chem-bond-dissociation
OfficialCompute bond dissociation energies fast.
System Documentation
What problem does it solve?
This Skill calculates homolytic and heterolytic bond dissociation energies for every eligible single bond in a molecule, turning structural inputs into actionable energetic rankings.
Core Features & Use Cases
- Homolytic BDEs from MLIP relaxations: Relaxes the intact molecule and both radical fragments, then computes BDEs from relaxed energies.
- Heterolytic BDEs with charge/spin-aware MLIPs: Evaluates both ionic polarity variants (minimum reported) for heavy-atom bonds when the selected model supports charge and spin.
- Bond-level outputs for screening: Produces per-bond JSON results plus relaxed geometries for intact and fragment structures, enabling weakest-bond identification and comparison across models.
Quick Start
Provide a SMILES string and run a BDE calculation for all single bonds (including heterolytic energies) with a charge/spin-capable model by executing one command like: run python .agents/skills/chem-bond-dissociation/scripts/calculate_bde.py with --smiles "CO", --all_bonds, --include_h_bonds, --cleavage both, --model_type mace, --model_name "MACE-OMOL-extra-large", and an --output_dir path.
Dependency Matrix
Required Modules
Components
💻 Claude Code Installation
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Please help me install this Skill: Name: chem-bond-dissociation Download link: https://github.com/learningmatter-mit/AtomisticSkills/archive/main.zip#chem-bond-dissociation Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
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