- name
- pharmaclaw-catalyst-design
- description
- Organometallic catalyst recommendation and novel ligand design for drug synthesis reactions. Recommends catalysts (Pd, Ru, Rh, Ir, Ni, Cu, Zr, Fe) for reaction types (Suzuki, Heck, Buchwald-Hartwig, metathesis, hydrogenation, click, etc.) from curated database with scoring. Designs novel ligand variants via RDKit (steric, electronic, bioisosteric modifications). Chains from chemistry-query/retrosynthesis (receives reaction type + substrate) and feeds into IP Expansion (novel ligands as patentable inventions). Triggers on catalyst, ligand, organometallic, cross-coupling catalyst, reaction conditions, catalyst selection, ligand design, cone angle, bite angle, phosphine, NHC, palladium catalyst, ruthenium catalyst.
Catalyst Design Agent v1.0.0
Overview
Recommends organometallic catalysts for drug synthesis steps and designs novel ligand modifications. Two core workflows: recommend (find the right catalyst) and design (create novel ligand variants).
Quick Start
# Recommend catalysts for a Suzuki coupling
python scripts/catalyst_recommend.py --reaction suzuki
# Recommend with constraints (prefer cheap, earth-abundant)
python scripts/catalyst_recommend.py --reaction "C-N coupling" --constraints '{"prefer_earth_abundant": true, "max_cost": "medium"}'
# Design novel ligand variants from PPh3
python scripts/ligand_designer.py --scaffold PPh3 --strategy all --draw
# Full chain: reaction → catalyst → ligand optimization
python scripts/chain_entry.py --input-json '{"reaction": "suzuki", "context": "retrosynthesis"}'Scripts
scripts/catalyst_recommend.py
Scores and ranks catalysts from curated database (12 catalysts, 28 reaction types).
--reaction <type> Required. e.g., suzuki, metathesis, C-N coupling, hydrogenation
--substrate <SMILES> Optional. Substrate context
--constraints <JSON> Optional. {prefer_metal, max_cost, prefer_earth_abundant}
--enantioselective Flag. Prioritize chiral catalystsScoring (0-100): reaction match (50), cost (15), metal preference (10), enantioselectivity (10), loading efficiency (5), advantages (5), earth-abundance (5).
scripts/ligand_designer.py
Generates novel ligand variants via three strategies:
| Strategy | Method | Output |
|---|---|---|
| steric | Add methyl/iPr/tBu to aromatic rings | Modified SMILES + properties |
| electronic | Add OMe/F/CF3 substituents | Modified SMILES + properties |
| bioisosteric | P→NHC, phenyl→pyridyl, phosphine→phosphite | Conceptual suggestions + rationale |
--scaffold <SMILES|name> Required. PPh3, NHC_IMes, NHC_IPr, PCy3, dppe, dppp, or raw SMILES
--strategy <type> steric|electronic|bioisosteric|all (default: all)
--draw Generate 2D grid PNG of variants
--output <path> Save JSON results to filescripts/chain_entry.py
Standard PharmaClaw chain interface. Accepts JSON, routes to recommend/design/both.
Input keys: reaction, scaffold/ligand, substrate/smiles, constraints, enantioselective, strategy, draw, context
If only reaction is given, also auto-runs ligand optimization on the top recommended catalyst's ligand.
Chaining
| From | Input | To | Output |
|---|---|---|---|
| Chemistry Query / Retrosynthesis | Reaction type needed for a synthesis step | Catalyst Design | Ranked catalysts + conditions |
| Catalyst Design | Top catalyst ligand SMILES | Ligand Designer | Novel ligand variants |
| Catalyst Design | Novel ligand SMILES | IP Expansion | Patent landscape check |
| Catalyst Design | Recommended conditions | Chemistry Query | Forward reaction simulation |
Database
references/catalyst_database.json — 12 catalysts, 8 metals, 28 reaction types. Includes SMILES, conditions, loading ranges, cost ratings, advantages/limitations, and literature DOIs.
Expandable: add entries following the existing schema.
Ligand Aliases
PPh3, PCy3, dppe, dppp, NHC_IMes, NHC_IPr — resolved automatically to SMILES.