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Organic and Biological

Molecules

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
2

Hydrocarbons

compounds composed of carbon and


hydrogen.
Saturated compounds (alkanes) have
the maximum number of hydrogen
atoms attached to each carbon atom
H H
H C

H H
3

Unsaturated compounds have


fewer hydrogen atoms attached
to the carbon chain than alkanes
Unsaturated: They contain
carbon-carbon multiple bonds
(double or triple)
H H
H
H C
H

C
H
4

22.1 Alkanes: Saturated hydrocarbons

Saturated hydrocarbons, CnH2n+2


Saturated because they cant take any more
hydrogen atoms
Normal straight chains (unbranched hydrocarbons)
H3C(CH2)n2CH3
Waxes, oils, & fuel gases as n decreases.

Alkanes: Saturated Hydrocarbons


The C-H Bonds in Methane

.The Lewis structure of ethane

Propane

Butane

The First 10 Normal Alkanes


Name
Isomers

Formula

M.P.

B.P.

# Structural

Methane CH4
-183 -162
C1
- C4 are
Ethane C2H
-172Gases
-89
6
Propane Cat
-187 -42
Temperature
3HRoom
8
Butane C4H10
Pentane C5H12
Hexane C6H14
Heptane
Octane

-138
-130

0
36

-95
-91

68
98

C7H16
C5
C16
are
Liquids
C8H18
-57 126

Room Temperature
Nonane Cat
-54 151
9H20
Decane C10H22
-30 174

1
1
1
2
3
5
9
18
35
75
10

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

11

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
12

13

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.

14

Normal vs Branched Alkanes

CH3

CH2

CH3

CH2

CH2

CH2

CH
CH3

CH3

CH3

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
15

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

n-pentane, C5H12
CH3

CH2

CH

CH3

CH3

2-methlbutane, C5H
16 12

Optical Isomerism
Arises when at least one carbon atom in a molecule is
bonded to four different atoms or groups, HCIBrCl is

chiral and the two forms are called enantiomers (optical


isomers)

Enantiomer s rotate the plane of polarized light clockwise or


, anticlockwise
When the two enantiomers are present in a sample in equal 17
amounts, we have a racemic mixture, no effect on plane-polarized

Exercise

18

Example : Show the structural formula


of 2,2-dimethylpentane

2
The parent chain is
4
CH2 5
CH2 3
indicated by the ROOT of
1
the name - pentane. This CH
CH3
CH2
3
means there are 5 carbons
in the parent chain.

dimethyl
dimethyl tells us that there are
TWO methyl branches on the
parent chain. A methyl branch is
made of a single carbon atom.

CH3
4

C
1

CH3

CH2

CH3

CH2

CH3
5

2,2-
2,2 tell us that BOTH methyl
branches are on the second
carbon atom in the parent chain.19

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

CH3

CH

CH

CH3
CH3

CH

CH2

CH2

CH2

2
1

CH3

CH2

CH2

CH2

CH2

H2C 6

CH3
2,4-dimethyl
2,4-dimethyl tells us there are
TWO methyl branches on the
parent chain, at carbons #2 and
#4.
CH3

3-ethyl-
3-ethyl tell us there is an ethyl
branch (2-carbon branch) on 20

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.

5
4

6
7

CH3 tells us there are


2,3,3-trimethyl
2,3,3-trimethyl
THREE
methyl
branches
CH
C
CH2 - one on
3
CH#2 andCH
CH2 #3.
carbon
two on carbon

5
4

6
7
8

CH3

CH3

CH2

CH2

4-propyl-
is a propyl
4-propyl tell us there
CH3
CH2
branch (3-carbon branch) on
3
carbon #4 of the CH
parent
chain. 21

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

CH3

CH2

CH
CH

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

5-ethyl-3,4-dimethyl octane

22

Reactions of alkanes

Combustion reactions

2C4H10 + 13 O2
H2O(g)

8CO2 + 10

Substitution Reactions

CH4 + Cl2

CH3Cl + HCl

CH3Cl + Cl2

CH2Cl2 + HCl

CH2Cl2 + Cl2

CH Cl3 + HCl

CHCl3 + Cl2

C Cl4
23

Dehydrogenation Reactions
CH3CH3

CH2
CH2
Ethylene

24

Cyclic alkanes
CnH2n

A cycloalkane is made of a hydrocarbon


chain that has been joined to make a ring.
H2
C

109.5 bond angle

CH3

CH2

CH3

n-propane
C3H8

H2C

60 bond angle
unstable!!

CH2

cyclopropane
C3H6

Note that two hydrogen atoms were lost in forming the ring
25

Ring Structures

26

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

27

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 C

Ethyne

CCC CC

2-pentyne
28

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
29

Alkenes, CnH2n

Cycle formation isnt the only possible


result of dehydrogenation.
Adjacent Cs can double bond, C=C,
making an (unsaturated) alkene.
Sp2

30

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
31

Nomenclature of alkenes
and alkynes

32

Cis and Trans Isomers

Double bond is fixed (rotation around the


double bond is restricted)
Cis/trans Isomers are possible

CH3

CH3

CH = CH

cis

CH3
CH = CH

trans

CH3
33

Reactions of alkenes and alkynes


1. Addition Reactions

in which (weaker) bonds are


broken and new (stronger) bonds
are formed to atoms being added.

