gjr-- 1

Unit One Part 2: naming and functional groups

To write and interpret IUPAC names for small, simple molecules
Identify some common functional groups found in organic molecules

H3C O CH3

N H
N O
N
N

H3C S O
N
O
N
H3C

viagra (trade name)

sildenafil (trivial name)
5-(2-ethoxy-5-(4-methylpiperazin-1-ylsulfonyl)phenyl)-1-methyl-3-propyl-1H-
pyrazolo[4,3-d] pyrimidin-7(6H)-one
dr gareth rowlands; g.j.rowlands@massey.ac.nz; science tower a4.12
http://www.massey.ac.nz/~gjrowlan
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Systematic (IUPAC) naming

PREFIX PARENT SUFFIX

substituents / minor number of C principal functional

functional groups AND multiple bond group
index

Comprises of three main parts

Note: multiple bond index is always incorporated in parent section

No. Carbons Root No. Carbons Root

Multiple-bond
1 meth 6 hex Bond index
2 eth 7 hept
CC an(e)
3 prop 8 oct
C=C en(e)
4 but 9 non
C C yn(e)
5 pent 10 dec
 gjr-- 3
Systematic (IUPAC) naming: functional groups
Functional group Structure Suffix Prefix General form
O
acid oic acid carboxy R-COOH
carboxylic acid
R OH
O O
anhydride oic anhydride R-C(O)OC(O)-R
carboxylic anhydride
R O R
O
acyl chloride oyl chloride chlorocarbonyl R-COCl
-carbonyl chloride
R Cl
O
ester oate alkoxycarbonyl R-COOR
carboxylate
R OR
O
amide amide carbamoyl R-CONH2
R NH2
carboxamide

nitrile R N nitrile cyano R-C N

O
aldehyde al oxo R-CHO
carbaldehyde
R H
O
ketone one oxo R-CO-R
R R
alcohol R OH ol hydroxy R-OH
amine R NH2 amine amino R-NH2
O
ether R R ether alkoxy R-O-R
alkyl bromide R Br bromo R-Br
(alkyl halide) (halo) (R-X)
 gjr-- 4

Nomenclature rules
1. Parent - root derived from number of carbon in longest unbranched chain
.containing functional group

CH3 CH3
OH
H3C 4 2
H3C CH3 5 3 1
4-methylheptane 2-propyl-1-pentanol

2. Suffix - basic name derived by adding ending of major functional group (FG)
O CH3 O

H3C OH H3C NH2

butanoic acid 3-methylbutanamide

3. Position - position of FG denoted by Arabic numeral placed before whole

....name or just before ending. Numbering achieves lowest number for FG
O

H3C CH3

2-pentanone
pentan-2-one
NOT 4-pentanone
 gjr-- 5

Nomenclature rules II
4. Prefix - substituents are designated by prefix & Arabic number indicating
....position (lowest possible numbering)
CH3 Cl CH3
H3C CH3
H3C CH3
H3C CH3 CH3
2,2,5-trimethylheptane 8-chloro-2,3-dimethylnonane
NOT 3,6,6-trimethylheptane NOT 2-chloro-7,8-dimethylnonane

5. FG - if more than one FG name & number based on principle FG. List of
....priorities given in course notes. Multiple bonds are added to parent (end),
....all others are prefixes
O O CH3
H3C OH
HO OH
H3C CH3 O
5-hydroxy-2,2-dimethylpentanoic acid 2-methyl-4-oxohex-2-enoic acid

6. Minor FG - halo-, nitro- (-NO2), nitroso- (-NO) & azo- (-N2-) are considered
....substituents & not FG for nomenclature only

7. Order - substituents are written in alphabetical order

 gjr-- 6

Examples: structure to name

OH O
OH O
H 3C N CH3
H3C N CH3 H
H N-ethyl-3-hydroxy-5-methylhept-6-enamide

Step 1: root
Step 7: complete

OH O OH O

H3C N CH3 H3C 5 3N CH3 1

H 4 H 2
hept 3-hydroxy-5-methylhept-6-enamide

Step 2: suffix Step 5: substituents

(prefix)

OH O OH O

H3C N CH3 H3C 3 N CH3 1

H H 2
hept amide 3-hydroxyhept-6-enamide
6 OH O
Step 3: multiple- Step 4: functional
bond index H3C 5 3 1 N CH3 groups (prefix)
4 2 H
hept-6-enamide
 gjr-- 7

Examples: name to structure

Draw the structure for 4-ethyl-3-hydroxycyclohexanone (please)

draw the root add major functional group

4-ethyl-3-hydroxycyclohexanone 4-ethyl-3-hydroxycyclohexanone
O O

OH

H3C H3C

add substituent add minor functional group

4-ethyl-3-hydroxycyclohexanone 4-ethyl-3-hydroxycyclohexanone
 gjr-- 8

Functional groups: alkanes

Saturated hydrocarbons - contain only C & H and no multiple bonds
Non-cyclic alkanes have the formula CnH2n+2

