George Mason University
General Chemistry 212
Chapter 15
Organic Chemistry
Acknowledgements
Course Text: Chemistry: the Molecular Nature of Matter and
Change, 7th edition, 2011, McGraw-Hill
Martin S. Silberberg & Patricia Amateis
The Chemistry 211/212 General Chemistry courses taught at George
Mason are intended for those students enrolled in a science /engineering
oriented curricula, with particular emphasis on chemistry, biochemistry,
and biology The material on these slides is taken primarily from the course
text but the instructor has modified, condensed, or otherwise reorganized
selected material.
Additional material from other sources may also be included.
Interpretation of course material to clarify concepts and solutions to
problems is the sole responsibility of this instructor.
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3/22/2016
1
1
Organic Chemistry

Life on earth is based on a vast variety of reactions and
compounds based on the chemistry of Carbon – Organic
Chemistry

Organic compounds contain Carbon atoms, nearly
always bonded to other Carbon atoms, Hydrogen,
Nitrogen, Oxygen, Halides and selected others (S, P)

Carbonates, Cyanides, Carbides, and other carboncontaining ionic compounds are NOT organic compounds

Carbon, a group 4A compound, exhibits the unique
property of forming bonds with itself (catenation) and
selected other elements to form an extremely large
number of compounds – about 9 million

Most organic molecules have much more complex
structures than most inorganic molecules
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2
Organic Chemistry

Bond Properties, Catenation, Molecular Shape
 The diversity of organic compounds is based on the
ability of Carbon atoms to bond to each other
(catenation) to form straight chains, branched chains,
and cyclic structures – aliphatic, aromatic
 Carbon is in group 4 of the Periodic Chart and has 4
valence electrons – 2s22p2
 This configuration would suggest that compounds of
Carbon would have two types of bonding orbitals each
with a different energy
 If fact, all four Carbon bonds are of equal energy
 This equalization of energy arises from the
hybridization of the 2s & 2p orbitals resulting in 4 sp3
hybrid orbitals of equal energy
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3
Organic Chemistry

Hybrid orbitals are orbitals used to describe bonding
that is obtained by taking combinations of atomic
orbitals of an isolated atom
 In the case of Carbon, one “s” orbital and three “p”
orbitals, are combined to form 4 sp3 hybrid orbitals
 The Carbon atom in a typical sp3 hybrid structure has
4 bonded pairs and zero unshared electrons,
therefore, Tetrahedral structure
AXaEb (a + b) 4 + 0 = AX4
 The four sp3 hybrid orbitals take the shape of a
Tetrahedron
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4
Organic Chemistry
sp3
2p
sp3
Energy
C-H bonds
2s
1s
C atom
(ground state)
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1s
C atom
(hybridized state)
1s
C atom
(in CH4)
5
Organic Chemistry
Shape of sp3 hybrid orbital
different than either s or p
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6
Organic Chemistry
 The bonds formed by these 4 sp3 hybridized
orbitals are short and strong
 The C-C bond is short enough to allow side-toside overlap of half-filled, unhybridized p
orbitals and the formation of “multiple” bonds
 Multiple bonds restrict rotation of attached
groups
 The properties of Organic molecules allow for
many possible molecular shapes
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7
Organic Chemistry

Electron Configuration, Electronegativity, and Covalent
Bonding
 Carbon ground-state configuration – [He 2s22p2]
 Hybridized configuration
–
4 sp3
 Forming a C4+ or C4- ion is energetically very difficult
(impossible?):
● Required energy
 Ionization Energy for C4+ - IE1<IE2<IE3<IE4
 Electron Affinity for C4- - EA1<EA2<EA3<EA4
 Electronegativity is midway between metallic and
most nonmetallic elements
 Carbon, thus, shares electrons to bond covalently in all
its elemental forms
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8
Organic Chemistry

Molecular Stability
 Silicon and a few other elements also catenate, but
the unique properties of Carbon make chains of
carbon very stable
 Atomic Size and Bond strength
● Bond strength decreases as atom size and bond
length increase, thus, C-C bond strength is the
highest in group 4A
 Relative Heats of Reaction
 Energy difference between a C-C Bond
(346 kJ/mol) vs C-O Bond (358 kJ/mol) is small
 Si-Si (226 kJ/mo) vs Si-O (368 kJ/mol) difference
represents heat lost in bond formation
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 Thus, Carbon bonds are more stable than Silicon
9
Organic Chemistry
 Orbitals available for Reaction
● Unlike Carbon, Silicon has low-energy “d”
orbitals that can be attacked by lone pairs of
incoming reactants
● Thus, Ethane (CH3-CH3) with its sp3
hybridized orbitals is very stable, does not
react with air unless considerable energy (a
spark) is applied
● Whereas, Disilane (SiH3 – SiH3) breaks down
in water and ignites spontaneously in air
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10
Organic Chemistry

Chemical Diversity of Organic Molecules
 Bonding to Heteroatoms (N, O, X, S, P)
 Electron Density and Reactivity
● Most reactions start (a new bond forms) when a region
of high electron density on one molecule meets a region
of low electron density of another
 C-C bond: “Nonreactive” – The electronegativities of
most C-C bonds in a molecule are equal and the
bonds are nonpolar
 C-H bond: “Nonreactive” – the bond is nonpolar and
the electronegativities of both H(2.1) & C(2.5) are
close
 C-O bond: “Reactive” – polar bond
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 Bonds to other Heteroatoms: Bonds are long &
weak, and thus, reactive
11
11
Carbon Geometry
The combination of single, double, and triple bonds in an organic
molecule will determine the molecular geometry
sp3
Tetrahedral
AX4
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sp2
trigonal planar
AX3
sp
linear
AX2
sp
linear
AX2
Review Chapter 11 – Multiple bonding in carbon compounds
12
Hydrocarbons

Compounds containing only C and H
 Saturated Hydrocarbons: Alkanes
only single () bonds
 Unsaturated Hydrocarbons:

Alkenes
Alkynes
Double (=) Bonds
Triple () bonds
 Aromatic Hydrocarbons (Benzene rings)
(6-C ring with alternating double and single bonds)
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13
Hydrocarbons



