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Molecule Lab (The Freshman Mole)
A free browser editor for 2D chemical structures, reaction schemes and interactive 3D molecular models.
Free. 36 of 65 checklist features confirmed.
Main canvas
No dark mode
Editor remained light under the dark appearance override.
Default drawings
Caffeine
Paclitaxel
Cholesterol in 3D
- The hosted editor was tested in an isolated WebKit window.
- SMILES imports resolve through PubChem and use its 2D structures.
- Paclitaxel's default drawing includes crowded overlapping labels.
- Local cholesterol 3D generation timed out; PubChem supplied a conformer.
- 3D PNG export failed with a renderer-size mismatch in WebKit.
Facts
- Version we tested
- 1.88.95
- Runs on
- Browser
- License
- Free hosted tool; redistribution terms unspecified.
- Price
- Free
- Relies on
- Kekule.js Composer, Kekule.js, RDKit, Open Babel, 3Dmol.js. Mounts Kekule.js Composer; adds RDKit validation, Open Babel conformers, and 3Dmol.js viewing.
- Draws with
- Kekule.js 2D canvas renderer; custom SVG exporter with HTML canvas PNG rasterization; Three.js and 3Dmol.js for 3D.
- Chemistry from
- Kekule.js; RDKit.js for validation and stereochemistry; Open Babel for 3D conformer generation.
- Interface
- Kekule.js widgets and custom JavaScript/HTML controls.
- Main language
- JavaScript
- Other languages
- C++: RDKit and Open Babel WebAssembly
- Renderer
- Borrowed: Kekule.js canvas; in-house SVG renderer
- Third-party licenses
- Includes GPL-2.0 (Open Babel) and GPL-noticed chemistry data; MIT/BSD components include GLmol with an LGPL-3.0 alternative.
- Naming, property and SMILES lookups depend on matching PubChem compounds.
- CDXML import omits annotations and rejects contracted groups.
- SVG export rejects query, coordination and non-Kekulé aromatic bonds.
In use
Screenshots from our test of this version.
Single, double and triple bonds
Single, double, and triple bond tools below the drawing.
Wedge, hash and wavy bonds
Solid and hashed wedges in the drawing and bond toolbar.
Ring tools
Aromatic rings on the canvas beside the ring tool.
3D model view
Ball-and-stick molecular model in the 3D preview.
High-resolution PNG
PNG output showing a caffeine structure.
Features
- Tested by running it
- Seen in the app
- The manual says yes
- Partly, with the reason shown
- Not supported
- Not established, which is not the same as no
Select a mark for its proof. A filled mark opens our screenshot, or the manual if the check left nothing to picture. A ring opens the manual.
Drawing structures
- Yes, tested by running it: Drew single, double, and triple bonds. Opens the screenshot.Single, double and triple bondsDrew single, double, and triple bonds.total-synthesis.com
- Partly: Drew solid and hashed wedges; wavy untested. Opens the screenshot.Wedge, hash and wavy bondsDrew solid and hashed wedges; wavy untested.total-synthesis.com
- Not establishedDative, hydrogen and quadruple bonds
- Not establishedChoose double-bond side
- Yes, tested by running it: Placed cyclohexane; aromatic ring tool also visible. Opens the screenshot.Ring toolsPlaced cyclohexane; aromatic ring tool also visible.total-synthesis.com
- Yes, according to the manual: Native chair and Haworth ring tools are retained. Opens the cited page.Chair and Haworth ringsNative chair and Haworth ring tools are retained.total-synthesis.com
- Yes, according to the manual: Native flexible-chain tool adjusts atom count while dragging. Opens the cited page.Chain toolNative flexible-chain tool adjusts atom count while dragging.github.com
- Partly: Boc placement added atoms but displayed an error and no drawing. Opens the cited page.Template libraryBoc placement added atoms but displayed an error and no drawing.total-synthesis.com
- Not establishedSave your own templates
- Yes, according to the manual. Opens the cited page.Group abbreviationstotal-synthesis.com
- Yes, according to the manual: Elements, charges and isotopes use native Atom controls. Opens the cited page.Charges, isotopes and atom labelsElements, charges and isotopes use native Atom controls.total-synthesis.com
- Yes, according to the manual: Radical and electron-pair tools are enabled. Opens the cited page.Radicals and lone pairsRadical and electron-pair tools are enabled.total-synthesis.com
- Yes, according to the manual. Opens the cited page.Keyboard drawingtotal-synthesis.com
- Yes, according to the manual: Lasso selection, rotation, flip and scale tools are enabled. Opens the cited page.Lasso select and transformsLasso selection, rotation, flip and scale tools are enabled.total-synthesis.com
- Not establishedTilt drawings in perspective
Reactions and mechanisms
- Yes, tested by running it: Drew forward and equilibrium arrows. Opens the cited page.Reaction arrowsDrew forward and equilibrium arrows.total-synthesis.com
- Yes, tested by running it: Drew full-head and single-electron curved arrows. Opens the cited page.Curved mechanism arrowsDrew full-head and single-electron curved arrows.github.com
