MOD.!

MOLECULAR STRUCTURES AND MODELS

Note: There is no need to write a pre-laboratory summary for this experiment, however you may
want to start work on the content. The laboratory period will run more like a tutorial, it’s “open
book”, you can work in groups and ask your TA about any concepts you don't understand.
Your grade for this laboratory is assessed based on an individual quiz at the end of the laboratory
period (run under examination conditions).

INTRODUCTION
This experiment uses a molecular model kit to help address and clarify the theoretical concepts of
covalent bonding and molecular structure. Molecular models are designed to reproduce molecular
structures in three dimensions, allowing many subtle features concerning shapes of molecules (such as
dipole moment, polarity, bond angle, and symmetry) to become clearer. Learning how to use a model kit
correctly can help you to realise how they may be able to help you answer questions about molecular
structure. Remember that you can use model kits during examinations to help you answer the questions
we might ask.
An important fundamental principle is that a molecule tends to position its atoms to give the
arrangement with the lowest possible energy. This allows us to predict the shape of a molecule, and the
subsequent physical and chemical properties to a very good approximation.
In this laboratory period you will learn how to use your model kit to help answer questions and
investigate:
• the implications of hybridisation on molecular shape
• aspects of isomerism
• conventions used in 2-D representations of 3-D molecules.
• counting types of atoms in a molecule (i.e. looking for equivalent groups, especially H and C)
• index of hydrogen deficiency
• chirality and chirality centers – R/Snomenclature
• Enantiomers and diastereomers – E/Z and cis/trans designation
• plane of symmetry, superimposable mirror images, enantiomers
• meso compounds

In preparation you should review the following concepts and terms from 1st year chemistry, 351 lectures
and / or tutorial materials:
• hybridisation and atomic orbital shape
• alkanes, functional groups, constitutional isomers, conformational isomers
• Newman projections; eclipsed/staggered, anti/gauche, potential energy diagrams
• cis/trans, E/Z and R/S nomenclature
• the implications of hybridisation on shape
• structural flexibility
 MOD.!2

• conventions used in the two dimensional representation of molecules and add that all important
third dimension.
• counting types of atoms in a molecule (i.e. looking for equivalent groups)
• index of hydrogen deficiency

MOLECULAR MODELS
The three dimensional shape of molecules results from the threedimensional arrangements of their
constituent atoms, and as such are often difficult to visualise in terms of a twodimensional diagram on a
page or computer screen. For this reason chemists often make use of molecular structure models (either
physical models or computer models). In addition to the qualitative appreciation of molecular structure,
scale models can be used to make approximate quantitative measurements. For this experiment you
should use your own set of models if you have them. We have a small number of the Molymod Molecular
Models that can be borrowed. From the Molymod Models we shall use the following components:

ATOMS Colour Atom No. of Holes Bond Angle

Black C 4 109° 28'
White H 1
Blue N 4 109° 28'
Red O 4 109° 28'
Green Cl 2
Orange Br 1

Atoms are joined together by inserting the appropriate bond into the holes in the atoms. The single
short rigid bond should be used to represent sigma (s) bond. Two curved pieces should be used to
represent a double bond and three curved pieces to represent a triple bond.
Sometimes more than one sensible structure may be drawn for a particular molecular formula. In
this case the arrangement of atoms must be determined experimentally. The different arrangements are
said to be "ISOMERS" of each other. Depending upon the relationship of the structures, the pair of
structures can be subcategorised as different types of isomers. This is schematically represented by the
isomer tree diagram on the following page and is an important part of the materials covered by this
experiment. At each branch in the tree, a “yes/no” question is asked in order to decide what path to
follow.

