What is a molecule? Atoms joined together, explained

A molecule is a group of two or more atoms held together by chemical bonds into a single, electrically neutral unit. A water molecule is two hydrogen atoms bonded to one oxygen atom; the oxygen you breathe is two oxygen atoms bonded to each other. A molecule is the smallest piece of a substance that still is that substance: split a water molecule and what is left is hydrogen and oxygen, not water.

In short

• A molecule is atoms bonded into one unit. Its formula, such as H₂O, says which atoms and how many.
• Molecules can be of one element (O₂) or of several (H₂O, which makes water a compound). Not every compound is made of molecules: table salt is a lattice of ions.
• Which atoms a molecule has matters, but so does their arrangement. The same atoms in a different shape can make a completely different substance.

How is a molecule different from an atom, an element, a compound and a mixture?

These five words are easy to mix up, because they describe overlapping things. An atom is a single particle of one element. A molecule is atoms bonded together. An element is a substance made of only one kind of atom, whether those atoms sit alone or in molecules. A compound is a substance made of two or more elements chemically bonded in fixed proportions. A mixture is different substances mingled without bonding to each other, so they can be separated again by physical means.

Example	Atom?	Molecule?	Element or compound?	What it is
Helium (He)	Yes	No, the atoms float alone	Element	A noble gas whose atoms don't bond
Oxygen gas (O₂)	Made of atoms	Yes, two O atoms	Element	Molecules of a single element
Water (H₂O)	Made of atoms	Yes, 2 H and 1 O	Compound	Molecules of a compound
Table salt (NaCl)	Made of ions	No discrete molecules	Compound	A crystal lattice of Na⁺ and Cl⁻ ions
Air	Made of atoms	Mostly molecules	Neither: a mixture	About 78% N₂, 21% O₂ and 0.9% argon, by volume

The salt row is the one that trips people up. Sodium chloride is a compound, but a grain of salt contains no salt molecules. Its sodium and chlorine atoms have swapped an electron to become charged ions, and every ion is held by all its neighbors at once in a repeating grid. The formula NaCl only gives the ratio, one sodium for each chlorine. Metals are similar: a lump of copper is a lattice of atoms sharing a sea of electrons, not a collection of molecules. Why atoms join in these different ways is the subject of the chemical bond note.

Air, the last row, shows the opposite case. Its nitrogen and oxygen molecules are not bonded to each other, so air can be cooled and separated into liquid nitrogen and liquid oxygen. Figures for Earth's atmosphere are from NASA's Earth fact sheet.

How do you read a chemical formula?

A molecular formula lists each element by its symbol, with a small number after it for how many atoms of that element the molecule contains. No number means one.

• H₂O: 2 hydrogen atoms, 1 oxygen atom. 3 atoms in all.
• CO₂: 1 carbon, 2 oxygen. 3 atoms.
• C₆H₁₂O₆, glucose: 6 carbon, 12 hydrogen, 6 oxygen. 24 atoms.

A number in front counts whole molecules: 3H₂O means three water molecules, so 6 hydrogen atoms and 3 oxygen atoms. That convention is how chemists balance the equation for a chemical reaction, making sure every atom on one side turns up on the other.

A worked example: how much does a molecule weigh, and how many are in a glass of water?

Each element has a standard atomic weight, the average mass of its atoms in atomic mass units, and the same number gives the mass in grams of one mole of those atoms. A mole is a fixed count: exactly 6.02214076 × 10²³ particles, a number called the Avogadro constant. To find a molecule's molar mass, add up its atoms.

For water, H₂O, using hydrogen at 1.008 and oxygen at 15.999:

1. Hydrogen: 2 × 1.008 = 2.016.
2. Oxygen: 1 × 15.999 = 15.999.
3. Molar mass: 2.016 + 15.999 = 18.015 grams per mole.

So 18 grams of water, a little more than a tablespoon, contains 6.02 × 10²³ molecules. A 250-gram glass of water holds 250 ÷ 18.015 = 13.9 moles, which is 13.9 × 6.02 × 10²³ = about 8.4 × 10²⁴ molecules. That is tens of trillions of times more molecules than there are stars in the Milky Way, which astronomers put at a few hundred billion.

For glucose, C₆H₁₂O₆, with carbon at 12.011:

1. Carbon: 6 × 12.011 = 72.066.
2. Hydrogen: 12 × 1.008 = 12.096.
3. Oxygen: 6 × 15.999 = 95.994.
4. Molar mass: 180.156 grams per mole, which matches the value of about 180.16 g/mol listed by PubChem.

A glucose molecule is ten times heavier than a water molecule, so a gram of sugar dissolved in water contains far fewer sugar molecules than a gram of water contains water molecules. Chemists use molar mass all the time to turn grams, which they can weigh, into numbers of molecules, which is what reactions actually count.

Why does a molecule's shape matter?

Two molecules can contain exactly the same atoms and still be different substances, because the atoms are joined in a different order. Ethanol, the alcohol in drinks, and dimethyl ether are both C₂H₆O. In ethanol the oxygen sits at one end with a hydrogen attached; in dimethyl ether it sits between the two carbons. Ethanol is a liquid that boils at 78 °C and mixes with water; dimethyl ether is a gas at room temperature, boiling at about −24 °C. Molecules like these, same formula, different structure, are called isomers.

Shape matters even when the connections are the same. Water is bent, with its two hydrogens at an angle of about 104.5°, while carbon dioxide is a straight line. Because of the bend, a water molecule has a slightly negative end and a slightly positive end, so water molecules cling to each other. That is why water is liquid at room temperature while carbon dioxide, a heavier molecule, is a gas. In biology, shape is nearly everything: an enzyme or a drug works by fitting another molecule the way a key fits a lock.

How big can a molecule get?

Most everyday molecules are tiny: a water molecule is about 0.3 nanometers across. But there is no upper limit to how many atoms can bond together. A protein may contain thousands of atoms folded into a precise shape. DNA is one of the largest molecules known: the DNA in human chromosome 1 is a single molecule about 249 million base pairs long, which stretched out would be roughly 8.5 centimeters. Plastics are long chains, called polymers, of the same small unit repeated many thousands of times.

How do scientists know molecules are real?

For most of the 1800s, many chemists used atoms and molecules as a bookkeeping device without being sure they existed. The decisive evidence came from Brownian motion, the jittery dance of pollen grains and other tiny specks in water. In 1905 Albert Einstein showed that the motion could be explained by water molecules constantly knocking into the specks, and predicted how far a speck should wander. In 1908 Jean Perrin measured it, matched the prediction, and from it estimated the Avogadro constant. Perrin won the 1926 Nobel Prize in Physics for work on what the Nobel committee called the discontinuous structure of matter.

Molecules are where atoms become substances, and where chemistry starts. Making and breaking the bonds that hold them together moves energy in or out, which is what powers a flame, a battery and every living cell.

Check yourself

• Without looking back, explain why water is a molecule and a compound, oxygen gas is a molecule but not a compound, and table salt is a compound but not made of molecules.
• How would you work out how many molecules are in 36 grams of water?
• How can ethanol and dimethyl ether have the same formula and still be different substances?

Sources

• Molecule — Wikipedia
• Glucose — PubChem, U.S. National Library of Medicine
• Water — PubChem, U.S. National Library of Medicine
• Avogadro constant — NIST, CODATA 2022
• Earth fact sheet — NASA Goddard Space Flight Center
• Jean Baptiste Perrin, Nobel Prize in Physics 1926 — Nobel Prize Outreach