Summary of Most Important Functional Groups

CMY 127 alkanes and cycloalkanes have no functional groups

H C
C C C C
O X

Organic Chemistry alkene alkyne alcohol / alkyl halide

hydroxy- halo-alkane
O

C C
The Chemistry of Carbon Compounds
C C
C H N C H O
S

aldehyde -amine / ether

alkanal amino- thiol alkoxy alkane
O O O O

Theme 1 C
C
C C
C
O
H
C
C
O
C
C
C
N

Structure and Bonding ketone carboxylic acid ester amide

alkanone alkanoic acid alkyl alkanoate alkyl alkanamide
Smith: Organic Chemistry
Extracts from Chapter 1 and Chapter 3  Blue text denotes IUPAC naming 3

Organic Chemistry & Lecture Classes

Big ideas in Organic Chemistry
1. Carbon is tetravalent
 Forms single, double and triple bonds

2. Organic molecules have 3D shape

 The shape with lowest energy is preferred
 This shape affects the physical, chemical and biological
properties of the compound

3. Functional groups are sites for chemical reactions

 The distribution of e-density in a FG determines the type of
reactions it can undergo
2 4

Theme 1-p1
 THE ELEMENT CARBON AND BONDING Molecular Shape: VSEPR Theory
 Carbon has 6 electrons with 4 electrons in its outer valence shell
and thus needs to accept 4 additional electrons to fill the valence shell
and satisfy the octet rule.
 Carbon is tetravalent i.e. it forms 4 bonds in stable neutral molecules.
Carbon can form single bonds, double bonds or even triple bonds.

C C C C C C

single bond double bond triple bond

 The intermediate electronegativity of carbon means that it forms
covalent or polar-covalent bonds (expressed as + and -).

H Li
O
C
C H H
H H H 5 7
H

H
Molecular Shape: VSEPR Theory Orbitals for bonding in methane
C
(Revise CMY 117)  The Structure of Methane: sp3 Hybridization
H H
H
 The structure of methane with its four identical tetrahedral bonds cannot be adequately
explained using the electronic configuration of carbon
Valence Shell Electron Pair Repulsion Theory is used to
predict the shape of a molecule 2p 2p

Energy
2s + Energy 2s
 Count how many regions of electron density there are
around an atom. 1s
1s
 All sets of valence electrons are considered including:
Bonding pairs involved in single or multiple bonds  Averaging (Hybridization) of the valence orbitals (2s and 2p) provides four new identical
Non-bonding pairs which are unshared orbitals which can be used for the bonding in methane.
 Orbital hybridization is a mathematical combination of the 2s and 2p wave functions to
 Electron pairs repel each other and tend to be as far apart obtain wave functions for the new orbitals (Quantum Mechanical Model)
as possible from each other  The Shape of the new hybrid orbital is an average of the shapes of the original orbitals.

6 8

Theme 1-p2
 When one 2s orbital and three 2p  Ethene (Ethylene): sp2 Hybridization
orbitals are hybridized four new and  The geometry around each carbon is trigonal planar
identical sp3 orbitals are obtained
 When four orbitals are hybridized, four 2s 2py 2px 2pz

orbitals must result +

hybridization hybridization
 Each new orbital has one part s omiting 2py
2py 2px 2pz 2py
character and 3 parts p character
 The four identical orbitals are oriented
4 sp3 orbitals 3 sp2 orbitals in the
in a tetrahedral arrangement x,z plane at 120°
 The four sp3 orbitals are then 2s A trigonal planar
combined with the 1s orbitals of four H arrangement!
hydrogens to give the -bonding of C
methane. H H The five lobes
H represent four orbitals:
tetrahedral methane
with 4 equal bonds three hybrid sp2 orbitals
and one 2p orbital

Energy
The 3-D shape of molecules has
very important consequences for
their reactivity
9 11

Bonding in Ethane:  bonds Pi () bonding

 Ethane (C2H6) There are three  bonds around each carbon of ethene and these are
formed by using the three sp2 hybridized orbitals on each carbon
 One sp2 orbital on each carbon overlaps head-on to form a carbon-
carbon  bond; the remaining sp2 orbitals overlap with hydrogen 1s
orbitals.

 The C-C bond is made from overlap of two sp3 orbitals to form a  bond
(single bond)
 The C-H bond is made from the overlap of an sp3 orbital and a 1s orbital.
It is also a  bond.
 The geometry for each C is tetrahedral with bond angles of 109°
 Generally there is relatively free rotation about  bonds The leftover 2p orbitals on each carbon overlap to form a bonding  bond
Very little energy is required to rotate around the C-C bond of ethane between the two carbons
 bond results from sideways overlap of p orbitals above and below the
 All single bonds in organic molecules are  bonds. plane of the  bond
10 12
A -bond has a nodal plane

Theme 1-p3
 Restricted Rotation and the Double Bond  In ethyne the sp orbitals on the two carbons overlap head-on to form a  bond.
There is a large energy barrier to rotation (about 264 kJ/mol) around the  The remaining sp orbitals overlap with hydrogen 1s orbitals also forming 
double bond bonds.
 This corresponds to the strength of a  bond  The p orbitals on each carbon overlap sideways to form two  bonds.
 The rotational barrier of a carbon-carbon  bond is 13-26 kJ/mol  The triple bond consists of one  and two  bonds.
This rotational barrier results because the p orbitals must be well aligned for
maximum overlap and formation of the  bond
Rotation of the p orbitals 90o totally breaks the  bond

Results in cis-trans isomers that do not interconvert

Cl Cl Cl H
C C C C
H H H Cl 13 15
cis-1,2-dichloroethene trans-1,2-dichloroethene

The Structure of Ethyne (Acetylene): sp Hybridization H C C H

Hybridisation of a carbocation (C+)
 The arrangement of atoms around each carbon is linear with bond angles 180°.
 The carbon in ethyne is sp hybridized:
 A “carbo-cat-ion” is a carbon atom with a positive charge. A
 One s and one p orbital are mixed to form two sp orbitals
carbocation has only 3 electrons in its valence shell.
 Two p orbitals are left unhybridized
 The carbocation makes 3 covalent bonds. It does not obey the
octet rule.
Hx H
VSEPR theory says 3 groups of electrons H
HxC C CH3
Energy

will have a trigonal planar geometry C H

o

CH3 H CH3
 Hybridisation is sp2

 The two sp orbitals are orientated 180° relative to eachother around the carbon
nucleus.
 The two p orbitals are perpendicular to the axis that
runs through the sp orbitals.

The 6 lobes in this picture represent  Notice the empty 2p orbital

4 orbitals = 2 hybrid sp orbitals + 2 2p orbitals 14 16

Theme 1-p4
 HYBRIDIZATION OF NITROGEN AND OXYGEN
Hybridisation of a carbanion (C)
 Hybridization also explains the molecular shape of simple molecules
 A “carb-an-ion” is a carbon atom with a negative charge. A containing N and O.
carbanion has 5 electrons in its valence shell.  The non-bonding electron pairs, called lone pairs, are accommodated
 The carbanion makes 3 covalent bonds and has a non-bonding in hybrid orbitals.
electron pair.  Nitrogen has 5 valence electrons. It can be sp3, sp2 or sp hybridised. Since
VSEPR theory says 4 groups of electrons
the N in NH3 has 4 e- domains, it is tetrahedral so the N is sp3 hybridised.
will have a tetrahedral geometry HxC o CH
3
x

H H CH3
H
 Hybridisation is sp3 hybridise

Energy
Energy

N
H H Geometry
 Compare with a nitrogen atom with 5 valence electrons. 17
107 o H around N = pyramidal 19

 Oxygen has 6 valence electrons. It can also be sp3, sp2 or sp hybridised.

 Summary In H2O, it is sp3 hybridised.

 Hybridized orbitals are obtained by mixing the wave functions of different types of
orbitals
hybridise

Energy
Four sp3 orbitals are obtained from mixing one s and three p orbitals
 The geometry of the four orbitals is tetrahedral
Three sp2 orbitals are obtained from mixing one s and two p orbitals
 The geometry of the three orbitals is trigonal planar
 The left over p orbital is used to make a pi bond
Two sp orbitals are obtained from mixing one s and one p orbital
 The geometry of the two orbitals is linear
 The two left over p orbitals are used to make two pi bonds

 When the N is sp3 hybridised it will be pyramidal and when the O is sp3
Hybridized orbitals overlap head-on to form Sigma (σ) bonds
hybridised it will be bent.
Pi (π) bonds result from sideways overlap of two unhybridized p orbitals
 The orbital pictures for ammonia and water can be used to predict the
orbital pictures for molecules with N and O bonding to C instead of H.
18 20

Theme 1-p5
 DETERMINING THE HYBRIDISATION OF A DRAWING ORBITAL PICTURES
SPECIFIC ATOM (NOT H)  Determine the hybridisation of each atom

 The nature of the hybridisation of an atom depends on the type of  Orientation:

covalent bonds that the atom is engaged in, i.e.  or bonds  hybrid orbitals forming bonds must be in a line
 The 2p orbitals are only used for bonds not for bonds.  p-orbitals forming bonds must be parallel
 The number of hybrid orbitals = no of lone pairs + no of bonds
and the no of hybrids tells you the type of hybrid

 E.g. What is the hybridisation of the carbon and oxygen atoms in  3D-representation:
Vitamin C?  Orbitals in plane of paper are drawn with a single thin line
 Orbitals projecting forward are drawn with a bold line
OH  Orbitals behind the plane are drawn with dotted lines
H2C CH
O
O
HO C C
H
C C
HO OH  Draw in the electrons – 4 for C, 5 for N, 6 for O & 1 for H
21 23

You must be able to do the following:

 Identify the hybridisation of the indicated atoms of  Name each orbital (1s, sp, sp2 , sp3 or unhybridised 2p)
caffeine.
 Show approximate bond angles – between 3 atoms (not between
atoms and lone pairs).
 Indicate types of bonds (or bonds)
 Specify the geometry of atoms bonded to each non-H atom (lone
pairs are not taken into account)
 Carbon: sp = linear, sp2 = trigonal planar, sp3 = tetrahedral
 Nitrogen: sp = no geometry, sp2 = bent, sp3 = pyramidal
 Oxygen: sp, sp = no geometry,
2 sp3 = bent

 Consider the unstable cations and anion drawn below and H

give the hybridization of the C atoms in these ions.
H C N H
H H
22 24
methylamine

Theme 1-p6
Exercise DRAWING STRUCTURES OF ORGANIC COMPOUNDS
 Draw complete orbital presentations for formaldehyde (H2CO),
and hydrogen cyanide (HCN). LEWIS STRUCTURES
H
H C O H
For Connect tuts
H H
Lewis structure
C O shows lone pairs

H
CONDENSED STRUCTURES (Smith 1.8A)
 All atoms drawn but bonds are omitted.
 Atoms are usually drawn next to atoms they’re bonded to
 Brackets are used around groups bonded to the same atom
 Structures are read from left to right, remember C is tetravalent, O is divalent, etc!

