Introduction To Organic Chemistry

Lecture 1 12.1 Introduction

Learning Outcomes:
At the end of the lesson the students should be able to : 1. List the elements that made up organic compounds C, H, O, N, P, S and halogens. 2. State the ability of carbon to form 4 covalent bonds with other carbons or elements. 3. Differentiate between saturated and unsaturated organic compounds. 4. Give examples of organic compounds used in medicine, engineering, biotechnology and agriculture.

WHAT IS ORGANIC CHEMISTRY? Organic chemistry is the chemistry of carbon compounds. Organic compounds contain H as well as C, while other common elements are O, N, the halogens, S and P. There are many varieties of organic compounds ( more than 10 millions!!!) They may exist as simple or complex molecules; as gases, liquids or solid and coloured or colourless.

 Examples :CH4 methane (a component of natural gas)

OCOCH3 COOH

methyl salicylic acid (aspirin-a drug)

O CH2 C NH O N COOH S

penicillin (an antibiotic)

Cl

CH CCl3

Cl

dichlorodiphenyltrichloroetane (DDT- a pesticide component)

 All organic compounds consist of carbon atom. Properties of carbon atom: -has 4 valence electrons. -can form 4 covalent bonds.
C C C C C C

Single bond

Double bond

Triple bond

Hydrocarbons

saturated
Contains only single bonds ( -C-C) Examples: alkanes, cycloalkanes

unsaturated
Contains at least one carboncarbon double bond (-C=C-) or triple bond (-C C-). Examples: alkenes, alkynes.

Uses of organic compounds

Medicine Antibiotics are used to fight bacterial and fungal infections Gasoline-as a fuel for internal combustion engines. Genetic information like DNA DDT-as insectisides to kill harmful insects.

Engineering

Biotechnology Agriculture

Lecture 2: 12.2 Molecular and Structural Formulae

Learning Outcomes:
At the end of the lesson the students should be able to : Define structural formula. Draw structural formula in the form of expanded, condensed and skeletal structures based on the molecular formula. Explain primary (1), secondary (2), tertiary (3) and quaternary (4) carbon.

 Structural formula shows how the atoms in a molecule are bonded to each other. 3 types of structural formula:
condensed structure expanded structure skeletal structure

2- Dimensional formula

Condensed Structure Does not show single bonds between carbon and hydrogen atoms, but double and triple bonds are shown. All atoms that are attached to a carbon are written immediately after that carbon.
C4H10 CH3CH2CH2CH3 (Condensed structure)

Examples: ii) Cyclohexane, C6H12 iii) Aldehyde, CH3CHO

H2C H2C

H2 C CH2 C H2 CH2

O CH3CH

Expanded Structure Expanded structures indicate how atoms are attached to each other but are not representations of the actual shapes of the molecules. C4H9Cl
Molecular Formula
H H H H C C H H H H

C C H Cl

Expanded structure

 Examples: i) Alcohol (C2H6O)

H H C H H C H OH

ii) Carboxylic acid (C3H6O2 )

H H C H H C H O C OH

Draw the expanded structure for the following molecules. a)(CH3)3CCH2CH=CH2

CH3 CH3 H H C C H H C C CH3 H

b)(CH3)3CCH=CHCH2-OH
CH3 CH3 H H C C H H OH

C C CH3

Skeletal Structure Shows only the carbon skeleton. Hydrogen atoms are not written. Other atoms such as O, Cl, N etc. are shown. When a line ends with nothing, the group at the end of it is CH3..
CH3

 When 2 lines intercept, the group at the intersection is CH2.

CH2

When 3 lines intercept, the group at the intersection is CH.

CH

i) CH3CH(Cl)CH2CH3

= Cl

ii)

H2C H2C

CH2 CH2

3- Dimensional formula ( wedge dashed wedge line formula )

Describes how the atoms of a molecule are arranged in space.

