Chem@HC

Secondary 4 Chemistry Olympiad

Name: ______________________ Class: Sec 4_____ Date: ________

Organic Chemistry Fundamentals

Types of Organic Formulae

We can choose to express the structures of organic compounds in one of several ways.

Empirical formula

 Simplest formula that shows the ratio of each kind of atom in a molecule

Molecular formula

 Shows the actual number of each kind of atom in a molecule

Full structural formula / Displayed formula

 Shows all the bonds and relative placing of all the atoms in a molecule.
 Common omission: students often forget to display the O–H bond.
 Exception: for ring structures (including benzene rings), all C and H atoms on the ring
are omitted.

Condensed structural formula

 Shows the arrangement of atoms in an unambiguous manner, without showing all the
bonds.

Skeletal formula

 Simplified representation of an organic formula, often used for larger and more
complicated molecules.
 C atoms and H atoms bonded to C atoms are omitted.
 Carbon chains are drawn in zig-zag lines, with each kink representing a C atom.
 Easy and quick to draw, yet unambiguously describes the organic molecule.
 This is what chemists use and you should learn to use it!

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The table below illustrates the various representations of two different organic compounds.

Hexane-1,6-diol Phenol
Empirical formula C3H7O C6H6O
Molecular formula C6H14O2 C6H6O
Displayed formula

HOCH2CH2CH2CH2CH2CH2OH
Condensed
or
structural formula or C6H5OH
HO(CH2 )6 OH

Skeletal formula

Table 1. Various representations of hexane-1,6-diol and phenol.

Structures of Organic Compounds

In organic chemistry, the simplest compound is the unbranched alkane, a single chain of
hydrocarbon connected by C-C single bonds. The name of the alkane depends on the
number of carbon atoms present in the chain. You should know the names by heart!

Number of carbon
Formula Name
atoms in alkane
1 CH4 Methane
2 CH3 CH3 Ethane
3 CH3CH2CH3 Propane
4 CH3 (CH2 )2 CH3 Butane
5 CH3 (CH2 )3 CH3 Pentane
6 CH3 (CH2 )4CH3 Hexane
7 CH3 (CH2 )5 CH3 Heptane
8 CH3 (CH2 )6 CH3 Octane
9 CH3 (CH2 )7 CH3 Nonane
10 CH3 (CH2 )8 CH3 Decane
Table 2. Names of the first ten straight-chain alkanes.

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Apart from straight chains, the hydrocarbon framework can also form branches. The types of
branching are shown below. We call a carbon atom that is bonded to only one other carbon
atom a primary carbon, a carbon atom that is bonded to two other carbon atoms a
secondary carbon, and one that is bonded to three other carbon atoms a tertiary carbon.

Hydrocarbons do not always have to contain C―C single bonds. Some chains and branches
may contain one or more C=C double bonds among the single bonds. Such a compound is
called alkene. Likewise, a hydrocarbon chain that contains a CC triple bond is called an
alkyne. A saturated organic compound contains only single bonds, while unsaturated ones
contain double or triple bonds.

Sometimes, you may see chemists using the letter ‘R’ in an organic structure. One way to
interpret ‘R’ is the rest of the molecule. For instance, we have used ‘R’ to represent an
unknown amino acid. When R  H, the amino acid is glycine; when R  CH3 , the amino acid
is alanine. When there are multiple different R groups, we use R1, R2 and so on (instead of
R2 as the latter means 2 same R groups).

Apart from straight and branched chains, organic compounds can also form rings. Below is a
list of common saturated organic ring structures.

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One of the most famous organic rings, however, is not saturated at all. Benzene is in fact
aromatic in nature (as opposed to aliphatic or alicyclic). All three double bonds are
conjugated in a circle giving rise to its aromatic properties (which we will not dwell into here).

Question 1:

Draw the following using (i) displayed formula and (ii) skeletal formula.

(a) CH2=CHCH3
(b) CH3CH2CH(CH3 )CH2OH
(c) C6H5NH2
(d) ClCH2C(CH3 )3

Question 2:

Convert the following structures into skeletal formulas.

