1. Organic Chemistry By Dr. Mehnaz Kamal Assistant Professor,
Pharmaceutical Chemistry
Prince Sattam Bin Abdulaziz University

2. 1-Defintion of Isomers.
2-How they could be Classified?
3- Naming of different isomers.
4-Some of their physical and chemical properties.

3. Stereochemistry
It is that part of the science which deals with structure in three dimensions
Study of the arrangement of atoms in space (three-dimensional shape “3D”) or molecules and how this affects their chemical and physical properties Z Y
2D vs 3D Y X X

4. Lecture Contents Isomerism Structural Isomerism Stereoisomerism
1. Chain isomerism
2. Position isomerism
3. Functional isomerism
Stereoisomerism
Optical active isomers.
Geometrical isomers.
Conformational isomers.

5. Isomerism
Isomerism
A phenomenon resulting from moleculs having the same molecular formula but different arrangement In space.
When two or more organic compounds have the same molecular formula but differ in their physical or chemical properties they are called Isomers and the phenomenon called isomerism.

6. Type of Isomerism….cont
1-Structural isomerism /Constitutional isomers.
They are different molecules. They have the same
formula, but they are connected together differently
You cannot convert one to the other without taking it apart and rebuilding it ( i.e., without breaking and remaking bonds).
All the physical properties of constitutional isomers are different
different melting points and boiling points, different solubility and densities, etc.
Thy include: A) Chain Isomerism (Or Skeletal Isomerism)
B) Positional Isomerism.
C) Functional Isomerism

7. Type of Isomerism….cont
1-Structural isomerism /Constitutional isomers..cont
Constitutional isomers include:
A. Chain isomers
C5H12
B. Position isomers
C3H7Br
C. Functional isomers
C2H6O

8. Type of Isomerism….cont
1-Structural isomerism /Constitutional isomers..cont

9. Type of Isomerism….cont
1-Structural isomerism /Constitutional isomers..cont
Examples
Write all of the constitutional isomers having the molecular formula C3H6O2
C4H10
CH3CH2CH2CH3
C3H8O
CH3CH2CH2CH2CH3
(CH3)4C
C6H6O2

10. Type of Isomerism….cont
2-Stereoisomerism
Greek, Stereos=occupying space).
The stereoisomers have the same structural formulas but differ in their arrangement of atoms in space but have the same bonding pattern.
In other words, stereoisomerism is exhibited by such compounds which have identical molecular structure but different configurations.
Stereoisomers are the same constitutional isomer, but have a difference in the way they are arranged in three-dimensional space at one or more of their atoms.

11. Type of Isomerism There are two main classes of isomers: Isomers
Structural isomerism
(Constitutional isomers)
Position of function groups
Skeleton or chain of carbon
Functional group
Stereoisomerism
Optical isomers
(Diastereomers
(Enantiomers
Geometrical
Cis & trans
There are two main classes of isomers:
Configurational
Conformational

12. Type of Isomerism….cont
2-Stereoisomerism
Conformational isomers
The atoms at either end of a single bond can rotate relative to one another.
compare
Free rotation of carbon- carbon single bonds 

13. Type of Isomerism….cont. 2-Stereoisomerism…cont.
Configuration Isomers
Differ only in arrangement of their atoms in space (3D geometry)
I-Diastereomers (Geometric isomerism)
Compounds which have the same molecular formula
but differ in arrangement of atoms or groups in space
different configuration
Diastereoisomers have different physical and chemical
properties, as solubility and boiling points
thus:
- if liquids……. Fractional distillation
- if solids …….. Fractional crystallization

14. Type of Isomerism….cont. 2-Stereoisomerism…cont.
I-Diastereomers (Geometric isomerism)
An isomerism resulting from rigidity in molecules and occurs only in two class of compounds
alkenes and cyclic compounds
Rigidity ≠ Flexibility
σ – bond free rotation ( flexibility )
 - bond C = C no free rotation ( rigidity )
σ – bond restricted rotation ( semi-flexible)

15. Type of Isomerism….cont. 2-Stereoisomerism…cont.
I-Geometric isomerism…cont
Restricted rotation of carbon-carbon double bonds 

16. Type of Isomerism….cont. 2-Stereoisomerism…cont.
I-Geometric isomerism…cont
i- Geometric isomerism in alkenes
The requirement for this type of isomerism is that each carbon
atom involved in the double bond has different substitution
D ≠ E
A ≠ B
On same side
cis
On different sides
trans

17. Geometrical Isomerism
cis/trans isomers
If a ≠ c and b ≠ d then there are 2 diastereomeric forms:
cis, Latin on this side trans, Latin across
cis-1,2-Dichloroethene
trans-1,2-Dichloroethene

18. COMPARE cis / trans ISOMERS IN RING COMPOUNDS
In alkenes cis / trans isomers used to be called geometric isomers,
a term generally not used for cyclic systems (rings). You may find the
term geometric isomers used in older books or papers.

