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

Nomenclature of organic

compounds

Dr. M. Abd-Elhakeem

Faculty of Biotechnology

Organic Chemistry

Chapter 2

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-nitrotolueneCH3

NO2

III- 1,2-dibromo-cyclopentane

VI- 2-hydroxy-hexanoic acid

II- 2-chloro-3-methyl-1-hexene

CH2CH3

Cl

CH3

CH3

OH

OH

O

Br

Br

V- 2,3,4-tri methyl pentane

VII- 4-chloro-2-butanone

VI- Ethanal CH3

O

CH3

O

Cl

CH3

CH3

CH3CH3

CH3

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.

H2CCH2

C

NHO O

H

N

O

O

H2CCH2

C

NH OO

H

N

O

O

L thalidomide (effective drug)

The body convert each enantiomer, so even pure L is

dangerous as it converts to D in the body.

D thalidomide (dangerous drug)

S limonene (lemons) R limonene (oranges)

CH3

HCCH2

CH3

CH3

H C CH2

H3C

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  

CH3 CH2

OH O CH3

CH3

CH2 C

O

HCH3

CH3

CH3

O

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 IsomerismGeometric isomers: different arrangement around

a carbon-carbon double bond

Alkenes

C CH H

CH3H3C

cis-2-butene trans-2-butene

C CH

H3C

CH3

H

Ring Compounds

Cis-trans isomers possible. Example: trans-1,3-dimethylcylohexane

CH3

H

H

CH3

CH3

H

H

CH3

CH3CH3

Cis -1,2-dimethyl-cyclopropanol

Example:

CHO

O

CH

CH

C

O

OH

fumaric acid, mp 287 C essential metabolite

o

HC

CC

H

C

O

OH

O

HO

maleic acid, mp 138 C toxic irritant

o

chapter 6

Cis and Trans Isomers are called together diastereoisomers

B. Chirality

chapter 6

Mirror image isomers (Enantiomers)

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.

OH

H

Cl

CH3

OH

H

Cl

CH3

Properties of IsomersDiastereomers 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) NomenclatureDifferent 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).

RulesAssign 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:

CH3

H Cl

Cl H

CH3

(S)

(S)

D and L System for nomenclature

CHO

H OH

CH2OH

D-(+)-glyceraldehyde

* CHO

H OH

HO H

H OH

H OH

CH2OHD-(+)-glucose

*

COOH

H2N H

CH2CH2COOH

L-(+)-glutamic acid

* >=

Special case for chiral compounds nomenclature

Optical ActivityRotation of plane-polarized lightEnantiomers rotate light in opposite

directions, but same number of degrees.

Polarimetry

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

Finally

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

End of Chapter 2