The many different possible arrangements of the same set of atoms is the main reason for the
enormous number (over a million) of known organic molecules. These different arrangements are
possible since carbon has a singular ability to form very strong bonds with itself (as carbon chains or
carbon rings), hydrogen atoms, or heteroatoms.
 MOD.!3

Do the compounds
have the same molecular
formulae ?
NO
Not isomers
YES
Isomers

Do the compounds have

the same connectivity ?
NO YES

Constitutional Stereoisomers

O
Can the compounds be
OH interconverted by rotation
about single bonds ?
(skeletal, positional, functional) NO YES

Configurational Conformational

Is the isomerism at a H 3C H H H
H H H
tetrahedral center ?
H
NO YES H CH 3 H 3C CH 3

Geometric Optical

Are the compounds

non-superimposable
mirror images ?
NO YES

Diastereomers Enantiomers

Cl H Cl Cl
H 3C H H 3C Cl
CH 3CH 2 H H CH 2CH 3
H H CH 3 H 3C
H 3C H 3C
Br Br
!

ISOMER TREE This figure helps you identify the type of isomer between a pair of structures. Note that
some classes are not always mutually exclusive (e.g. technically geometric isomers and conformational
isomers are also diastereomers). In general, it is usually best to use the more specific term.

EXPERIMENTAL PROCEDURE
"Tutorial" work in pairs, open book. Work through the following tutorial questions using your model kit, text
book etc. and record your answers, talking to your TA as you work through them. At the end of the
laboratory period, you will be given a hands on assessment to be done individually.
A. CARBON:
 MOD.!4

3
Tetrahedral sp carbon
Since four single bonds are formed, the carbon atom is situated at the centre of a tetrahedron. This is
the largest number of sbonds carbon can form and hence the carbon is termed a "saturated carbon".
Construct an ethane molecule with the medium straight bonds and confirm that the carbon atoms are
both at the centre of a tetrahedron.
H H
H C C H ethane
! H H
The molecule is flexible; grasp one carbon atom and view the molecule along the CC axis. Now rotate the
front C atom about the CC bond for a full 360° rotation. The relative positions of the hydrogen atoms on
the different carbon atoms are constantly changing, and every different relative arrangement is called a
"CONFORMATION" or they can be described as "CONFORMATIONAL ISOMERS" or "CONFORMERS".
There are two extreme conformations, and these have important names.

! 

staggered conformation eclipsed conformation

It is often useful to inspect interactions between groups on adjacent atoms by viewing along the CC bond.
This particular projection, represented above, is known as the "Newman Projection". (Groups attached
to the front carbon intersect at the centre of the circle; those attached to the rear carbon project only as
far as the edge of the circle). Another convention very frequently used for the diagrammatic
representation of threedimensional molecules is the wedge-hash diagram.

! bond in the plane of the paper

! bond projecting behind the plane of the paper
! bond projecting in front of the plane of the paper

Therefore a staggered conformation of ethane could be represented in a wedge-hash diagram as:

H H
H
C C
H H
! H
At room temperature the rotation about CC bonds takes place many thousands of times per second,
however the different conformations do not have identical energies. The staggered and eclipsed
conformations are the two extreme energy conformations since the electrostatic repulsion of the pairs of
electrons in bonds (or lone pairs) when they are spatially in close proximity destablises the eclipsed
 MOD.!5

conformation (note there are other explanations of the reasons for the difference in the energies of the
two conformations). Thus the staggered conformation is the more stable conformation. This
destabilization effect tends to get larger as the groups involved get larger. In real terms, that means that it
is at a minimum for two H atoms.

Replace one of the hydrogen atoms on each carbon atom with chlorine to form 1,2-dichloroethane.
Starting with the 2 C-Cl bonds lined up with each other in an eclipsed conformation shown below.
Cl Cl

C C
H H
! H H
Now for a definition:
Torsional or dihedral angle. Let’s look at an example. The torsional angle is the angle between the pair
of C-X and C-Y bonds that are part of an X-C-C-Y system when viewed along the middle C-C bond.
Rotation about the C-C bond will change this torsional angle. This angle is also known as a dihedral
angle. Thinking of “torsional” as “twisting” and this may help you remember and understand the term and
differentiate it from a simple “bond angle”.

