Isomers were quite confusing for early chemists, before atomic theory was widely accepted, and people where thinking mostly in terms of proportions of equations, related: Section "Isomers suggest that atoms exist".
Exist because double bonds don't rotate freely. Have different properties of course, unlike enantiomer.
Key exmaple: d and L amino acids. Enantiomers have identical physico-chemical properties. But their biological roles can be very different, because an enzyme might only be able to act on one of them.

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TODO definition. Appears to be isomers
Example:
Molecules that are the same if you just look at "what atom is linked to what atom", they are only different if you consider the relative spacial positions of atoms.

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Molecule by Codex 0 Created 2026-10-13 Updated 2026-10-20
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, , contains two hydrogen and one oxygen chemical atom. One molecular oxygen molecule, , contains two oxygen chemical atoms; a molecule need not contain different chemical elements. One carbon dioxide molecule, , 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.
Figure 1.
Discrete neutral molecules versus an extended ionic crystal
. Original explanatory cartoons of water, molecular oxygen, carbon dioxide, and a patch of sodium chloride. The right panel uses a two-dimensional alternating arrangement to explain counting, not the full three-dimensional ionic crystal. Dotted neighbor guides are not localized covalent bonds; the box selects a count without isolating a molecule. Neither panel is a measured molecular image; positions, sizes, and connections are schematic. Details.
Ordinary crystalline sodium chloride, , contains an extended arrangement of sodium cations and chlorine anions . 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, . A molecular ion formed by removing an electron from intact water, , retains the same atom inventory but has net electric charge . 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.
A molecule is a group of two or more atoms that are bonded together by chemical forces. Molecules can consist of the same type of atoms, such as in diatomic molecules like oxygen (O₂) and nitrogen (N₂), or different types of atoms, such as in water (H₂O) and carbon dioxide (CO₂). Molecules can be classified into different categories: 1. **Elementary Molecules**: Formed from atoms of the same element (e.g.