Thushan Hettige

VCE Unit 3 Chemistry

AREA OF STUDY 2: ORGANIC CHEMICAL PATHWAYS

Principles:
Remember, organic chemistry is instinct after a while!
It is about opposite charges attracting!
STUDY DESIGN:
structure including molecular, structural and semi-structural formulae, and International Union
of Pure and Applied Chemistry (IUPAC) nomenclature of alkanes, alkenes, amines, haloalkanes,
alkanols (CnH2n+1OH), alkanoic acids (CnH2n+1COOH) and esters up to C10
common reactions of organic compounds including equations: addition reactions of alkenes (addition
of hydrogen halides and water limited to symmetrical alkenes), substitution reactions of alkanes
and primary haloalkanes, oxidation of primary alkanols, and esterification
chemical bonding:
primary, secondary and tertiary structures of proteins
the role of the tertiary structure of proteins in enzyme action
denaturing of proteins: effect of changes in pH and temperature on bonding
primary and secondary structure of DNA
organic reaction pathways including appropriate equations and reagents:
production of esters from alkenes
condensation reactions that produce lipids (limited to triglycerides)
condensation and polymerisation reactions that produce large biomolecules including
carbohydrates, proteins and DNA
production of biochemical fuels including the fermentation of sugars to produce ethanol
function of organic molecules in the design and synthesis of medicines including the production
of aspirin from salicylic acid.

A summarised version of AOS 2:

General Organic Chemistry
1.
2.
3.
4.
5.

IUPAC Organic Nomenclature

Isomerism
Reactions of Functional Groups
Organic Reaction Pathways (Roadmaps)
IR and NMR*

Biochemistry
6. Carbohydrates
7. Fats
8. Proteins; structure, function as enzymes, markers of disease
9. Nucleotides/DNA, use in forensics
10. Biochemical fuels
11. Medicines Aspirin Production
*IR and NMR analysis will also be in this section, because they coincide with organic
very well. In study design they are found in AOS 1.
HIGHLY RECOMMEND this website: www.chemguide.co.uk

Thushan Hettige
VCE Unit 3 Chemistry

1.

IUPAC ORGANIC NOMENCLATURE

IUPAC systematic nomenclature aims to allow organic chemists to determine the structure of
a molecule from its name and vice-versa. The systematic names of organic molecules may
seem long and daunting, but they are really parts of words shoved together into one long
word. They range from the simplest type of name methane to something ridiculously
complex, such as:
methyl (1R,2R,3S,5S)-3- (benzoyloxy)-8-methyl-8-azabicyclo[3.2.1] octane-2-carboxylate
also known as cocaine. Massive textbooks have been written that are dedicated to organic
nomenclature, but we only need to be able to name the simpler compounds in VCE.
Nomenclature for all non-ester molecules that will be tested by VCAA:
Note: in reality, the IUPAC nomenclature rules are insanely complex, but the below method
simplifies it (without making it wrong) to cover only the molecules in the scope of the VCE
Unit 3 course.
First, let us look at the general structure of a name:
[substituents]||||[main part of molecule] this can be divided further into:
{[substituent][substituent].}|||[number of carbons][double bond?][principal functional group]
Steps in writing the name of an organic compound:
1.

Identify the longest carbon chain which contains a principal functional group
and/or a C=C double bond.
This will give you the [number of carbons] part, which will be as per the following table
(which you do need to remember):
Number of C atoms in longest carbon
chain
1
2
3
4
5
6
7
8
9
10

2.

[number of carbons]
meth
eth
prop
but
pent
hex
hept (not sept)
oct
non
dec

Determine the presence of any principal functional groups.

Thushan Hettige
VCE Unit 3 Chemistry

This will give you the [principal functional group] part.

There can only be one principal functional group in the molecule. The possible principal
functional groups, in order from highest to lowest priority, are:
carboxy (COOH)
hydroxyl (OH)
amino (NH2)
This means that if there is, for instance, a carboxy and a hydroxyl group in the molecule,
the carboxy group will be the principal functional group, and the hydroxyl group will be
simply a substituent. If there are all three in the same molecule, both the hydroxyl and
amino groups will be substituents and the carboxy will be the principal functional group.
The [principal functional group] part will be as per the following table:
Principal functional group
carboxy
hydroxy
amino

[principal functional group]

oic acid
ol
amine

If there is no principal functional group in the molecule, omit the [principal functional
group] part.
3.

Number the carbons if necessary.

The carbon atoms must be numbered, so we can easily say to which carbon each of the
functional groups are bonded.
We are aiming to count in the direction in which we get the lowest number/sum of
numbers on the principal functional group.
If there is no principal functional group (or if the principal functional group position
cannot determine numbering direction), attempt to determine direction of numbering by
looking to get the lowest sum of numbers on the C=C double bond positions. If there
is neither a principal functional group nor a C=C double bond, determine direction of
numbering by looking to get the lowest sum of numbers on the substituents.

4.

Determine the presence of any C=C double bonds.

If there is a C=C double bond, then [double bond?] = en(e).
If there is no C=C double bond, then [double bond?] = an(e).
Determine the double bond position by taking the lower-numbered carbon in the double
bond (note that direction may already have been determined by the presence of any
principal functional groups).

5.

Determine the presence of any substituents.

