7
BONDING IN
ORGANIC MOLECULES
CHAPTER
7.1 Petroleum Refining and the Hydrocarbons
7.2 The Alkanes
7.3 The Alkenes and Alkynes
7.4 Aromatic Hydrocarbons
7.5 Fullerenes
7.6 Functional Groups and Organic Reactions
7.7 Pesticides and Pharmaceuticals
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7.1 PETROLEUM 307
REFINING AND
THE
HYDROCARBONS
Organic Chemistry:
the study of the compounds
of carbon
Hydrocarbons:
compounds of carbon and
hydrogen
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7.2 THE ALKANES
 Normal alkanes, n-alkanes
~ straight-chain (linear) alkanes, CnH2n+2
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s(sp3-s)
s(sp3-sp3)
s(sp3-s)
Fig. 7.1. Bonding in alkanes involves sp3 hybridized orbitals.
‘staggered’ conformer
‘eclipsed’ conformer
Fig. 7.2. Rotation about C–C bond  variable conformations
Conformers (conformations) are isomers that can be
interconverted via bond rotations. They are stereoisomers.
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London
dispersion
force
Two conformations of C16H34
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Fig. 7.5. Fractional distillation of petroleum.
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Cyclic Alkanes: Carbon atoms arranged in rings
- cycloalkanes have one ring: CnH2n
- angle strain energy reducing the stability of small rings (< C5)
CCC bond angle smaller than the sp3 tetrahedral angle of 109.5o
Cyclopropane, C3H6
Cyclobutane, C4H8
angle strained
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Cyclohexane, C6H12
unstrained
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H
H
H C
H
H2
C
H
C H
C
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H2 C
CH2
or
H C
H
C
C
H
H
H
H
H2 C
CH2
or
C
H2
Cyclohexane, C6H12
Fig. 7.7. Conformations of cyclohexane. (a) Chair. (b) Boat.
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Branched-Chain Alkanes and Isomerism
-Branched chain hydrocarbons contain only C-C and C-H
single bonds, but not in a straight chain. They are constitutional
(structural) isomers of normal alkanes. Isomers are different
structures with the same molecular formula.
Fig. 7.8. Two isomeric hydrocarbons with the molecular formula C4H10.
(a) Butane. (b) 2-Methylpropane (branched chain isomer).
 Constitutional isomers have different atomic connectivities:
they can be interconverted only by bond-breaking and bondmaking processes.
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ISOMERS
Slide 9
Slide 18
CONSTITUTIONAL
ISOMERS
Branch isomers
Position isomers
Functional group
isomers
Slide 33
Differ in atomic
connectivity
STEREOISOMERS
Geometric isomers
Optical isomers
Conformers
Slide 18
Slide 17
Slides 4 & 8
Have same atomic
connectivity, but
differ in spatial
arrangement of
atoms
 Interconversion of all isomers, except conformers, requires
bond breaking and remaking
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 Nomenclature for isomeric alkanes
(IUPAC: International Union of Pure and Applied Chemistry)
1. Find the longest (backbone) alkane chain (= root, named
according to slide 3)
2. Alkyl groups (branches)
Methyl –CH3
Ethyl
–CH2CH3
Propyl –CH2CH2CH3 Isopropyl –CH(CH3)2
3. Numbering of carbon atoms
(lowest number for the attached position)
4. Prefixes for many alkyl groups
di-, tri-, tetra- , penta5. Alphabetical order for different alkyl groups
(E.g. ethyl before methyl before propyl)
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EXAMPLE 7.1
Name the following branched-chain alkane:
1
2 3
4 5
6
4-ethyl-2,4-dimethylhexane
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 Octane number
Straight-chain alkanes burn very unevenly  “knocking”
Heptane (octane number, 0)  Isooctane (octane number, 100)
Octane number, 90  90% (by vol) isooctane + 10% heptane
Anti-knocking additive: tetraethyllead, Pb(C2H5)4 (now banned!)