Functional Groups

Thus far, we have covered the different types of hydrocarbon structures, which determine
the overall shape of the molecule. However, what is more interesting is the functional
group, which determines its reactivity. One of the main aims of learning organic chemistry is
to understand how each of the functional groups reacts. There are too many functional
groups in organic chemistry to list out here and each has its own unique set of reactions
which will be covered in subsequent lessons on organic chemistry. For starters, you should
familiarize yourself with some of the more common functional groups and learn to recognise
them.

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 General structural
Functional group Example Name of example
formula

Alkene pent-1-ene

Alkyne hex-2-yne

Alcohol butan-1-ol

Alkyl halide 1-bromobutane

(X  Cl, Br, I)

Ether 1-methoxypropane

Amine propan-1-amine

Aldehyde butanal

Ketone hexan-3-one

Carboxylic acid butanoic acid

Ester methyl butanoate

Amide butanamide

Arene ethylbenzene

Aryl halide bromobenzene

Phenol 2-bromophenol

Table 3. Common functional groups.

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Question 3:

Identify all the functional groups in the following molecules.

IUPAC Nomenclature

In general, there are two ways of naming organic compounds. Trivial names or common
names are what scientists and most people use in everyday scientific conversations. They
are short, easy to pronounce and used for well-known, frequently referred-to compounds.

However, with over 40 million known organic compounds, it is impossible to give trivial
names to all of them. For this reason, the International Union of Pure and Applied Chemistry
(IUPAC) have developed systematic nomenclature, a set of rules that allows any
compound to be given a unique name that can be deduced directly from its chemical
structure. Conversely, a chemical structure can be deduced from its systematic name. We
refer to this as the IUPAC nomenclature. Although the IUPAC name can be quite
challenging to pronounce for complicated molecules (sometimes it is even impossible to
name!), but it is still used for many small and medium compounds without a trivial name. The
usefulness of the IUPAC nomenclature is that it allows chemists to draw out the structure
from the name or vice versa – a skill which you should master.

We do not have enough time to go through all the rules for the IUPAC nomenclature, neither
is there a necessity to do so. Nonetheless, we will introduce a few basic principles which you
should know.

Systematic names can be divided into three parts: one describes the hydrocarbon
framework, one describes the functional groups, and one indicates the positions of the
functional groups on the skeleton.

After identifying the principal carbon chain or ring, the name of a functional group can be
added to the name of a hydrocarbon framework either as a suffix or as a prefix. Some
examples follow.

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Sometimes a number can be included in the name to indicate which carbon atom the
functional group is attached to. None of the above needed a number—check that you can
see why not for each one. When numbers are used, the carbon atoms are counted from one
end. In most cases, either of two numbers could be used (depending on which end you
count from); the one chosen is always the lower of the two. Again, some examples will
illustrate this point. Notice again that some functional groups are named by prefixes, some
by suffixes, and that the number always goes directly before the functional group name.

One carbon atom can have as many as four functional groups: this limit is reached with
tetrabromomethane, CBr4 . Here are some other examples of compounds with more than one
functional group.

Again, the numbers indicate how far the functional groups are from the end of the carbon
chain. Counting must always be from the same end for each functional group. Notice how
we use di-, tri-, and tetra- if there is more than one of the same functional group.

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With cyclic compounds, there is no end to the chain, but we can use numbers to show the
distance between the two groups—start from the carbon atom carrying one of the functional
groups, then count round. These rules work for hydrocarbon frameworks that are chains or
rings, but many skeletons are branched. We can name these by treating the branch as
though it were a functional group.

Question 4:

Draw skeletal structures for the compounds with the following IUPAC systematic names.

(a) 2-aminopropanoic acid

(b) 5-bromohex-1-ene
(c) 2,3-dihydroxypropanal
(d) 4-methylpent-2-yne
(e) 2,4,4-trimethylpent-1-ene
(f) ethyl 3-oxobutanoate

Question 5:

Provide the IUPAC systematic names for the following compounds.