Thushan Hettige
VCE Unit 3 Chemistry

Any functional groups or branches that have not been named yet are substituents.
Determine the carbon number to which each substituent is bonded too. Substituents go in
alphabetical order.
Each [substituent] will be as follows:
Substituent
methyl (CH3), ethyl (CH3CH2)
chloro (Cl), bromo (Br), iodo (I)
hydroxy (OH)
amino (NH2)

When numbering the carbon atom to which the substituent or principal functional group,
or the position of the double bond, write the number immediately before the [substituent]
or [principal functional] or [double bond] bit, separated by a hyphen.
o

eg. propan-1-ol. Note that whilst 1-propanol can be accepted, this is not the
systematic IUPAC name, and therefore writing it in the exam is a gamble.

If there are more than one of the same substituent or C=C double bond or principal
functional group, then write the number of carbon to which each of the same
substituent/PFG/DB is bonded, separated by a comma. Then, immediately preceding the
[substituent] or [principal functional] or [double bond] write -di if there are two of the
same, -tri if there are three, and -tetra if there are four.
o

[substituent]
methyl, ethyl
chloro, bromo, iodo
hydroxy
amino

eg. propane-1,2-diol

As a general rule, if youre writing a letter and a number next to each other, separate
them with a hyphen (eg. 1-chlorobutane) and if youre writing two numbers next to each
other, write a comma between them (eg. 1,1-dichlorobutane).

Worked examples:
(ATARnotes Unit 3 Study Guide, AOS 2 Test 1, Question 1)
Name the following molecules:
CH3CH2CH=CHCH3
CH2ClCH2CH(OH)CH(CH3)2
CH3CH(OH)COOH

Naming Esters:

Thushan Hettige
VCE Unit 3 Chemistry

The general name of the ester is as follows:

[number of carbons (1)]yl [number of carbons (2)]anoate

If we have a look at the general structure of an ester RCOOR (where R and R can be any
alkyl chain):

[number of carbons (1)] will refer to the number of carbons in the R section
[number of carbons (2)] will refer to the number of carbons in the RC section

Dont forget to include the carbonyl (C=O) carbon!

Worked Examples:
Name the following molecules:
CH3CH2COOCH2CH3
HCOOCH2CH2CH3

2.

ISOMERISM

Thushan Hettige
VCE Unit 3 Chemistry

Isomers have the same molecular formula yet a different structural formula (the atoms are
arranged differently.
Sometimes, you are asked to determine all the isomers with a particular molecular formula.
There is a systematic way to do this. Let us go through this way, using the example of
C3H5Cl.
1.

Determine the number of double bonds in the molecule using the molecular formula.
You could either do this intuitively, or use the following formula (the double bond
equivalent formula, which will give you the number of double bonds + rings).

2 + 1 1 + 3
2

where n(C) = number of carbons, n(1 bond) = number of atoms that form 1 bond (like H,
F, Cl, Br, I), n(3 bonds) = number of atoms that form 3 bonds (like N and P).
In this case, C3H5Cl has 1 double bond.
2.

Draw all the possible arrangements for all atoms that form more than one bond (eg. C, O,
N, etc) dont forget to factor in double bonds!
In this case of C3H5Cl, there is only one arrangement for these atoms (which are all
carbon atoms), that being the arrangement C=C-C.

3.

Using the skeletons you draw in step 2, draw all the possible arrangements of all atoms
that form single bonds apart from hydrogen.
In this case of C3H5Cl, the Cl atom can go on any of the three carbon atoms.

4.

Complete all the structures of the isomers by adding in all the hydrogen atoms.
So the isomers would be:
CHCl=CHCH3
CH2=CClCH3
CH2=CHCH2Cl

Worked Example: Draw and name all the isomers of C6H11Cl.

Thushan Hettige
VCE Unit 3 Chemistry

Worked Example: Draw all isomers of C3H6O2 that are not ethers (ROR) or peroxy
compounds (ROOR).

3.

REACTIONS OF COMMON FUNCTIONAL GROUPS

Thushan Hettige
VCE Unit 3 Chemistry

A. Alkanes
General formula = CnH2n+2
Alkanes are quite boring compounds, and they are relatively unreactive; they undergo few
reactions. The below reactions you will need for the VCE are:
Combustion: alkanes burn in oxygen to produce carbon dioxide and water
Substitution: alkane + Cl2 chloroalkane + HCl (UV catalyst needed)
Combustion:
Alkanes burn in excess oxygen to form carbon dioxide and water.
Eg. methane in water:
CH4 (g) + 2O2 (g) CO2 (g) +2H2O (g) [VCAA accepted H2O (l) in a past exam though]
Substitution:
Remembering alkanes are quite non-polar and unreactive, in order to force a functional group
into an alkane, we need something really unstable...Cl atoms (really really reactive, they have
only 7 electrons around the outer shell)
How to form Cl atoms though? Get a Cl2 molecule and stick in UV or heat!
Hence the reason why we need UV or heat when trying to chlorinate an alkane!
CH4 (g) + Cl2 (g) CH3Cl (g) + HCl (g) - stick in UV/heat on top of the arrow!
Now, if they ever ask you to write an equation of substitution (they shouldnt), then use the
states mentioned above; this reaction can also be done in organic phase (org), but its not in
the course.

