Organic Chemistry IStructure and Nomenclature

Indra Yudhipratama

Outline

Representation of organic molecules Nomenclature of organic chemistry Structure of hydrocarbons (alkanes, alkenes,

and alkynes) and aromatic benzene. Isomerism

Representation of the Organic MoleculesHow to draw it?

Mainly there are 4 ways to draw organic molecules

CH3CH2CH2CH3

3D formula

Skeletal FormulaeStructural Formulae

CH3

H5C2

H

H

Representation of the Organic molecules

In this course, you are expected to understand the organic molecules in skeletal form.

How to draw skeletal form? Draw H attached to O, N, S (or other elements except C) Do not draw H attached to C (unless it is important) Use uniform bond lengths (give your best effort) Use uniform bond angles (give your best effort)

120o for single bond and double bonds 180o for triple bonds

Representation of the Organic molecules

Example:

H2N

O

OH

Why skeletal formula?

CH

CH

CH

N

CHCH2

CH2

CH2

CH3

CO O

CH3

O

C

O

C

CH

CH

CH

CH

CH

C

C

C

N

CC

C

C

C

CO O

C

O

C

O

C

C

C

C

C

CHH

H

HH

H

HH

H

H

H

HH

H

H

H

H

H

H

H

H

Why skeletal formula?

Just simply makes your life easier

With this structure you can easily spot the functional group and reaction centre

N

O O

O

O

Nomenclature Select the longest continuous carbon chain.

This determines the base name.

Consider each branch and name similarly except change the name from –ane to –yl.

Number the C atoms so that substituents have the lowest possible number.

NomenclatureName each substituent according to its identity and the number of the C atom to which it is attached.

Use di, tri, tetra as appropriate.

Separate numbers from one another by commas.

List substituents alphabetically by name.

Functional groupsWhat is functional group?

An atom or group of atoms which gives rise to an homologous series

Nomenclature example

4-propylcyclohex-2-en-1-one

O

Cl

O

O

O

cyclohexyl 4-methylhex-2-ynoate

1-chloropropan-2-one

3-ethyl-4,5-dimethyloctane

However, More complicated organic molecule sometimes is known

by its trivial name NOT IUPAC systematic name

N

O O

O

O

methyl 8-methyl-3-[(phenylcarbonyl)oxy]-8-azabicyclo[3.2.1]octane-2-carboxylateCocaine

And a bit messy now …

Calicheamicin 𝛾1S-[(2R,3S,4S,6S)-6-({[(2R,3S,4S,5R,6R)-5-{[(2S,4S,5S)-5-(Ethylamino)-4-methoxytetrahydro-2H-pyran-2-yl]oxy}-4-hydroxy-6-{[(2S,5Z,9S,13E)-9-hydroxy-12-[(methoxycarbonyl)amino]-13-[2-(methyltrisulfanyl) ethylidene]-11-oxobicyclo[7.3.1]trideca-1(12),5-diene-3,7-diyn-2-yl]oxy}-2-methyltetrahydro-2H-pyran-3-yl]amino}oxy)-4-hydroxy-2-methyltetrahydro-2H-pyran-3-yl] 4-{[(2S,3R,4R,5S,6S)-3,5-dihydroxy-4-me thoxy-6-methyltetrahydro-2H-pyran-2-yl]oxy}-3-iodo-5,6-dimethoxy-2-methylbenzenecarbothioate

Structure of HydrocarbonsAlkanes (e.g. Ethane)

The carbon-carbon bond is made from overlap of two sp3 orbitals to form

a s bond The molecule is

approximately tetrahedral around each

carbon

Structure of HydrocarbonsAlkenes (e.g. Ethenes) The geometry around each carbon is called trigonal planar The three sp2 hybridized orbitals come from mixing one s and

two p orbitals One p orbital is left unhybridised

Restricted rotation due to overlap on p orbitals (π bonding).

Result: Cis/trans isomerism

Benzene (delocalisation Structure)

Each carbon has p orbital that forms π bonding The π bonds not only with the adjacent carbon, but with all carbon π electrons are delocalised give delocalisation structure Delocalisation can takes place whenever two double bonds are

separated by single bond or a lone pair is separated from a double bond by one single bond

Delocalisation structure

Structure of Hydrocarbon

Alkynes (e.g. ethyne) The arrangement of atoms around each carbon is linear with

bond angles 180o

The carbon in ethyne is sp hybridized One s and one p orbital are mixed to form two sp orbitals

Two p orbitals are left unhybridized The triple bond consists of one s and two p bonds

Isomerism

Structural Isomer Same chemical formula, but behave differently The

structure is different. E.g. C4H10

It can be drawn in two ways:

Quick Review:

Name all the isomers of C4H10.

CH3

CH3

CH3

Structural Isomer E.g. A organic molecule has formula C4H10O. It

has isomers with alcohol FG:

Quick Review:

Draw the other isomer with alcohol FG

and name it.

OHOH

C 4H 10OC 4H 10O

Structural Isomer C4H10O also can be drawn with another functional

group.

Because they have different functional, so it’s called the functional group isomerism

Quick Review:

Name the functional group of those molecules above.

OCH3 CH3O

CH3CH3

Stereoisomerism

Related to the geometrical/spatial arrangement Two types of stereoisomerism:

Cis/trans isomerism occurs mainly at alkenes

Optical isomerism Chiral centre.

CH3

CH3

CH3 CH3

trans-but-2-ene cis-but-2-ene

COOH

OH

CH3H

HOOC

OH

CH3H

(2S)-2-hydroxypropanoic acid (2R)-2-hydroxypropanoic acid

Cis-trans isomers Cis-trans isomers are the result of restricted rotation about

double bonds These isomers have the same connectivity of atoms and

differ only in the arrangement of atoms in space One molecule is designated cis (groups on same side) and

the other is trans (groups on opposite side)

Cis-trans isomerism is not possible if one carbon of the double bond has two identical groups

Optical isomerism What is Chiral Centre?

A Carbon atom in a molecule attached to four different groups.

Chiral centre Chiral molecules

Cannot be superimposed, but are mirror images each others

COOH

OH

CH3H

HOOC

OH

CH3H

(2S)-2-hydroxypropanoic acid (2R)-2-hydroxypropanoic acid

Quick Review

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