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Introduction to Molecular Shape
Animated image: Nanorex, Inc., www.nanorex.com
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<font size="4" face="Verdana, Arial, Helvetica, sans-serif">The shape of a
molecule is a critical factor in what it can do. For example, the
interaction of an enzyme with its substrate has been compared to the
fitting of a key into a lock - the correct shape allows the key to fit
into the lock and turn to open it. In a similar way, molecules must have
the correct shape because they must fit together in order to work. </font>
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<font size="4" face="Verdana, Arial, Helvetica, sans-serif">A key with
just a slight difference in shape may fit in a lock, but not be able to
open it. Drugs that block the function of molecules that cause disease
often are like these mishapen keys. They have almost the right shape,
and so they fit into the place for the molecular "key", blocking the
correct one from being inserted.</font>
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<font size="3" face="Verdana, Arial, Helvetica, sans-serif">Ritonavir
(blue), a drug that fights AIDS, fits closely inside the HIV protease
(green). Ritonavir blocks the protease's function by virtue of its shape. </font>
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<font size="4" face="Verdana, Arial, Helvetica, sans-serif">Also, the
closer the fit between the molecules of a substance, the more energy is
required to melt or boil it. This accounts for the difference between
butter - a solid at room temperature, and oil - a liquid at room
temperature. Attempts to make "healthier butter" involve changing the
shapes of oil molecules so that they fit together better, becoming solid
or "spreadable" at room temperature. </font>
<p>
<font size="4" face="Verdana, Arial, Helvetica, sans-serif">The shape of
a molecule is determined by its electrons. Electrons are so negatively
charged that they are attracted intensely to the (positive) nuclei of
nearby atoms. But they also repel each other. Electrons adopt positions
as far away from each other, but as close to the nuclei as they can. The
interplay of these attractions and repulsions resolves itself into a
sort of skeleton for the molecule. </font>
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<font size="4" face="Verdana, Arial, Helvetica, sans-serif">For every
configuration of electrons around an atom, an arrangement that maximizes
attraction and minimizes repulsions is achieved. These arrangements,
called molecular geometries, give rise to characteristic molecular
shapes. The shapes, in turn, give rise to the phenomena we see in
everyday life: from drugs that cure diseases, to the need to heat butter
before you can pour it on your popcorn. </font>
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<font size="3" face="Verdana, Arial, Helvetica, sans-serif">The fat
molecules in butter (upper panel) fit together well, so butter remains a
solid at room temperature. Oil molecules (lower panel) vary in shape and
do not pack well, so oil is a liquid at room temperature, and requires a
lower temperature to solidify. </font>
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