Functional isomers are structural isomers that have the same molecular formula (that is, the same number of atoms of the same elements), but the atoms are connected together in different ways so that the groupings are dissimilar. These groups of atoms are called functional groups, functionalities, or moieties.

Another way to say this is that two compounds with the same molecular formula, but different functional groups, are functional isomers.

For two molecules to be functional isomers, they must contain key groups of atoms arranged in particular ways. Some of the best examples come from organic chemistry. C₂H₆O is a molecular formula. Depending on how the atoms are arranged, it can represent two different compounds:

dimethyl ether CH₃-O-CH₃

ethanol CH₃CH₂-O-H

Dimethyl ether and ethanol are functional isomers. The first is an ether. The carbon chain-oxygen-carbon chain functionality is called an ether. The second is an alcohol. The carbon chain-oxygen-hydrogen functionality is called an alcohol.

If the functionalities stay the same, but their locations change, the structural isomers are not functional isomers. 1-Propanol and 2-propanol are stuctural isomers, but they are not functional isomers. Both of them are alcohols.

1-propanol CH₃CH₂CH₂OH

2-propanol CH₃CH(OH)CH₃

The functional group (carbon chain-O-H) is present in both of these compounds, but they are not the same.

While some chemists use the terms structural isomer and functional isomer interchangeably, not all structural isomers are functional isomers.

Some examples of functional groups are given below. R represents any carbon chain. When R appears more than once in a formula, it does not mean the two carbon chains are required to be identical.

alcohol ROH

aldehyde RC(O)H

amide R-C(O)-NH₂

amine NX3 (X = H or R, but not all H)

carboxylic acid RCO₂H

disulfide R-S-S-R

ester R-C(O)-OR

ether R-O-R

halide R-X (X = F, Cl, Br, or I)

ketone R-C(O)-R

imine X₂-C=NX (X = H or R)

mercaptan R-S-H

nitrile R-CN

phenyl C₆H₅-R

sulfonic acid R-SO₃H

Functional isomers are most often identified in chemistry using infrared spectroscopy. Infrared radiation corresponds to the energies associated primarily with molecular vibration. The alcohol functionality has a very distinct vibration called OH-stretch that is due to hydrogen bonding. All alcohols in liquid and solid form absorb infrared radiation at certain wavelengths.

Compounds with the same functional groups will all absorb certain wavelengths of infrared light because of the vibrations associated with those groups. In fact, the infrared spectrum is divided into two regions. The first part is called the functional group region. Dimethyl ether and ethanol would have dissimilar infrared spectra in the functional group region.

The second part of the infrared spectrum is called the fingerprint region; it is associated with types of motion allowed by the symmetry of the molecule and influenced by the bond energies. The fingerprint region is more specific to an individual compound. Even though 1-propanol and 2-propanol have similar infrared spectra in the functional group region, they differ in the fingerprint region.