Organic Chemistry

ByDr. Mehnaz KamalAssistant Professor,

Pharmaceutical ChemistryPrince Sattam Bin Abdulaziz University

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

2D vs 3DX

Y

X

Y

Z

StereochemistryIt 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

Isomerism Structural Isomerism

1 .Chain isomerism2 .Position isomerism

3 .Functional isomerism Stereoisomerism

1. Optical active isomers. 2. Geometrical isomers. 3. Conformational isomers.

Lecture Contents

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.

A phenomenon resulting from

moleculs having the same molecular

formula but different arrangement

In space.

IsomerismIsomerism

This is a branched-chainalkane.

Type of Isomerism….cont

You cannot convert one to the other without taking it apart and rebuilding it ( i.e., without breaking and remaking bonds).

They are different molecules. They have the same formula, but they are connected together differently

All the physical properties of constitutional isomers are different

different melting points and boiling points, different solubility and densities, etc.

1-Structural isomerism /Constitutional isomers.

Thy include: A) Chain Isomerism (Or Skeletal Isomerism) B) Positional Isomerism. C) Functional Isomerism

A. Chain isomers

CH3CH2

CH2CH2

CH3 CH3C

CH2CH3 CH3

CCH3

CH3 CH3H CH3

2,2-dimethylpropanen-pentane 2-methylbutane

B. Position isomers

C5H12

C3H7BrBr

2-bromopropane

Br

1-bromopropane

C. Functional isomers

C2H6OCH3

OH3C

Dimethyl ether

OHCH3C

H

H

Ethanol

Constitutional isomers include:

Type of Isomerism….cont

1-Structural isomerism /Constitutional isomers..cont

Type of Isomerism….cont

1-Structural isomerism /Constitutional isomers..cont

Write all of the constitutional isomers having the molecular formula C3H6O2

O

O

HO

O

H

O

OH

OOO

O

1-Structural isomerism /Constitutional isomers..cont

Type of Isomerism….cont

Examples

C4H10 CH3CH2CH2CH3

CH3

CH3-CH-CH3

C3H8O CH3CH2CH2CH2CH3

CH3

CH3-CH-CH2CH3 (CH3)4C

C6H6O2

OHOH

Catechol

OH

Resorcinol

OH

OH

Hydroquinone

OH

2-StereoisomerismGreek, 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.

Type of Isomerism….cont

Isomers

Structural isomerism)Constitutional isomers(

Position of function groups

Skeleton or chain of carbon Functional group

Stereoisomerism

Optical isomers

)Diastereomers)Enantiomers

GeometricalCis & trans

ConformationalConfigurational

Type of IsomerismThere are two main classes of isomers:

compare

The atoms at either end of a single bond can rotate relative to one another.

Type of Isomerism….cont2-Stereoisomerism

Conformational isomers

Free rotation of carbon- carbon single bonds 

• 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

Type of Isomerism….cont.2-Stereoisomerism…cont.

I-Diastereomers (Geometric isomerism)

Configuration IsomersDiffer only in arrangement of their atoms in space (3D geometry)

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)

Type of Isomerism….cont.2-Stereoisomerism…cont.

I-Diastereomers (Geometric isomerism)

Restricted rotation of carbon-carbon double bonds 

Type of Isomerism….cont.

2-Stereoisomerism…cont.I-Geometric isomerism…cont

i- Geometric isomerism in alkenesThe requirement for this type of isomerism is that each carbon atom involved in the double bond has different substitution

C CE

A

B

D

D ≠ E A ≠ B

CH

Cl

H

Cl

C

CH

H

Cl

Cl

C

On same side cis On different sides

trans

Type of Isomerism….cont.

2-Stereoisomerism…cont.I-Geometric isomerism…cont

Geometrical Isomerism

If a ≠ c and b ≠ d then there are 2 diastereomeric forms:

C C

b

d

a

c

cis/trans isomers

cis, Latin on this side trans, Latin across

C C

H

Cl

Cl

H

C C

Cl

H

Cl

Hcis-1,2-Dichloroethene trans-1,2-Dichloroethene

C C

R

H

R

H

C C

H

R

R

H

RR

R

R

COMPARE cis / trans ISOMERS IN RING COMPOUNDS

cis trans

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.

C C

Cl

Cl

Cl

HC C

Cl

Cl

H

H

1,1-dichloroethene 1,1,2-trichloroethene

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?

H2C CHCH2CH3 H2C C(CH3)2

H3CHC CHCH3 H3CH2CHC CHCl

• 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

Summary

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

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 > ……

C C

H

H2C=HC

H

CH3

C C

H

H3C

Br

Cl

C C

H

H3C

CH2CH2CH3

OH

cis

trans

cis

Type of Isomerism….cont.

2-Stereoisomerism…cont.I-Geometric isomerism…cont

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

C C

H

H3C

CH2OH

CH2NH2

C C

H

H3C

CH2CH2CL

CH2CH2Br

C C

H

H3C

CH2CH2CH3

CH2CH3

transtrans

cis

Sequence Rule or Priority Order

I-Geometric isomerism…cont

2-Stereoisomerism…cont.

3- Atoms attached to double or triple bonds are given single-bond equivalencies, each doubly bonded atom is duplicated (or triplicated for triple bonds)

R-C-R

O

R-C-R

O

R-C-OH

O

R-C-OH

O

R-C-H

O

R-C

N N

N

NCR

O

O

OHCR

O

O

RCR

RCH2OH RCN -CH=CR2> > > > > >

2-Stereoisomerism…cont.

I-Geometric isomerism…cont

Sequence Rules or Priority Order

E / Z SYSTEM OF NOMENCLATURE

Diastereoisomers can also be designated by:

1- E instead of trans

2- Z instead of cis

IC C

Cl

F

Br

cis or trans?

E and Z Based on Priority:

Cahn- Ingold-Prelog: 1. Atomic Number2. Atomic number of the next atom

----------------

35

53 1

2 17

9 2

1

Higher priority at the opposite side of pi bond (E) Higher priority at the same side of pi bond (Z)

(E)-1-bromo-2-chloro-2-fluoro-1-iodoethene

In this system the two groups attached to each carbonare assigned a priority ( 1 or 2 ).

If priority 1 groups are both on same side of double bond:

11

2 2

21

2 1

Z EIf priority 1 groups on opposite sides of double bond:

E isomer = entgegen = opposite (in German)

Z isomer = zusammen = together (in German)

sameside opposite

sides

ASSIGNING PRIORITIES1. Look at the atoms attached to each carbon of the double bond.2. The atom of higher atomic number has higher (1) priority.

example IF

H Br

1

2

1

2F > H I > Br

Since the 1’s are on the same side, this compound is Z

(Z)-1-bromo-2-fluoro-1-iodoethene

notice use of parentheses

Br

Cl

ClH2CH2C

H3C

3 4dc

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

CH

CR2 C N CH2OH

O

H

O

R

O

OH

Increasing priority

BrCl

CO2HH2N

CO2HCl

BrH2N

Z E

CO2HH H

CO2H

E Z

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

C C

H

H3C

CHO

COOH

C C

H

H3C

CH2NH2

CN

C C

H2C=HC COOH

OCH3

cis cis cis

C C

H3CC CCH2Cl

Cl

O O

ClH2C

C C

H3CC Cl

CCH2Cl

O

ClH2C

O

CisZ

Trans E

Sequence Rules or Priority Order

Examples

http://www.chemeddl.org/resources/stereochem/definitions1.htm

http://orgchem.chem.uconn.edu/courses/243f97-rs-practice.html

Useful resources