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How to label an isotope (deuterium, carbon-13)

Type D, T or 13C on an atom the way you type any label, or select the atom and enter the mass number in Properties › Isotope. The atom shows ¹³C or D, and the formula, both masses, SMILES and MOL files carry the isotope.

Steps

  1. Select the atom with Select (V), or move to it with Alt+. and press Enter. Properties shows that atom.

  2. In Isotope, type the mass number, such as 13, and press Enter. The 13C and 14C buttons beside it set the common carbon isotopes in one press.

  3. The atom's label shows the isotope, here H₃¹³C, and the structure's formula and mass in Layers change with it.

    Acetic acid with its methyl carbon set to carbon-13: the label reads H3 13C, and Properties shows Isotope 13.Acetic acid with its methyl carbon set to carbon-13: the label reads H3 13C, and Properties shows Isotope 13.

To go back to the natural element, clear the Isotope box. Blank means natural.

Type it on the atom

Typing the label does the same thing. Point at an atom and press Enter, or click it with the Text tool (T), then type:

Type You get
D Deuterium (hydrogen-2)
T Tritium (hydrogen-3)
13C, 15N, 18O That element with that mass number

See atom labels for how typing a label works.

What carries the isotope

  • The formula and masses. The molecular formula, the exact mass and the molecular weight all use the isotope's mass.
  • SMILES and MOL files. Copy or export and the isotope goes with it ([13CH3]C(=O)O in SMILES, the mass field in a MOL file), so other programs read it too.

Note

A mass number that no isotope of that element has is refused, with "That mass number is not possible for" the element.

Atoms, bonds and ringsAtom propertiesSelect an atom and open Properties. It shows the Label, Charge, Isotope and Hydrogens, the Query atom settings for substructure searches, and Shape at this atom with the steric number, AXE class, geometry, hybridization and ideal angle.Text and labelsHow to type atom labels like CO2Et or NHBocWith the Text tool (T), click an atom, type its label and press Enter. Or point at the atom with any tool and press Enter. Elements and known groups such as CO2Et, NHBoc and OMe are read as atoms.Workspace and settingsThe Properties panelProperties changes with the selection. With nothing selected it shows the document settings; with a structure, its name, formula and Display switches; with one atom, its label, charge, query settings and VSEPR shape; with a shape, its position and behavior.

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Last updated Nov 12, 2026