A descriptor is in chemical nomenclature a prefix placed before the systematic substance name, which describes the configuration or the stereochemistry of the molecule. Some listed descriptors are only of historical interest and should not be used in publications anymore as they do not correspond with the modern recommendations of the IUPAC. Stereodescriptors are often used in combination with locants to clearly identify a chemical structure unambiguously.
The descriptors, usually placed at the beginning of the systematic name, are not taken into account in the alphabetical sorting.
cis (left) and trans (right) configured double bound: maleic acid and fumaric acid
cis (left) and trans isomerism (right) in a ring system.
The descriptors cis (lat. on this side of) and trans (lat. over, beyond) are used in various contexts for the description of chemical configurations.
In organic structural chemistry, the configuration of a double bond can be described with cis and trans,
in case it has a simple substitution pattern with only two residues.
The position of two residues relative to one another at different points
in a ring system or a larger molecule can also be described with cis and trans if the structure’s configuration is rigid and does not allow simple inversion.
Violet leaf aldehyde, systematic name (E,Z)-nona-2,6-dienal, is a compound having one (E)- and one (Z)-configured double bond
The descriptors (E) (from German entgegen, opposite) and (Z)
(from German zusammen, together) are used to provide a distinct
description of the substitution pattern for alkenes, cumulenes or other
double bond systems such as oximes.
For the attribution of (E) or (Z) is based on the
relative position of the two substituents of highest priority are on
each side of the double bond, while the priority is based on the CIP
nomenclature. The (E)/(Z) nomenclature can be applied to
any double bond systems (including heteroatoms), but not to substituted
ring systems. The descriptors (E) and (Z) are always
capitalized, set italic, and surrounded by parentheses that are set as
normal just like additional locants or commas.
The abbreviation o- (short for ortho, from Greek orthós for upright, straight), m- (meta, Greek (roughly) for between) and p- (para, from Greek pará for adjoining, to the side) describe the three possible positional isomers of two substituents on a benzene ring. These are usually two independent single substituents, but in case of fused ring systems, ortho-fusing is also mentioned unless the substitution pattern is regarded in the name like in [2.2]paracyclophane. In the current systematic nomenclature, o-, m- and p- are often replaced by using locants (1,2-dimethylbenzene instead of o-xylene).
o-, m- and p- (written out ortho-, meta- and para-) are written in lowercase letters and italic.
exo (from Greek = outside) or endo (from Greek endon = inside)
denotes the relative configuration of bridged bicyclic compounds. The
position of a substituent in the main ring relative to the shortest
bridge is decisive for the assignment of exo or endo (according to IUPAC: the bridge with the highest locant digits in the bridged ring system). The substituent to be classified is attributed with the exo descriptor when facing the bridge. It is endo configured when facing away from the bridge. If two different substituents are located on the same C atom, the exo/endo assignment is based on the substituent with higher priority according to the CIP rules.
If a bridged bicyclic system carries a substituent at the shortest bridge, the exo or endo descriptor can not be used for its assignment. Such isomers are classified by the syn/anti notation. If the substituent to be assigned points towards the ring with the highest number of segments it is syn configured (from Greek syn = together). Otherwise it is attributed with the anti descriptor (Greek anti = against).
If both rings possess an equal number of segments the ring with the
most significant substituent according to the CIP rules is chosen.
The use of syn and anti to indicate the configuration of double bonds is nowadays obsolete, especially in case of aldoximes and aldehydes derived from hydrazones. Here, the compounds were designated as syn configured when the aldehyde H and the O (of the oxime) or the N (of the hydrazone) were cis aligned. These compounds are now described by the (E)/(Z) nomenclature. Aldoximes and hydrazones classified as syn are therefore by now described as (E) configurated.
When talking of diastereomers, syn and anti are used to describe groups on the same or opposite sites in zigzag prijection, see Diastereomer#Syn_/_anti
syn and anti are always written small and italic, locants (if used) are placed in front of the word and separated by hyphens.
fac, mer
The terms fac (from Latin facies) and mer (from meridonal)
can specify the arrangement of three identical ligands around the
central atom in octahedral complexes. Today, this nomenclature is
considered obsolete, but is still permissible. The prefix fac describes the situation when the three identical ligands occupy the three vertices of an octahedron triangular surface. In mer configuration the three ligands span a plane in which the central atom is located.
fac-[CoCl3(NH3)3]
mer-[CoCl3(NH3)3]
fac and mer are prefixed in small and italic to the complex name.
n, iso, neo, cyclo
The prefixes n (normal), iso (from Greek ísos = equal), neo (Greek néos = young, new) and cyclo (Greek kyklos = circle) are primarily used to describe the arrangement of atoms, usually of carbon atoms in carbon skeleton. n, iso and neo are no longer used in the systematic nomenclature, but still frequently in trivial names and in laboratory jargon.