B. Chloroalkanes

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VCE Unit 3 Chemistry

Chloroalkanes are more reactive, especially at the carbon that is bonded to the chlorine.
Chlorine is more electronegative, and pulls electron density away from the carbon atom,
giving the carbon atom a slight positive charge, making it more vulnerable to attack more
reactive.
The reaction (in the VCE course) that chloroalkanes undergo is:
Substitution: RCH2Cl + OH- RCH2OH + Cl- (no catalyst needed here)
Substitution:
Chloroalkanes are rather different in their nature of substitution in that it is a lot easier to
perform a substitution reaction on a chloroalkane than on an alkane. This is because:
chloroalkanes are more polar, and the carbon containing the Cl is partially positively
charged
hence OH-, being negatively charged, can attack the carbon more easily (this is also known
as backside attack)
Cl- is kicked off into solution, and its quite unreactive (the ION is unreactive, that is)
if we tried to kick off H- that is no good, that is quite reactive

Thushan Hettige
VCE Unit 3 Chemistry

C. Alkenes
Alkenes are a fair bit more reactive especially at their double bond. Two of the electrons in
that double bond actually reside above and below the molecule, so theyre exposed. This
makes the double bond quite vulnerable to attack by positive charge.
The reactions that alkenes undergo are:
Combustion: C2H4 (g) + 3O2 (g) 2CO2 (g) + 2H2O (l or g)
Addition of X2: RCH=CHR + X2 RCHXCHXR (where X is any halogen)
Addition of HX: RCH=CHR + HX RCHXCH2R or RCH2CH2XR
Addition of H2O: RCH=CHR + H2O RCH(OH)CH2R or RCH2CH(OH)R (H+needed!)
Addition of H2: RCH=CHR + H2 RCH2CH2R (Pt, Pd/C or Ni needed)
Combustion:
Alkenes undergo combustion as well (although they are more susceptible to incomplete
combustion, where carbon is produced).
Example:
C2H4 (g) + 3O2 (g) 2CO2 (g) + 2H2O (g)
Addition:
Chlorine
Alkenes are a lot more reactive than alkanes, and hence a hell of a lot more interesting than
alkanes! Think about the double bond as being a lot more reactive refer to the diagram
opposite. The location of the second pair of electrons in the C=C bond is above and below the
molecule...they are exposed and susceptible to attack.
Cl2 can add to alkenes; the Cl-Cl bond can be broken by the exposed electrons on the C=C
bond as shown in the figure opposite. HCl, being polar, is even more susceptible to this:
Addition of chlorine you can replace this with Br2 or I2 (I2 tends to react really really slowly
FYI)
H2C=CH2 + Cl2 CH2ClCH2Cl Note: NO UV needed here, the alkene is reactive enough
anyway!
Addition of HCl can replace with HBr or HI (although you need to make HI in situ mix
KI/H2SO4 dont need to know for VCE though)
H2C=CH2 + HCl CH3CH2Cl

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VCE Unit 3 Chemistry

Note that I didnt put in any states here; this is because you generally perform reactions
between alkenes and HX or X2 (where X is a halogen) in organic phase (so in a solvent like
say diethyl ether CH3CH2OCH2CH3). The reactions between ethene and chlorine or HCl can
all occur in gas phase though. Hopefully VCAA doesnt spring you a question about states in
these kinds of reactions.

Water
You can also add water to alkenes, but we have a problem. But the double bond has a big
electron cloud as shown on the right. So we need something with a nice positive charge to
catalyse the reaction, say...H+.
Hence:
H2C=CH2 (aq) + H2O (l) CH3CH2OH (aq) [H+ catalyst needed!]
Why the states? Well, I can confidently say that this reaction is in aqueous solution as water is
one of the reactants.
This reaction is called a hydration reaction (addition of water). Dont get confused with
hydrolysis which means the breaking up of a molecule using water as a reactant.

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VCE Unit 3 Chemistry

Hydrogen
Youd think that we could do the same with hydrogen as we could with chlorine, but
hydrogen is a very small molecule with the electrons very close to the nucleus. Its very
difficult to polarise the molecule to make one of the H atoms positively charged. Hence, a Pt
or Pd/C or Ni catalyst is needed.

D. Alcohols
Alcohols can undergo the following reactions:
Combustion in O2 to form CO2 and H2O.
Oxidation to carboxylic acid (primary alcohol only) by MnO4-/H+ or Cr2O72-/H+
Combustion
C2H5 OH (l) + 3O2 (g) 2CO2 (g) + 3H2O (g) is an example. The state of the alcohol at
room temperature can be found in the last page of the Data Book.
Oxidation
Oxidation is the loss of electrons. In organic chemistry, it simply means forcing oxygen or
ripping hydrogen from an organic compound which is still losses of electrons.
All primary alcohols are oxidised to the carboxylic acid. Common oxidising agents include:

Cr2O7 2-/H+ (aq) (acidified dichromate, nasty stuff)

MnO4 /H+(aq) (acidified permanganate, nasty stuff)

Oxygen gas (O2 (g)) does oxidise alcohols to carboxylic acids too, but we would not use it as
a laboratory oxidising agent as wed probably end up igniting the alcohol (combustion)
rather than turning it into a carboxylic acid. But if you expose alcohol to air for a while...it
does oxidise. Think about wine going sour ethanol into ethanoic acid (taste of vinegar??)

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VCE Unit 3 Chemistry

Why only primary alcohols?

