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How to map reaction atoms

Select the reaction and choose Object › Chemistry › Map reaction atoms automatically. Each atom gets a map number, matched across the arrow, and new bonds are marked. Object › Clear atom mapping removes it.

Map automatically

  1. Draw the reaction, for example ethanol and acetic acid to ethyl acetate, and select it.

  2. Choose Main menu › Object › Chemistry › Map reaction atoms automatically.

  3. Each heavy atom gets a map number, such as :3, and the product atom it becomes carries the same number. A bond that forms in the reaction is marked in green.

    Ethanol and acetic acid to ethyl acetate, mapped: the ester oxygen :3 comes from ethanol, and the new C-O bond is marked.Ethanol and acetic acid to ethyl acetate, mapped: the ester oxygen :3 comes from ethanol, and the new C-O bond is marked.

In this Fischer esterification the ester oxygen (:3) comes from ethanol, and the acid's OH leaves as water.

Map by hand

Select one atom on each side and choose Main menu › Object › Map these two atoms. Object › Clear atom mapping removes the numbers.

Reactions and arrowsHow to draw a reaction schemeDraw or insert the reactants, press W and drag a reaction arrow after them, write the conditions above it with the Text tool, then add the products after the arrow. Or press / and type the whole reaction as reaction SMILES.Reactions and arrowsHow to make a stoichiometry tableDraw the reaction and choose View › Stoichiometry table. Pick the limiting reagent and its mass; the other amounts follow from their equivalents, with the theoretical yield below.

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Last updated Nov 12, 2026