Unit One Part 2:naming & functional groups

N

NNN

SN

NH3C

H3C O

O

CH3

H3C O

O

H

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

N

NNN

SN

NH3C

H3C O

O

CH3

H3C O

O

H

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

Don’t panic!We won’t do anything

this complicated

Unit OnePart2Naming molecules (pg 11-16)Introducing functional groups (pg 16-9)

remember...read the study guide it

contains all you need

how do wename molecules?

NH2

O

OH

2-amino-4-methylpentanoic acid

prefixsubstituents

minor functional groups

parentcarbon chain

(& multiple bonds)

suffixprincipal functional

groups

NH2

O

OH

2-amino-4-methylpentanoic acid

prefixsubstituents

minor functional groups

parentcarbon chain

(& multiple bonds)

suffixprincipal functional

groups

there are three parts to any name...even Viagra’s real name

obeys this.

NH2

O

OH

2-amino-4-methylpentanoic acid

prefixsubstituents

minor functional groups

parentcarbon chain

(& multiple bonds)

suffixprincipal functional

groups

the prefix can become a nightmare as it contains most

information

five steps to success!

works for all molecules but the

whole system takes volumes to explain...

five steps to success!

parentlongest carbon chain containing a functional group1H3C CH3

CH3

4-methylheptane

H3C

CH3OH

2-propyl-1-pentanol1

23

45

page 12/13 of guide

parentlongest carbon chain containing a functional group1H3C CH3

CH3

4-methylheptane

H3C

CH3OH

2-propyl-1-pentanol1

23

45

7 bigger than 5 he says patronisingly

parentlongest carbon chain containing a functional group1H3C CH3

CH3

4-methylheptane

H3C

CH3OH

2-propyl-1-pentanol1

23

45

now use pent- as we have to start

our chain from the functional group

suffixm a j o r functional g r o u p

H3C OH

O

butanoic acidH3C NH2

OCH3

3-methylbutanamide

2 list of major groups pg 13

order of priority pg 14

suffixm a j o r functional g r o u p

H3C OH

O

butanoic acidH3C NH2

OCH3

3-methylbutanamide

2only one major

group per molecule

BrH3C

CH3

1-bromo-2-methylpropane

minor FGnot all groups are equal: halo- & nitro- (-NO2) are prefixes2

NO

O

nitroethane

a

no idea why!But please remember they are functional groups. It is only for naming that they

do not count

H3C CH3

O

2-pentanonepentan-2-one

NOT 4-pentanone

O

HO

5-methylheptanoic acid

positionof functional group from end of chain3 number longest

chain (parent) from start to

finish...

H3C CH3

O

2-pentanonepentan-2-one

NOT 4-pentanone

O

HO

5-methylheptanoic acid

positionof functional group from end of chain3

...giving major functional group lowest possible

value

H3C CH3

O

2-pentanonepentan-2-one

NOT 4-pentanone

O

HO

5-methylheptanoic acid

positionof functional group from end of chain3

it doesn’t matter where number

goes but I think the second example avoids confusion

later

H3C CH3

CH3

CH3

Cl

8-chloro-2,3-dimethylnonaneNOT 2-chloro-7,8-dimethylnonane

H3C CH3

H3C CH3

CH3

2,2,5-trimethylheptaneNOT 3,6,6-trimethylheptane

prefixsubstituents (and minor functional g r o u p s ) 4

H3C CH3

CH3

CH3

Cl

8-chloro-2,3-dimethylnonaneNOT 2-chloro-7,8-dimethylnonane

H3C CH3

H3C CH3

CH3

2,2,5-trimethylheptaneNOT 3,6,6-trimethylheptane

prefixsubstituents (and minor functional g r o u p s ) 4

numbering should start with major functional group

(like previous slide)

H3C CH3

CH3

CH3

Cl

8-chloro-2,3-dimethylnonaneNOT 2-chloro-7,8-dimethylnonane

H3C CH3

H3C CH3

CH3

2,2,5-trimethylheptaneNOT 3,6,6-trimethylheptane

prefixsubstituents (and minor functional g r o u p s ) 4

if no major functional group then have

lowest numbering for the majority of substituents

H3C CH3

CH3

CH3

Cl

8-chloro-2,3-dimethylnonaneNOT 2-chloro-7,8-dimethylnonane

H3C CH3

H3C CH3

CH3

2,2,5-trimethylheptaneNOT 3,6,6-trimethylheptane

prefixsubstituents (and minor functional g r o u p s ) 4

note: group identical substituents (or

functional groups) together

H3C CH3

CH3

CH3

Cl

8-chloro-2,3-dimethylnonaneNOT 2-chloro-7,8-dimethylnonane

H3C CH3

H3C CH3

CH3

2,2,5-trimethylheptaneNOT 3,6,6-trimethylheptane

prefixsubstituents (and minor functional g r o u p s ) 4

so trimethyl not 2-methyl-2-methyl-6-

methylheptane

H3C CH3

CH3

CH3

Cl

8-chloro-2,3-dimethylnonaneNOT 2-chloro-7,8-dimethylnonane

H3C CH3

H3C CH3

CH3

2,2,5-trimethylheptaneNOT 3,6,6-trimethylheptane

prefixsubstituents (and minor functional g r o u p s ) 4

bizarrely, halides don’t count as functional groups...don’t ask...

