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A molecule, using the International Union of Pure and Applied Chemistry (IUPAC) convention, is an electrically neutral entity containing two or more chemical atoms. Its constituents form a bound unit through chemical bonds; merely drawing a boundary around neighboring particles does not make a molecule. The neutrality requirement concerns total electric charge, not the absence of internal charge separation: water is a polar molecule with zero total electric charge.^[ref]

One water molecule, ${\mathrm{H}}_2\mathrm{O}$, contains two hydrogen and one oxygen chemical atom. One molecular oxygen molecule, ${\mathrm{O}}_2$, contains two oxygen chemical atoms; a molecule need not contain different chemical elements. One carbon dioxide molecule, $\mathrm{C}{\mathrm{O}}_2$, contains one carbon and two oxygen chemical atoms. The molecular formula records these inventories, while molecular geometry describes their arrangement. Water and carbon dioxide are chemical compounds; molecular oxygen is a form of one chemical element.

Ordinary crystalline sodium chloride, $\mathrm{NaCl}$, contains an extended arrangement of sodium cations $\mathrm{N}{\mathrm{a}}^{+}$ and chlorine anions $\mathrm{C}{\mathrm{l}}^{-}$. Its formula unit specifies one of each for compositional accounting, without selecting a unique isolated pair. Bulk neutrality therefore does not imply a material consists of neutral molecules. This statement concerns the ionic crystal; the physical state and conditions matter when deciding what particles a chemical formula represents.^[ref]

A polyatomic ion is a charged bound group of chemical atoms, such as hydronium, ${\mathrm{H}}_3{\mathrm{O}}^{+}$. A molecular ion formed by removing an Electron from intact water, ${\mathrm{H}}_2{\mathrm{O}}^{\bullet +}$, retains the same atom inventory but has net electric charge $+e$. Neither satisfies the neutral-molecule definition. Distinguishing these entities makes molecular count and amount of substance and mass spectrometry interpretable: say whether the count is of chemical atoms, neutral molecules, ions, or formula units.

The useful surprise is that a molecule can be treated as one particle for motion and counting while retaining internal structure. Its molar mass connects a particle inventory to bulk mass; molecular rotation and molecular vibration reveal internal organization. The continuum approximation uses bulk fields in place of individual molecular positions and motions.