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Reaction Workflows

The reaction tools are for workflows that involve two endpoints — a reactant structure and a product structure.

What You Need to Start​

Two structures that represent the two ends of the reaction. In practice this means:

  • A two-frame XYZ file with reactant and product as separate frames, or
  • Two structures loaded together into the viewer

Atom Mapping​

Atom mapping identifies which atom in the reactant corresponds to which atom in the product. It:

  • Reorders product atoms into a reaction-aware correspondence with the reactant
  • Highlights which bonds are formed or broken
  • Makes the structures ready for downstream reaction tools

Run this first before any other reaction workflow. Getting the atom correspondence right is what makes the rest work correctly.

TS Geodesic​

TS geodesic interpolation builds a smooth pathway between the mapped reactant and product. This pathway is an initial guess for the transition state — better than a hand-edited structure and a good starting point for a TS optimization.

Typical use: Run atom mapping → run TS geodesic → use the resulting path as the input for a transition state optimization.

Reaction Network Generation​

Reaction network generation is a single-structure workflow rather than a two-endpoint reactant/product workflow, but it lives alongside the other reaction tools in Run Mode.

When you run Net Gen, the viewer:

  • Enumerates a reaction network from the current structure's SMILES representation
  • Evaluates single-point energies for the generated species with the currently selected browser model
  • Colors network edges relative to the reaction-energy range present in that specific network
  • Shows reaction-energy labels in Hartree next to the reaction nodes

Networks loaded from file are shown as imported and are not recolored automatically.

Cancellation​

Longer workflows can be cancelled from the Run Mode panel. Use this when you realize an input was wrong or you want to try different parameters.

Tips​

  • Run atom mapping before anything else — the TS tools depend on it.
  • After getting a TS geodesic path, switch to View Mode and step through the trajectory to check that it looks chemically reasonable before starting a TS optimization.