34

Hydrogenation reaction
Adds

a hydrogen atom to each


carbon atom of a double bond
H H
H H
catalyst

HC=CH + H2

H C C H

CH3-CH3

H H
Ethene

Ethane
35

Halogenation reaction
Adds

a halogen atom to each


carbon atom of a double bond
H H
H H
catalyst

HC=CH + Cl2

HCCH

Cl Cl
Ethene
ethane

Dichloro
36

Halogenation Reactions

CH2

CHCH2CH2CH2 + Br2
CH2Br

CHBrCH2CH2CH2

1,2-dibromopentane

37

Alkynes, CnH2n2
sp triple bonding makes a rigid 180
segment in a hydrocarbon.

Carbon-carbon triple bonds


Names end in -yne
HCCH
HCC-CH3

ethyne(acetylene)
propyne
38

The Bonding in
Acetylene

39

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

2-butyne

CH3CH CHCH3

40

Question
Write the IUPAC name for each of the
following unsaturated compounds:
A.

CH3CH2CCCH3

CH3

2-pentyne

CH3
B.

CH3C=CHCH3
methyl-2-butene-2

C.
3-methylcyclopentene
41

Question

Name the following compound


CH3CH2C CCHCH2CH3
CH2
CH3
1

4 5

CH3CH2C CCHCH2CH3
CH2
CH3
5-ethyl-3-heptyne

42

Additions reactions:Hydrogenation and


Halogenation
Hydrogens and halogens also add to
the triple bond of an alkyne.
Br Br
CH3C CCH2CH3

+ Br2

CH3C CCH2CH3
Br Br

43

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

44

Benzene C6H6
structure is
often preserved in
benzene chemical
reactions
Aromatic rings
do not add, they
substitute instead
The

sp2

sp2

sp2

45

Shorthand notation for benzene rings

The bonding in the


benzene ring is a
combination of different
Lewis structures
46

Aromatic Hydrocarbons
Substitution reaction
Nitroobenzene
Chlorobenzene

Cl

+ Cl2
benzene

FeCl 3


HNO3
CH3Cl

-NO2
-CH3
Toluene

+ HCl
+H2O
+HCl

47

48

Nomenclature of benzene derivatives

49

More Complex Aromatic Systems

50

Hydrocarbon Derivatives 22.4


(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
51

The Common Functional Groups


Class
General
Formula
Halohydrocarbons
R X
Alcohols
R OH
Ethers
RO O R
Aldehydes

C H

52

Class
Formula
Ketones
Carboxylic Acids
Esters

General
R

O
C R'

O
C OH

O
C OR'

NH2

Amines
53

Some Types of Functional


Groups
Haloalkane
Alcohol
Ether
CH3

-F, -Cl, -Br CH3Cl


-OH
CH3OH
-OO
C H

Aldehyde
Ketone

CH3-OO
CH 3CH

CH3CCH3
54

More Functional Groups


Carboxylic acid
Ester
Amine
Amide

-COO-NH2
-CONH2

-COOH

CH3COOH

CH3COOCH3
CH3NH2
CH3CONH2

55

56

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

57

rC
B
lC
l

Name the following:

bromocyclopentane

1 2
3

1,3dichlorocyclohexane
58

Substituents
List other attached atoms or groups
in alphabetical order
Br = bromo, Cl = chloro
Cl
Br
1

CH3CHCH2CHCH2CH2CH3
4-bromo-2-chloroheptane
59

Nomenclature
The name of this compound is:
Cl

CH3

CH3CH2CHCH2CHCH3
4-chloro-2-methylhexane

60

Alcohols: ROH
The OH makes alcohol polar enough
to hydrogen bonding
Thus, they are water soluble
Ethanol is produced by the
fermentation of glucose
C6H12O6
Glucose

yeast

2CH3CH2OH
Ethanol

+ 2 CO2

Methanol is produced industrially by hydrogenation


of carbon monoxide

CO + 2H2O

CH3OH
Methanol
61

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

62

Classes of alcohols
Alcohols can be classified according to the
number of hydrocarbon fragments bonded to
the carbon where the OH group is attached

CH2OH Primary alchol

R
CHOH Secondary alcohol
R'
R
R' C OH Tertiary alcohol
R"

63

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)
64

OH

Phenol
(Aromatic alcohol)
65

Some Typical Alcohols


OH
Rubbing alcohol

CH3CHCH3

2-propanol (isopropyl alcohol)


Antifreeze

HO-CH2-CH2-OH

1,2-ethanediol (ethylene glycol)

66

Naming Alcohols

IUPAC names for longer chains number


the chain from the end nearest the -OH
group.

