Build a Molecule Lesson Plan: Atoms, Bonds and Shapes
Updated 2026-10-02
This build a molecule lesson plan uses a free simulation in which students drag atoms together and the molecule either works or it doesn't. Hydrogen takes one bond, oxygen two, nitrogen three, carbon four, and the simulation tells students when an atom is full. A finished molecule shows its formula, its name and a 3D model with its shape and bond angle. You get learning goals, setup, predictions, a step-by-step sequence with what students should see, a five-question set for the class link, a VSEPR extension for older students, and ideas for differentiation. Every formula, shape and angle below comes from the simulations' own model code.
Lesson at a glance
- Level: grades 7–10 (ages 12–16). The VSEPR extension suits grades 10–12.
- Time: one 50–60 minute period, plus an optional 20-minute extension.
- Prior knowledge: atoms and elements, chemical symbols. Bonding as "atoms sharing electrons" helps but isn't required.
- Format: pairs on laptops or tablets. Dragging atoms works on phones too, but the table is small.
- Simulation: Building molecules – atoms, valence, formulas and 3D shapes. Extension: Molecule shapes – bonds, lone pairs and bond angles (VSEPR).
Learning goals
By the end of the lesson, students can:
- Use valence (H one bond, O two, N three, C four) to build simple molecules and to say why some combinations fail.
- Write the formula of a molecule they have built.
- Classify a molecule as an element or a compound.
- Describe the shapes of H₂O, CO₂, NH₃ and CH₄ and give their bond angles.
- Explain how two different molecules can share one formula (isomers).
What the simulation does
Students drag atoms out of bins at the bottom of the screen and drop them next to another atom. If both atoms still have a free bond, they join. Tapping a bond cuts it; with a mouse, a ✂ appears when you point at a bond. When every atom has used exactly its valence, the molecule is complete and a label shows its formula and name, such as "H₂O – water", with a 3D button. The status line explains what happened, for example "Made H₂O (water) – compound of H, O."
The simulation uses these valences: H, F, Cl and Br one bond; O two; N, P and B three; C and Si four; S two (more only when bonded to O). It builds open chains only, no rings, and its catalog holds 58 substances.
It has three screens:
- Make Molecules: four collection boxes and one or more kits with a limited number of atoms. ◀ ▶ switch kits. A finished molecule goes into the box with the matching formula. Collection 1 asks for CO₂, CO, H₂O₂ and Cl₂. Kit 1 holds 3 C and 4 O. Kit 2 holds 2 H, 3 O and 3 Cl. Each kit has a spare atom or two, so students must plan. Reset Screen brings back the same Collection 1.
- Multiples: each box needs two or three molecules of the same substance. Collection 1 asks for 2 Cl₂, 2 CH₄, 3 CO and 3 HF.
- Playground: four kits with unlimited atoms (H C N O · H C O F Cl · H N O S P · H C Br B Si), up to 40 atoms on the table per kit.
The 3D view rotates by drag and gives the shape and bond angle: "Shape: bent around O (bond angle ≈ 104.5°)." Underneath, it counts each element and says whether the molecule is an element or a compound.
Materials and setup before class
Materials: one device per pair, and a record sheet with columns for formula, name, element or compound, shape and bond angle.
Setup (10 minutes, once):
- Open the simulation. The defaults are the Make Molecules screen, familiar substances and names shown.
- Click Share and create a link for each class, for example "Science · Period 1". The link pins these starting values. For a class that knows organic chemistry, a second link with Collection goals set to Extended (incl. organic) gives harder boxes.
- Optional: on the Questions tab, enter the question set below and attach it to the link.
- Post the link, or open it in present mode and show the QR code.
Lesson sequence
1. Hook and predictions (7 minutes)
Show a glass of water and ask: "We write water as H₂O. Why not HO, or H₃O?" Collect a few answers. Then students commit to two predictions, on paper or on the link:
- P1. "You have one carbon atom and plenty of hydrogen. How many H atoms will bond to the C before the molecule is complete? 2 / 3 / 4 / 6"
- P2. "What shape do you expect a water molecule to have? A straight line / bent / a flat triangle / a pyramid"
Many students draw water as a straight H–O–H line. Don't correct anyone yet.
