Substituent
Encyclopedia
- For other meanings see substitutionSubstitutionSubstitution may refer to:- Sciences :* Substitution , a syntactic transformation on strings of symbols of a formal language* Substitution of variables* Substitution cipher, a method of encryption...
.
In organic chemistry
Organic chemistry
Organic chemistry is a subdiscipline within chemistry involving the scientific study of the structure, properties, composition, reactions, and preparation of carbon-based compounds, hydrocarbons, and their derivatives...
and biochemistry
Biochemistry
Biochemistry, sometimes called biological chemistry, is the study of chemical processes in living organisms, including, but not limited to, living matter. Biochemistry governs all living organisms and living processes...
, a substituent is an atom or group of atoms substituted in place of a hydrogen
Hydrogen
Hydrogen is the chemical element with atomic number 1. It is represented by the symbol H. With an average atomic weight of , hydrogen is the lightest and most abundant chemical element, constituting roughly 75% of the Universe's chemical elemental mass. Stars in the main sequence are mainly...
atom on the parent chain of a hydrocarbon
Hydrocarbon
In organic chemistry, a hydrocarbon is an organic compound consisting entirely of hydrogen and carbon. Hydrocarbons from which one hydrogen atom has been removed are functional groups, called hydrocarbyls....
. The terms substituent, side-chain, group, branch, or pendant group
Pendant group
A pendant group or side group is a group of molecules attached to a backbone chain of a long molecule. Usually, this molecule would be a polymer...
are used almost interchangeably to describe branches from a parent structure, though certain distinctions are made in the context of polymer
Polymer
A polymer is a large molecule composed of repeating structural units. These subunits are typically connected by covalent chemical bonds...
chemistry. In polymers, side chains extend from a backbone structure. In protein
Protein
Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...
s, side chains are attached to the alpha carbon
Alpha carbon
The alpha carbon in organic chemistry refers to the first carbon that attaches to a functional group . By extension, the second carbon is the beta carbon, and so on....
atoms of the amino acid
Amino acid
Amino acids are molecules containing an amine group, a carboxylic acid group and a side-chain that varies between different amino acids. The key elements of an amino acid are carbon, hydrogen, oxygen, and nitrogen...
backbone.
The suffix yl is used when naming organic compound
Organic compound
An organic compound is any member of a large class of gaseous, liquid, or solid chemical compounds whose molecules contain carbon. For historical reasons discussed below, a few types of carbon-containing compounds such as carbides, carbonates, simple oxides of carbon, and cyanides, as well as the...
s that contain a single bond replacing one hydrogen; -ylidene and -ylidyne are used with double bond
Double bond
A double bond in chemistry is a chemical bond between two chemical elements involving four bonding electrons instead of the usual two. The most common double bond, that between two carbon atoms, can be found in alkenes. Many types of double bonds between two different elements exist, for example in...
s and triple bond
Triple bond
A triple bond in chemistry is a chemical bond between two chemical elements involving six bonding electrons instead of the usual two in a covalent single bond. The most common triple bond, that between two carbon atoms, can be found in alkynes. Other functional groups containing a triple bond are...
s, 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 isomer
Isomer
In chemistry, isomers are compounds with the same molecular formula but different structural formulas. Isomers do not necessarily share similar properties, unless they also have the same functional groups. There are many different classes of isomers, like stereoisomers, enantiomers, geometrical...
s. The polar effect
Polar effect
The Polar effect or electronic effect in chemistry is the effect exerted by a substituent on modifying electrostatic forces operating on a nearby reaction center...
exerted by a substituent is a combination of the inductive effect
Inductive effect
In chemistry and physics, the inductive effect is an experimentally observable effect of the transmission of charge through a chain of atoms in a molecule by electrostatic induction...
and the mesomeric effect
Mesomeric effect
The mesomeric effect or resonance effect in chemistry is a property of substituents or functional groups in a chemical compound. The effect is used in a qualitative way and describes the electron withdrawing or releasing properties of substituents based on relevant resonance structures and is...
. Additional Steric effects
Steric effects
Steric effects arise from the fact that each atom within a molecule occupies a certain amount of space. If atoms are brought too close together, there is an associated cost in energy due to overlapping electron clouds , and this may affect the molecule's preferred shape and reactivity.-Steric...
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 ruleMarkovnikov's ruleIn organic chemistry, Markovnikov's rule or Markownikoff's rule is an observation based on Zaitsev's rule. It was formulated by the Russian chemist Vladimir Vasilevich Markovnikov in 1870....
predicts that the hydrogen adds to the carbon of the alkene functional group that has the greater number of hydrogen substituents. - Zaitsev's ruleZaitsev's ruleIn chemistry, Zaitsev's rule, Saytzeff's rule or Saytsev's rule named after Alexander Mikhailovich Zaitsev is a rule that states that if more than one alkene can be formed during dehalogenation by an elimination reaction, the more stable alkene is the major product...
predicts that the major reaction product is the alkene with the more highly substituted (more stable) double bond.
Nomenclature
The suffixAffix
An affix is a morpheme that is attached to a word stem to form a new word. Affixes may be derivational, like English -ness and pre-, or inflectional, like English plural -s and past tense -ed. They are bound morphemes by definition; prefixes and suffixes may be separable affixes...
yl is used in Organic chemistry
Organic chemistry
Organic chemistry is a subdiscipline within chemistry involving the scientific study of the structure, properties, composition, reactions, and preparation of carbon-based compounds, hydrocarbons, and their derivatives...
to form names of radical
Radical (chemistry)
Radicals are atoms, molecules, or ions with unpaired electrons on an open shell configuration. Free radicals may have positive, negative, or zero charge...
s, either separate or chemically bonded parts of molecules. It can be traced back to the word methylene
Methylene
Methylene is a chemical species in which a carbon atom is bonded to two hydrogen atoms. Three different possibilities present themselves:* the -CH2- substituent group: e.g., dichloromethane ....
