As defined in an earlier introductory section, isomers are different compounds that have the same molecular formula. When the group of atoms that make up the molecules of different isomers are bonded together in fundamentally different ways, we refer to such compounds as constitutional isomers.

For example, in the case of the C₄H₈ hydrocarbons, most of the isomers are constitutional. Shorthand structures for four of these isomers are shown below with their IUPAC names.

Note that the twelve atoms that make up these isomers are connected or bonded in very different ways. As is true for all constitutional isomers, each different compound has a different IUPAC name. Furthermore, the molecular formula provides information about some of the structural features that must be present in the isomers.

Since the formula C₄H₈ has two fewer hydrogens than the four-carbon alkane butane (C₄H₁₀), all the isomers having this composition must incorporate either a ring or a double bond. A fifth possible isomer of formula C₄H₈ is CH₃CH=CHCH₃.

This would be named 2-butene according to the IUPAC rules; however, a close inspection of this molecule indicates it has two possible structures. These isomers may be isolated as distinct compounds, having characteristic and different properties. They are shown here with the designations cis and trans.

The bonding patterns of the atoms in these two isomers are essentially equivalent, the only difference being the relative orientation or configuration of the two methyl groups (and the two associated hydrogen atoms) about the double bond.

In the cis isomer the methyl groups are on the same side; whereas they are on opposite sides in the trans isomer. Isomers that differ only in the spatial orientation of their component atoms are called stereoisomers.

Stereoisomers always require that an additional nomenclature prefix be added to the IUPAC name in order to indicate their spatial orientation, for example, cis (Latin, meaning on this side) and trans (Latin, meaning across) in the 2-butene case.

As chemists studied organic compounds isolated from plants and animals, a new and subtle type of configurational stereoisomerism was discovered.

For example, lactic acid ( a C₃H₆O₃ carboxylic acid) was found in sour milk as well as in the blood and muscle fluids of animals. The physical properties of this simple compound were identical, regardless of the source (m.p, 53 ºC & pK_a 3.80), but there was evidence that the physiological behavior of the compound from the two sources was not the same.

Another natural product, the fragrant C₁₀H₁₄O ketone carvone, was isolated from both spearmint and caraway. Again, all the physical properties of carvone from these two sources seemed to be identical (b.p. 230 ºC), but the odors of the two carvones were different and reflected their source.

Other examples of this kind were encountered, and suspicions of a subtle kind of stereoisomerism were confirmed by the different interaction these compounds displayed with plane polarized light.

We now know that this configurational stereoisomerism is due to different right and left-handed forms that certain structures may adopt, in much the same way that a screw may have right or left-handed threads but the same overall size and shape. Isomeric pairs of this kind are termed enantiomers (from the Greek enantion meaning opposite).