In organic chemistry and biochemistry, a substituent is an atom or group of atoms which replaces one or more hydrogen atoms on the parent chain of a hydrocarbon, becoming a moiety of the resultant new molecule. The terms substituent and functional group, as well as other ones (e.g. side chain, pendant group) are used almost interchangeably to describe branches from a parent structure, though certain distinctions are made in the context of polymer chemistry. In polymers, side chains extend from a backbone structure. In proteins, side chains are attached to the alpha carbon atoms of the amino acid backbone.
The suffix -yl is used when naming organic compounds that contain a single bond replacing one hydrogen; -ylidene and -ylidyne are used with double bonds and triple bonds, respectively. In addition, when naming hydrocarbons that contain a substituent, positional numbers are used to indicate which carbon atom the substituent attaches to when such information is needed to distinguish between isomers. The polar effect exerted by a substituent is a combination of the inductive effect and the mesomeric effect. Additional steric effects result from the volume occupied by a substituent.
The phrases most-substituted and least-substituted are frequently used to describe molecules and predict their products. In this terminology, methane is used as a reference of comparison. Using methane as a reference, for each hydrogen atom that is replaced or "substituted" by something else, the molecule can be said to be more highly substituted. For example:
The suffix -yl is used in organic chemistry to form names of radicals, either separate species (called free radicals) or chemically bonded parts of molecules (called moieties). It can be traced back to the old name of methanol, "methylene" (from Ancient Greek: μέθυ méthu, 'wine' and ὕλη húlē, 'wood'), which became shortened to "methyl" in compound names, from which -yl was extracted. Several reforms of chemical nomenclature eventually generalized the use of the suffix to other organic substituents.
The use of the suffix is determined by the number of hydrogen atoms that the substituent replaces on a parent compound (and also, usually, on the substituent). According to the 1993 IUPAC recommendations:
The suffix -ylidine is encountered sporadically, and appears to be a variant spelling of "-ylidene"; it is not mentioned in the IUPAC guidelines.
For multiple bonds of the same type, which link the substituent to the parent group, the prefixes di-, tri-, tetra-, etc., are used: -diyl (two single bonds), -triyl (three single bonds), -tetrayl (four single bonds), -diylidene (two double bonds).
For multiple bonds of different types, multiple suffixes are added: -ylylidene (one single and one double), -ylylidyne (one single and one triple), -diylylidene (two single and one double).
The parent compound name can be altered in two ways:
Note that some popular terms such as "vinyl" (when used to mean "polyvinyl") represent only a portion of the full chemical name.
According to the above rules, a carbon atom in a molecule, considered as a substituent, has the following names depending on the number of hydrogens bound to it, and the type of bonds formed with the remainder of the molecule:
|methyl group or methanyl||one single bond to a non-hydrogen atom|
|methylene group or methanylidene or methylidene||one double bond|
|methylene bridge or methandiyl or methdiyl||two single bonds|
|≡CH||methanylidyne group or methylidyne||one triple bond|
|=CH−||methine group or methanylylidene or methylylidene||one single bond and one double bond|
|>CH−||methantriyl group or methtriyl||three single bonds|
|≡C−||methanylylidyne group or methylylidyne||one triple bond and one single bond|
|=C=||methandiylidene group or methdiylidene||two double bonds|
|>C=||methandiylylidene group or methdiylylidene||two single bonds and one double bond|
|>C<||methantetrayl group or methtetrayl||four single bonds|
In a chemical structural formula, an organic substituent such as methyl, ethyl, or aryl can be written as R (or R1, R2, etc.) It is a generic placeholder, the R derived from radical or rest, which may replace any portion of the formula as the author finds convenient. The first to use this symbol was Charles Frédéric Gerhardt in 1844.
One cheminformatics study identified 849,574 unique substituents up to 12 non-hydrogen atoms large and containing only carbon, hydrogen, nitrogen, oxygen, sulfur, phosphorus, selenium, and the halogens in a set of 3,043,941 molecules. Fifty substituents can be considered common as they are found in more than 1% of this set, and 438 are found in more than 0.1%. 64% of the substituents are found in only one molecule. The top 5 most common are the methyl, phenyl, chlorine, methoxy, and hydroxyl substituents. The total number of organic substituents in organic chemistry is estimated at 3.1 million, creating a total of 6.7×1023 molecules. An infinite number of substituents can be obtained simply by increasing carbon chain length. For instance, the substituents methyl (-CH3) and pentyl (-C5H11).