25 27

SKELETAL (LINE) STRUCTURES (Smith 1.8B)

Drawing an orbital picture for bigger molecules
H O  This is the most common way to draw structures in
Label the hybridization of
modern organic chemistry
H C C O H each non-H atom and the
bond angles.
H H O H O O
It is usually best to plan to show the  bond from the side. H C C H
C C OH OH OH
C C
H C O H O O
H C H H H
O C O O
H H H H

Lewis structure 1. Remove C atoms skeletal structure

2. Remove ──H (atoms
& bonds) attached to C

26
 Structures are uncluttered and easy to read 28

Theme 1-p7
 Rules for drawing skeletal structures ALKANES and STRUCTURAL ISOMERISM
1. Carbon atoms are not shown.  Alkanes are saturated hydrocarbons
Assume there is a carbon at every intersection of two lines (bonds) and at the end  Straight chain or branched alkanes have formula CnH2n+2
of each line (bond) if no atom is specified.  Cyclic alkanes have 2 H’s fewer than the max for each ring
2. Hydrogen atoms and their bonds to carbon are not shown.
Hydrogen atoms are shown when they form part of the functional group i.e. are
 Molecules can fold into different three-dimensional
bonded to any heteroatom or to a carbonyl carbon in an aldehyde. arrangements but remain the same molecule.
Remember Carbon is tetravalent! - All missing bonds must be to hydrogen
3. All atoms other than C and H are always shown.
4. Bond angles and molecular shape must be represented as accurately as
possible. Which of the structures below are incorrectly represented?  These are two different compounds with the same molecular
 sp3carbons with at least one H (which is not shown) are drawn with 120° angles to formula. They are called structural (or constitutional) isomers.
make an even zig-zag chain

 Propose line structures for C5H12:

How many C’s in:
31
29

Exercise  There are 5 structural isomers for C6H14.

 Write molecular formulae (CxHyXaNbOcSd) for the following

compounds:
O

S OH
NH2
 The number of structural isomers increases dramatically with the
methionine Adrenaline
size of the alkane. There are 75 structural isomers for C10H22
Hint: Draw in all missing atoms and make sure all carbons are tetravalent before
determining the molecular formula and 366 319 for C20H42.
 Saturated C’s are classified as primary (1°), secondary (2°),
Checking the molecular formula tertiary (3°) or quarternary (4°) according to the number of
attached C groups.
 Degrees of unsaturation = Tot no of rings and -bonds  Identify 1°, 2°, 3° and 4° C atoms in the structures above.
= [(2 x nC+2) – (nH – nN + nX)]/2 Ignore O  Draw a structural isomer of C7H16 that has a 3° and 4° C.
See Smith 10.2, sample problem 10.2.
30 32

Theme 1-p8
 ALKYL GROUPS
 An alkyl group is part of a larger molecule attached by a  bond
 An alkyl group is named according to the alkane that it would
have been if it had been bonded to a H atom instead of the larger
molecule.
Theme 2
Saturated Hydrocarbons H3C- CH3CH2- CH3CH2CH2- CH3(CH2)3-
methyl ethyl n-propyl n-butyl etc.
Me Et Pr Bu
Smith: Organic Chemistry
Extracts from Chapter 4  Common names of branched alkyl groups indicate the total
number of carbons and the branch point
H H
H C H
C C
 Use R to specify an Alkyl group H H H H
which is any hydrocarbon group 3

Condensed Skeletal
Alkane Name Abbreviation
NAMING BRANCHED ALKANES structure structure
 The IUPAC nomenclature system (revision of matric) n
3 H3C CH2 CH2 n-propyl group Pr
Prefix --- PARENT --- Suffix H3C CH CH3 isopropyl group i
Pr
PARENT = Number of carbon atoms in the main chain
H3C CH2 CH2 CH2 n-butyl group n
Suffix = Identifies the most important functional group 4 Bu
Prefix = Where and what are the substituents on the main chain H3C CH2 CH CH3 sec-butyl group s
Bu
Substituent = Atom or group of atoms attached to the main chain H3C CH CH2 i
isobutyl group Bu
e.g. an alkyl group CH3
# C’s 1 2 3 4 5 6 7 8 9 10 H3C C CH3 t
tert-butyl group Bu
Prefix Meth- Eth- Prop- But- Pent- Hex- Hept- Oct- Non- Dec- CH3

CH4 CH3CH3 H3C CH CH2 CH2 isopentyl group

5
CH3 4
methane ethane propane butane pentane etc. 2

Theme 2 - p1
Exercise: EXERCISE
Identify all the alkyl groups on the following backbone Give an IUPAC name for the following:

Br

Draw line structures for the following:

1. sec-butyl bromide Note: These are

trivial names of
small molecules.
2. isopentyl alcohol The structures can
also be named
using the IUPAC
3. t-butyl chloride system.

Name HALOALKANES as ALKANES with halogens as

4. diisopropylamine 5
substituents named fluoro-, chloro-, bromo- and iodo- 7

PROPERTIES OF ALKANES
IUPAC name for a simple branched alkane Revision of Matric
 Physical properties
1. Find the PARENT hydrocarbon
 Bp and Mp increase with size
 Choose the longest continuous carbon chain
 With the most substituents
2. Number the atoms in the main chain
 Begin at the end nearest a branch
 Soluble in organic solvents,
3. Name and number the substituents not soluble in water Kerosene
Natural Petroleum Petrol
Crude oil Fuel for rockets
 Group identical substituents and use the  Chemical properties
gas ether Fuel for cars
and jet engine

prefix di-, tri-, tetra-, etc.

 Generally unreactive but React with O2 to produce CO2 and H2O
4. Write the complete name Branched chain alkanes burn slower than straight chain alkanes
 Arrange the substituents in alphabetical giving more even piston movement in engines. Combustion that is
order. too fast gives jerky piston movement and a knocking sound.
 Add the parent and suffix. 3-ethyl-2,4-dimethylhexane If petrol contains too many straight chain alkanes, they add anti-
Note: Separate numbers by commas and separate knock agents such as tert-butyl methyl ether (TBME)
numbers from letters by hyphens. There are no
spaces in the name of an alkane 6 8

Theme 2 - p2
 CONFORMATIONS OF ALKANES Bond rotation in butane
 Steric (van der Waals) strain arises when atoms or groups come
 The conformation of a compound is its complete 3-dimensional
closer than the sum of their van der Waals’ radii.
shape at any given instant that rotation about  bonds is frozen.
H3C CH3 H3C H3C H H3C
H CH3 H H
H H H H H
H H H H H H H H H H
H H rotate C-C H H H H H H
H H CH3
H CH3
H H H H H H
HH -bond H
H
staggered staggered
gauche anti-periplanar
eclipsed staggered

Newman projections

 Electrons in  bonds repel each other so prefer to orientate

themselves as far apart as possible. 0° 60° 120° 180°
Torsional strain
 This means that a staggered conformation is more stable than
an eclipsed conformation. 9
Steric strain    x 11
Me - Me residual 2x Me - H
Me - Me

 This type of conformational drawing is called a Newman projection.

CH3
H H

H H
CH3
Line structure that
Lowest energy most accurately
Newman projection represents shape
 This information justifies the zig-zag drawing of carbon chains in line structures.
Energy

The lowest energy conformation is the most common conformation of the molecule
Exercise:
Consider 2-methylbutane (isopentane). Sighting along the C2-C3 bond, draw
0° 60° 120° 180° 240° 300° 360°
Newman projections of the most stable and the least stable conformations.
H H H
H H H H
H H H H H H H H H H H H H H
H H H H
H H H H H H
HH H HH H HH H HH

Torsional strain: Resistance to free rotation about C-C bonds due

to the repulsion between bonding electron clouds 10 12

Theme 2 - p3
 Drawing Newman Projections CYCLOALKANES CnH2n
 Build a line structure and look at the model from a new angle.
 Look along a C-C bond such that one C is at the front and the
other C is directly behind it. CIS-TRANS ISOMERISM
 The ring structure prevents free rotation about -bonds, fixing the
position of substituents relative to the plane of the ring.
 Substituents on the same side of the ring are CIS
1. Draw the three bonds to other groups outwards from the front C
 Substituents on opposite sides of the ring are TRANS
exactly as they are bonded.
2. Draw a circle to represent the back C.
3. From the edge of the circle draw the three bonds from the back C
to other groups exactly as they are bonded.