A close relationship exists among Bond Order, Bond
Length, and Bond Energy
Two nuclei are more strongly attracted to two shared
electrons pairs than to one: The atoms are drawn closer
together and are more difficult to pull part
For a given pair of atoms, a higher bond order results in
a shorter bond length and a higher bond energy, i.e.,
A shorter bond is a stronger bond
The Relation of Bond Order, Bond Length, and Bond Energy
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14
Hydrocarbons

Alkanes (Aliphatic Hydrocarbons)
 Normal-chain: linear series of C atoms
C-C-C-C-C-C Branched-chain: branching nodes for C atoms
Methyl Propane
 Cycloalkanes: C atoms arranged in rings
Cyclohexane
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15
Hydrocarbons

Alkanes: CnH2n+2
 Straight Chained Alkanes
H
H
C
H
H
H
H
H
H
C
C
C
H
H
H
Propane
Methane
H
H
H
C
C
H
H
Ethane
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H
H
H
H
H
H
H
C
C
C
C
H
H
H
H
Butane
H
16
Hydrocarbons

Branched Chained Alkanes
3-Ethyl-4-MethylHexane

Cycloalkanes
Cyclobutane
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Methylcyclopropane
17
Hydrocarbons

Molecular Formulas of n-Alkanes
 Methane:
C-1:
CH4
 Ethane:
C-2:
CH3CH3
 Propane:
C-3:
CH3CH2CH3
 Butane:
 Pentane:
 Hexane:
 Heptane:
 Octane:
 Nonane:
 Decane:
C-4:
C-5:
C-6:
C-7:
C-8:
C-9:
C-10:
CH3CH2CH2CH3
CH3CH2CH2CH2CH3
CH3(CH2)4CH3
CH3(CH2)5CH3
CH3(CH2)6CH3
CH3(CH2)7CH3
CH3(CH2)8CH3
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18
Hydrocarbons

Straight Chain (n) Alkanes
Physical Properties of Straight–Chain Alkanes
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19
Hydrocarbons

Petroleum Fractions
Boiling
Point
Name
Carbon
Atoms
Gases
C1 to C4
Heating,
Cooking
20-200 0C
Gasoline
C5 to C12
Fuel
200-300 0C
Kerosene
C12 to C15
Fuel
300-400 0C
Fuel oil
C15 to C18
Diesel Fuel
over C18
Lubricants,
Asphalt, Wax
< 20
> 400
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0C
0C
Use
20
Hydrocarbons

Cycloalkanes: CnH2n
H
H
H
H
C
H
C
C
H
H
C
C
H
C
H
H
H
H
H
H
H
C
H
Cyclopropane
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H
H
H
C
C
H
H
C
C
H
H
H
Cyclohexane
H
C
C
H
Cyclobutane
21
Hydrocarbons

Structural Isomers

Structural (or constitutional) isomers are compounds
with the same molecular formula, but different structural
formulas. Created by branching, etc.
H3C
H
H
C
C
H
H
Butane
C4H10
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CH3
CH3
H3C
C
CH3
H
Isobutane
C4H10
22
Hydrocarbons

Structural Isomers of Pentane
C5H12
Pentane
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2-Methylbutane 2,2-Dimethylpropane
23
Hydrocarbons

Chiral Molecules & Optical Isomerism
 Another type of isomerism exhibited by some alkanes
and many other organic compounds is called
Stereoisomerism
 Sterioisomers are molecules with the same
arrangement of atoms but different orientations of
groups in space
 Optical Isomerism is a type of stereoisomerism, where
two objects are mirror images of each other and
cannot be superimposed (also called enantiomers)
 Optical isomers are not superimposable because each
is asymmetric: there is no plane of symmetry that
divides an object into two identical parts
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24
Hydrocarbons

Chiral Molecules & Optical Isomerism
 An asymmetric molecule is called “Chiral”
 The Carbon atom in an optically active asymmetric (l)
organic molecule (the Chiral atom) is bonded to four
(4) different groups.
Mirror images
1C1 & 1C2 of molecule 1 (left) can be
moved to the right to sit on top of
2C1 & 2C2 of molecule 2, i.e.,
1C & 2C groups can be superimposed
But, the two groups on C3 are opposite
Optical Isomers of
3-methylhexane
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 The two forms are optical isomers and
cannot be superimposed, i.e., no plane
of symmetry to divide molecule into
equal parts
 C-3 is the “Chiral” Carbon
25
Hydrocarbons

Optical Isomers
 In their physical properties, Optical Isomers differ only
in the direction each isomer rotates the plane of
polarized light
● One of the isomers – dextrorotary isomer - rotates
the plane in a clockwise direction (d or +)
● The other isomer – levorotary isomer - rotates the
plane in a counterclockwise direction (l or -)
● An equimolar mixture of the dextrorotary (d or
+) and levorotary (l or -) isomers:
recemic mixture
does not rotate the plane of light because the
dextrorotation cancels the levoratation
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26
Hydrocarbons

Optical Isomers
 In their chemical properties, optical isomers differ
only in a chiral (asymmetric) chemical
environment
● An optically active isomer is distinguished by
the chiral atom being attached to 4 distinct
groups
If the attached groups are not distinct the
molecule is NOT optically active
● An isomer of an optically active reactant added
to a mixture of optically active isomers of an
another compound will produce products of
different properties – solubility, melting point,
etc.
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27
Nomenclature of Alkanes




Determine the longest continuous chain of carbon
atoms. The base name is that of this straight-chain
alkane.
Any chain branching off the longest chain is named
as an “alkyl” group,
changing the suffix –ane to –yl
For multiple alkyl groups of the same type, indicate
the number with the prefix di, tri, …
Ex. Dimethyl, Tripropyl, Tertbutyl
The location of the branch is indicated with the
number of the carbon to which is attached
Note: The numbering of the longest chain begins
with the end carbon closest to the carbon with the
first substituted chain or functional group
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28
Nomenclature Example
CH3
HC
CH3
H2C
CH2
CH3
CH2
CH3
CH
HC
CH3
(Con’t)
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29
Nomenclature Example

