Markdown chemical structure drawer

Draw a molecule from its SMILES string. Type the formula and get a clean chemical structure to embed in notes or teaching material.

The editor format

The editor writes one small text block, fenced as ```smiles. The first line is the keyword chemistry. Every line after that is one molecule: a SMILES string, then an optional label in double quotes. Lines starting with # are comments.

You write

chemistry
c1ccccc1 "Benzene"
CC(=O)O "Acetic acid"
CCO "Ethanol"

You get

Line	Meaning
`chemistry`	The first line — names the format
`c1ccccc1`	A molecule, drawn from its SMILES string
`CCO "Ethanol"`	A molecule with a caption in double quotes
`# note`	A comment, ignored when drawing

A SMILES primer

SMILES writes a molecule as a short string of atoms. Letters are atoms, atoms next to each other are bonded, and hydrogens are filled in for you. Here is each piece you can write.

Atoms and bonds

Write element symbols in a row. Neighbouring atoms are joined by a single bond.

You write

CCO

You get

Double and triple bonds

Put = for a double bond or # for a triple bond between atoms.

You write

CC(=O)O

You get

Branches

Open a branch with a round bracket and close it to return to the main chain.

You write

CC(C)CO

You get

Rings

Match a pair of digits to close a ring, or use lowercase letters for an aromatic ring.

You write

c1ccccc1

You get

Cheat sheet

Write this	You get
`C`	A carbon atom, with hydrogens added for you
`O` `N` `S`	Other atoms by element symbol
`CC`	A single bond between neighbours
`=`	A double bond
`#`	A triple bond
`( )`	A branch off the main chain
`1 ... 1`	Matching digits close a ring
`c1ccccc1`	Lowercase letters make an aromatic ring

Common molecules

Handy SMILES snippets to paste into the SMILES box.

Molecule	SMILES
Water	`O`
Ethanol	`CCO`
Acetic acid	`CC(=O)O`
Benzene	`c1ccccc1`
Phenol	`Oc1ccccc1`
Aspirin	`CC(=O)Oc1ccccc1C(=O)O`
Caffeine	`Cn1cnc2c1c(=O)n(C)c(=O)n2C`
Glucose	`OCC1OC(O)C(O)C(O)C1O`