GCE

Chemistry

Context study

Edexcel Advanced Subsidiary GCE in Chemistry

(8CH01)

Edexcel Advanced GCE in Chemistry (9CH01)

Supramolecular Chemistry

October 2007
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Contents

Introduction 1
Supramolecular chemistry 2
So what is it? 2
Potential uses of supramolecules 5
Key words for searching the internet 5
Introduction

This document is designed to help teachers to understand the contemporary context of

supramolecules. It should give teachers information on this context and on how to research it
further if they wish. This document could also be given to students as introductory material.

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Supramolecular chemistry

Supramolecular chemistry is a relatively new but rich area of chemistry that has developed
since the late 1960s: it was recognised as being of great importance when a Nobel Prize for
chemistry was awarded to Donald Cram, Charles Pedersen and Jean-Marie Lehn in 1987 for
their ground-breaking developments in this area of science.

So what is it?
It has numerous broad definitions ranging from the ‘chemistry of molecular assemblies and the
intermolecular bond’ to the more brief ‘the chemistry of the non-covalent bond’ and
‘nonmolecular chemistry’. These all mean the same thing as they describe the study of the
building of large ‘supramolecules’ through the formation of non-covalent bonds between
molecules.
In the simplest case this supramolecular chemistry is complexation (like we see with transition
metals and ligands) between a host molecule (usually quite big) and a guest (smaller): this is
called host-guest chemistry. For example, common hosts are large cyclic molecules
(macrocycles) with a sizeable hole in the middle. Common guests can be anions, cations or
small neutral molecules. For complexation to occur the host and the guest must interact
through a non-covalent bond.

Figure 1 — This is a picture generated from crystal structure data reported by Wade A.
Freeman in Acta Crystallographica Section B: Structural Science, year 1984, pages 382-387. It
shows a p-xylylenediammonium (the guest) bound within a cucurbit[6]uril (the host)

The inspiration for this type of work came from biology and enzyme chemistry where
molecules are brought into the active site, using the lock and key concept, of complicated
proteins. Once inside the active site some reaction happens within the guest — normally a
reaction that couldn’t occur without the presence of the enzyme or host. It was for synthetic,
man-made versions of this type of host-guest chemistry that the Noble prize was awarded. The
degree of efficiency, sophistication and specificivity provided by nature has yet to be
matched, but great strides are being made.

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For a host and a guest to interact favourably, their chemical properties must match each
other. For example, if the guest is a hydrogen bond donor, eg water, then the host molecule
must be able to form hydrogen bonds with it; it must contain nitrogen, oxygen or fluorine
atoms with available lone pairs. The host must be a hydrogen bond acceptor: the host and the
guest will interact well with each other if they are complimentary.
Similarly, it must be easy for the host and the guest to react — the host must not have to
change shape too much to form favourable interactions with the guest. A well-matched host is
often termed pre-organised to bind particular guests. By well-matched we also mean
selective, and it is this selectivity that supramolecular chemists are often aiming for. A rigid
host that cannot change shape too easily will only bind a select band of guests, but it will bind
them strongly. This should be contrasted with a conformationally flexible host that can bend
and stretch its shape — this can bind a wide range of guests but none of them very well. So,
one of the main goals in supramolecular chemistry is to design a host that is selective for a
particular guest.

Figure 2 — This is a picture generated from a crystal structure reported by Julius Rebek, Jr.
and coworkers in Chemistry-A European Journal, 1996, 2, 989-991. It shows a dimeric
molecular assembly that contains a single nitrogen molecule (in grey)

Numerous non-covalent interactions have been used in the construction of host-guest

