Unit One Part 2:

naming & functional groups

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
Unit One Part 2:
naming & functional groups
H3C O CH3

N H
N O
N
N

H3C S O
N
O
N
H3C

viagra™ (trade name)

sildenafil (trivial name)Don’t panic!
5-(2-ethoxy-5-(4-methylpiperazin-1-ylsulfonyl)phenyl)-1-
We won’t do anything
methyl-3-propyl-1H-pyrazolo[4,3-d]pyrimidin-7(6H)-one
this complicated
Unit One
Part 2
Naming molecules (pg 11-16)
Introducing functional
groups (pg 16-9)
remember...read the
study guide it
contains all you need
 how do we
name molecules?
 O

OH
NH2

2-amino-4-methylpentanoic acid

prefix parent suffix

substituents carbon chain principal
minor functional (& multiple functional
groups bonds) groups
 O

OH
NH2

2-amino-4-methylpentanoic acid

there are three parts

to any name...even
Viagra’s real name
prefix parent suffix
obeys this.

substituents carbon chain principal

minor functional (& multiple functional
groups bonds) groups
 O

OH
NH2

2-amino-4-methylpentanoic acid
the prefix can
become a nightmare
as it contains most
information

prefix parent suffix

substituents carbon chain principal
minor functional (& multiple functional
groups bonds) groups
seven steps to
success!
seven steps to
success!

works for all

molecules but the
whole system takes
volumes to
explain...
1
parent
longest carbon
chain containing a
functional group page 12 of guide

CH3 CH3
OH
H3C CH3 H3C 4 2
5 3 1
4-methylheptane 2-propyl-1-pentanol
1
parent
longest carbon
chain containing a
functional group

CH3 7 bigger than

CH35 he
says patronisingly
OH
H3C CH3 H3C 4 2
5 3 1
4-methylheptane 2-propyl-1-pentanol
1
parent
longest carbon
chain containing a
functional group

CH3 CH3
now use pent- as OH
H3C we have to start
CH3 H3C 4 2
5 3 1
our chain from the
4-methylheptane
functional group 2-propyl-1-pentanol
2
suffix
major
functional
group
list of major
groups pg 13
order of priority
pg 14

O CH3 O

H3C OH H3C NH2

butanoic acid 3-methylbutanamide
2
suffix
major
functional
group

O CH3 O

H3C OH H3C NH2

butanoic acid 3-methylbutanamide
only one major
group per
molecule
3
position
of functional
group from number longest

end of chain chain (parent)

from start to
finish...

O
HO
H3C CH3
O
2-pentanone 5-methylheptanoic acid
pentan-2-one
NOT 4-pentanone
3
position
of functional
group from
end of chain

O
HO ...giving major
H3C CH3 functional group
lowest possible
O value
2-pentanone 5-methylheptanoic acid
pentan-2-one
NOT 4-pentanone
3
position
of functional
group from
end of chain

it doesn’t matter
O where number
HO goes but I think the
H3C CH3 second example
avoids confusion
O later
2-pentanone 5-methylheptanoic acid
pentan-2-one
NOT 4-pentanone
4
prefix
substituents
(and minor
functional
groups)

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
4
prefix
substituents
(and minor
functional
groups)

CH3 Cl CH3
numbering should
H3C CH3 start with major
H3C CH
functional group3
H3C CH3 (like previous
CH3 slide)
2,2,5-trimethylheptane 8-chloro-2,3-dimethylnonane
NOT 3,6,6-trimethylheptane NOT 2-chloro-7,8-dimethylnonane
4
prefix
substituents
(and minor
functional
groups)

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
if no major functional
group then have
lowest numbering for
the majority of
substituents
4
prefix
substituents
(and minor
functional
groups)

CH3 Cl CH3
H3C CH3 note: group identical
H3C substituentsCH
(or 3
functional groups)
H3C CH3 CH3
together
2,2,5-trimethylheptane 8-chloro-2,3-dimethylnonane
NOT 3,6,6-trimethylheptane NOT 2-chloro-7,8-dimethylnonane
4
prefix
substituents
(and minor
functional
groups)

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

so trimethyl not 2-
methyl-2-methyl-6-
methylheptane
4
prefix
substituents
(and minor
functional
groups)