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7.3 THE ALKENES AND ALKYNES
 Unsaturated hydrocarbons
Alkene ~ double bonds E.g. Ethene (Ethylene), C2H4
Alkyne ~ triple bonds
E.g. Ethyne (Acetylene), C2H2
Fig. 7.10. Reaction with KMnO4.
(a) No reaction with hexane.
(b) Redox reaction with 1-hexene.
Products: MnO2 and
CH3(CH2)3CH(OH)CH2OH
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Ethylene, H2C=CH2
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Acetylene, HC≡CH
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 Optical isomerism and chirality
 Optical isomers:
Non-superimposable mirror image structures are called
enantiomers
Same physical properties but with different optical activity
Chemical properties can differ when they interact with other
optically active molecules → Pharmaceutically important!
 Optical activity:
Rotating the plane polarized light clockwise or anti-clockwise
Chirality (handedness) ~ C*: chiral center
Fig. 7.9. Non-superimposable optical isomers of a molecule CHBrClF.
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 Position isomers of alkenes and alkynes
C4H8: CH2=CH-CH2-CH3
1-butene
C4H6:
HCC–CH2–CH3
1-butyne
CH3-CH=CH-CH3
2-butene
H3C–CC–CH3
2-butyne
 Geometric isomers of alkenes
E.g. 2-butene
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Fig. 7.13. The overlap between the two p orbitals decreases when the
2-butene molecule is twisted about the C=C bond.
Fig. 7.14. Configurational change of the trans isomer of 2-butene
to its cis isomer upon absorbing UV light.   * transition.
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 Polyenes
1,3-butadiene, CH2=CH–CH=CH2
conjugated
 electron
system
Fig. 7.15. The four  MOs
formed from four 2pz AOs in
1,3-butadiene. Only the two
lowest orbitals are occupied
in the ground state.
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7.4 AROMATIC HYDROCARBONS
 Benzene, C6H6
Fig. 7.16. The six 
molecular
orbitals Ifor benzene.
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 BTX (benzene-toluene-xylene)
(methylbenzene)
(1,2; 1,3; 1,4-dimethylbenzenes)
- hydrodealkylation: from toluene to benzene, 550-650 oC, 40-80 atm
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 Reforming reactions:
producing BTX aromatics from straight chain alkanes
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7.5 FULLERENES
- Buckminsterfullerene: the third allotrope of carbon
- a whole family of closed-cage carbon molecules
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The Nobel Prize in Chemistry 1996
“for their discovery of fullerenes”
Robert F. Curl, Jr.
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Harold W. Kroto
Richard E. Smalley
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Carbon Nanotubes (CNTs)
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Carbon nanotubes : one of the purest carbon forms
• Single-walled nanotubes (SWNTs)
- a single graphite sheets wrapped into a cylindrical tube
• Multi-walled nanotubes (MWNTs)
- an array of concentrically nested nanotubes
Baughman, R. H. et al. Science 2002, 297, 787
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Graphene-Based Materials
• graphenes – monolayers of carbon
atoms arranged in a honeycomb
network
• simply prepared by pulling an atomic
layer off of a graphite crystal with a
piece of sticky tape
• a giant aromatic macromolecule that
conducts both electricity and heat well
in two dimensions
• high specific surface area,
high mechanical strength
comparable to CNTs
• production cost lower than
that of CNTs
D. Li et al. Science 2008, 320, 1170
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7.6 FUNCTIONAL GROUPS AND ORGANIC
REACTIONS
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325
 Halides
R–X (X = F, Cl, Br, I)
Halo-
 Free radical chain reaction
250 400 C, h

