Atoms in groups
Most of the matter around you is not made of single atoms but of molecules: small fixed groups of atoms held together by shared electrons. Water is two hydrogen atoms attached to one oxygen. The oxygen you breathe is two oxygen atoms locked together. Every molecule of a given substance has exactly the same atoms in exactly the same arrangement, and that arrangement is what makes the substance what it is.
The bond
Atoms join because their outer electrons are unfinished. Two hydrogen atoms, each with one electron, can share the pair between them so that both feel complete. That shared pair is a covalent bond, drawn in the scene as a stick. Sometimes atoms share two pairs, a double bond, or three, a triple bond. Oxygen molecules are held by a double bond; nitrogen by a triple, which is why nitrogen in the air is so reluctant to react with anything.
Try it: choose Oxygen, then Nitrogen, and count the sticks between the two atoms.
Shape is destiny
The atoms in a molecule settle into the shape that keeps their electron pairs as far apart as possible. Two things attached to a central atom sit in a straight line, so carbon dioxide is straight. Four sit at the corners of a tetrahedron, so methane is a little pyramid. Water has two hydrogens and two unshared electron pairs on its oxygen, and the four of them spread out into a tetrahedron too, which leaves the hydrogens bent at an angle of about 104 degrees.
That bend has consequences. Oxygen pulls the shared electrons toward itself, so the oxygen end of water is slightly negative and the hydrogen end slightly positive. In carbon dioxide the two pulls point in opposite directions and cancel; in bent water they do not. Slide to Space filling and the colours show it: water’s oxygen side turns red and its hydrogens blue, while carbon dioxide has a red end on each side of a blue middle, balanced. Water molecules therefore stick to each other and to charged things, which is why water dissolves salt, climbs up paper towels, and takes so much heat to boil.
Sticks or spheres
Chemists draw molecules two ways. Ball-and-stick shows which atoms are joined and at what angles, with the atoms shrunk so the bonds can be seen. Space-filling draws each atom at the size it actually takes up, and the molecule becomes a lumpy blob with no gaps and no visible bonds. The second is nearer the truth; the first is easier to read. The scene blends between them. At the space-filling end the usual element colours give way to a charge map, the way chemists colour a molecule’s surface: red where it is slightly negative, white where it is neutral, blue where it is slightly positive. Oxygen and nitrogen molecules stay white all over, because two identical atoms share their electrons evenly.
Molecules moving
A molecule is never still. Its bonds stretch and compress, and the whole thing tumbles and vibrates, harder as it gets hotter. Warm one enough and a bond can snap, freeing the atoms to find new partners. That is a chemical reaction, and everything from burning to digestion is atoms leaving one set of molecules to form another.