The prefix n describes a straight-chain carbon skeleton without branches, whereas iso describes a branched skeleton, without specifying any further details. More generally, iso is a compound which is isomeric to the n compound (a compound in which individual atoms or atomic groups are rearranged)
neo is a non-specific term for "new", usually synthetically produced substances or isomers of long-known n compounds or natural substances (for example neomenthol derived from menthol or neoabietic acid from abietic acid). According to IUPAC neo is only recommended in neopentane or the neopentyl residue.
cyclo is a frequently used prefix for all cyclic and heterocyclic compounds. In many proper names of chemical substances cyclo is not used as a prefix but directly part of the name, for example in cyclohexane or cyclooctatetraene.
While n, iso and neo are written in small and italic letters, for cyclo this is only the case in inorganic compounds.
In organic compounds, "cyclo" is frequently used as a name component,
not separated by a hyphen and also considered in alphabetical sorting.
The prefixes sec and tert are used to indicate the
substituent environment in a molecule. Thus, not the exact position of
the substituent is described but only the substitution pattern of the
adjacent atom (usually a carbon atom). In n-butanol, the OH group is attached to a primary carbon atom, in sec-butanol to a secondary carbon and in tert-butanol to a tertiary carbon atom.
The terms sec and tert are considered obsolete and should only be used for unsubstituted sec-butoxy, sec-butyl or tert-butyl groups. There are various spellings such as "sec-butyl", "s-butyl", "sBu" or "bus" which are also considered obsolete.
The prefix "spiro" followed by a Von-Baeyer descriptor describes in
the nomenclature of organic compounds ring systems linked by only one
common atom, the spiro atom. If several spiro atoms are present in the
molecule, the prefix "spiro" is provided with a prefix ("dispiro",
"trispiro", etc.) corresponding to the number of spiro atoms. Typically
"spiro" is set as normal.
catena
The term catena is used in the inorganic nomenclature to describe linear, chain-like polymers from identical polyatomic units. One example is are catenatriphosphazenes. Related compounds in organic chemistry are the catenanes.
Configuration
assignment of the stereo center "X", the substituents are decreasingly
prioritized from "A" → "D" according to the CIP rules.
The stereochemical descriptors (R) (from Latin rectus = right) and (S) (from lat. sinister = left) are used to describe the absolute configuration of a stereocenter (usually a chiral carbon atom).
For this purpose, all substituents at the stereocentre are prioritized
according to the CIP rules and the substituent with the lowest priority
("D") is pointed backwards (away from the viewing direction). The
stereocenter is (S) configured if the remaining substituents describe a circle descending in priority ("A" → "B" → "C") to the left. The (R) configuration is assigned to the stereocenter if the direction of rotation is directed to the right.
If one molecule contains several stereocenters, a locant must be placed before the descriptor (for example, in (1R, 2S)-2-amino-1-phenylpropan-1-ol, the systematic designation of norephedrine). If all stereocenters are configured the same, the naming of the locants can be omitted in favor of an "all-R" or "(all-S)" spelling.
Typographically, (R) and (S) are placed in
uppercase and italic; the frequently preceding locants, the enclosing
round brackets and the commas, on the other hand, as normal.
The descriptors (r) and (s) are used to describe the absolute configuration of pseudoasymmetric (pseudochiral) centers.
Pseudoasymmetry occurs when four different substituents are attached to
one carbon atom, two of which differ only by their absolute
stereochemical configuration. Examples of such are meso compounds such the tropane alkaloids; the parent compound is tropine, whose systematic name is (1R, 3r, 5S)-8-methyl-8-azabicyclo[3.2.1]octane-3-ol. In this structure, the C3 atom—the carbon to which the hydroxyl group
is attached—is pseudo-asymmetric; therefore, the stereochemical
descriptor in the systematic name is written in lower-case italics
rather than upper-case italics as for regular chiral atoms.