CH3

OH

O

OH3C

2-methyl-4-oxohex-2-enoic acid

HO OH

O

H3C CH35-hydroxy-2,2-dimethyl

pentanoic acid

Prefixcontains everything except major functional group and multiple bonds4

multiple bonds combined with parent

CH3

OH

O

OH3C

2-methyl-4-oxohex-2-enoic acid

HO OH

O

H3C CH35-hydroxy-2,2-dimethyl

pentanoic acid

Prefixcontains everything except major functional group and multiple bonds4

multiple bonds combined with parent

functional groups listed on pg 13

CH3

OH

O

OH3C

2-methyl-4-oxohex-2-enoic acid

HO OH

O

H3C CH35-hydroxy-2,2-dimethyl

pentanoic acid

Prefixcontains everything except major functional group and multiple bonds4

multiple bonds combined with parent

major functional group is suffix and is

the start of numbering

CH3

OH

O

OH3C

2-methyl-4-oxohex-2-enoic acid

HO OH

O

H3C CH35-hydroxy-2,2-dimethyl

pentanoic acid

Prefixcontains everything except major functional group and multiple bonds4

multiple bonds combined with parent

all other groups are prefix

CH3

OH

O

OH3C

2-methyl-4-oxohex-2-enoic acid

HO OH

O

H3C CH35-hydroxy-2,2-dimethyl

pentanoic acid

Prefixcontains everything except major functional group and multiple bonds4

multiple bonds combined with parent

alkenes and alkynes are

normally part of the parent

ordera, b, c...hope y o u k n o w your alphabet!5

HO OH

O

NH

3-hydroxy-2-(methylamino)pentanoic acidNOT 2-(methylamino)-3-hydroxypentanoic

acid

prefixes are ordered alphabetically

(although descriptors like tert are ignored)

name this molecule...

H3C NH

O

CH3

OH

hept

1parent

H3C NH

O

CH3

OH

1parent

select longest carbon chain (with major functional

group in it)

H3C NH

O

CH3

OH

amide

2suffixhept

identify major functional group –

this will be the suffix

3position

H3C NH

O

CH3

OH

12

34

5

6

hept amide

number chain starting with major

functional group

H3C NH

O

CH3

OH

12

34

5

6

5-methyl

4prefixhept amide

add prefixes (and remember to tell us

where they are by giving a position number)

4functional groups

H3C NH

O

CH3

OH

12

34

5

3-hydroxy 6-en

6

hept amide 5-methyl

repeat with all remaining

functional groups

H3C NH

O

CH3

OH

12

34

5

N-ethyl

6

4the resthept amide 5-methyl 3-hydroxy 6-en

and the last bit (which throws a nasty curve

ball in but don’t worry...)

5order

H3C NH

O

CH3

OH

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

5order

H3C NH

O

CH3

OH

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

to be honest order not too important

as long as name is not ambiguous

N-ethyl?

(methylamino)?

what the@&!!#?

©Renaissance Pictures

DON’TPANIC!

only simple examples in test

2exampleOn the next slide there

is a skeletal structure and four possible names.

Which is correct?

4-amino-3,5-dihydroxy-5-oxopentanoic acidA

4-amino-3,5,6-trihydroxyhexanoic acidB

3-amino-2,4-dihydroxy-1-oxo-6-hexanoic acidC

4-amino-3,5-dihydroxy-6-oxohexanoic acidD

OHC

OHOH

NH2OH

O

A 4-amino-3,5-dihydroxy-5-oxopentanoic acid

4-amino-3,5,6-trihydroxyhexanoic acidB

3-amino-2,4-dihydroxy-1-oxo-6-hexanoic acidC

4-amino-3,5-dihydroxy-6-oxohexanoic acidDwrong

OHC

OHOH

NH2OH

O

A 4-amino-3,5-dihydroxy-5-oxopentanoic acid

4-amino-3,5,6-trihydroxyhexanoic acidB

3-amino-2,4-dihydroxy-1-oxo-6-hexanoic acidC

4-amino-3,5-dihydroxy-6-oxohexanoic acidDwrong

OHC

OHOH

NH2OH

O

The parent contains 6 C. The carbon C of CHO still

counts!