(a) CH3CH(OH)CH2CH(CH3 )2
(b) CH3 CO2CH2CH2CH3

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Isomerism

Isomers are compounds that have the same molecular formula but different structures.

In organic chemistry, there are two main types of isomerism:

(i) Structural isomerism: atoms are linked together in different ways.

(ii) Stereoisomerism: atoms have the same connectivity but different spatial
arrangements.

These general classes can be sub-divided into different categories which describe more
precisely the various isomers.

Isomerism

Structural
(constitutional) Stereoisomerism
isomerism

Chain Cis-trans
isomerism isomerism

Positional
Enantiomerism
isomerism

Functional
group
isomerism

Structural Isomerism

There are three types of structural (constitutional) isomerism.

Chain Isomerism

Chain isomers are molecules with the same molecular formula and same functional group,
but different carbon skeleton. Chain isomers have similar chemical properties but different
physical properties.

hexane 3-methylpentane

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Positional Isomerism

Positional isomers are molecules with the same molecular formula, same functional group
and same carbon chain, but differ in the position of that functional group.

Functional Group Isomerism

Functional group isomers are molecules that have the same molecular formula but different
functional groups. For instance, these two isomers both have the molecular formula C 4H10O
but different functional groups.

Note that these three types of structural isomerism are merely guidelines to help you draw
out possible isomers given a particular molecular formula. When it comes to finding all the
possible isomers, the only sure method is to draw everything out systematically, changing
one thing at a time.

Question 6:

Draw the skeletal structures of all possible structural isomers for the following:

(a) C5H11Br
(b) C4H8Cl2
(c) C6H14
(d) C3H6O

Cis-trans Isomerism

Cis-trans isomerism occurs because of restricted rotation about double bonds or in ring
systems.

All double bonds, by virtue of their π bond, confer rigidity to a molecule by restricting rotation
about the double bond itself. The C=C bond cannot undergo free rotation because the π
bond would have to be broken which would require too much energy. This is in contrast to
the C―C single bond in alkanes around which free rotation is possible.

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Figure 1. Restricted rotation about alkenes. Figure taken from Organic Chemistry (2e) by Clayden, Greeves and
Warren.

Figure 2. Free rotation about alkanes. Figure taken from Organic Chemistry (2e) by Clayden, Greeves and
Warren.

As a result, cis-trans isomers are unable to interconvert to each other under normal
conditions and remain distinct from each other.

Cis-trans isomerism also occurs in ring systems because rotation around single bonds in a
ring is prevented by the linkages in the ring.

Not all double bonds have cis-trans isomerism. For cis-trans isomerism to exist, the two
groups on each C of the double bond must not be identical.

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The word cis is used to describe substituents on the same side whereas trans is used to
describe substituents on opposite sides. Note that the cis-trans convention is ambiguous
with tetrasubstituted alkenes. In this case, the E/Z convention is used, which we will not go
into detail here.

Cis-trans isomers generally have similar chemical reactivity but different physical properties
(e.g. melting point, boiling point).

Question 7:

Draw all possible isomers (including cis-trans isomers) for C5H10.

Enantiomerism

Enantiomerism occurs when a molecule is not superimposable on its mirror image. 2-

hydroxypropanoic acid (also known as lactic acid) shown below is an example of
enantiomerism. Since 2-hydroxypropanoic acid displays enantiomerism, we call it a chiral
molecule. Conversely, a molecule that is superimposable on its mirror image (such as
methane) is termed an achiral molecule. We call the two non-superimposable mirror images
of 2-hydroxypropanoic acid enantiomers.

A point to note on stereochemical projections: the bold wedge bond ( ) comes out in front
of the plane of paper while the dashed bond ( ) goes behind the plane of paper.

NOTE: This topic of enantiomerism requires good three-dimensional visualisation. You

should aim to be able to rotate the three-dimensional molecules in your head to compare
whether they superimposable. However, this takes practice for some of you. If you
encounter difficulties in the beginning, you may use some online software or molecular
modelling kits to help you. You may try this link:
http://www.chemtube3d.com/Main%20Page.html.

