cluster-Model Study. A. Ursachi. Submitted to ACS Applied Engineering
Materials, 2026. Preprint (v8): https://doi.org/10.21203/rs.3.rs-8935698/v1
(v9 correction will be posted upon acceptance).

CONTACT

contact@andreiursachi.eu