Organic Chemistry

It is the chemistry of compounds containing carbon

How they are bonded to themselves or different atoms such
as oxygen, nitrogen, sulfur and halogens to form molecules.
How do these molecules interact with the environment that
they are in. O
O CH2CH3
O C N
C OH
CH2CH3
O C CH3

CH3
DEET
Acetylsalicylic Acid (ASA) N,N-Diethyl-m-toluamide

CH3 O
H3C H3C
CH CH2 CH C CH CH2 O C
OH H3C OH
H3C
C Juicy Fruit
Ibuprofen, Advil, Nuprin
O

Sec. 1 - Nomeclature 1
 Extraction Synthetic Viagra is a synthetic
O molecule designed
OH H specifically to fit into
N
O HN an enzyme and
H3CO N
HO O O compete with the
N naturally produced
O C H molecule, cGMP
OH
HO Sildenafil
O
vanillin β-D-glucoside O S O
Vigra
N N
HN
H3CO
O N H2N N N

HO C H O
cGMP
OH
Vanillin O
O
P
Vanilla is the only edible fruit of the orchid
O OH
family. Synthetic vanilla contains only one
It is a potent selective inhibitor of the enzyme
organic component - vanillin - the flavor
phosphodiesterase (PDE-5), which destroys cyclic
and fragrance that we most associate with
guanosine monophosphate (cGMP), itself a dilator
vanilla. Because pure vanilla contains so
of blood vessels in the body. Viagra thus allows
many other flavor and fragrance
cyclic GMP to persist and this property has led to
components, it has a much richer smell
its use for the oral treatment of male erectile
and taste than vanillin does by itself dysfunction:
http://www.kitchenproject.com/vanilla http://www.ch.ic.ac.uk/motm/viagra.html
/Vanilla_Bean_Page.html
Sec. 1 - Nomeclature 2
 Molecular Switch

The conduction path in a

conventional microelectronics
transistor
is turned on using an applied
voltage at the gate electrode.
Similarly, the conduction path
through a molecular switch is
turned on by an applied voltage.

The applied voltage is believed to

cause a conformational shift
which, in concert with the
charging of the molecule, opens
the conduction pathway. NH2
O
S C CH3

O2N

http://www.eng.yale.edu/reedlab/research/device/mol_devices.html#overview
Sec. 1 - Nomeclature 3
 Two complementary strategies can be employed in
the fabrication of molecular biological materials. In
the ‘top-down’ approach, biomaterials are generated
by stripping down a complex entity into its
component parts. This contrasts sharply with the
‘bottom-up’ approach, in which materials are
assembled molecule by molecule and in some cases
even atom by atom to produce novel supramolecular
architectures. The latter approach is likely to
become an integral part of nanomaterials
manufacture and requires a deep understanding of
individual molecular building blocks, their
structures, assembling properties and dynamic
behaviors. Two key elements in molecular
fabrication are chemical complementarity and
structural compatibility, both of which confer the
weak and noncovalent interactions that bind building
blocks together during self-assembly. Significant
advances have been achieved at the interface of
biology and materials science, including the
fabrication of nanofiber materials for 3-D cell
cultures, tissue engineering and regenerative
medicine, the peptide detergents for stabilizing, and
crystallizing membrane proteins as well as
nanocoating molecular for cell organizations.
Molecular fabrications of nanobiomateirals have
fostered diverse scientific discoveries and
technological innovations. Sec. 1 - Nomeclature 4
http://web.mit.edu/lms/www/
Sec. 1 - Nomeclature 5
Langmuir Trough

Amphiphilic Molecules (Soap)

connection between hydrophilic and
hydrophobic liquids

Compression organizes monolayer

Monolayer can be transferred onto a solid

support

hydrophilic
bilayers can also be made
hydrophobic
hydrophilic

Sec. 1 - Nomeclature 6
 NE 122 Lab

LAB EXPERIMENT #1 STARTS:

January 5th , 2006: Sections 20(1,2,3)

January 12th 2006 Sections 20(4,5,6)
Starts at 7:00 pm in ESC-342

The Lab Manual is found online in your UW-ACE

Be prepared for the first experiment
Make sure to fill in the Prelab before you come to the lab

Don’t forget safety glasses!

