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Molecular structure is of central importance for our
everyday lives. Before we explore molecular structure, we
explore the nature and structure of atoms. We show how, with
the aid of the computer, we can understand how these complex
(and unbelievably tiny) objects bind together to form
molecules - the problem that is at the heart of chemistry.
Molecules use simple geometrical tricks - chain and ring
formation - to achieve complexity. We then consider the
aggregates of molecules and the fascinating question of the
balance between order and disorder at the atomic and
molecular level. Consideration of order will lead to
describing how in crystals nature builds beautiful, ordered
(if often very complex) structures in three dimensions;
while disorder takes us naturally to structures of
liquids and glasses. Three dimensional objects like crystals
are bounded by a surface; models for surfaces and
interfaces are the subject of this section. And
consideration of surfaces leads us naturally to discuss
films and membranes that play such important roles in
technology and living matter. Molecules and other atom
assemblies are, of course, omnipresent. The pen used to
write the draft of these words and the paper on which they
were written were made out of molecules: chain molecules,
molecules whose typical structures are illustrated below.
Chain or polymer molecules
Metals
are three dimensional ordered
arrangements of atoms; atoms arranged in arrays at the atomic
level as shown here.
However, molecules are not static objects: they are in
constant motion; vibrating, rotating or translating. So when
I feel a breeze on my face, unimaginable numbers of
molecules are colliding with my skin; and when a solid
melts, the molecules that were previously fixed at
particular sites in the solid, are able to move, to wander
through the liquid.
Molecules change: they lose and gain
atoms; they break up and reform, and as they do so they gain
or lose energy. So when we light natural gas which is made
from the simple molecule methane, the molecule breaks up and
forms new molecules - carbon dioxide and water - by
combining with the oxygen atoms from the air; energy in the
form of heat is given out, as is light. When metal rusts,
the atoms from the crystalline metallic solid again combine
with the oxygen from the air to make a new crystalline
material - an oxide - which has very different physical and
mechanical properties from that of the metal.
Molecules and molecular
processes are, of course, "in the news". As we
have just seen, the molecule carbon dioxide is produced by
burning gas and other carbon containing fuels. It is the end
product of combustion - a chemical reaction which unlocks
the energy stored in molecules like methane. The carbon
dioxide enters the atmosphere. But it has the key property
of being able to absorb the heat carrying infra red
radiation emitted from the earth's surface. So it acts as a
blanket, keeps the heat in the atmosphere; and as carbon
dioxide accumulates owing to the increased generation of
energy by burning fuels, the atmosphere will soon warm up,
with incalculable consequences for mankind. The ability of
carbon dioxide to absorb infra red radiation is a
consequence of its molecular structure. The radiation
excites vibrations in the molecule; and as it does so, the
energy of the radiation is absorbed. Many other molecules,
including methane and water, also absorb this type of
radiation. Our concerns focus on carbon dioxide because of
its release in unprecedented quantities in modern industrial
societies.
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Ozone is another molecule that plays a crucial role in
controlling the transmission of radiation through the
atmosphere. The molecule is built out of three oxygen atoms
(unlike "ordinary" molecular oxygen that simply
comprises two atoms stuck together). Unlike CO2 that absorbs the low energy, heat
carrying radiation, ozone absorbs the high energy ultra
violet radiation present in the sun's rays. And the
"ozone layer" high up in the earth's atmosphere
protects the surface of the earth by absorbing a high
proportion of this damaging radiation. Ozone can, however,
easily decompose; the molecules rearrange to form
"ordinary" molecular oxygen. This decomposition is
helped by reactive atoms such as chlorine. Such reactive
atoms are not normally present in appreciable concentrations
in the earth's atmosphere. They are, however, made by the
action of sunlight on chlorine molecules known as CFCs,
widely used in refrigerators, as they form volatile liquids
at low temperatures. Sufficient of these molecules have
leaked into the earth's atmosphere and reached the
stratospheric heights where they have decomposed, releasing
chlorine atoms which have depleted the ozone layer.
Fortunately, the chemical industry has now succeeded in
designing replacements for CFCs that do not have these
environmentally damaging consequences.
Molecules and molecular processes control our lives; indeed,
as we shall discuss later in this book, life is a molecular
process. But there is nothing magical about the molecules of
life. They can be understood using the same principles as
are applied to all molecular species. And they have been
fashioned by billions of years of evolution into a high
level of complexity necessary for their achieving a precise
function.
To conclude we recall the words of John Tyndall - one of the
many great men who have developed scientific knowledge
within The Royal Institution in London. In his address to
the British Association in 1870, he considered, among other
matters, the growth of living tissues. He made the following
prophetic remark.
"An intellect the same in kind as our own would, if
only sufficiently expanded, be able to follow the whole
process from beginning to end. It would see every molecule
placed in its position by the specific attractions and
repulsions exerted between it and other molecules, the whole
process and its consummation being an instance of the play
of molecular force."
With the aid of the marvelous modeling power of modern
computers, we are beginning to realize Tyndall's vision.
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