Example : Bromoethane
Br H C H H

Br C H H H

or

C H H

Br or

C H Br H

Indication ::bonds that lie in the plane :bonds that lie behind the plane :bonds that project out of the plane

Classification of C atoms:
A carbon atom can be classified as primary carbon(1o) bonded to 1 C atom secondary carbon(2o) bonded to 2 C atoms tertiary carbon(3o) bonded to 3 C atoms quarternary carbon(4o) bonded to 4 C atoms

H H C CH3
10 carbon 10 carbon

CH3 H C H
20 carbon

CH3

CH3 H C CH3
30 carbon

CH3

H H CH3 H C
1

CH3 C CH3
1

C CH2

CH3

H H H

H H CH3 H C C
2

CH3 C CH3
2

C CH2

CH3

H H H

H H CH3 H C C
3

CH3 C
4

C CH2

CH3

H H H

CH3

Question
Expanded Structure Condensed Structure Skeletal Structure

CH3CH2CCl(CH3)2

CH3 H C C CH H H CH3

H H

FUNCTIONAL GROUPS AND HOMOLOGOUS SERIES

Lecture 3 Functional Group and Homologous Series

Learning Outcomes: At the end of the lesson the students should be able to : Define functional group. Name functional groups and classify organic compounds according to their functional groups. Define homologous series and explain general characteristics of its members.

Functional group
is an atom or group of atoms in an organic molecule which characterised the molecule and enables it to react in specific ways which determines its chemical properties.

Example Halogenation of Alkenes

(i) In inert solvent (CH2Cl2) y Alkenes react rapidly with chlorine or bromine in CH2Cl2 at room temperature to form vicinal dihalides.

Cl2

CH2Cl2

Cl Cl

Functional groups are important for three reasons:

i.

A basic by which organic compounds are divided into different classes. ii. A basic for naming organic compounds iii. A particular functional group will always undergo similar types of chemical reactions.

Homologous Series
is series of compounds where each member differs from the next member by a constant CH2 unit Members of the same homologous series are called homologs. CH3CH2CH3 - propane CH3CH2CH2CH3 - butane

Homologs Features
1. Obey a general formula: Examples: Alkane: CnH2n+2 Alkene: CnH2n Alcohol : CnH2n+1OH

2. Differ from the successive homolog by a CH2 unit. 3. Show a gradual change in the physical properties. (eg. increasing boiling point) 4. Have same functional group. 5. Have similar chemical properties.
6. Can be prepared by similar general methods.

Classification of organic compound Class of Compound (homologous series) Alkane Functional Group Example Structure Name CH3-CH3 carbon-carbon double bond carbon-carbon triple bond

Alkene

-C=C-

CH3CH=CH2

Alkyne

-C C-

CH3C CCH3

Aromatic

Benzene ring

-CH3 CH3Cl CH3-OH OH

Haloalkane

X (F, Cl, Br, I) Halogen

Alcohol

-OH

Hydroxyl

Phenol

-OH

Hydroxyl

Ether

-C-O-C-

Alkoxide

CH3-O-CH3

Aldehyde

-C=O H R-C=O R -C=O OH -C-O-CO -C=O Cl

Carbonyl

CH3-C=O H CH3-C=O CH3 CH3-C=O OH

Ketone Carboxylic acid

Carbonyl

Carboxyl

Ester

CH3-C=O Carboxyalkoxy OCH3 CH3-C=O Cl

Acyl chloride

Anhydride Amide

O O -C-O-C-C=O N-NH2 -C N

O O CH3C-O-CCH3 Carboxamide CH3-C=O NH2 Amino Cyano group CH3-NH2 CH3C N

Amine Nitrile

Exercises: 1. Identify the functional group in the following molecules a)(CH3)3CCH2CH=CH2

carboncarbon-carbon double bond

b)(CH3)3CCH=CHCH2-OH
Hydroxyl carboncarbon-carbon double bond

c)

O C OH

O C

O O C O C CH3 NH2 CH3

CH3 CH2 OH CH2 CH3 C C C C CH O

NH2 CH

CH2 O

Carboxyl

O C OH

O C

O O C O C CH3
Carboxyalkoxy

CH3

anhydride

CH3 CH2 OH CH2 CH3

Amino

Carboxamide

C C

CH
Hydroxyl

NH2

NH2 CH

CH2 O
carboncarbon-carbon double bond

Identify the functional group in the following molecules

NH2 C O CH2 CH NH2 COOH

Carboxyl

Carboxamide Amino

O Cl C

O C Cl

Acyl chloride

Benzene ring

Lecture 4: Isomerism
Learning Outcomes: At the end of the lesson the students should be able to : Define isomerism. Explain constitutional isomerism. chain isomers positional isomers functional group isomer