CH3 Cl CH3
H3halides
bizarrely, C don’t CH3
count as functional H3C CH3
groups...don’t
H3C ask...
CH3 CH3
2,2,5-trimethylheptane 8-chloro-2,3-dimethylnonane
NOT 3,6,6-trimethylheptane NOT 2-chloro-7,8-dimethylnonane
5
functional groups FG
principle FG suffix &
numbering; all others
prefix

O O CH3
H3C OH
HO OH
H3C CH3 O
5-hydroxy-2,2-dimethyl 2-methyl-4-oxo
pentanoic acid hex-2-enoic acid

multiple bonds combined with parent

5
functional groups FG
principle FG suffix &
numbering; all others
prefix functional groups
listed on pg 13

O O CH3
H3C OH
HO OH
H3C CH3 O
5-hydroxy-2,2-dimethyl 2-methyl-4-oxo
pentanoic acid hex-2-enoic acid

multiple bonds combined with parent

5
functional groups FG
principle FG suffix &
numbering; all others
prefix

O O CH3
major functional
group is suffix and
H3isC OH
HO OH the start of
numbering
H3C CH3 O
5-hydroxy-2,2-dimethyl 2-methyl-4-oxo
pentanoic acid hex-2-enoic acid

multiple bonds combined with parent

5
functional groups FG
principle FG suffix &
numbering; all others
prefix

O O CH3
H3C OH
all other groups
HO OH are prefix
H3C CH3 O
5-hydroxy-2,2-dimethyl 2-methyl-4-oxo
pentanoic acid hex-2-enoic acid

multiple bonds combined with parent

5
functional groups FG
principle FG suffix &
numbering; all others
prefix alkenes and
alkynes are
normally part of
the parent

O O CH3
H3C OH
HO OH
H3C CH3 O
5-hydroxy-2,2-dimethyl 2-methyl-4-oxo
pentanoic acid hex-2-enoic acid

multiple bonds combined with parent

6
minor FG
not all groups are
equal: halo- & nitro-
(-NO2) are prefixes

H3C O
Br N
CH3 O
1-bromo-2-methylpropane nitroethane
7
order
a, b, c...hope
you know prefixes are ordered
alphabetically
your alphabet! (although descriptors
like tert are ignored)

NH
HO OH

3-hydroxy-2-(methylamino)pentanoic acid
NOT 2-(methylamino)-3-hydroxypentanoic
acid
name this
molecule...
 OH O

H3C N CH3
H
hept

1
parent
 OH O

H3C N CH3
H

select longest
carbon chain (with
major functional

1
group in it)

parent
 OH O

H3C N CH3
H
amide

2
suffix
hept
identify major
functional group –
this will be the
suffix
 6 OH O

H3C 5 3 1 N CH3
4 2 H

number chain
starting with major

3
functional group

hept amide

position
 6 OH O

H3C 5 3 1 N CH3
4 2 H
5-methyl

4
prefix
hept amide
add prefixes (and
remember to tell us
where they are by giving
a position number)
 6 OH O

H3C 5 3 N1 CH3
4 2 H
3-hydroxy 6-en

repeat with all

remaining

5
functional groups

hept amide 5-methyl

functional groups
 and the last bit (which
throws a nasty curve
ball in but don’t
worry...)
6 OH O

H3C 5 3 1 N CH3
4 2 H
N-ethyl

6
the rest
hept amide 5-methyl 3-hydroxy 6-en
 OH O

H3C N CH3
H

N-ethyl-3-hydroxy-5-methylhept-6-enamide

7
order
 OH O

H3C N CH3
H

N-ethyl-3-hydroxy-5-methylhept-6-enamide

to be honest order

7
not too important
as long as name is
not ambiguous

order
N-ethyl?

(methylamino)?
 what the
©Renaissance Pictures
@&!!#?
DON’T
PANIC !
only simple examples in test
draw the molecule
with the following
name...
4-ethyl-3-hydroxycyclohexanone
4-ethyl-3-hydroxycyclohexanone

1 parent
4-ethyl-3-hydroxycyclohexanone

2 suffix
4-ethyl-3-hydroxycyclohexanone

4
H3C

prefix
4-ethyl-3-hydroxycyclohexanone
numbering starts
from major functional
group

