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Molecular Geometry
The shape of a molecule can be very important
to the way it interacts with other molecules.
For example, water molecules have a bent
shape, and the oxygen atom, which attracts
extra electrons more strongly than do the
hydrogen atoms, draws the electron shells over
to its side a little bit.
in science textbooks, and the one on the right
shows a more realistic view of the molecule.
The four hydrogen atoms are at the four points
of a shape called a tetrahedron, the shape
below
This makes the molecule polar, meaning that
one side is negatively charged while the other
side is positively charged. Polar molecules
attach themselves to other polar molecules,
and water is a good solvent as a result: the
molecules cling to molecules of things like
sugar, surround them, and separate them from
the solid sugar.
There are many other important consequences
of the shapes of molecules. Many of the
molecules that make up our bodies have
intricate shapes on which the molecule’s
function depends. They’re like little machines,
and a machine needs to have a reliable
structure in order to function.
Pairs of Valence Electrons
Below are depictions of a methane molecule,
𝐶𝐻4. The figure on the left shows the
traditional ball and stick depiction that you see
This configuration puts them as far from each
other as they can get without leaving the
carbon atom. This happens because of the
repulsion of electrons from each other. Recall
that in a covalent bond like the ones here, each
of the two atoms share a pair of electrons. So
each of the hydrogen atoms in the methane
molecule above share 2 electrons with the
carbon atom. The two electrons in each pair
stay close together, but each pair repels the
other pairs, and so the four pairs move
themselves to the far corners of the carbon
atom.
Water molecules have this tetrahedral shape
too. Below are the two depictions of a water
molecule (ball & stick and a more realistic view)
The two hydrogen atoms are positioned at two
of the four corners of the tetrahedron. So,
what are at the other corners? At the other
corners are pairs of electrons that are valence
electrons of the oxygen atom, but there are no
hydrogen atoms there. Look at the periodic
table below.
Below is a depiction of a lysine molecule (the
realistic view is not shown because the
structure is not very clear in that view). Lysine
is an amino acid, one of the 20 building blocks
of all the proteins of all life forms on Earth.
The red atoms are oxygens, the blacks are
carbons, the blues nitrogens, and the whites are
hydrogens. All but the hydrogens have their
bonds arranged in the tetrahedral way. You can
see this if you look closely.
Covalently bonded atoms don’t always have 4
valence pairs when bonded to other atoms, and
so the arrangement of the bonds is not always
tetrahedral. An extreme example is shown in
the figure below: a molecule of Iodine
heptafluoride, 𝐼𝐹7 .
Oxygen is in the sixth position of the second
row, which means it has 6 electrons in its
valence shell, and two empty spaces. Only two
hydrogen atoms are required to provide the
oxygen atom with enough electrons to
complete its valence shell. The valence shell
still has four pairs of valence electrons, but only
two of them are pairs that are involved in
bonds. All four pairs repel each other and so
the water molecule is shaped in this way, giving
water its important properties.
The iodine atom is bonded to 7 fluorine atoms.
Geometry of Metallic Crystals
Metallic elements form metallic bonds between
their atoms: the valence shells of individual
atoms join to form a vast valence shell that
surrounds the remaining ions. We thus can’t
really speak of the number of valence pairs on
each atom. Instead, a sea of electrons attracts
the ions to each other, and they pack
themselves together as closely as the forces can
pull them.
If you were to stack glass marbles together in a
way that minimizes the space that they take up,
as in the figure below, how many other marbles
would each marble be touching?
The answer is 12. This is typically the way that
metal atoms arrange themselves when they
form a solid. So, metal atoms are bonded to 12
other atoms when they’re in a solid form. This
is what gives metals like steel their tremendous
strength.