Notes for teachers
A free, point-and-click ball-and-stick model kit that runs in the browser. Pupils plug atoms into each other's holes, as with a plastic kit, and the finished molecule is named for them. No logins, no installs, and nothing to tidy away.
← Back to the kitThe kit in two minutes
| Build | Pick an atom from the box, then click an atom in the model: the new one snaps into the nearest free hole (a preview shows where). Or drag an atom out of the box onto a hole. Fill with H puts a hydrogen in every free hole. |
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| Link | Drag from one atom to another to join them; this closes rings. Link the same two atoms again for a double bond, and a third time for a triple bond, as with the flexible links of a real kit. |
| Delete | Turns the view's edge red. Hover an atom or link and everything that a click would remove shows in red; click to remove it. Undo puts it back. |
| Look around | Drag empty space to turn the view; pinch, scroll or use + and − to zoom; two fingers, right-drag or Shift-drag to pan. Drag an atom to turn its piece; drag a single bond to twist one end. |
| Ions | The box's Ions section has lithium, sodium, potassium, magnesium and calcium ions (Li⁺, Na⁺, K⁺, Mg²⁺, Ca²⁺) and fluoride, chloride, bromide and oxide ions (F⁻, Cl⁻, Br⁻, O²⁻). Each has six holes set square, so they build ionic lattices; the panel names the compound from its ions. |
| Examples | About 60 ready-made models, from water to caffeine, ice, graphite and a buckyball. |
| Save and Load | Save writes the model to a file (in Chrome, Edge and on Chromebooks pupils choose the folder; in other browsers it goes to Downloads), so work can be handed in. Load opens a saved file. The current model is also kept in the browser, so a refresh doesn't lose it. |
Every ball has one hole for each bond it makes: hydrogen 1, oxygen 2, nitrogen 3, carbon 4. A model with every hole filled is a real molecule, and the panel names it using PubChem, the US National Library of Medicine's chemistry database.
Where it fits
England: KS3 science
- Atoms, elements and compounds; chemical symbols and formulae.
- Simple molecules, and the difference between a molecule and a giant structure.
GCSE chemistry (AQA, OCR, Edexcel and others)
- Covalent bonding, including double and triple bonds.
- Structure and properties: small molecules; giant covalent structures (diamond, graphite, silica); fullerenes and the buckyball; the giant ionic lattice of sodium chloride.
- Organic chemistry: alkanes, alkenes, alcohols and carboxylic acids; structural isomers.
- Hydrogen bonding and the structure of ice.
- The limitations of ball-and-stick and 3D models (see below).
US middle school (NGSS)
- MS-PS1-1: develop models to describe the atomic composition of simple molecules and extended structures.
Activities
1. Holes are bonds
Look at the box: hydrogen has 1 hole, oxygen 2, nitrogen 3, carbon 4. Build water, ammonia and methane: one atom, then Fill with H.
Why can't you add a third hydrogen to the oxygen? What does the number of holes tell you about each element?
2. The alkane staircase
Start with one carbon and Fill with H (methane). Undo the fill, add a second carbon, fill again (ethane). Keep going: propane, butane, pentane. Record each formula from the panel.
What's the pattern? Predict the formula for 10 carbons, then build it to check. (CnH2n+2.)
3. Same formula, different molecule
Build two different molecules with the formula C4H10: a straight chain and a branched one. Then two with C2H6O. The panel names each, so pupils can see they've made different substances (butane and isobutane; ethanol and dimethyl ether).
If the formula is the same, why are the names different? Why might they boil at different temperatures?
4. Double and triple bonds
Build two joined carbons and Fill with H: that's ethane. Undo the fill, then in Link mode drag from one carbon to the other to add a second link, and Fill with H: ethene. Undo the fill again and add a third link: ethyne. Then build carbon dioxide, with two double bonds. Try dragging each bond to twist it.
How does the shape change from ethane to ethene to ethyne? Why will a single bond twist but a double bond won't?
5. One element, three structures
Load the diamond chunk, graphite and the buckyball from Examples. Count the links on a carbon in each.
Diamond's carbons use all four holes; graphite's use three, leaving one spare. How does that explain diamond's hardness, graphite's slippery layers, and why pencil lead conducts electricity?
6. Molecules or giant structures?
Compare carbon dioxide (a small molecule) with silica (a giant structure of silicon and oxygen) and the salt crystal (a lattice of ions). Note how the formula of a giant structure is a ratio: NaCl, not one molecule.
Then build a lattice from the Ions section: alternate Na⁺ and Cl⁻ for sodium chloride, then Mg²⁺ and O²⁻ for magnesium oxide. Now try Mg²⁺ with Cl⁻ and read what the panel says.
CO2 is a gas but sand (SiO2) is a hard solid. What's different about how their atoms are joined? Why is magnesium chloride MgCl2 and not MgCl?
7. Ice and hydrogen bonds
Load ice. The dotted lines are hydrogen bonds between water molecules; they aren't links. Turn it to look down on the six-sided rings.
Where do snowflakes get their six sides? Why does ice float on water?
8. Mystery molecules
Give pupils only a formula or a name, such as C3H6O or "vinegar", and ask them to build it. The panel tells them what they've actually made.
9. What does the model leave out?
Good for the GCSE "limitations of models" point. Things to notice:
- Atoms aren't coloured balls, and they aren't drawn to scale.
- Bonds are shared electrons, not sticks; electrons and lone pairs aren't shown (oxygen has two holes, but four pairs of electrons).
- A real double bond isn't two bent links.
- Real molecules vibrate and bonds have different lengths; the kit keeps them tidy.
- Charges only appear on the ions in the Ions section; the uneven sharing of electrons inside molecules isn't shown.
Practicalities
- Runs in any up-to-date browser: Chromebooks, iPads, Windows and Macs, and phones. Nothing to install and no accounts.
- Everything runs from this site; the only other site it contacts is PubChem, to name molecules. If a school network blocks PubChem, building still works but molecules won't be named.
- To hand work in, pupils Save to a file and upload or email it; Load opens it again.
- It's free and open source (AGPL-3.0); the code is on GitHub.
Privacy
- No accounts, no logins, no cookies, no adverts, and no tracking or analytics scripts.
- The model being built is kept in the browser's own storage on that device, so it survives a refresh. It isn't sent to us.
- To name a molecule, its structure (a line of text describing the atoms and bonds, called SMILES) is sent to PubChem. Nothing about the pupil is sent.
- Saved files stay wherever the pupil saves them.
- Like any website, the web server keeps standard access logs.