B

4-amino-3,5-dihydroxy-5-oxopentanoic acidA

4-amino-3,5,6-trihydroxyhexanoic acid

3-amino-2,4-dihydroxy-1-oxo-6-hexanoic acidC

4-amino-3,5-dihydroxy-6-oxohexanoic acidD wrong

OHC

OHOH

NH2OH

O

B

4-amino-3,5-dihydroxy-5-oxopentanoic acidA

4-amino-3,5,6-trihydroxyhexanoic acid

3-amino-2,4-dihydroxy-1-oxo-6-hexanoic acidC

4-amino-3,5-dihydroxy-6-oxohexanoic acidD wrong

OHC

OHOH

NH2OH

OThere are only two alcohol/

hydroxy groups. This OH is part of the acid (all bonds to one C).

B

4-amino-3,5-dihydroxy-5-oxopentanoic acidA

4-amino-3,5,6-trihydroxyhexanoic acid

3-amino-2,4-dihydroxy-1-oxo-6-hexanoic acidC

4-amino-3,5-dihydroxy-6-oxohexanoic acidD wrong

OHC

OHOH

NH2OH

OThis is not an alcohol OH because of the position of the C. The C needs four bonds so

must have C=O

B

4-amino-3,5-dihydroxy-5-oxopentanoic acidA

4-amino-3,5,6-trihydroxyhexanoic acid

3-amino-2,4-dihydroxy-1-oxo-6-hexanoic acidC

4-amino-3,5-dihydroxy-6-oxohexanoic acidD wrong

OHC

OHOH

NH2OH

OThis is not an alcohol OH because of the position of the C. The C needs four bonds so

must have C=O

An alcohol would be HOH2C-

A

B

C

D

4-amino-3,5-dihydroxy-5-oxopentanoic acid

4-amino-3,5,6-trihydroxyhexanoic acid

3-amino-2,4-dihydroxy-1-oxo-6-hexanoic acid

4-amino-3,5-dihydroxy-6-oxohexanoic acid

wrong

OHC

OHOH

NH2OH

O

A

B

C

D

4-amino-3,5-dihydroxy-5-oxopentanoic acid

4-amino-3,5,6-trihydroxyhexanoic acid

3-amino-2,4-dihydroxy-1-oxo-6-hexanoic acid

4-amino-3,5-dihydroxy-6-oxohexanoic acid

wrong

OHC

OHOH

NH2OH

O

Major functional group controls the numbering,

so the acid is 1.

4-amino-3,5-dihydroxy-5-oxopentanoic acidA

4-amino-3,5,6-trihydroxyhexanoic acidB

3-amino-2,4-dihydroxy-1-oxo-6-hexanoic acidC

4-amino-3,5-dihydroxy-6-oxohexanoic acidD

OHC

OHOH

NH2OH

O

3example

A

B

C

D

2-amino-3-phenylpropanoic acid

2-amino-1-phenylpropanoic acid

2-amino-1-hydroxy-3-phenylpropanone

2-amino-nona-4,6,8-trienoic acid

NH2

OH

O

A

B

C

D

2-amino-3-phenylpropanoic acid

2-amino-1-phenylpropanoic acid

2-amino-1-hydroxy-3-phenylpropanone

2-amino-nona-4,6,8-trienoic acid

NH2

OH

O

A

B

C

D

2-amino-3-phenylpropanoic acid

2-amino-1-phenylpropanoic acid

2-amino-1-hydroxy-3-phenylpropanone

2-amino-nona-4,6,8-trienoic acid

NH2

OH

O

...or phenylalanine for those of you of a more biological disposition...

A

B

C

D

2-amino-3-phenylpropanoic acid

2-amino-1-phenylpropanoic acid

2-amino-1-hydroxy-3-phenylpropanone

2-amino-nona-4,6,8-trienoic acidwrong

NH2

OH

O

A

B

C

D

2-amino-3-phenylpropanoic acid

2-amino-1-phenylpropanoic acid

2-amino-1-hydroxy-3-phenylpropanone

2-amino-nona-4,6,8-trienoic acidwrong

NH2

OH

O

Major functional group controls the numbering, so the acid is 1 and not

the phenyl group

A

B

C

D

2-amino-3-phenylpropanoic acid

2-amino-1-phenylpropanoic acid

2-amino-1-hydroxy-3-phenylpropanone

2-amino-nona-4,6,8-trienoic acid

wrongNH2

OH

O

A

B

C

D

2-amino-3-phenylpropanoic acid

2-amino-1-phenylpropanoic acid

2-amino-1-hydroxy-3-phenylpropanone

2-amino-nona-4,6,8-trienoic acid

wrongNH2

OH

O

Both the carbonyl group and the hydroxyl are attached to the same carbon so they are the same

functional group (a carboxylic acid)

