Structural isomer
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In
chemistry Chemistry is the scientific study of the properties and behavior of matter. It is a physical science within the natural sciences that studies the chemical elements that make up matter and chemical compound, compounds made of atoms, molecules a ...
, a structural isomer (or constitutional isomer in the
IUPAC The International Union of Pure and Applied Chemistry (IUPAC ) is an international federation of National Adhering Organizations working for the advancement of the chemical sciences, especially by developing nomenclature and terminology. It is ...
nomenclature) of a compound is a compound that contains the same number and type of atoms, but with a different connectivity (i.e. arrangement of bonds) between them. The term metamer was formerly used for the same concept. For example, butanol , methyl propyl ether , and
diethyl ether Diethyl ether, or simply ether, is an organic compound with the chemical formula , sometimes abbreviated as . It is a colourless, highly Volatility (chemistry), volatile, sweet-smelling ("ethereal odour"), extremely flammable liquid. It belongs ...
have the same molecular formula but are three distinct structural isomers. The concept applies also to polyatomic ions with the same total charge. A classical example is the cyanate ion and the fulminate ion . It is also extended to ionic compounds, so that (for example)
ammonium cyanate Ammonium cyanate is an inorganic compound with the formula . It is a colorless, solid salt. Structure and reactions The structure of this salt was verified by X-ray crystallography. The respective C–O and C–N distances are 1.174(8) and 1.192 ...
and
urea Urea, also called carbamide (because it is a diamide of carbonic acid), is an organic compound with chemical formula . This amide has two Amine, amino groups (–) joined by a carbonyl functional group (–C(=O)–). It is thus the simplest am ...
are considered structural isomers,William F. Bynum, E. Janet Browne, Roy Porter (2014)
''Dictionary of the History of Science''
page 218.
and so are methylammonium formate and ammonium acetate . Structural isomerism is the most radical type of
isomer In chemistry, isomers are molecules or polyatomic ions with identical molecular formula – that is, the same number of atoms of each element (chemistry), element – but distinct arrangements of atoms in space. ''Isomerism'' refers to the exi ...
ism. It is opposed to stereoisomerism, in which the atoms and bonding scheme are the same, but only the relative spatial arrangement of the atoms is different. Examples of the latter are the
enantiomer In chemistry, an enantiomer (Help:IPA/English, /ɪˈnænti.əmər, ɛ-, -oʊ-/ Help:Pronunciation respelling key, ''ih-NAN-tee-ə-mər''), also known as an optical isomer, antipode, or optical antipode, is one of a pair of molecular entities whi ...
s, whose molecules are mirror images of each other, and the ''cis'' and ''trans'' versions of 2-butene. Among the structural isomers, one can distinguish several classes including skeletal isomers, positional isomers (or regioisomers), functional isomers, tautomers, and structural isotopomers.


Skeletal isomerism

A skeletal isomer of a compound is a structural isomer that differs from it in the atoms and bonds that are considered to comprise the "skeleton" of the molecule. For
organic compound Some chemical authorities define an organic compound as a chemical compound that contains a carbon–hydrogen or carbon–carbon bond; others consider an organic compound to be any chemical compound that contains carbon. For example, carbon-co ...
s, such as alkanes, that usually means the carbon atoms and the bonds between them. For example, there are three skeletal isomers of
pentane Pentane is an organic compound with the chemical formula, formula C5H12—that is, an alkane with five carbon atoms. The term may refer to any of three structural isomerism, structural isomers, or to a mixture of them: in the IUPAC nomenclature, h ...
: ''n''-pentane (often called simply "pentane"), isopentane (2-methylbutane) and neopentane (dimethylpropane). If the skeleton is acyclic, as in the above example, one may use the term chain isomerism.


Position isomerism (regioisomerism)

Position isomers (also positional isomers or regioisomers) are structural isomers that can be viewed as differing only on the position of a
functional group In organic chemistry, a functional group is any substituent or moiety (chemistry), moiety in a molecule that causes the molecule's characteristic chemical reactions. The same functional group will undergo the same or similar chemical reactions r ...
,
substituent In organic chemistry, a substituent is one or a group of atoms that replaces (one or more) atoms, thereby becoming a moiety in the resultant (new) molecule. The suffix ''-yl'' is used when naming organic compounds that contain a single bond r ...
, or some other feature on the same "parent" structure. For example, replacing one of the 12 hydrogen atoms –H by a hydroxyl group –OH on the ''n''-pentane parent molecule can give any of three different position isomers: Another example of regioisomers are α-linolenic and γ-linolenic acids, both octadecatrienoic acids, each of which has three double bonds, but on different positions along the chain.


