Molecule builder

A molecule builder lets you put a molecule together atom by atom and see its 3D shape. Our Molecule Builder checks every atom against the octet rule as you build, then gives the molecular formula, the VSEPR shape at each atom, the bond angles, whether the molecule is polar, and a stable or unstable verdict with the reason shown on the atom at fault.

It opens on ethanol, C₂H₆O, as a 3D model you can turn with a finger, the mouse or the arrow keys.

Try it

Molecule Builder

Build molecules atom by atom in 3D and check if they are stable

Open the simulatorGo to its page

How to use the molecule builder

1. Under Start from, choose a molecule to begin with, such as methane, benzene or sulfur hexafluoride, or build from the atom already on the stage.
2. Under Build, tap an atom on the model to pick it, choose an element (C, H, O, N, F, Cl, Br, I, S, P, B, Si or Xe) and a Single, Double or Triple bond, and press Add.
3. Press Fill with hydrogens to fill the picked atom's spare bonds. Use Join to bond two atoms already on the stage, which is how you close a ring, Change to to swap an element, and Remove to take one away.
4. Read the formula, the verdict, the shape at the picked atom, the degree of unsaturation and the total bond enthalpy.
5. Turn on Bond angles, Lone pairs or Dipole to show them on the model, and open Stability for the reasons behind the verdict.

Molecules can have up to 64 atoms, with chains, branches and rings. Practice and help sets questions on shapes, lone pairs and unsaturation, with worked solutions.

Molecular shapes and bond angles: VSEPR

Electron pairs round a central atom repel each other and spread as far apart as they can. Lone pairs repel more strongly than bonding pairs, so each lone pair squeezes the bond angles a little. The builder names the shape at every central atom with its AXE notation, where A is the central atom, X a bonded atom and E a lone pair. These shapes come from its quick starts:

A double or triple bond counts as one region of electrons, so CO₂, with two double bonds, is linear. The builder shows the measured angles for its quick starts, such as 104.5° for water. Try one in the course, then press Mark:

Worked examples you can check in the builder

Example 1: ethanol

The opening molecule, ethanol, has the formula C₂H₆O. Pick either carbon and the builder says tetrahedral (AX₄); pick the oxygen and it says bent (AX₂E₂), with two lone pairs. The verdict is stable: every atom has a full outer shell. It is polar, because its bond dipoles do not cancel, and its O-H group can hydrogen bond with water, which is why the two mix.

Example 2: why water is bent and polar

Choose Water. Oxygen has two bonding pairs and two lone pairs, four regions in a tetrahedral arrangement, but only the two hydrogens count in the shape, so it is bent. The two lone pairs push the bonds closer together than 109.5°, to 104.5°. The bond dipoles point the same way, so they do not cancel: water is polar. Turn on Dipole to see the arrow.

Example 3: polar bonds, non-polar molecule

Carbon dioxide has two polar C=O bonds, but the molecule is linear, so the two dipoles point in opposite directions and cancel. The builder says non-polar: the bond dipoles cancel. SF₆ and XeF₄ are non-polar for the same reason, by symmetry. For SF₆ the verdict also notes that sulfur has 12 electrons around it, an expanded octet, which atoms from period 3 on can hold.

Example 4: an unstable structure

Build methane, then remove one hydrogen to leave CH₃. The builder says unstable: carbon has 7 electrons, one of them unpaired, so it is a radical that reacts at once. Try instead to add a fifth hydrogen to carbon, and it says the structure cannot exist: carbon would have 5 bonds, 10 electrons, and a period 2 atom can hold only eight.

Degree of unsaturation and bond enthalpy

The degree of unsaturation counts rings plus π bonds. Each double bond has one π bond and each triple bond two. Benzene, C₆H₆, has one ring and three double bonds in the builder's model, so its degree of unsaturation is 4. From a formula with C carbons and H hydrogens, it is (2C + 2 − H) ÷ 2:

The total bond enthalpy adds up the energy of every bond, using data-booklet values. For methane it is 4 × 413 = 1,652 kJ/mol, and the builder gives 1,652 kJ/mol. Where the data booklet has no figure for a bond, such as S-F in SF₆, the builder says so instead of giving a total.

What the builder does not do

• No names for your molecules. It names a molecule only when it matches one of the quick starts. Work out IUPAC names yourself.
• Small molecules only. Up to 64 atoms, so proteins and DNA are too big, and there is no file import from a database.
• No reactions. It gives the bond enthalpy of one molecule. For an enthalpy change, add up bonds broken minus bonds made by hand.
• Covalent molecules only. Ionic lattices and metals are not built here.

Common mistakes

• Counting a double bond as two regions. A double or triple bond is one region of electron density for VSEPR.
• Forgetting lone pairs. NH₃ has four electron regions but only three bonds, so it is pyramidal, not trigonal planar.
• Naming the shape from the electron arrangement. The shape describes where the atoms are. Water's electron pairs are tetrahedral, but the molecule is bent.
• Calling every molecule with polar bonds polar. In a symmetrical molecule like CO₂ or CCl₄, the dipoles cancel.
• Using 109.5° for every carbon. A carbon with a double bond is trigonal planar, about 120°.

Practise bonding in a short timed paper

Molecular shapes, bond angles and polarity come up in Honors Chemistry and College General Chemistry practice, and in A-level Chemistry: Year 1 in the UK. Each daily paper is a short timed paper of 8 questions worth 25 to 35 marks, and the papers mix topics. The Chemical Bonding course covers bonding from the start, and our covalent bonding guide explains shared pairs.

Read next

Chemistry · Bonding and structureShapes of molecules A-level Chemistry: VSEPR and anglesShapes of molecules for A-level Chemistry: electron pair repulsion, counting pairs, every shape from linear to octahedral with bond angles, and examples.