O
1
2

3
4

4
H3C

prefix
4-ethyl-3-hydroxycyclohexanone

O
1
2
3

4 OH

5
H3C

functional groups
functional groups

these are listed on

pg 17
alkanes
H

H C H
H
methane
CH4

propane
C3H8

CnH2n+2
alkanes
H

H C H
H
methane
CH4

propane
open chains (no C3H8
rings) have this
general formula

CnH2n+2
alkanes
H

H C H
H
methane
CH4

alkanes are
tetrahedral in
shape...we shall see
why later
propane
C3H8

CnH2n+2
alkanes
H

H C H
H
methane
CH4

alkanes are
boring...normally
fuels or solvents
propane
C3H8

CnH2n+2
structural
isomers

pentane 2-methylbutane 2,2-dimethyl

C5H12 C5H12 propane
bp 36.2˚C bp 28˚C C5H12
bp 9.6˚C
structural
isomers

same number of
atoms – but bonding
different

pentane 2-methylbutane 2,2-dimethyl

C5H12 C5H12 propane
bp 36.2˚C bp 28˚C C5H12
bp 9.6˚C
structural
isomers

can make big

pentane 2-methylbutane
differences in
2,2-dimethyl
C5H12 C5H12 properties...as propane
bp 36.2˚C bp 28˚Cwe shall see later C5H12
bp 9.6˚C
alkenes

H H

H H
ethene
trigonal planar
alkenes

more exciting as the

double bond is
reactive! H H

H H
ethene
trigonal planar
alkenes
means it is flat with
three groups
attached to central
atom

H H

H H
ethene
trigonal planar
 configurational
(stereoisomers)
isomers

1-butene 2-methylpropene cyclobutane

C4H8 C4H8 C4H8

CH3

H3C CH3
H3C
trans-2-butene cis-2-butene
C4H8 C4H8

no rotation around C=C bond

 configurational
(stereoisomers)
isomers
these 2 are structural
isomers

1-butene 2-methylpropene cyclobutane

C4H8 C4H8 C4H8

CH3

H3C CH3
H3C
trans-2-butene cis-2-butene
C4H8 C4H8

no rotation around C=C bond

 configurational
(stereoisomers)
isomers

these 2 are
stereoisomers. Same
1-butene
atoms and bonds but 2-methylpropene cyclobutane
C4different
H8 orientation in C4H8 C4H8
space

CH3

H3C CH3
H3C
trans-2-butene cis-2-butene
C4H8 C4H8

no rotation around C=C bond

 configurational
(stereoisomers)
isomers

1-butene 2-methylpropene cyclobutane

occurs becomes
C4H8 C4H8 alkene cannot C4H8
rotate

CH3

H3C CH3
H3C
trans-2-butene cis-2-butene
C4H8 C4H8

no rotation around C=C bond

 configurational
(stereoisomers)
isomers

a whole world of pain

1-butene
is coming your way 2-methylpropene cyclobutane
C4H8when we discuss C4H8 C4H8
stereoisomers!

CH3

H3C CH3
H3C
trans-2-butene cis-2-butene
C4H8 C4H8

no rotation around C=C bond

alkenes
in nature

H3C CH3
CH3
H3C
CH3
H3C
(1R,5R)-2,6,6-trimethylbicyclo[3.1.1]hept-2-ene
α-pinene
alkenes
in nature

H3C CH3
CH3
H3C
CH3
H3C
(1R,5R)-2,6,6-trimethylbicyclo[3.1.1]hept-2-ene
α-pinene
yup...it smells of
pine...and is a very
useful compound in
chemistry
alkynes
H H
triple bond makes
ethyne alkynes long
C2H2 cylinders

O
O

OMe O

O O

H3C O

OH O
MeHN
HO
O
CH3
OH
neocarzinostatin chromophore A
alkynes
H H
ethyne
C2H2

O
they are found in O
nature...this nasty OMe O
beast cleaves DNA
O O

H3C O

OH O
MeHN
HO
O
CH3
OH
neocarzinostatin chromophore A
cyclic compounds

cyclohexane benzene
C6H12 C6H6
cyclic compounds

some cyclic
molecules are
flat...because they
have flat double
bonds

cyclohexane benzene
C6H12 C6H6
cyclic compounds

some look flat

flat...but are not due
to tetrahedral alkane
structure (see lct 7)

cyclohexane benzene
C6H12 C6H6
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
alcohols

OH
ethanol
C2H6O
alcohols
need OH attached to
alkane (not alkene,
alkyne or benzene)

OH
ethanol
C2H6O
alcohols
found in many
biological systems...

