1

Organic and Biological

Molecules

Chapter 22

2

Organic Chemistry and Biochemistry

The study of carbon-containing

compounds and their properties.

The vast majority of organic

compounds contain chains or rings

of carbon atoms.

The study of the chemistry of living

matter

3

Hydrocarbons

compounds composed of carbon and

hydrogen.

Saturated compounds (alkanes) have

the maximum number of hydrogen

atoms attached to each carbon atom

H C

H

H

C

H

H

H

4

Unsaturated compounds have fewer

hydrogen atoms attached to the carbon

chain than alkanes

Unsaturated: They contain carbon-carbon

multiple bonds (double or triple)

H C

H

H

C

H

C

H

H

5

22.1 Alkanes: Saturated hydrocarbons

Saturated hydrocarbons, CnH2n+2

“Saturated” because they can’t take

any more hydrogen atoms

Normal straight chains (unbranched

hydrocarbons)

H3C–(CH2)n–2–CH3

Waxes, oils, & fuel gases as n

decreases.

6

Alkanes: Saturated Hydrocarbons

The C-H Bonds in Methane

7

The Lewis structure of ethane.

8

Propane

9

Butane

10

The First 10 “Normal” Alkanes

Name Formula M.P. B.P. # Structural Isomers

Methane CH4 -183 -162 1

Ethane C2H6 -172 -89 1

Propane C3H8 -187 -42 1

Butane C4H10 -138 0 2

Pentane C5H12 -130 36 3

Hexane C6H14 -95 68 5

Heptane C7H16 -91 98 9

Octane C8H18 -57 126 18

Nonane C9H20 -54 151 35

Decane C10H22 -30 174 75

C1 - C4 are Gases

at Room Temperature

C5 - C16 are Liquids

at Room Temperature

11

IUPAC Rules for Naming Branched Alkanes

• Find and name the parent chain in the hydrocarbon -

this forms the root of the hydrocarbon name

• Number the carbon atoms in the parent chain

starting at the end closest to the branching

• Name alkane branches by dropping the “ane” from

the names and adding “yl”. A one-carbon branch is

called “methyl”, a two-carbon branch is “ethyl”,

etc…

• When there are more than one type of branch (ethyl

and methyl, for example), they are named

alphabetically

• Finally, use prefixes to indicate multiple branches

12

Rules for Naming Alkanes

1. For alkanes beyond butane, add -ane to

the Greek root for the number of

carbons.

C-C-C-C-C-C : hexane

2. Alkyl substituents: drop the -ane and

add -yl

-C2H5 is ethyl

13

14

Rules for Naming Alkanes

3. Positions of substituent groups are specified by numbering the longest chain sequentially.

C C-C-C-C-C-C

3-methylhexane

Start numbering at the end closest to the branching

4. Location and name are followed by root alkane name. Substituents are given in alphabetical order and use di-, tri-, etc.

15

Normal vs Branched Alkanes

Normal alkanes consist of

continuous chains of

carbon atoms

Alkanes that are NOT

continuous chains of

carbon atoms contain

branches

The longest continuous

chain of carbons is called

the parent chain

CH3

CH2

CH2

CH2

CH3

CH3

CH2

CH

CH3

CH3

16

Structural Isomerism

Structural isomers are

molecules with the same

chemical formulas but

different molecular

structures - different

“connectivity”.

They arise because of the

many ways to create

branched hydrocarbons.

CH3

CH2

CH2

CH2

CH3

CH3

CH2

CH

CH3

CH3

n-pentane, C5H12

2-methlbutane, C5H12

17

Example : Show the structural formula

of 2,2-dimethylpentane

The parent chain is indicated by the ROOT of the name - “pentane”. This means there are 5 carbons in the parent chain.

CH3

CH2

CH2

CH2

CH3

• “dimethyl” tells us that there are

TWO methyl branches on the

parent chain. A methyl branch is

made of a single carbon atom.

• “2,2-” tell us that BOTH methyl

branches are on the second

carbon atom in the parent chain.

CH3

1

C

CH23

CH2

4

CH35

CH3

CH3

1

2

3

4

5

18

Example: Structural formula of 3-ethyl-2,4-dimethylheptane?

