Draw chemistry, not just pictures.
ChemPencil is a fast, native 2D chemical structure editor for chemists, students, and educators — on macOS and Windows. Sketch molecules the way you think about them, and move your work freely between every tool you and your collaborators already use.
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 window with ball-and-stick or plain stick view — orbit, zoom, and reset 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.
Native on Mac and Windows
AppKit build for macOS (universal for Apple silicon and Intel) and a WPF build for Windows 10 and 11. Explorer / Finder thumbnail and preview handlers on both. Sandboxed, offline — no telemetry, no accounts, 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
.chempXML - SMILES, MOL, CDXML, InChI, InChIKey, SMARTS
Try it today.
ChemPencil runs on macOS 12 (Monterey) and later — universal for Apple silicon and Intel — and on Windows 10 version 1809 (build 17763) and later, including Windows 11.