Nomenclature of organic compounds Faculty of Biotechnology Organic Chemistry Chapter 2 Nomenclature of organic compounds Dr. M. Abd-Elhakeem

Name the following compounds according to IUPAC rules

Drawing structure from name 1- Start to draw the parent chain (at the end of the name). 2- Add the function group in the correct position. 3- add the substitution(s).

Draw the structure of the following compounds I- 3-nitrotoluene II- 2-chloro-3-methyl-1-hexene VI- 2-hydroxy-hexanoic acid III- 1,2-dibromo-cyclopentane

V- 2,3,4-tri methyl pentane VI- Ethanal VII- 4-chloro-2-butanone

Primary, Secondary, Tertiary A primary carbon has one other C directly bonded to it. A secondary carbon is directly bonded to two other C’s. A tertiary carbon is directly bonded to three other C’s. Multivalent atoms are 1º, 2º, or 3º by bonding to C’s. Univalent atom or group not really 1º, 2º, or 3º on its own - ID depends on type of carbon it is bonded to.

Nomenclature of Isomers

Isomerism Isomerization It is the similarity between organic molecules in molecular formula (number of atoms) and different in way of arrangement of atom

Biological Significance chapter 6

Many drugs have chiral centre , with one enantiomer (form) only having the beneficial effect. In the case of some drugs, the other enantiomer can even be harmful, e.g. thalidomide.

In the 1960’s thalidomide was given to pregnant women to reduce the effects of morning sickness. This led to many disabilities in babies and early deaths in many cases.

D thalidomide (dangerous drug) L thalidomide (effective drug) The body convert each enantiomer, so even pure L is dangerous as it converts to D in the body.

S limonene (lemons) R limonene (oranges)

Isomerism Structural Geometric

1. Structural Isomers compounds have the same number of carbon and hydrogen but they are different in the way of carbon atom attachment.

Also some function groups are isomer to each other as shown in the following examples  

2. Stereoisomerism   The atoms are joined up in the same order, but still manage to have a different spatial arrangement.(Three dimensional arrangements). It consists of two types.

A. Geometrical Isomerism Geometric isomers: different arrangement around a carbon-carbon double bond

Alkenes

Ring Compounds Cis-trans isomers possible. Example: trans-1,3-dimethylcylohexane Cis -1,2-dimethyl-cyclopropanol

Cis and Trans Isomers are called together diastereoisomers Example: o o Cis and Trans Isomers are called together diastereoisomers chapter 6

B. Chirality Mirror image isomers (Enantiomers) chapter 6

It takes place when one carbon attached to four different groups. This carbon name chiral carbon and compound name chiral compound and it has an optical activity. The groups are arranged two different ways and the two isomers are mirror images of each other.

Properties of Isomers Diastereomers have different physical properties: m.p., b.p. They can be separated easily. Enantiomers differ only in reaction with other chiral molecules and the direction in which polarized light is rotated. Enantiomers are difficult to separate.

(R), (S) Nomenclature Different molecules (enantiomers) must have different names. Usually only one enantiomer will be biologically active. Configuration around the chiral carbon is specified with (R) and (S).

Rules Assign a priority number to each group attached to the chiral carbon. Atom with highest atomic number assigned the highest priority #1. In case of ties, look at the next atoms along the chain. Double and triple bonds are treated like bonds to duplicate atoms.

(R) and (S) Clockwise 1-2-3 is (S) and counterclockwise 1-2-3 is (R). Example: (S) (S)

D and L System for nomenclature Special case for chiral compounds nomenclature * * * =>

Optical Activity Rotation of plane-polarized light Enantiomers rotate light in opposite directions, but same number of degrees.

Polarimetry Clockwise = dextrorotatory = d or (+) Counterclockwise = levorotatory = l or (-)

Finally Please differentiate between D –L and d- l (+ , -) D – L and R – S

End of Chapter 2