Isomerism

Structural/ Constitutional Isomerism

Stereoisomerism

Chain Isomerism

Positional Isomerism

Functional Group Isomerism

diastreomer

enantiomer

cis-trans isomerism

other diastereomers

 Isomerism is the existence of different compounds with the same molecular formula but different structural formulae. Different structural formula that have the same molecular formula are called isomers.
Molecular formula C5H12

CH3CH2CH2CH2CH3
pentane

CH3CHCH2CH3 CH3
2- methylbutane

1) Constitutional isomers (Structural isomers) are isomers with the same molecular formula but differ in the order of attachment of atoms. 2) Stereoisomers are isomers with the same molecular formula but different arrangement of atoms in space

Constitutional isomerism Isomerism resulting from different order of attachment of atoms. a) b) c) Three types Chain/skeletal isomerism Positional isomerism Functional group isomerism

a) Chain/skeletal isomerism The isomers differ in the carbon skeleton or parent chain(different carbon chain). They possess the same functional group and belong to the same homologous series. Example:

C5H12 CH3CH2CH2CH2CH3 CH3 CH3CHCH2CH3 CH3 CH3CCH3 CH3

b)Positional isomerism These isomers have a substituent group/ functional group in different positions. ( but same parent chain) Examples C3H7Cl
substituent group

CH3CHCH3 Cl
2-chloropropane

CH3CH2CH2Cl 1-chloropropane

C4H8

functional group

CH2=CHCH2CH3 1-butene

CH3CH=CHCH3 2-butene

CH3 CH3

C8H10

C H3

1,21,2-dimethylbenzene
CH3

C H3 1,41,4-dimethylbenzene

CH3

1,31,3-dimethylbenzene

 C6H13N
NH2 CH3
H2N CH3

CH3
CH2NH2

NH2

c)Functional group isomerism These isomers have different functional groups and belong to different homologous series with the same general formula. Different classes of compounds that exhibit functional group isomerism :General formula CnH2n+2O ; n > 1 CnH2nO ; n CnH2nO2 ; n CnH2n ; n 3 3 2 Classes of compounds alcohol and ether aldehyde and ketone carboxylic acid and ester alkene and cycloalkane

 Examples C2H6O

CH3CH2OH ethanol

CH3OCH3 dimethyl ether

C3H6O

CH3CCH3
propanone

CH3CH2CH
propanal

C3H6O2

CH3CH2COH O
propanoic acid

CH3COCH3 O
methyl ethanoate

Exercise:

1. State how many are isomers with the following molecular formulae, identify the type of isomerism and draw the structural formula of the isomers. a) C5H10 b) C5H10O2 c) CH3CH=C(Cl)CH3 d) C4H6Cl2 e) CH3CH2CH(OH)CH(Br)CH2CH3

CH3CH2CH2CH=CH2 A

CH3CH2CH=CHCH3 B

CH3CH2C=CH3 CH3 C

CH3CHCH=CH3 CH3 D

CH3CH=CCH3 CH3 E F

A&B

Positional isomerism Chain isomerism Positional isomerism Functional group isomerism

A&D C&D A&F

C5H10O2 CH3CHCH2C-OH CH3

||
CH3CH2CH2CH2C-OH A O

||
B O

||
CH3CH2CHC-OH CH3 O C O CH3C(CH3)2C-OH

||
D

||
CH3CH2CH2C-OCH3 E O

||
CH3CH2C-OCH2CH3 F

||
CH3CHC-OCH3 CHCCH3 G

Type of isomerism E&F B&C A&C C&D A&G

Chain isomerism Positional isomerism Chain isomerism Chain isomerism Functional group isomerism

Lecture 5 Isomerism
Learning Outcomes: At the end of the lesson the students should be able to : Define stereoisomerism. Describe cis-trans isomerism due to restricted rotation about C=C bond and CC bond in cyclic compounds Identify cis-trans isomerism of a given structural formula.