CH3CH2CH2OH

1-propanol

OH
CH3CHCH3
CH3

2-propanol
2

OH

CH3CHCH2CH2CHCH3 5-methyl-2-hexanol
67

Example
Name the following alcohols:
OH
CH3CHCHCH2CH3
CH3
3-methyl-2-pentanol
68

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

CH3-C-CH3

carbonyl group
69

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 butyr(4C)
O
O
O

methane
propane
ethane
H-C-H CH3-C-H
CH3CH2C-H
methanal
ethanal propanal

(formaldehyde) (acetaldehyde)
(propionaldehyde)

70

Aldehydes as Flavorings
O

CH

CH

O
CH=CH CH

HO
OCH3
Benzaldehyde
(almonds)

Vanillin
(vanilla beans)

Cinnamaldehyde
(cinnamon)

71

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
butane

propane

CH3 -C-CH3
2-Propanone

cyclohexane

CH3-C-CH2-CH3
2-Butanone

(Dimethyl ketone) (Ethyl methyl ketone)

Cyclohexanone
Acetone

72

Name the following compounds


O

A. CH3CH2CCH3

O
B.

2-butanone (ethyl methyl ketone)


CH3

C. CH3-C-CH2CH
cyclohexanone
CH3
3,3-dimethylbutanal
73

Draw the structural formulas for each of the following


compounds

CH3

A. 3-Methylpentanal
Br O

CH3CH2CHCH2CH

B. 2,3-Dibromopropanal

Br-CH2CHCH
O

C. 3-Methyl-2-butanone

CH3CHCCH3

CH3
74

Preparation of aldehydes and


Ketones
They are produced by oxidation of
alcohols:
O
Oxidation

CH
3CH
2OH
Primary
alcohol

CH3CHCH3
OH

Oxidation

CH3C

acetaldehyde

ethanal

CH3CCH3 acetone
propanone
O

Secondary alcohol
75

Carboxylic Acids and Esters


Carboxylic acids contain the carboxyl
group as carbon 1.
O
R

CH3 COH
CH3COOH
carboxyl group
General formula
RCOOH
76

Nomenclature of Carboxylic Acids


Formula IUPAC
alkan -oic acid
HCOOH

Common
prefix ic acid

methanoic acid

CH3COOH

ethanoic acid

CH3CH2COOH

propanoic acid

CH3CH2CH2COOH butanoic acid

formic acid
acetic acid
propionic acid
butyric acid

77

IUPAC nomenclature for


Carboxylic acids

Identify longest chain


Number carboxyl carbon as 1
CH3
| 2
1
CH3 CHCH2 COOH
3-methylbutanoic acid

78

CH3
|
CH3CHCOOH
2-methylpropanoic acid;

79

Reaction of carboxylic acid with alcohol

Esterification
O
CH3C OH
Carboxylic acid

H OCH2CH3
Alcohol

O
CH3C OCH2CH3

H2O

Ester

80

Esters
In ester, the H in the carboxyl group is
replaced with an alkyl group

CH3 CO CH3
CH3

CH3COO

ester group

Esters give fruity odors


81

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 CO CH3
Ethanoate
methyl ethanoate (IUPAC)
(acetate)
methyl acetate (common)
82

Amines
Organic compounds of nitrogen N;
derivatives of ammonia
Classified as primary, secondary, tertiary
CH3
CH3

CH3NH2
CH3NH
CH3N CH3

Primary

Secondary

one N-C
bond

two N-C
bonds

Tertiary

three N-C
bonds
83

Naming Amines
IUPAC aminoalkane

Common alkylamine

CH3CH2NH2
aminoethane
(ethylamine)

NH2

N H2
|
CH3CHCH3
2-aminopropane
(isopropylamine)

Aniline
84

Organic Reactions
In general, we look at what occurs and try to
learn how it happens
Common patterns describe the changes
Addition reactions two molecules combine

Elimination reactions one molecule splits into


two

85

Organic Reactions
Substitution Reactions parts from
two molecules exchange

Rearrangement reactions a molecule undergoes


changes in the way its atoms are connected

86

Exercise

87

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
88

Some common synthetic polymers, their


monomers and applications

89

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)

90

Addition Polymerization
H
H
C C
H
H

H H
H C C
OH H

A species with
an unpaired
electron such as
hydroxyl free radical

OH
The polymerization process
Is initiated by a free radical

H
H
C C
H
H
H H
H C C

H H H H
H C C C C
OH H H H

Free radical attacks and break


The bond of ethylene molecule
To form a new free radical

OH H

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.
91

Condensation Polymerization
Formation of Nylon
H

O
O
N (CH2)6 N
C (CH2)4 C
H
H
H O
O H
Adipic acid
Hexamethylendiamine
Diamine
H
H

Dicarboxylic acid

H O
O
(CH2)6 N C (CH2)4 C
O H
Dimer

+ H2O

Small molecule such as H2O is formed


from each extension of the polymer chain
both ends are free to react
92

Nylon
H
(

H O
O
(CH2)6 N C (CH2)4 C )n

93

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