The parent chain is

indicated by the ROOT

of the name -

“heptane”. This means

there are 7 carbons in

the parent chain.

CH3

CH2

CH2

CH2

CH2

CH2

CH3

• “2,4-dimethyl” tells us there are

TWO methyl branches on the

parent chain, at carbons #2 and

#4.

• “3-ethyl-” tell us there is an ethyl

branch (2-carbon branch) on

carbon #3 of the parent chain.

1

2

3

4

5

7 6

CH3

CH

CH

CH

CH2

CH2

CH3

CH2

CH3

CH3

CH3

19

Example: 2,3,3-trimethyl-4-propyloctane

The parent chain is indicated

by the ROOT of the name -

“octane”. This means there

are 8 carbons in the parent

chain.

• “2,3,3-trimethyl” tells us there are

THREE methyl branches - one on

carbon #2 and two on carbon #3.

• “4-propyl-” tell us there is a propyl

branch (3-carbon branch) on

carbon #4 of the parent chain.

1

2

3

4

5

7

6

8

1

2 3

4

5

7

6

8

CH

C

CH

CH2

CH2

CH2

CH3

CH3

CH3

CH3

CH3

CH2

CH2

CH3

20

Example : Name the molecules shown

parent chain has 5 carbons -

“pentane”

two methyl branches - start

counting from the right - #2

and #3

2,3-dimethylpentane

CH3

CH2

CH

CH

CH3

CH3

CH3

parent chain has 8 carbons - “octane”

two methyl branches - start counting

from the left - #3 and #4

one ethyl branch - #5

name branches alphabetically

3,4-dimethyl

4 3

octane

5

5-ethyl-

21

Reactions of alkanes

Combustion reactions

2C4H10 + 13 O2 8CO2 + 10 H2O(g)

Substitution Reactions

CH4 + Cl2 CH3Cl + HCl

CH3Cl + Cl2 CH2Cl2 + HCl

CH2Cl2 + Cl2 CH Cl3 + HCl

CHCl3 + Cl2 C Cl4

22

Dehydrogenation Reactions

CH3CH3 CH2 CH2

Ethylene

23

Cyclic alkanes

CnH2n

A cycloalkane is made of a hydrocarbon

chain that has been joined to make a

“ring”.

CH

3

CH2

CH3 CH

2

C

H2

CH2

n-propaneC3H8

cyclopropaneC3H6

60° bond angleunstable!!

109.5° bond angle

•Note that two hydrogen atoms were lost in forming the ring

24

Ring Structures

25

Cyclohexane - Boat & Chair Conformations

Cyclohexane is NOT a planar molecule. To achieve

its 109.5° bond angles and reduce angle strain, it

adopts several different conformations.

The BOAT and CHAIR (99%) are two conformations

Boat

chair

26

22.2 Alkenes and Alkynes

Alkenes: hydrocarbons that contain a

carbon-carbon double bond. [CnH2n]

C=C Ethene

CC=C propene

Alkynes: hydrocarbons containing a

carbon-carbon triple bond. [CnH2n-2]

C ΞC Ethyne

CCC Ξ CC 2-pentyne

27

Alkenes & Alkynes

Alkenes are

hydrocarbons that

contain at least one

carbon-carbon double

bond

Alkynes are

hydrocarbons that

contain at least one

carbon-carbon triple

bond

The suffix for the parent

alkane chains are

changed from “ane” to

“ene” and “yne”

e.g. ethene, ethyne

Where it is ambiguous,

the BONDS are

numbered like branches

so that the location of the

multiple bond may be

indicated

28

n2Hnnes, CeAlk

Cycle formation isn’t the only possible

result of dehydrogenation.

Adjacent C’s can double bond, C=C,

making an (unsaturated) alkene.

Sp2

29

Nomenclature for Alkenes

1. Parent hydrocarbon name ends in -ene

C2H4; CH2=CH2 is ethene

2. With more than 3 carbons, double bond

is indicated by the lowest numbered

carbon atom in the bond.

C=C-C-C is 1-butene

30

Nomenclature alkenes and alkynes

31

Cis and Trans Isomers

Double bond is fixed (rotation around the

double bond is restricted)

Cis/trans Isomers are possible

CH3 CH3 CH3

CH = CH CH = CH

cis trans CH3

32

Reactions of alkenes and alkynes

in which (weaker) bonds are broken

and new (stronger) bonds are formed

to atoms being added.

