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, C
n
H
2n+2

Saturated because they cant take
any more hydrogen atoms
Normal straight chains (unbranched
hydrocarbons)
H
3
C(CH
2
)
n2
CH
3
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 CH
4
-183 -162 1
Ethane C
2
H
6
-172 -89 1
Propane C
3
H
8
-187 -42 1
Butane C
4
H
10
-138 0 2
Pentane C
5
H
12
-130 36 3
Hexane C
6
H
14
-95 68 5
Heptane C
7
H
16
-91 98 9
Octane C
8
H
18
-57 126 18
Nonane C
9
H
20
-54 151 35
Decane C
10
H
22
-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
-C
2
H
5
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
CH
3
CH
2
CH
2
CH
2
CH
3
CH
3
CH
2
CH
CH
3
CH
3
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.
CH
3
CH
2
CH
2
CH
2
CH
3
CH
3
CH
2
CH
CH
3
CH
3
n-pentane, C
5
H
12

2-methlbutane, C
5
H
12

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.
CH
3
CH
2
CH
2
CH
2
CH
3
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.
CH
3
1
C
CH
2
3
CH
2
4
CH
3
5
CH
3
CH
3
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.
CH
3
CH
2
CH
2
CH
2
CH
2
C H
2
CH
3
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
CH
3
CH
CH
CH
CH
2
CH
2
CH
3
CH
2
CH
3
CH
3
CH
3
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
CH
2
CH
2
CH
2
CH
3
CH
3
CH
3
CH
3
CH
3
CH
2
CH
2
CH
3
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
CH
3
CH
2
CH
CH
CH
3
CH
3
CH
3
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
2C
4
H
10
+ 13 O
2
8CO
2
+ 10 H
2
O(g)
Substitution Reactions
CH
4
+ Cl
2
CH
3
Cl + HCl
CH
3
Cl

+ Cl
2
CH
2
Cl
2
+ HCl
CH
2
Cl
2
+ Cl
2
CH

Cl
3
+ HCl
CHCl
3
+ Cl
2
C

Cl
4
22
Dehydrogenation Reactions
CH
3
CH
3
CH
2
CH
2

Ethylene
23
Cyclic alkanes
C
n
H
2n
A cycloalkane is made of a hydrocarbon
chain that has been joined to make a
ring.



CH
3
CH
2
CH
3
CH
2
C
H
2
C H
2
n-propane
C
3
H
8
cyclopropane
C
3
H
6
60 bond angle
unstable!!
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. [C
n
H
2n
]
C=C Ethene
C C=C propene
Alkynes: hydrocarbons containing a
carbon-carbon triple bond. [C
n
H
2n-2
]
C C Ethyne
C C C C C 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
n 2
H
n
nes, C e Alk
Cycle formation isnt the only possible
result of dehydrogenation.
Adjacent Cs can double bond, C=C,
making an (unsaturated) alkene.

Sp
2

29
Nomenclature for Alkenes
1. Parent hydrocarbon name ends in -ene
C
2
H
4;
CH
2
=CH
2
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

CH
3
CH
3
CH
3


CH = CH CH = CH
cis trans CH
3

32
Reactions of alkenes and alkynes

in which (weaker) t bonds are broken
and new (stronger) o 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
HC=CH + H
2
HCCH

H H

Ethene Ethane
CH
3
-CH
3
34
Halogenation reaction
Adds a halogen atom to each carbon atom of
a double bond

H H H H
catalyst
HC=CH + Cl
2
HCCH

Cl Cl

Ethene Dichloro ethane
35
Halogenation Reactions
CH
2
CHCH
2
CH
2
CH
2
+ Br
2

CH
2
Br

CHBrCH
2
CH
2
CH
2

1,2-dibromopentane
36
Alkynes, C
n
H
2n2
Carbon-carbon triple bonds
Names end in -yne
HCCH ethyne(acetylene)
HCC-CH
3
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
CH
2
=CHCH
2
CH
3
1-butene
CH
3
CH=CHCH
3
2-butene
CH
3
CH CHCH
3
2-butyne


39
Question
Write the IUPAC name for each of the following
unsaturated compounds:
A. CH
3
CH
2
CCCH
3

CH
3

B. CH
3
C=CHCH
3
C.



CH
3
2-pentyne
2-methyl-2-butene
3-methylcyclopentene
40
Question
Name the following compound
CH
3
CH
2
C
CCHCH
2
CH
3
CH
2
CH
3
CH
3
CH
2
C
CCHCH
2
CH
3
CH
2
CH
3
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.