Determine the longest chain in the molecule
 7 Carbons
CH3
HC
CH3
H2C
CH2
CH3
CH2
CH3
CH
HC
CH3
Substituted Heptane (7 C)
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(Con’t)
30
Nomenclature Example

The base chain is 7 carbons – Heptane

Add the name of each chain substituted on the base
chain
“methyl” groups at Carbon 3 and Carbon 5
“ethyl” group at Carbon 4
CH3
CH3
H2C
HC
CH2
3
2
CH 4
CH3
1
HC
5
CH3
7
CH2
6
CH3
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3,5-dimethyl-4-ethylheptane
31
Nomenclature Example

Guidelines for numbering substituted carbon
chains
 The numbering scheme used in developing
the name of a organic compound begins with
the end carbon closest to the carbon with the
first substituted group or functional group
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32
Hydrocarbons

Reactions of Alkanes
 Combustion (reaction with oxygen) – Burning
C5H12(g) + 8 O2(g)  5 CO2(g) + 6 H2O(l)
 Substitution (for a Hydrogen)
C5H12(g) + Cl2(g)  C5H11Cl(g) + HCl(g)
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33
Hydrocarbons

Alkenes
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
When a Carbon atom forms a
double bond with another
Carbon atom, it is now bonded
to 2 other atoms instead of 3
as in an Alkane

The Geometry now changes
from 4 sp3 orbitals (Tetrahedral
AX4E0) to 3 sp2 hybrid orbitals
and 1 unhybridized 2p orbital
(AX3E0 Trigonal Planar) lying
perpendicular to the plane of
the trigonal sp2 hybrid orbitals
Review Chapter 10 - Geometry
34
Hydrocarbons

Alkenes
 Two sp2 orbitals of each carbon form C – H
sigma () bonds by overlapping the 1 s
orbitals of the two H atoms
 The 3rd sp2 orbital forms a C-C () bond with
the other Carbon
 A Pi () bond forms when the two
unhybridized 2p orbitals (one from each
carbon) overlap side-to-side, one above and
one below the C-C sigma bond
 A double bond always consists of 1  and 1 
bond
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Hydrocarbons

Alkenes: CnH2n
Alkenes substitute the single sigma bond () with
a double bond – a combination of a sigma bond
and a Pi () bond
The double-bonded (-C=C-) atoms are sp2
hybridized
The carbons in an Alkene structure are bonded to
fewer than the maximum 4 atoms
Alkenes are considered: unsaturated hydrocarbons
H
H
H
H
C
C
C
C
H
H
H
CH3
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Ethene
or
Ethylene
Propene
36
Hydrocarbons


Molecular Formulas of Alkenes
 Ethene:
 Propene:
CH2=CH2
CH2=CHCH3
 Butene:
 Pentene:
 Decene:
CH2=CHCH2CH3
CH2=CHCH2CH2CH3
CH2=CH(CH2)7CH3
Conjugated Molecules
Alkene (or aromatic) with alternating Sigma bonds
and Pi bonds)
Ex. 2,5-Dimethyl-2,4-Hexadiene
CH3CH3=CH-CH=C(CH3CH3)
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37
Hydrocarbons

Reactions of Alkenes
 Addition Reactions
CH3CH=CH2 + HBr  CH3CHBrCH(H2)
 Why does the Bromine (Br) attach to the middle
carbon?
Markownikov’s Rule:
When a double bond is broken, the H atom being added
adds to the carbon that already has the most Hydrogens
CH2 → CH3
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38
Hydrocarbons
 An addition reaction occurs when an unsaturated
reactant (alkene, alkyne) becomes saturated
( bonds are eliminated)
● Carbon atoms are bonded to more atoms in the
“Product” than in the reactant (Ethene is reduced)
 Addition Reaction – Heat of Formation
Reactants (bonds broken
1 C = C = 614 kJ
4 C – H = 1652 kJ
1 H – C = 427 kJ
Total
= 2693 kJ
Product (bonds formed)
1 C – C = – 347 kJ
5 C – H = – 2065 kJ
1 C – Cl = – 339 kJ
Total = – 2751 kJ
o
o
ΔH orxn = ∑ ΔH bondsbroken
+ ∑ ΔHbondsformed
= 2693 kJ + (-2751 kJ) = - 58 kJ
Reaction is Exothermic
Formation of two strong  bonds from a single 
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bond and a relatively weak  bond
39
Hydrocarbons
 Elimination Reactions
● The reverse of “addition reaction”:
A saturated molecule becomes “unsaturated”
 Typical groups “Eliminated” include:
 Pairs of Halogens – Cl2, Br2, I2
 H atom and Halogen – HCL, HBr
 H atom and Hydroxyl (OH) –
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 Driving force – Formation of a small, stable
molecule, such as HCl, H2O, which increases
Entropy of the system
40
Hydrocarbons
 Substitution Reactions
● A substitution reaction occurs when an atom (or
group) from an added reagent substitutes for an
atom or group already attached to a carbon
 Carbon atom is still bonded to the same number
of atoms in the product as in the reactant
 Carbon atom may be saturated or unsaturated
 “X” & “y” may be many different atoms (not C)
 Reaction of “Acetyl Chloride” and
“isopentylalcohol” to form “banana oil”, an ester
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41
Hydrocarbons

Nomenclature of Alkenes
 Alkenes (-C=C-) are named just as alkanes,
except that the –ane suffix is changed to –ene
 Alkynes (-CC-) are named in the same way,
except that the suffix –yne is used
 In either case, the position of the double bond
is indicated by the number of the carbon
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42
Hydrocarbons

Nomenclature of Alkenes - Example
 First, find the longest carbon chain containing the
double bond
CH2CH3
6
H3CHC
1 2
C
3
CH2CHCH3
4
5
CH2CH2CH3
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7
3-propyl-5-methyl-2-heptene
43
Hydrocarbons