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The most common organic compounds that display enantiomerism, and the ones we are
most concerned with, are those that contain a chiral carbon (or stereogenic carbon). A
chiral carbon is any carbon atom with 4 different substituents. This carbon atom is also
known as a chiral centre (or stereogenic centre). For instance, 2-hydroxypropanoic acid
has one chiral carbon marked with an asterisk (*) that has 4 different substituents (―H,
―OH, ―CH3 and ―CO2H). Other examples of chiral carbons are shown below. In skeletal
structures, it is important to remember the ‘hidden’ hydrogen atoms when searching for
chiral carbons.

Due to the presence of a chiral carbon, the above molecules are non-superimposable with
their mirror image and hence are chiral. However, it is important to note that the presence
of chiral carbons is not a definitive indicator of chirality. The following guidelines serve
as a good rule of thumb:

1. If a molecule only has only one chiral carbon, then the molecule is definitely chiral.
2. If a molecule has multiple chiral carbons but contains a plane of symmetry, then it is
achiral.

A molecule has a plane of symmetry if we can draw a plane which divides the molecule into
two symmetrical halves.

Figure 3. Molecules with planes of symmetry. Figure taken from Organic Chemistry (2e) by Clayden, Greeves
and Warren.

To better understand why having chiral carbons do not necessarily imply a chiral molecule,
consider 2,3-dihydroxybutanedioic acid, with isomers A, B, and C. Compounds A, B and C
all have two chiral carbons each. You can check that compounds A and B are non-
superimposable mirror images of each other. As such, they are both chiral, and are in fact a
pair of enantiomers. Compound C looks very similar but it possesses a plane of symmetry
and is achiral. In fact, we call compound C a meso compound. Meso compounds are
molecules which have chiral carbons but are not chiral themselves.

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To describe the relationship between compounds A, B and C, we call A and B enantiomers
because they are non-superimposable mirror images of one another. We call C a
diastereoisomer of A and B (and vice versa). Diastereoisomers are simply stereoisomers
which are not mirror images. Note that cis-trans isomers are also diastereoisomers.

To calculate the total number of stereoisomers in a compound, you can use the formula
below, where n is the sum of the number of chiral carbons and C=C double bonds where cis-
trans isomerism is present. However, this formula only gives a maximum due to the
possibility of meso compounds and other exceptions.
n
Maximum number of stereoisomers  2

Question 8:

Identify the chiral carbons in the following compounds using an asterisk (*).

Question 9:

Draw all possible stereoisomers for the compound below. Which of these are chiral/achiral?
Which of these are enantiomers? Which of these are diastereoisomers?

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Optical Activity

An enantiomerically pure solution contains only one enantiomer. If you shine plane-
polarised light through an enantiomerically pure solution of (+)-2-hydroxypropanoic acid, the
light rotates clockwise. If you shine the same light through another solution containing the
other enantiomer (-)-2-hydroxyropanoic acid, the light rotates anticlockwise.

CH3 CH3

C C H
H CO2H HO2C
HO OH

(+)-2-hydroxypropanoic acid (-)-2-hydroxypropanoic acid

At this point in time, you may ask: what is plane-polarised light? A beam of ordinary light
consists of electromagnetic waves that oscillate in an infinite number of planes at right
angles to the direction of light travel. When a beam of ordinary light passes through a device
called a polariser, however, only the light waves oscillating in a single plane pass through
and the light is said to be plane-polarised. Light waves in all other planes are blocked out.

Not all organic compounds are able to rotate plane-polarised light. Only chiral compounds
can do so and hence they are said to be optically active.

The angle of rotation can be measured with an instrument called a polarimeter, represented
by the schematic below. A solution of optically active organic molecules is placed in a
sample tube, plane-polarised light is passed through the tube, and rotation of the polarisation
plane occurs. The light then goes through a second polariser called the analyser. By rotating
the analyser until the light passes through it, we can find the new plane of polarisation and
can tell to what extent rotation has occurred.