D-glucose in the Fischer projection. Red: Group with highest priority, Blue: For determination of D-/L- relevant group, Violet: Group with achiral carbon atom
The stereoscriptors D- (from Latin dexter, right) and L- (Latin laevus, left) are used to describe the configuration of α-amino acids and sugars.
First, the three-dimensional molecule must be transformed in a defined
notation as a two-dimensional image ("Fischer projection").
For this, the C atom with the highest priority according to the normal
nomenclature rules is arranged on top and the further carbon chain is
arranged vertically underneath. The chiral C-atom most remote from the
group with the highest priority is used for the assignment of D- or L-. If the residue located on this carbon atom (usually an OH group) points to the left, the molecule originates from the L-series. If the residue points to the right, the descriptor D- is used.
The descriptors D- and L- are written as small capitals and separated by a hyphen from the rest of the name.
d-, l-
Sometimes the small capital D- and L- stereodescriptors mentioned above are mistakenly confused with the obsolete italic d- and l- stereodescriptors, which are equivalent with dextrorotatory and levorotatoryoptical rotation, i.e. (+)- and (−)- stereodescriptors, respectively.
Isomers do not necessarily share similar chemical or physical properties. Two main forms of isomerism are structural or constitutional isomerism, in which bonds between the atoms differ; and stereoisomerism or spatial isomerism, in which the bonds are the same but the relative positions of the atoms differ.
Isomeric relationships form a hierarchy. Two chemicals might be
the same constitutional isomer, but upon deeper analysis be
stereoisomers of each other. Two molecules that are the same
stereoisomer as each other might be in different conformational forms or
be different isotopologues. The depth of analysis depends on the field
of study or the chemical and physical properties of interest.
The English word "isomer" (/ˈaɪsəmər/) is a back-formation from "isomeric", which was borrowed through Germanisomerisch from Swedishisomerisk; which in turn was coined from Greek ἰσόμερoς isómeros, with roots isos = "equal", méros = "part".
Structural isomers have the same number of atoms of each element (hence the same molecular formula), but the atoms are connected in distinct ways.
Example: C 3H 8O
For example, there are three distinct compounds with the molecular formula :
The first two isomers shown of are propanols, that is, alcohols derived from propane. Both have a chain of three carbon atoms connected by single bonds, with the remaining carbon valences being filled by seven hydrogen atoms and by a hydroxyl group comprising the oxygen
atom bound to a hydrogen atom. These two isomers differ on which carbon
the hydroxyl is bound to: either to an extremity of the carbon chain propan-1-ol (1-propanol, n-propyl alcohol, n-propanol; I) or to the middle carbon propan-2-ol (2-propanol, isopropyl alcohol, isopropanol; II). These can be described by the condensed structural formulas and .
The third isomer of is the ethermethoxyethane (ethyl-methyl-ether; III).
Unlike the other two, it has the oxygen atom connected to two carbons,
and all eight hydrogens bonded directly to carbons. It can be described
by the condensed formula .
The alcohol "3-propanol" is not another isomer, since the
difference between it and 1-propanol is not real; it is only the result
of an arbitrary choice in the ordering of the carbons along the chain.
For the same reason, "ethoxymethane" is not another isomer.
1-Propanol and 2-propanol are examples of positional isomers, which differ by the position at which certain features, such as double bonds or functional groups, occur on a "parent" molecule (propane, in that case).
Example: C 3H 4
There are also three structural isomers of the hydrocarbon:
I Propadiene
II Propyne
III Cyclopropene
In two of the isomers, the three carbon atoms are connected in an open chain, but in one of them (propadiene or allene; I) the carbons are connected by two double bonds, while in the other (propyne or methylacetylene, II) they are connected by a single bond and a triple bond. In the third isomer (cyclopropene; III)
the three carbons are connected into a ring by two single bonds and a
double bond. In all three, the remaining valences of the carbon atoms
are satisfied by the four hydrogens.
Again, note that there is only one structural isomer with a
triple bond, because the other possible placement of that bond is just
drawing the three carbons in a different order. For the same reason,
there is only one cyclopropene, not three.