H C H
H
methane propane pentane cyclopentane
CH4 C3H8 C5H12 C5H10

CH4

Alkanes are a little dull - used as solvents or burnt as fuel

Methane is a fuel, a chemical feedstock & a green house gas propane
 gjr-- 9

Functional groups: alkanes II

isooctane
2,2,4-trimethylpentane
C8H18

Isooctane is used in petrol - branched structure means it burns smoothly

Octane is a long change and burns explosively
Octane number of petrol is based on isooctane = 100 & heptane = 1
Unleaded 91 petrol = 91% isooctane & 9% heptane
Structural isomers have same formula but different atoms joined differently
Isomers can have very different properties

pentane 2-methylbutane 2,2-dimethylpropane

bp 36.2C bp 28C bp 9.6C
 gjr-- 10

Functional groups: alkenes

H H

H H
ethene

Ethene - simplest alkene. Very important industrially

Carbon is trigonal planar - flat and triangular!
New form of isomerism - configurational isomers
All atoms bonded in the same manner but different orientation in space

CH3

H3C CH3
H3C
1-butene 2-butenecis-2-butene
trans-2-butene 2-methylpropene cyclobutane
C4H8 C4H8 C4H8 C4H8

H3C CH3
CH3
H3C
CH3
H3C
(1R,5R)-2,6,6-trimethylbicyclo[3.1.1]hept-2-ene
-pinene
 gjr-- 11

Functional groups: alkynes & cyclic structures

O

H H OH O
O
H3C OME
ethyne pent-3-yn-1-ol O O
C2H2 NOT pent-2-yn-5-ol
H3C O

OH O
MeHN
Ethyne is an explosive gas HO
O
Triple bond makes molecular linear (cylinder) OH
CH3

Examples found in nature (example cleaves DNA) neocarzinostatin chromophore A

Cycloalkanes and cycloalkenes

H3C CH3
cyclopropane 1,3-dimethylcyclohexane cyclohexene benzene

Cyclic hydrocarbons are common - note that most are not flat
 gjr-- 12

Cyclic structures in nature

H3C
CH3

CH3 H CH3

H H H3C

(8R,9S,10S,13R,14S,17R)-10,13-dimethyl-17-(6-
methylheptan-2-yl)-hexadecahydro-1H-
cyclopenta[a]phenanthrene
cholestane - steroid

Ring systems are common in natural products & pharmaceuticals

Example below shows the importance of another form of isomerism -
stereoisomers

H3C CH3 H3C CH3

H H
(R)-1-methyl-4-(prop-1-en-2- (S)-1-methyl-4-(prop-1-en-2-
yl)cyclohex-1-ene yl)cyclohex-1-ene
(R)-limonene (S)-limonene
smells of oranges smells of lemons
 gjr-- 13

Functional groups: alcohols

H3C CH3
primary tertiary
(1) CH3 (3)
CH3 CH3
CH3 H CH3
H3C OH
H3C OH
H H H3C
HO CH3
(R)-3,7-dimethyloct-6-en-1-ol cholesterol (R)-1-isopropyl-4-
citronellol all animals methylcyclohex-3-enol
citronella oil secondary terpinen-4-ol
(2) tea tree oil

Alcohols contain OH (hydroxy) group

Found in many natural systems (especially on Friday night)
Three classes depending on how many C attached to COH
Compounds can have more than one OH (improves water solubility)
HO

HO O
OH HO
HO OH
HO
1,2-ethandiol 6-(hydroxymethyl)-tetrahydro-
ethylene glycol 2H-pyran-2,3,4,5-tetraol
antifreeze glucose
sugar I guess!
 gjr-- 14

Functional groups: phenols and ethers

Phenols
Cl
OH
OH

Cl Cl
phenol 2,4,6-trichlorophenol
carbolic acid TCP
antiseptic

Phenols are distinct from alcohols as attached to phenyl ring - acidic OH

Ethers
O
O O
O
H3C O CH3
O O
ethoxyethane O
diethyl ether tetrahydrofuran
ether THF 18-crown-6

Most commonly used as solvents

18-Crown-6 enables metal cations (M+) to dissolve in organic solvents
 gjr-- 15

Functional groups: alkyl halides and thiols

Cl Cl
H F Cl
Cl
O
Cl H Cl F
Cl Cl Cl H
Cl
dichloromethane dichlorodifluoromethane dieldrin H
DCM Freon (refrigerant)
a CFC

Alkyl halides are incredibly useful compounds - used extensively

Down side is they appear to be bad for us and the environment
Thiols
SH CH3
HS CH3 O
HS SH
H3C HS
H2N H H3C CH3 H3C CH3
CO2H CH3
(R)-2-amino-3- 2-(4-methylcyclohex-3- propane-2,2-dithiol 4-methyl-4-
sulfanylpropanoic acid enyl)propane-2-thiol sulfanylpentan-2-one
cysteine taste of grapefruit

