The Chemistry Lab
Molecule Explorer.
Zoom into real molecules. Click any atom to see its bonds, its lone pairs and where the electrons really are.
Every cloud comes from the electrons.
Put it into practice 01
Click the most δ− atom
Click an atom in the 3D model to answer.
Preparing your molecule…
Atom colours follow the CPK convention. Clouds show where each pair of electrons is found; they are calculated, not drawn.
Click any atom in the model to begin.
Pick a molecule
Molecule library
Know your molecule
Molecule facts
Measured in the model
Bond lengths
Follow your curiosity
What happens if…
Understand this model
Each structure started as a PubChem 3D conformer and was re-optimised with density functional theory (B3LYP/def2-TZVP). Bond lengths agree with gas-phase experiment to within about 0.01 Å.
The coloured clouds are intrinsic bond orbitals: the calculation's own electron pairs, sorted into bonds and lone pairs. They are drawn where the electron wave has a set size, so their edges are a choice of cut-off, not a hard boundary. Two colours in one cloud show the two signs of the wave, not two different pairs.
GCSE diagrams draw the two lone pairs on oxygen as identical. The calculation separates them into one with more s character and one p-type pair. Both are valid ways to describe the same four electrons.
Charges are shared-electron estimates (δ+ and δ−) and are rounded; different methods give slightly different numbers but the same signs. The charge map shows the electrostatic potential on the molecule's electron-density surface: red is electron-rich, blue is electron-poor.
Learn more: PubChem ↗ · NIST CCCBDB experimental geometries ↗