Molecule 3D Viewer

Guess the atoms

A fun check: one atom is circled in gold and all labels are hidden. Use the colours to guess what it is, then pick from the list. The list only shows elements that are actually in this molecule.

How it works

Every molecule is a set of atoms joined by bonds, and a flat drawing hides how it really sits in space. This viewer takes the real 3D coordinates of a molecule from PubChem (the free chemistry database run by the US National Library of Medicine) and draws it as a ball-and-stick model: each atom is a coloured ball, each bond is a line, and you can drag to turn the molecule around and zoom in on any part of it.

Worked example — ethanol. Tap "Ethanol" above, then pick the result. The viewer shows 9 atoms: 2 carbons (dark grey), 6 hydrogens (pale grey) and 1 oxygen (red), with the formula C₂H₆O and a molecular weight of 46.07 g/mol. Count the lines and you will find 8 bonds, all single: the carbon–carbon bond, the carbon–oxygen bond, the oxygen–hydrogen bond, and five carbon–hydrogen bonds. A single bond is one pair of electrons shared between two atoms. Double bonds show up in red and triple bonds in blue, so a quick look tells you where the stronger bonds are.

Below the viewer you get the numbers that matter for a first look: molecular weight, SMILES (the one-line text code for the structure), XLogP (a rough measure of how greasy the molecule is), how many hydrogen-bond donors and acceptors it has, and how many bonds can rotate. The "Chemistry in easy words" box turns those numbers into plain sentences. And if you want to test yourself, the "Guess the atoms" game hides the labels, circles one atom in gold, and asks you to name it from its colour alone.

Structures and data come live from PubChem. If PubChem has no 3D shape for a compound, the details still show and the viewer says so honestly. For learning only.