Isomers are chemical compounds that have the same molecular formulas — meaning that they are composed of the same number of the same types of atoms — but have different structures or arrangements in space. For example, pentane is an organic compound composed of five carbon atoms and 12 hydrogen atoms. Two isomers of pentane include unbranched pentane, in which the carbons are arranged in a linear chain, and isopentane or methylbutane, in which four carbons are arranged in a linear chain while the fifth branches off from one of the interior carbon atoms. Both of these have the same molecular formulas, but the actual arrangements of their atoms are different. Isomers are important because compounds with different structures, even if they contain the same atoms, can have drastically different chemical properties.
Compounds with the same molecular formulas may differ structurally in two ways. First, structural isomers differ in the actual structural arrangements of atoms. The functional groups that make up the compounds are joined together in different ways and in different arrangements. Stereoisomers, on the other hand, are arranged in the same way in terms of the position of functional groups but differ in their relative positions in space. Two molecules may, for instance, have the same atoms and the same structure but may also be non-overlapping mirror images of each other and would, therefore, be isomers.
Isomers are very important because different compounds, even if they have the same molecular formulas, can have different chemical properties. This is even true of stereoisomers, which are, superficially, nearly identical. One compound may, for instance, be an important active ingredient in a drug while its non-overlapping mirror image isomer may be utterly ineffective or even harmful. Compounds with different arrangements often react in drastically different ways with other atoms and compounds. They may differ in which chemicals they react with or in the rates at which they react with various chemicals.
Many chemical reactions produce a mix of different isomers — this is particularly true of stereoisomers — so chemists must often use various methods to isolate the particular isomer in which they are interested. Many different methods based on various chemical properties can be used to separate isomers. Some compounds with identical molecular formulas may, for instance, boil at different temperatures, so distillation can be used to separate them. Others react with different compounds, so chemical reactions can be used to remove one isomer while leaving the compound of interest unaltered.