 Compounds with the same molecular formula and the atom bonding
pattern, but different spatial arrangement of their atoms are called
13
stereoisomers. 15

Showing 3-dimensional structure CONFORMATIONS OF CYCLOALKANES

 Plain lines are used to draw the carbon backbone of a  Cyclopropane

molecule in the plane of the paper.
 Bonds projecting forward are drawn with a wedge
H2
 Bonds projecting behind the plane of paper are drawn
with hashed lines C
Draw the given Newman projection as a line structure showing three dimensions.
H2C CH2
Et
F H

Cl i
Pr HO  Angle strain: Bond angle is 60° not 109.5°
OH  Torsional strain: All bonds are eclipsed
The four bonds of sp3
carbons will always consist of two plain bonds, a  Poor orbital overlab = weak bonds
forward bond and a bond projecting backwards. Missing forward or  Very reactive towards ring opening reactions
backward bonds imply H’s 14 16

Theme 2 - p4
  Cyclohexane
 Cyclobutane

H H
H H

 In the flat line structure bond angles are 120° - much bigger
H H than 109.5°!
H H
 The stable low-energy conformation of cyclohexane is
puckered to give a chair conformation with all bond angles
 Angle strain due to 90° angles the ideal 109.5°
 Most stable conformation is puckered not flat to reduce  In the chair conformation, cyclohexane has no angle strain
torsional strain and no torsional strain

17 19

Axial and Equatorial Bonds in Cyclohexane

 Cyclopentane
 The chair conformation has two kinds of positions for
substituents on the ring: axial and equatorial positions
 Chair cyclohexane has 6 axial H’s perpendicular to the ring and
6 equatorial H’s near the plane of the ring

 Bond angles are 108°  no angle strain H H

 In flat conformation, all bonds are eclipsed so H H
torsional strain is high HH HH
 Ring puckers to give an envelope H H
conformation to reduce torsional H H
strain rotate 60°, 120° or 180°

H H
H H
 Molecular vibration means that
H HH
each CH2 takes a turn at being H
the point of the envelope 18 H H 20
H H

Theme 2 - p5
 Conformational Mobility of Cyclohexane  Drawing a chair conformation line structure

 Observe 3 pairs of parallel lines.

 This is a cyclohexane chair line structure (no ─H’s) with the
backrest to the left.
 Now draw a cyclohexane chair with the backrest to the right.

 Notice how axial and equatorial positions have been

exchanged! 21 23

Relative stereochemistry Drawing the H substituents (not a true line structure)

H H
H H
 A ring flip does not change the relative stereochemistry. H
H H
Atoms that are cis to one another remain cis after a ring flip. H
H
 Hydrogens do not swap sides in a ring flip. H
H
H H
H H Ring H F H
H F flip H H H H
H H
H
H
HF HH F H
H H
 Draw the 6 axial C-H bonds - vertical with 3 pointing up and
H H
H H H H 3 pointing down
 Draw the 6 equatorial C-H bonds parallel to lines already
making the ring. Don’t use hash and wedge bonds.
 Notice 4 black bonds are parallel, 4 red bonds are
parallel and 4 blue bonds are parallel
 Note: Never use wedge or hash bonds on a chair
22 conformational drawing! ( or ) x x 24

Theme 2 - p6
 Substituted cyclohexanes 3. Draw the least stable conformation of trans-1-isopropyl-4-methylcyclohexane.

 A ring flip will produce two different conformations for

substituted cyclohexanes
CH3 Ring flip

CH3 4. Which is more stable, cis-1,3-dimethylcyclohexane or trans-1,3-

dimethylcyclohexane? Draw chair conformations of both and explain your
become answer.
axial groups equatorial groups
 The two different conformations are not equal in energy
because of steric strain between axial substituents
H
H H
H
H H
5 1 Ring flip
H CH3
3

1,3-diaxial interaction more stable conformation 25 27

STERIC STRAIN less strain

 As the size of the substituent increases, so does the strain from a Isomerism: The relationship between two structures with the
1,3-diaxial interaction. same molecular formula
H < Br < OH < Me < Et < iPr << tBu
Connectivity Orientation in Can be interconverted
space without breaking bonds
Structural different different no
isomers
O H
 Increasing the number of axial substituents also increases the strain. e.g. C3H6O
O O
O
Exercises
Stereoisomers identical different no
1. Identify whether the following molecules have cis or trans stereochemistry.
Me
Et e.g. cis vs trans
i Me
Pr cis trans

Conformers identical different yes

2. Draw the most stable conformation of cis-1-isopropyl-4-methylcyclohexane. (Identical molecules
not strictly isomers)
26
e.g. ring flips 28

Theme 2 - p7
 TERM DESCRIPTION
Summary Primary, secondary, A saturated carbon atom bonded to one, two, three
tertiary or quaternary or four other carbon atoms, respectively
 Names  Conformations carbon
 IUPAC  Eclipsed
Structural Compounds with the same molecular formula, but
 Drawings  Staggered (Constitutional) isomers different connectivity (bond pattern) of the atoms
 Line  Gauche
 Newman  Antiperiplanar Alkyl group (-R) Part of a structure that is named according to the
 Chair alkane that it would have been if it was bonded to
 Chair
hydrogen rather than to the rest of molecule
 Axial and equatorial
 Isomerism
 Strain Conformation The exact three-dimensional shape of a molecule at
 Constitutional Isomers
 Torsional any given instant, assuming that rotation around
 Cis/Trans Stereoisomers single bonds is frozen at that instant
 Steric
 vs Identical molecules but
 Angle Conformers Structures that differ only in the rotation around
conformers
single bonds

Newman projection A way of viewing a molecule’s spatial arrangement by

29 looking end-on at a specific carbon-carbon bond 31

TERM DESCRIPTION Use of molecular model sets

Functional group An atom or a group of atoms that is part of a larger
molecule and has a characteristic chemical reactivity  Carbon is black  Nitrogen is blue
Hydrocarbon A compound that consists of only hydrogen and carbon
atoms  sp3  sp3
Saturated A compound that has only single bonds
 sp2  sp2
Carbonyl group The C=O functional group
 sp  sp
Lewis dot A representation of a molecule showing covalent bonds as
structure pairs of electron dots between atoms
 Hydrogen is white  Oxygen is red
Lewis structure A representation of a molecule showing covalent bonds as
lines and lone pairs are shown as dots.
s  sp3
Condensed A shorthand way of writing structures in which bonds are
structure understood rather than shown
 Halogens (Cl, Br, I)  sp2
Skeletal or line A shorthand way of drawing structures that shows only
structure bonds, not atoms (except in functional groups) 30 are green

Theme 2 - p8
 HO2C CO2H HO2C CO2H

OH NH2 OH NH2
Chirality = Handedness
N N  Left and Right hands are mirror images of one another.
H H
These mirror images are not identical. The mirror images
2700 x sweeter
than 5% sucrose Theme 3 50 x sweeter than
5% sucrose are non-superimposable.

 Systems which are non superimposable on their mirror

Stereochemistry: Chiral Molecules images are termed CHIRAL.
A study of the three-dimensional bonding arrangement of
atoms in molecules and its effect on the properties of
 Some objects have mirror images that are identical (i.e.
compounds.
are superimposable and therefore not chiral = achiral).
These objects all have a plane of symmetry which means
Smith: Organic Chemistry that half the object is a mirror image of the other half.
Extracts from Chapter 5
1 3

The stereochemistry of one bond can make a big difference!

OH
Chirality = Handedness
O
HO
OH
 Organic molecules that are not superimposable on their
ax
OH
O eq
O mirror images are said to be CHIRAL
HO

OH  These molecules do not have an internal plane of

O
symmetry in any of their conformations

CH3CH(OH)COOH

This OH can be
Lactic acid
axial or equatorial

Mirror
 This chiral molecule and its mirror image are a
pair of enantiomers
 Chirality is most commonly due to the presence of a
stereogenic centre in a molecule.
2 4

Theme 3 - p1
  Determining if a molecule is chiral
 Stereogenic centres = stereocentres (= chiral centres) no
 A stereogenic centre is an atom with tetrahedral geometry Stereocentre(s)? Achiral
and 4 different substituents. yes
e.g. an sp3 hybridised asymmetric carbon atom.
yes
 C=C, C≡C and C=O are not tetrahedral so can not be Plane of symmetry? Achiral
stereocentres
no
 -CH3 and -CH2- groups do not have 4 different
substituents so can not be stereocentres CHIRAL

 The configuration of a stereocentre is its 3-D

arrangement of atoms that can only be changed by
breaking bonds
 Enantiomers have different configurations
5 7

 The Biological Importance of Chirality

 Identify all the stereogenic centres in the following
compounds by marking them with asterisks.  The binding specificity of a chiral receptor site for a chiral
molecule is usually only favorable in one way
Cl
OH

COOH

I I

HO  Chiral molecules are like hands and receptors are like gloves
6 8

Theme 3 - p2
 Absolute Configuration
3. For purposes of comparison, consider multiple bonds to be
 There are only two different arrangements possible for equal to the same number of single bonds to the same
the four groups bonded to an asymmetric carbon atom
X X O (O) (C)
 
C consider as C O
W Y Y W
Z Z OH O H
[8,8,8] [6,1]
 These are non-superimposable mirror images and
therefore are enantiomers This C has 3 bonds to O
 Specifying the absolute configuration of a molecule as
R or S is a way of describing the complete structure of  Rate the four substituents on the stereogenic carbon for
the molecule. relative priority (high 1 > 2 > 3 > 4 low)
 The process starts by using the Cahn-Ingold-Prelog
Sequence rules to assign priorities to the four
substituents on the stereocentre
9 11

Cahn-Ingold-Prelog Sequence Rules Assigning the configuration as R or S

 Replace the substituents on the stereogenic centre with the
1. Priority of substituents is determined by atomic assigned priorities
number. Bigger number = higher priority
Br > Cl > F > O > N > C > H
35 17 9 8 7 6 1

2. First compare atoms 1 bond away from the  Build a model and orientate the molecule with the lowest
stereogenic Carbon. If atoms are the same, look at priority group (4) pointing away from the observer
atoms 2 bonds away from the stereogenic C, etc.