Tautomers
Tautomers are structural isomers which readily interconvert, so that two or more species co-exist in equilibrium such as
The structure of some molecules is sometimes described as a resonance between several apparently different structural isomers. The classical example is 1,2-methylbenzene (o-xylene), which is often described as a mix of the two apparently distinct structural isomers:
However, neither of these two structures describes a real compound;
they are fictions devised as a way to describe (by their "averaging" or
"resonance") the actual delocalized bonding of o-xylene, which is the single isomer of with a benzene core and two methyl groups in adjacent positions.
Stereoisomers have the same atoms or isotopes connected by bonds of
the same type, but differ in their shapes — the relative positions of
those atoms in space — apart from rotations and translations.
In theory, one can imagine any special arrangement of the atoms
of a molecule or ion to be gradually changed to any other arrangement in
infinitely many ways, by moving each atom along an appropriate path.
However, changes in the positions of atoms will generally change the
internal energy
of a molecule, which is determined by the angles between bonds in each
atom and by the distances between atoms (whether they are bonded or
not).
A conformational isomer is an arrangement of the atoms of the molecule or ion for which the internal energy is a local minimum;
that is, an arrangement such that any small changes in the positions of
the atoms will increase the internal energy, and hence result in forces
that tend to push the atoms back to the original positions. Changing
the shape of the molecule from such an energy minimum to another energy minimum will therefore require going through configurations that have higher energy than and . That is, a conformation isomer is separated from any other isomer by an energy barrier:
the amount that must be temporarily added to the internal energy of the
molecule in order to go through all the intermediate conformations
along the "easiest" path (the one that minimizes that amount).
Molecular
models of cyclohexane in boat and chair conformations. The carbon
atoms are colored amber or blue according to whether they lie above or
below the mean plane of the ring. The C–C bonds on the ring are light
green.
A classic example of conformational isomerism is cyclohexane. Alkanes generally have minimum energy when the
angles are close to 110 degrees. Conformations of the cyclohexane
molecule with all six carbon atoms on the same plane have a higher
energy, because some or all the
angles must be far from that value (120 degrees for a regular hexagon).
Thus the conformations which are local energy minima have the ring
twisted in space, according to one of two patterns known as chair (with the carbons alternately above and below their mean plane) and boat (with two opposite carbons above the plane, and the other four below it).
If the energy barrier between two conformational isomers is low enough, it may be overcome by the random inputs of thermal energy that the molecule gets from interactions with the environment or from its own vibrations.
In that case, the two isomers may as well be considered a single
isomer, depending on the temperature and the context. For example, the
two conformations of cyclohexane convert to each other quite rapidly at
room temperature (in the liquid state), so that they are usually treated
as a single isomer in chemistry.
In some cases, the barrier can be crossed by quantum tunneling of the atoms themselves. This last phenomenon prevents the separation of stereoisomers of fluorochloroamine or hydrogen peroxide, because the two conformations with minimum energy interconvert in a few picoseconds even at very low temperatures.
Conversely, the energy barrier may be so high that the easiest
way to overcome it would require temporarily breaking and then reforming
or more bonds of the molecule. In that case, the two isomers usually
are stable enough to be isolated and treated as distinct substances.
These isomers are then said to be different configurational isomers or "configurations" of the molecule, not just two different conformations.
(However, one should be aware that the terms "conformation" and
"configuration" are largely synonymous outside of chemistry, and their
distinction may be controversial even among chemists.)
Interactions with other molecules of the same or different compounds (for example, through hydrogen bonds)
can significantly change the energy of conformations of a molecule.
Therefore, the possible isomers of a compound in solution or in its
liquid and solid phases many be very different from those of an isolated
molecule in vacuum. Even in the gas phase, some compounds like acetic acid will exist mostly in the form of dimers or larger groups of molecules, whose configurations may be different from those of the isolated molecule.
Enantiomers
Two compounds are said to be enantiomers
if their molecules are mirror images of each other, that cannot be made
to coincide only by rotations or translations — like a left hand and a
right hand. The two shapes are said to be chiral.
A classical example is bromochlorofluoromethane (). The two enantiomers can be distinguished, for example, by whether the path
turns clockwise or counterclockwise as seen from the hydrogen atom. In
order to change one conformation to the other, at some point those four
atoms would have to lie on the same plane — which would require severely
straining or breaking their bonds to the carbon atom. The
corresponding energy barrier between the two conformations is so high
that there is practically no conversion between them at room
temperature, and they can be regarded as different configurations.