φ torsional angle
X
. Y

!
There are some specific terms associated with certain torsional angles between a pair of substituents
(such as the two Cl atoms in 1,2-dichloroethane):
Syn torsional angle = 0o
Gauche torsional angle = 60o
Anti torsional angle = 180o


Eclipsed conformations will have the largest amounts of torsional strain due to the electrostatic repulsions
between the pairs of electrons in the eclipsing bonds. The conformations that brings atoms (or groups of
atoms), especially large atoms, closer together in space than the van der Waals radii allow will have the
largest amounts of van der Waals strain. Take your model of 1,2-dichloroethane and rotate the molecule
about the middle C-C and observe the equivalent and non-equivalent eclipsed and staggered
conformations.
1) Draw the Newman projections for the three eclipsed conformations. Circle the eclipsed
conformation(s) with the highest energy.

2) Draw the Newman projections for the three staggered conformations. Circle the staggered
conformation(s) with the lowest energy.
 MOD.!6

3) For the diagrams you drew in qu 1 and qu 2, identify the conformations where the chlorine atoms are
syn, gauche or anti.

4) Sketch the following potential energy diagram, and indicate the positions where each of the six
conformations (three eclipsed and three anti) of 1,2-dichloroethane would fall:

The connectivity and molecular motion due to bond rotations within a molecule can result in atoms that
are considered to be equivalent or non-equivalent types. For example, the six hydrogen atoms in
ethane are considered to be chemically equivalent (i.e. of the same type). Each individual hydrogen atom
is in an identical environment (attached to a carbon atom that is linked to 2 other hydrogens and one
methyl group). The ability to recognise the number of types of H (or indeed other atoms such as C) is a
very important and a useful concept. For example, counting types of H is very important in
spectroscopy (especially nuclear magnetic resonance) and in reactions (e.g. radical halogenation of
alkanes). It will be revisited several times in later questions in this exercise and applied in other
components of the course.

There are three methods one can use to establish the number of kinds of H (similar methods can be
used for other atoms such as C). We recommend that you start with the first method, and over time as
you get better at the task, you will gradually and naturally migrate through the second method to the third:

1. Substitution method. This method is based on the idea is that you replace each H in turn with a
"dummy" atom to see if you get a different product (e.g. 1-chlorobutane and 2-chlorobutane). If you
have a new product, then the H was different to those already considered.

2. By "verbal" description. The verbal method requires that you describe the position of the H within
the molecule. If you need to use different words to describe two H atoms, then they represent
different types of H. For example an -OH is different to a -CH (based on what they are attached to),
and a -CH3 is different to a -CH2- (because the number of H at that C are different). Other
differences could be position on a chain, across a ring or double bond, hybridisation etc.
 MOD.!7

3. Symmetry. The symmetry method is the most sophisticated but the quickest method and requires
that you look for mirror planes, rotation axes or inversion centers that interchange H atoms. H
atoms that can be interchanged are equivalent to each other.

Try replacing different H atoms in 1,2-dichloroethane to determine how many different types of H there
are in 1,2-dichloroethane.

CAUTION: Remember that rotation about bonds produces different conformations (conformational
isomers or conformers) only, not different molecules.

5)How many different types of H are there in each of the following hydrocarbons: methane, ethane,
propane, butane, 2-methylpropane.

CONSTITUTIONAL ISOMERS are compounds that have the same molecular formula, but differ in the
way that the atoms are connected to each other (i.e. due to different branching patterns or functional
groups). They cannot be interconverted unless bonds are broken and made. Note that constitutional
isomers have different names (i.e. beyond differences in stereochemistry such as cis, trans, E/Z or R/S).

6) Using line diagrams, sketch and name all possible constitutional isomers with the molecular
formula of C3H7I.
7) How many different types of hydrogen atoms are present in the structures that you
have drawn?

2
Trigonal sp carbon

Three sbonds are formed with the carbon atom at the centre of a triangle. The other bond formed to
2
carbon is a pbond (remember, carbon is TETRAVALENT!). The simplest hydrocarbon with an sp carbon
is ethene.
H H
C C
!H H
Construct an ethene molecule using the long flexible bonds and satisfy yourself it is flat. Try to rotate the
molecule about the C=C bond. It’s only possible if you break the pbond.
Replace one of the H atoms with a Cl atom.

