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

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 the 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 them 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.