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

2. Name the following compounds according to IUPAC rules

3. 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).

4. 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

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

6. 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.

7. Nomenclature of Isomers

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

9. Biological Significance
chapter 6

10. 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.

11. 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.

12. 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.

13. S limonene (lemons)
R limonene (oranges)

14. Isomerism
Structural
Geometric

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

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

17. 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.

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

19. Alkenes

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

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

22. B. Chirality
Mirror image isomers (Enantiomers)
chapter 6

23. 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.

24. 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.

25. (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).

26. 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.

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

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

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

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

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

32. End of Chapter 2