CH
3
C CCH
2
CH
3
+
Br
2
CH
3
C CCH
2
CH
3
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 t bonds
possess a great stability
thus benzene does not
react like unsaturated
hydrocarbons
43
Benzene C
6
H
6

sp
2
sp
2
sp
2
The t 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
+ Cl
2
FeCl
3

Cl
+ HCl
+H
2
O
+HCl
benzene
Chlorobenzene
H
N
O
3
HNO
3
CH
3
Cl
-NO
2
-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 NH
2
52
Some Types of Functional Groups
Haloalkane -F, -Cl, -Br CH
3
Cl
Alcohol -OH CH
3
OH

Ether -O- CH
3
-O-CH
3

Aldehyde

Ketone
C H
O
CH
3
CH
O
C
O
CH
3
CCH
3
O
53
More Functional Groups
Carboxylic acid -COOH CH
3
COOH

Ester -COO- CH
3
COOCH
3


Amine -NH
2
CH
3
NH
2


Amide -CONH
2
CH
3
CONH
2

54
55
Haloahydrocarbons
An alkane in which one or more H atoms is
replaced with a halogen (F, Cl, Br, or I)

CH
3
Br bromomethane
Br (methyl bromide)

CH
3
CH
2
CHCH
3
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

CH
3
CHCH
2
CHCH
2
CH
2
CH
3

4-bromo-2-chloroheptane



1
2
3
4
5
58
Nomenclature
The name of this compound is:
Cl

CH
3


CH
3
CH
2
CHCH
2
CHCH
3

4-chloro-2-methylhexane



59
Alcohols: ROH
The OH makes alcohol polar enough to
hydrogen bonding
Thus, they are water soluble
Ethanol is produced by the fermentation of
glucose
yeast
C
6
H
12
O
6
Glucose
2CH
3
CH
2
OH
Ethanol
+ 2 CO
2
CO

+ 2H
2
O CH
3
OH
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:
CH
2
=CH
2
+ H
2
O CH
3
CH
2
OH
61
Classes of alcohols
R CH
2
OH

Primary alchol
CHOH
R'
R
Secondary alcohol
C
R'
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.
CH
4
methane
CH
3
OH methanol (methyl alcohol)
CH
3
CH
3
ethane
CH
3
CH
2
OH ethanol (ethyl alcohol)
63
OH
Phenol
(Aromatic alcohol)
64
Some Typical Alcohols
OH

Rubbing alcohol CH
3
CHCH
3

2-propanol (isopropyl alcohol)

Antifreeze HO-CH
2
-CH
2
-OH
1,2-ethanediol (ethylene glycol)

65
Naming Alcohols
IUPAC names for longer chains number the chain
from the end nearest the -OH group.
CH
3
CH
2
CH
2
OH 1-propanol
OH

CH
3
CHCH
3
2-propanol
CH
3
OH

CH
3
CHCH
2
CH
2
CHCH
3
5-methyl-2-hexanol

5
2
66
Name the following alcohols:
OH

CH
3
CHCHCH
2
CH
3


CH
3





Example
3-methyl-2-pentanol

67
Aldehydes and Ketones
In an aldehyde, an H atom is attached to a carbonyl
group
O carbonyl group

CH
3
-C-H
In a ketone, two carbon groups are attached to a
carbonyl group
O carbonyl group