Thiols are the sulfur analogue of alcohols - and they smell, bad...
Humans can detect 2x105 ppb of the second compound (1 drop in a lake)
One of the last two compounds is the smelliest known - but no one is
...prepared to make them again to find out which!
 gjr-- 16

Functional groups: amines

CH3 O

H3C N NH2
H2N OH
H2N H
CH3
triethylamine butane-1,4-diamine (S)-2-amino-3-phenylpropanoic acid
smells of fish putrescine phenylalanine
smells of decay amino acid

Vital in biological systems

Many smell (bad but not as bad as thiols)
Found in many compounds that are physiologically active...

CH3 O
N
CH3
O
N
H O
CH3
N
O
(S)-3-(1- methyl 3-(benzoyloxy)-8-methyl-
methylpyrrolidin-2-yl) 8-aza-bicyclo[3.2.1]octane-2-
pyridine carboxylate
nicotine cocaine
 gjr-- 17

Functional groups: amines II

H H3C N CH
H N H H3C NH2 N 3
H H3C CH3 H3C
ammonia methylamine dimethylamine trimethylamine
1 amine 2 amine 3 amine

Just to confuse, amines are labeled by the number of C attached

This is different to alcohols (labeled by C attached to COH)
secondary
position H
(2)
H3C N CH
CH3 O H3C
3

H3C OH trimethylammonium ion

4 ammonium (salt)
NH2

primary
valine If add four groups
amine everything changes!
(1)
 gjr-- 18

Functional groups: the carbonyl group

Carbonyl group C=O analogous to alkene
Two groups, aldehydes RCHO and ketones R2C=O
Aldehyde
O OH OH
O O
O
H HO
H H H3C H
OH OH H
methanal ethanal benzaldehyde (2R,3S,4R,5R)-2,3,4,5,6-
formaldehyde acetaldehyde pentahydroxyhexanal
glucose

Ketones
CH3 CH3
O O
O

H3C CH3 HO H3C O

H3C H H CH3

propanone (R)-2-methyl-5-(prop-1-en- (S)-2-methyl-5-(prop-1-en- 4-(4-hydroxyphenyl)

acetone 2-yl)cyclohex-2-enone 2-yl)cyclohex-2-enone butan-2-one
(R)-carvone (S)-carvone raspberry ketone
spearmint caraway
 gjr-- 19

Functional groups: carboxylic acids & derivatives

H oxidation H oxidation H oxidation OH
R C H R C H R C R C
reduction reduction reduction
H OH O O
hydrocarbon alcohol aldehyde carboxylic
acid

Many of the functional groups are 'linked'

If we replace one CH at a time by a CO we see how these groups relate

H3C CH3 CH3

O
O
HO2C CO2H H3C
OH
H3C OH CO2H
OH O CH3
ethanoic acid maleic acid (S)-2-hydroxypropanoic acid (2Z,4E)-3-methyl-5-(2,6,6-
acetic acid L-(+)-lactic acid trimethyl-4-oxocyclohex-2-
vinegar enyl)penta-2,4-dienoic acid
abscisic acid
leaf fall
 gjr-- 20

Functional groups: derivatives

O O
+ NaOH Na + HOH
H3C OH H3C O
ethanoic sodium sodium ethanoate water
acid hydroxide carboxylate ion

Reaction of a carboxylic acid with a base (eg. NaOH) gives carboxylate ion
Derivatives
O O
O
H3C CH3
O Cl
H3C O CH3
CH3
ethyl ethanoate 2-methylpropyl propanoate benzoyl chloride
ethyl acetate isobutyl propionate acid chloride
solvent smell of rum
ester ester
NH2 O
H
HO2C N
OMe O O
O
H3C O CH3
aspartame ethanoic anhydride
sweetener acetic anhydride
amide acid anhydride
 gjr-- 21

Classification of functional groups

Functional groups can be classed by the degree of oxidation (removal of H)
increasing degree of oxidation

alkanes
(removal of hydrogen)

alkyl
alcohols ethers amines thiols
halides

aldehydes ketones

carboxylic acyl acid

esters amides chlorides
acids anhydrides nitriles

H oxidation H oxidation H oxidation OH

R C H R C H R C R C
reduction reduction reduction
H OH O O
hydrocarbon alcohol aldehyde carboxylic
acid
 gjr-- 22

Overview

What have we learnt?

How to name simple organic molecules
To recognise common functional groups
Common examples of these functional groups

What's next?
To looking at the bonding in molecules in detail
To understand how bonding effects the shape of molecules

dr gareth rowlands; g.j.rowlands@massey.ac.nz; science tower a4.12

http://www.massey.ac.nz/~gjrowlan