Introduction To Organic Chemistry

Lecture 1 12.1 Introduction Learning Outcomes: At the end of the lesson the students should be able to : List the elements that made up organic compounds C, H, O, N, P, S and halogens. State the ability of carbon to form 4 covalent bonds with other carbons or elements. Differentiate between saturated and unsaturated organic compounds. 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) methyl salicylic acid (aspirin-a drug)

penicillin (an antibiotic) 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 unsaturated Contains only single bonds ( -C-C- ) Examples: alkanes, cycloalkanes Contains at least one carbon-carbon 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 Engineering Gasoline-as a fuel for internal combustion engines. Biotechnology Genetic information like DNA Agriculture DDT-as insectisides to kill harmful insects.

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.

3 types of structural formula: 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. C4H9Cl CH3CHCH2CH3 (Condensed structure)

Examples: ii) Cyclohexane, C6H12 iii) Aldehyde, CH3CHO 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 Expanded structure C C C C H Cl

Examples: i) Alcohol (C2H6O) ii) Carboxylic acid (C3H6O2 )

Shows only the carbon skeleton. Hydrogen atoms are not written. Skeletal Structure Shows only the carbon skeleton. Hydrogen atoms are not written. Other atoms such as O, Cl, N etc. are shown. i) CH3CH(Cl)CH2CH3 = Cl ii) =

3- Dimensional formula ( wedge – dashed wedge – line formula ) Describes how the atoms of a molecule are arranged in space.

Example : Bromoethane or or 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 secondary carbon(2o) → bonded to 2 C tertiary carbon(3o) → bonded to 3 C quarternary carbon(4o) → bonded to 4 C

H H C H CH3 10 carbon 10 carbon

CH3 H C CH3 CH3 30 carbon

1 H 1 H CH3 CH3 1 1 H C C C CH2 C CH3 H H H CH3 1

H H CH3 CH3 2 H C C C CH2 C CH3 2 H H H CH3

H H CH3 CH3 3 4 H C C C CH2 C CH3 H H H CH3

Question CH3(CH2)CCl(CH3)2 Expanded Structure Condensed Structure Skeletal Structure

12.3 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.

Functional groups are important for three reasons: A basic by which organic compounds are divided into different classes. A basic for naming organic compounds 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.

Homologs Features Obey a general formula: Examples: Alkane: CnH2n+2 Alkene: CnH2n Alcohol : CnH2n+1OH Differ from the successive homolog by a CH2 unit Show a gradual change in the physical properties

Have same functional group Have similar chemical properties Can be prepared by similar general methods

Classification of organic compound Class of Compound Structure Name Example Functional Group Alkane CH3-CH3 Alkene -C=C- carbon-carbon double bond CH3CH=CH2 -C C- Alkyne carbon-carbon triple bond CH3C CCH3

Aromatic Benzene ring -CH3 Haloalkane X (F, Cl, Br, I) Halogen CH3Cl Alcohol -OH Hydroxyl CH3-OH Phenol Ether -C-O-C- Alkoxide CH3-O-CH3

Aldehyde -C=O H Carbonyl CH3-C=O Ketone R-C=O R CH3 Carboxylic acid OH Carboxyl Ester -C-O-C- O Carboalkoxy OCH3 Acyl chloride Cl

Anhydride O O -C-O-C- CH3C-O-CCH3 Amide -C=O N- Carboxamide CH3-C=O NH2 Amine -NH2 Amino CH3-NH2 Nitrile -C N Cyano group CH3C N

Exercises: 1. Identify the functional group in the following molecules (CH3)3CCH2CH=CH2 (CH3)3CCH=CHCH2-OH

CH3 C CH NH2 O CH2 OH c)

12.4 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

Constitutional Isomerism Structural/ Constitutional Isomerism Stereoisomerism diastreomer enantiomer Chain Isomerism Positional Isomerism Functional Group Isomerism 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.

