Substituent Information

In organic chemistry and biochemistry, a substituent is an atom or group of atoms substituted in place of a hydrogen atom on the parent chain of a hydrocarbon. The terms substituent, side chain, group, branch, or pendant group are used almost interchangeably to describe branches from a parent structure,^[1] though certain distinctions are made in the context of polymer chemistry.^[2] 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. This word may also be confused with the word substitute such as a substitute teacher.

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 is attached to when such information is needed to distinguish between structural 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. For example:

• Markovnikov's rule predicts that the hydrogen adds to the carbon of the alkene functional group that has the greater number of hydrogen substituents.
• Zaitsev's rule predicts that the major reaction product is the alkene with the more highly substituted (more stable) double bond.

Nomenclature

The suffix -yl is used in Organic chemistry to form names of radicals, either separate or chemically bonded parts of molecules. It can be traced back to the word methylene (methy = "wine" + hȳlē = wood), evolving through the gradual regularization of chemical names to its current meaning.

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 1993 IUPAC guidelines:^[3]

• -yl means that one hydrogen is replaced.

• -ylidene means that two hydrogens are replaced by a double bond between parent and substituent. The term "-ylidine" is encountered sporadically, and is often used synonymously with -ylidene. The spelling "-ylidine" seems to be a rare usage in some contexts, but it appears notably in manufacturer's publications about Sunitinib ^[4] PubChem indexes 740110 results for "-ylidene", of which 14 use synonyms that replace the suffix freely with "-ylidine". An additional four compound entries contain "-ylidine" without listing "-ylidene" as a synonym. The word "-ylidine" is not in IUPAC guidelines.
• -ylidyne means that three hydrogens are replaced by a triple bond between parent and substituent.

• -di, -tri, -tetra indicate multiple bonds of the same type link the substituent and parent group (-diyl, -triyl, -tetrayl, -diylidine), and multiple suffixes are added to indicate different bond types (-ylylidine, -ylylidyne, -diylylidine)

The parent compound name can be altered in two different ways.

• For many common compounds the substituent is linked at one end (the 1 position), which is therefore not explicitly numbered in the formula. The substituent name is modified by stripping "-ane" (see Alkane) and adding the appropriate suffix. This is "recommended only for saturated acyclic and monocyclic hydrocarbon substituent groups and for the mononuclear parent hydrides of silicon, germanium, tin, lead, and boron". Thus, if there is a carboxylic acid called "X-ic acid", an alcohol ending "X-anol" (or "X-yl alcohol"), or an alkane called "X-ane", then "X-yl" typically denotes the same carbon chain lacking these groups but modified by attachment to some other parent molecule.

• The more general method omits only the terminal "e" of the substituent name, but requires explicit numbering of each -yl prefix, even at position 1 (except for -ylidyne, which as a triple bond must terminate the substituent carbon chain). Pentan-1-yl is an example of a name by this method, and is synonymous with Pentyl from the previous guideline.

Note that some popular terms such as "vinyl" represent only a portion of the full chemical name.

Structures

In a chemical structural formula, an organic substituent such as methyl, ethyl, aryl can be written as R (or R₁, R₂, etc.) This 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.

The symbol X is often used to denote electronegative substituents such as the halides. ^[5]

Number crunching

One cheminformatics study ^[1] identified 849,574 unique substituents up to 12 non-hydrogen atoms large and containing only C,H,N,O,S,P,Se and the halogens in a set of 3,043,941 molecules. Fifty common substituents are found in only 1% of this set, and 438 in 0.1%. 64% of the substituents are unique to just one molecule. The top 5 consists of the phenyl, chlorine, methoxy, hydroxyl, and ethyl substituent. The total number of organic substituents in organic chemistry is estimated at 3.1 million, creating a total of 6.7×10²³ molecules. Or, since you can increase the carbon chain length of a substituent an infinite amount, provided it is not long enough to become part of the parent carbon chain (which can also be infinite in length), you can have an infinite number of substituents, simply by increasing carbon chain length. For instance, the substituents methyl (-CH₃) and pentyl (C₅H₁₁)

See also

• Functional groups are a subset of substituents

External links

• Database of 21,000 substituents and 49,000 linkers extracted from bioactive molecules

References

1. ^ Cheminformatics Analysis of Organic Substituents: Identification of the Most Common Substituents, Calculation of Substituent Properties, and Automatic Identification of Drug-like Bioisosteric Groups Peter Ertl J. Chem. Inf. Comput. Sci.; 2003; 43(2) pp 374 – 380 Abstract Download reprint

1. ^ D.R. Bloch (2006). "Organic Chemistry Demystified". http://books.google.com/books?id=yVPcSIn5xjAC&pg=PT88&lpg=PT88.
2. ^ "PAC, 1996, 68, 2287. Glossary of basic terms in polymer science (IUPAC Recommendations 1996)". IUPAC Gold Book. doi:doi:10.1351/pac199668122287. http://goldbook.iupac.org/src_PAC1996682287.html. This distinguishes a pendant group as neither oligomeric nor polymeric, whereas a pendant chain must be oligomeric or polymeric.
3. ^ "R-2.5 Substituent Prefix Names Derived from Parent Hydrides". IUPAC. 1993. http://www.acdlabs.com/iupac/nomenclature/93/r93_271.htm.
4. ^ http://www.pfizerpro.com/product_info/sutent_pi_description.aspx
5. ^ Jensen, W. B. (2010). "Why Is “R” Used To Symbolize Hydrocarbon Substituents?". Journal of Chemical Education 87: 360–361. doi:10.1021/ed800139p.

6. wikipedia.org

Categories: Organic chemistry | Chemical nomenclature

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