How Are Molecules Named - Organic Chemistry from Examville.com

8/9/2019 How Are Molecules Named - Organic Chemistry from Examville.com

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Unit One Part 2:naming & functional groups

N

N

N

N

SN

NH3C

H3C

O

O

CH3

H3CO

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


2/113

Unit One Part 2:naming & functional groups

N

N

N

N

SN

NH3C

H3C

O

O

CH3

H3CO

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

Dont panic!

We wont do anything

this complicated


3/113

Unit One

Part2

Namingmolecules (pg 11-16)Introducing functional

groups (pg 16-9)remember...read the

study guide it

contains all you need


4/113

how do wename molecules?


5/113

NH2

O

OH

2-amino-4-methylpentanoic acid

prefixsubstituents

minor functionalgroups

parentcarbon chain

(& multiplebonds)

suffixprincipalfunctional

groups


6/113

NH2

O

OH


prefixsubstituents


parentcarbon chain

(& multiplebonds)


groups

there are three parts

to any name...even

Viagras real name

obeys this.


7/113

NH2

O

OH


prefixsubstituents


parentcarbon chain

(& multiplebonds)


groups

the prefix can

become a nightmare

as it contains most

information


8/113

sevensteps tosuccess!


9/113

sevensteps tosuccess!

works for all

molecules but thewhole system takes

volumes to

explain...


10/113

parentlongest carbon

chain containing afunctional group1H3C CH3

CH3

4-methylheptane

H3C

CH3

OH

2-propyl-1-pentanol

1

2

3

4

5

page 12 of guide


11/113



CH3

4-methylheptane

H3C

CH3

OH

2-propyl-1-pentanol

1

2

3

4

5

7 bigger than 5 he

says patronisingly


12/113



CH3

4-methylheptane

H3C

CH3

OH

2-propyl-1-pentanol

1

2

3

4

5

now use pent- aswe have to start

our chain from the

functional group


13/113

suffixm a j o r

functionalg r o u p

H3C OH

O

butanoic acid

H3C NH2

OCH3

3-methylbutanamide

2 list of majorgroups pg 13order of priority

pg 14


14/113

suffixm a j o r

functionalg r o u p

H3C OH

O

butanoic acid

H3C NH2

OCH3

3-methylbutanamide

2only one major

group per

molecule


15/113

H3C CH3

O

2-pentanonepentan-2-one

NOT 4-pentanone

O

HO

5-methylheptanoic acid

positionof functional

group fromend of chain3 number longestchain (parent)from start tofinish...


16/113

H3C CH3

O


NOT 4-pentanone

O

HO



group fromend of chain3...giving major

functional group

lowest possible

value


17/113

H3C CH3

O


NOT 4-pentanone

O

HO



group fromend of chain3it doesnt matterwhere number

goes but I think the

second exampleavoids confusion

later

fi


18/113

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

functionalg r o u p s )4

fi


19/113

H3C CH3

CH3

CH3

Cl


H3C CH3

H3C CH3

CH3



functionalg r o u p s )4numbering should

start with majorfunctional group

(like previous slide)

fi


20/113

H3C CH3

CH3

CH3

Cl


H3C CH3

H3C CH3

CH3




if no major functional

group then have

lowest numbering for

the majority ofsubstituents

fi


21/113

H3C CH3

CH3

CH3

Cl


H3C CH3

H3C CH3

CH3



functionalg r o u p s )4note: group identical

substituents (or

functional groups)

together

fi


22/113

H3C CH3

CH3

CH3

Cl


H3C CH3

H3C CH3

CH3




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

methylheptane

fi


23/113

H3C CH3

CH3

CH3

Cl


H3C CH3

H3C CH3

CH3



functionalg r o u p s )4bizarrely, halides dont

count as functional

groups...dont ask...


24/113

CH3

OH

O

O

H3C

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

HO OH

O

H3C CH3

5-hydroxy-2,2-dimethylpentanoic acid

functional groups FGprinciple FG suffix &

numbering; all othersprefix5

multiple bonds combined with parent


25/113

CH3

OH

O

O

H3C


HO OH

O

H3C CH3





functional groups

listed on pg 13


26/113

CH3

OH

O

O

H3C


HO OH

O

H3C CH3





major functionalgroup is suffix and is

the start of

numbering


27/113

CH3

OH

O

O

H3C


HO OH

O

H3C CH3





all other groups

are prefix

G

5


28/113

CH3

OH

O

O

H3C


HO OH

O

H3C CH3





alkenes and

alkynes are

normally part of

the parent

i FG

6


29/113

BrH3C

CH3

1-bromo-2-methylpropane

minor FGnot all groups are

equal: halo- & nitro-(-NO2) are prefixes6N

O

O

nitroethane

d

7


30/113

ordera, b, c...hope

y o u k n o wyour alphabet!7HO OH

O

NH

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

acid

prefixes are orderedalphabetically

(although descriptors

like tertare ignored)


31/113

name thismolecule...


