ChemPencil

ChemPencil is a fast, native Mac scientific 2D chemical structure
editor for chemists, students, and educators. Sketch molecules the
way you think about them, work with real chemistry data — not just
pretty pictures — and move files freely between the tools you and
your collaborators already use.

DRAWING
• Single, double, and triple bonds with left/right/center alignment
• Wedge, hashed, wavy, bold, and dashed stereo bonds
• Ring palette: 3- to 8-membered rings, benzene, cyclopentadiene,
cyclohexane chairs
• Reaction arrows (forward, equilibrium, retrosynthetic) with
conditions above and below the shaft
• Curved mechanism arrows (double-barbed and fishhook)
• Brackets (square, round, curly), text labels, formal charges,
isotopes, highlights, and element coloring
• "Magic Hotkeys" for fast atom and bond editing without switching
tools

CHEMISTRY, NOT JUST GRAPHICS
• Implicit hydrogens with live valence and over-valence checking
• Calculated properties: formula, MW, monoisotopic mass, TPSA,
cLogP, H-bond donors/acceptors, rotatable bonds, degree of
unsaturation, formal charge
• Simulated isotopic mass spectrum
• Nicknames library (Me, Et, Ph, Bn, Ac, Ts, OMe, NO₂, CF₃, CO₂H…)
with one-click set / expand
• Clean Up Structure, Auto-Orient, Equalize Bond Angles

NOMENCLATURE & SEARCH
• Generate IUPAC name from structure
• Structure from IUPAC name
• Find and Replace substructure, query atoms, query bonds,
atom lists, SMARTS

REACTIONS
• Reaction conditions editor
• Atom-to-atom mapping
• Reaction stoichiometry panel

INTEROPERABILITY
• Read and write native .chemp, MOL, SDF, RXN, RDF, SMILES, CDXML
• Copy InChI, InChIKey, SMILES, MOLfile, CDXML, SMARTS
• Export PDF (vector), SVG, PNG, TIFF
• Rich clipboard: paste vector + raster + native into any app
• QuickLook thumbnails and previews in Finder

3D VIEWER
• Interactive SceneKit 3D window for any 2D structure

DESIGNED FOR MAC
• Universal binary (Apple silicon + Intel)
• Sandboxed and hardened, no telemetry, no account required
• AppleScript automation
• Multiple document windows, page setup, and printing

Includes ready-made sample documents (aspirin synthesis, caffeine,
amino acids, and more) to explore right after you launch.