The simple answer to this is because the carboxy functional group is always at carbon-1, and
therefore the hydroxy group (before the alcohol is oxidised) has to be at the same carbon
atom carbon-1. Only in primary alkanols is the hydroxy group in carbon-1.
E. Carboxylic acids
General formula: RCOOH.
The reactions that carboxylic acids can undergo (in the scope of the course) are:
Combustion
Acid-base reactions (as carboxylic acids are acids)
Esterification (by reactions with alcohols)
Combustion
Self-explanatory.
Acid-base reactions
As its name suggests, carboxylic acids are weakly acidic, and exhibit properties like any other
acid. They can oxidise metals (as an acid), they can undergo acid-base reactions, etc.
Esterification
Below is the general structure of an ester:

Now, esters can be formed from carboxylic acids reacting with alcohols.
Consider the structures of these two compounds:

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VCE Unit 3 Chemistry

It seems as though that the ester functional group looks similar to the carboxy functional
group so this is a good way to remember that esters are formed from a carboxylic acid
and an alcohol. A concentrated sulphuric acid (H2SO4 (l)) catalyst is needed.
Example reaction:
CH3OH (l) + CH3COOH (l) CH3COOCH3 (l) + H2O (l) [H2SO4 (l) catalyst]
Water is produced in this reaction; this is thus a condensation reaction.
F. Polymerisation
Addition Polymerisation
Addition polymerisation is the type in which none of the atoms in the organic compound
form a second product. In the scope of the VCE course, this happens with molecules with
C=C double bonds.
Examples:

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VCE Unit 3 Chemistry

Condensation Polymerisation
Here, water is a product of the reaction!
Think about condensation polymerisation as a series of condensation reactions repeated over
and over again to form a large molecule.
What condensation reactions do we know?
carboxylic acid + alcohol ester + water
carboxylic acid + amine amide + water [covered in biochem]
The nature of the monomers could be such that:
there is a carboxylic acid in one end and an alcohol in the other end
there is a carboxylic acid in one end and an amine in the other end (eg. amino acid)
you could have two monomers one being a diol (alcohols on both ends) or a
diamine (amines on both ends) and a dicarboxylic acid (carboxylic acids on both
ends)
Examples:

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VCE Unit 3 Chemistry

4.

ORGANIC ROADMAPS (REACTION PATHWAYS)

Synthetic organic chemists make many organic compounds from a limited range of organic
compounds. In VCE, we are going to do the same thing from a smaller scale, for example
synthesising ethyl ethanoate from ethane or ethene.
All you need to do is be able to instinctively deduce the reactions needed to form the complex
compounds from the simpler ones.
Worked Examples:
ethyl ethanoate from ethane

ethyl ethanoate from ethene

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VCE Unit 3 Chemistry

5.

ORGANIC ANALYSIS (IR/NMR/MS)

IR Spectroscopy

Mechanics: all you need to know about the mechanics of IR is that molecules vibrate
and stretch when they absorb IR radiation. Specific bonds stretch at specific
wavelengths. The energy (and therefore the wavenumber) is dependent on mass of the
atoms and the bond length.
Wavenumber is 1/wavelength wavelength in cm! Thats why units of wavenumber is
cm-1

Tips for analysing an IR spectrum:

Anything that is at 1500 cm-1 or under ignore. Hardly any useful information here,
except for identifying compounds like a fingerprint would identify a person.

Although you get a Data Book, it is useful to recognise some characteristic absorption
bands:
o ~1670-1750 cm-1 strong absorption here indicates presence of C=O, in the
scope of VCAA the compound could either be an ester or a carboxylic acid,
although they did put in a ketone in 2008!
Below is the IR spectrum of acetone, whose structure is below:
strong absorption band @ ~1700
cm-1 C=O

Structure:

(Wikipedia)

IR Spectrum (SDBS):

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VCE Unit 3 Chemistry

o ~2800-3000 cm-1 strong absorption here shows the presence of a C-H bond,
but it is generally always going to be there, although it COULD indicate an OH (acid) bond. The O-H (acid) bond tends to be fat and somewhat fused with
the C-H stretch.
Below is the IR spectrum (SDBS) of hexane (CH3(CH2)4CH3), which only
contains C-C
and C-H bonds:
strong, sharp absorption band @
~2900 cm-1 C-H

Compare this to the IR spectrum of ethanoic acid:

strong, sharp absorption band @
~2900 cm-1 C-H
Structure:

(Wikipedia)

IR Spectrum (SDBS):

strong, fat absorption band @ ~3000 cm-1 O-H

(acid) fused with the C-H stretch
O
O

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VCE Unit 3 Chemistry

o ~3000-3500 cm-1 strong and fat band here indicates O-H (alcohol). A
medium-strong and sharp, sometimes two-pronged band indicates the
presence of an NH2 group.
For example, consider the IR spectrum of ethanol; you may or may not have
had personal experiences with this particular chemical, pleasant or otherwise:

Structure (Wikipedia):
IR Spectrum (SDBS):
strong, fat absorption band @ ~3200 cm-1 O-H
(alcohol) distinct from the C-H stretch
strong, sharp absorption band @
O
~2900 cm-1 C-H
O

Now try pentan-1-amine:

medium-weak, sharp, (in this case two pronged)

absorption band @ ~3200 cm-1 N-H
O
O

IR spectrum (SDBS):