A

B

C

D

2-amino-3-phenylpropanoic acid

2-amino-1-phenylpropanoic acid

2-amino-1-hydroxy-3-phenylpropanone

2-amino-nona-4,6,8-trienoic acid

wrong

NH2

OH

O

A

B

C

D

2-amino-3-phenylpropanoic acid

2-amino-1-phenylpropanoic acid

2-amino-1-hydroxy-3-phenylpropanone

2-amino-nona-4,6,8-trienoic acid

wrong

NH2

OH

O

The benzene ring can be considered as a functional group with the name phenyl (if it has 1 substituent) or benzene (if it has more than 1

substituent). It should not be called cyclohexa-1,3,5-triene or any variant.

4example

A

B

C

D

2-carbamoyl-4-nitrobenzenol

2-carbamoyl-4-nitrophenol

1-(aminomethyl)-2-hydroxy-5-nitrobenzaldehyde

2-hydroxy-5-nitrobenzamide

O NH2

OH

O2N

A

B

C

D

2-carbamoyl-4-nitrobenzenol

2-carbamoyl-4-nitrophenol

1-(aminomethyl)-2-hydroxy-5-nitrobenzaldehyde

2-hydroxy-5-nitrobenzamidewrong

O NH2

OH

O2N

A

B

C

D

2-carbamoyl-4-nitrobenzenol

2-carbamoyl-4-nitrophenol

1-(aminomethyl)-2-hydroxy-5-nitrobenzaldehyde

2-hydroxy-5-nitrobenzamidewrong

O NH2

OH

O2N

Most of this name is wrong. The amide takes priority and is the

suffix (benzamide). If the OH took priority it would be a phenol.

A

B

C

D

2-carbamoyl-4-nitrobenzenol

2-carbamoyl-4-nitrophenol

1-(aminomethyl)-2-hydroxy-5-nitrobenzaldehyde

2-hydroxy-5-nitrobenzamidewrong

O NH2

OH

O2N

A

B

C

D

2-carbamoyl-4-nitrobenzenol

2-carbamoyl-4-nitrophenol

1-(aminomethyl)-2-hydroxy-5-nitrobenzaldehyde

2-hydroxy-5-nitrobenzamidewrong

O NH2

OH

O2N

Amide still takes priority so it is not a phenol

A

B

C

D

2-carbamoyl-4-nitrobenzenol

2-carbamoyl-4-nitrophenol

1-(aminomethyl)-2-hydroxy-5-nitrobenzaldehyde

2-hydroxy-5-nitrobenzamide

wrong

O NH2

OH

O2N

A

B

C

D

2-carbamoyl-4-nitrobenzenol

2-carbamoyl-4-nitrophenol

1-(aminomethyl)-2-hydroxy-5-nitrobenzaldehyde

2-hydroxy-5-nitrobenzamide

wrong

O NH2

OH

O2N

Both the C=O and the C–N are the same carbon so this is one functional group. It is an amide not an aldehyde and an amine.

A

B

C

D

2-carbamoyl-4-nitrobenzenol

2-carbamoyl-4-nitrophenol

1-(aminomethyl)-2-hydroxy-5-nitrobenzaldehyde

2-hydroxy-5-nitrobenzamide

O NH2

OH

O2N

draw the molecule with the following name...

4-ethyl-3-hydroxycyclohexanone

4-ethyl-3-hydroxycyclohexanone

1parent

O

4-ethyl-3-hydroxycyclohexanone

2suffix

O

4-ethyl-3-hydroxycyclohexanone

4prefix

O

H3C

O

4-ethyl-3-hydroxycyclohexanone

4prefix

O

H3C

numbering starts from major functional

group

12

34

O

H3C

OH

O

4-ethyl-3-hydroxycyclohexanone

4functional groups

12

3

4

2example

2-hydroxy-3,3-dimethylpentanoic acid

CO2H

OH

CO2H

OH

CO2H

OH OHOHO

A B

C D

CO2H

OH

CO2H

OH

CO2H

OH OHOHO

A B

C D

2-hydroxy-3,3-dimethylpentanoic acid

✔✗

✗ ✗

CO2H

OH

CO2H

OH

CO2H

OH OHOHO

A B

C D

2-hydroxy-3,3-dimethylpentanoic acid

✔✗

✗ ✗

Hydroxyl group in wrong position. Numbering starts with the major

functional group, thecarboxylic acid

CO2H

OH

CO2H

OH

CO2H

OH OHOHO

A B

C D

2-hydroxy-3,3-dimethylpentanoic acid

✔✗

✗ ✗

CO2H

OH

CO2H

OH

CO2H

OH OHOHO

A B

C D

2-hydroxy-3,3-dimethylpentanoic acid

✔✗

✗ ✗

CO2H

OH

CO2H

OH

CO2H

OH OHOHO

A B

C D

2-hydroxy-3,3-dimethylpentanoic acid

✔✗

✗ ✗

The carbon chain is too short (pent = 5)

CO2H

OH

CO2H

OH

CO2H

OH OHOHO

A B

C D

2-hydroxy-3,3-dimethylpentanoic acid

✔✗

✗ ✗

CO2H

OH

CO2H

OH

CO2H

OH OHOHO

A B

C D

2-hydroxy-3,3-dimethylpentanoic acid

✔✗

✗ ✗

No carboxylic acid present. Instead we have erroneously

have an aldehyde and an alcohol.