Which can be purchased at CHEM Stores ESC-121
If you have questions contact Josephine Simon
Organic Labs ESC-342
email: josimon@uwaterloo.ca

Sec. 1 - Nomeclature 7
 Nomenclature
Introduction
• In the middle of the nineteenth century, the structures of many
organic compounds were unknown and were given names to
illustrate their origins or their properties. Some compounds were
named after friends and relatives.
• The carboxylic acid HCO2H came from the distillation of red ants.
This acid was given the common name formic acid from the Latin
Formica, which means “ants”
• muratic acid  hydrochloric acid
• In the late nineteenth century a systematized organic
nomenclature was created. The system developed is called the
IUPAC system - International Union of Pure and Applied
Chemistry.

Sec. 1 - Nomeclature 8
Basic Nomenclature
n-Alkanes the Simplest Organic Compounds
The straight-chain alkanes make up a family of hydrocarbons that
have the general formula H−(CH2)n−H or CnH2n+2.

Alkanes are sometimes called saturated hydrocarbons. This term

means that the carbon skeleton is “saturated” with hydrogen.
In saturated hydrocarbons there are only single bonds with bond that
form a tetrahedral.

Sec. 1 - Nomeclature 9
methane CH4 Tetrahedral
H Same plane as page
methyl alcohol or wood alcohol 109.5o
C H into page
Greek methy (wine) hyle (wood)
H H
Same plane as page
out of page
ball and stick
H H
ethane CH3-CH3 C2H6
H C C
H
Greek- aithein “to kindle or blaze” H H

propane CH3-CH2-CH3 C3H8

Taken from Propionic acid
Greek proto (first) and pion (fat)
H H
H H
C
C C
H H
H H

σ bonds free rotation stick structure

Sec. 1 - Nomeclature 10
butane CH3-(CH2)2-CH3 C4H10

Taken from butyric acid

odorous component of rancid butter Latin butyrum (butter) 2
4
1
each vertex and end is a carbon 3
with the appropriate number of hydrogens

pentane CH3-(CH2)3-CH3 C5H12

Greek
hexane CH3-(CH2)4-CH3 C6H14

Greek
heptane CH3-(CH2)5-CH3 C7H16

Greek
octane CH3-(CH2)6-CH3 C8H18

Greek
nonane CH3-(CH2)7-CH3 C9H20

Latin
decane CH3-(CH2)8-CH3 C H
Sec. 1 10 22
- Nomeclature Stick Structures 11
Greek
Know the first 10

Sec. 1 - Nomeclature 12
Functional Groups

Sec. 1 - Nomeclature 13
Functional Groups

Sec. 1 - Nomeclature 14
Nomenclature of Unbranched Alkyl groups
The unbranched alkyl groups are obtained by removing one
hydrogen from the alkane and named by replacing the -ane of
the corresponding alkane with -yl

Sec. 1 - Nomeclature 15
 Nomenclature of Branched-Chain Alkanes (IUPAC)

What is the name of the follow compound?

6 2 2- methyl
7 4- ethyl 1
5
1
4-ethyl-2-methyl heptane
1 2 4 6
5 7 6 4 2
3 3
7 5 1

Find the longest continuous chain (the parent chain), which may or may not
be shown in a straight line and name this chain.

Number the principal chain from one end in such a way that the smaller
number is used at the first point of difference.

Name each appendage group that is attached to this principle chain.

Alphabetize the appendage groups.

Assign to each appendage group a number signifying its point of attachment

to the principal chain.

