Manual Mapping

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In situations that require manual mapping of atoms, you can use the Reaction Atom-Atom Map tool. This might be necessary when the automatic mapping is applied to complicated reactions. In these cases you can manually readjust the reaction mapping.

The following figure shows how to amend the initial mapping by using the Reaction Atom-Atom Map tool.

When you perform manual mapping with the Reaction Atom-Atom Map tool, you can suppress automatic re-mapping of atoms other than your target atom.

To suppress automatic re-mapping:

1. From the File menu, choose Preferences.

2. On the General tab, select Automatic Reaction Mapping.

3. Click OK.

To use the Reaction Atom-Atom Map tool to supplement the automatic mapping:

1. Click the Reaction Atom-Atom Map tool .

2. Point to the atom in the reactant whose mapping you want to establish. For example, in the following drawing you would point to the acyclic carbon adjacent to the ether oxygen.

3. Drag from the reactant atom to the corresponding product atom.

The remaining atoms are automatically mapped based on the manual mapping you performed.

You can continue to set or change the mapping for other atoms in the reaction if necessary until you get exactly the mapping you want. For this example additional manual mapping is not necessary.