Functional isomerism

Functional isomers are structural isomers which have different
functional group In organic chemistry, a functional group is any substituent or moiety (chemistry), moiety in a molecule that causes the molecule's characteristic chemical reactions. The same functional group will undergo the same or similar chemical reactions r ...
s, resulting in significantly different chemical and physical properties. An example is the pair propanal H3C–CH2–C(=O)-H and
acetone Acetone (2-propanone or dimethyl ketone) is an organic compound with the chemical formula, formula . It is the simplest and smallest ketone (). It is a colorless, highly Volatile organic compound, volatile, and flammable liquid with a charact ...
H3C–C(=O)–CH3: the first has a –C(=O)H functional group, which makes it an aldehyde, whereas the second has a C–C(=O)–C group, that makes it a
ketone In organic chemistry, a ketone is an organic compound with the structure , where R and R' can be a variety of carbon-containing substituents. Ketones contain a carbonyl group (a carbon-oxygen double bond C=O). The simplest ketone is acetone ( ...
. Another example is the pair
ethanol Ethanol (also called ethyl alcohol, grain alcohol, drinking alcohol, or simply alcohol) is an organic compound with the chemical formula . It is an Alcohol (chemistry), alcohol, with its formula also written as , or EtOH, where Et is the ps ...
H3C–CH2–OH (an
alcohol Alcohol may refer to: Common uses * Alcohol (chemistry), a class of compounds * Ethanol, one of several alcohols, commonly known as alcohol in everyday life ** Alcohol (drug), intoxicant found in alcoholic beverages ** Alcoholic beverage, an alco ...
) and dimethyl ether H3C–O–CH2H (an ether). In contrast, 1-propanol and
2-propanol Isopropyl alcohol (IUPAC name propan-2-ol and also called isopropanol or 2-propanol) is a colorless, flammable, organic compound with a pungent alcoholic odor. Isopropyl alcohol, an organic polar molecule, is miscible in water, ethanol, an ...
are structural isomers, but not functional isomers, since they have the same significant functional group (the hydroxyl –OH) and are both alcohols. Besides the different chemistry, functional isomers typically have very different infrared spectra. The infrared spectrum is largely determined by the vibration modes of the molecule, and functional groups like hydroxyl and esters have very different vibration modes. Thus 1-propanol and 2-propanol have relatively similar infrared spectra because of the hydroxyl group, which are fairly different from that of methyl ethyl ether.


Structural isotopomers

In chemistry, one usually ignores distinctions between
isotope Isotopes are distinct nuclear species (or ''nuclides'') of the same chemical element. They have the same atomic number (number of protons in their Atomic nucleus, nuclei) and position in the periodic table (and hence belong to the same chemica ...
s of the same element. However, in some situations (for instance in Raman,
NMR Nuclear magnetic resonance (NMR) is a physical phenomenon in which atomic nucleus, nuclei in a strong constant magnetic field are disturbed by a weak oscillating magnetic field (in the near and far field, near field) and respond by producing ...
, or microwave spectroscopy) one may treat different isotopes of the same element as different elements. In the second case, two molecules with the same number of atoms of each isotope but distinct bonding schemes are said to be structural isotopomers. Thus, for example,
ethene Ethylene (IUPAC name: ethene) is a hydrocarbon which has the formula or . It is a colourless, flammable gas with a faint "sweet and musky" odour when pure. It is the simplest alkene (a hydrocarbon with carbon–carbon double bonds). Ethy ...
would have no structural isomers under the first interpretation; but replacing two of the hydrogen atoms (1H) by deuterium atoms (2H) may yield any of two structural isotopomers (1,1-dideuteroethene and 1,2-dideuteroethene), if both carbon atoms are the same isotope. If, in addition, the two carbons are different isotopes (say, 12C and 13C), there would be three distinct structural isotopomers, since 1-13C-1,1-dideuteroethene would be different from 1-13C-2,2-dideuteroethene. And, in both cases, the 1,2-dideutero structural isotopomer would occur as two stereoisotopomers, ''cis'' and ''trans''.


Structural equivalence and symmetry


Structural equivalence

Two molecules (including polyatomic ions) A and B have the same structure if each atom of A can be paired with an atom of B of the same element, in a one-to-one way, so that for every bond in A there is a bond in B, of the same type, between corresponding atoms; and vice versa. This requirement applies also to complex bonds that involve three or more atoms, such as the delocalized bonding in the benzene molecule and other aromatic compounds. Depending on the context, one may require that each atom be paired with an atom of the same isotope, not just of the same element. Two molecules then can be said to be structural isomers (or, if isotopes matter, structural isotopomers) if they have the same molecular formula but do not have the same structure.


