What is SMILES? 

The Simplified Molecular Input Line Entry System, or SMILES, is a notation that uses simple text characters to represent chemical structures. Developed by David Weininger in the 1980s, it provides a compact and human-readable way to describe molecules. While modern chemical drawing software is now common, SMILES remains a cornerstone in cheminformatics for storing and exchanging molecular information.

Examples

• Ethanol: CCO

• Benzene: c1ccccc1

SMILES basics: atoms, bonds, branching, rings

• Atoms: C, N, O, Cl, Br, etc.

• Single bonds are implicit: CC = C–C

• Double = and triple # bonds: C=O (carbonyl), C#N (nitrile)

• Branching uses parentheses: CC(O)C = isopropanol

• Rings use numbers to label ring closure points: c1ccccc1 = benzene (lowercase c indicates aromatic carbon).

To visualize these, we can use the Python library RDKit. The function Chem.MolFromSmiles() converts a SMILES string into a molecule object that can then be displayed.

RDKit example

The following codes can be used to generate a butane (C4H10) structure (Figure 1).

Code:

butane = Chem.MolFromSmiles("CCCC")

butane

2. Pentane C5H12 (Figure 2).

Code:

pentane = Chem.MolFromSmiles("CCCCC")

pentane

3. Butanol C4H10OH (Figure 3).

Code:

butanol = Chem.MolFromSmiles("CCCCO")

butanol