2. Valence in the Playground (10 minutes)
Open Playground with Kit 1 (H, C, N, O). Pairs build and record:
| Build | Bonds on the central atom | Result |
|---|---|---|
| O with 2 H | 2 | H₂O – water |
| N with 3 H | 3 | NH₃ – ammonia |
| C with 4 H | 4 | CH₄ – methane |
| C with 2 O | 4 (two double bonds) | CO₂ – carbon dioxide |
Then ask them to break the rules on purpose:
- C with only 2 H: no name appears, and the status line says "Some atoms still have unused (or wrong) valence, so this is not a complete molecule yet."
- A fifth H on methane: it won't bond. The status line says the atom it touched "has used up its valence", for example "The C atom has used up its valence (IV), so it cannot form more bonds."
- H–O–O–O–H: every atom is satisfied, but the label says "H₂O₃ – not in the catalog". The rules allow it on paper. Ask: "Does that mean it exists?" A nice moment to separate a model's rules from real chemistry.
Note the double bonds in CO₂: students only drop atoms, and the simulation draws the double bonds once every valence is satisfied. Check P1 now.
3. Make Molecules: plan your atoms (10 minutes)
Switch to Make Molecules. Kit 1 (3 C, 4 O) has to supply CO₂ and CO. Kit 2 (2 H, 3 O, 3 Cl) has to supply H₂O₂ and Cl₂.
The trap is in Kit 2. A student who builds water first uses both hydrogen atoms and has none left for H₂O₂. Let them fall into it. Then ask: "What do you need to undo?" They drag the water back down to the bins, which returns its atoms, and rebuild. Students who finish early press New Collection.
A note on CO, in case students ask: real carbon monoxide has a triple bond. The simulation sticks to simple valence rules, gives carbon a valence of II here and draws a double bond.
4. Elements and compounds (5 minutes)
Each time a molecule is completed, the status line classifies it. O₂ gives "Made O₂ (oxygen) – element (only O)." H₂O gives "Made H₂O (water) – compound of H, O." Ask them to sort everything they built into two columns. Cl₂, H₂, O₂ and N₂ are elements. H₂O, CO₂, NH₃, CH₄ and H₂O₂ are compounds.
5. Shapes in 3D (8 minutes)
Students open 3D on each molecule and complete the table:
| Molecule | Shape in the 3D view | Bond angle shown |
|---|---|---|
| H₂O | bent around O | ≈ 104.5° |
| CO₂ | linear around C | 180° |
| NH₃ | trigonal pyramidal around N | ≈ 107° |
| CH₄ | tetrahedral around C | 109.5° |
| HCN | linear around C | 180° |
Check P2. Ask: "Water and carbon dioxide both have three atoms. Why is one bent and the other straight?" Oxygen keeps two pairs of electrons that aren't in bonds, and they push the hydrogens down. Carbon in CO₂ has none. The extension below makes this visible.
6. Isomers (5 minutes)
In the Playground, students build two molecules from 2 C, 6 H and 1 O. One gives "C₂H₅OH – ethanol", the other "CH₃OCH₃ – methoxymethane (dimethyl ether)". Same atoms, different connections, different substances. The 3D view of each shows tetrahedral carbons and a bent oxygen.
7. Exit check (5 minutes)
Use questions 3–5 of the set below. Then open View answers and compare the Prediction and After columns for P1 and P2.
Question set for this lesson
Enter these on the simulation's Questions tab. Suggested Instructions for students: "Use the Playground with Kit 1 (H, C, N, O). Open the 3D view to read shapes and angles."
1. Multiple choice · Before, as a prediction · Ask again after the simulation
- Question: "You have one carbon atom and plenty of hydrogen. How many H atoms will bond to the C before the molecule is complete?"
- Options: 2 / 3 / 4 (correct) / 6
- Explanation: "Carbon has a valence of four: it forms four bonds. Hydrogen forms one. So one carbon holds four hydrogens, which gives CH₄, methane. With fewer, the carbon still has free bonds and the molecule isn't complete."
2. Multiple choice · Before, as a prediction · Ask again after the simulation
- Question: "What shape do you expect a water molecule to have?"
- Options: a straight line / bent (correct) / a flat triangle / a pyramid
- Explanation: "Water is bent, with an H–O–H angle of about 104.5°. The oxygen atom has two pairs of electrons that are not in bonds. They push the two O–H bonds closer together, so the molecule can't be straight."
3. Multiple choice · After the simulation
- Question: "Which of these molecules is an element, not a compound?"
