Mapping Atoms in AutoTS

AutoTS automatically determines the correspondence between atoms in the reactant and product structures. When the mapping between reactant and product is ambiguous, the automatic mapping may not correctly identify which atoms correspond, which can cause the transition state search to fail or find an incorrect reaction path.

To resolve this, set the i_user_AutoTS_Atom_Class atom property on the reactant and product structures to explicitly specify the mapping. Each atom that needs to be tracked is assigned an integer value, and atoms with the same value on the reactant side and the product side are treated as corresponding atoms. For example, if atom 1 in a reactant maps to atom 3 in a product, assign both the same integer value.

You do not need to assign atom classes to every atom. Labeling the reaction center — the atoms whose bonds are being broken or formed — is enough to disambiguate the mapping for the rest of the structure.

The atom classes must be consistent between reactants and products: each class value must appear on the same number of atoms on both sides of the reaction. AutoTS checks this at the start of the calculation and reports an error if the classes are inconsistent.

Setting Atom Classes in Maestro

Set the i_user_AutoTS_Atom_Class property using the Change Atom Properties Panel (Other Edits → Change Atom Properties in the 3D Builder).

To create the property and assign it to the first set of atoms:

  1. In the Workspace, select the atom or atoms that should share a class value.

  2. In the panel, choose Other from the Property option menu.

  3. Click Add to open the Add Property dialog box. Set the type to Integer, set the name to i_user_AutoTS_Atom_Class, and enter the integer class value. The value is added to the selected atoms.

  4. Click Apply to commit the change.

To assign additional class values to other atoms (with the panel still open):

  1. In the Workspace, select the next atom or atoms that should share a class value.

  2. With Other still chosen in the Property option menu, select i_user_AutoTS_Atom_Class in the Properties list. The selected atoms appear in the Atoms table.

  3. Edit the value cells in the Atoms table to set the class value. To set the same value across multiple atoms in one step, select the table rows, edit one cell, and press Ctrl+ENTER (⌘ENTER).

  4. Click Apply.

Repeat for the corresponding atoms in the product structure, using the same integer values to mark corresponding pairs. Apply all class assignments before closing the panel — the panel settings are cleared when it is closed.