8) How many different monochloroethenes can you make? How many different kinds of H are there
in ethene?
 MOD.!8

Replace another H atom by a Cl atom. Because of the lack of rotation about the C=C bond it is possible
to construct THREE DIFFERENT dichloroethenes.

Cl Cl Cl H
H Cl

H Cl H H H Cl

! 1,1-dichloroethene (Z)-1,2-dichloroethene (E)-1,2-dichloroethene

The "Z" prefix indicates that the two groups of higher priority according to the CahnIngoldPrelog Rules**
(see notes at the end) are situated on the same side (German word Zusammen = together) of the double
bond. Conversely, "E" (German word Entgegen = opposite) indicates these groups are across from each
other. Note ONLY in the very simplest cases does Z correspond to cis and E to trans, e.g. see Qu 11
below.

9)How many different kinds of H are there in chloroethene?

Make a model of the Z isomer and then convert this to the E isomer. Note that in order to do this, a
chemical bond must be broken, so they are not conformational isomers.
The two isomers have the same atoms bonded to each other, but in a different spatial arrangement, so
they are called STEREOISOMERS. Note that stereoisomers have the same names except for
differences in stereochemistry such as cis, trans, E/Z or R/S, e.g. cis-but-2-ene and trans-but-2-ene, (R)-
butan-2-ol and (S)-butan-2-ol.
The interconversion of stereoisomers requires that bonds are broken. For example, in alkenes, this
requires that the pbond be broken. This general kind of isomerism is called CONFIGURATIONAL
ISOMERISM and specifically this type is E/Z, or a type of GEOMETRIC ISOMERISM. These molecules
are quite different and have different physical and chemical properties. This is in complete contrast to
CONFORMATIONAL ISOMERS (see above) which are different stereoisomers of the SAME molecule,
differeing due to rotation about CC single bonds.

10) How many different trichloroethenes are there?

Construct, and draw a model of (E)-2-bromo-2-butene. Replace the hydrogen atom at carbon 3 with a
chlorine atom.

11) Reassign priorities and specify the configuration (E or Z) of each the 2-bromo-3-chloro-2-
butene(s).

The Index of Hydrogen Deficiency (IHD) is a measure of the number of units (or degree) of
unsaturation in a molecule. A saturated hydrocarbon is one that has the maximum number of H atoms (or
single bonds) for the given number of carbon atoms. The IHD is a count of how many molecules of H2
need to be added to a structure in order to obtain the corresponding saturated, acyclic species. Remake
 MOD.!9

a model of ethene. The IHD is equal to the number of units of unsaturation, that is the number of π bonds
plus the number of rings present (i.e. π + r ). IHD can be deduced from a structure by counting these
features or it can be calculated from a molecular formula. Both methods are useful. If we have a
molecule with the general molecular formula CcHhNnOoXx, then the following equation can be derived,

IHD = 0.5 * [2c+2-h-x+n]

see http://www.chem.ucalgary.ca/courses/351/Carey5th/useful/ihd.html

12) How many hydrogen atoms need to be added to the ethene to turn it into ethane? How many
molecules of H2 does that correspond to? (This is the IHD for ethene)

Linear sp carbon
Two sbonds are formed; the other two bonds to carbon are both pbonds. The angle between the
sbonds is 180°.
Make a model of but-1-yne
H C C CH2CH3
!
13) What is the relative spatial relationship of the carbon atoms in the triple bond of but-1-yne?
14) How many different kinds of H and C atoms are there and what is the index of hydrogen
deficiency (IHD) of but-1-yne?

Rearrange these atoms to form but-2-yne

H3C C C CH3
!

15) How many different kinds of H and C atoms are there and what is the index of hydrogen
deficiency (IHD) of but-2-yne?