19. Which of the following alkenes can exist as cis-trans isomers?
1,1,2-trichloroethene
1,1-dichloroethene
cis-trans isomerism is not possible if one carbon atom of the double bond bears 2 identical groups.
Which of the following alkenes can exist as cis-trans isomers?
Draw their structures?

20. Summary
Cis-trans isomers differ from one another in the way the atoms/ groups are positioned in space
Cis –same, trans –across
They have different physical and chemical properties
They interact differently with enzymes/ receptor sites
They cannot be interconverted by rotation around C-C bonds
Rotation is restricted by double bond or cyclic structure

21. Type of Isomerism….cont. 2-Stereoisomerism…cont.
I-Geometric isomerism…cont
Diastereoisomers are designed cis or trans according to the priority order or sequence rule
[ atomic number]
53I > 35Br > 17Cl > 16S > 9F > 8O > 7N > 6C > 1H

22. Type of Isomerism….cont. 2-Stereoisomerism…cont.
I-Geometric isomerism…cont
Sequence Rule or Priority Order
1- If the two atoms in question are different, the atom of
highest atomic number receives the highest priority
I > Br > Cl > ……
trans
cis
cis

23. 2-Stereoisomerism…cont.
I-Geometric isomerism…cont
Sequence Rule or Priority Order
2- If the two atoms are identical, the atomic numbers of next
atoms are used, until the priority is determined at the first
point of difference along the chain
cis
trans
trans

24. 2-Stereoisomerism…cont.
I-Geometric isomerism…cont
Sequence Rules or Priority Order
3- Atoms attached to double or triple bonds are given single-bond equivalencies, each doubly bonded atom is duplicated (or triplicated for triple bonds)
>
>
>
>
>
>
RCH2OH
RCN
-CH=CR2

25. E / Z SYSTEM OF NOMENCLATURE

26. Diastereoisomers can also be designated by:
1- E instead of trans
2- Z instead of cis

27. 1 1 cis or trans? 35 2 17 ---------------- 53 Cahn- Ingold-Prelog:
E and Z Based on Priority: 35 2 17 1 53
Cahn- Ingold-Prelog:
1. Atomic Number
2. Atomic number of the next atom 1 9 2
(E)-1-bromo-2-chloro-
2-fluoro-1-iodoethene
Higher priority at the opposite side of pi bond (E)
Higher priority at the same side of pi bond (Z)

28. In this system the two groups attached to each carbon
are assigned a priority ( 1 or 2 ).
If priority 1 groups are both on same side of double bond:
Z isomer = zusammen = together (in German)
same
side
opposite
sides Z E
If priority 1 groups on opposite sides of double bond:
E isomer = entgegen = opposite (in German)

29. ASSIGNING PRIORITIES
1. Look at the atoms attached to each carbon of the double bond.
2. The atom of higher atomic number has higher (1)
priority. 1 1
example
F > H
I > Br 2 2
Since the 1’s are on the same side, this compound is Z
(Z)-1-bromo-2-fluoro-1-iodoethene
notice use of parentheses

30. On carbon c, the chloroethyl substituent is of higher priority than methyl
On carbon d, the bromine substituent is of higher priority than chlorine
IUPAC name is (Z)-1-bromo-1,4-dichloro-2-methylbut-1-ene

31. E Z

32. E Z

33. cis/trans Geometry of Alicyclic Compounds
The cyclic systems use the traditional cis/trans nomenclature.
trans-1,2-dimethylcyclobutane
cis-1,2-dimethylcyclobutane
trans-1,2-dimethylcyclohexane
cis-1,2-dimethylcyclohexane

34. Sequence Rules or Priority Order
Examples
cis
cis
cis
Cis Z
Trans E

35. Useful resources