Numbers are separated by commas and number and names are separated by
a dash. Sec. 1 - Nomeclature 16
When two chains of equal length compete to be parent, choose
the chain with the greatest number of substituents

When branching first occurs at an equal distance from either end

of the parent chain, choose the name that gives the lower
number at the first point of difference

Sec. 1 - Nomeclature 17
Nomenclature of Branched Alkyl Chains

Sec. 1 - Nomeclature 18
 The neopentyl group is a common branched alkyl group

Examples 1 2 3 4 5 6 7

1 2 3 4 5 6 7 8

Sec. 1 - Nomeclature 19
Classification of Carbons and Hydrogen Atoms
Primary (1o) is a carbon bonded to one other carbon
Secondary (2o) is a carbon bonded to two other carbons
Tertiary (3o) is a carbon bonded to three other carbons
Quaternary (4o) is a carbon bonded to four other carbons

CH3

H3C CH2 CH C CH3

CH2 CH2

Hydrogens take their classification from the carbon they are attached to:

Sec. 1 - Nomeclature 20
 Nomenclature of Alkyl Halides

In IUPAC nomenclature halides are named as substituents on the

parent chain
Halo and alkyl substituents are considered to be of equal ranking

In common nomenclature the simple haloalkanes are named as alkyl

halides

Common nomenclature of simple alkyl halides is accepted by IUPAC

and still used

Sec. 1 - Nomeclature 21
 Also – nitro for NO2 and phenyl for R

benzene
What is the name of the follow compound?

fluoro
F

5 3 1
6 4 2
nitro
NO2
Br
bromo

phenyl

Sec. 1 - Nomeclature 22
 Cycloalkenes
The prefix cyclo- is added to the name of the alkane with the same
number of carbons

When one substituent is present it is assumed to be at position

one and is not numbered

When two alkyl substituents are present the one with alphabetical
priority is given position 1

Numbering continues to give the other substituent the lowest

number
Hydroxyl has higher priority than alkyl and is given position 1

If a long chain is attached to a ring with fewer carbons, the

cycloalkane is considered the substituent

Sec. 1 - Nomeclature 23
 Alkenes and Alkynes
Alkenes
Alkynes

H H
C C
H H

no rotation around double bond

H H
sideview C C
H H

Sec. 1 - Nomeclature 24
 Alkenes are named after their alkane parents, but with the -ane
ending changed to -ene for double bonds and -yne for triple bonds

CH3CH3 CH2=CH2 CH≡CH

ethane ethene ethyne

(ethylene) (acetylene)

Hydrocarbons with two and three double bonds are called dienes and trienes
respectively

The prefix number specifies the carbon atom in the chain where the double bond
begins. Note, an a is inserted before the di to ease the pronunciation.

When the parent contains four or more carbons, a prefix number must be used to
indicate the position of the double or triple bond.

The chain is numbered so as to give the double or triple bond as low a number as
possible, even if the prefix group must then receive a higher number.
The locant for the alkene suffix may precede the parent name or be placed
immediately before the suffix

Sec. 1 - Nomeclature 25
What is the name of the follow compounds?

CH3 methyl 1 2 3 4 5
methyl

CH3CHCH2CH2C CH CH2=CHCH=CHCH3 4 2
6 5 4 3 2 1 1
3

chloro 1
Cl 6 2
3 1
7 5

6 H3C 5 3 CH3
4 2
4

methyl
ethyl

Carbon atoms of the double bond

are at positions 1 and 2 and assign
the lowest numbers to the substituents

Sec. 1 - Nomeclature 26
Unbranched hydrocarbons with both double and triple bond
• If there is a choice, the double bond receives the lower number.
HCΞC-CH=CH2 1-butene-3-yne
4 3 2 1

The double bond has the higher priority but the prefix numbers are chosen to
be a low as possible

HCΞC-CH=CH-CH3 3-penten-1-yne (not 2-penent-4-yne)