 If the sequence 1→2→3 is clockwise the configuration is R

10
and if it is anticlockwise the configuration is S 12

Theme 3 - p3
Exercise Drawing enantiomers – Draw a Mirror Image
 Method 1: Put a mirror at the side of the molecule and see the reflection in
the mirror. Now wedges remain wedges and dashes remain dashes just on
the opposite side.

 Method 2: Change all wedges into dashes and all dashes into wedges.
This is the same a putting a mirror behind the molecule, then look into the
mirror.
Br

13 15

Exercises Properties of Enantiomers: Optical Activity

 Draw the enantiomer of ()-Lactic acid and assign the  Enantiomers have identical physical properties (melting point, boiling point,
configuration. density, solubility) except optical rotation.
A polarimeter: an instrument to measure optical rotation

()-Lactic acid

 Draw (S)-3-bromo-2-butanone (a ketone at carbon-2)

 If the light is rotated clockwise the rotation is (+)

 If the light is rotated counterclockwise the rotation is (-)
 The ability of a chiral molecule in solution to rotate the plane of polarised
light = Optical Activity
14 16
 Optical Rotation (α) is an angle measured in degrees

Theme 3 - p4
 Specific Rotation, [α]D Algorithm for Chirality
 An empty sample tube or one containing an achiral molecule will not no
rotate the plane-polarized light Stereogenic centre(s)? Achiral
 An optically active substance (e.g. one pure enantiomer ) will yes
rotate the plane-polarized light
 The amount of rotation depends on the sample concentration and the
yes
Plane of symmetry? Achiral
sample path length
MESO
 The standard value specific rotation [α]D can be calculated from the no
observed rotation 
[α]D = ObservedRotation(α)
pathlength×concentration CHIRAL

no
Optical activity? Racemic
yes

17 Enantiomeric Excess 19

Enantiomers and Optical Rotation

Enantiomers
 The specific rotation of the two pure enantiomers of 2-butanol are
 Same molecular formula, identical connectivity pattern
equal but opposite
 Not superimposable due to different spacial arrangement of
substituents
 Occur in pairs that are mirror images of each other (R vs S)
 Identical Physical properties, except optical rotation
 Identical chemical properties (undergo the same reactions)
 Usually very different biological properties
 There is no correlation between the R,S designation of an
enantiomer and the direction [(+) or (-)] in which it rotates plane
polarized light
 Racemic mixture = A 1:1 mixture of enantiomers
 No net optical rotation
 Often designated as (±)
e.g. (±)-2-butanol or (±)-CH3CH2CHOHCH3
18  Racemates are a 50:50 mixture of enantiomers 20

Theme 3 - p5
 Stereoisomers Diastereomers
TWO stereoisomers  Same molecular formula, identical connectivity pattern
ONE stereogenic centre
a pair of enantiomers  Include saturated compounds with more than one stereogenic centre
or cis-trans diastereomers in alkenes
R S
 Not superimposable due to different spatial arrangement for at least
one stereogenic centre
TWO stereogenic centres FOUR stereoisomers
two pairs of enantiomers  Two diastereomers are not mirror images of each other
 Have different physical properties including optical rotation
R,R S,S R,S S,R  Have the same chemical properties (undergo the same reactions)
 Usually have very different biological properties
Diastereomers

"n" stereogenic centres maximum2n stereoisomers

 Enantiomers have opposite configurations at all stereogenic centres.

 Diastereomers are stereoisomers that are not mirror images.
Diastereomers include compounds that differ in configuration at some
21 23
but not all stereogenic centres.

Example Drawing Diastereomers

 How many stereoisomers exist for 2,3-dihydroxybutanoic acid?
 Switch some not all bond directions. Now you have a
molecule with a new 3D bonding pattern, but it is not a mirror
image of the first

 Assign the configuration at each stereogenic centre.

22

Theme 3 - p6
 Summary  Remember the test for Chirality:
 Plane of symmetry
An imaginary plane that bisects a molecule in such a way that the two
 For each stereogenic carbon, there are only two possible halves of the molecule are mirror images of each other
arrangements of substituents A molecule with a plane of symmetry can not be chiral
 So, for a compound with one stereogenic centre:
 Meso compound:
 There are 2 configurations which are mirror images achiral despite the presence of stereogenic centers
 These are enantiomers because they are not superimposable. Has more than one stereogenic centre
 For a compound with more than one stereogenic centre: Has a plane of symmetry
 There are only two configurations for each asymmetric carbon Superimposable on its mirror image
 A compound with n different stereogenic centres, can exist as 2n
different stereoisomers (n = 1, 2, 3, …)
 When two stereoisomers are compared, they could either be
mirror images (enantiomers) or
NOT mirror images (diastereomers)

 Exercise: Draw a meso isomer of 1,2-dimethylcyclohexane

25 27

Exceptions to the rule:

How many stereoisomers exist for tartaric acid? Example
HOOC OH
 Physical properties of stereoisomers of tartaric acid
* *

HOOC OH

 Number of stereogenic centres = 2

 Maximum number of stereoisomers = 22 = 4

Stereoisomer (+)-R,R ()-S,S Meso-R,S Racemate (±)

Melting Point (°C) 171 171 146 206
Density (g.cm-3) 1.76 1.76 1.67 1.79
Solubility (g/100 mL H2O) 139.0 139.0 125.0 20.6
Optical Rotation []D +13 13 0 0
 However, because of the symmetry of the tartaric acid molecule, only Figure 5.12 p 201 Smith V
three stereoisomers exist: (S,S), (R,R) and (S,R)- MESO. 26 28

Theme 3 - p7
 Isomerism Exercises
– the relationship between any two structures  What is the stereochemical relationship between the given pairs of
compounds?
Different compounds Remember: conformers ≠ isomers
(not superimposable)
But are identical compounds with
with the same
different spacial orientation.
molecular formula
1.
Isomers with the same
connectivity but different
arrangement of atoms
in space
Isomers whose atoms
have a different
connectivity 2.

3.
29 31

Algorithm for Isomerism

Looking ahead to Theme 4
No
Same molecular formula? Different compounds  Chemical reactions might lead to the formation of
Yes molecules with new stereocentres. The products might
No
contain a mixture of stereoisomers.
Same connectivity? Structural isomers
 For example:
Yes
No H Cl
Superimposable? Stereoisomers + H Cl
Identical,
Yes
Same compound  How many stereoisomers are there for this product?
Mirror images?

Identical conformation? Yes No

No
Enantiomers Diastereomers
Conformer
30 32

Theme 3 - p8
 Theme 4 Double Bond Substitution
Unsaturated Hydrocarbons Monosubstituted Disubstituted
Alkenes, Alkynes and Aromatic Compounds A B
A
B A A B

Trisubstituted Tetrasubstituted

A C

B D
Any of A, B, C or D could
be equal to each other
Smith: Organic Chemistry
Extracts from Chapters 6, 8, 10, 11 and 17 We can’t use cis and trans to distinguish between different
1 geometric isomers of tri- or tetra-substituted double bonds. 3

Stereoisomerism: Geometric Isomers IUPAC nomenclature for alkene geometry

 Alkene double bonds can not rotate  The E,Z-system works for di-, tri- and tetrasubstituted
 Rotation would break the -bond alkenes Ze zame zide
 Z-alkenes have high priority groups on the same side
(zusammen = together in German)
 E-alkenes have high priority groups on the opposite side
(entgegen = opposite in German)
High High
Low
 This results in the possibility of cis-trans diastereomers also Low Low Low Low Low Br
called geometric isomers
Low
High High High High High High Low

Z E Z E
cis-2-butene trans-2-butene
 Each alkene C has two groups attached. One is given High
 Which would have more strain? priority and the other Low. Priority is determined by the
Cahn-Ingold-Prelog sequence rules.
2 4

Theme 4 - p1
 Assigning alkene geometry cont… Exercises
Cahn-Ingold-Prelog Sequence Rules OH
1. Priority of substituents is determined by atomic number. Bigger
number = higher priority Br
2. First compare atoms 1 bond away from each alkene Carbon. If
both are the same, look at atoms 2 bonds away from the =C, etc.
3. Expand multiple bonds into complementary single bonds. O
 Rate the two substituents on a single alkene carbon for
relative priority (high and low). OH
 Compare substituents on both alkene carbons. Are high
priority groups on the same side (Z) or opposite sides (E)?  Draw (E)-3-chloro-2-ethyl-1,3-hexadiene

[17] > [6] 6C H 1H [6] > [1]

High Low High Low
17Cl Cl 6C
5 7

Example Including geometry in IUPAC name

1. If one d.b. needs E/Z geometry, then use E/Z for all d.b.’s
HO otherwise cis/trans may be used
2. Geometry comes before the IUPAC name
 Cis/Trans no brackets, linked with a hyphen
 E/Z in brackets, linked with a hyphen
 For more than one double bond, indicate numerical position
within the bracket

6 8

Theme 4 - p2
 Kinds of Organic Reactions Hydrohalogenation:
 Reactions in CMY 127 can be divided into 3 main groups: Addition of HX to an alkene
1. Addition
H H  General Reaction
C C + H2 C C
H X H X
H OH
C C C C
2. Elimination H+ Ether
C C C C + H2O