3example

3-bromo-5-methylbenzoic acid

O OH

Br

O OH

Br

O OH

Br

O

BrHO

A B

C D

3-bromo-5-methylbenzoic acid

O OH

Br

O OH

Br

O OH

Br

O

BrHO

A B

C D

✔

✗

✗

✗

3-bromo-5-methylbenzoic acid

O OH

Br

O OH

Br

O OH

Br

O

BrHO

A B

C D

✔

✗

✗

✗This is not a carboxylic

acid. Instead it has both an aldehyde and an

alcohol. Carboxylic acids have the C=O and the OH

on the same carbon atom.

3-bromo-5-methylbenzoic acid

O OH

Br

O OH

Br

O OH

Br

O

BrHO

A B

C D

✔

✗

✗

✗

3-bromo-5-methylbenzoic acid

O OH

Br

O OH

Br

O OH

Br

O

BrHO

A B

C D

✔

✗

✗

✗Bromo is part of the prefix so is attached

directly to the benzene ring

3-bromo-5-methylbenzoic acid

O OH

Br

O OH

Br

O OH

Br

O

BrHO

A B

C D

✔

✗

✗

✗Bromo is part of the prefix so is attached

directly to the benzene ring

If it was attached to the methyl group then it would be grouped with the

methyl (e.g. 3-(bromomethyl)benzoic acid)

3-bromo-5-methylbenzoic acid

O OH

Br

O OH

Br

O OH

Br

O

BrHO

A B

C D

✔

✗

✗

✗

3-bromo-5-methylbenzoic acid

O OH

Br

O OH

Br

O OH

Br

O

BrHO

A B

C D

✔

✗

✗

✗Numbering is wrong. Carboxylic acid takes priority so the numbering within the ring starts from the carbon attached to the acid. The

drawing shows 2-bromo-5-methylbenzoic acid.

3-bromo-5-methylbenzoic acid

O OH

Br

O OH

Br

O OH

Br

O

BrHO

A B

C D

✔

✗

✗

✗

functional groups

these are listed on pg 17

Read functional groups (Pg16-29)

©hebedesign@flickr

I will not have time to go through these

HC

HHH

methaneCH4

alkanes

CnH2n+2

propaneC3H8

HC

HHH

methaneCH4

alkanes

CnH2n+2

propaneC3H8open chains (no

rings) have this general formula

CnH2n+2

Reference

C6H2x6+2

H

H H

H H

H H

H H

H HH

H H

C6H14

CnH2n+2

Functional groups

C6H12 ≠ CnH2n+2

CnH2n+2

Functional groups

C6H12 ≠ CnH2n+2if a molecule does not agree with this

formula, it has either a ring or functional group (look at double bond equivalence (dbe)

if you are interested).

HC

HHH

methaneCH4

alkanes

CnH2n+2

propaneC3H8

alkanes are tetrahedral in

shape...we shall see why later

HC

HHH

methaneCH4

alkanes

CnH2n+2

propaneC3H8

alkanes are boring...normally fuels or solvents

2,2-dimethylpropane

C5H12bp 9.6˚C

2-methylbutaneC5H12

bp 28˚C

pentaneC5H12

bp 36.2˚C

structuralisomers

2,2-dimethylpropane

C5H12bp 9.6˚C

2-methylbutaneC5H12

bp 28˚C

pentaneC5H12

bp 36.2˚C

structuralisomers

same number of atoms – but bonding

different

2,2-dimethylpropane

C5H12bp 9.6˚C

2-methylbutaneC5H12

bp 28˚C

pentaneC5H12

bp 36.2˚C

structuralisomers

can make big differences in properties...as

we shall see later

alkenes

trigonal planarH

H H

Hethene

alkenes

trigonal planarH

H H

Hethene

more exciting as the double bond is

reactive!

