# Stereochemistry

Stereochemistry, a subdiscipline of chemistry, studies the spatial arrangement of atoms that form the structure of molecules and their manipulation. The study of stereochemistry focuses on the relationships between stereoisomers, which are defined as having the same molecular formula and sequence of bonded atoms (constitution) but differing in the geometric positioning of the atoms in space. For this reason, it is also known as 3D chemistry—the prefix "stereo-" means "three-dimensionality". Stereochemistry applies to all kinds of compounds and ions, organic and inorganic species alike. Stereochemistry affects biological, physical, and supramolecular chemistry.
Stereochemistry reactivity of the molecules in question (dynamic stereochemistry).

## History

In 1815, Jean-Baptiste Biot's observation of optical activity marked the beginning of organic stereochemistry history. He observed that organic molecules were able to rotate the plane of polarized light in a solution or in the gaseous phase. Despite Biot's discoveries, Louis Pasteur is commonly described as the first stereochemist, having observed in 1842 that salts of tartaric acid collected from wine production vessels could rotate the plane of polarized light, but that salts from other sources did not. This was the only physical property that differed between the two types of tartrate salts, which is due to optical isomerism. In 1874, Jacobus Henricus van 't Hoff and Joseph Le Bel explained optical activity in terms of the tetrahedral arrangement of the atoms bound to carbon. Kekulé explored tetrahedral models earlier, in 1862, but never published his work; Emanuele Paternò probably knew of these but was the first to draw and discuss three dimensional structures, such as of 1,2-dibromoethane in the Giornale di Scienze Naturali ed Economiche in 1869. The term "chiral" was introduced by Lord Kelvin in 1904. Arthur Robertson Cushny, a Scottish Pharmacologist, first provided a clear example in 1908 of a bioactivity difference between enantiomers of a chiral molecule viz. (-)-Adrenaline is two times more potent than the (±)- form as a vasoconstrictor and in 1926 laid the foundation for chiral pharmacology/stereo-pharmacology (biological relations of optically isomeric substances). Later in 1966, the Cahn-Ingold-Prelog nomenclature or Sequence rule was devised to assign absolute configuration to stereogenic/chiral center (R- and S- notation) and extended to be applied across olefinic bonds (E- and Z- notation).

## Significance

Cahn–Ingold–Prelog priority rules are part of a system for describing a molecule's stereochemistry. They rank the atoms around a stereocenter in a standard way, allowing unambiguous descriptions of their relative positions in the molecule. A Fischer projection is a simplified way to depict the stereochemistry around a stereocenter.

### Thalidomide example

Stereochemistry has important applications in the field of medicine, particularly pharmaceuticals. An often cited example of the importance of stereochemistry relates to the thalidomide disaster. Thalidomide is a pharmaceutical drug, first prepared in 1957 in Germany, prescribed for treating morning sickness in pregnant women. The drug was discovered to be teratogenic, causing serious genetic damage to early embryonic growth and development, leading to limb deformation in babies. Several proposed mechanisms of teratogenicity involve different biological functions for the (R)- and (S)-thalidomide enantiomers. In the human body, however, thalidomide undergoes racemization: even if only one of the two enantiomers is administered as a drug, the other enantiomer is produced as a result of metabolism. Accordingly, it is incorrect to state that one stereoisomer is safe while the other is teratogenic. Thalidomide is currently used for the treatment of other diseases, notably cancer and leprosy. Strict regulations and controls have been implemented to avoid its use by pregnant women and prevent developmental deformities. This disaster was a driving force behind requiring strict testing of drugs before making them available to the public.
In yet another example, the drug ibuprofen can exist as (R)- and (S)-isomers. Only the (S)-ibuprofen is active in reducing inflammation and pain.

## Types
### Atropisomers

Atropisomerism derives from the inability to rotate about a bond, such as due to steric hindrance between functional groups on two sp$^2$-hybridized carbon atoms. Usually atropisomers are chiral, and as such they are a form of axial chirality. Atropisomerism can be described as conformational isomerism

### Cis-Trans isomers

Cis-Trans isomers are often associated alkene double bonds.
    cis-pent-2-ene   trans-pent-2-ene
The more general E/Z nomenclature refers to the concept of cis/trans isomerism, and is especially useful for more complex compounds.
    (Z)-1-Bromo-1,2-dichloroethene   (E)-1-Bromo-1,2-dichloroethene

### Diastereomers

Diastereomers are non-superposable, non-identical stereoisomers. A common example of diastereomerism is when two compounds differ from each other by the (R)/(S) absolute configuration at some, but not all corresponding stereocenters. Epimers are diastereomers that differ at exactly one such position. cis/trans isomerism is another type of diastereomeric relationship.
* Example: The below pair can also be classified as epimers.

### Enantiomers

Enantiomers are pairs of non-superposable mirror images. Each member of the pair has a distinct R.

### Epimers

Epimers are a subcategory of diastereomers that differ in absolute configuration configurations at only one corresponding stereocenter. They are commonly found in sugar chemistry, where two sugars can differ by the configuration of a single carbon atom.
* Example: D-glucose and D-galactose are epimers, differing only at the C-4 position in their structure. (see sugar numbering)