Stereoisomers are compounds that have atoms in a different spatial, three-dimensional orientation, even though the atoms are connected in the same order and have the same molecular formula. The classic example of these is that of a mirror image between compounds, like a right and left hand. Compounds that differ in this manner are known as enantiomers. They can be differentiated in how they rotate polarized light. One compound can have different atoms that have stereoisomers, and these are known as chiral centers.
Differences in stereoisomerism can profoundly affect the biological properties of the compounds. For instance, there were enantiomers of the drug thalidomide that caused many birth defects in the mid-1900s. Only one of the enantiomers caused the birth defects. With most chiral compounds, only one form is found in nature.
Enantiomers are also known as optical isomers. Traditionally, compounds that were chemically-related to a known right-handed compound were known as D compounds. Their enantiomers were known as L compounds. This nomenclature is still applied to amino acids and carbohydrates. Most naturally-occurring amino acids are in the L form, while those of carbohydrates, such as the biologically-active form of glucose, are in the D form.
The nomenclature of these stereoisomers has been updated to negate the need for a reference compound. Each chiral location in a molecule is assigned an R or S, deriving from the Latin rectus for right, or sinister for left. There is a code for assigning priorities to the atoms attached to the chiral center.
There is another type of stereoisomer that is not a mirror image. These have double bonds with a substitution for hydrogen on either side of bond. These compounds are known as cis-trans isomers. This terminology also comes from Latin.
Imagine two carbon atoms connected by a double bond. There are two chlorine atoms at either end of the molecule, along with two hydrogen atoms. Both of the chlorine atoms can be on the same side of the double bond, or they can be on opposite sides. The atoms on the same side are cis, for on this side. If they are on the other side, they are trans, for across.
There is a newer, additional stereoisomer naming system due to some ambiguity. This system is based on German terminology, and uses the atomic number of the substituents to assign priority. If the atoms with the higher atomic number are on the same side, the molecule is Z for zusammen,or together. If they are on different sides, the compound is E for entgegen, or opposite. This is not always interchangeable with cis and trans.
It is worth noting that compounds can have the same molecular formula, but not be stereoisomers. This is the case for structural isomers, which have their atoms in differ orders. For instance, there are multiple forms of bromobutane. CH3CH2CH2CH2Br and CH2BrCH2CH2CH3 share the same atoms, but are not stereoisomers.