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. Three types a) Chain/skeletal isomerism b) Positional isomerism c) Functional group isomerism

C5H12 CH3CH2CH2CH2CH3 CH3CHCH2CH3 CH3CCH3 CH3 CH3 a) Chain/skeletal isomerism The isomers differ in the carbon skeleton (different carbon chain). They possess the same functional group and belong to the same homologous series. Example: C5H12 CH3CH2CH2CH2CH3 CH3CCH3 CH3 CH3CHCH2CH3 CH3

CH3CH2CH2Cl CH3CHCH3 Cl 2)Positional isomerism These isomers have a substituent group/ functional group in different positions. Examples C3H7Cl CH3CH2CH2Cl 1-chloropropane CH3CHCH3 Cl 2-chloropropane

C4H8 C8H10 C H CH2=CHCH2CH3 CH3CH=CHCH3 1-butene 2-butene 1,2-dimethylbenzene 1,3-dimethylbenzene 1,4-dimethylbenzene

C6H13N

3)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 Classes of compounds CnH2n+2O ; n > 1 alcohol and ether CnH2nO ; n ≥ 3 aldehyde and ketone CnH2nO2 ; n ≥ 2 carboxylic acid and ester CnH2n ; n ≥ 3 alkene and cycloalkane

Examples C2H6O C3H6O C3H6O2 CH3CH2OH CH3OCH3 ethanol dimethyl ether propanone propanal propanoic acid methyl ethanoate

Exercise: 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

Lecture 5 12.4 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 CC 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: Enantiomers (mirror image) Diastereomers (non-mirror image)

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 trans-2-butene cis-2-butene CH3 H H CH3 cis-1,2-dimethylcyclohexane trans-1,2-dimethylcyclohexane

If one of the doubly bonded carbons has 2 identical groups, geometric isomerism is not possible. Example No cis – trans isomer

Lecture 6 12.4 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

The requirements for optical isomerism :- molecule contains a chiral carbon or chirality centre or stereogenic centre (a sp3-hybridized carbon atom with 4 different groups attached to it) ii) molecule is not superimposable with its mirror image. PQRS *designates chiral centre

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

ii) 2-hydroxypropanoic acid, enantiomers

12.4.9 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 plane-polarized 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)

REACTIONS OF ORGANIC COMPOUNDS

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 : X X + X free radicals X X  

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 is more electronegative. 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 :   (CH3)3C — Cl (CH3)3C+ + Cl- carbocation 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:   (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 Cl – Cl uv Cl● + Cl ●

ii) C C ● C + ● C iii) ● H ● + H H3C 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 group) stabilise the positive charge on the carbocation. The stability of carbocation increases with the number of alkyl groups present.

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

Free Radical Stability : H H R C . Tertiary 30 H H C R H R C H C . < . < . < methyl radical Primary 10 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.

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

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 ).

Lecture 7 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) Electrophilic Addition b) Nucleophilic Addition

CH3CH=CH2 + Br2 CH3CHBrCH2Br electrophile 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 CH3CHBrCH2Br electrophile CCl4 Room temperature

b) Nucleophilic Addition Initiated by a nucleophile, which attacks an electrophilic site of a molecule. Typical reaction of carbonyl compounds.  CN O + HCN CH3 C CH3 CH3 C CH3  OH

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.

CH3CH3 + Cl2 uv light CH3CH2Cl + HCl a) Free-radical Substitution Substitution which involves free radicals as intermediate species. Example : CH3CH3 + Cl2 uv light CH3CH2Cl + 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. + Br2 Br + HBr electrophile Example: Fe catalyst

c) Nucleophilic Substitution Typical reaction of saturated organic compounds bearing polar bond as functional group, such as haloalkane with alcohol. Example :   CH3CH2Br + OH-(aq) CH3CH2OH + Br-(aq) nucleophile Δ

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 : H tautomerisme H C C R H C C R H H O OH

Exercises 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 3. Which would you expect to be the most stable free radical ? CH2CH3 , (CH3)2 CH , CH3 ,  CH3