Alkenes – Geometric Isomerism
 In Alkanes, the C-C bond allows rotation of bonded
groups; the groups continually change relative
positions
 In Alkenes with the C=C bond, the double bond
restricts rotation around the bond
 Geometric isomers are compounds joined together in
the same way, but have different geometries
 The similar groups attached to the two carbon atoms
of the C=C bond are on the same side of the double
bond in one isomer and on the opposite side for the
other isomer
CH3
H3C
C
H
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H3C
H
C
C
H
cis-2-butene
H
C
CH3
trans-2-butene
44
Hydrocarbons
 Alkynes
 General Formula - CnH2n-2
 The Carbon-Carbon (-C-C-) bond is replaced by a
triple bond
 Each Carbon of an Alkyne structure (-CC-) can only
bond to one other Carbon in a linear structure
 Each C is sp hybridized (sp – linear geometry)
 Alkyne compound names are appended by the
suffix “yne”
 The  electrons in both alkenes (-C=C-) and alkynes
(-CC-) are “electron rich” and act as functional
groups
 Alkenes and alkynes are much more “reactive” than
alkanes
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45
Hydrocarbons

Alkynes
H
H
H3C
C
C
CH2
C
H
C
CH3
C
C
Ethyne
or
Acetylene
Propyne
A Terminal Acetylene
CH2
CH3
3-Hexyne
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46
Aromatic Hydrocarbons




Aromatic Hydrocarbons are “Planar” molecules consisting
of one or more 6-carbon rings
Although often drawn depicting alternating  and 
bonds, the 6 aromatic ring bonds are identical with
values of length and strength between those of –C-C– &
–C=C – bonds
The actual structure consists of 6  bonds and 3 pairs of
 electrons “delocalized” over all 6 carbon atoms
The bond between any two carbons “resonates”
between a single bond and a double bond
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The orbital picture shows the
two “lobes” of the delocalized
 cloud above and below the
hexagonal plane of the - 47
bonded carbon atoms
47
Aromatic Hydrocarbons

Molecular Orbitals of Benzene
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Aromatic Hydrocarbons
H
H
H
H
C
H
H
C
H
C
C
C
C
C
C
C
C
C
H
H
H
C
H
H
Benzene
Benzene
Condensed Resonance
Form of Benzene
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49
Aromatic Hydrocarbons

Substituted Benzenes
CH3
CH3
CH3
C2CH3
Methylbenzene
(Toluene)
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3,4-Dimethyl-ethylbenzene
m,p-Dimethyl-ethylbenzene
50
Aromatic Compounds

Substituted Benzenes
Toluene
Methyl Benzene
Anisole
(Methoxybenzene)
Methoxybenzoate
Dinitroanizole
Nitrobenzene
Tribromobenzene (isomers)
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51
Aromatic Compounds

Benzene ring naming conventions - ring site locations
 Starting at the carbon containing the first substituted
group, number the carbons 1 thru 6 moving clockwise
 Alternate names: 2 (ortho); 3 (meta); 4 (para)
CH3
CH3
1
1
6 (o)
CH3
2 (o)
5 (m)
3 (m)
4 (p)
6 (o)
CH3
1
2 (o)
3 (m)
5 (m)
4 (p)
CH3
6 (o)
2 (o)
5 (m)
3 (m)
4 (p)
CH3
ortho-toluene
1,2-dimethylbenzene
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meta-toluene
1,3-dimethylbenzene
para-toluene
1,4-dimethylbenzene
52
Reactions of Aromatic Compounds

The stability of the Benzene ring favors
“substitution” reactions

The “delocalization” of the pi bonds makes it
very difficult to break a –C=C- bond for an
“addition” reaction
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Reactivity – Alkenes vs Aromatics

The double bond (-C=C-) is electron–rich

 Electrons are readily attracted to the partially positive
H atoms of hydronium atoms (H3O+) and hydrohalic
acids (HX), to yield alcohols and alkyl Halides,
respectively
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Reactivity – Alkenes vs Aromatics





The pi electrons in an alkene double bond represent a
localized overlap of unhybridized 2p orbitals, where two
regions of electron density are located above and below
the  bond
The localized nature of alkene double bonds is very
different from the “delocalized” unsaturation of aromatic
structures
Although aromatic rings are commonly depicted as
having alternating sigma () and () bonds, the ()
bonds are actually delocalized over all 6 –C– () bonds
The reactivity of benzene is much less than a typical
alkene because the  electrons are “delocalized”
requiring much more energy to break up the ring
structure to accommodate an “addition” reaction
“Substitution” is much more likely from an energy
perspective because the delocalization is retained
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55
Redox Processes in Organic Reactions


“Oxidation Number” is not applicable for carbon atoms
Oxidation-Reduction in organic reactions is based on
movement of “electron density” around Carbon atom
 The number of bonds joining a carbon atom and a
“more” electronegative atom (group) vs. the number
of bonds joining a carbon atom to a “Less”
electronegative atom (group)
 The more electronegative atoms will attract electron
density away from the carbon atom
 Less electronegative atoms will donate electron
density to the carbon atom
 When a C atom forms more bonds to Oxygen or fewer
bonds to Hydrogen, the compound is oxidized
 When a C atom forms fewer bonds to Oxygen or more
bonds to Hydrogen, the compound is reduced
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Redox Processes in Organic Reactions

Combustion Reactions (burning in Oxygen)
2CH 3 - CH 3 + 7O2  4CO2 + 6H 2O
 Ethane is converted to Carbon Dioxide (CO2) and
water (H2O)
 Each Carbon in CO2 has more bonds to Oxygen than
in ethane (none) and few bonds to Hydrogen
Reaction is “Oxidation”
 Oxidation of Propanol
● C-2 has one fewer bonds to H and one more bond
to O in 2-propanone - Oxidation
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Redox Processes in Organic Reactions

Hydrogenation of Ethene

Pd
CH 2 = CH 2 + H 2 
 CH 3 - CH 3
 Each carbon has more bonds to H in Ethane than in
Ethene
Ethene is reduced, H2 is oxidized (loses e-)
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Organic Reactions

