Bicyclic molecule

Nomenclature and terminology

Bridgehead atoms are the carbons that form three C-C bonds. The parent (that is, unsubstituted) bicyclic hydrocarbons have two bridgehead carbon atoms.

In spiro compounds, two rings share one single atom, the spiro atom, which is usually a quaternary carbon. An example of a spirocyclic compound is the photochromic switch spiropyran.

The naming of bicyclic molecules is described by IUPAC nomenclature. The root of the compound name depends on the total number of atoms in all rings together, possibly followed by a suffix denoting the functional group with the highest priority. Numbering of the carbon chain always begins at one bridgehead atom (where the rings meet) and follows the carbon chain along the longest path, to the next bridgehead atom. Then numbering is continued along the second longest path and so on. Fused and bridged bicyclic compounds get the prefix bicyclo, whereas spirocyclic compounds get the prefix spiro. In between the prefix and the suffix, a pair of brackets with numerals denotes the number of carbon atoms between each of the bridgehead atoms. These numbers are arranged in descending order and are separated by periods. For example, the carbon frame of norbornane contains a total of 7 atoms, hence the root name heptane. This molecule has two paths of 2 carbon atoms and a third path of 1 carbon atom between the two bridgehead carbons, so the brackets are filled in descending order: [2.2.1]. Addition of the prefix bicyclo gives the total name bicyclo[2.2.1]heptane.

The carbon frame of camphor also counts 7 atoms, but is substituted with a carbonyl. Numbering of the carbon frame starts at the bridgehead atom with the highest priority (methyl goes before proton), hence the bridgehead carbon in front gets number 1, the carbonyl gets number 2 and numbering continues along the carbon chain following the longest path, until the doubly substituted top carbon (number 7). Norbornane has two paths of 2 carbon atoms and one path of 1 carbon atom between the two bridgehead carbons, so the numbers within the brackets stay [2.2.1].

When naming simple fused bicyclic compounds, the same method as for bridged bicyclic compounds is applied, except the third path between the two bridgehead atoms now consists of zero atoms. Therefore, fused bicyclic compounds have a "0" included in the brackets. For example, decalin is named bicyclo[4.4.0]decane. The numbers are sometimes omitted in unambiguous cases. For example, bicyclo[1.1.0]butane is typically called simply bicyclobutane.

Heteroatom substitutions

The bicyclic structures emphasized apply to many compounds where CH₂ and CH site are replaced by other elements. CH₂ is often replaced by O, NH and NR, as well as S. CH is often replaced by N and P. The heterocyclic molecule DABCO has a total of 8 atoms in its bridged structure, hence the root name octane. The two bridgehead atoms are nitrogen instead of carbon atoms. Its official name is 1,4-diazabicyclo[2.2.2]octane.

Occurrence

Of the major classes of biomolecules, only the purines are bicyclic. Otherwise, bicyclic compounds are restricted to cofactors and secondary metabolites. Terpenes and alkaloids, which are known for their structural complexity, are often bicyclic or still more complex.