supramolecular assemblies. They are: ion-ion (ionic bonding, bond energy = 100 −
350 kJ mol−1); ion-dipole (between a polar molecule and an ion, bond energy = 50 − 200 kJ
mol−1) — these include coordinate or dative bonds in metal complexes; dipole-dipole (bond
energy 0.5 − 10 kJ mol-1), hydrogen bonds (bond energy = 4 − 120 kJ mol−1), and instantaneous
dipole–induced dipole forces (bond energy 2 − 50 kJ mol−1).
Along with these well-known types of interaction several new types of interaction have been
discovered through research into supramolecular chemistry, including cation − π interactions
between s-block metal ions and delocalized electrons (bond energy ≈ 75 kJ mol−1) and π − π
‘stacking’ interactions (bond energy = 1 − 50 kJ mol−1) between electron-rich π-systems (eg
phenol) and electron poor ones (eg C6F6). The latter type has been shown to help stabilize,
along with H-bonds, the double helix in DNA through π − π interactions between the paired
nucleobases.
The type of non-covalent interaction should suit the purpose of the assembly: strong host-
guest interactions are used when the host is to be used as a ‘sink’ — for example, when toxic
metals (a guest) are to be removed from water, where the binding is irreversible. Weak
interactions are favoured when the assembly is used as a sensor to detect the quantity,
presence or absence of the guest species. Here the guest reversibly binds to the host, where it
is detected by some response on formation of the assembly (eg a colour change), and then
released. Similarly weak interactions are required when the host is used to ‘carry’ a guest
from one place to another, through an area impermeable to the guest alone, where again it is
released. This is the principle behind drug delivery agents.

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One of the main reason for work in this area is the synthesis of molecular devices. Again
inspiration for this kind of work has been from nature, from molecular biology. In biology, the
supramolecular hosts are the receptor sites of enzymes, genes, antibodies of the immune
system and ionophores. The guests are substrates, inhibitors, cofactor drugs or antigens. All of
these components exhibit supramolecular properties such as molecular recognition, self-
assembly, self-organisation and complementarity: as such nature displays supramolecular
chemistry perfectly. These aggregates of molecules carry out a defined process and can, as
such, be viewed as a molecular device. Supramolecular chemists are aiming to mimic biology,
building complex yet specific aggregates that have predefined or pre-programmed properties.
This desire for supramolecules with increased complexity has been satisfied through
application of so-called ‘self-assembly’ techniques. Here, incredibly complex systems can be
made using incredibly simple experimental techniques. By allowing pre-organised and
complimentary molecules (hosts and guests) to interact slowly with each other, at a particular
pH and temperature, large aggregates can be formed.
One of the main reasons for the success of this approach is that self-assembly processes
normally converge on one product out of the countless possibilities from the starting reagents:
the system converges on the most thermodynamically stable product of all. How does this
work? The key issue is that normally the interactions holding together the aggregates are quite
weak. So, if some of the starting materials take the wrong ‘turn’ to form the wrong products
they can easily dis-assemble, then re-assemble quickly in the right way, leading to the single
most stable product. This sounds easy but as you can imagine, it can be difficult to control.
The skill comes in designing hosts and guests that will come together in a pre-programmed
way to form the desired large supramolecule.

Figure 3 — This is a picture generated from a crystal structure data reported by Kenneth E.
Maly, Eric Gagnon, Thierry Maris, and James D. Wuest in the Journal of the American
Chemical Society 2007, volume 129, pages 4306-4322. It shows a portion of a crystal structure
in which the molecules have been engineered to assemble into sheets by hydrogen-bonding
with six of their neighbors. Hydrogen bonds are red

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The experimental techniques are simple as, at the final stage, all that is normally necessary is
to mix molecules you wish to interact and wait. The thermodynamically stable configuration
will form through self-assembly. The simplicity of this approach has the added advantage that
these reactions are cheap. The complex molecules formed would be much more expensive if
they were made from using traditional chemical reactions, as numerous reactions would be
required. The economic advantage of this type of synthesis has obviously great appeal to
industry and commerce: supramolecular chemistry is one of the main strands of
nanotechnology.
One of the main current themes in nanotechnology and supramolecular chemistry is the
possible construction of molecular machines. These are individual molecules or discrete
aggregates of molecules that perform a specific process — machines on this scale would be
much more efficient and obviously take up less space than their larger cousins. A simple
supramolecular example of such a machine is a rotaxane. These molecules consist of a
macrocyclic molecule wrapped around a molecule that looks like a dumbbell.

Figure 4 — A schematic diagram of rotaxane supramolecule

The macrocycle can shuttle between the two ends when an external influence (pH, potential
difference) is applied. The position of the macrocycle changes the properties of the molecule.
These molecules have been developed as logic switches in molecular electronics.

Potential uses of supramolecules

Hydrogen storage devices (metal organic frameworks) for green fuel technology, high
performance catalysts, treating radioactive waste, information storage devices, contrast
agents in MRI and CAT scans, drug delivery and high-technology sensor devices.

Key words for searching the internet

Supramolecular, host-guest chemistry, self-assembly, nanochemistry, nanotechnology.

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October 2007

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