Stereoisomers are a type of isomer where the order of the atoms in the two molecules is the same but their arrangement in space is different.
To understand this we need to take a look at the ways that organic molecules can and cannot move. Again, usingthree-dimensional models is a great tool to visualize this and almost essential for most people to grasp these concepts clearly.
With cyclo-alkanes, we observe that a group placed on one side of a ring stays on that same side. Except in very large rings (13+ carbons) the carbons are not free to rotate all of the way around their axes. This means that a group that is axial will not move into an equatorial position, and vice versa.
Stereoisomerism is the arrangement of atoms in molecules whose connectivity remains the same but their arrangement in space is different in each isomer.
The two main types of stereoisomerism are:
- DiaStereomerism (including 'cis-trans isomerism')
- Optical Isomerism (also known as 'enantiomerism' and 'chirality')
Main article: Diastereomers
Cis/trans isomerism occurs when a double bond is present, because the pi bond involved prevents that bond from being "twisted" the same way that a single bond can be. A good example is 1,2-dichloroethene: C2H2Cl2. Consider the two examples below:
The two molecules shown above are cis-1,2-dichloroethene and trans-1,2-dichloroethene.
This is more specifically an example of diastereomerism. These two molecules are stereoisomers because the two carbon atoms cannot be rotated relative to each other, due to the rigidity caused by the pi bond between them. Therefore, they are not "superimposeable" - they are not identical, and cannot take each other's place. However, the isomers are not mirror images of one another, so they are not enantiomers; therefore they must be diastereomers.
Diastereomers usually have different chemical and physical properties and can exhibit dramatically different biological activity.
There are two forms of these isomers; the cis and trans versions. The form in which the substituent hydrogen atoms are on the same side of the bond that doesn't allow rotation is called cis; the form in which the hydrogens are on opposite sides of the bond is called trans. An example of a small hydrocarbon displaying cis-trans isomerism is 2-butene.
Alicyclic compounds can also display cis-trans isomerism. As an example of a geometric isomer due to a ring structure, consider 1,2-dichlorocyclohexane:
Main article: Chirality
Optical isomers are stereoisomers formed when asymmetric centers are present, for example, a carbon with four different groups bonded to it. Enantiomers are two optical isomers (i.e. isomers that are reflections of each other). Every stereocenter in one isomer has the opposite configuration in the other.
Compounds that are enantiomers of each other have the same physical properties, except for the direction in which they rotate polarized light and how they interact with different optical isomers of other compounds.
In nature, most biological compounds, such as amino acids, occur as single enantiomers. As a result, different enantiomers of a compound may have substantially different biological effects.
When a molecule has more than one source of asymmetry, two optical isomers may be neither perfect reflections of each other nor superimposeable: some but not all stereocenters are inverted. These molecules are diastereomers, not enantiomers. Diastereomers seldom have the same physical properties.
Optical isomerism is a form of isomerism (specifically stereoisomerism) where the two different isomers are the same in every way except being non-superposable  mirror images of each other. Optical isomers are known as chiral molecules (pronounced ki-rall) .