SMILES notation explained simply

What is SMILES?

SMILES (Simplified Molecular Input Line Entry System) describes a molecule with a single line of text. It’s the most widely used format for exchanging structures between software, databases and publications.

Atoms

Each atom is written with its symbol, and hydrogens are implicit: C is methane, CH₄, and CCO is ethanol. Atoms outside the “organic subset” (B, C, N, O, P, S, F, Cl, Br, I), or carrying a charge, go in square brackets: [Na+], [NH4+].

Bonds

• single: nothing (or -), CC for ethane
• double: =, C=C for ethylene
• triple: #, C#C for acetylene

Branches

A branch goes in parentheses: acetic acid is CC(=O)O, isobutane CC(C)C.

Rings

A ring opens and closes with the same digit: cyclohexane is C1CCCCC1.

Aromaticity

Aromatic atoms are written in lowercase: benzene is c1ccccc1, pyridine c1ccncc1.

Stereochemistry

/ and \ describe double-bond geometry (F/C=C/F is trans-1,2-difluoroethylene), and @ and @@ the configuration of stereocenters.

Examples to open in the editor

• CCO ethanol
• CC(=O)O acetic acid
• c1ccccc1 benzene
• CC(=O)Oc1ccccc1C(=O)O aspirin
• CN1C=NC2=C1C(=O)N(C(=O)N2C)C caffeine

One SMILES, or several?

The same molecule can have several valid SMILES: OCC and CCO are both ethanol. To compare structures, software computes a canonical SMILES, unique to each molecule.