Structural symmetry and equivalent atoms

Structural symmetry of a molecule can be defined mathematically as a
permutation In mathematics, a permutation of a set can mean one of two different things: * an arrangement of its members in a sequence or linear order, or * the act or process of changing the linear order of an ordered set. An example of the first mean ...
of the atoms that exchanges at least two atoms but does not change the molecule's structure. Two atoms then can be said to be structurally equivalent if there is a structural symmetry that takes one to the other. Thus, for example, all four hydrogen atoms of
methane Methane ( , ) is a chemical compound with the chemical formula (one carbon atom bonded to four hydrogen atoms). It is a group-14 hydride, the simplest alkane, and the main constituent of natural gas. The abundance of methane on Earth makes ...
are structurally equivalent, because any permutation of them will preserve all the bonds of the molecule. Likewise, all six hydrogens of
ethane Ethane ( , ) is a naturally occurring Organic compound, organic chemical compound with chemical formula . At standard temperature and pressure, ethane is a colorless, odorless gas. Like many hydrocarbons, ethane is List of purification methods ...
() are structurally equivalent to each other, as are the two carbons; because any hydrogen can be switched with any other, either by a permutation that swaps just those two atoms, or by a permutation that swaps the two carbons and each hydrogen in one methyl group with a different hydrogen on the other methyl. Either operation preserves the structure of the molecule. That is the case also for the hydrogen atoms in cyclopentane,
allene In organic chemistry, allenes are organic compounds in which one carbon atom has double bonds with each of its two adjacent carbon atoms (, where R is hydrogen, H or some organyl group). Allenes are classified as diene#Classes, cumulated dienes ...
, 2-butyne, hexamethylenetetramine, prismane,
cubane Cubane is a synthetic hydrocarbon compound with the Chemical formula, formula . It consists of eight carbon atoms arranged at the corners of a Cube (geometry), cube, with one hydrogen atom attached to each carbon atom. A solid crystalline substanc ...
, dodecahedrane, etc. On the other hand, the hydrogen atoms of
propane Propane () is a three-carbon chain alkane with the molecular formula . It is a gas at standard temperature and pressure, but becomes liquid when compressed for transportation and storage. A by-product of natural gas processing and petroleum ref ...
are not all structurally equivalent. The six hydrogens attached to the first and third carbons are equivalent, as in ethane, and the two attached to the middle carbon are equivalent to each other; but there is no equivalence between these two equivalence classes.


Symmetry and positional isomerism

Structural equivalences between atoms of a parent molecule reduce the number of positional isomers that can be obtained by replacing those atoms for a different element or group. Thus, for example, the structural equivalence between the six hydrogens of
ethane Ethane ( , ) is a naturally occurring Organic compound, organic chemical compound with chemical formula . At standard temperature and pressure, ethane is a colorless, odorless gas. Like many hydrocarbons, ethane is List of purification methods ...
means that there is just one structural isomer of
ethanol Ethanol (also called ethyl alcohol, grain alcohol, drinking alcohol, or simply alcohol) is an organic compound with the chemical formula . It is an Alcohol (chemistry), alcohol, with its formula also written as , or EtOH, where Et is the ps ...
, not 6. The eight hydrogens of
propane Propane () is a three-carbon chain alkane with the molecular formula . It is a gas at standard temperature and pressure, but becomes liquid when compressed for transportation and storage. A by-product of natural gas processing and petroleum ref ...
are partitioned into two structural equivalence classes (the six on the methyl groups, and the two on the central carbon); therefore there are only two positional isomers of propanol ( 1-propanol and
2-propanol Isopropyl alcohol (IUPAC name propan-2-ol and also called isopropanol or 2-propanol) is a colorless, flammable, organic compound with a pungent alcoholic odor. Isopropyl alcohol, an organic polar molecule, is miscible in water, ethanol, an ...
). Likewise there are only two positional isomers of butanol, and three of pentanol or hexanol.