32/113

H3C NH

O

CH3

OH

hept

1parent


33/113

H3C NH

O

CH3

OH

1parent

select longest

carbon chain (with

major functional

group in it)


34/113

H3C NH

O

CH3

OH

amide

2suffix heptidentify major

functional group

this will be the

suffix


35/113

3position

H3C NH

O

CH3

OH

12

34

5

6

hept amide

number chain

starting with major

functional group


36/113

H3C NH

O

CH3

OH

12

34

5

6

5-methyl

4prefix hept amideadd prefixes (and

remember to tell us

where they are by giving

a position number)


37/113

5functional groups

H3C NH

O

CH3

OH

12

34

5

3-hydroxy6-en

6

hept amide 5-methyl

repeat with all

remaining

functional groups

and the last bit (which


38/113

H3C NH

O

CH3

OH

12

34

5

N-ethyl

6

6the resthept amide 5-methyl 3-hydroxy6-en

(

throws a nasty curve

ball in but dont

worry...)


39/113

7order

H3C NH

O

CH3

OH

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


40/113

7order

H3C NH

O

CH3

OH

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

to be honest order

not too important

as long as name isnot ambiguous


41/113

N-ethyl?

(methylamino)?


42/113

what the

@&!!#?Renaissance Pictures


43/113

DONTPANIC!

only simple examples in test


44/113

draw the moleculewith the followingname...

4 th l 3 h d l h


45/113

4-ethyl-3-hydroxycyclohexanone

4 th l 3 h d l h


46/113


1parent 4 th l 3 h d l h


47/113

O


2suffix 4 th l 3 h d l h


48/113

O


4prefix

O

H3C


49/113

4 th l 3 h d l h


50/113

O

H3C

OH

O


5functional groups

1

2

3

4


51/113

functional groups

these are listed on

pg 17

alkanes


52/113

H

CH

H

H

methane

CH4

alkanes

CnH2n+2

propane

C3H8

alkanes


53/113

H

CH

H

H

methane

CH4

alkanes

CnH2n+2

propane

C3H8open chains (norings) have this

general formula

alkanes


54/113

H

CH

H

H

methane

CH4

alkanes

CnH2n+2

propane

C3H8

alkanes are

tetrahedral in

shape...we shall see

why later

alkanes


55/113

H

CH

H

H

methane

CH4

alkanes

CnH2n+2

propane

C3H8

alkanes are

boring...normally

fuels or solvents

structural


56/113

2,2-dimethylpropane

C5H12bp 9.6C

2-methylbutaneC5H12

bp 28C

pentaneC5H12

bp 36.2C

structuralisomers

structural


57/113

2,2-dimethylpropane

C5H12bp 9.6C

2-methylbutaneC5H12

bp 28C

pentaneC5H12

bp 36.2C

structuralisomers

same number of

atoms but bonding

different

structural


58/113

2,2-dimethylpropane

C5H12bp 9.6C

2-methylbutaneC5H12

bp 28C

pentaneC5H12

bp 36.2C

structuralisomers

can make bigdifferences in

properties...as

we shall see later

alkenes


59/113

alkenes

trigonal planar

H

H H

H

ethene

alkenes


60/113

alkenes

trigonal planar

H

H H

H

ethene

more exciting as the

double bond is

reactive!

alkenes


61/113

alkenes

trigonal planar

H

H H

H

ethene

means it is flat withthree groups

attached to central

atom

configurational


62/113

trans-2-buteneC4H8

H3C

CH3

H3C CH

3

cis-2-buteneC4H8

1-butene

C4H8

2-methylpropene

C4H8

cyclobutane

C4H8

configurational(stereoisomers)