Figure 4. Rotation of plane-polarised light by an optically active sample. Figure taken from Organic Chemistry
(8e) by McMurry.

In addition to determining the extent of rotation, we can also find the direction. From the
vantage point of the observer looking directly at the analyser, some optically active
molecules rotate polarised light to the left (anticlockwise) and are said to be levorotatory,
whereas others rotate polarised light to the right (clockwise) and are said to be
dextrorotatory. By convention, rotation to the left is given a minus sign (-) and rotation to
the right is given a plus sign (+).
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The extent of rotation observed in a polarimetry experiment depends on the species of
organic compound, its concentration, and the extent to which it is enantiomerically pure. If a
sample of (+) enantiomer is contaminated with more of the (-) enantiomer, than the angle of
rotation will be lower. When you have equal amounts of the (+) and (-) enantiomers in the
solution, you get a racemic mixture or a racemate. Racemic mixtures do not rotate plane-
polarised light and are hence optically inactive. Do not confuse chirality with enantiomerically
pure and racemic. Both an enantiomerically pure solution and a racemic mixture must
contain chiral compounds.

Physical & Chemical Properties of Enantiomers

To end off the topic of enantiomers, let us take some time to find out why it is important to
distinguish between enantiomers.

Enantiomers have identical physical properties (e.g. melting point, boiling point) except for
the rotation of plane-polarised light.

Enantiomers have identical chemical properties except for when they interact with other
chiral molecules. This has immense biological significance because our bodies are chiral
environments. The amino acids and sugars in our bodies are chiral and produced
enantiomerically pure.

For instance, the two compounds between are

enantiomers of carvone. (-)-carvone smells of mint
while (+)-carvone smells of caraway seeds. This is
because our smell receptors form a chiral
environment for carvone to bind to.

Enantiomerism can have far worse consequences. In the 1960s, thalidomide was sold as a
sedative for pregnant women suffering from morning
sickness. Thousands of pregnant women took the
drug to relieve their symptoms. Although (+)-
thalidomide was effective against morning sickness,
its enantiomer (-)-thalidomide was found to be
teratogenic and caused birth defects. When this was
discovered, it was already too late and many babies
across Europe were born with missing, extra or
deformed limbs.

O O O O
NH NH
N O N O

O O
(+)-thalidomide (-)-thalidomide
effective against morning sickness teratogen

In contrast, diastereoisomers have different physical and chemical properties.

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Summary

You have encountered quite a few new terminologies in this topic of enantiomerism. It is
important for you to be able to understand, differentiate between and use these terms
accurately.

To describe individual Chiral carbon/ A carbon atom that is bonded to four

atoms stereogenic carbon different substituents
Chiral centre/ Any atom (including but not limited
stereogenic centre to carbon) that is bonded to four
different substituents.
To describe individual Chiral Molecule is not superimposable with
molecules its mirror image.
Achiral Molecule is superimposable with its
mirror image.
Meso compound Molecule contains at least two chiral
centres, but is achiral.
To describe Enantiomers/optical A pair of molecules which are non-
relationships between isomers superimposable mirror images of
molecules each other.
Diastereoisomers Molecules that are stereoisomers
but not enantiomers.
To describe mixtures Enantiomerically pure Solution contains only one type of
enantiomer.
Racemic Solution contains equal amounts of
both enantiomers.

Online Resources for Organic Chemistry

ChemSpider

http://www.chemspider.com/StructureSearch.aspx

This is the Google for organic molecules. Not only can you search by name but it has a
drawing function for you to search by structure. And if you do not know the IUPAC name, it
can help you generate from your drawn structure.

ChemSketch

http://www.acdlabs.com/resources/freeware/chemsketch/

You can download this free organic molecule drawing software to produce professional-
looking organic structures. This is extremely useful for those of you doing chemistry research
projects. It can also generate IUPAC names.

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