Stereoisomerism / optical isomerism : Isomerism that resulting from different spatial arrangement of atoms in molecules. Two subdivisions of stereoisomers: i) Enantiomers (stereoisomers that are mirror image and non-superimposable isomers ) ii) Diastereomers (stereoisomers that are not mirror images of each other)

Diastereomer
Cis-Trans Isomerism  The requirements for geometric isomerism : i) restricted rotation about a C=C,double bond in alkenes, or a C-C single bond in cyclic compounds. ii) each carbon atom of a site of restricted rotation has two different groups attached to it.

 Examples
H C H3C
transtrans-2-butene

CH3 C H

H3C C H
ciscis-2-butene

CH3 C H

Diastereomers both isomers are not mirror images of each other.

CH3 CH3
cis-1,2cis-1,2-dimethylcyclohexane

CH3

CH3

trans-1,2trans-1,2-dimethylcyclohexane

 If one of the doubly bonded carbons has 2 identical groups, geometric isomerism is not possible. Example

H3C C C H3C

CH3

H No cis trans isomer

Which of the following compounds can exist as a pair of cis-trans isomers? Draw each cis-trans pair and indicate the geometry of each isomer.

a. CH3CH2CH=CHCH3 b. ClCH=CHBr c. (CH3)2C=CHCH3 d. CH3CH=CH2

a. CH3CH2CH=CHCH3 H C=C H3CH2C Cis- isomer CH3

b. ClCH=CHBr Cl C=C H Br H

trans- isomer

H C=C H3CH2C trans- isomer

H CH3 H Cl Cis- isomer C=C

H Br

c. (CH3)2C=CHCH3 H3C C=C H3C H CH3 No cis and trans isomers

d. CH3CH=CH2 H C=C H3C H H No cis and trans isomers

Lecture 6 Isomerism
Learning Outcomes: At the end of the lesson the students should be able to : Identify cis-trans isomerism of a given structural formula. Define chirality centre and enantiomers. Identify chirality centre in a molecule. Explain optical activity of a compound. Draw a pair of enantiomers using 3-dimensional formula. Define racemate. State the applications of chiral compounds in daily life.

Enantiomer
Optical Isomerism Optically active compounds have the ability to rotate plane-polarized light to the right (dextrorotary) and to the left (levorotary) The angle of rotation can be measured with an instrument called polarimeter.

Polarimeter

Clockwise rotation

Dextrorotatory isomer (d or +)

Anti-Clockwise rotation

Levorotatory isomer (l or -)

The requirements for optical isomerism :i) molecule contains a chiral carbon or chirality centre or stereogenic centre (a sp3-hybridized carbon atom with 4 different groups attached to it)
P Q C* S

P{Q{R{S *designates chiral centre

R not superimposable with its mirror ii) molecule is image.

CH3CH2OH

CI

* CH3CCH2CH3
CI

OH

CH3CCH2CH3 CH3
CI OH C molecule contains a chiral carbon: B and D

* * CH3CCH2 CHCH3
OH
D

 Enantiomers  a pair of mirror-image that are not superimposable. Example:i) 2-butanol , *

CH3CHCH2CH3 OH

CH2CH3 H3 C C* H OH
enantiomers

CH2CH3 C H CH3 OH

H CH3CH(NH2)COOH CH3CCOOH NH2 H C * COOH NH2 enantiomers HOOC NH2 H

H3C

CH3

The optically active compounds -have chiral carbon -can rotate plane polarized light

ii) 2-hydroxypropanoic acid,

COOH H CH3 OH
HO

COOH H CH3

enantiomers

ISOMERISM
Molecules with 2 or more chiral centre, diastereomer may exist diastereomer : stereoisomers that are not mirror images of each other

CH3
2 C*H

e.g. CH3

C*CH2CH3

OH OH
1C

C H H H

H O

O H

H O

CH3 H 2C H
5

H3C C H 2C H
(II)

O H

4C

(I)

C H H O

C H H H

O H

H3 C C H 2C H

OH

HO C H 2C H
(IV)

CH3

(III)

CH3 HO HO H CH3 CH2CH3

(I)

CH3 H H3C OH OH CH2CH3

(II) (I) And (II) : enantiomer (III) And (IV) :enantiomer (I) And (III) : diastereomer (I) And (IV) : diastereomer (II) And (III) : diastereomer (II) And (IV) : diastereomer

CH 3 HO H3 C H OH CH 2CH 3
(III)

CH 3 H HO OH CH3 CH 2CH 3
(IV)

Racemate
A racemic mixture or racemate is an equimolar mixture of enantiomers which is optically inactive because the two components rotate plane-polarized light equally (same degree of rotation) but in opposite directions. Hence it does not give a net rotation of planepolarized light.

