Organic Chemistry/Isomerism, Chirality and Stereochemistry

Isomerism
In chemistry, isomers are molecules or polyatomic ions with identical molecular formulas — that is, same number of atoms of each element — but distinct arrangements of atoms in space.[1] Isomerism is existence or possibility of isomers.

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.

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: C3H8O
For example, there are three distinct compounds with the molecular formula :

The first two isomers shown 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 H3C–CH2–CH2OH and H3C–CH(OH)–CH3.

The third isomer is the ether methoxyethane (ethyl-methyl-ether). 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–O–CH2–CH3.

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, "ethoxy- methane" 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).

Point chirality
Many chiral molecules have point chirality, namely a single stereogenic center that coincides with an atom. This stereogenic center usually has four or more bonds to different groups, and may be carbon (as in many biological molecules), phosphorus (as in many organophosphates), silicon, or a metal (as in many chiral coordination compounds). However, a stereogenic center can also be a trivalent atom whose bonds are not in the same plane, such as phosphorus in P-chiral phosphines (PRR′R″) and sulfur in S-chiral sulfoxides (OSRR′), typically due to a lone-pair being present instead of a fourth bond.

Chirality can also arise from isotopic differences between atoms, such as in the deuterated benzyl alcohol PhCHDOH; which is chiral and optically active ([α]D = 0.715°), even though the non-deuterated compound PhCH2OH is not.

If two enantiomers easily interconvert, the pure enantiomers may be practically impossible to separate, and only the racemic mixture is observable. This is the case, for example, of most amines with three different substituents (NRR′R″), because of the low energy barrier for nitrogen inversion. 1,1′-Bi-2-naphthol is an example of a molecule lacking point chirality. While the presence of a stereogenic center describes the great majority of chiral molecules, many variations and exceptions exist. For instance it is not necessary for the chiral substance to have a stereogenic center. Examples include 1-bromo-3-chloro-5-fluoroadamantane, methylethylphenyltetrahedrane, certain calixarenes and fullerenes, which have inherent chirality. The C2-symmetric species 1,1′-bi-2-naphthol (BINOL), 1,3-dichloroallene have axial chirality. (E)-cyclooctene and many ferrocenes have planar chirality.

When the optical rotation for an enantiomer is too low for practical measurement, the species is said to exhibit cryptochirality. Chirality is an intrinsic part of the identity of a molecule, so the systematic name includes details of the absolute configuration (R/S,  D/L , or other designations).

Stereochemistry
Stereochemistry is another name for the optical activity that a molecule expresses. Optical activity is a property of organic molecules. You have seen (+) or (-) or D or L in from of vitamins and drugs well this is the direction of light rotation. In short, for a carbon atom to have optical activity it must be chiral or have 4 different groups attached to it.