---

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 catalysts

Scoring (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 file

scripts/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.