What is the shape of a molecule? - George Zaidan and Charles Morton

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A molecule is nearly all empty space, apart from the extremely dense nuclei of its atoms and the clouds of electrons that bond them together. When that molecule forms, it arranges itself to maximize attraction of opposite charges and minimize repulsion of unlike. George Zaidan and Charles Morton shape our image of molecules.

Lesson by George Zaidan and Charles Morton, animation by Bevan Lynch.

What is the shape of a molecule?

Well, a molecule is mostly empty space.

Almost all of its mass is concentrated

in the extremely dense nuclei of its atoms.

And its electrons,

which determine how the atoms

are bonded to each other,

are more like clouds of negative charge

than individual, discrete particles.

So, a molecule doesn't have a shape

in the same way that, for example,

a statue has a shape.

But for every molecule,

there's at least one way

to arrange the nuclei and electrons

so as to maximize the attraction

of opposite charges

and minimize the repulsion

of like charges.

Now, let's assume that the only electrons

that matter to a molecule's shape

are the outermost ones from each participating atom.

And let's also assume

that the electron clouds in between atoms,

in other words, a molecule's bonds,

are shaped kind of like sausages.

Remember that nuclei are positively charged

and electrons are negatively charged,

and if all of a molecule's nuclei

were bunched up together

or all of its electrons were bunched up together,

they would just repel each other and fly apart,

and that doesn't help anyone.

In 1776, Alessandro Volta,

decades before he would eventually invent batteries,

discovered methane.

Now, the chemical formula of methane is CH4.

And this formula tells us

that every molecule of methane

is made up of one carbon and four hydrogen atoms,

but it doesn't tell us what's bonded to what

or how they atoms are arranged in 3D space.

From their electron configurations,

we know that carbon can bond

with up to four other atoms

and that each hydrogen can only bond

with one other atom.

So, we can guess

that the carbon should be the central atom

bonded to all the hydrogens.

Now, each bond represents

the sharing of two electrons

and we draw each shared pair of electrons as a line.

So, now we have a flat representation

of this molecule,

but how would it look in three dimensions?

We can reasonably say

that because each of these bonds

is a region of negative electric charge

and like charges repel each other,

the most favorable configuration of atoms

would maximize the distance between bonds.

And to get all the bonds

as far away from each other as possible,

the optimal shape is this.

This is called a tetrahedron.

Now, depending on the different atoms involved,

you can actually get lots of different shapes.

Ammonia, or NH3, is shaped like a pyramid.

Carbon dioxide, or CO2, is a straight line.

Water, H2O, is bent like your elbow would be bent.

And chlorine trifluoride, or ClF3,

is shaped like the letter T.

Remember that what we've been doing here

is expanding on our model of atoms and electrons

to build up to 3D shapes.

We'd have to do experiments

to figure out if these molecules

actually do have the shapes we predict.

Spoiler alert:

most of the do, but some of them don't.

Now, shapes get more complicated

as you increase the number of atoms.

All the examples we just talked about

had one obviously central atom,

but most molecules,

from relatively small pharmaceuticals

all the way up to long polymers

like DNA or proteins, don't.

The key thing to remember

is that bonded atoms will arrange themselves

to maximize the attraction between opposite charges

and minimize the repulsion between like charges.

Some molecules even have two or more

stable arrangements of atoms,

and we can actually get really cool chemistry

from the switches between those configurations,

even when the composition of that molecule,

that's to say the number and identity of its atoms,

has not changed at all.