Symmetry breaking by substitutions

Once a substitution is made on a parent molecule, its structural symmetry is usually reduced, meaning that atoms that were formerly equivalent may no longer be so. Thus substitution of two or more equivalent atoms by the same element may generate more than one positional isomer. The classical example is the derivatives of
benzene Benzene is an Organic compound, organic chemical compound with the Chemical formula#Molecular formula, molecular formula C6H6. The benzene molecule is composed of six carbon atoms joined in a planar hexagonal Ring (chemistry), ring with one hyd ...
. Its six hydrogens are all structurally equivalent, and so are the six carbons; because the structure is not changed if the atoms are permuted in ways that correspond to flipping the molecule over or rotating it by multiples of 60 degrees. Therefore, replacing any hydrogen by chlorine yields only one chlorobenzene. However, with that replacement, the atom permutations that moved that hydrogen are no longer valid. Only one permutation remains, that corresponds to flipping the molecule over while keeping the chlorine fixed. The five remaining hydrogens then fall into three different equivalence classes: the one opposite to the chlorine is a class by itself (called the ''para'' position), the two closest to the chlorine form another class (''ortho''), and the remaining two are the third class (''meta''). Thus a second substitution of hydrogen by chlorine can yield three positional isomers: 1,2- or ''ortho''-, 1,3- or ''meta''-, and 1,4- or ''para''-dichlorobenzene. For the same reason, there is only one
phenol Phenol (also known as carbolic acid, phenolic acid, or benzenol) is an aromatic organic compound with the molecular formula . It is a white crystalline solid that is volatile and can catch fire. The molecule consists of a phenyl group () ...
(hydroxybenzene), but three
benzenediol In organic chemistry, dihydroxybenzenes (benzenediols) are organic compounds in which two hydroxyl groups () are Electrophilic aromatic substitution, substituted onto a benzene ring (). These aromatic compounds are classed as phenols. There are t ...
s; and one
toluene Toluene (), also known as toluol (), is a substituted aromatic hydrocarbon with the chemical formula , often abbreviated as , where Ph stands for the phenyl group. It is a colorless, water Water is an inorganic compound with the c ...
(methylbenzene), but three toluols, and three xylenes. On the other hand, the second replacement (by the same substituent) may preserve or even increase the symmetry of the molecule, and thus may preserve or reduce the number of equivalence classes for the next replacement. Thus, the four remaining hydrogens in ''meta''-dichlorobenzene still fall into three classes, while those of ''ortho''- fall into two, and those of ''para''- are all equivalent again. Still, some of these 3 + 2 + 1 = 6 substitutions end up yielding the same structure, so there are only three structurally distinct trichlorobenzenes: 1,2,3-, 1,2,4-, and 1,3,5-. If the substituents at each step are different, there will usually be more structural isomers.
Xylenol Xylenols are organic compounds with the formula (CH3)2C6H3OH. They are volatile colorless solids or oily liquids. They are derivatives of phenol with two methyl groups at various positions relative to the hydroxyl group. Six isomers exist, of whi ...
, which is benzene with one hydroxyl substituent and two methyl substituents, has a total of 6 isomers:


Isomer enumeration and counting

Enumerating or counting structural isomers in general is a difficult problem, since one must take into account several bond types (including delocalized ones), cyclic structures, and structures that cannot possibly be realized due to valence or geometric constraints, and non-separable tautomers. For example, there are nine structural isomers with molecular formula C3H6O having different bond connectivities. Seven of them are air-stable at room temperature, and these are given in the table below. Two structural isomers are the enol tautomers of the carbonyl isomers (propionaldehyde and acetone), but these are not stable. CRC Handbook of Chemistry and Physics 65th ed.


See also

* Coordination isomerism * Descriptor (chemistry) * Stereoisomer * Metamerism (disambiguation)


References

online ver. 3.0.1 2019. Frederick A. Bettelheim, William H. Brown, Mary K. Campbell, Shawn O. Farrell (2009): ''Introduction to Organic and Biochemistry''. 752 pages. Peter P. Mumba (2018): ''Useful Principles in Chemistry for Agriculture and Nursing Students'', 2nd Edition. 281 pages. Jim Clark (2000)
"Structural isomerism"
in ''Chemguide'', n.l.
D. Brynn Hibbert, A.M. James (1987): ''Macmillan Dictionary of Chemistry''. page 263. Zdenek Slanina (1986):
Contemporary Theory of Chemical Isomerism
'. 254 pages.
H. Stephen Stoker (2015): ''General, Organic, and Biological Chemistry'', 7th edition. 1232 pages. Jean-Loup Faulon, Andreas Bender (2010): ''Handbook of Chemoinformatics Algorithms''. 454 pages. Barry G. Hinwood (1997): ''A Textbook of Science for the Health Professions''. 489 pages. {{isbn, 9780748733774
Isomerism es:Isomería estructural he:איזומרים מרחביים