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VCE Unit 3 Chemistry

Here is one band that may come up in the exam hasnt yet a C=C bond that
absorbs around ~1600 cm-1, just to the right of a C=O stretch. It tends to be somewhat
sharper and weaker than the C=O stretch.
Consider the compound vinyl acetate, whose structure (SDBS) and IR spectrum
(SDBS) is shown below:

strong absorption band @ ~1750

cm-1 C=O
strong, but weaker and sharper
absorption band to the right of C=O @
~1600 cm-1 C=C

And perhaps even the compound pent-1-ene (you tell me where the C=C band is):

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VCE Unit 3 Chemistry

NMR Spectroscopy

Background Information

This information is simply to give you an understanding of the principles of NMR. You
do not need to know this information; I will italicise anything here that I think you need
to know.
Based on nuclei; we generally analyse 1H and 13C nuclei.
Mechanics:

NMR is based on spin of nuclei what exactly that means, I dont know, but just
think about it as a property of the nucleus. For now, think about the nuclei as arrows.
Normally, these arrows are pointing at random directions.

Stick in a strong magnetic field, and the arrows will all point in the one direction
with the field.

With this strong field, the arrows can be in one of two directions, with the field, and
against the field.

Stick in radio waves of a specific frequency (and hence a specific energy), say 300
MHz. Shoot them at the nuclei.

Radio waves can cause nuclei spin to flip if they have enough energy to break the
magnetic field. When spin flips, the radio waves are absorbed, and a peak is generated.

The stronger the magnetic field experienced by the nucleus, the more energy required
to force nucleus to flip.

Vary magnetic field, keep radio waves constant. A high magnetic field means radio
waves not enough to allow arrows to spin away from field. A low magnetic field
means radio waves are enough to make arrows spin away from field.

Ok, so what causes the variation in the required magnetic field to cause a flip? Well, just
because I throw say 300 units of magnetism on a nucleus doesnt mean the nucleus
experiences 300 units. Whats around the nucleus that stops it from experiencing the full 300
units? Electrons. They shield nuclei from the magnetic field. Hence, we can generalise:

the more exposed the nucleus is, the lower the magnetic field required to force the
nuclei arrows to spin towards the field.
nuclei that are next to more electronegative atoms are generally more exposed
because there is less electron density around them

In a molecule, different nuclei are surrounded by different things protons and electrons.
How do we describe this location of protons and electrons relative to the nucleus? We call it a
chemical environment. So nuclei in different chemical environments need different strength
magnetic fields to force them to flip with the field.

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VCE Unit 3 Chemistry

How can we tell whether two nuclei are in the same chemical environment? Protons are in the
same chemical environment if and ONLY if they are bonded to EXACTLY the same things
(not just locally, but considering the whole molecule).
Let us keep the frequency (and hence the energy) of the radio
waves constant and vary the magnetic field. Remember that an
exposed nucleus requires a lower magnetic field to allow it to
rebel. But how do we measure a scale for the magnetic
field? We need a reference point, otherwise how can we
perform measurements? We use TMS- tetramethylsilane.
Why? All the protons are in the same chemical environment,
bonded to same things, hence one peak. Silicon is LESS
electronegative than carbon (refer to structure below) hence the
1
H nuclei are most shielded as the electron density is closer to
carbons than towards silicon. Since nuclei are most shielded, it
requires a BIG magnetic field to force the nuclei to behave, to
turn towards field; in fact, few organic compounds have
environments that need a higher magnetic field for flipping.
Hence, we can designate the peak at TMS = 0.
Now, the units for the magnetic field are chemical shift measured in parts per million. A
peak at x ppm means that the magnetic field required to cause flipping of the nucleus is x
millionths less than that of the 1H nuclei of TMS. So, a higher chemical shift means a more
exposed nucleus in general.

Analysis of 1H NMR spectra

Things to look out for:

Number of peaks = number of chemical environments. This gives you an idea into
whether there is any symmetry in the molecule, say if there are more carbons than
environments.
Integration pattern: If available, look at the relative AREA under the peaks. This gives
you the relative number of hydrogen atoms in each particular environment.
Typical characteristics:
o a 3H peak (peak with an area of 3 units) often indicates
that the peak represents a CH3 (methyl) group

a 6H peak often indicates symmetry within the molecule,

or there is an isopropyl group as shown on the right:

a 9H peak indicates a tert-butyl group as shown on the

right:

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VCE Unit 3 Chemistry

Location of peaks: remember the principle that the more

exposed the nucleus is, the higher the chemical shift. In
particular, look for and recognise these points:
o
o

~ 1.0 ppm, generally indicates a CH3 or CH2 group. Check integration

and splitting for confirmation
~ 5 7 ppm, you may have a proton bonded to an alkenyl group (C=C)
Consider the structure of propene (CH2=CHCH3) and its NMR spectrum
(SDBS) ignore the scary-looking splitting; alkenes undergo pretty nastylooking splitting. Note the peaks at ~5-6 ppm.