Functional groups
 A functional group is a reactive portion of a molecule
that undergoes predictable reactions
 The reaction of an organic compound takes place at
the functional group
 A functional group is a combination of bonded atoms
that reacts as a group in a characteristic way
 Each functional group has its own pattern of reactivity
 The distribution of electron density in a functional
group affects its reactivity
 Vary from carbon-carbon bonds (single, double, triple)
to several combinations of carbon-heteroatom bonds
 A particular bond may be a functional group itself or
part of one or more functional groups
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Organic Reactions

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Functional Groups (Con’t)
 Electron density can be low at one end of a bond and
higher at the other end, as in a dipole, an intermolecular
force
 The Intermolecular Forces that affect physical properties
and solubility also affect reactivity
 Alkene (-C=C-) and Alkyne (-CC-) bonds have high
electron density, thus are functional groups with high
reactivity
 Classification of Functional Groups
● Functional groups with only single bonds undergo
“substitution” reactions
● Functional groups with “double” or “triple” bonds
undergo “addition” reactions
● Functional groups with both single and double bonds
undergo substitution reactions
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60
Functional Groups

Oxygen containing functional groups:
alcohols, ethers, aldehydes, ketones, esters,
carboxylic acids, anhydrides, acid halides

Nitrogen containing functional groups:
amines, amides, nitriles, nitro

Compounds containing Carbonyl Group (C=O)
acids, esters, ketones, aldehydes,
anhydrides, amides, acid halides

Compounds containing Halides
alkyl halides, aryl halides, acid halides

Compounds containing double & triple bonds
alkenes, alkynes, aryl structures (benzene rings)
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Functional Groups
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62
Functional Groups
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63
Alcohols

Functional Groups with “only” single bonds
 An alcohol, general formula – R-OH, is a
compound obtained by substituting an -OH
group for an –H atom in a hydrocarbon
● primary alcohol: one carbon attached to the
carbon with the –OH group
● secondary alcohol: two carbons attached to
the carbon with the –OH group
● tertiary alcohol: three carbons attached to
the carbon with the –OH group
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Alcohols
CH3 – CH2 – CH2 – OH
Propanol (n-propyl alcohol)
(primary alcohol)
t-butanol
(tertiary alcohol)
sec-butanol
(secondary alcohol)
Alcohol Nomenclature
Drop final “e” from hydrocarbon and add suffix “ol”
OH
CH3CH2CH2CH2CH3
CH2CH2CH2CH3
CH3
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4,6-dimethyl-3-octanol (a secondary alcohol)
65
Alcohols

Alcohol Reactions
 Alcohol structure similar to water
(R-OH
vs
H-OH)
 Alcohols react with very active metals to release H2
 Alcohols form strongly basic “Alkoxide (R-O-) Ions
 High melting points and boiling points of alcohols
result from Hydrogen Bonding
 Alcohols dissolve “Polar” molecules
 Alcohols dissolve “some” salts
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Alcohols

Alcohol Reactions
 Elimination Reactions
● Elimination of a H atom and a hydroxide ion (OH)
from a cyclic compound in the presence of acid
results in the formation of an “alkene”
● Removal of 2 H atoms from a secondary alcohol in
the presence of an oxidizing agent, such as K2CrO7
results in the formation of a “Ketone”
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Alcohols

Alcohols Reactions
 Oxidation
● For Alcohols with the OH group at the end of a
chain (primary alcohol) oxidation to an organic acid
can occur in air
 Substitution Reactions
● Substitution results in products with other single
bonded functional groups, such as the formation of
Haloalkanes
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Haloalkanes

A Haloalkane (Alkyl Halide) is a Halogen
(X = F, Cl, Br, I) bonded to a carbon atom
 Elimination Reactions
● Elimination of HX in the presence of a
strong base will produce an Alkene
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Haloalkanes

Haloalkanes
 Substitution Reactions
● Halides of Carbon and most other non-metals, such
as Boron (B), Silicon (Si), Phosphorus (P), all
undergo substitution reactions
● The process involves an attack on the slightly
positive central atom, such as C, etc. by an OHgroup
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● -CN, -SH, -OR, and –NH2 groups also substitute for
the halide
70
Ethers

H-O-H
water

R-O-H
alcohol
(OH group – Hydroxyl group)

R-O-R
ether
(R-O group – Alkoxy group)
where R = any group

Ether Nomenclature:
 If R-C-O-CH3 group is part of structure,
add “Methoxy” to name
 If R-C-O-CH2-CH3 group is part of structure,
add “Ethoxy” to name
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Ether Nomenclature
OCH2CH3
CH3CH2CH2CH2CH3
4 3
2
1
5 6 7 8
CH2CH2CH2CH3
CH3
4,6-dimethyl-3-ethoxyoctane
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Amines

An Amine is a compound derived by substituting one or more
Hydrocarbon groups for Hydrogens in Ammonia, NH3
 Naming convention
● Drop the final “e” from the alkane name and add
“amine” (ethanamine) or append “amine” to alkyl name
(Methylamine)
 Types
● primary amine: one carbon attached to the Nitrogen
● secondary amine: two carbons attached to the Nitrogen.
● tertiary amine: three carbons attached to the Nitrogen
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H
N
CH3
H
Methylamine
(Primary Amine)
H
N
CH3
CH3
Dimethylamine
(Secondary Amine)
CH3
:
:
:
Amine Examples
N
CH3
CH3
Trimethylamine
(Tertiary Amine)
Trigonal pyramidal
Shape – AX3E
The pair of “unbonded” electrons common to all amines is the
key to all amine reactivity
Amines act as bases by donating the pair of unshared electrons
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Amines

Reactions
 Primary and secondary Amines can form H–bonds
● Higher melting points and boiling points than
Hydrocarbons or Alkyl Halides of similar mass
● Trimethyl Amines cannot form Hydrogen Bonds and
have generally lower melting points
● Amines of low molecular mass are water soluble
and weakly basic (donate electrons)
 Reaction with water proceeds slowly and
produces OH- ions
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Amines