OH
ethanol
C2H6O
alcohols ...especially on
Saturday nights...

OH
ethanol
C2H6O
alcohols in
the real world

HO

O or Sunday HO
HO mornings... OH
HO OH
HO
6-(hydroxymethyl)-tetrahydro- 1,2-ethandiol
2H-pyran-2,3,4,5-tetraol ethylene glycol
glucose antifreeze
sugar I guess!
three classes
of alcohol H3C
CH3
CH3 CH3
secondary (2°)
CH3 H CH3
H3C OH
H H H3C
primary (1°) HO
(R)-3,7-dimethyloct-6-en-1-ol cholesterol
citronellol all animals
citronella oil CH3

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

depends on the tertiary (3°)

number of carbonsH3C OH
attached to the
C–OH unit CH3
(R)-1-isopropyl-4-methylcyclohex-3-enol
terpinen-4-ol
tea tree oil
three classes
of alcohol H3C
CH3
CH3 CH3
secondary (2°)
...this one has 1
CH3 H carbon attached so is
primary. the nextCH3
H3C OH
has 2 so is
H H secondaryH3C etc.
primary (1°) HO
(R)-3,7-dimethyloct-6-en-1-ol cholesterol
citronellol all animals
citronella oil CH3

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

this controls the tertiary (3°)

H
reactivity of the 3 C OH
alcohols as you
shall see in future CH3
lectures
(R)-1-isopropyl-4-methylcyclohex-3-enol
terpinen-4-ol
tea tree oil
phenols
CH3

H3C
OH HO
H
H3C N
O
phenol O
carbolic acid
(E)-N-(4-hydroxy-3-methoxybenzyl)-
8-methylnon-6-enamide
capsaicin
chilli peppers
phenols looks like an
alcohol BUT is not
(as it is not
CH3 to an
attached
alkane)
H3C
OH HO
H
H3C N
O
phenol O
carbolic acid
(E)-N-(4-hydroxy-3-methoxybenzyl)-
8-methylnon-6-enamide
capsaicin
chilli peppers
phenols thus has very
different
properties...I should CH3
whistle ‘ring of fire’
now...
H3C
OH HO
H
H3C N
O
phenol O
carbolic acid
(E)-N-(4-hydroxy-3-methoxybenzyl)-
8-methylnon-6-enamide
capsaicin
chilli peppers
ethers
O
O O
O
H3C O CH3
O O
ethoxyethane O
diethyl ether tetrahydrofuran
ether THF 18-crown-6
replace one carbon
in an alkyl chain and
you have an ether.
Often used as
solvents
18-crown-6
and potassium
cation
halides organic molecules
containing fluorine,
chlorine, bromine or
iodine

H F

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

Pic: NASA
halides often toxic and some
are responsible for
the hole in the ozone
H F layer

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

Pic: NASA
thiols
SH
HS SH CH3 O
HS
H2N H H3C CH3 H3C CH3
CO2H
(R)-2-amino-3- propane-2,2-dithiol 4-methyl-4-
sulfanylpropanoic acid sulfanylpentan-2-one
cysteine these are the
sulfur version of
alcohols...found in
nature (and us)
thiols
SH
HS SH CH3 O
HS
H2N H H3C CH3 H3C CH3
CO2H
(R)-2-amino-3- propane-2,2-dithiol 4-methyl-4-
sulfanylpropanoic acid sulfanylpentan-2-one
cysteine
one of these is the
smelliest chemical
known...but no one wants
to repeat the experiment
to find out which!
 CH3

2x10 -5 ppb
HS
H3C

CH3
2-(4-methylcyclohex-3-
enyl)propane-2-thiol
taste of grapefruit

can smell nice...garlic,

truffles etc...And incredibly
small amounts are the taste
of grapefruit!
 CH3

2x10 -5 ppb
HS
H3C

CH3
2-(4-methylcyclohex-3-
enyl)propane-2-thiol
taste of grapefruit
this value is similar to
1 drop in a lake...
amines
CH3

H3C N NH2
H2N H2N NH2

CH3
triethylamine butane-1,4-diamine pentane-1,5-diamine
smells of fish putrescine cadaverine
smells of decay smells of decay

