ChemPencil › Tutorials

How to draw a chemical structure from SMILES

Tutorial · macOS and Windows

SMILES strings are everywhere: in papers, supplier catalogues, PubChem and your colleagues' emails. ChemPencil turns a SMILES string into a clean, properly laid-out drawing in one step, including stereochemistry, and gives you canonical SMILES back from anything you draw.

Draw a structure from a SMILES string

1. Copy the SMILES string, for example aspirin: CC(=O)Oc1ccccc1C(=O)O.
2. In ChemPencil choose Structure › Insert from SMILES… (⇧⌘M on Mac, Ctrl+Shift+M on Windows). The field is already filled in when the clipboard holds a SMILES string.
3. Click OK. The structure is laid out with standard bond lengths and angles and placed in the middle of the visible canvas.

To start a fresh document instead, use Structure › New from SMILES…. You can also simply paste: text containing SMILES (or a Molfile) pasted onto the canvas with ⌘V / Ctrl+V becomes a structure.

Stereochemistry is drawn for you

Stereo marks in the SMILES become real wedges and double-bond geometry. N[C@@H](C)C(=O)O is drawn as L-alanine with a solid wedge to the amine, and C/C=C/C as trans-but-2-ene. ChemPencil reads the wedges back when it names the structure, so the (R)/(S) labels always match the drawing. See drawing wedge and hash bonds.

Copy SMILES from a drawing

1. Draw or open the structure.
2. On Mac choose Structure › Copy SMILES; on Windows choose Edit › Copy As › SMILES (Ctrl+Shift+C).
3. Paste the result wherever you need it.

The SMILES is canonical: the same structure always gives the same string, however you drew it, with stereochemistry included. For L-alanine you get:

When a document holds several molecules they are joined with a .. To label a structure with its SMILES on the canvas, select it, right-click it and choose Generate SMILES for Selection.