chem-bond-dissociation

Bond Dissociation Energy Skill

Goal

Calculate the homolytic and/or heterolytic bond dissociation energy (BDE) for each single bond in a molecule using Machine Learning Interatomic Potentials (MLIPs).

Homolytic BDE (radical fragments): $$\text{BDE}_\text{homo}(A{-}B) = E(A\bullet) + E(B\bullet) - E(A{-}B)$$

Heterolytic BDE (ionic fragments, minimum over both polarity variants): $$\text{BDE}_\text{hetero}(A{-}B) = \min!\bigl(E(A^+)+E(B^-),; E(A^-)+E(B^+)\bigr) - E(A{-}B)$$

[!IMPORTANT] This skill computes BDEs by relaxing both the intact molecule and fragments with an MLIP. For purpose-trained GNN models that predict BDE directly from SMILES (MAE ~0.6 kcal/mol), consider ALFABET or BonDNet instead.

Background

BDE is a fundamental thermodynamic quantity that determines:

• Drug metabolism: CYP450 enzymes abstract H from the weakest C–H bond
• Electrolyte stability: Which bonds break first under electrochemical voltage
• Combustion chemistry: Rate-determining bond-breaking steps in fuel oxidation
• Polymer degradation: Weakest links in polymer backbone chains

A 2024 study (Zubatyuk et al., JCTC) demonstrated that MACE potentials achieve BDE RMSE of 1.37 kcal/mol for aliphatic C–H bonds in drug-like molecules, outperforming semi-empirical methods and ALFABET for BDE ranking.

1. Prerequisites

• Conda Environment: mace-agent (includes RDKit, ASE, and MACE)
• Input: SMILES string or structure file (.sdf, .mol2)
• RDKit: Required for bond identification and molecular fragmentation

2. Choosing a Foundation Potential

Refer to the foundation-potentials skill for model selection.

[!IMPORTANT] Model requirements by cleavage mode:

Mode	Recommended model	supports_charge_spin	Validated?
homolytic	MACE-OFF23-small/medium/large	Not required	✅
heterolytic or both	MACE-OMOL-extra-large (env: mace-agent)	✅ Required	✅
heterolytic or both	MACE-MH-1 with omol head (env: mace-agent)	✅ Required	✅
heterolytic or both	FairChem uma-s-1p1 with --task_name omol (env: fairchem-agent)	✅ Required	✅

Setting charge/spin on MACE models: use atoms.info["charge"] and atoms.info["spin"] (the calculator's default info_keys maps "charge" → total_charge / "spin" → total_spin). Both MACE-OMOL and MACE-MH use joint_embedding to condition the network on these scalars.

If you request --cleavage both with a model that does not support charge/spin, the skill will log a warning and silently fall back to homolytic-only. Using --cleavage heterolytic with an unsupported model raises an error.

Note on single-atom fragments: When a bond produces a bare H (or other single atom), heterolytic BDE is automatically skipped — neither MACE nor FairChem UMA has signed single-atom energies (only neutral H, C, N, O… are in the reference tables).