Applications of chiral compounds in daily life.

e.g:  () Dopa is used for treatment of Parkinson s disease but (+) dopa is toxic to human.  (S)-Ibuprofen the popular analgesic(the active ingredient in motrin, advil, and many other nonaspirin analgesics)

Lecture 7 12.5 Reactions of Organic Compounds Learning Outcomes: At the end of the lesson the students should be able to : Explain covalent bond cleavage:
homolytic heterolytic

Types of Covalent Bond Cleavage/Fission  All chemical reactions involved bond breaking and bond making.  Two types of covalent bond cleavage : Homolytic cleavage  Heterolytic cleavage

a)

Homolytic Cleavage

Occurs in a non-polar bond involving two atoms of similar electronegativity. A single bond breaks symmetrically into two equal parts, leaving each atom with one unpaired electron. Formed free radicals.

Example:
X Xy
y

Xy + Xy
free radicals

X y yX
Br Br
y y

Bry + Bry
free radicals

b) Heterolytic cleavage
Occurs in a polar bond involving unequal sharing of electron pair between two atoms of different electronegativities. A single bond breaks unsymmetrically. Both the bonding electrons are transferred to the more electronegative atom. Formed cation and anion.

A:+ B+ anion cation A:B A is more electronegative. A+ + B:cation anion B is more electronegative.

Reaction Intermediates
a) Carbocation b) Carbanion c) Free Radical They are unstable and highly reactive.

a)

Carbocation

Also called carbonium ion. A very reactive species with a positive charge on a carbon atom. Carbocation is formed in heterolytic cleavage.

Example : H H (CH3)3C Cl

(CH3)3C+ + Clcarbocation anion

Chlorine is more electronegative than carbon and the C Cl bond is polar. The C Cl bond breaks heterolitically and both the bonding electrons are transferred to chlorine atom to form anion and carbocation.

b) Carbanion is an anion counterpart a species with a negative charge on a carbon atom. Carbanion is formed in heterolytic cleavage.

example: H- H+ (CH3)3C Li

(CH3)3C- + Li+ carbanion kation

b)

Free Radical

A very reactive species with an unpaired electron. Formed in homolytic cleavage. Examples:
i)

free radicals
yy

Cl Cl
uv

Cl + Cl

ii)

C
iii)

yy

H3C y y H

H3C

Lecture 7 12.5 Reactions of Organic Compounds

Learning Outcomes:
At the end of the lesson the students should be able to: State the relative stabilities of primary, secondary and tertiary free radicals, carbocations and carbanions. Explain the inductive effect of alkyl group towards the stability of carbocations and carbanions. Define electrophile and nucleophile.

Relative Stabilities of Carbocations, Carbanions and Free Radicals

Carbocation, carbanion and free radical can be classified into: Primary Secondary Tertiary

Carbocation Stability The alkyl groups(electron-releasing/donating group) stabilise the positive charge on the carbocation. The stability of carbocation increases with the number of alkyl groups (R) present. R = - CH3 , -CH2CH3 , -CH2CH2CH3 etc

Carbocation Stability: H R R H H C H < H C R <H C R < R C R + + + + Methyl Primary Secondary Tertiary cation 10 20 30

Increasing stability

Carbanion Stability Alkyl group and other electron-donating groups destabilise carbanions. Electron withdrawing group (e.g: halogen) stabilise carbanions through the inductive withdrawal of electron density

Carbanion Stability: H R R H H C H > H C R >H C R > R C R Methyl anion Primary 10 Secondary 20 Tertiary 30

Increasing stability

Free-radical stability The stability of free radical increases as more alkyl groups are attached to the carbon atom with unpaired electron.

H H C H < H C R < H . . methyl radical Primary 10

Free Radical Stability : R H C .