3. Substitution H H The reaction is REGIOSELECTIVE, following Markovnikov’s rule

h  H adds to the carbon with fewer alkyl substituents
H + Cl2 H + HCl
H Cl  X adds to the carbon with more alkyl substituents
H H

 Bonds are breaking and reforming

HCl Cl H Cl
not
O
9 11

Writing Organic Reactions

Examples
B
A C
solvent, temperature

HBr Br Br
solvent +
A + B C Ether
temperature
unsymmetrical alkene
but equally substituted 50:50 mixture of 2 products

Br
 Reactions are seldom completely balanced HBr
 Assume excess of inorganic reagents unless specifically stated Et2O
otherwise (e.g. a catalyst is not needed in stoichiometric amounts) symmetrical alkene
10 12

Theme 4 - p3
 Exercise Reaction Mechanisms:
 Predict the product(s) of the following reactions: How do reactions happen?
 Bonds form and bonds break
 Bonds consist of electrons
To understand what is happening in a reaction, we
must look at what the electrons in the molecules are
doing!
 We show what the electrons are doing by using curved
arrows
 Curved arrows show where electrons start from and
 Predict the substrate of the following reaction: where they move to

Br H   H
HBr -
or O + H Cl O +H + Cl
H H
13 15

Exercise
 H   H
 Write the hydrohalogenation reaction which will produce each of the products. -
Include all possible answers.   + H Cl O +H + Cl
H O H

 A pair of electrons from an electron rich part of a

molecule will attack an electron poor atom
 The electron rich reactant molecule which donates a pair
of electrons is called a nucleophile (Nu: or Nu–)
[Nucleophile = (+) nucleus lover]
 The reactant molecule with an electron poor atom that
accepts the electron pair is called an electrophile (E+)
[Electrophile = (-) electron lover]
 There is an electrostatic attraction between the –
nucleophile and the + electrophile.

 Do not duplicate the same starting material

16
 Tick all starting materials for which a Z isomer will also give the product. 14

Theme 4 - p4
 Good curved arrows Mechanism of the hydrohalogenation reaction
 A lone pair makes a new bond
H
H H X X H
O
H O Ether
H
 A bond makes a lone pair
 Look at the polarity of the reactants H-X and the alkene:
Cl Cl
 The H-X bond is polarised so that the H is  and the X is 
 The alkene has no polarised bonds, but the -electrons are not
 A bond breaks to make a new bond held tightly and are able to be donated. The alkene will act as a
nucleophile.
- electrons represent an electron rich area of a molecule.
 Since the alkene can only act as a nucleophile, there will be an
electrostatic attraction between the alkene’s -electrons and the 
H of the H-X molecule. Thus H-X will act as an electrophile.
 When drawing an arrow from a bond, always draw it
17 19
from the middle of the bond.

H H
 Do NOT do this!  To understand what happens when drawing the mechanism
O O
H H H H with line structures, we will look at the mechanism using
Lewis structures to help us count electrons
  The -electrons from the alkene move to
H Cl form a bond between one of the alkene C’s
 Draw the intermediates formed as the curved arrows indicate: H Cl
H H and the H. The -bond breaks and a new
C
x
x
x
C -bond forms. H can only make 1 bond
*
H * C*H
x
H so the -bond to the Cl breaks.
*
H

Cl Cl The result now leaves an alkene carbon

H H short of an e– so that C has a + charge.
H x
H C xC x H The Cl has an extra e– so the Cl has a –
 Add curved arrows to explain product formation: H * x
H * C* H H charge.
H3C H *
H
18 20
End of part 1 of the mechanism

Theme 4 - p5
 Cl Cl
Stability of Carbocation Intermediates
H H Cl H Cl
H x x H
H C xC x H
H C xC x H H
H * H
H3C H * C* H
x
H *
H * C* H H
x
 (Most stable) 3° > 2° > 1° > methyl (Least stable)
H * * H3C H
H H  -bonding electrons in alkyl groups help to stabilise the
 The product has not yet formed, we have made two ionic species
empty 2p orbital and the + Carbon.
called intermediates.
 The Cl intermediate is negatively charged. It is an anion [an-ion] and
will act as a nucleophile. H CH3
H H H
 The organic intermediate is positively charged. It is a cation [cat-ion] H H H H H
H H
and will act as an electrophile. Because the charge is on a carbon we C+ has 3 valence e- and
call this intermediate a carbocation. e- in -bond help More alkyl substituents =
3 shared e- so does not
stabilise the + more -bond e- = more
 The electrostatic attraction between two ions is much stronger than have complete octet and
is very unstable. charge on the C. stability of the carbocation
between neutral molecules. Thus the intermediates react quickly.
The Cl– donates an electron pair to form a -bond with the C+.
 At the end of part 2 of the mechanism, we have the product.
21 23

A note about Carbocation intermediates Mechanism for hydrohalogenation of

unsymmetrical alkenes
 A carbocation intermediate is formed during the course
of most alkene addition reactions
 It is reactive and can not be isolated.
 Carbocations are sp2 hybridised and are trigonal planar

H Cl
H
+ Cl
2 2 2 3
sp -sp sp -sp

 Carbocations may be 3° ; 2° ; 1° or methyl

R H H H
>

R = alkyl group R > C+ R > C+ H C+ H C+

>

>

>

R R R H
22 24

Theme 4 - p6
Exercise Hydration of an alkene
 General Reaction

H OH
HBr H2O, H+catalyst
C C C C
250°C

 This reaction requires strong acid and high temperatures

 It is suitable for industrial applications, not lab scale reactions

 Mechanism
 Similar to HX addition
 The reaction is therefore regioselective following Markovnikov’s rule
 The reaction requires an extra step to produce the alcohol product.
 The acid is a catalyst because it is regenerated in the reaction.
It is not used up.
25 27

Example of an exam question Mechanism for hydration of unsymmetrical alkenes

Question 4: Mechanisms of Organic Reactions [Marks: 10]

4.1 Use line structures and write a complete mechanism for the
hydrobromination of 4-methyl-2-pentene, clearly indicating the
following:
i) flow of electrons,
ii) position of charges,
iii) nature of all possible intermediates (Electrophiles or Nucleophiles),
iv) hybridization changes of all C-atoms taking part in the transformation.
(8)
4.2 Is the reaction in question 4.1 regiospecific? Explain fully. (2)

26 28

Theme 4 - p7
Exercise Halogenation of an alkene
What products do you expect from the following reactions?  General Reaction (Observed in practical)
It is not necessary to show the mechanism in your answer.

 This reaction occurs with anti stereochemistry

 This reaction works best with Cl2 and Br2
 It is used in industry for the synthesis of the substrate for PVC

Cl2 Cl OH
Cl Cl PVC
vinyl chloride
 Mechanism
 The mechanism explains why the product has anti stereochemistry
29 31

Draw line structures for all the substrates that can be Mechanism of Halogenation
used for the synthesis of 3-methyl-3-pentanol
Step i textbook = ia + ib
X
X Loosly held e s of X2
molecule are repelled by X
C=C e s to temporarily X
polarize the X2 molecule.

ia

Draw line structures for all the substrates that can be X

used for the synthesis of 3-methyl-2-pentanol i
X
X+ blocks one side
ib so X attacks from
X
This imaginary intermediate opposite side
is added to the mechanism ii X
for clarity

30 X X anti 32

Theme 4 - p8
Exercise Halohydrin formation
 Complete the mechanism of the addition of Br2 to cis-3-
hexene. Show curved arrows and three dimensions of the  Treatment of an alkene with a halogen X2 and H2O
products. forms a halohydrin.

 The reaction occurs with anti stereochemistry

because the mechanism involves a halonium ion.
 The reaction is regioselective:
 the X adds to the less substituted carbon and
 the OH adds to the more substituted carbon.
 Alternative reagents are NBS (Br2 source) in DMSO
33 (solvent) with H2O. 35

Mechanism of Halohydrin formation

 Predict the products of the following reactions: (Show the
anti stereochemistry and identify new stereocentres *)

 The mechanism begins in the same way as in the formation

of an anti dihalide.
 BUT now there is lots more H2O than Br, thus H2O acts
 Complete: as the nucleophile in the second step.
 H2O also acts as a base to remove a proton and give
the neutral product (a chlorohydrin or a bromohydrin).
Br2
2,3-dibromo-5-methylhexane  H3O+ and Br are the byproducts of the reaction.
CH2Cl2 34
36

Theme 4 - p9
Exercise Catalytic hydrogenation of alkenes
 Complete the mechanism of the addition of Cl2 to 1-butene in  General Reaction
H2O. Remember that the reaction is regioselective. Show
curved arrows and three dimensions of the products.

(Enantiomers)
 This reaction occurs with syn stereochemistry
 Catalysts are either PtO2 or Pd/C (also written Pd-C)
 Polar organic solvents are used e.g. ethanol
 The catalysts are not soluble in the solvent, so there is a solid
phase, a liquid phase and a gas phase in the reaction. This makes
+
the process HETEROGENEOUS, not homogeneous

 Mechanism
 The mechanism explains why the product has syn stereochemistry
 What is the relationship between the two products? 37 39

Exercise Mechanism (not examinable)

 Complete the following reactions:

38 40

Theme 4 - p10
 Hydrogenation of other functional groups Examples
 Draw line structures for the products of the following hydrogenation
 The following FG’s will survive H2/Pd-C or H2/PtO2 reactions. How many moles of H2 are absorbed per mole of substrate?
O O O O

H OH OR

 Under super-high pressure aromatic rings can be reduced

H2(136 atm), Pt

 Draw line structures of substrates for the following reactions.