The compound chlorofluoromethane, in contrast, is not chiral: the mirror image of its molecule is also obtained by a half-turn about a suitable axis.
Another example of a chiral compound is 2,3-pentadiene
a hydrocarbon that contains two overlapping double bonds. The double
bonds are such that the three middle carbons are in a straight line,
while the first three and last three lie on perpendicular planes. The
molecule and its mirror image are not superimposable, even though the
molecule has an axis of symmetry. The two enantiomers can be
distinguished, for example, by the right-hand rule. This type of isomerism is called axial isomerism.
Enantiomers behave identically in chemical reactions, except when reacted with chiral compounds or in the presence of chiral catalysts, such as most enzymes.
For this latter reason, the two enantiomers of most chiral compounds
usually have markedly different effects and roles in living organisms.
In biochemistry and food science, the two enantiomers of a chiral molecule — such as glucose — are usually identified, and treated as very different substances.
Each enantiomer of a chiral compound typically rotates the plane of polarized light
that passes through it. The rotation has the same magnitude but
opposite senses for the two isomers, and can be a useful way of
distinguishing and measuring their concentration in a solution. For this
reason, enantiomers were formerly called "optical isomers". However, this term is ambiguous and is discouraged by the IUPAC.
Stereoisomers that are not enantiomers are called diastereomers. Some diastereomers may contain chiral center, some not.
Some enantiomer pairs (such as those of trans-cyclooctene)
can be interconverted by internal motions that change bond lengths and
angles only slightly. Other pairs (such as CHFClBr) cannot be
interconverted without breaking bonds, and therefore are different
configurations.
Cis-trans isomerism
A
double bond between two carbon atoms forces the remaining four bonds
(if they are single) to lie on the same plane, perpendicular to the
plane of the bond as defined by its π orbital.
If the two bonds on each carbon connect to different atoms, two
distinct conformations are possible, that differ from each other by a
twist of 180 degrees of one of the carbons about the double bond.
The classical example is dichloroethene , specifically the structural isomer
that has one chlorine bonded to each carbon. It has two conformational
isomers, with the two chlorines on the same side or on opposite sides of
the double bond's plane. They are traditionally called cis (from Latin meaning "on this side of") and trans ("on the other side of"), respectively; or Z and E in the IUPAC
recommended nomenclature. Conversion between these two forms usually
requires temporarily breaking bonds (or turning the double bond into a
single bond), so the two are considered different configurations of the
molecule.
More generally, cis–trans isomerism
(formerly called "geometric isomerism") occurs in molecules where the
relative orientation of two distinguishable functional groups is
restricted by a somewhat rigid framework of other atoms.
For example, in the cyclic alcohol inositol (a six-fold alcohol of cyclohexane), the six-carbon cyclic backbone largely prevents the hydroxyl and the hydrogen
on each carbon from switching places. Therefore, one has different
configurational isomers depending on whether each hydroxyl is on "this
side" or "the other side" of the ring's mean plane. Discounting isomers
that are equivalent under rotations, there are nine isomers that differ
by this criterion, and behave as different stable substances (two of
them being enantiomers of each other). The most common one in nature (myo-inositol) has the hydroxyls on carbons 1, 2, 3 and 5 on the same side of that plane, and can therefore be called cis-1,2,3,5-trans-4,6-cyclohexanehexol. And each of these cis-trans
isomers can possibly have stable "chair" or "boat" conformations
(although the barriers between these are significantly lower than those
between different cis-trans isomers).
The two isomeric complexes, cisplatin and transplatin, are examples of square planar MX2Y2 molecules with M = Pt.
For more complex organic molecules, the cis and trans labels are ambiguous. The IUPAC recommends a more precise labeling scheme, based on the CIP priorities for the bonds at each carbon atom.
Centers with non-equivalent bonds
More generally, atoms or atom groups that can form three or more non-equivalent single bonds (such as the transition metals
in coordination compounds) may give rise to multiple stereoisomers when
different atoms or groups are attached at those positions. The same is
true if a center with six or more equivalent bonds has two or more
substituents.
For instance, in the compound , the bonds from the phosphorus atom to the five halogens have approximately trigonal bipyramidal geometry.
Thus two stereoisomers with that formula are possible, depending on
whether the chlorine atom occupies one of the two "axial" positions, or
one of the three "equatorial" positions.
For the compound , three isomers are possible, with zero, one, or two chlorines in the axial positions.