~ 6.5-8.0 ppm, indicates aromatic protons, hydrogens around a benzene

ring. If you see peaks at 7-8 ppm, you have a benzene ring in the structure.
VCAA have not sprung benzene for analysis yet though, but maybe this
year...just keep that in the back of your head.
Consider p-aminobenzoic acid and its NMR spectrum (SDBS) (you do not
need to know how to name this!):

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VCE Unit 3 Chemistry

~810 ppm indicates the presence of a methanoate (or aldehyde out of the
course) (HCOOR or RCHO). Beware of the amide though (CONH) if
nitrogen is present in the compound.
Here is the NMR spectrum of ethyl methanoate:

~11-12 ppm indicates the presence of a carboxylic acid (COOH)

Consider the NMR spectrum (SDBS) of propanoic acid:

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VCE Unit 3 Chemistry

Splitting:
o
Individual peaks can be split into many different peaks. For VCE purposes,
we follow the n+1 rule. Multiplicity rule?
o
A peak is split into n+1 subpeaks, if the number of hydrogens on the
neighbouring carbons is equal to n.
o
Characteristic splitting patterns to look out for:
a quartet with a 2H integration (2 hydrogens in environment) at a
relatively low ppm CH2 CH3
a triplet with a 3H integration at a very low (1.0) ppm CH3 CH2
singlets at 1-6 ppm generally indicate OH or NH2 (check integration
trace)
singlets at 9-13 ppm indicate carboxylic acid (or 8-10 ppm for
methanoate)

Analysis of 13C NMR spectra

Things to look out for:
o

Number of peaks = number of chemical environments. This gives you an idea into
whether there is any symmetry in the molecule, say if there are more carbons than
environments.

Location of peaks: you do get a Data Book, but here is a little something that you
could remember to make your analysis very quick:

C-C ~0-50 ppm

C-O ~50-100 ppm
C=C ~100-150 ppm
C=O ~ 150+ ppm
This is not gospel; this is a generalisation. But its very useful.

Also, 13C NMR does not have splitting or integration traces.

Look at this example of a 13C NMR spectrum of an ester. Can you identify the bonds
corresponding to each peak?

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Mass Spectrometry
The mass spectrometer separates species based on their relative molecular mass by the
following process.

The sample (say ABC) is injected, and electrons bombard the sample to knock off
electrons to form ABC+.
o These ions can be unstable, and they split into fragment ions
eg. ABC+ AB++ C

The positively charged ions are accelerated through the chamber using an electric
potential.
The ions are deflected by a magnetic field
o smaller ions are deflected MORE than larger ions

The detector detects ions with particular m/z values (mass/charge, and generally
charge (z) = 1) by adjusting its position to only detect ions that go through one
particular path

The ion with the highest abundance produces a peak called the base peak and is
assigned a relative value of 100. All other abundances are measured relative to that
peak.

Information you can get out of a mass spectrum:

you can effectively only get the molar mass of the compound by looking at the peak
with the largest m/z; this represents the molecular ion, the ion that has not been
fragmented

you can get an idea on how many atoms are in the compound based on the number of
peaks; the more atoms there are, the more fragments, the more peaks.
o for an example, see the VCAA 2010 exam paper.

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Combining these techniques

A generic question involving all these techniques where you have to find the structural
formula of the compound could give you:

microanalytical data (percentage of C, H, O in compound)

IR spectrum
NMR (C or H)
mass spectrum

To tackle this type of problem:

microanalytical data (percentage of C, H, O in compound)

o work out empirical formula

mass spectrum
o work out molecular formula

Work out the number of double bonds in the molecule (you can use the DBE
formula) this is extremely useful

IR

NMR

o look for possible functional groups (C=O), OH, NH2, look at DBEs!
o look for possible functional groups (through singlets => OH or NH2)
o look for location of the different groups in the molecule by looking at splitting,
integration, and location of peaks

In summary, its a logic puzzle!!

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Worked Example:
(ATARnotes Chemistry Unit 3 Study Guide, AOS 2 Test 4, Question 3 modified)
A compound with empirical formula CH2O and molar mass 60 g/mol has the following highresolution 1H NMR and IR spectra (SDBS):

Determine the structure of the molecule.

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6.

BIOCHEMISTRY (CARBIOHYDRATES)

There is no Biochemistry, just Chemistry Trent Wallis

Biochemistry is just APPLIED chemistry. The principles of chemistry are still there.
Carbo + hydrates = carbon + water. Hence the empirical formula CH2O (applies to
monosaccharides only!)
Carbohydrates are composed of rings of carbon (with an oxygen present in the ring too), and
serve a variety of functions, including:

source of energy (via cellular respiration) and energy storage

structural (cellulose)
receptors on cells!

Carbohydrates can be further classified into:

mono|saccharides one ring (eg. glucose, fructose, galactose)

di|saccharides two rings (eg. sucrose [glucose+fructose], maltose [glucose+glucose])
poly|saccharides many rings (eg. starch, glycogen, cellulose)

Examples:
glucose

fructose

sucrose

Note: Youre given the structure of sucrose on the Data Book. Should you have to use the
structure of glucose or fructose, derive it from sucrose!
Polysaccharides are polymers; treat these polymers like you would any other polymer.
However, the difference lies in the type of reaction. As many esterification reactions form a
polyester, many substitution reactions between hydroxyl groups of glucose molecules can
form a polysaccharide. The O- link between sugar rings is called a glycosidic or ether
linkage. The polymerisation reaction is a condensation reaction, so water is lost.

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7.