Amine Reactions
 Substitution Reactions
● The pair of unbonded electrons on the Nitrogen
attacks the partially positive Carbon in Alkyl Halides
to displace the Halogen (X-) and form a “larger”
amine
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Carbonyl Group

Functional Groups with Double Bonds

The Carbonyl group is a Carbon doubly bonded to an Oxygen (C=O)

Very versatile group appearing in several types of compounds
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
Aldehydes

Ketones

Carboxylic acids

Esters

Anydrides

Acid Halides

Amides
77
Aldehydes and Ketones
An Aldehyde is distinguished from a Ketone by
the Hydrogen atom attached to the Carbonyl
Carbon
 If two Hydrogens are attached to the Carbonyl
atom, the compound is specific – Formaldehyde
(CH2O)

C
R
Aldehyde
(- al)
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R
H
H
C
O
O
H
Formaldehyde
C
O
R
Ketone
(-one)
78
Aldehydes and Ketones

Aldehydes
 In Aldehydes the Carbonyl group always appears at
the end of a “chain
Butanal
(Butyraldehyde)
 Aldehyde names drop the final “e” from the alkane
names and “-al” – Propanal, Isobutanal, etc.
 Alternate naming conventions:
● Benzaldehyde, Propionaldehyde
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Aldehydes and Ketones

Ketones
 The Carbonyl Carbon always occurs within a chain as
it is bonded to two other Alkyl groups (R, R’)
 Ketones are named by numbering the carbonyl C,
dropping the final “e” from the alkane name, and
adding “-one”, 4-Heptanone
4-Heptanone
(Dipropylketone)
 Alternate naming conventions:
● Use the Alkyl root and add “ketone”
Methylisopropylketone
(3-methyl-2-butanone)
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Aldehydes and Ketones

Like the –C=C= bond, the Carbonyl (–C=O) bond is
electron-rich

Unlike the –C=C= bond, the –C=O bond is highly polar
 A - The  and  bonds that make up the C═O bond of
the carbonyl group
 B - The charged resonance form shows that the C═O
bond is polar (ΔEN = 1.0)
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Aldehydes and Ketones

Aldehydes and Ketones are formed by oxidation of
Alcohols

The C=O is an unsaturated structure, thus, carbonyl
compounds can undergo “addition” reactions and be
reduced (forms more bonds to H) to form alcohols
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Aldehydes and Ketones

Organometallic compounds
 The Carbonyl group exhibits polarity with the
Carbon atom bearing a slight positive charge
and the Oxygen bearing a negative charge
 An addition reaction to the Carbonyl group
would involve an electron-rich group bonding
to the positive carbon and an electron-poor
group bonding to the negative Oxygen
 Organometallic compounds have a metal atom
(Li or Mg) attached to an “R” group through a
polar covalent bond
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Aldehydes and Ketones
 Organometallic compounds
 The two-step addition of an organometallic
compound to a Carbonyl group produces an Alcohol
with a different Carbon skeleton
 Aldehyde & Lithium Organometallic
 Acetone (ketone) & Ethyllithium
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Carboxylic Acids

Carboxylic Acids are formed by adding an
“Hydroxyl” group to the Carbonyl Carbon

Different R groups lead to many different
carboxylic acids

Carboxylic Acids have the “- oic” suffix with
“acid”

Example: Ethanoic acid (Acetic acid) – C2H4O2
HO
Acidic Hydrogen
(Hydroxyl Group)
Carboxyl Group
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C
O
CH3
Carbonyl Group
85
Carboxylic Acids
Carboxylic Acids are named by dropping the “-e” from
the alkane name and adding “-oic acid”
 Common names are often used
 Carboxylic Acids are “Weak Acids” in solution
 Typically >99% of an organic acid is “undissociated”

Carboxylate
anion
 Carboxylic acid molecules react completely with strong
base to form salt & water
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Carboxylic Acids

Carboxylic acids with long hydrocarbon chains
are referred to as “fatty acids”
 Fatty acid skeletons have an “even” number of
Carbon atoms (16-18 most common)
 Animal fatty acids have “saturated”
hydrocarbon chains
 Vegetable sources are generally “unsaturated”,
with the -C=C- in the “cis” configuration
 Fatty acid salts are the “soaps”, with the
“cation” usually from Group 1A of 2A
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Examples

Straight chain saturated (Aliphatic) carboxylic
acids
Name
Formula
Methanoic (Formic) Acid
HCOOH
Ethanoic (Acetic) Acid
CH3COOH
Propionic Acid
CH3CH2COOH
Butanoic (Butyric) Acid
CH3CH2CH2COOH
Pentanoic Acid
CH3CH2CH2CH2COOH
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88
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88
Esters

Esterification is a dehydration-condensation reaction between
a Carboxylic acid and an alcohol to form an Ester

The Hydroxyl group (OH) from the Alcohol reacts with the
Carboxyl group to form the Ester and Water
R1COOH + R2OH  R1COOR2 + H2O

Ester group occurs commonly in “Lipids,” a large group of
fatty biological substances, such as “triglycerides
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Esters

Hydrolysis is the opposite of Dehydration-Condensation
(Esterification) in which the Oxygen atom from water is
attracted to the partially positive Carbon of the ester
carbonyl group, cleaving (lysing) the molecule into two
parts
 One part gets the –OH and one part gets the H
 In Saponification, the process used in the
manufacture of soap, the ester bonds in animal or
vegetable fats are “Hydrolyzed” with a strong base
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Amides

Amides are derived from the reaction of an Amine with a
Carboxylic acid or an Ester

Amides are named by denoting the “amine” portion from
the amine and the replacing the “-oic acid” from the
Carboxylic acid with “-amide”
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Amides

The partially negative N (2 unbonded e-) of the amine is
attracted to the partially positive carbonyl carbon of the
ester
 In the Amine & Acid reaction water is lost
R1COOH + R2NH2  R1CONHR2 + H2O
 In the Amine & Ester reaction an alcohol (ROH) is lost
 Amides can be “Hydrolyzed” in hot water to reform
the acid and the amine
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Functional Groups with Triple Bonds