1. Addition Reactions

33

Hydrogenation reaction

Adds a hydrogen atom to each carbon atom

of a double bond H H H H catalyst

H–C=C–H + H2 H–C–C–H H H Ethene Ethane

CH3-CH3

34

Halogenation reaction

Adds a halogen atom to each carbon atom of

a double bond H H H H catalyst

H–C=C–H + Cl2 H–C–C–H Cl Cl Ethene Dichloro ethane

35

Halogenation Reactions

CH2 CHCH2CH2CH2 + Br2

CH2Br CHBrCH2CH2CH2

1,2-dibromopentane

36

Alkynes, CnH2n–2

Carbon-carbon triple bonds

Names end in -yne

HCCH ethyne(acetylene)

HCC-CH3 propyne

•sp triple bonding makes a rigid 180°

segment in a hydrocarbon.

37

The Bonding in Acetylene

38

Naming Alkenes and Alkynes

When the carbon chain has 4 or more C atoms,

number the chain to give the lowest number to the

double or triple bond.

1 2 3 4

CH2=CHCH2CH3 1-butene

CH3CH=CHCH3 2-butene

CH3CHCHCH3 2-butyne

39

Question

Write the IUPAC name for each of the following

unsaturated compounds:

A. CH3CH2CCCH3

CH3

B. CH3C=CHCH3 C.

CH32-pentyne

2-methyl-2-butene 3-methylcyclopentene

40

Question

Name the following compound

CH3CH2C CCHCH2CH3

CH2

CH3

CH3CH2C CCHCH2CH3

CH2

CH3

1 2 3 4 5 6 7

5-ethyl-3-heptyne

41

Additions reactions:Hydrogenation and

Halogenation

Hydrogens and halogens also add to

the triple bond of an alkyne.

CH3C CCH2CH3 + Br2 CH3C CCH2CH3

Br Br

Br Br

42

22.3 Aromatic hydrocarbons

Unsaturated Cyclic hydrocarbons

Alternating single/double bond

cycles occur in many organic molecules

This class is called “aromatic” (by

virtue of their aroma).

• Delocalized bonds

possess a great stability

thus benzene does not

react like unsaturated

hydrocarbons

43

Benzene C6H6

sp2

sp2 sp2

The structure is

often preserved in

benzene chemical

reactions

Aromatic rings

do not add, they

substitute instead

44

Shorthand notation for benzene rings

The bonding in the

benzene ring is a

combination of different

Lewis structures

45

Aromatic Hydrocarbons

Substitution reaction

+ Cl2

FeCl3

Cl

+ HCl

+H2O

+HCl

benzene

Chlorobenzene

H

N

O

3

HNO3

CH3Cl

-NO2

-CH3

Nitroobenzene

Toluene

46

47

Nomenclature of benzene derivatives

48

More Complex Aromatic Systems

49

22.4 Hydrocarbon Derivatives

(Functional Groups)

Molecules that are fundamentally hydrocarbons

but have additional atoms or group of atoms

called functional groups

Part of an organic molecule where chemical

reactions take place

Replace an H in the corresponding alkane

Provide a way to classify organic compounds

50

The Common Functional Groups

Class General Formula

Halohydrocarbons RX

Alcohols ROH

Ethers ROR

Aldehydes R C

O

H

51

Class General Formula

Ketones

Carboxylic Acids

Esters

Amines

R C

O

R'

R C

O

OH

R C

O

OR'

R NH2

52

Some Types of Functional Groups

Haloalkane -F, -Cl, -Br CH3Cl

Alcohol -OH CH3OH

Ether -O- CH3-O-CH3

Aldehyde

Ketone

C H

O

CH3CH

O

C

O

CH3CCH3

O

53

More Functional Groups

Carboxylic acid -COOH CH3COOH

Ester -COO- CH3COOCH3

Amine -NH2 CH3NH2

Amide -CONH2 CH3CONH2

54

55

Haloahydrocarbons

An alkane in which one or more H atoms is

replaced with a halogen (F, Cl, Br, or I)