1 2 3 4 5
The double bond prevents free rotation around a double bond. Consequently,
some alkenes exhibit geometric isomerism. This topic will be discussed in
greater depth in the section on stereochemistry.
H H H CH3
opposite side C C
same side C C
H3C CH3 H3C H
cis-2-butene trans-2-butene
(Z)-2-butene (E)-2-butene

trans – Latin – across

cis – Latin – on the same side
(E) – German – Entgegen - opposite
(Z) – German – Zusanen together
Sec. 1 - Nomeclature 27
 6
1 CH3
H H 5 CH3
C C nitro H
H3CH2C CH2NO2 4
3 2
2 H
5 4 1 H3C H3C
3
cis-1-nitro- 2-petene
trans- 1,4-dimethylcylcohexane

Alkynes are linear molecules and therefore do not exhibit geometric isomerism.

Note: The older system of naming alkynes used acetylene (HC≡CH) as the parent
compound.

5
3 2 1
C CH 4

IUPAC: phenylethyne 2-pentyne

Trivial: phenylacetylene ethylmethylacetylene

Sec. 1 - Nomeclature 28
 Functional Groups with a Carbon

Carboxylic acids
A carboxyl group, must be at the beginning of a
carbon chain and contains the first carbon atom
(carbon 1).

A number is not needed in the name and the ending

for a carboxylic acid is -oic acid.

O O

R C OH H 3C C OH Cl O
carboxylic acid 2 1
H3C CH H2C C OH
group ethane
4 3 2 1

butane
O

H3C C

acetyl group
Sec. 1 - Nomeclature 29
 The first word of the name is the stem name of the alkyl group
Esters attached to oxygen. The part derived form the alcohol. The
second name is the name of the parent acid with the suffix -ic
replaced with –ate or –oate.
O
CH3 O CH3
H3C C O CH3 2 1
H3C C O C CH CH3
removal of 1 2 3
H2O CH3
O
2-methylpropanoic acid
H3C C OH H O CH3
H2O
1,1-dimethylethyl -2-methylpropanoate
carboxylic acid alcohol
or
ethanoic acid methanol
tert-butyl -2-methylpropanoate

methyl ethanoate
or
methyl acetate
Sec. 1 - Nomeclature 30
Amides Amides are named by dropping the suffix -ic or -oic from
the name of the parent acid and adding the suffix -amide.

methyl
O
CH3
O CH3CH2 C N
3 2 1 H
H3C C NH2
2 1
ethanamide
or phenyl
acetamide O

H3C C N

CH2CH3 ethyl

Sec. 1 - Nomeclature 31
 Because an aldehyde (RCHO) contains a carbonyl group
bonded to a hydrogen atom, the aldehyde group must be
Aldehydes at the beginning of a carbon chain.

The aldehyde carbon is considered carbon 1; therefore,

no number is used in the name to indicate the position.
The ending for an aldehyde name is -al.
O has to be
carbonyl group carbon #1
6 4 2
1 H
O
O 5 3
C O
H H H3C C H

methane ethanal
methanal or
acetaldehyde
(formaldehyde)

Sec. 1 - Nomeclature 32
 A nitrile group, like an aldehyde group, must be at the beginning of
Nitrile a carbon chain and again contains the first carbon atom (carbon 1).
With trivial names the -ic or -oic is replaced by -onitrile

CH3C≡N CH3CH2C≡N BrCH2CH2CH2CH2CH2C≡N

ethanenitrile propanenitrile 6-bromohexanenitrile

or acetonitrile

Ketones A keto group by definition cannot be at the beginning of a carbon

chain. Therefore, except for propanone and a few simple
ketones, a prefix number is necessary.
The chain should be numbered to give the carbonyl group the
lowest possible number. The ending for a ketone is -one.

O O O Cl
4
C
H3C CH3 2 4 5
2 1 3
1 3
propanone
or acetone 2-butanone
Sec. 1 - Nomeclature 33
 Functional Groups without a Carbon

Alcohols In the IUPAC system, the name of an alcohol is the same of

the parent hydrocarbon with the final -ane changed to ol.
Prefix numbers are used when necessary; the hydroxyl
group (-OH) receives the lowest prefix number possible.