 Alkynes are reduced completely to alkanes with H2/Pd-C
1eq H2, Pd/C
H H 2-methylbutane
2 H2, Pd/C

H H 1eq H2, PtO2

1,1-dimethylcyclohexane
41 43

Reduction and Oxidation in Organic Chemistry

Hydrogenation of alkynes to alkenes
 Reduction of a molecule
 Hydrogenation of alkynes can be stopped at the alkene  Increase in hydrogen content e.g. hydrogenation
stage if the right catalyst is used  Decrease in oxygen content
 This will give a cis-alkene
 Oxidation of a molecule
H2  Increase in oxygen content
Lindlar catalyst
H H  Decrease in hydrogen content

 Loss or Addition of H2O does not count as oxidation

H2, Pd/C or reduction

H2
Lindlar catalyst
42 44

Theme 4 - p11
 Summary – Addition Reactions of Alkenes
and Alkynes Zaitsev’s Rule (Smith 8.5)
alkyne
H2  Elimination reactions yield the more highly substituted
Lindlar catalyst H2 alkene as the major product
cis alkene Pd/C or PtO2
H2 Examples
H X Pd/C or
HX H H
PtO2

alkyl halide syn alkane

Cl2 or Br2
H+/H2O Cl2 CH3CH2ONa
H2O
Markovnikov Br2 +
X EtOH
OH Br 81% 19%
HO X X
anti 1,2-halohydrin

alcohol anti 1,2- 45 47

dihalide

Elimination reactions – prep of alkenes Exercises

Smith 10.7
A. Dehydration – loss of H2O HO H+

H2 O
OH
H+
 Best for 3° alcohols and not used for 1° alcohols - H2O
 Usually conc H+ = conc H2SO4 or TsOH
Br
B. Dehydrohalogenation – loss of HX EtONa
H X EtOH
base
C C C C + H2O + X-
HONa

 Usually X = Br Br
46 48
 Possible bases: hydroxide and alkoxides e.g. CH3O– and EtO–

Theme 4 - p12
 Aromatic Compounds
Stability of aromatic compounds
 Name comes from “aroma” because all the first known  Benzene does not react like alkenes!
aromatic compounds had fruity smells, but other  Benzene is more stable and less reactive than alkenes
functional groups also have fruity smells
 Aromatic compounds have benzene-like rings HX

Examples H2O, H+

OH COOH Br2 no reaction

COOH
COOH H2N
Benzene H2N
H2N H2, Pd/C
N HN
NH
N O OH
Pyrimidine Paracetamol Phenyl alanine Tyrosine Tryptophan H2 (136 atm), Pt

Amino acids 49 51

The structure of benzene Nomenclature

 Benzene shape  A benzene ring attached to a carbon chain is named as a phenyl-
 Planar
substituent (formula C6H5—)
 Perfect hexagon not
4-methyl-3-phenylheptane
 All bond angles 120°
Ph
 Bond Length
In line structures Ph = the phenyl group
 Normal single bond lengths are 154 pm
 Normal double bond lengths are 134 pm  A substituent with a benzene ring attached to a CH2 is called a
 Bond lengths in benzene are all 139 pm benzyl group (PhCH2— or C6H5CH2— or Bn— )
H H
 Hybridisation and Bonding H  Give IUPAC names for the following compounds:
H
 All C’s are sp2 hybridised H H
 All C’s have 3 -bonds
 All C’s have 1 p-orbital with a single e- for -
bonding H H
  electrons are located in delocalised bonds not H H
3 distinct -bonds H H
50 52
 Draw a line structure for (Z)-3-methyl-4-benzyl-2-hexene

Theme 4 - p13
 Theme 5 Exercise
Saturated Compounds with X, O and N  Provide suitable reagents and the structures of the
products for the conversion of the following alcohols
Extracts from Chapters 7, 8, 9,
Smith: Organic Chemistry
to alkyl chlorides and alkyl bromides:

OH
12 and 25

OH

OH

1 3

The Chemistry of the Alkyl Halides Remember the tests for 1°, 2° and 3° alcohols
 Preparation from alkenes (addition reactions)
 Only 3° alcohols react with HCl
HCl
i) Markovnikov Addition HCl
Positive result
OH Cl
within 5 minutes
ii) Br2 trans-1,2-dibromo product
as a racemic mixture  2° and 3°alcohols react with Lucas reagent
OH Cl
 Preparation from alcohols (substitution reactions) HCl, ZnCl2 Positive result
within 5 minutes
C OH C X
SOCl2 or PBr3  1° alcohols react too slowly in these experiments for
1º or 2º alcohol 1º or 2º alkyl halide the reaction to be observed in the time frame of a 2
hour practical.
HCl (g) or HBr Very slow reaction
3º alcohol 3º alkyl halide OH Br
takes 24 hours
HBr (g) 2 4

Theme 5 - p1
 Typical Reactions of Alkyl halides The chemistry of Amines
 Substitution of 1º Alkyl halides (CMY284) sp3
N geometry around
nitrogen is pyramidal
Br OH
OH Br approx 109°

 Amines, like ammonia, are basic because of the lone

 Elimination of 2º or 3º Alkyl halides (Prep of alkenes) pair electrons on nitrogen
Br
C C OH C C H2O Br Et3N: H Cl Et3N H Cl
H RO ROH
triethylamine triethylammonium chloride
Zaitsev’s Rule: The major product will be the more substituted alkene

Br OH

major minor
5 7

How do elimination reactions happen? The Chemistry of Alcohols

Br
 5.3.1 Physical Properties
H R R
C C C C H O Br sp3 O
O geometry around O
H H H H H
H3C H oxygen is bent
HO O O
approx 109° R R
 Exercise – Complete the following reactions:
 Boiling points are high compared to alkanes because of hydrogen bonding
 Soluble in water (up to C5) because of hydrogen bonding
? NaOH Br2  Can act as weak bases – donating an electron pair (like water)
OH Cl ? ?

 Can act as weak acids donating H+ (like water)

HCl(g) NaOEt ?
OH ? ? Br

Br  Better preparation of alkoxides is with Na or K metal

PBr3 ? Cl2
? ?
6 8

Theme 5 - p2
 Preparation of Alcohols Examples
 From Alkenes (Revision)

H+/H2O H OH Markovnikov
C C C C addition

 Complete the following reactions:

 From Carbonyl Compounds – Reduction

 Carboxylic acids are not reduced by NaBH4, and esters react

9 11
too slowly

Explaining the reduction Reactions of Alcohols

 Sodium borohydride reagent = Na BH4
 Formation of Alkoxides
 A hydride carrier
 Dehydration to alkenes – Elimination with conc acid
H proton 1 proton, 0 electrons
H OH
H radical 1 proton, 1 electron Zaitsev
3º alcohol conc H2SO4
H hydride 1 proton, 2 electrons
C C C C + H2O Rule

 Substitution to alkyl halides

 A two step mechanism
 1º and 2º alcohols react with SOCl2 or PBr3
 3º alcohols react with HCl(g) or HBr(g)
Cl H2 O
H H Cl H H Cl
O O Cl

 Methanol is used as a reagent and a solvent HCl (g) is better than HCl (aq) = H3O+ + Cl-
10
 Oxidation to carbonyl compounds 12

Theme 5 - p3
 Oxidations of alcohols CrO3
OH [O] d) H2O+
NO REACTION HO
PCC
CH2Cl2
3º alcohol [O] = oxidising agent
OH [O] O CrO3 in H2SO4 (Jones’ reagent) CrO3
OH
PCC (Pyridinium chlorochromate) H2O+
e)
2º alcohol Ketone PCC
CH2Cl2

OH [O] O [O] O

H OH CrO3
1º alcohol Aldehyde Carboxylic acid O
H2O+
f) H
PCC
• Normally 1º alcohols oxidise to give carboxylic acids
CH2Cl2
• PCC in CH2Cl2 is used to stop the oxidation of 1º alcohols at the
13 15
aldehyde oxidation level

Multistep Synthesis : Doing a sequence of different

Excercise reactions to get from a starting material to a product.
 Complete the following reactions:
 Identify the functional groups in the starting material and the product and find the
O
functional groups that link them on the reaction map.
a)
[O] Propose synthetic sequences for the following conversions:

b) [O]
H

c)
[O] O
14 16

Theme 5 - p4
 Theme 6 and 7 A. Carbohydrates
Carbonyl Compounds
 Carbon and water – formula Cn(H2O)n
& Carbohydrates
 Simple carbohydrates
Smith: Organic Chemistry  Monosaccharides – e.g. glucose and fructose
Extracts from Chapters
 Disaccharides – e.g. sucrose and lactose
19, 20, 21, 22 and 27
 Complex carbohydrates - Polysaccharides
 For structure – cellulose and lignin
 For storage – starch and glycogen

 Glycoproteins = carbohydrate linked to protein

 Glycolipids = carbohydrate linked to lipid

1 3

The Carbonyl Group O Monosaccharides

C  Contain 3 – 7 carbons, formula CnH2nOn
 Possess a C=O group and all other carbons are bonded to OH groups,
 Hybridisation except if specifically stated otherwise, eg. 2-deoxyribose
 Bond angles aldehyde H O
C
 Geometry
H C OH aldose = sugar with aldehyde FG
 Bond Polarity
H C OH

H C OH
ketone C O ketose = sugar with ketone FG
 The + Carbon will be attacked by nucleophiles
H C OH
 The lone pair e- on the Oxygen can be protonated by a
strong acid
2  C3 = triose, C4 = tetrose, C5 = pentose, C6 = hexose 4

Theme 6/7 - p1
 Combining the names gives:  Convert the following Fischer projections into line structures with
stereochemistry and assign the absolute configuration of the
 an Aldotriose  a Ketotriose
stereocentres:
e.g. glyceraldehyde e.g. dihydroxyacetone
COOH CHO CH3
H2 N H H OH H CHO
CH3 CH3 HO H
CH2CH3
 steroisomers
 an Aldohexose  a Ketohexose
e.g. glucose e.g. fructose

CHO CH2OH
H C OH C O
OH H O
HO C H HO C H
H C OH H C OH O O H
H C OH H C OH
CH2OH CH2OH
5 7
 stereoisomers  stereoisomers

Representing Stereochemistry D and L Sugars

 Every carbohydrate except dihydroxyacetone contains 1 or more  In D sugars the OH on the penultimate carbon is on the right hand
stereocentres, so will have optically active stereoisomers side and in L sugars it is on the left hand side.
 Fischer Projections are a standard way of representing the  The terms D and L come from glyceraldehyde where the D is dextrorotatory
stereochemistry of sugars and the L is levorotatory BUT
 Vertical lines point into the page (away from you) D and L do not predict the sign of optical rotation because they refer
 Horizontal lines point out of the page (towards you) to only one of many stereocentres.
 C’s at centre are omitted CHO Classify the following monosaccharides for type of C=O, no of C’s and D
CHO or L…
H OH
H OH = HO H
=
CH2OH H OH
H OH
CH2OH

 H’s and their bonds on centre C’s may be omitted.