LIPIDS

Lipids are biomolecules that are characteristically insoluble in water. Examples include:\

fats (solid at room temperature)

oils (liquid at room temperature)
waxes, steroids

The fats and oils are all triglycerides, which are composed of three fatty acid molecules
and glycerol. Fatty acid molecules are essentially really long chain carboxylic acid
molecules, and can have C=C double bonds. The structure of glycerol and the fatty acid is
shown below:

To form the triglyceride, each fatty acid reacts with one of the hydroxyl groups on the
glycerol. This is just another example of an esterification reaction; a carboxylic acid
(COOH) reacting with a hydroxyl group (OH) to form an ester and water! This is again a
condensation reaction.
Triglycerides can be saturated, monounsaturated or polyunsaturated.

saturated no C=C double bonds

monounsaturated one C=C double bond
polyunsaturated two or more C=C double bonds

You may be asked to determine how many C=C double bonds there are in a fatty acid
molecule. There are two possible ways:
1. Consider the saturated fatty acid formula: CnH2n+1COOH. For every C=C double
bond you have, you take away 2 Hs.
eg. C17H33COOH C17H35COOH is saturated, and we take away 2 Hs. Hence we
have 1 C=C double bond.
2. Use the DBE formula (in Organic Analysis section) to get the number of double
bonds. Careful! There is also a C=O double bond in a fatty acid.
eg. C17H33COOH C18H34O2 (molecular formula). DBE = (38-34)/2 = 2. There is a
C=O double bond, hence there is one C=C double bond.
In digestion, the triglycerides are split into glycerol and fatty acid molecules. Whats the
reaction? Remember, the rules of chemistry dont change. This is simply applied
chemistry.

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8.

PROTEINS

Amino acids
Before we look at proteins, we should examine its monomer, the amino acid.
Below is the general structure of an amino acid. If you forget the general structure, you can
look inside the Data Book at the different amino acids to jog your memory.

Each amino acid has a different Z group. All amino acids (of those listed in your Data Book)
are 2-amino acids or -amino acids as the amino group is connected to carbon 2. A carbon
adjacent to a C=O group is known as an -carbon.
So, proteins have an amino group and a carboxyl group. The amino group is a base and the
carboxylic acid group is...well...an acid. Stick an amino acid into water, and youll most likely
get this species being dominant on the diagram below:

These species are known as zwitterions. Zwitterions have a positive and negative charge at
different parts of the molecule, but the net charge is zero.
Now, add some HCl (aq) into this amino acid solution. We are now effectively forcing H+
onto the COO- groups, and we get the species below:

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Now, add an excess of NaOH (aq) into the amino acid solution. The OH- ion is a very strong
base; it likes ripping off protons. So it rips protons off the NH3+ group and the COOH
group, and you get the species below:

The fact that when you stick H+ or OH- into a solution and lots of it reacts with the amino acid
molecules means that amino acid solutions are excellent buffers. Buffers are solutions that
keep pH relatively constant. When you stick in lots of H+ or OH- only some stays in solution;
the rest is neutralised by the amino acid molecules, so pH does not change much.
Also, just a note: the Z group could itself be acidic or basic; and this could affect its acid-base
properties. However, the principles dont change.
Proteins
A carboxylic acid functional group can react with an amino functional group to form an
amide, as shown below.

The carboxylic acid functional group of one amino acid can react with the amino functional
group of another to form an amide linkage. Does this scenario look familiar? Polymerisation
can occur here too! Here is another example of how biochemistry is just chemistry.
Individual amino acids polymerise to form polypeptides. Large polypeptides are called
proteins. Also, only when the amide linkage is between two amino acids do we refer to it
instead as a peptide linkage. All peptide linkages are amides, but not all amides are
peptides.

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Proteins have four levels of structure:

Primary Structure:
o Type of bonding: Covalent (peptide linkages)
o This is the specific sequence of amino acids bonded by peptide linkages.

Secondary Structure:
o Type of bonding: Hydrogen bonding (between the C=O of one peptide linkage
and the NH group of another peptide linkage)
o This localised bonding causes the formation of:
alpha-helices
beta-pleated sheets (careful not to say beta sheets, this lost you a mark
in the 2009 VCAA biology exam)
random coils

Tertiary Structure
o Type of bonding: hydrogen bonding, ionic interactions, covalent interactions
(disulfide bridge) and dispersion forces
The disulfide bridge occurs between the Z groups of cysteine (Z group
= CH2-SH). With the bridge it is Cys-CH2-S-S-CH2-Cys [for the
purposes of this example only Cys refers to the cysteine molecule
minus the Z group]
o The interactions of the Z groups are responsible for this type of bonding. The
tertiary structure of a protein is its 3-D shape.

Quaternary Structure
o The bonding between multiple polypeptide chains to form an overall protein;
proteins can be made from one or more individual polypeptides
This is for interests sake only. Quaternary structure is NOT on the
course.

Proteins as Enzymes
Enzymes are protein molecules that catalyse biological reactions. The site of reaction is called
the active site.
Typical characteristics of enzymes relative to inorganic catalysts:

produce much faster reaction rates

operate at body temperature
catalyse ONE type of reaction
o enzymes are highly specific; for instance catalase catalyses the decomposition
of hydrogen peroxide and that reaction only
are sensitive to temperature and pH
o well expand on this dot point in the sensitivity section

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Mechanism:

The substrate (reactant/s) enters the active site of the enzyme.