OH alcohol (CH3)2COHCH2CHCH2
methyl H3C

CH CH2 CH3
CH CH3
H3C 4 3 2 1
H3C C CH2 CH CH2
5 1 2 3 4 5
OH

Sec. 1 - Nomeclature 34
Amines Simple amines are usually named by the functional-group
system. The alkyl or aryl group is named then the ending -amine
is added. Amines can also be named in a substitutive way like
an alcohol which is the most common way of naming amines.

NH2
3-nitro- 2-butylamine functional group system
4
3 or
2 1
3-nitro- 2-butanamine substitutive (same as alcohols)
NO2
like butanol
1
H3C H
N-methyl isopropylamine or N-methyl-2-propylamine
CH N
H3C 2 or
CH3
3 N-methyl-2-propanamine

1 N,N-dimethyl-2-butylamine
N or
4 2 N,N-dimethyl-2-butanamine
3
Sec. 1 - Nomeclature 35
 If a functional group of higher nomenclature priority is
Amines
present, an amino prefix is used.
2 1
NH2CH2CH2OH 2-aminoethanol

NHCH3 N-methylamine

CH3CHCOOH
3 2 1

Ethers The common names of ether are derived by naming the two
alkyl groups and adding the word ether
In the IUPAC system ethers are named as alkoxyalkanes. The
larger alkyl group is chosen as the stem.

CH3OCH2CH3 methoxy ethane (IUPAC) or ethylmethyl ether

larger group
CH3CH2OCH2CH3 ethoxy ethane (IUPAC) or diethyl ether
Sec. 1 - Nomeclature 36
 Nomenclature priorities of selected functional groups

Partial Structure Name

R-COOH -oic acid

R-COOR -oate
R-NONH2 -amide
increasing R-C≡N -nitrile
priority R-COH -al
R-CO-R -one
R-OH -ol
R-NH2 -amine
R-O-R -oxy
R2C = CR2 -ene
RC≡CR -yne
C6H5-, Cl-, Br-, NO2- etc prefix substituents

Sec. 1 - Nomeclature 37
 Common Alkenes and Functional Group Suffixes

Trivial Names
StructureName Example
CH2= methylene**
CH2

methylenecyclohexane
CH2=CH− vinyl CH2=CHCl

vinyl chloride (chloroethene)

CH2=CHCH2− allyl CH2=CHCH2Br

allyl bromide (3-bromopropene)

**The term methylene is also used to refer to a disubstituted sp3 hybridized carbon
(RCH2R’) i.e. CH2Cl2 → methylene chloride

Sec. 1 - Nomeclature 38
Memorize this chart for the Nomenclature Test
I will give you the names and you must draw the structures
alcohol R3C OH alkane contains only C-C alkene R3C CR3 alkyne R3C C C CR3
and C-H single bonds C C
O R3C CR3 R R
aldehyde R C H amine R3C N R
R arene R R
carboxylic acid O O
O O anhydride R3C C O C CR3 R R
R carboxylic R3C C
amide R C N
R acid OH
O O
O ester R3C C O CR3
epoxide R C C R
ether R3C O CR3 R
ketone R3C C CR3 R

n-propyl CH3CH2CH2 R3C C N peroxide R O O R

isopropyl CH3CH nitrile
n-butyl CH3CH2CH2CH2 CH3
CH2
CH3 phenyl benzyl
sec-butyl CH3CH2CH t-butyl H3C C
CH3 CH3
neopentyl
CH3 CH3CHCH2 H H H H
isobutyl vinyl C C allyl C C
H3C CCH2 CH3 H CH2
H
CH3
R = H or alkyl group
= bond to functional group

Primary, secondary and tertiary carbons

Illustrated using an alcohol as the functional group
CH3
H CH3
H3C C OH
H3C C OH H 3C C OH
2° 3°
1° CH3
H H

Sec. 1 - Nomeclature 39