B. NITROGEN and OXYGEN:

Many organic molecules contain nitrogen and / or oxygen atoms. The formation of bonds to nitrogen
and oxygen and the arrangements and shapes that result may be considered in terms similar to those
3
discussed for carbon. Nitrogen is often trivalent; the N atom is sp hybridised forming 3 sbonds and the
fourth group attached to the nitrogen is a lone pair of electrons. These four groups are arranged
tetrahedrally around the central nitrogen atom. A further bond may be formed to the trivalent nitrogen
using the lone pair of electrons from the nitrogen. If this takes place the coordinating group (the term
"coordinating" implies that one atom, in this case the nitrogen, supplied both electrons to the bond)
occupies the fourth corner of the tetrahedron and the nitrogen becomes positively charged to give a
"substituted ammonium cation".
The simplest example of a molecule containing trivalent nitrogen is ammonia; one of the simplest
organic nitrogencontaining molecules is methanamine:
 MOD.!10

NH (ammonia) CH NH (methanamine)
3 3 2
Construct models of ammonia and methanamine. Confirm that they both have the same relative
arrangements of atoms at the nitrogen atom.

16) What is the VSEPR description of the shape of the arrangement at nitrogen in both these
molecules?
17) What is the N hybridisation in each structure?
18) Are ammonia and methanamine saturated compounds?
19) What is the index of hydrogen deficiency (IHD) for each of these compounds?

From inspection of the models it would seem that the bond angles are the same, as if the nitrogen were
Å
carbon. This is only true if there are four identical groups attached to the nitrogen (e.g. as in the NH
4

cation).
The actual measured bond angles are:
NH CH NH
3 3 2
HNH 107.3 ± 0.2° HNH 105.8°
HCH 109.5°
In fact, deviations from the ideal angle of 109.5° for a regular tetrahedron are often observed. Factors
which influence this angle include bond length, size of group or atom attached, and in particular, the
presence of a lone pair of electrons. It is found that a lone pair will repel bonding pairs more than will
another bonding pair; in the presence of one or more lone pairs the angle between bonding pairs is
significantly compressed (VSEPR). An example of a molecule with nitrogen bonded to four groups is the
neurotransmitter acetylcholine.

O CH3
⊕
H3C C O C C N CH3 OH
H2 H2
CH3
!
This compound is the chemical mediator which bridges the gap ("synapse") between the endings of two
nerve cells. It is by means of this chemical that the nerve impulse is transmitted.
Nitrogen is biochemically a very important element. It is found in a large number of biologically active
molecules and is often intimately involved in the biological function of the molecule.
Oxygen is a commonly occurring element in many organic molecules. The simplest, and most
3
abundant molecule containing oxygen is water. In this molecule the oxygen may be considered sp
hybridised with two lone pairs.* Again, the lone pairs compress the angle between the bond pairs as was
observed in the ammonia molecule. Methanol, CH OH, is a simple organic molecule containing an OH
3
 MOD.!11

group. If the second H atom of water is also substituted by a methyl (CH ) group then a molecule of
3
dimethyl ether results.

..O.. H ..O.. ..O..

H H C H CH3 CH3
H H
H O H 104.45o C O H 108.9o C O C 110o
H C H 109.3o
! water methanol dimethyl ether
* Other treatments of the bonding are also possible.
Construct models of molecules of water, methanol, and dimethyl ether.

20) What is the VSEPR description of the shape of the arrangement at the oxygen in these
molecules?
21) What is the O hybridisation in each structure?
22) Draw a wedge-hash diagram to show the groups around the O in each structure.
23) Are water, methanol and dimethyl ether saturated compounds?
24) What is the index of hydrogen deficiency (IHD) for each of these compounds?

2
Both nitrogen and oxygen can occur in an sp hybridised state and form double bonds, and nitrogen

can also form a triple bond when the nitrogen is sp hybridized. (e.g. in an alkyl cyanide such as CH CºN,
3

or a ketone such as CH3C=OCH3).

25) What is the IHD of acetonitrile, CH CºN?

3

26) What is the C-C-N bond angle?