R R <R C R . Tertiary 30

Secondary 20

Increasing stability

Reagents and sites of organic reactions

A) Electrophile Means electron loving . An electron-deficient species and accepting electron from an attacking nucleophile. Can be either neutral or positively charged

Examples of electrophiles : cations such as H+, H3O+, NO2+ etc. carbocations. Lewis acids such as AlCl3, FeCl3, BF3 etc. oxidizing agents such as Cl2, Br2 and etc. Molecules with incomlpete octet element. (Al, B, Be)

electrophilic sites are molecules with low electron density around a polar bond Examples: ii) i) H+ HH+ H-C = O (carbonyl) ; -C X (haloalkanes)
iii)

H+ H-C OH (hydroxy compounds)

b)Nucleophile means nucleus loving An electron-rich species and electron-pair donor. A nucleophile can be either neutral or negatively charged.

Examples of nucleophiles : anions such as OH-, RO-, Cl-, CN- etc. carbanions ( species with a negative charge on carbon atoms ). double bond between two carbon atoms. molecule with lone pair electron ( NH3). Molecules with expanded octet elements. (S-12e , P-10e)

Classify the following species as nucleophiles or electrophiles: electrophiles:

H+ H2O OHCNBr+

E N N N E

NO2+ NH3 SO3 CH3CH2OHBr

E N N N E

Br2

Lecture 8 12.5 Reactions of Organic Compounds

Learning Outcomes: At the end of the lesson the students should be able to explain the main types of organic reactions: addition: electrophilic and nucleophilic substitution: electrophilic, nucleophilic and free radical elimination rearrangement

4 Types of Organic Reactions

    Addition Substitution Elimination Rearrangement

I) Addition Reaction
A reaction in which atoms or groups add to adjacent atoms of a multiple bond. Two types of addition :a) b) Electrophilic Addition Nucleophilic Addition

a)Electrophilic Addition Initiated by an electrophile accepting electron from an attacking nucleophile. Typical reaction of unsaturated compounds such as alkenes and alkynes. Example :

CH3CH=CH2 + Br2

CCl4 Room temperature

CH3CHBrCH2Br CHBrCH

electrophile

b)

Nucleophilic Addition

Initiated by a nucleophile, which attacks an electrophilic site of a molecule.

Typical reaction of carbonyl compounds.

OH CH3 C CH3 + HCN H

nucleophile electrophilic site

OH CH3 C CN CH3

II) Substitution Reaction

A reaction in which an atom or group in a molecule is replaced by another atom or group. Three types of substitution :a) free radical substitution. b) electrophilic substitution. c) nuclephilic substitution.

a) Free-radical Substitution Substitution which involves free radicals as intermediate species. Example :

CH3CH3 + Cl2

uv light

CH3CH2Cl

+ HCl HCl

b)

Electrophilic Substitution

Typical reaction of aromatic compounds. The aromatic nucleus has high electron density, thus it is nucleophilic and is prone to electrophilic attack. Example: + Br2 electrophile
H H H = H H

Fe catalyst

Br + HBr

high electron density

H

c)

Nucleophilic Substitution
Typical reaction of saturated organic compounds bearing polar bond as functional group, such as haloalkane with alcohol.

Example : H H CH3CH2Br + OH-(aq) nucleophile

CH3CH2OH

+ Br-(aq) Br-

III) Elimination Reaction

An atoms or groups are removed from adjacent carbon atoms of a molecule to form a multiple bond (double or triple bond). Results in the formation of unsaturated molecules. Example : CH3CH2OH conc. H2SO4 CH2= CH2 + H2O (

IV) Rearrangement Reaction

A reaction in which atoms or groups in a molecule change position. Occurs when a single reactant reorganizes the bonds and atoms. Example :

C H

tautomerisme C R H C OH

H C R O

Exercises 1. Explain how the free radicals are formed in homolytic cleavage. 2. Write an equation for the bromine-bromine bond cleavage in the bromination of methane. State the type of bond cleavage.

3.

Which would you expect to be the most stable free radical ?

yCH2CH3 , (CH3)2 CHy , yCH3 , y

CH3

State the type of reaction for each of the following reactions

1. CH2 CHOH CH3CHO CH3CHBr C6H5CH3 + HCl CH2CH2 + H2O CH3CH2OH + HCl

2. CH2CH2 + HBr 3. C6H6 + CH3Cl 4. CH3CH2OH 5. CH3CH2Cl + NaOH

Past year session 2001/02