isomers

no rotation around C=C bond configurational


63/113

trans-2-buteneC4H8

H3C

CH3

H3C CH

3

cis-2-buteneC4H8

1-butene

C4H8

2-methylpropene

C4H8

cyclobutane

C4H8


isomers

no rotation around C=C bond

these 2 are structural

isomers

configurational


64/113

trans-2-buteneC4H8

H3C

CH3

H3C CH

3

cis-2-buteneC4H8

1-butene

C4H8

2-methylpropene

C4H8

cyclobutane

C4H8


isomers


these 2 are

stereoisomers. Sameatoms and bonds but

different orientation inspace

configurational


65/113

trans-2-buteneC4H8

H3C

CH3

H3C CH

3

cis-2-buteneC4H8

1-butene

C4H8

2-methylpropene

C4H8

cyclobutane

C4H8


isomers


occurs becomes

alkene cannotrotate

configurational


66/113

trans-2-buteneC4H8

H3C

CH3

H3C CH

3

cis-2-buteneC4H8

1-butene

C4H8

2-methylpropene

C4H8

cyclobutane

C4H8


isomers


a whole world of pain

is coming your way

when we discussstereoisomers!


67/113

alkenes


68/113

alkenesin nature

CH3

H3C

H3C

CH3

CH3H3C

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

yup...it smells of

pine...and is a veryuseful compound in

chemistry

alkynes


69/113

alkynes

O

O

O

O

O

O

O

H3C

OMe

OH

O

OH

HO

CH3

MeHN

neocarzinostatin chromophore A

H Hethyne

C2H2

triple bond makes

alkynes longcylinders

alkynes


70/113

alkynes

O

O

O

O

O

O

O

H3C

OMe

OH

O

OH

HO

CH3

MeHN

neocarzinostatin chromophore A

H Hethyne

C2H2

they are found in

nature...this nasty

beast cleaves DNA

cyclic compounds


71/113

cyclohexaneC6H12

cyclic compounds

benzene

C6H6

cyclic compounds


72/113

cyclohexaneC6H12

cyclic compounds

benzene

C6H6

some cyclic

molecules are

flat...because they

have flat double

bonds


73/113

cyclic structures


74/113

yin 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]phenanthrene

cholestane - steroid

alcohols


75/113

alcohols

OH

ethanol

C2H6O

alcohols


76/113

alcohols

OH

ethanol

C2H6O

need OH attached to

alkane (not alkene,alkyne or benzene)

alcohols


77/113

alcohols

OH

ethanol

C2H6O

found in manybiological systems...

alcohols...especially on

Saturday nights...


78/113

alcohols

OH

ethanol

C2H6O

alcohols inh l ld


79/113

HOOH

1,2-ethandiolethylene glycol

antifreeze

OHO

HO

HO

HO

OH

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

glucosesugar I guess!

the real world

or Sunday

mornings...

three classesf l h l


80/113

H3C OH

CH3 CH3

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

citronellolcitronella oil

CH3

CH3

H3C

H3C

CH3

H H

H

HOcholesterolall animals

CH3

OHH3C

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

terpinen-4-ol

tea tree oil

ofalcohol

tertiary (3)

secondary (2)

primary (1)



81/113

H3C OH

CH3 CH3



CH3

CH3

H3C

H3C

CH3

H H

H

HOcholesterolall animals

CH3

OHH3C


terpinen-4-ol

tea tree oil

ofalcohol

tertiary (3)

secondary (2)

primary (1)

depends on the

number of carbons

attached to the

COH unit



82/113

H3C OH

CH3 CH3



CH3

CH3

H3C

H3C

CH3

H H

H

HOcholesterol

all animals

CH3

OHH3C


terpinen-4-ol

tea tree oil

ofalcohol

tertiary (3)

secondary (2)

primary (1)

...this one has 1

carbon attached so isprimary. the next

has 2 so is

secondary etc.



83/113

H3C OH

CH3 CH3



CH3

CH3

H3C

H3C

CH3

H H

H

HOcholesterol

all animals

CH3

OHH3C


terpinen-4-ol

tea tree oil

ofalcohol

tertiary (3)

secondary (2)

primary (1)

this controls thereactivity of the

alcohols as you

shall see in future

lectures

phenols


84/113

phenols

OH

phenolcarbolic acid

HO

OH3C

H

N

O

CH3

H3C

(E)-N-(4-hydroxy-3-methoxybenzyl)-

8-methylnon-6-enamidecapsaicinchilli peppers

phenols


85/113

phenols

OH

phenolcarbolic acid

HO

OH3C

H

N

O

CH3

H3C



looks like an

alcohol BUT is not(as it is not

attached to an

alkane)

phenols


86/113

phenols

OH

phenolcarbolic acid

HO

OH3C

H

N

O

CH3

H3C



thus has very

different

properties...I should

whistle ring of firenow...