 Monosaccharides are written with the carbon backbone vertical and the
C=O nearest the top 6  An aldohexose has 4 stereocentres, so 16 stereoisomers. Half of8
these are D-sugars and half are L-sugars.

Theme 6/7 - p2
Fig 27.4 Configurations of D-aldoses
Cyclisation of Monosaccharides
* Memorise
 Cyclisation of monosaccharides is spontaneous in aqueous solution.
*  The sp2 carbonyl carbon becomes sp3 forming a new stereocentre. This
carbon is called the anomeric carbon.

* *
 This is an equilibrium reaction and the two stereoisomers (called anomers) will
slowly interconvert.
 The six-membered ring form of a sugar is called a pyranose.
 This structural representation (a flat ring with O in upper right position and
substituents on vertical lines – up or down) is called a HAWORTH projection

* * * 9 11
All altruists gladly make gum in gallon tanks!

Isomerism  and  anomers

 D-glucose and L-glucose are enantiomers.  The  anomer of a D-monosaccharide has the OH group drawn
down, trans to the CH2OH group at C5.
 The  anomer of a D-monosaccharide has the OH group drawn up,
cis to the CH2OH group at C5.

 Epimers – differ in configuration at only 1 stereocentre

 D-glucose and D-mannose are epimeric at C2
 D-glucose and _____________ are epimeric at C4
 D-glucose and L-__________ are epimeric at C5  Names: -D-glucopyranose and -D-glucopyranose

 Are epimers enantiomers or diastereomers?  What about L-sugars,

 What is the relationship between D-fructose and D-glucose?
e.g. -L-glucopyranose?
10 12
 Are D-glucose and D-xylose isomers?

Theme 6/7 - p3
Mutarotation of Anomers
CHO
Stable conformation of Pyranose sugars
CH2OH CH2OH
O H OH O OH
HO H
OH OH  Both Fischer and Haworth projections are poor
H OH
HO OH H OH HO representations of the real shape of monosaccharides.
OH CH2OH OH  Six membered pyranose rings will adopt a chair
 - anomer open chain  - anomer conformation with the substituents axial or equatorial
 The chair conformation with the most equatorial
 Solution of pure -D-glucopyranose in water has []D = +112.2 substituents will be most stable.
 Solution of pure -D-glucopyranose in water has []D = +18.7
CH2OH HOH2C
 After time, a glucose solution that reached equilibrium has []D = HOH2C OH 1
O O OH
+52.7 implying 1/3 is in  form and 2/3 is in  form HO
OH OH 1 HO
O OH
1 OH
3 3
 This spontaneous change in optical rotation as a pure anomer HO OH
3 OH OH
equilibrates to a mixture of anomers is MUTAROTATION
 Mutarotation is slow at pH7, but is much faster when catalysed by -D-mannopyranose
acid 13 15

Cyclisation of Fructose B. Aldehydes and Ketones

 Preparation of aldehydes and ketones: Oxidation of
alcohols
 Aldehydes from 1o alcohols
PCC
OH CH2Cl2 O

 Forms a 5-membered cyclic hemiacetal  Ketones from 2o alcohols

 Shape of furan, so is called a furanose
O [O]
remember
tetrahydrofuran

 Called -D-fructofuranose and -D-fructofuranose OH O

14 16

Theme 6/7 - p4
Reactions of aldehydes and ketones Mechanism for acetal formation
1. Nucleophilic addition to Aldehydes and Ketones
 The + Carbon will be attacked by nucleophiles.
 The Oxygen lone pair e- can be protonated by strong acid
 O
 Mechanism

Nu

 Negatively charged nucleophiles such as H¯ from NaBH4

 These reactions are followed by addition of H3O+
 Neutral nucleophiles such as ROH
 These reactions work faster with an acid catalyst

H
O

Nu 17 19

Addition of Alcohol – Acetal formation More about hemiacetals

 Hemiacetals are intermediates in the formation of acetals.

 Hemiacetals are the product when a hydroxyl group and a
carbonyl group are part of the same molecule and no other
alcohol is present, e.g. sugars.
 Le Chatelier’s principle applies to the equilibrium
 Removing water from the system forms more acetal. Use c. H2SO4
 Adding excess water forms more ketone / aldehyde. Use H3O+

 Acetals are stable in neutral and basic medium but are

 If another alcohol is present then the hemiacetal will be
hydrolysed by aqueous acid 18
converted to the acetal. 20

Theme 6/7 - p5
 Examples Exercise
O 2 OH a) b)
a) b)
2 CH3OH conc H+ H+
O
H+ H +
ethanol HO CHO

H O
acetal acetal
c) d)
O OH OH O
H3O+ c. H+

c) OH O
H H+ H+
HO
e) O
O
hemiacetal acetal +
H3O OH
H HO

O
d) f) c. H+ O
H+
O O
carbonyl compound + 2 alcohol acetal 21 23

Identification of acetals and hemiacetals

Acetal formation in sugars = Glycoside formation
 One carbon atom bonded to two oxygen substituents with single
bonds
O OH H+ O OR
O ROH H2O
O O OH
O O
O
O
 The acetal of a sugar is called a glycoside
 The bond to the external alcohol is called a glycoside bond
OH OH  The alcohol can be as simple as methanol or it can be the
hydroxyl group of a monosaccharide OH
O O
HO HO OH HO HO O Lactose O
HO OH
OH
OH OH HO
O HO HO
O
 Specify the starting materials (Ketone / Aldehyde and HO O OH
OH HO
alcohol) from which the above compounds were made. OCH3
OH
22 24
Methyl -D-glucopyranoside -(1, 4') glycoside bond

Theme 6/7 - p6
Exercises 2. Oxidation of aldehydes
 Find the glycoside bond(s) in maltose, cellulose and the most
common form of starch – amylopectin.
 What kind of glycoside bond will it be ( or ) (1,4’ or 1,6’)?  Easily oxidised by many oxidising agents because the H can be
removed during oxidation
HO
O O
HO O O [O] [O] = CrO3/H+ or Tollens reagent
HO HO
HO O
HO OH R H R OH
HO O O O
OH O O HO Amylopectin
OH
OH O O O O
Maltose HO HO HO AgNO3
OH OH
O O Tollens' Test H OH Ag
HO
OH NH4OH
HO HO HO HO O

O O
O
O
O O
O O  Ketones are not oxidised because of strong C-C bonds
HO HO O
HO HO
OH OH OH OH
Cellulose

 Which sugars make up these glycosides? 25 27

Exercise Oxidation of carbohydrates

 Give the products, substrates or reagents for the
following reactions:
CH2OH CH2OH
O O
OH OH OH OH
HO OH HO O

HO HO
HO O HO O
OH
HO
OH OCH
HO
OH
Aldoses are called “reducing” sugars because, in the process
HO
3
OCH2CH3 of being oxidised, they reduce the oxidising agent
+ O
H HO
CH2OH
 Tollens reagent: AgNO3, NH4OH (Ag+ → Ag0 silver mirror)

OH
HO
H3O+
O
HO OH
O
HOHO OH O
CH2OH
OH 26 28

Theme 6/7 - p7
 C. Carboxylic Acids
Predicting reducing sugars
Physical properties of carboxylic acids
(mono- and disaccharides)
 Shape
CH2OH COOH O H O
 Hybridisation
OH
O OH  Bond angles R C C R
Tollens' test HO
OH
OH
Ag0  Geometry around C
O H O
HO OH
 Boiling points
OH CH2OH
 Exceptionally high
D-glucose D-gluconic acid
 Dimer due to hydrogen bonding
O
MM: 62 g.mol-1 MM: 60 g.mol-1
 All aldoses bp: -10 ºC
F OH
bp: 118 ºC

 No ketoses  Water solubility

 No glycosides  C1 to C4 are soluble, C5 is partly soluble, >C5 insoluble
 Alkali metal carboxylate salts are more soluble in water
 Except certain disaccharides
O O
 Reducing sugars show mutarotation NaOH H2O
29
OH O Na 31

Identify the reducing sugars: Acidity of carboxylic acids

 Remember
CH2OH
O HO HA + H 2O A - + H 3O +
HO O
OH OH
HO
HO [H 3 O +][A -]
HO OH OH OCH CH2OH Ka = pK a = - log K a
HO O
HO
3
O
[HA]
HO
OH O O HO OH OH  Given pKa values, and doing the calculations means
OH OH
Maltose HO O HO O HCl CH 3COOH H 2O
OH HO
CH2OH pK a = -7 4.75 15.75
HO OH
7 -4.75
HO O
HO
OH O Ka = 10 10 10-15.75
HO OH
OH O HO
OH
HO
% dissociated = 99.97% 0.45% 0.000001%
O
Sucrose
O OH O OH  Carboxylic acids are weak acids compared to HCl but much
HO
HO OH
stronger acids than water and alcohols
CH2OH Lactose
30 32

