Isomer

In chemistry, isomers are molecules or polyatomic ions with an identical molecular formula – that is, the same number of atoms of each element – but distinct arrangements of atoms in space. Isomerism refers to the existence or possibility of isomers.
Isomers do not necessarily share similar chemical or physical properties. Two main forms of isomerism are structural isomerism, in which bonds between the atoms differ; and stereoisomerism, 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" is a back-formation from "isomeric", which was borrowed through German isomerisch from Swedish isomerisk; which in turn was coined from Greek ἰσόμερoς, with roots = "equal", = "part".

Structural isomers

Structural isomers have the same number of atoms of each element, but the atoms are connected in distinct ways.

Example:

For example, there are three distinct compounds with the molecular formula C3H8O:
The first two isomers shown of C3H8O 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 -OH 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 or to the middle carbon propan-2-ol. These can be described by the condensed structural formulas H3C-CH2-CH2OH and H3C-CH-CH3.
The third isomer of C3H8O is the ether methoxyethane. 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 H3C-CH2-O-CH3.
The alcohol "3-propanol" is not another isomer, since the difference between it and 1-propanol is the result of a choice in the direction of numbering the carbons along the chain. For the same reason, "ethoxymethane" is the same molecule as methoxyethane, 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.

Example:

There are also three structural isomers of the hydrocarbon C3H4:


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 the carbons are connected by two double bonds, while in the other they are connected by a single bond and a triple bond. In the third isomer 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

s are structural isomers which readily interconvert, so that two or more species co-exist in equilibrium such as
H-X-Y=Z <=> X=Y-Z-H.
Important examples are keto-enol tautomerism and the equilibrium between neutral and zwitterionic forms of an amino acid.

Stereoisomers

Stereoisomers have the same atoms or isotopes connected by bonds of the same type, but differ in the relative positions of those atoms in space. Two broad types of stereoisomers exist, enantiomers and diastereomers. Enantiomers have identical physical properties but diastereomers do not.

Enantiomers

Two compounds are said to be enantiomers if their molecules are mirror images of each other and 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 classic example is bromochlorofluoromethane. The two enantiomers can be distinguished, for example, by whether the path F->Cl->Br 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 CH2ClF, 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 H3C-CH=C=CH-CH3, 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 reacting 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.
Some enantiomer pairs can be interconverted by internal motions that change bond lengths and angles only slightly. Other pairs cannot be interconverted without breaking bonds, and therefore are different configurations.

Diastereomers

Stereoisomers that are not enantiomers are called diastereomers. Some diastereomers may contain chiral centers, and some may not.

Cis–trans isomerism

A double bond between two carbon atoms forces the remaining four bonds 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 C2H2Cl2, specifically the structural isomer Cl-HC=CH-Cl 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 and trans, respectively, or Z and E in the IUPAC recommended nomenclature. Conversion between these two forms usually requires temporarily breaking bonds, so the two are considered different configurations of the molecule.
More generally, cis–''trans 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 6, the six-carbon cyclic backbone largely prevents the hydroxyl -OH and the hydrogen -H 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. The most common one in nature 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.
Image:Cisplatin and transplatin.svg|class=skin-invert-image|thumb|right|320px|The two isomeric complexes, cisplatin and transplatin, are examples of square planar MX₂Y₂ molecules with M = Pt.
Cis and trans isomers also occur in inorganic coordination compounds, such as square planar MX2Y2 complexes and octahedral MX4Y2 complexes.
For more complex organic molecules, the cis and trans'' labels can be ambiguous. In such cases, a more precise labeling scheme is employed based on the Cahn-Ingold-Prelog priority rules.

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 on an ethane molecule yields two distinct structural isomers, depending on whether the substitutions are both on the same carbon or one on each carbon ; as if the substituent was chlorine instead of deuterium. The two molecules 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 molecule is not chiral and has a single isomer, the substitution creates a pair of chiral enantiomers of CHDClF, which could be distinguished 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 D were replaced by H, the two dideuteroethanes would both become ethane and the two deuterochlorofluoromethanes would both become CH2ClF.
The concept of isotopomers is different from isotopologs or isotopic homologs, which differ in their isotopic composition. For example, C2H5D and C2H4D2 are isotopologues and not isotopomers, and are therefore not isomers of each other.