...also smell bad but

are vital for life (and
the smell of death).
amines in
nature

O CH3 O

OH H3C OH
H2N H NH2
(S)-2-amino-3- (S)-2-amino-3-
phenylpropanoic acid methylbutanoic acid
phenylalanine valine
amino acid amino acid

amino acids are an

obvious source of
amines
amines in nature N
CH3 O
CH3
O
O

O
methyl 3-(benzoyloxy)-8-methyl-
8-aza-bicyclo[3.2.1]octane-2-
carboxylate
cocaine

Scarface (1983): Universal Pictures

amines in nature N
CH3 O
CH3
O
O

O
methyl 3-(benzoyloxy)-8-methyl-
8-aza-bicyclo[3.2.1]octane-2-
carboxylate
cocaine

but there is a problem

bigger than drugs...

Scarface (1983): Universal Pictures

five kinds of amine

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

H3C N CH
3
H3C
trimethylammonium ion
4° ammonium (salt)
five kinds of amine

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

H but primary,
secondary & tertiary
H3C N CH mean something
3 different than when
H3C
we used them with
trimethylammonium ion alcohols!
4° ammonium (salt)
five kinds of amine

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

H
...now refer to the
number of C attached H3C N CH
to the N...but it gets 3
worse...
H3C
trimethylammonium ion
4° ammonium (salt)
the problem
with amines primary amine
because only 1
primary amine carbon attached
(1°)

NH2
H3C OH

CH3 O

secondary position
(2°)
the problem
with amines but in a secondary
primary amine
position (like alcohol
(1°)naming) as this carbon
has 2 carbons
attached!

NH2
H3C OH

CH3 O

secondary position
(2°)
carbonyl:
aldehydes O
O O
H
H H H3C H

methanal ethanal benzaldehyde

formaldehyde acetaldehyde

OH OH
O
HO
OH OH H
(2R,3S,4R,5R)-2,3,4,5,6-
pentahydroxyhexanal
glucose
carbonyl:
aldehydes O
O O
H
H H H3C H

methanal ethanal C=Obenzaldehyde

is the cornerstone
formaldehyde acetaldehyde of organic synthesis.
Aldehydes = CHO and
are more reactive than...
OH OH
O
HO
OH OH H
(2R,3S,4R,5R)-2,3,4,5,6-
pentahydroxyhexanal
glucose
carbonyl:
ketones
CH3 CH3
O O
O

H3C CH3
H3C H H CH3

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

2-yl)cyclohex-2-enone acetone 2-yl)cyclohex-2-enone
(R)-carvone (S)-carvone
spearmint caraway
carbonyl:
ketones
ketones, which have
CH3 C=O bonded to two
CH3
carbon groups
O O
O

H3C CH3
H3C H H CH3

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

2-yl)cyclohex-2-enone acetone 2-yl)cyclohex-2-enone
(R)-carvone (S)-carvone
spearmint caraway
carboxylic acid
derivatives: acids
H3C CH3 CH3
O
O
H3C
OH
H3C OH CO2H
OH O CH3
ethanoic acid (S)-2-hydroxy- (2Z,4E)-3-methyl-5-(2,6,6-
acetic acid propanoic acid trimethyl-4-oxocyclohex-2-
vinegar L-(+)-lactic acid enyl)penta-2,4-dienoic acid
abscisic acid
C=O bonded to 1 leaf fall
carbon and an OH
group
carboxylic acid
derivatives: others
O
O
H3C CH3
Na O
H3C O
CH3
sodium ethanoate 2-methylpropyl propanoate
carboxylate ion isobutyl propionate
smell of rum
ester
NH2 O
H
HO2C N many different
OMe derivatives
depending on what
O is attached to C=O

aspartame
sweetener
amide
how are functional
groups related?
 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

carboxylic acids
alcohols
esters
ethers
aldehydes amides
alkanes amines
ketones acyl halides
halides
acid anhydrides
thiols
nitriles
parts 3 & 4
are combined
word of
warning...next 2
units will not be in
the same order as
study guide...
what have
....we learnt? • naming (simple)
HO molecules
HO
• recognise
functional groups
OH
Me O
Me O O
NH2 O
Cl
OH O O

HO Cl OH
O O O
H H
O N N NHMe
N N N
H H H
HN O O O Me
molecules may look
HO2C complicated but simply
NH2 Me into
break them down
their functional groups
OH (amides in red)
HO OH
Vancomycin