CH3Br bromomethane

Br (methyl bromide)

CH3CH2CHCH3 2-bromobutane

Cl

chlorocyclobutane

56

Name the following:

bromocyclopentane

1,3-dichlorocyclohexane

Br

Cl

Cl

1 2

3

57

Substituents

List other attached atoms or groups in

alphabetical order

Br = bromo, Cl = chloro

Cl Br

CH3CHCH2CHCH2CH2CH3

4-bromo-2-chloroheptane

1 2 3 4 5

58

Nomenclature

The name of this compound is:

Cl CH3

CH3CH2CHCH2CHCH3

4-chloro-2-methylhexane

59

Alcohols: R–OH The –OH makes alcohol polar enough to

hydrogen bonding

Thus, they are water soluble

Ethanol is produced by the fermentation of

glucose

yeast C6H12O6

Glucose 2CH3CH2OH

Ethanol + 2 CO2

CO + 2H2O CH3OH

Methanol

• Methanol is produced industrially by hydrogenation

of carbon monoxide

60

Uses of alcohols

Methanol is used to synthesize adhesives, fibers,

plastics and recently as motor fuel

It is toxic to human and can lead to blindness and

death

Ethanol can be added to gasoline to form gasohol

and used in industry as solvent

Commercial production of ethanol:

CH2=CH2 + H2O CH3CH2OH

61

Classes of alcohols

R CH2OH

Primary alchol

CHOHR'

RSecondary alcohol

CR'R

R"OH

Tertiary alcohol

Alcohols can be classified according to the

number of hydrocarbon fragments bonded to

the carbon where the –OH group is attached

62

Naming Alcohols

In IUPAC name, the -e in alkane name is

replaced with -ol.

CH4 methane

CH3OH methanol (methyl alcohol)

CH3CH3 ethane

CH3CH2OH ethanol (ethyl alcohol)

63

OH

Phenol

(Aromatic alcohol)

64

Some Typical Alcohols

OH

“Rubbing alcohol” CH3CHCH3

2-propanol (isopropyl alcohol)

Antifreeze HO-CH2-CH2-OH

1,2-ethanediol (ethylene glycol)

65

Naming Alcohols

IUPAC names for longer chains number the chain from the end nearest the -OH group.

CH3CH2CH2OH 1-propanol

OH

CH3CHCH3 2-propanol

CH3 OH

CH3CHCH2CH2CHCH3 5-methyl-2-hexanol

5 2

66

Name the following alcohols:

OH

CH3CHCHCH2CH3

CH3

Example

3-methyl-2-pentanol

67

Aldehydes and Ketones

In an aldehyde, an H atom is attached to a carbonyl

group

O carbonyl group

CH3-C-H

In a ketone, two carbon groups are attached to a

carbonyl group

O carbonyl group

CH3-C-CH3

68

Naming Aldehydes

IUPAC name: Replace the -e in the alkane name by -al

Common Add aldehyde to the prefixes form (1C), acet (2C), propion(3), and butry(4C)

O O O H-C-H CH3-C-H CH3CH2C-H

methanal ethanal propanal

(formaldehyde) (acetaldehyde) (propionaldehyde)

methane ethane propane

69

Aldehydes as Flavorings

CH

O

CH

O

HO

OCH3

CH=CH CH

O

Benzaldehyde Vanillin Cinnamaldehyde(almonds) (vanilla beans) (cinnamon)

70

Naming Ketones

IUPAC name: the -e in the alkane name is replaced with –one

and a number to indicate the position of carbonyl group when

needed.

In the common name, add the word ketone

after naming the alkyl groups attached to the

carbonyl group

O O

CH3 -C-CH3 CH3-C-CH2-CH3

2-Propanone 2-Butanone

(Dimethyl ketone) (Ethyl methyl ketone)

O

Cyclohexanone

Acetone

propane

butane

cyclohexane

71

Name the following compounds

O

A. CH3CH2CCH3 B.

2-butanone (ethyl methyl ketone)

CH3 O

C. CH3-C-CH2CH cyclohexanone CH3

3,3-dimethylbutanal

O

72

Draw the structural formulas for each of the following

compounds

CH3 O

A. 3-Methylpentanal CH3CH2CHCH2CH

Br O

B. 2,3-Dibromopropanal Br-CH2CHCH

O

C. 3-Methyl-2-butanone CH3CHCCH3

CH3

73

Preparation of aldehydes and Ketones

They are produced by oxidation of alcohols:

CH3CH2OH Oxidation

CH3CHCH3

OH

Oxidation CH3CCH3

O

CH3C

O

Hacetaldehyde

acetone

Primary alcohol

Secondary alcohol

ethanal

propanone

74

Carboxylic Acids and Esters

Carboxylic acids contain the carboxyl group as

carbon 1.