- Options: H₂O / CO₂ / NH₃ / O₂ (correct)
- Explanation: "An element is made of one kind of atom. O₂ contains only oxygen atoms. H₂O, CO₂ and NH₃ each contain two different elements, so they are compounds."
4. Number · After the simulation
- Question: "Build NH₃ and open its 3D view. What bond angle does it show, in degrees?"
- Answer: 107, tolerance ± 1, unit °
- Explanation: "Ammonia is trigonal pyramidal, with H–N–H angles of about 107°. That's a little less than the 109.5° of methane, because nitrogen's lone pair pushes the three bonds closer together."
5. Short answer · After the simulation
- Question: "Ethanol and methoxymethane both contain 2 C, 6 H and 1 O. How are the two molecules different?"
- Accepted answers (optional): leave empty and read the answers yourself.
- Model answer: "The atoms are joined in a different order. In ethanol the oxygen sits at the end of the carbon chain, bonded to one C and one H. In methoxymethane the oxygen sits between the two carbon atoms. Different structures make different substances, called isomers."
Questions 1 and 2 are the predictions, asked again after the simulation. For more on why predictions matter, see Predict–Observe–Explain with simulations.
Extension: why molecules have these shapes (VSEPR)
For grades 10–12, or a second lesson, the shapes simulation shows the reason behind the angles. On its Model screen, students add single, double or triple bonds and lone pairs to a central atom A, up to six in total. The bonds and lone pairs push each other as far apart as possible. Students can drag an atom away and watch it spring back. Tick Bond angles and Electron geometry to see the numbers and names.
Ask pairs to fill in this table:
| Around A | Molecular geometry | Bond angle | Real example |
|---|---|---|---|
| 2 bonds | linear | 180.0° | CO₂ |
| 3 bonds | trigonal planar | 120.0° | BF₃ |
| 4 bonds | tetrahedral | 109.5° | CH₄ |
| 3 bonds + 1 lone pair | trigonal pyramidal | 107.0° | NH₃ |
| 2 bonds + 2 lone pairs | bent | 104.5° | H₂O |
Three points to draw out:
- Lone pairs push harder than bonds. Four electron domains give 109.5° with no lone pairs, 107.0° with one and 104.5° with two.
- A double bond counts as one direction. Two double bonds on A still give a linear 180.0°, which is CO₂.
- Models have limits. On the Real molecules screen, choose SO₂. The readout gives "Measured bond angles: 119.0° · model: 114.7°". Ask students why a simple repulsion model could miss by four degrees.
Differentiation
Support:
- Stay in the Playground with Kit 1 and give the four target molecules on a card.
- Give a valence card: "H one hand, O two hands, N three hands, C four hands. Every hand must hold another."
- Leave Show names on so students can check their own work.
Stretch:
- Build both C₃H₇OH isomers (propan-1-ol and propan-2-ol) and explain the difference.
- Build ethene (C₂H₄) and ethyne (C₂H₂) and compare the angles at carbon: 120° and 180°.
- In the extension, predict the shape of a central atom with 4 bonds and 2 lone pairs before building it.
English learners: the simulation is available in six languages. Create a second link in the student's language so the labels are familiar while the discussion stays in English.
Standards alignment
This lesson matches NGSS MS-PS1-1: develop models to describe the atomic composition of simple molecules and extended structures. The VSEPR extension supports high school chemistry units on covalent bonding and molecular shape, and exercises the Developing and Using Models practice. It fits the bonding topics of GCSE Chemistry and introductory chemistry courses.
For more chemistry activities, see interactive chemistry lesson ideas, where the build an atom activity makes a good lesson before this one. For classroom routines, see how to use interactive simulations in the classroom. The balancing chemical equations lesson plan uses the same molecules next.
FAQ
Why won't two atoms bond when I drop them together?
At least one of them has no free bond left, or the drop was too far away. The status line says which atom is full. Drop the new atom right next to an atom that still has room.
Why can't students build benzene or other rings?
The simulation builds open chains only. Rings and charged ions are outside this model, so it suits introductory bonding rather than organic chemistry.
The 3D button doesn't open. What now?
The 3D view needs WebGL. On an old device, the simulation shows a message instead. Try another browser or turn on hardware acceleration. The rest of the lesson works without 3D.
Does every molecule a student builds exist?
No. A molecule that satisfies every valence but isn't in the 58-substance catalog shows "not in the catalog", like H₂O₃. That's a good prompt: the rules of a model don't guarantee that a substance is stable.