Guide

Best Tools for Drawing Chemical Structures (2026)

Free and paid chemical structure drawing tools compared: MolDraw, Sciicons Molecules, Ketcher, ChemSketch, JSME, PubChem Sketcher, Avogadro and ChemDraw.

Sciicons · Published October 11, 2026 · Last updated October 11, 2026

Last updated: October 11, 2026. Licences and prices were checked on the official sites linked under Sources on that date.

Quick answer: The best free tools for drawing chemical structures in 2026 are MolDraw and Sciicons Molecules for fast browser drawing and figure export, Ketcher (open source) and PubChem Sketcher for web-based editing, ACD/ChemSketch freeware for desktop work, and Avogadro for 3D models. ChemDraw remains the paid industry standard for advanced chemistry features.

What is a chemical structure drawing tool?

A chemical structure drawing tool (a "chemical sketcher" or "molecule editor") is software that lets you draw atoms and bonds as a 2D skeletal formula, check the structure, and export it as an image or a chemical file format such as MOL, SDF or SMILES. Most tools also convert names or SMILES into drawings and some generate 3D coordinates.

Which chemical drawing tools are best? Comparison table

What do MolDraw, Sciicons Molecules and LabCanvas offer?

MolDraw

MolDraw is a free online chemical drawing tool. Its site lists a 2D structure editor, a reaction drawer, SMILES input, a 3D viewer and image export, with no installation. It positions itself as a free ChemDraw alternative for everyday drawing tasks such as worksheets, slides and figure panels.

Sciicons Molecules

Sciicons Molecules searches compounds by name or SMILES (backed by PubChem) and renders clean 2D and 3D structure drawings styled to sit next to Sciicons illustrations. The preview is free; SVG and PNG downloads are part of Sciicons Pro. It is designed for figure-making, not for reaction mechanisms or spectroscopy.

LabCanvas Blender addon

The LabCanvas Blender addon adds scientific generators to Blender, including a Molecule importer that searches PubChem and imports SDF, MOL, PDB, XYZ and CDXML files. It is a paid, one-time purchase aimed at 3D renders for journal covers, posters and talks rather than 2D skeletal formulas.

Which free tools are best for 2D structures?

Ketcher

Ketcher is EPAM's open-source web editor for small molecules, reactions and biomolecules, licensed under Apache 2.0. Because it is open source, many chemistry databases and electronic lab notebooks embed it. It exports MOL, SDF, SMILES and image formats.

PubChem Sketcher

PubChem Sketcher is a free web editor run by the NCBI. It reads and writes SMILES, SMARTS, InChI and Molfile, and it is the quickest way to draw a structure and immediately search PubChem for it.

JSME

JSME is a free JavaScript molecule editor released under a BSD licence and described in a 2013 Journal of Cheminformatics paper. It is small and fast, which makes it popular for teaching pages and web forms.

ACD/ChemSketch Freeware

ChemSketch Freeware from ACD/Labs is a Windows desktop program for drawing structures, reactions and lab diagrams. The freeware licence is for personal and academic use only, not commercial work.

Which tool is best for 3D molecules?

Avogadro is a free, cross-platform molecular editor for building 3D structures and running quick geometry optimisations; the current Avogadro 2 source is released under the permissive BSD 3-clause licence. For rendered, illustration-quality 3D images, export coordinates from Avogadro or PubChem and render them in Blender with LabCanvas, or use Sciicons Molecules for flat 3D-style graphics.

Is ChemDraw still worth paying for?

ChemDraw by Revvity Signals is the long-standing professional standard. It adds features the free tools lack, such as extensive templates, name-to-structure and structure-to-name, NMR prediction, journal style sheets and ELN integration. It is subscription-only; at the time of writing, Revvity's online shop listed ChemDraw Professional at about US$1,355 per named user per year, and many universities provide it through a site licence. Check your institution first.

Chemaxon's Marvin tools are another professional option; Chemaxon (now part of Certara) changed its academic licensing in 2026, so check the current academic terms before relying on a free licence.

How do you draw a publication-quality chemical structure?

1. Start from a trusted identifier. Paste the SMILES or name from PubChem rather than drawing from memory; this avoids missing hydrogens or wrong stereochemistry.
2. Check stereochemistry and charges. Confirm wedge and hash bonds, E/Z geometry and formal charges against the source record.
3. Use consistent drawing settings. Keep one bond length, font and line width for every structure in the figure. Journals such as ACS publish ChemDraw style templates for this purpose.
4. Export as vector. Save SVG, PDF or EPS so the structure stays sharp when the journal resizes it.
5. Assemble in a layout tool. Place structures next to illustrations (for example Sciicons chemistry illustrations or the Computational Chemistry pack) in Inkscape, Affinity or Illustrator.
6. Keep the source file. Save MOL/SDF or the SMILES string with the figure so you can edit it during revision.

Which tool should you choose?

• You need a structure in a slide in two minutes: MolDraw or PubChem Sketcher.
• You are building a figure panel in a consistent style: Sciicons Molecules plus Sciicons illustrations.
• You need to embed an editor in your own website or ELN: Ketcher (Apache 2.0) or JSME (BSD).
• You work offline on Windows: ChemSketch Freeware.
• You need 3D geometry: Avogadro; for rendered art, LabCanvas in Blender.
• You need name-to-structure, NMR prediction and journal templates: ChemDraw, ideally through a site licence.

Common mistakes when drawing structures

• Mixing bond lengths and fonts across panels, which makes figures look assembled from different sources.
• Exporting low-resolution PNGs instead of vector files. Most publishers ask for at least 300 dpi for raster images and much higher for line art (Elsevier asks for 1000 dpi for line art).
• Dropping stereochemistry when copying between tools. Re-check wedges after every import.
• Using colour as the only cue for atoms or groups. Pair colour with labels so the structure works in greyscale and for colour-blind readers.

Sources

• MolDraw: https://www.moldraw.com/ (checked 11 Oct 2026)
• LabCanvas Blender addon: https://blender.labcanvas.com/ (checked 11 Oct 2026)
• Ketcher (EPAM) and licence: https://lifescience.opensource.epam.com/ketcher/index.html, https://github.com/epam/ketcher/blob/master/LICENSE
• PubChem Sketcher: https://pubchem.ncbi.nlm.nih.gov/edit/
• JSME: https://jsme-editor.github.io/ and Bienfait & Ertl, J. Cheminform. 2013: https://pmc.ncbi.nlm.nih.gov/articles/PMC3662632/
• ACD/ChemSketch Freeware: https://www.acdlabs.com/resources/free-chemistry-software-apps/chemsketch-freeware/
• Avogadro: https://avogadro.cc/
• ChemDraw Professional subscription listing: https://shop.revvitysignals.com/product/chemdraw-professional-named-user-subscription-includes-support-and-maintenance/01tHs000009rOzeIAE
• Chemaxon academic programme: https://www.certara.com/chemaxon-academic-discount/
• Elsevier artwork types (resolution): https://www.elsevier.com/about/policies-and-standards/author/artwork-and-media-instructions/artwork-types

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