O

R

CH3 — C—OH CH3—COOH

carboxyl group

General formula R—COOH

75

Nomenclature of Carboxylic Acids

Formula IUPAC Common

alkan -oic acid prefix – ic acid

HCOOH methanoic acid formic acid

CH3COOH ethanoic acid acetic acid

CH3CH2COOH propanoic acid propionic acid

CH3CH2CH2COOH butanoic acid butyric acid

76

IUPAC nomenclature for Carboxylic acids

Identify longest chain

Number carboxyl carbon as 1

CH3

|

CH3 — CH—CH2 —COOH

3-methylbutanoic acid

1 2 3 4

77

CH3

|

CH3CHCOOH

2-methylpropanoic acid;

78

Reaction of carboxylic acid with alcohol

CH3CO

OH + H OCH2CH3

CH3C

O

OCH2CH3 + H2O

Ester

Carboxylic acid Alcohol

Esterification

79

Esters

In ester, the H in the carboxyl group is replaced with

an alkyl group

O

CH3 — C—O —CH3 CH3—COO —CH3

ester group

•Esters give fruity odors

80

Naming Esters

• The parent alcohol is named first with a –yl ending

• Change the –oic ending of the parent acid to –ate

acid alcohol

O

methyl

CH3 — C—O —CH3

Ethanoate methyl ethanoate (IUPAC)

(acetate) methyl acetate (common)

81

Amines

Organic compounds of nitrogen N; derivatives of ammonia

Classified as primary, secondary, tertiary

CH3 CH3

CH3—NH2 CH3—NH CH3—N — CH3

Primary Secondary Tertiary

one N-C two N-C three N-C

bond bonds bonds

82

Naming Amines

IUPAC aminoalkane Common alkylamine

CH3CH2NH2

aminoethane

(ethylamine)

NH2

|

CH3CHCH3

2-aminopropane Aniline

(isopropylamine)

NH2

83

22.5 Polymers

Poly= many; mers=parts

Polymers are large, usually chainlike

molecules that are built from small

molecules called monomers joined by

covalent bonds

Monomer Polymer

Ethylene Polyethylene

Vinyl chloride Polyvinyl

chloride

Tetrafluoroethylene Teflon

84

Some common synthetic polymers, their

monomers and applications

85

Types of Polymerization

Addition Polymerization: monomers “add

together” to form the polymer, with no other

products. ( Polyethylene and Teflon)

Condensation Polymerization: A small

molecule, such as water, is formed for each

extension of the polymer chain. (Nylon)

86

Addition Polymerization

OH

C CH

H

H

HC

OH

H C

H

H

H

C CH

H

H

H

C

OH

H C

H

H

H

C

OH

H C

H

H

H

C CH H

H H

The polymerization process

Is initiated by a free radical

A species with

an unpaired

electron such as

hydroxyl free radical

Free radical attacks and break

The bond of ethylene molecule

To form a new free radical

• Repetition of the process thousands of times creates a long chain

polymer

• The process is terminated when two radicals react to form a bond;

thus there will be no free radical is available for further repetitions.

87

Condensation Polymerization

Formation of Nylon

N

H

H(CH2)6 N

H

H CO

O(CH2)4H

CO

O H

Hexamethylendiamine Adipic acid

N

H

H(CH2)6 N

H

C (CH2)4 CO

O H

O

+ H2O

• Small molecule such as H2O is formed

from each extension of the polymer chain

• both ends are free to react

Dimer

Diamine Dicarboxylic acid

88

N

H

(CH2)6 NH

( C (CH2)4 COO

)n

Nylon