27) What is the IHD of propan-2-one CH3C=OCH3?
28) What is the C-C-O bond angle?

C. CYCLIC SYSTEMS:
Carbon atoms, in addition to forming long carbon backbone chains, can also form rings. e.g.
cycloalkanes These rings differ in size and to a limited extent in their chemical properties, particularly in
the case of the smallsized rings (e.g. 3 or 4 carbons – which tend to be very reactive) otherwise rings
generally have similar reactivity to the analogous acyclic systems.
Construct a molecule of cyclopropane using sigma bonds (use the medium, straight pieces)
H H
C
H C C H
! H H
 MOD.!12

29) How many different kinds of H are there in cyclopropane?

30) Is cyclopropane saturated?
31) How many H atoms need to be added to make the related acyclic alkane propane?
32) What is the index of hydrogen deficiency (IHD) of cyclopropane?
H2 / Ni H2 / Pd

!
cyclopropane propane propene

You should have concluded that the cyclic system has the same degree of unsaturation as an alkene unit,
a fact that is emphasised by the two reactions shown above: C3H6 is the molecular formula for both
cyclopropane and propene, which are CONSTITUTIONAL ISOMERS. The ring strain of cyclopropane
even makes its reaction resemble an alkene. The index of hydrogen deficiency (IHD) or degree of
unsaturation is just a count of the number of π bonds and / or rings. An alternative way to deduce the
degree of unsaturation of a cyclic system is to count how many bonds you have to break to make a chain
system.

Many other polycyclic ring systems are possible, and you will encounter some during your organic
chemistry courses. We will investigate a few examples below:

Build a model of adamantane.

adamantane C10H16
!
33) What in the index of hydrogen deficiency (IHD) of adamantane ?
How many types of H are there in adamantane?

Now build a model of cubane.

cubane C8H8
!
34) What in the index of hydrogen deficiency (IHD) of cubane ? (it is probably a good idea to
determine this by breaking a bond at a time until you have an acyclic structure).
How many types of H are there in cubane?

D. AROMATIC RINGS:
There is a whole branch of organic chemistry based upon structures containing rings of mainly carbon
2
in an sp hybridised state, but also including nitrogen and oxygen in some cases. Compounds
 MOD.!13

2
comprising rings of sp hybridised atoms where there are 6,10,14,18.. electrons in porbitals are called
AROMATIC and show properties quite different from any other organic structures. The commonest and
most familiar of all these compounds is benzene.
H
H H
C
H H 1.39A
C C C C
1.10A
benzene H C C H
C 120o
C 120o C C
H H
C H 120o H

! H
The structure as represented in the left hand diagram has alternating double and single bonds, and it is in
this form that you have to construct a benzene ring with your model kit. In reality all the CC bonds are the
same length, 1.39Å, intermediate between double and single, and the ring is completely flat. The angles
and bond lengths for benzene are shown in the righthand diagram. This ring is rigid; there is no flexibility
2
as in the carbon skeleton. The internal angle of a regular hexagon is 120° and so the trigonal sp angle of

120° is accommodated without strain.

Build a model of benzene. Now determine the degree of unsaturation, by either counting the number of
bonds you need to break or taking half the number of H atoms you need to add (equal to counting H2
molecules) to get a saturated acyclic structure.

35) What in the index of hydrogen deficiency (IHD) of benzene?

Build a model of chlorobenzene. Now, in turn, replace each of the hydrogens with a second chlorine
atom.

36) How many different dichlorobenzenes are there?

37) For each dichlorobenzene, how many different types of H and C atoms are there and what is the
index of hydrogen deficiency of each compound?

Now take your model of chlorobenzene and replace each of the hydrogens in turn with a bromine atom.

38) How many different bromochlorobenzenes are there ?

39) For each bromochlorobenzene, how many different types of H and C atoms are there?