Theme 6/7 - p8
 Hydrolysis of esters
Reactions of carboxylic acids
 The reaction adds water to the ester to break it into the
carboxylic acid and alcohol from which it was made
 Reaction with a base to form a salt
O O
 Acid catalysed hydrolysis is the reverse of Fischer
OH NaOH O Na+ H2O H+
water ester alcohol carboxylic acid
O O
H 3 O+
O OH HO
 Or
 Reaction with an alcohol to form an ester
 Base induced hydrolysis – Saponification
O O
O O
conc H+ OH
OH EtOH O H2O
O O HO
rancid butter pineapple
 See manufacture of soap
33 35

D. Esters
Fischer Esterification – formation of esters Mechanism of saponification

H+
carboxylic acid alcohol ester water

excess remove to shift equilibrium

use as solvent to give product formation
O OH H+
+
OH

O
OH H+
OH + Write the products of the following saponification reaction:

CO2H H+
EtOH 34 36

Theme 6/7 - p9
 Hemiacetals, acetals or esters – when do you Peptides
O get what?
c H2SO4 O O
H H H H
EtOH
H2N C COOH N N
N N
O
H O H O
c H2SO4
R EtOH
O
 The amide bond is very stable. It forms the backbone of
c H2SO4
OH proteins.
EtOH
 The amide bond between two amino acids is called a peptide
bond.
Why the difference?
 Amino acids linked in this way are called peptides or
polypeptides.
 When the polypeptide is big enough, it is called a protein.
 Restricted rotation of the amide bond is important for protein
structure and activity.
37 39

E. Amides Hydrolysis of Amides

O O O
O O
H R R
N N N H2O H
N OH N
H H R'
 Amides are completely non-basic (c.f. amines)
because the lone pair is delocalised towards the carbonyl group and is not  Requires prolonged heating with aqueous acid or base.
available for bonding to H+ (6M HCl at 100 ºC for 12 h)

O O O  The chemical form of the products (carboxylic acid and
 amine) depends on the pH of the solution.
H H H
N N N
H H H O H3O+ O
NH4
NH2  OH
 Resonance forms = Normal line structures that do not accurately represent the
amide structure. These line structures differ only in the position of their -
electrons. We say these line structures are imaginary. O OH O
NH3
 Resonance hybrid = The true structure. Average of all resonance forms. NH2  O
38 40

Theme 6/7 - p10

 Remember inorganic chemistry Summary of CMY127 reactions
Alkynes
NH3(aq) + HCl(aq) NH4+(aq) + Cl-(aq)

NH4+(aq) + OH-(aq) NH3(aq) + H2O Alkylhalides Alkenes Alkanes

CH3COOH(aq) + OH-(aq) CH3COO-(aq) + H2O

Alcohols Esters
- -
CH3COO (aq) + HCl(aq) CH3COOH(aq) + Cl (aq)

 It is impossible to have NH3 or RCOO in an acidic Hemiacetals Aldehydes

solution Acetals Ketones
Carboxylic
 It is impossible to have NH4+ or RCOOH in a basic acids
solution
41
Amides 43

H H
Exercise Reaction Scheme
- Overview CMY127 X X X OH
halohydrin
alkane

H2
 Draw line structures of the products obtained after both acid 1,2-dihalide Cl2 H2
Br2 X2, H2O Pd/C Pd/C or PtO2
or PtO2

and base hydrolysis of the following amides. H X

OH- H H H2
Lindlar catalyst
HX
alkylhalide alkene alkyne

NH N H+/H2O
conc.
H2SO4

O
SOCl2
O O O R
or
SOCl2
orPBr3 HX OH
Na (or K)
O
PBr3
ester alkoxide
2o alcohol 3o alcohol Jones
1o alcohol no
reactio
H2O + H+ ROH, H+ n
or OH- Jones
NaBH4 PCC NaBH4 Jones or PCC

O
Jones H H+, ROH O O
O R R
OH O
orTollens
H+, H2O
carboxylic acid aldehyde ketone acetal

 How about hydrolysis of the corresponding esters? H+, H2O

R
O O
R
H+, ROH H
42 44
acetal

Theme 6/7 - p11

 The Full IUPAC nomenclature system Functional Groups and the Parent
Stereoisomerism Substituents Parent Unsaturation Functional group  Identify all the functional groups and choose the highest
priority group to give the suffix of the IUPAC name.
 Stereoisomerism: Indicates whether double bonds are cis/trans or  Use the unsaturation block to indicate alkenes, alkynes or
E/Z, and indicates stereocentres (R, S). alkanes.
 Substituents: Are groups coming off the main chain, including  The parent chain or ring must include as many functional
alkyl chains and other functional groups. Halides & ethers are groups as possible. The longest carbon chain or ring with all
always substituents the functional groups gives the parent name. For equal lengths
 Parent: Is the number of carbons in the main chain. choose to have as many side chains as possible .
 Avoid branched alkyl substituents near the ends of the parent chain.
 Unsaturation: Indentifies if there are any double or triple bonds.
 For rings, add “cyclo” to the start of the parent.
 Functional group: The most important functional group in the
molecule (see data sheet).
carbonyls > alcohols > thiols > amines > alkenes > alkynes > alkanes

45
47

Functional Groups in IUPAC names Naming substituents

Name Formula Suffix when When named as  All extra functional groups as well as ethers and halogens get
a principal FG a Substituent named as substituents.
Carboxylic acid RCO2H, -oic acid  Alkyl branches from the parent get named as substituents
Ester RCO2R’ -oate indicating the number of carbons and the shape of the branch.
Aldehyde RCHO -al  Use di, tri, and tetra to indicate if there are 2, 3 or 4 of the
Ketone RCOR’ -one same type of substituent.
Alcohol ROH -ol hydroxy  List the substituents in alphabetical order according to the
Thiol RSH -thiol sulfanyl name of the substituent.
Amine RNH2,RNHR’,RNR’2 -amine amino (NH2)
Alkene -ene
Alkyne -yne
Alkane -ane
Ether ROR alkoxy
Halide RX halo
46 48

Theme 6/7 - p12

 Exercises
Numbering
 Name the following compounds:
 After finding the parent and naming the substituents, SH Br
OH
choose the direction of numbering. Br OH OH
 If there is a functional group, numbering is easy: NH2
 number the chain from the end closest to the functional NH2
group OR
 number the ring with 1 at the C with the functional group, or
no 1 and 2 for the C’s of an alkene then proceed around the
ring to give the next functional group the smallest number.
 If there is no functional group revert to rules for
branched alkanes:

49 51

Exercises

 Draw structures for the following compounds:

 3-Chloro-2-isopropyl-1-butanethiol
 trans-2-sec-Butyl-6-methyl-1,4-heptadien-3-ol
 3-Methyl-2-cyclopentenol
 (E)-6-Bromo-5-heptene-3,4-diamine

50

Theme 6/7 - p13

Interpreting IUPAC names Example:

To read an IUPAC name, you need to recognise the components of IUPAC

nomenclature.

Functional
Stereochemistry Substituents Parent Saturation
Group
answer:
Read the name from the back: O CH3 H Br CH3 H
4
Br
3 5
1. The Functional Group (suffix) identifies the most important (principal) functional H C C C C C C C C H H 1
6
7 8
2
group in the molecule according to IUPAC naming priorities. 1 2
H
4
H
6
CH3 H
7 8
H O Line structure
Lewis structure
2. The saturation indicates if there are any alkene or alkyne functional groups in
the molecule in addition to the most important functional group. [an indicates
there is no additional unsaturation; en suggests and alkene and yn suggests an Table 1: Parent Chain length
alkyne, enyn suggests both.] # C’s 1 2 3 4 5 6 7 8 9 10
3. The parent gives the number of carbon atoms in the longest consecutive
sequence in the molecule (Table 1). Parent meth‐ eth‐ prop‐ but‐ pent‐ hex‐ hept‐ oct‐ non‐ dec‐
4. Substituents indicate all other branches or functional groups in the molecule.
Note that a functional group name will look different when it is a substituent Table 2: Lists of Functional groups and the IUPAC nomenclature system
compared to when it is the principal functional group e.g. alcohols (Table 2). Suffix as principal
Name Formula Prefix as substituent
5. Stereochemistry may be used to indicate three dimensional arrangements in the Functional Group
Carboxylic acid RCO2H ‐oic acid
molecule e.g. double bond geometry E and Z or stereochemistry R and S)
Ester RCO2R’ ‐oate
Aldehyde RCHO ‐al
Drawing the structure:
Ketone RCOR’ ‐one
1. Draw the parent chain Alcohol ROH ‐ol hydroxy
2. Find the number closest the principal functional group and draw the functional Thiol RSH ‐thiol sulfanyl
group on the correct carbon. (Note that for cycloalkanes, carboxylic acids and Amine RNH2,RNHR’,RNR’2 ‐amine amino (NH2)
Alkene ‐ene
aldehydes, no number is given for the principal functional group because it is Alkyne ‐yne
always on carbon number 1.) Alkane ‐ane
3. Draw the unsaturation starting on the given number and moving to the next Ether ROR alkoxy
Halide RX fluoro, chloro, bromo, iodo
higher number.
4. Draw any other functional groups at their correct positions.
Table 3: Names of special substitutents
5. If specified, test the stereochemistry as drawn and redraw if necessary (Theme 2
onwards).
6. Remember that di, tri, tetra are used to indicate more than one of the same
functional group or substituent. There should be sufficient numbers given to
indicate the position of every occurrence of the group.