ISOMERISM IN ORGANIC COMPOUNDS

In organic chemistry, we distinguish two types of isomerism: structural isomers and stereoisomers. Isomerism is the existence of compounds that have the same molecular formula but different arrangements of atoms; those compounds are called Isomers. Isomers have different physical or/and chemical properties and the difference may be great or small depending on the type of isomerism.
                                  STRUCTURAL ISOMERS
In structural isomers we distinguish:

1. Chain isomers: Molecules with the same molecular formula but different arrangement of atoms or different chain length.
   
2. Positional isomers: Molecules have the same molecular formula but with different position of unsaturation or other functional groups
3. Functional isomers: Where we have the same empirical formula into different classes
   

                            STEREOISOMERS

Note that in this type of isomerism, molecules have the same empirical formula and the same connection of atoms but different arrangement in space. We distinguish two types: geometric isomers and diastereoisomers.
GEOMETRIC ISOMERS:  The order of atoms bonding is the same but different arrangement in space (geometry is different). We distinguish Cis/Trans isomers and E/Z isomers.

• Cis/Trans isomers:  When carbon atoms are connected by single bond, we have free rotation which is impossible when double bond is present.
  Sothat for molecules of the type 
  Exist in two forms: The two R may be on the same side (Cis-isomers) or on opposite sides (Trans-isomers) with respect to the position of double bonds.
• E/Z isomers: The Cis/Trans system is applicable to the disubstituted alkenes, for a tri or tetra substituted alkenes this system is no longer applicable and contary the E/Z system is used.
  

In cases like this we use the Cahn-Ingold-Prelog convention based on priority of groups. On each carbon belonging to the double bond, we choose an atom or group of atoms of high priority. The priority is given to the atoms according to their atomic masses.

* When atoms of high priority are on the same side, the alkene is of Z-configuration, from the german word Zusammen meaning together.

* When atoms of high priority are on opposite sides, the alkene is of E-configuration, from the german word Entgegen meaning opposite.

CAHN- INGOLD- PRELOG (CIP) RULES OF PRIORITY

1. Atoms of higher atomic mass are of higher priority.
2. When we have identical atoms attached to the atom belonging to the double bond, you have to compare the following atoms till the point where appears the difference.
3. For an atom linked to the other one by multiple bonds, this will give priority.
   

DIASTEREOISOMERS OR OPTICAL ISOMERS

This is applicable to the asymmetric carbon. According to Vant Hoff and Lebel, a carbon with four different substituents is called asymmetric carbon or chiral carbon. Chemicals with chiral carbon show two isomers which are mirror images of each other but non superimposable known as optical isomers.

To name these isomers, we assign priorities to the groups according to the Cahn-Ingold-Prelog.

High priority (1)

Low priority (2)

The above isomers are said to have R or S configurations. We impose the rotation to the molecule such that the atom of priority (4) is oriented towards behind the plane in the axis of the viewer. If the eyes see the sequence of atoms of priority (1), (2), (3) in the clockwise direction (dextrose) and the configuration of chiral carbon is R (rectus) to mean right. If the eyes see the sequences in the counterclockwise direction, the configuration of that chiral carbon is S (sinister) to mean left.

OPTICAL ACTIVITY
Nonsuperimposable mirror image molecules are called enantiomer (from the greek enantion which means opposite). Enantiomers share many of the same properties:
They have the same boiling points, the same melting points, and the same solubilities. All physical properties are the same except those that arise from how groups are boned to the asymmetric carbon are arranged is space. One of them is their interaction with polarized light.
What is polarized light?
Normal light consist of electromagnetic waves that oscillate in all directions. Plane of polarized light or simply polarized light in contrast, oscillate only in a single plane passing through the path of propagation. Polarized light is produced by passing normal light through a polarizer such as polarized lens or Nicol prism.

When polarized light passes through a solution of achiral molecules, the right emerges from the solution with its plane of polarization unchanged. Achiral molecule does not rotate the plane of polarization, it is said to be optically inactive.
But when polarized light passes through a solution of a chiral compound, the light emerges with its plane of polarization changed. Chiral compounds rotates the plane of polarization either in clockwise or counterclockwise direction.

If an enantiomer rotates the plane of polarized light in clockwise direction, its mirror image will rotate the plane of polarized light exactly the same amount counterclockwise.
A compound that rotates the plane of polarization clockwise, it is called dextrogyre (dextrorotatory), indicated by (+). And when an optically active compound rotates the plane of polarized light counterclockwise it is called Levogyre (levorotatory) indicated by (-).
Dextro and Levo are latin prefixes for "to the right" and "to the left" respectively.
Sometimes lowercase d and l are used insted of (+) and (-).
Do not confuse (+) and (-) with R and S. The (+) and (-) symbols indicate the direction in which an optically active compound rotates the plane of polarized light whereas R and S indicate arrangement of groups about an asymmetric carbon. Some compounds with the R configuration are (+) and some are (-). A mixture of equal amounts of two enantiomers (+) and (-) is caleed a "racemic mixture" or a "racemate". Racemic mixtures do not rotate the plane of polarized light since their rotations cancel.

DISCRIMINATION OF ENANTIOMERS BY BIOLOGICAL MOLECULES

ENZYMES:
Enantiomers react in the same way with achiral reagents. But chiral molecules recognizes  only one enantiomer sothat if a synthesis is carried out using a chiral reagent or a chiral catalyst, only one enantiomer will undergo the reaction. The example of a chiral catalyst is an enzyme for example D-aminoacid oxidase that catalyses the reaction of the R enantiomer and leaves the S enantiomer unchanged.

RECEPTORS:
A receptor is a protein that binds a particular molecule. Because a receptor is chiral it will bind one enantiomer better than the other. many drugs exert their physiological activity by binding to receptors. If the drug has an asymetric carbon, the receptor will preferentially bind to one of the enantiomers. Note that in drugs, enantiomers can have the same physiological activity, different degrees of the same activity or very different activity.
Thalidomide tradegy:
Thalodomide is a sedative which has been used in pregnant women with anxiety.

Later on they discovered the the drug was teratogenic (cause malformation in new babies). They found the medicine to have two optical isomers R and S. One of then S, is a good sedative whereas mixed with R due to errors in synthesis even in small amount R causes malformation to new babies and since then the medicine was removed on the market. Recently, Thalidomide was approved in some diseases like leprosy and melanomas.