alkenes

trigonal planarH

H H

Hethene

means it is flat with three groups

attached to central atom

trans-2-buteneC4H8

H3C

CH3H3C CH3

cis-2-buteneC4H8

1-buteneC4H8

2-methylpropeneC4H8

cyclobutaneC4H8

configurational (stereoisomers)

isomers

no rotation around C=C bond

trans-2-buteneC4H8

H3C

CH3H3C CH3

cis-2-buteneC4H8

1-buteneC4H8

2-methylpropeneC4H8

cyclobutaneC4H8

configurational (stereoisomers)

isomers

no rotation around C=C bond

these 2 are structural isomers

trans-2-buteneC4H8

H3C

CH3H3C CH3

cis-2-buteneC4H8

1-buteneC4H8

2-methylpropeneC4H8

cyclobutaneC4H8

configurational (stereoisomers)

isomers

no rotation around C=C bond

these 2 are stereoisomers. Same atoms and bonds but different orientation in

space

trans-2-buteneC4H8

H3C

CH3H3C CH3

cis-2-buteneC4H8

1-buteneC4H8

2-methylpropeneC4H8

cyclobutaneC4H8

configurational (stereoisomers)

isomers

no rotation around C=C bond

occurs becomes alkene cannot

rotate

trans-2-buteneC4H8

H3C

CH3H3C CH3

cis-2-buteneC4H8

1-buteneC4H8

2-methylpropeneC4H8

cyclobutaneC4H8

configurational (stereoisomers)

isomers

no rotation around C=C bond

a whole world of pain is coming your way when we discuss stereoisomers!

alkenes in nature

CH3H3C

H3C

CH3CH3H3C

(1R,5R)-2,6,6-trimethylbicyclo[3.1.1]hept-2-eneα-pinene

alkenes in nature

CH3H3C

H3C

CH3CH3H3C

(1R,5R)-2,6,6-trimethylbicyclo[3.1.1]hept-2-eneα-pinene

yup...it smells of pine...and is a very useful compound in

chemistry

alkynes

O

O

O

O

OO

O

H3C

OMe

OH

OOH

HO

CH3

MeHN

neocarzinostatin chromophore A

H HethyneC2H2

triple bond makes alkynes long

cylinders

alkynes

O

O

O

O

OO

O

H3C

OMe

OH

OOH

HO

CH3

MeHN

neocarzinostatin chromophore A

H HethyneC2H2

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

cyclohexaneC6H12

cyclic compounds

benzeneC6H6

cyclohexaneC6H12

cyclic compounds

benzeneC6H6

some cyclic molecules are

flat...because they have flat double

bonds

cyclohexaneC6H12

cyclic compounds

benzeneC6H6

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

cyclic structures in nature

CH3

CH3

H3C

H3C

CH3

H H

H

(8R,9S,10S,13R,14S,17R)-10,13-dimethyl-17-(6-methylheptan-2-yl)-hexadecahydro-1H-

cyclopenta[a]phenanthrenecholestane - steroid

alcohols

OHethanolC2H6O

alcohols

OHethanolC2H6O

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

alcohols

OHethanolC2H6O

found in many biological systems...

alcohols

OHethanolC2H6O

...especially on Saturday nights...

HOOH

1,2-ethandiolethylene glycol

antifreeze

alcohols in the real world

or Sunday mornings...O

HOHO

HO

HOOH

6-(hydroxymethyl)-tetrahydro-2H-pyran-2,3,4,5-tetraol

glucosesugar I guess!

H3C OH

CH3 CH3

(R)-3,7-dimethyloct-6-en-1-olcitronellol

citronella oil

CH3

CH3

H3C

H3C

CH3

H H

H

HOcholesterolall animals

CH3

OHH3C

CH3(R)-1-isopropyl-4-methylcyclohex-3-enol

terpinen-4-oltea tree oil

three classes of alcohol

tertiary (3°)

secondary (2°)

primary (1°)

H3C OH

CH3 CH3

(R)-3,7-dimethyloct-6-en-1-olcitronellol

citronella oil

CH3

CH3

H3C

H3C

CH3

H H

H

HOcholesterolall animals

CH3

OHH3C

CH3(R)-1-isopropyl-4-methylcyclohex-3-enol

terpinen-4-oltea tree oil

three classes of alcohol

tertiary (3°)

secondary (2°)

primary (1°)

depends on the number of carbons

attached to theC–OH unit

H3C OH

CH3 CH3

(R)-3,7-dimethyloct-6-en-1-olcitronellol

citronella oil

CH3

CH3

H3C

H3C

CH3

H H

H

HOcholesterolall animals

CH3

OHH3C

CH3(R)-1-isopropyl-4-methylcyclohex-3-enol

terpinen-4-oltea tree oil

three classes of alcohol

tertiary (3°)

secondary (2°)

primary (1°)

...this one has 1 carbon attached so is

primary. the next has 2 so is

secondary etc.