87/113


88/113

halidesorganic molecules

containing fluorine,


89/113

halidesH

HCl

Cl

dichloromethaneDCM

F

FCl

Cl

dichlorodifluoromethaneFreon (refrigerant)

a CFC

ClCl

Cl

ClCl

Cl H

H

O

dieldrin

Pic: NASA

g ,

chlorine, bromine or

iodine


90/113

thiols


91/113

thiols

H3

C CH3

H3C CH

3

HS SH OCH3HS

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

H2N

SH

H

CO2H

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

cysteine these are thesulfur version of

alcohols...found innature (and us)

thiols


92/113

thiols

H3

C CH3

H3C CH

3

HS SH OCH3HS

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

H2N

SH

H

CO2H

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

cysteineone of these is the

smelliest chemicalknown...but no one wants

to repeat the experiment

to find out which!

CH3HS

2x10-5 ppb


93/113

CH3

H3C

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 tasteof grapefruit!

CH3HS

2x10-5 ppb


94/113

CH3

H3C

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

2x10 5 ppb

this value is similar to

1 drop in a lake...

amines


95/113

amines

CH3

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).


96/113


97/113

amines in nature OCH3

NCH3


98/113

O

O

O

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

carboxylate

cocaine

Scarface (1983): Universal Pictures

but there is a problem

bigger than drugs...

five kinds ofamine


99/113

NH

H

H

ammonia

H3

C NH2

methylamine1 amine

H3C

HN

CH3dimethylamine

2 amine

NCH

3

H3C

H3Ctrimethylamine

3 amine

NCH3

H3C

H3C

trimethylammonium ion

4 ammonium (salt)

H

five kinds ofamine


100/113

NH

H

H

ammonia

H3C NH2

methylamine1 amine

H3C

HN

CH3dimethylamine

2 amine

NCH

3

H3C

H3Ctrimethylamine

3 amine

NCH3

H3C

H3C


4 ammonium (salt)

H but primary,secondary & tertiary

mean something

different than when

we used them with

alcohols!

five kinds ofamine


101/113

NH

H

H

ammonia

H3C NH2

methylamine1 amine

H3C

HN

CH3dimethylamine

2 amine

NCH

3

H3C

H3Ctrimethylamine

3 amine

NCH3

H3C

H3C


4 ammonium (salt)

H...now refer to the

number of C attachedto the N...but it gets

worse...

the problemwith amines

primary amine


102/113

with aminesprimary amine

(1)

secondary position

(2)

H3C OH

CH3 O

NH2

p ybecause only 1

carbon attached


103/113

carbonyl:


104/113

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:


105/113

carbonyl:aldehydes

H H

O

methanalformaldehyde

H3C H

O

ethanalacetaldehyde

H

O

benzaldehyde

HO

O

OH

OH

OH

OH

H

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

glucose

C=O is the cornerstoneof organic synthesis.Aldehydes = CHO and

are more reactive than...

carbonyl:


106/113

carbonyl:ketones

H3C CH3

O

propanoneacetone

CH3

H

O

H3C

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

spearmint

CH3

H

O

CH3

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

caraway

carbonyl:


107/113

carbonyl:ketones

H3C CH3

O

propanoneacetone

CH3

H

O

H3C

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

spearmint

CH3

H

O

CH3

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

caraway

ketones, which haveC=O bonded to two

carbon groups

carboxylic acidd i ti id


108/113

derivatives:acids

H3C OH

O

ethanoic acidacetic acid

vinegar

H3C

O

OH

OH

(S)-2-hydroxy-propanoic acid

L-(+)-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 acidabscisic acidleaf fallC=O bonded to 1

carbon and an OHgroup

carboxylic acidd i ti th


109/113

derivatives:others

H3C O

O

Na

sodium ethanoatecarboxylate ion

H3CO

CH3O

CH32-methylpropyl propanoate

isobutyl propionatesmell of rum

ester

HO2CHN

OMe

NH2

O

O

aspartamesweetener

amide

many different

derivativesdepending on what

is attached to C=O


110/113

how arefunctional

groups related?


111/113


112/113

what havewe learnt? naming (simple)


113/113

NH

HN

HN

NH

HN

NH

NHMe

Me

Me

O

O

O

O

O

O O

O

NH2

OHHO

O

Cl

Cl

O

HO

HOOH

OOMe

NH2OH

Me

HO2C

O

....welearnt? naming(simple)molecules

recognisefunctional groups

molecules may look

complicated but simply

break them down into

their functional groups

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How Are Molecules Named - Organic Chemistry from Examville.com