 CH3Cl + HCl
o
CH4 + Cl2
+ other products
chloromethane
Cl2 → 2 Cl ∙
(initiation)
Cl ∙ + CH4 → HCl + ∙ CH3
(propagation)
∙ CH3 + Cl2 → CH3Cl + Cl ∙
(propagation)
 Addition and elimination reactions
CH2=CH2 + Cl2 → ClCH2CH2Cl
1,2-dichloroethane
500 C, charcoal
ClCH2CH2Cl  CH2=CHCl + HCl
o
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vinyl chloride (chloroethene)
monomer of PVC
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 Alcohols R–OH
– OH group -ol, hydroxy-
 Methanol (methyl alcohol), CH3OH
CH4(g) + H2O(g) → CO(g) + 3 H2(g) (reforming reaction)
CO(g) + 2 H2(g) → CH3OH
synthesis gas
 Ethanol (ethyl alcohol), C2H5OH
CH2=CH2 + H2O → CH3CH2OH
 CH3CH2CH2OH: 1-propanol (propyl alcohol)
Position isomers
CH3CH(OH)CH3: 2-propanol (isopropyl alcohol)
H


+

HSO4


H2O


CH3CH(OH)CH2CH3: 2-butanol or 2-hydroxybutane
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 Types of Alcohols
 Primary alcohol: RCH2–OH
ethanol
 Secondary alcohol: R2CH–OH
2-butanol
 Tertiary alcohol: R3C–OH
2-methyl-2-propanol
tertiary-butyl alcohol or tert-butanol
(CH3)3COH
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 Phenols C6H5OH or Carbolic acid
 Weak acid, but stronger than EtOH
 Partial oxidation of benzene, distillation of coal
 Toxic: lethal dosage, 1g
 Major Synthetic Process (the cumene process)
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 Ethers R–O–R’ –O– group
CH3CH2–O–CH2CH3, diethyl
ether
- methyl t-butyl ether (MTBE)
- cyclic ethers: epoxides
E.g. epoxyethane (ethylene oxide)
 Alcohols and ethers of same molecular formula are
functional group isomers
E.g. ethanol (CH3CH2OH) and dimethyl ether (CH3OCH3), both C2H6O
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O
 Aldehydes
C
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-CHO group –al
(H)R
H
▶ HCHO, methanal (formaldehyde)
 “Formalin” : aqueous solution of HCHO
preservation of biological specimens
 ‘Sick house syndrome’
▶ CH3CHO, ethanal (acetaldehyde)
Fig. 7.23.
Bonding in
formaldehyde
involves sp2
hybrid orbitals
of both
C and O.
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O
 Ketones
C
>CO group
–one
R
R'
 (CH3)2CO, propanone (acetone)
Good solvent, miscible with water
Oxidation of secondary alcohol:
 CH3CH2CH2COCH3, 2-pentanone
 CH3CH2COCH2CH3, 3-pentanone
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Position isomers
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 Carboxylic Acids R–COOH –oic acid
O
▶ Carboxyl group:
C
OH
 HCOOH,
methanoic acid (formic acid)
 CH3COOH, ethanoic acid (acetic acid)
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O
 Esters
–oate
C
R
OR'
 Product of the reaction between a carboxylic acid
and an alcohol
 Fragrant odors, flavors of fruits
Ethyl ethanoate (ethyl acetate)
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★ Fats
 Hydrogenation of oils (esters of cis-unsaturated fatty
acids)
Triglyceride ester
+ 6H2 → saturated fats
 Saturated fats with higher m.p.:
→ solid, good for baking and extended shelf-life
 Remaining double bonds converted from
cis to trans isomers → bad for health!
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R'(H)
 Amines
>N- group –amine (or amino-)
N
(H)R''
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Weak bases
R
 Primary amine: RNH2
Secondary amine: R2NH Tertiary amine: R3N
◆ Amides: R–(CO)–(NH)–R’ -CONH- group -amide
(or amido-)
 Condensation product of an amine with a carboxylic acid
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an amide
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Functional Groups in Proteins
 Amino acids, NH2–R–COOH
~ bifunctional molecules
 Glycine, NH2CH2COOH
α-amino acid, +H3NCH2CO2– (pH = 7)
‘zwitterion’
 Peptide
~ Condensation product of two or more amino acids
 Peptide bonds –(CO)–(NH)– (amide bonds)
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 Protein ~ Polypeptide
primary, secondary, tertiary, quaternary structures
tertiary structure of the
enzyme chymotrypsin
expanded view of the
active site of chymotrypsin
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binding of phenylalanine in the
active site of chymotrypsin
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7.7 PESTICIDES AND PHARMACEUTICALS
 Insecticides (살충제)
 First-generation
Copper, Lead, Arsenic, Nicotine → aphid
 Second-generation
DDT (dichlorodiphenyltrichloroethane):→lice
Methyl parathion
 Third-generation
Target oriented, environmentally degradable
E.g. sex attractant, Juvenile hormone ~
Methoprene
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 Herbicides (제초제)
 2,4-D (2,4-dichlorophenoxyacetic acid)
 2,4,5-T (“Agent Orange,” or 2,4,5-trichlorophenoxyacetic
acid) → Defoliant used during Vietnam war
→ Contains trace amount (10 ppb) of TCDD
 TCDD (“dioxin,” or 2,3,7,8-tetrachlorodibenzo-p-dioxin)
Extremely toxic ! Waste-burning incinerator
→ major source of dioxin in the environment
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 Analgesics (진통제)
 Aspirin (acetylsalicylic acid)
Analgesic (pain reliever), Antipyretic (reduces fever),
Prevents heart disease (thins the blood)
Carboxylic acid  Irritates stomach
 Acetaminophen (4-acetaminophenol)
“Tylenol” ~ weakly acidic phenol
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 Much more powerful pain relievers
 Morphine ~ natural product from “opium poppy”
 Codeine ~ also cough suppressant and analgesic
 Heroin ~ 3,6-diacetylmorphine
2~3 times powerful than morphine and more addictive
Morphine
General Chemistry I
Codeine
Heroin
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A Little Joke on Nomenclature
A research chemist walked into a pharmacy
and asks, “Do you have (5a,6a)-7,8-didehydro-4,5epoxy-3-methoxy-17-methylmorphinan-6-ol?”
The pharmacist scratched her head and
said, “Do you mean codeine?”
“That’s it!”, said the chemist, “I can
never remember that word!”
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 Antibacterial Agents (Antibiotics)
 Sulfanilamide
Bacteria mistake sulfanilamide for p-aminobenzoic acid
→ Interferes with bacteria’s synthesis of folic acid,
 Penicillin ~ natural product formed by certain molds
~ Total synthesis by John C. Sheehan (1957)
~ Fermentation (more economic)
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 Steroids: derived from cholesterol
“Steroid nucleus” 3 six-atom rings and 1 five-atom ring
Cholesterol ~ synthesized in the liver from acetate units
via the ‘mevalonate pathway’. It is the biological precursor
to most other steroids
Cortisone ~ secreted from adrenal glands
~ controls metabolism of sugars, fats, and proteins
Progesterone, Estrogen
~ Female sex hormones, oral contraceptives
Testosterone ~ male sex hormone
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10 Problem Sets
For Chapter 7,
4, 12, 20, 28, 30, 32, 40, 44, 46, 50
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