H3C OH

CH3 CH3

(R)-3,7-dimethyloct-6-en-1-olcitronellol

citronella oil

CH3

CH3

H3C

H3C

CH3

H H

H

HOcholesterolall animals

CH3

OHH3C

CH3(R)-1-isopropyl-4-methylcyclohex-3-enol

terpinen-4-oltea tree oil

three classes of alcohol

tertiary (3°)

secondary (2°)

primary (1°)

this controls the reactivity of the alcohols as you

shall see in future lectures

important terms & common mistakes

X

HH

X

H

X

primarygroup

secondarygroup

tertiarygroup

not just true of alcohols but all

functional groups

phenolsOH

phenolcarbolic acid

HO

OH3C

HN

O

CH3

H3C

(E)-N-(4-hydroxy-3-methoxybenzyl)-8-methylnon-6-enamide

capsaicinchilli peppers

phenolsOH

phenolcarbolic acid

HO

OH3C

HN

O

CH3

H3C

(E)-N-(4-hydroxy-3-methoxybenzyl)-8-methylnon-6-enamide

capsaicinchilli peppers

looks like an alcohol BUT is not

(as it is not attached to an

alkane)

phenolsOH

phenolcarbolic acid

HO

OH3C

HN

O

CH3

H3C

(E)-N-(4-hydroxy-3-methoxybenzyl)-8-methylnon-6-enamide

capsaicinchilli peppers

thus has very different

properties...I should whistle ‘ring of fire’

now...

important terms & common mistakes

R

OH

RR

alcohol(R = C or H)

OH

phenol1 million times

more acidic than an aliphatic alcohol

OH

enolyou can

ignore this one

ethers

H3C O CH3

ethoxyethanediethyl ether

ether

O

tetrahydrofuranTHF

OO

OO

O

O

18-crown-6replace one carbon

in an alkyl chain and you have an ether.

Often used as solvents

18-crown-6 and potassium cation

halidesH

HClCl

dichloromethaneDCM

F

FClCl

dichlorodifluoromethaneFreon (refrigerant)

a CFCClCl

Cl

ClCl

Cl HH

O

dieldrin

Pic: NASA

organic molecules containing fluorine, chlorine, bromine or

iodine

halidesH

HClCl

dichloromethaneDCM

F

FClCl

dichlorodifluoromethaneFreon (refrigerant)

a CFCClCl

Cl

ClCl

Cl HH

O

dieldrin

Pic: NASA

often toxic and some are responsible for

the hole in the ozone layer

thiols

H3C CH3 H3C CH3

HS SH OCH3HS

propane-2,2-dithiol 4-methyl-4-sulfanylpentan-2-one

H2N

SH

HCO2H

(R)-2-amino-3-sulfanylpropanoic acid

cysteine these are the sulfur version of

alcohols...found in nature (and us)

thiols

H3C CH3 H3C CH3

HS SH OCH3HS

propane-2,2-dithiol 4-methyl-4-sulfanylpentan-2-one

H2N

SH

HCO2H

(R)-2-amino-3-sulfanylpropanoic acid

cysteineone of these is the smelliest chemical

known...but no one wants to repeat the experiment

to find out which!

CH3

H3C

CH3HS

2-(4-methylcyclohex-3-enyl)propane-2-thioltaste of grapefruit

2x10-5 ppb

can smell nice...garlic, truffles etc...And incredibly small amounts are the taste

of grapefruit!

CH3

H3C

CH3HS

2-(4-methylcyclohex-3-enyl)propane-2-thioltaste of grapefruit

2x10-5 ppbthis value is similar to

1 drop in a lake...

aminesCH3

NH3C

CH3

H2NNH2

triethylaminesmells of fish

butane-1,4-diamineputrescine

smells of decay

H2N

pentane-1,5-diaminecadaverine

smells of decay

NH2

...also smell bad but are vital for life (and the smell of death).

amines in nature

H2N HOH

O

(S)-2-amino-3-phenylpropanoic acid

phenylalanineamino acid

H3C OH

CH3 O

NH2

(S)-2-amino-3-methylbutanoic acid

valineamino acid

amino acids are an obvious source of

amines

amines in nature

O

O

O

OCH3

NCH3

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

carboxylatecocaine

Scarface (1983): Universal Pictures

amines in nature

O

O

O

OCH3

NCH3

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

carboxylatecocaine

Scarface (1983): Universal Pictures

but there is a problem bigger than drugs...

five kinds of amine

NHH

Hammonia

H3C NH2

methylamine1° amine

H3CHN

CH3dimethylamine

2° amine

NCH3

H3CH3C

trimethylamine3° amine

NCH3

H3CH3C

trimethylammonium ion4° ammonium (salt)

