Build a reaction network

Build a reaction network by validating your starting mixture and proposed elementary steps first, then attaching simulation, transition-state, and DFT evidence to each step.

1. Dry-run your proposed network

Open your project in the web workspace or connect an AI agent via the chemistry MCP server.

Before writing anything to the project, validate the full network with checkReactionNetwork. If you are using an MCP-connected agent, ask:

Run checkReactionNetwork for my project using these starting species, elementary reaction SMILES, and target species. List any atom/charge balance errors, missing reactants, or unreachable targets.

checkReactionNetwork takes:

• startingSpecies — Reactants, reagents, catalysts, and solvents present at the start.
• reactions — Proposed elementary steps (one bond-breaking/forming event per step) with SMILES and source rationale.
• targets — Products or intermediates you expect the network to reach.
• projectId (optional) — Includes species already saved in your project.

2. Fix validation errors before running calculations

checkReactionNetwork runs the exact same chemistry rules used when saving proposals and returns a valid topological write order. Fix any reported issues first:

• Atom and charge balance: Every reaction must conserve both elemental counts and net charge.
• Single elementary steps: Split multi-step shorthand reactions into individual elementary transformations with explicit intermediates.
• Reachable reactants: Every reactant in a step must either be in startingSpecies, already exist in the project, or be produced by an earlier step.
• Sourced rationale: Literature or mechanistic proposals must include their source reference and rationale.

3. Save the validated network

Once checkReactionNetwork passes with zero errors, save the network atomically with addReactionNetwork:

• Batch write (addReactionNetwork): Saves all starting species and reactions in dependency order in a single transaction. If any item fails validation, nothing is written.
• Single additions (addSpeciesProposal / addReactionProposal): Add one species or elementary step to an existing network.

Important: A saved reaction proposal is a hypothesis, not proof that the pathway occurs.

4. Attach calculation evidence to each pathway

Once your proposed steps are in the project, run calculations to test which pathways actually operate and compete:

Keep charge, spin multiplicity, and level of theory consistent whenever you compare competing barriers across the network.