E OPTICAL ISOMERS : ENANTIOMERS and DIASTEREOMERS

There is a further spatial relationship between atoms in molecules that we must consider, and it is a
more subtle than those considerer above. There is a type of isomerism called OPTICAL ISOMERISM
3
that can arise as a result of the tetrahedral arrangement of an sp hybridised carbon or nitrogen atom.
 MOD.!14

Build two models of CH2ClBr. Position the two molecules of CH2ClBr such that they are ‘reflected’
through an imaginary mirror that runs between them. Try putting one molecule ‘on top’ of the other such
that all the matching atoms line up.

40) Is CH2ClBr superimposable on its mirror image?

41) Does interchanging any two atoms (Cl, Br, or H’s) create a new molecule?

Looking at only one of the models for now, note the plane of symmetry that bisects the C, Cl and Br
atoms. This molecule has an internal plane of symmetry and because of this, it is superimposable on
its mirror image. To test this out take a black, tetrahedral C atom and add a white, an orange, a purple
and a green piece to the C to make a simple tetrahedral molecule, CHClBrF. Now ignore this one and
make as many other models as you can from your model kit (4 or 5 minimum: cooperate with another
group if you need to). Now compare them all. Separate them into distinguishable types. You should
have only two groups, all those within a group are superimposable on each other and they are all non-
superimposable mirror images of all those in the other group.
Superimposable means that two models can be placed side by side in such a way that they look
identical (i.e. they can be superimposed in each other).
Non-superimposable means that when two models are placed side by side, they can always be
distinguished.
Enantiomers are non-superimposable mirror images.
Compare the structures you built and make sure you understand the principle of superimposability.
CHClBrF has no internal plane of symmetry, and forms a pair of enantiomers and is said to be chiral
(molecules that lack this property are said to be achiral).

42) What happens when any pair of substituents within these structures are interchanged? (i.e.
remove one substituent and switch it with another then see if it belongs to the original group or the other
group)

Build each of the following structures and its mirror image, then check for superimposability: 2-
chloropropane, 2-chlorobutane, and 2,3-pentadiene.

43) Which of the structures listed above have non-superimposable mirror images?

The most common scenario that leads to this type of isomerism arises if four different groups are
attached to a central atom, then two different molecules can exist depending on the 3D-sequence in
which the four groups are attached. The relationship between these two molecules is such that they are
nonsuperimposable and mirror images of each other; they are given the name OPTICAL ISOMERS or
 MOD.!15

ENANTIOMERS*. If the four groups are different there is no element of symmetry (mirror plane, rotation
axis, inversion center) in the molecule and the central atom is termed an asymmetric atom. The reason
for the term OPTICAL ISOMERS is that most physical and chemical properties of these isomers are
identical. However, they have a different effect on a beam of plane polarised light, hence their name.
Molecules with no asymmetric atom have no effect they are optically inactive. One other difference has
considerable biochemical significance optical isomers typically react at different rates with another
optically active compound such as an enzyme or a receptor.
Normally in chemical reactions conducted in the laboratory where a molecule with an asymmetric
carbon is generated, equal amounts of the two optical isomers are formed giving a racemic mixture. In
natural systems the converse is true. It is a general rule that only one of the pair of enantiomers will be
found, also biochemical reactions are so specific that usually the other enantiomer would not give a
particular reaction.

Build a model of the isomer of the 1,2-dibromo-1,2-dichloroethane system shown below and its mirror
image.
H H
C C
Br Br
Cl Cl
!
44) Are these structures superimposable on each other?
45) Are there any chirality centers?

This type of compound is a special type of stereoisomer, known as a MESO compound. Note the special
relationship of the asymmetric centers. To be considered to be a MESO compound a molecule MUST
have two (or more) chiral centers and be superimposable on its mirror image – if there are NO chiral
centers (e.g. CH2BrCl) the molecule is NOT considered to be MESO.
Keep the last two models and now build the isomer shown below, and its mirror image.
H H
C C
Br Cl
Cl Br
!
46) Are these two new models superimposable on each other or either of the other isomers of 1,2-
dibromo-1,2-dichloroethane you have built?
47) Are there any chirality centers?