- Partly: CDXML reaction steps require one horizontal arrow and one row. Opens the cited page.Machine-readable reactionsCDXML reaction steps require one horizontal arrow and one row.total-synthesis.com
- Not establishedAtom mapping
- Yes, according to the manual: Enabled glyph palette includes plus, heat and light symbols. Opens the cited page.Orbitals and symbolsEnabled glyph palette includes plus, heat and light symbols.github.com
Figures and layout
- Yes, according to the manual. Opens the cited page.Rich text captionstotal-synthesis.com
- Yes, according to the manual: Enabled glyph tools provide editable line segments and curves. Opens the cited page.Shapes, brackets and curvesEnabled glyph tools provide editable line segments and curves.github.com
- Yes, according to the manual. Opens the cited page.Align and distributetotal-synthesis.com
- Yes, according to the manual. Opens the cited page.Group and ungrouptotal-synthesis.com
- Yes, according to the manual. Opens the cited page.2D structure cleanuptotal-synthesis.com
- Partly: ACS-inspired publication defaults only. Opens the cited page.Journal drawing stylesACS-inspired publication defaults only.total-synthesis.com
- Not establishedReusable custom styles
- Not establishedColor control
- Partly: Selection halos only; SVG and PNG exports omit them. Opens the cited page.Color highlightingSelection halos only; SVG and PNG exports omit them.github.com
- Not establishedPage layout and multipage
- Not establishedImported pictures
- Not establishedTLC plates and tables
Chemistry intelligence
- Yes, according to the manual. Opens the cited page.Structure checkingtotal-synthesis.com
- Yes, according to the manual: RDKit computes R/S and E/Z overlays. Opens the cited page.R/S and E/Z labelsRDKit computes R/S and E/Z overlays.total-synthesis.com
- Partly: PubChem lookup returned caffeine formula and molecular weight. Opens the cited page.Formula and massPubChem lookup returned caffeine formula and molecular weight.total-synthesis.com
- Partly: PubChem lookup returned XLogP and TPSA. Opens the cited page.Property estimatesPubChem lookup returned XLogP and TPSA.total-synthesis.com
- Partly: Aspirin imported through PubChem name lookup. Opens the cited page.Name to structureAspirin imported through PubChem name lookup.total-synthesis.com
- Partly: Caffeine drawing returned PubChem IUPAC name. Opens the cited page.Structure to nameCaffeine drawing returned PubChem IUPAC name.total-synthesis.com
- Not establishedNMR prediction
- Not establishedR-groups and query structures
- Not establishedPolymers and repeat units
- Not establishedPeptides and nucleic acids
- Not establishedImage to structure
- Yes, tested by running it: PubChem returned caffeine, paclitaxel, cholesterol, and aspirin. Opens the cited page.Online structure lookupPubChem returned caffeine, paclitaxel, cholesterol, and aspirin.total-synthesis.com
- Yes, tested by running it: PubChem conformer loaded; fresh cubane model rotated by dragging. Opens the screenshot.3D model viewPubChem conformer loaded; fresh cubane model rotated by dragging.total-synthesis.com
- Not establishedCrystal structures
Files and exchange
- Yes, tested by running it: Exported caffeine CDXML and reimported its atom and bond text. Opens the cited page.CDXML import and exportExported caffeine CDXML and reimported its atom and bond text.total-synthesis.com
- No: Binary CDX import is explicitly rejected. Opens the cited page.CDX import and exportBinary CDX import is explicitly rejected.total-synthesis.com
- Partly: Exported 3D SDF; no MOL import or export found. Opens the cited page.MOL and SDFExported 3D SDF; no MOL import or export found.total-synthesis.com
- Partly: PubChem-backed SMILES import and lookup output worked. Opens the cited page.SMILESPubChem-backed SMILES import and lookup output worked.total-synthesis.com
- Not establishedInChI
- Not establishedRXN files
- Yes, tested by running it: Exported all three drawings as SVG. Opens the cited page.SVG exportExported all three drawings as SVG.total-synthesis.com
- No: No PDF export command in File menu. Opens the cited page.PDF exportNo PDF export command in File menu.
- Partly: 2D PNG exported; no print DPI control observed. Opens the screenshot.High-resolution PNG2D PNG exported; no print DPI control observed.total-synthesis.com
- Partly: CDXML-text paste in; copy-out uses PNG. Opens the cited page.Paste to and from ChemDrawCDXML-text paste in; copy-out uses PNG.total-synthesis.com
- Not establishedEditable in Word or PowerPoint
- Not establishedWindows Office OLE
APIs and automation
- Not establishedPython API
- Not establishedJavaScript or TypeScript API
- Not establishedCommand-line tool
- Not establishedAI agent control
- Not establishedBuilt-in AI assistant
Embedding and extension
- Not establishedPlugins
- Not established: No embed documentation; headers alone cannot confirm iframe support.Embed in your own appNo embed documentation; headers alone cannot confirm iframe support.total-synthesis.com