As another example, a complex with a formula like , where the central atom M forms six bonds with octahedral geometry, has at least two facial–meridional isomers, depending on whether the three bonds (and thus also the three bonds) are directed at the three corners of one face of the octahedron (fac isomer), or lie on the same equatorial or "meridian" plane of it (mer isomer).
Rotamers and atropisomers
Two
parts of a molecule that are connected by just one single bond can
rotate about that bond. While the bond itself is indifferent to that
rotation, attractions and repulsions between the atoms in the two parts
normally cause the energy of the whole molecule to vary (and possibly
also the two parts to deform) depending on the relative angle of
rotation φ between the two parts. Then there will be one or more special
values of φ for which the energy is at a local minimum. The
corresponding conformations of the molecule are called rotational
isomers or rotamers.
Thus, for example, in an ethane molecule , all the bond angles and length are narrowly constrained, except that the two methyl groups can independently rotate about the
axis. Thus, even if those angles and distances are assumed fixed, there
are infinitely many conformations for the ethane molecule, that differ
by the relative angle φ of rotation between the two groups. The feeble
repulsion between the hydrogen atoms in the two methyl groups causes the
energy to minimized for three specific values of φ, 120° apart. In
those configurations, the six planes or are 60° apart. Discounting rotations of the whole molecule, that configuration is a single isomer — the so-called staggered conformation.
Rotation between the two halves of the molecule 1,2-dichloroethane ( also has three local energy minima, but they have different energies due to differences between the , , and interactions. There are therefore three rotamers: a trans isomer where the two chlorines are on the same plane as the two carbons, but with oppositely directed bonds; and two gauche isomers, mirror images of each other, where the two groups are rotated about 109° from that position. The computed energy difference between trans and gauche is ~1.5 kcal/mol, the barrier for the ~109° rotation from trans to gauche is ~5 kcal/mol, and that of the ~142° rotation from one gauche to its enantiomer is ~8 kcal/mol. The situation for butane is similar, but with sightly lower gauche energies and barriers.
If the two parts of the molecule connected by a single bond are
bulky or charged, the energy barriers may be much higher. For example,
in the compound biphenyl — two phenyl
groups connected by a single bond — the repulsion between hydrogen
atoms closest to the central single bond gives the fully planar
conformation, with the two rings on the same plane, a higher energy than
conformations where the two rings are skewed. In the gas phase, the
molecule has therefore at least two rotamers, with the ring planes
twisted by ±47°, which are mirror images of each other. The barrier
between them is rather low (~8 kJ/mol). This steric hindrance effect is more pronounced when those four hydrogens are replaced by larger atoms or groups, like chlorines or carboxyls. If the barrier is high enough for the two rotamers to be separated as stable compounds at room temperature, they are called atropisomers.
Topoisomers
Large molecules may have isomers that differ by the topology
of their overall arrangement in space, even if there is no specific
geometric constraint that separate them. For example, long chains may
be twisted to form topologically distinct knots, with interconversion prevented by bulky substituents or cycle closing (as in circular DNA and RNAplasmids). Some knots may come in mirror-image enantiomer pairs. Such forms are called topological isomers or topoisomers.
Also, two or more such molecules may be bound together in a catenane
by such topological linkages, even if there is no chemical bond between
them. If the molecules are large enough, the linking may occur in
multiple topologically distinct ways, constituting different isomers. Cage compounds, such as helium enclosed in dodecahedrane (He@C 20H 20) and carbon peapods, are a similar type of topological isomerism involving molecules with large internal voids with restricted or no openings.
Isotopes and spin
Isotopomers
Different
isotopes of the same element can be considered as different kinds of
atoms when enumerating isomers of a molecule or ion. The replacement of
one or more atoms by their isotopes can create multiple structural
isomers and/or stereoisomers from a single isomer.
For example, replacing two atoms of common hydrogen () by deuterium (, or ) on an ethane
molecule yields two distinct structural isomers, depending on whether
the substitutions are both on the same carbon (1,1-dideuteroethane, ) or one on each carbon (1,2-dideuteroethane, ); as if the substituent was chlorine instead of deuterium. The two compounds do not interconvert easily and have different properties, such as their microwave spectrum.
Another example would be substituting one atom of deuterium for one of the hydrogens in chlorofluoromethane (). While the original compound is not chiral and has a single isomer, the substitution creates a pair of chiral enantiomers of , which could be distinguished (at least in theory) by their optical activity.
