Pd-allyl

Pd-allyl demonstrates composition of a caller-supplied MM3 base with an OPT-only publication field and an exact frozen/active scalar partition.

Source and membership

• Article: Wahlers et al., Nature Communications 2021, 12, 6508 (Zotero QVKE99W3).
• Derivation: Wahlers, Ph.D. Dissertation, University of Notre Dame, 2021, Chapter 3, 10.7274/k930bv76q4n (Zotero AAZ6I5V3).
• Primary set: TS1–TS21.
• Auxiliary oxazole-fitting set: TS22–TS25.
• Force field: eight physical OPT blocks composed with an external MM3 base.

Current claims

Row	Status	Substantiation
21 primary cases, repository-geometry-eigenmatrix-v1	partial_repository_reproduction	Primary/auxiliary evidence
Complete eight-block rederivation across 25 cases	blocked_historical_record	Missing TS22–TS25 Hessian blocker

No charge, torsion, or equilibrium-tether source target is silently substituted by the compatibility profile.

Run

python examples/publication/pd-allyl/run.py \
  --supporting-info /path/to/publication-data \
  --mm3-base /path/to/mm3_base.fld \
  --output-root /path/to/output \
  --bounded-ci