H

five kinds of amine

NHH

Hammonia

H3C NH2

methylamine1° amine

H3CHN

CH3dimethylamine

2° amine

NCH3

H3CH3C

trimethylamine3° amine

NCH3

H3CH3C

trimethylammonium ion4° ammonium (salt)

H but primary, secondary & tertiary

mean something different than when we used them with

alcohols!

five kinds of amine

NHH

Hammonia

H3C NH2

methylamine1° amine

H3CHN

CH3dimethylamine

2° amine

NCH3

H3CH3C

trimethylamine3° amine

NCH3

H3CH3C

trimethylammonium ion4° ammonium (salt)

H...now refer to the

number of C attached to the N...but it gets

worse...

the problem with amines

primary amine(1°)

secondary position(2°)

H3C OH

CH3 O

NH2

primary amine because only 1 carbon attached

the problem with amines

primary amine(1°)

secondary position(2°)

H3C OH

CH3 O

NH2

but in a secondary position (like alcohol

naming) as this carbon has 2 carbons

attached!

carbonyl:aldehydes

H H

O

methanalformaldehyde

H3C H

O

ethanalacetaldehyde

H

O

benzaldehyde

HOO

OH

OH

OH

OH

H(2R,3S,4R,5R)-2,3,4,5,6-pentahydroxyhexanal

glucose

carbonyl:aldehydes

H H

O

methanalformaldehyde

H3C H

O

ethanalacetaldehyde

H

O

benzaldehyde

HOO

OH

OH

OH

OH

H(2R,3S,4R,5R)-2,3,4,5,6-pentahydroxyhexanal

glucose

C=O is the cornerstone of organic synthesis.

Aldehydes = CHO and are more reactive than...

carbonyl:ketones

H3C CH3

O

propanoneacetone

CH3

H

O

H3C

(R)-2-methyl-5-(prop-1-en-2-yl)cyclohex-2-enone

(R)-carvonespearmint

CH3

H

O

CH3

(S)-2-methyl-5-(prop-1-en-2-yl)cyclohex-2-enone

(S)-carvonecaraway

carbonyl:ketones

H3C CH3

O

propanoneacetone

CH3

H

O

H3C

(R)-2-methyl-5-(prop-1-en-2-yl)cyclohex-2-enone

(R)-carvonespearmint

CH3

H

O

CH3

(S)-2-methyl-5-(prop-1-en-2-yl)cyclohex-2-enone

(S)-carvonecaraway

ketones, which have C=O bonded to two

carbon groups

carboxylic acid derivatives: acids

H3C OH

O

ethanoic acidacetic acid

vinegar

H3CO

OHOH

(S)-2-hydroxy-propanoic acidL-(+)-lactic acid

O CH3

H3C CH3 CH3

CO2H

(2Z,4E)-3-methyl-5-(2,6,6-trimethyl-4-oxocyclohex-2-enyl)penta-2,4-dienoic acid

abscisic acidleaf fallC=O bonded to 1

carbon and an OH group

carboxylic acid derivatives: others

H3C O

ONa

sodium ethanoatecarboxylate ion

H3CO

CH3

O

CH32-methylpropyl propanoate

isobutyl propionatesmell of rum

ester

HO2CHN

OMe

NH2

O

O

aspartamesweetener

amide

many different derivatives

depending on what is attached to C=O

important terms & common mistakes

atoms attached to the same carbon count as one functional group

OH

RR

alcoholR = C or H

O

aldehyde

O

OHNOT

an aldehyde+

an alcohol

O

OHcarboxylic

acid

atoms attached to the same carbon count as one functional group

important terms & common mistakes

NH2

RR

amineR = C or H

O

aldehyde

O

NH2

NOTan aldehyde

+an amine

O

NH2

amide

OHC-R ≠ HOC-R

OC

H R≠ O

CR

H

This actually meaningless as the C does not have 4 bonds

important terms & common mistakes

Learn to draw accurately

how are functional groups related?

R CH

HH

hydrocarbon

R COH

HH R C

O

HR C

O

OH

alcohol aldehyde carboxylicacid

oxidation

reduction

oxidation

reduction

oxidation

reduction

alkanes

alcoholsethersamineshalidesthiols

aldehydesketones

carboxylic acidsestersamides

acyl halidesacid anhydrides

nitriles

Read this unit againLearn the functional groups

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NH

HN

HN

NH

HN

NH

NHMe

Me

Me

OO

O

O

O

HO OHOH

O O

O

NH2

OHHO

O

Cl

Cl

O

HOHO

OH

OOMe

NH2OH

Me

HO2CO

Vancomycin

what have....we learnt? •naming (simple)

molecules•recognise functional groups

molecules may look complicated but simply break them down into their functional groups

(amides in red)

parts 3 & 4are combined

word of warning...next 2

units will not be in the same order as

study guide...

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readPages 35, 37, 41-42, 45-47