(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:
- -yl means that one hydrogen is replaced.
- -ylidene means that two hydrogens are replaced by a double bondDouble bondA double bond in chemistry is a chemical bond between two chemical elements involving four bonding electrons instead of the usual two. The most common double bond, that between two carbon atoms, can be found in alkenes. Many types of double bonds between two different elements exist, for example in...
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 in manufacturer's publications about SunitinibSunitinibSunitinib is an oral, small-molecule, multi-targeted receptor tyrosine kinase inhibitor that was approved by the FDA for the treatment of renal cell carcinoma and imatinib-resistant gastrointestinal stromal tumor on January 26, 2006...
PubChemPubChemPubChem is a database of chemical molecules and their activities against biological assays. The system is maintained by the National Center for Biotechnology Information , a component of the National Library of Medicine, which is part of the United States National Institutes of Health . PubChem can...
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 bondTriple bondA triple bond in chemistry is a chemical bond between two chemical elements involving six bonding electrons instead of the usual two in a covalent single bond. The most common triple bond, that between two carbon atoms, can be found in alkynes. Other functional groups containing a triple bond are...
between parent and substituent.
- 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 bond 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 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 AlkaneAlkaneAlkanes are chemical compounds that consist only of hydrogen and carbon atoms and are bonded exclusively by single bonds without any cycles...
) 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 acidCarboxylic acidCarboxylic acids are organic acids characterized by the presence of at least one carboxyl group. The general formula of a carboxylic acid is R-COOH, where R is some monovalent functional group...
called "X-ic acid", an alcoholAlcoholIn chemistry, an alcohol is an organic compound in which the hydroxy functional group is bound to a carbon atom. In particular, this carbon center should be saturated, having single bonds to three other atoms....
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 bondTriple bondA triple bond in chemistry is a chemical bond between two chemical elements involving six bonding electrons instead of the usual two in a covalent single bond. The most common triple bond, that between two carbon atoms, can be found in alkynes. Other functional groups containing a triple bond are...
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
Vinyl
A vinyl compound is any organic compound that contains a vinyl group ,which are derivatives of ethene, CH2=CH2, with one hydrogen atom replaced with some other group...
" (when used to mean "polyvinyl
Polyvinyl
Polyvinyl is a group of polymers derived from vinyl monomers.Polyvinyl may also refer to:* Polyvinyl chloride* Polyvinyl acetate* Polyvinyl alcohol* Polyvinyl Record Co., an independent record label...
") represent only a portion of the full chemical name.
Structures
In a chemical structural formulaStructural formula
The structural formula of a chemical compound is a graphical representation of the molecular structure, showing how the atoms are arranged. The chemical bonding within the molecule is also shown, either explicitly or implicitly...
, an organic substituent such as methyl, ethyl
Ethyl group
In chemistry, an ethyl group is an alkyl substituent derived from ethane . It has the formula -C2H5 and is very often abbreviated -Et.Ethylation is the formation of a compound by introduction of the ethyl functional group, C2H5....
, or aryl
Aryl
In the context of organic molecules, aryl refers to any functional group or substituent derived from an aromatic ring, be it phenyl, naphthyl, thienyl, indolyl, etc....
can be written as R (or R1, R2, etc.) This is a generic placeholder, the R derived from radical
Radical (chemistry)
Radicals are atoms, molecules, or ions with unpaired electrons on an open shell configuration. Free radicals may have positive, negative, or zero charge...
or rest
Rest
Rest may refer to:* Leisure* Human relaxation* SleepRest may also refer to:* Rest , a pause in a piece of music* Rest , the relation between two observers* Rest , a 2008 album by Gregor Samsa...
, which may replace any portion of the formula as the author finds convenient. The first to use this symbol was Charles Frédéric Gerhardt
Charles Frédéric Gerhardt
Charles Frédéric Gerhardt was a French chemist.-Biography:He was born in Strasbourg, where he attended the gymnasium. He then studied at the Karlsruhe Institute of Technology, where Friedrich Walchner's lectures first attracted his interest to chemistry...
in 1844.
The symbol X is often used to denote electronegative substituents such as the halides.
Number crunching
One cheminformaticsCheminformatics
Cheminformatics is the use of computer and informational techniques, applied to a range of problems in the field of chemistry. These in silico techniques are used in pharmaceutical companies in the process of drug discovery...
study 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
Chlorine
Chlorine is the chemical element with atomic number 17 and symbol Cl. It is the second lightest halogen, found in the periodic table in group 17. The element forms diatomic molecules under standard conditions, called dichlorine...
, methoxy
Methoxy
In chemistry , methoxy refers to the functional group consisting of a methyl group bound to oxygen. This alkoxy group has the formula O–CH3.The word is used in organic nomenclature usually to describe an ether...
, hydroxyl
Hydroxyl
A hydroxyl is a chemical group containing an oxygen atom covalently bonded with a hydrogen atom. In inorganic chemistry, the hydroxyl group is known as the hydroxide ion, and scientists and reference works generally use these different terms though they refer to the same chemical structure in...
, and ethyl
Ethyl group
In chemistry, an ethyl group is an alkyl substituent derived from ethane . It has the formula -C2H5 and is very often abbreviated -Et.Ethylation is the formation of a compound by introduction of the ethyl functional group, C2H5....
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 the carbon chain length of a substituent can be increased by an infinite amount, provided it is not long enough to become part of the parent carbon chain (which can also be infinite in length), an infinite number of substituents can be obtained simply by increasing carbon chain length. For instance, the substituents methyl (-CH3) and pentyl (C5H11)