Principal Groups with triple bonds
 Alkynes (Acetylenes) -CC● Addition reactions with H2O, H2, HX, X2, others
 Nitriles -CN
● Produced by substituting a cyanide ion (-C N-) for
a Halide ion (X-) in a reaction with an alkyl halide
● Nitriles can be reduced to form amines or
hydrolyzed to carboxylic acids
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Polymers

Polymers are extremely large molecules consisting of
“monomeric” repeating units

Naming polymers
 Add prefix “poly-” to the monomer name
Polyethylene Polystyrene Polyvinyl chloride

Polymer Types
 Addition
● Monomers undergo addition with each other (chain
reactions)
● Monomers of most addition polymers have the group
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Addition Polymers
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95
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95
Addition Polymers

Free-radical polymerization of Ethene, CH2=CH2 ,to
polyethylene
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Condensation Polymers

Condensation polymers have “two” functional groups
A–R–B
 Monomers link when group A on one undergoes a
“dehydration-condensation” reaction with a B group on
another monomer

Many condensation polymers are “Copolymer”, consisting of
two or more different repeating units
 Condensation of Carboxylic acid & Amine monomers forms
“polyamides” (nylons)
 Carboxylic Acid and Alcohol monomers form polyesters
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Biological Macromolecules

Natural Polymers
 Polysaccharides
 Proteins
 Nucleic acids
 Intermolecular forces stabilize the very large
molecules in the aqueous medium of living cells
 Structures that make wood strong; hair curly,
fingernails hard
 Speed up many natural reaction inside cells
 Defend living organisms against infection
 Possess genetic information organisms need to
synthesis other biomolecules
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Sugars & Polysaccharides

Carbohydrates – substances that provide energy through
oxidation

Monosaccharides
 Glucose & simple sugars
 Consist of carbon chains with attached hydroxyl and
carbonyl groups
 Serve as monomer units of polysaccharides

Polysaccharides
Consist mainly of Glucose units with differences in
aromatic ring position of the links, orientation of
certain bonds and the extent of cross-linking
 Cellulose
 Starch
 Glycogen
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Sugars & Polysaccharides
Cellulose
 Most abundant organic chemical on earth
 50% of carbon in plants occurs in stems &
leaves
 Cotton is 90% cellulose
 Wood strength comes from Hydrogen bonds
between cellulose chains
 Humans lack enzyme to links to the C1 & C4
bonds between units making it impossible to
digest
 Other animals – cows, sheep, termites,
however, have microorganisms in their
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digestive tracts that can digest cellulose

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Sugars & Polysaccharides

Starch
 A mixture of polysaccharides of glucose
 Energy store in plants
● Starch is broken down by hydrolysis of the
bonds between units, releasing glucose, which
is oxidized in a multistep process

Glycogen
 Energy storage molecule in animals
 Occurs in molecules made from 1000 to 500,000
glucose units
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 The cross-linking between the C1 & C4 bonds is
similar to starch, but is more highly cross-linked
between the C1 & C6 bonds
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101
Amino Acids & Proteins

Amino Acids
 An amino acid has a carboxyl group (COOH) and an amine
group (NH2) attached to an “-carbon”, the 2nd C atom in a
Carbon-Carbon (C-C) chain
 In the aqueous cell fluid, the NH2 (amino) and COOH
(carboxyl) groups of amino acids are charged because the
carboxyl group transfers an H+ ion to H2O to form H3O+
(acid), which transfers the H+ to the amine group
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Amino Acids & Proteins

Proteins
 Proteins are unbranched polyamide polymers made up
of amino acids linked together by “Peptide” bonds”
 A “Peptide” (amide) bond is formed by a dehydrationcondensation reaction in which the Carboxyl group of
one monomer reacts with the Amine group of the next
monomer releasing water
“dipeptide”
 A “Polypeptide chain” is a polymer formed by the
linking of many amino acids by peptide bonds
 A “Protein” is a polypeptide with a “biological” function
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Amino Acids & Proteins

Peptide Bonds
C=O
:N-H
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Amino Acids & Proteins

About 20 different amino acids occur in proteins
See Examples on Next Slide

The R groups are screened gray

The -carbons (boldface), with carboxyl and amino
groups, are screened yellow

The amino acids are shown with the charges they
have under physiological conditions

They are grouped by polarity, acid-base character, and
presence of an aromatic ring

The R groups, which dangle from the -carbons on
alternate sides of the chain, play a major role in the
shape and function of proteins
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Amino Acids & Proteins
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106
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106
Amino Acids & Proteins

Hierarchy of Protein Structure
 Each type of protein has its own amino acid composition –
a specific number and proportion of various amino acids
 The role of a protein in a cell, however, is not determined
by its composition
 The “sequence” of amino acids determines the protein’s
shape and function in the cell
 Proteins range from 50 to several thousand amino acids
 The number of possible sequences of the 20 types of
amino acid, even in the smaller proteins, is extremely large
(20n where ‘n’ is the number of amino acids)
 Only a small fraction of the possible combinations occur in
actual proteins – 105 for a human being
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Amino Acids & Proteins

Protein Native Shapes
 Proteins have unique shapes that unfold during
synthesis in a cell
Simple
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Complex
Long rods
Baskets
Undulating sheets
Y-Shapes
Spheroid Blobs
Globular Forms
108
Amino Acids & Proteins
 Hierarchy of Protein Structure
● Primary
(1o) – Basic Level (sequence of
covalently bonded amino
acids
in polypeptide chain)
● Secondary (2o) – Shapes called -helices and
-pleated sheets formed as a
result of H bonding between
nearby peptide groupings
● Tertiary
(3o) – 3-dimensional folding of
whole polypeptide chain
● Quarternary (4o) – Most complex, proteins
made up of several
polypeptide chains
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Amino Acids & Proteins
Structural Hierarchy of Proteins
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110
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110
Amino Acids & Proteins