When two isomers would be identical if all isotopes of each element were replaced by a single isotope, they are described as isotopomers or isotopic isomers. In the above two examples if all were replaced by , the two dideuteroethanes would both become ethane and the two deuterochlorofluoromethanes would both become .
The concept of isotopomers is different from isotopologs or isotopic homologs, which differ in their isotopic composition. For example, and are isotopologues and not isotopomers, and are therefore not isomers of each other.
Spin isomers
Another type of isomerism based on nuclear properties is spin isomerism, where molecules differ only in the relative spins
of the constituent atomic nuclei. This phenomenon is significant for
molecular hydrogen, which can be partially separated into two spin
isomers: parahydrogen, with the spins of the two nuclei pointing in
opposite ways, and orthohydrogen, where the spins point the same way.
Ionization and electronic excitation
The same isomer can also be in different excited states, that differ by the quantum state of their electrons. For example, the oxygen molecule can be in the triplet state or one of two singlet states.
These are not considered different isomers, since such molecules
usually decay spontaneously to their lowest-energy excitation state in a
relatively short time scale.
Likewise, polyatomic ions and molecules that differ only by the addition or removal of electrons, like oxygen or the peroxide ion are not considered isomers.
Isomerization is the process by which one molecule is transformed
into another molecule that has exactly the same atoms, but the atoms are
rearranged. In some molecules and under some conditions, isomerization occurs spontaneously. Many isomers are equal or roughly equal in bond energy,
and so exist in roughly equal amounts, provided that they can
interconvert relatively freely, that is the energy barrier between the
two isomers is not too high. When the isomerization occurs intramolecularly, it is considered a rearrangement reaction.
An example of an organometallic isomerization is the production of decaphenylferrocene, [(η5-C5Ph5)2Fe] from its linkage isomer.
Synthesis of fumaric acid
Industrial synthesis of fumaric acid proceeds via the cis-trans isomerization of maleic acid:
Topoisomerases are enzymes that can cut and reform circular DNA and thus change its topology.
Medicinal chemistry
Isomers having distinct biological properties are common; for example, the placement of methyl groups. In substituted xanthines, theobromine, found in chocolate, is a vasodilator with some effects in common with caffeine; but, if one of the two methyl groups is moved to a different position on the two-ring core, the isomer is theophylline, which has a variety of effects, including bronchodilation and anti-inflammatory action. Another example of this occurs in the phenethylamine-based stimulant drugs. Phentermine is a non-chiral compound with a weaker effect than that of amphetamine.
It is used as an appetite-reducing medication and has mild or no
stimulant properties. However, an alternate atomic arrangement gives dextromethamphetamine, which is a stronger stimulant than amphetamine.
In medicinal chemistry and biochemistry, enantiomers are a special concern because they may possess distinct biological activity.
Many preparative procedures afford a mixture of equal amounts of both
enantiomeric forms. In some cases, the enantiomers are separated by chromatography using chiral stationary phases. They may also be separated through the formation of diastereomeric salts. In other cases, enantioselective synthesis have been developed.
As an inorganic example, cisplatin
(see structure above) is an important drug used in cancer chemotherapy,
whereas the trans isomer (transplatin) has no useful pharmacological
activity.
History
Isomerism was first observed in 1827, when Friedrich Wöhler prepared silver cyanate and discovered that, although its elemental composition of was identical to silver fulminate (prepared by Justus von Liebig the previous year), its properties were distinct. This finding challenged the prevailing chemical understanding of the time, which held that chemical compounds could be distinct only when their elemental compositions differ. (We now know that the bonding structures of fulminate and cyanate can be approximately described as ≡ and , respectively.)
Additional examples were found in succeeding years, such as Wöhler's 1828 discovery that urea has the same atomic composition () as the chemically distinct ammonium cyanate. (Their structures are now known to be and , respectively.) In 1830 Jöns Jacob Berzelius introduced the term isomerism to describe the phenomenon.
In 1848, Louis Pasteur observed that tartaric acid
crystals came into two kinds of shapes that were mirror images of each
other. Separating the crystals by hand, he obtained two version of
tartaric acid, each of which would crystallize in only one of the two
shapes, and rotated the plane of polarized light to the same degree but
in opposite directions.
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