ChemPencil
ChemPencil app icon

Draw chemistry, not just pictures.

ChemPencil is a fast, native Mac 2D chemical structure editor for chemists, students, and educators. Sketch molecules the way you think about them, and move your work freely between every tool you and your collaborators already use.

Download on the Mac App Store See what's inside

Everything you need to draw and reason about molecules.

A polished drawing surface backed by a real chemistry engine — no plugins, no cloud round-trips.

Full drawing toolkit

Single / double / triple bonds, wedge, hashed, wavy, bold, and dashed stereo bonds. Rings from three- to eight-membered, benzene, cyclopentadiene, and cyclohexane chairs.

Reactions and mechanisms

Forward, equilibrium, and retrosynthetic arrows with conditions above and below the shaft. Curved mechanism arrows (double-barbed and fishhook) for clean electron pushing.

Magic Hotkeys

Change an atom's element, formal charge, or a bond's order and stereochemistry with a single keypress — no tool switching, no dialog boxes.

IUPAC name ↔ structure

Generate an IUPAC name from any structure, or build a structure from a name. Covers common functional groups including acid halides, esters, amines, ethers, and ketones.

Calculated properties

Molecular formula, molecular weight, monoisotopic mass, TPSA, cLogP, H-bond donors and acceptors, rotatable bonds, degree of unsaturation, formal charge — updated live as you draw.

Mass spectrum simulator

Simulated isotopic distribution for any molecule, ready to compare against your real MS data.

Standard InChI & SMILES

One-click Copy InChI, InChIKey, and SMILES for reliable lookups in PubChem, ChemSpider, and your ELN.

Query & substructure search

Query atoms, query bonds, atom lists, SMARTS, plus Find and Replace Substructure — search and edit motifs across your document.

Nicknames library

Me, Et, Ph, Bn, Ac, Ts, OMe, NO₂, CF₃, CO₂H, and more — set and expand in one click.

Interactive 3D viewer

See any 2D structure in an interactive 3D SceneKit window without leaving the app.

Publication-ready output

Export vector PDF and SVG, or high-resolution PNG and TIFF. Rich clipboard pastes vector + raster + native into Keynote, Pages, Word, PowerPoint, or your ELN.

Designed for Mac

Universal binary for Apple silicon and Intel. Sandboxed, hardened, and offline — no telemetry, no accounts, and no data leaves your machine.

Fits into your workflow.

Every file format chemists actually use — and every output format you'll paste into a paper, poster, or slide.

Read

  • ChemPencil .chemp
  • MDL Molfile .mol
  • MDL SDF .sdf
  • MDL RXN .rxn
  • MDL RDF .rdf
  • SMILES .smi
  • CDXML .cdxml

Write

  • ChemPencil .chemp
  • MOL / SDF / RXN / RDF
  • SMILES
  • CDXML

Export

  • PDF (vector)
  • SVG (vector)
  • PNG (300 dpi)
  • TIFF (300 dpi)

Clipboard

  • Vector PDF + raster PNG / TIFF
  • Native .chemp XML
  • SMILES, MOL, CDXML, InChI, InChIKey, SMARTS

Try it today.

ChemPencil runs on macOS 12 (Monterey) and later, on Apple silicon and Intel Macs.

Download on the Mac App Store