What you have just worked through covers a slightly different type of stereoisomers. Stereoisomers that
are non-superimposable mirror images are ENANTIOMERS. Stereoisomers that are not enantiomers are

* The term enantiomer comes from the Greek enantios = opposite.

 MOD.!16

DIASTEREOMERS (note that this description is quite broad and therefore includes other types of
stereisomers that can be better described by more specific terms).
Unlike enantiomers, DIASTEREOMERS typically have different chemical and physical properties, a factor
that often makes them much easier to separate and purify.

48) What is the relationship of last two structures you built to the previous two?

The next optically active molecules we will consider are amino acids. A generic representation is shown
below in the Fischer# and wedge/hash projections. The (L) differentiates which of the enantiomers we are
referring to and is an historical convention that was initially adopted for this purpose. This has been
superseded by the modern CahnIngoldPrelog Rules (see the end).

All of the amino acids obtained from the hydrolysis of proteins exist as one enantiomer only and those
obtained from the animals and the higher plants all have the same arrangement of groups around the
asymmetric carbon atom as shown generically below. By the old convention these are the Lamino acids.
Based on the R/S convention some are R but most are S. For this reason, the older convention is often
retained when describing amino acids particularly (especially by biochemists).

CO2H CO2H
H NH2 H NH2
R R

! Fischer wedge/hash
Common representations of α−amino acids

49) When R=H in the above formula, the amino acid is called glycine. Can glycine exist as a pair of
enantiomers ? If not, why not?

Phenylalanine (R = -CH2C6H5) is an essential amino acid that is not synthesised in the body and so
must be ingested in the diet. Whole egg, for instance, contains 5.4% (L)phenylalanine. It is also one of
the two amino acids that make up the artificial sweetener, “Aspartame”. Make a model of naturally
occurring phenylalanine.
H
O
CH2 C
OH
NH2

! (L)- or (S)-phenylalanine

# In a Fischer projection horizontal lines indicate the substituent in front of the plane; vertical lines project
backwards.
 MOD.!17

50) To convert this enantiomer to its mirror image, the (D) or (R)enantiomer, which groups can be
interchanged ?

(Note: to convert one enantiomer to the other requires bond breaking and hence these molecules are
configurational isomers).

REFERENCES
1. a.M. Jones and S.A. Fleming in "Organic Chemistry", Norton, 4th ed. See Ch2 (for
hybridisation and conformations), Ch3 (alkene stereoisomers, alkynes, index of hydrogen deficiency),
Ch4 (stereochemistry, chirality, enantiomers, diastereomers).
b.
http://www.chem.ucalgary.ca/courses/351/Carey5th/Ch02/ch2-3.html
http://www.chem.ucalgary.ca/courses/351/Carey5th/Ch03/ch3-0.html
http://www.chem.ucalgary.ca/courses/351/Carey5th/Ch05/ch5-1.html
http://www.chem.ucalgary.ca/courses/351/Carey5th/Ch09/ch9-1.html
http://www.chem.ucalgary.ca/courses/351/Carey5th/useful/ihd.html
http://www.chem.ucalgary.ca/courses/351/Carey5th/Ch07/ch7-0.html

2. D.H.R. Barton, Experientia, 6, 316 (1950).

3. D.H.R. Barton, O. Hassel, K.S. Pitzer and V. Prelog, Science, 119, 49 (1953), Nature, 172, 1096
(1953).
4. D.H.R. Barton, Science, 169, 539 (1970).
5. E.L. Eliel, and S.H. Wilen, in "Stereochemistry of Organic Compounds", Wiley, New York, 1994, or E.L.
Eliel, "The Stereochemistry of Organic Compounds", McGrawHill, New York, 1962.
6. R.S. Cahn, C.K. Ingold and V. Prelog, Experientia, 12, 81 (1956).
http://www.chem.ucalgary.ca/courses/351/Carey5th/Ch07/ch7-6.html
http://www.chem.ucalgary.ca/courses/351/orgnom/stereo/stereo-03.html
http://www.chem.ucalgary.ca/courses/351/orgnom/stereo/stereo-02.htm