CH
3
-C-CH
3


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 CH
3
-C-H CH
3
CH
2
C-H
methanal ethanal propanal
(formaldehyde) (acetaldehyde) (propionaldehyde)





methane
ethane
propane
69
Aldehydes as Flavorings
CH
O
CH
O
HO
OCH
3
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

CH
3
-C-CH
3
CH
3
-C-CH
2
-CH
3

2-Propanone 2-Butanone
(Dimethyl ketone) (Ethyl methyl ketone)



O
Cyclohexanone
Acetone
propane
butane
cyclohexane
71
Name the following compounds
O

A. CH
3
CH
2
CCH
3
B.
2-butanone (ethyl methyl ketone)
CH
3
O

C. CH
3
-C-CH
2
CH
cyclohexanone
CH
3
3,3-dimethylbutanal
O
72
Draw the structural formulas for each of the following
compounds

CH
3
O


A. 3-Methylpentanal CH
3
CH
2
CHCH
2
CH
Br O

B. 2,3-Dibromopropanal Br-CH
2
CHCH
O

C. 3-Methyl-2-butanone CH
3
CHCCH
3


CH
3

73
Preparation of aldehydes and Ketones
They are produced by oxidation of alcohols:

CH
3
CH
2
OH
Oxidation
CH
3
CHCH
3
OH
Oxidation
CH
3
CCH
3
O
CH
3
C
O
H
acetaldehyde
acetone
Primary alcohol
Secondary alcohol
ethanal
propanone
74
Carboxylic Acids and Esters
Carboxylic acids contain the carboxyl group as
carbon 1.
O
R ,,
CH
3

COH CH
3
COOH

carboxyl group
General formula RCOOH

75
Nomenclature of Carboxylic Acids
Formula IUPAC Common
alkan -oic acid prefix ic acid

HCOOH methanoic acid formic acid
CH
3
COOH ethanoic acid acetic acid
CH
3
CH
2
COOH propanoic acid propionic acid
CH
3
CH
2
CH
2
COOH butanoic acid butyric acid


76
IUPAC nomenclature for Carboxylic acids
Identify longest chain
Number carboxyl carbon as 1
CH
3

|
CH
3

CHCH
2
COOH
3-methylbutanoic acid

1
2
3
4
77


CH
3

|
CH
3
CHCOOH
2-methylpropanoic acid;

78
Reaction of carboxylic acid with alcohol
CH
3
C
O
OH + H OCH
2
CH
3
CH
3
C
O
OCH
2
CH
3

+
H
2
O
Ester
Carboxylic acid
Alcohol
Esterification
79
Esters
In ester, the H in the carboxyl group is replaced with
an alkyl group

O
,,
CH
3

CO CH
3
CH
3
COO CH
3



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
CH
3

CO CH
3

Ethanoate methyl ethanoate (IUPAC)
(acetate) methyl acetate (common)


81
Amines
Organic compounds of nitrogen N; derivatives of
ammonia
Classified as primary, secondary, tertiary
CH
3
CH
3

| |
CH
3
NH
2
CH
3
NH CH
3
N CH
3

Primary Secondary Tertiary
one N-C two N-C three N-C
bond bonds bonds
82
Naming Amines
IUPAC aminoalkane Common alkylamine
CH
3
CH
2
NH
2
aminoethane
(ethylamine)

NH
2

|
CH
3
CHCH
3

2-aminopropane Aniline
(isopropylamine)
NH
2
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 C
H
H
H
H
C
OH
H C
H
H
H
C C
H
H
H
H
C
OH
H C
H
H
H
C
OH
H C
H
H
H
C C
H
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 t 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
(CH
2
)
6
N
H
H
C
O
O
(CH
2
)
4
H
C
O
O H
Hexamethylendiamine
Adipic acid
N
H
H
(CH
2
)
6
N
H
C (CH
2
)
4
C
O
O H
O
+

H
2
O
Small molecule such as H
2
O is formed
from each extension of the polymer chain
both ends are free to react
Dimer
Diamine
Dicarboxylic acid
88
N
H
(CH
2
)
6
N
H
(
C (CH
2
)
4
C
O
O
)
n
Nylon