The Z-groups of the enzyme form intermolecular bonds with the
substrate/s, optimising them for reaction (for example by
weakening bonds within substrate)
o eg. ion-dipoles, hydrogen bonds, ionic interactions...

Sensitivity:
The active site MUST have a specific shape, complementary to that of the substrate. What
determines this shape? Hydrogen bonds, covalent bonds (disulfide linkages) and ionic
interactions between Z groups. If we disturb these interactions, then the enzyme molecule
would change its shape. How do we disturb these interactions?
Its easy to break hydrogen bonds heat. Note that cold temperatures would simply slow
down the function of enzymes because of slower molecular motion, but they would not
destroy the enzymes function (generally). Heating the enzyme, then cooling it again...doesnt
work.
Its also easy to disturb ionic interactions pH (because we can protonate the COO- or
deprotonate the NH3+).

When the biological activity of the protein is changed as a result of its change in structure
(again, the structure function link) it is denatured and its function is lost. What can happen
then is that the protein can adopt a random shape and form bonds with other random protein
molecules, so we get this clumping called coagulation.

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9.

DNA

DNA (deoxyribonucleic acid) is well known, and its functions are:

codes for our genes that make protein

DNA is a polymer, and we are going to examine its monomer, the nucleotide.
Nucleotides
The general structure of a nucleotide is below.

The nitrogenous bases on DNA are adenine, thymine, cytosine and guanine. The two-ringed
bases are called purines (if it helps to remember, purine, pure, awesome, big, two-rings) and
the one-ringed bases are called pyrimidines. Which is which? Check your data book.
Below we have a condensation reaction (why condensation?) in which the base, deoxyribose
and the phosphate react to form the nucleotide.

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DNA as a polymer
Each nucleotide reacts with the next via condensation reactions to form the DNA polymer, as
shown below. The encircled group is called a

DNA is directional; at one end there is a free phosphate group, and at the other there is a free
OH group. How do we describe these ends? Well, first consider the numbering of the
carbons in the ribose:
We can see that the free OH group is bonded to the 3 carbon, hence this end is called the 3
end. The free phosphate group is bonded to the 5 carbon, so this end is known as the 5 end.
However, DNA is generally double-stranded. What does this structure look like and how is it
held? Hydrogen bonding. Also, we find that in DNA the base adenine is always directly
opposite thymine, and cytosine with guanine (A-T, G-C). This is known as complementary
base pairing.
There are three hydrogen bonds between C and G, but only two between A and T. The
hydrogen bonding between A and T is weaker.
Also, the DNA strands are antiparallel, as the following diagram shows.

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10. BIOCHEMICAL FUELS

biochemical fuel: a fuel derived from living plant material
We need to know about three biochemical fuels: ethanol, biodiesel and biogas.
Advantages of biofuels: carbon neutral, renewable.
Ethanol
How do we make ethanol in making wine? Throw yeast into grape juice. Ethanol can
combust too. Why not throw it into our petrol tank?
We can obtain the glucose from sugar cane, and ferment it:
C6H12O6 (aq) 2CH3CH2OH (aq) + 2CO2 (g)
The ethanol is isolated via evaporation and dehydration to get rid of the water. We also add
up to 5% petrol, otherwise people would drink the alcohol, and there are issues there.
Biodiesel
Biodiesel is a mixture of esters. The synthesis works like this:
1. We start with triglycerides (oils, vegetable oils). We need to break the glycerol off.
Hence, we need to break the ester linkages. Something that is good at attacking the
C=O carbon is CH3O- (methoxide, an extremely strong base). How do we form this?
We mix CH3OH with solid KOH (so we have KOH dissolved in methanol).

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2. The CH3O- will attack the C=O carbons, and bond with the fatty acid parts to form
biodiesel. In doing so, glycerol is displaced. This biodiesel can be added to regular
diesel. It is also biodegradable.

Biogas
Biogas is a mixture of carbon dioxide and methane in equal proportions. It is derived from
decay of organic material.
11. ORGANIC CHEMISTRY IN MEDICINE
The principles of organic chemistry and biochemistry have been used to extract or synthesise
drugs and medicines. In this unit we need to know about the synthesis of aspirin from salicylic
acid, and the principle of the drugs inhibiting the functions of the relevant proteins.
Aspirin acetylsalicylic acid
Here is the reaction:

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VCE Unit 3 Chemistry

What kind of reaction is this? Esterification, condensation.

Chemistry of salicylic acid:

It is weakly acidic (but stronger than most weak acids) because of the COOH group
and the Ph-OH group phenols are weak acids too.
It is bitter and causes stomach bleeding.
Not particularly soluble in water.

Chemistry of acetylsalicylic acid:

It is weakly acidic because of the COOH group and weaker than salicylic acid
It is tasteless and causes no stomach bleeding.
It is not very soluble in water, hence we convert it to sodium acetylsalicylate
o Why is sodium acetylsalicylate more soluble?
But salicylic acid is the actual thing we need in our blood. So what happens? In
intestines, in high pH, what happens?
o Hydrolysis of aspirin:

I think thats all we need to know about aspirin.

A final note: the drugs we make often target proteins and react with them, often disabling their
function as their structure changes. Remember that a proteins structure dictates its function.
12. AFTERWORD
Remember to try and learn the PRINCIPLES of what we learnt. Understanding and problem
solving is what they are looking for!
Good luck for the Unit 3 exam!

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