As you have probably learnt in school all of us and our things are made out of atoms. These atoms are the building blocks for all living and non-living things. So it is basically like having a really big number of really small Lego bricks stacked together, right?

Well yes and no. Almost everything is made out of atoms being combined, so in that regard they are like small Lego. It turns out however, that things on that micro-scale behave differently than things in our normal macro-scale world. Atoms and molecules don’t “snap” together like Lego bricks would (in some cases they might actually repel!). Intuitions from our everyday lives on how things move and interact can not be directly applied to an atomic scale.

My assumption is that developing an intuitive understanding of how things interact at this micro-scale is both possible as well as greatly beneficial for understand how our world works. For this in this article I want to introduce the most basic of all atoms - the hydrogen atom.

What are atoms made of?

Atoms were originally thought to be smallest possible building blocks of reality. However it turns out that Atoms can be further subdivided into a combination of Protons, Neutrons and Electrons¹. Protons and Neutrons are the heavy part of the atoms, centered in the middle. The Protons and Neutrons together are also called the Nucleus².

While the nucleus gives the atom (most of) its mass, it is the electrons that do all of the interesting stuff: They are responsible for bonding and thus creating molecules. Most of chemistry and molecular biology is basically interaction of electrons! So getting a good understanding of how they behave is crucial for understanding our world on a micro-scale level.

So how does an atom look like?

So let’s just dive in! How does that all look like? You have probably seen the model of an atom where electrons orbit the nucleus like planets orbit the sun. That picture is inaccurate. Electrons do not orbit atoms - they don’t orbit at all as they don’t even have a well defined position in the first place! So what do they do? And where are they?

Instead of electrons orbiting a nucleus, it is better to visualize electrons as “probability clouds” around the nucleus.

This is a hydrogen atom with a single electron. The fuzzy cloud shows the area where the electron is likely to exist. The brighter the area, the more likely the electron is to exist there.

Shells

Wait, is that it? You might remember from school that there are different “layers” of orbits around the atom - like rings in an onion. An electron does not just exist around an electron - it usually has a specific energy associated with it. The higher the energy the bigger the orbit gets. For example if you “excite” (increase the energy) of the electron in the Hydrogen atom you get this:

As you can see the cloud has gotten a bit bigger (and more colorful, but more on that later)! The electron is more “spread out”. Also there is a now a gap! there is an outer ring and an inner ring. The electron in this state can exist anywhere in the inner or outer ring, but it will never be in the gap.

What happens when we further increase the energy? The electron cloud will increase getting bigger and have more gaps.

What we have done here is increase the “shell” of the electron, usually denoted with the letter $n$. At first (in the ground state) the electron is in the first shell ($n=1$). As you increase the energy of the electron you get to the next shell ($n=2$). With every further shell the energy of the electron increases. Thus if you want ot excite an electron to a higher shell you need to infuse it with energy - such as light. Usually the electron wants to fall back to its lowest possible energy state. When doing so it releases the energy that it has stored as light.

Subshells

For every shell (denoted by $n$) there are a number of subshells, usually denoted with the letter $l$. The number of the subshells is always equal to the number of the shell. So for the first shell ($n=1$) there is exactly one subshell. For the second shell ($n=2$) there are two subshells, etc. - the higher the shell (the higher $n$), the more subshells exist.

The subshells is where the electron clouds will start to look interesting! We have already seen what the first subshell ($l=0$) for every shell looks like above. Also for shell $n=1$ we have already seen all subshells, as there is only one. However for $n=2$ we have seen only one subshell yet! The second subshell looks like this:

The electron cloud is now dumbbell shaped with a gap between them! Now we have already seen all subshells for $n=2$ (because there are only two). For $n=3$ we have not yet seen the second and third subshell. This is how they look like:

Second subshell:

Third subshell:

Isn’t it pretty? Actually there is even more variation for the subshells! For every subshell there are many orbitals! So for the the higher the subshell number the higher the number of possible orbitals. The first subshell has one orbital. The second subshell has two more, so three orbitals. Then every next subshell gains two new orbitals.

In the case the the third subshell for our third shell we have a total of five different orbitals. This is one of those:

Uh oh now everything is so colorful! What happened? The colors of the electron cloud represent the “phase of the wave function”. What does that mean? When calculating the electron cloud one calculates something called the “wave function”. This function tells you for every position how likely it is to find an electron. It is also “waving” similar to a water wave. When two water ripples collide the peaks and troughs cancel each other out, while two peaks or two troughs combine to even higher peaks and lower troughs.

Just as water waves have peaks and troughs, the wave functions has peaks and troughs. However unlike water where the wave displaces water up or down, the wave function here can wiggle in any direction on the circle! Where the wave function points to at a given point is visualized with the rainbow color. When two wave functions collide, opposite colors would cancel each other out, and equal colors would amplify the wave.

Sources and Annotations

Footnotes

1. Home Bookshelves General Chemistry Map: Structure and Properties (Tro) 1: Atoms 1.8: Subatomic Particles - Protons, Neutrons, and Electrons / 1.8: Subatomic Particles - Protons, Neutrons, and Electrons. source: https://chem.libretexts.org/Bookshelves/General_Chemistry/Map%3A_Structure_and_Properties_(Tro)/01%3A_Atoms/1.08%3A_Subatomic_Particles_-_Protons_Neutrons_and_Electrons ↩

2. Wikipedia contributors. (2025, February 12). Atomic nucleus. In Wikipedia, The Free Encyclopedia. Retrieved 08:33, February 16, 2025, from https://en.wikipedia.org/w/index.php?title=Atomic_nucleus&oldid=1275363392 ↩