Protein Structure and Function
 Two broad classes of proteins differ in the complexity
of their amino acid composition and sequence, thus,
their structure and function
● Fibrous Proteins
 Relatively simple amino acid compositions and
correspondingly simple structures
 Includes “Colagen”, the most common animal
protein (30% glycine; 20% proline)
● Globular Proteins
 More complex, containing up to all 20 amino
acids in varying proportions
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Amino Acids & Proteins
Nucleotides and Nucleic Acids
 Nucleic Acids – Unbranched polymers that consist of
linked monomer units called mononucleotides
● Mononucleotides consist of:
 Nitrogen-containing base
 Sugar
 Phosphate group
 Nucleic Acid Types
● Ribonucleic Acid (RNA)
● Deoxyribonucleic Acid (DNA)
● RNA & DNA differ in sugar portions of
mononucleotides
 RNA contains Ribose, a 5-Carbon sugar
 DNA contains deoxyribose (H substitutes for OH
on the 2’ position of Ribose
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
112
Amino Acids & Proteins

Nucleic Acid Precursors
 Nucleoside Triphosphates – Cellular precursors that
form a nucleic acid
 Dehydration-condensation reactions between cellular
precursors:
● Releases inorganic diphosphate (H2P2O72-)
● Creates Phosphodiester bonds to form a
“polynucleotide”
● Sets up the repeating pattern of the nucleic acid
backbone
– sugar – phosphate – sugar – phosphate –
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113
Amino Acids & Proteins
 DNA
 Phosphate group
 2’-deoxyribose (a Sugar)
 Base: Attached to each sugar is one of four Ncontaining bases, either
 a Pyrimidine (six-membered ring)
 Pyrimidines – Thymine (T) & Cytosine (C)
or
 a Purine (six- and five- membered rings sharing a
side)
 Purines
– Guanine (G) & Adenine (A)
 RNA
● Sugar in RNA is Ribose
● Uracil (U) substitutes for Thymine (T)
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Amino Acids & Proteins
Nucleic Acid Precursors
 In a cell, nucleic acids are
constructed from nucleoside
triphosphates, precursors of the
mononucleic units
 Each mononucleic unit consists
of:
 an N-containing base
 a sugar
 a triphosphate group
 Nitrogen Containing Bases:
 Pyrimidines
● Thymine (DNA) Uracil
(RNA)
● Cytosine
 Purines
● Guanine
● Adenine
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
115
Amino Acids & Proteins

Base Pairing
 In the nucleus of a cell, DNA exists as two chains
wrapped around each other in a “double Helix”
 Each base in one chain “Pairs” with a base in the
other through Hydrogen Bonding
 A double-helical DNA molecule may contain many
millions of H-Bonded bases
 Base Pair Features
● A Pyrimidine (Pyr) is always paired with a Purine
(Pur)
● Each base is always paired with the same partner
 Thymine (T) (Pyr) with Adenine (A) (Pur)
 Cytosine (C) (Pyr) with Guanine (G) (Pur)
● Thus, base sequence on one chain is the
complement of the sequence on the other chain
Ex. A-C-T on one chain paired with T-G-A on
another
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Practice Problem
Write the sequence of the complimentary DNA strand that
pairs with each of the following:
a.
GGTTAC
Ans: CCAATG
b.
CCCGAA
Ans: GGGCTT
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Practice Problem
Write the base sequence of the DNA template from which
the RNA sequence below was derived
Ans:
GUA UCA AUG AAC UUG
(RNA)
CAT AGT TAC TTG AAC
(DNA)
(note: Uracil (U) substitutes for Thymine (T) in RNA)
How many amino acids are coded for in this sequence?
Ans: five (CAT) (AGT) (TAC) (TTG) (AAC)
Each 3-base sequence is a word, each word codes for
a specific amino acid
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Nucleic Acids (N-Containing Bases)
Pyrimidines
Thymine
Uracil
Cytosine
Purines
Guanine
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Adenine
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Nucleic acid precursors and their linkage
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The Double Helix of DNA
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Amino Acids & Proteins

Protein Synthesis
 A protein consists of a sequence of Amino Acids
 The Protein’s Amino Acid sequence determines its
structure, which in turn determines its function
SEQUENCE  STRUCTURE  FUNCTION
 The DNA base sequence contains an information template
that is carried by the RNA base sequence (messenger and
transfer) to create the protein amino acid sequence
 In other words, the DNA sequence determines the RNA
sequence, which determines the protein amino acid
sequence
● In Genetic Code, each base acts as a “Letter”
● Each three-base sequence is a “Word”
● Each word codes for a specific Amino Acid
Ex. C-A-C codes for Histidine
A-A-G codes for Lysine
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Amino Acids & Proteins
 One Amino Acid at a time is positioned and linked to the
next in the process of protein synthesis
 Outline of Synthesis
● DNA occurs in cell nucleus
● Genetic message is decoded outside of cell
● RNA serves as messenger to synthesis site
● Portion of DNA is unwound and one chain segment acts
as a template for the formation of a complementary
chain of messenger RNA (mRNA)
● mRNA made by individual mononucleoside triphosphates
linking together
● The DNA code words are transcribed into RNA code
words through base pairing
● mRNA leaves the nucleus and binds, again through
base-pairing, to an RNA rich-rich particle called a
“Ribosome”
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Amino Acids & Proteins
 Synthesis Outline (con’t)
● The words (3-base sequences) in the RNA are then
decoded by molecules of transfer RNA (tRNA)
● The smaller nucleic acid “shuttles” have two key
portions on opposite ends of their structures
 A three-base sequence (word) which is a
complement of a word on the nRNA
 A binding site for the amino acid coded by that word
● The Ribosome moves along the bound mRNA, one word
at a time, while tRNAs bind to the mRNA
● The Amino acids are positioned near one another in
preparation of peptide bond formation and synthesis of
the protein
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Amino Acids & Proteins
 Synthesis Outline (con’t)
● Net result
Protein Synthesis involves the DNA message of threebase words being transcribed into the RNA message of
three-base words, which is then translated into a
sequence of amino acids that are linked to make a
protein
DNA Base Sequence  RNA Base Sequence 
Protein Amino Acid Sequence
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