In chemistry and physics class, they visualise them as plastic marbles with sticks to connect them to eachother, but what is the true shape of an atom? It also contains quarks and has spinning electrons and neutrons around it. Is it a cloud? How does atomic matter actually look?
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The center is a dense cluster of neutrons and protons. Around this are “clouds” of electrons; because of quantum effects it is impossible to pinpoint exactly where the electons are. There is a lot of space between the electrons and the nucleus.
Almost nothing whatsoever.
There are tiny particle-like things whizzing around a center of other tiny particle-like things also whizzing around, but at any scale in which you can reasonably depict it, it’s mostly nothing all the way through.
The analogy for electron/neutron for instance is that if the neutron was a pea in the middle of a stadium, an electron would be whizzing around the outside of the stadium, and would be 1/1000th the size of the pea. Almost the entirely of the “atom” is nothing at all. There’s no real “structure” in that sense. It’s just a handy diagrammatic depiction.
Imagine standing in the middle of the stadium and seeing a pea at your feet and then trying to spot a speck of dust running around the stadium. That’s literally ALL the atom is. Everything else is forces of those things pushing each other (a bit like magnets, but ultra-strong in comparison at this scale… magnets the size of a pea that literally keep that speck of dust orbiting even at that distance and not letting it escape). Take away the stadium and everything else and just leave the pea and the dust-speck, and there’s basically nothing there.
And even the “orbiting” thing is a bit of a misnomer, the particles themselves are not what you think of as particles, and they’re moving at ridiculous speeds so much so that we can’t even tell where they are, but they “look” like they’re orbiting at a given distance (however when it comes to shrinking/growing the atom by adding more electrons, for instance, they almost immediately “jump” to a different orbit with basically almost no “time” where they are between the two states).
And from that we draw cute little diagrams like planets orbiting or spheres, and none of that has any real relevance to the actual structure of the object of an atom itself.
Then you get into the quantum / quark stuff… nobody knows. At that scale things break down and even light doesn’t help us picture anything. You’re talking about things “smaller than light itself”, if you like. We can only imagine.
It doesn’t really have a shape in the sense we normally mean. A lumpy cloud is probably the closest easy analogy.
You can’t define it’s shape by the boundaries where you can touch it, like we do with macro scale solids, because it doesn’t have any defined boundaries you can touch.
You can’t define it’s shape by what it looks like because it’s so small that we can’t see it with any light our eyes can work with. Extremely high energy particles can “see” it in a sense but they are so powerful that they distort the shape when they interact with the atom.
The particles themselves aren’t the little spheres your old high school marble models suggest…they’re spread out in space like tiny waves with basically a cloud of probability for where they’re likely to be found at a particular time.
At some scale terms like “looks like” don’t actually make any sense any more. Like, you could not look at an atom and see it in any reasonable meaning of the word. All you get there are probabilistic clouds of “things” that can’t even decide if they are particles or waves.
It’s tough to pin down a defined shape when things get this small. Even an atom is mostly empty space. The nucleus makes up a tiny point in the center. But we don’t know how to pin down the position of an electron with any certainty, ajd it’s not clear that the concept of a “position” actually applies in the way we usually think of it. We can calculate the *orbitals* of electrons -probability graphs showing where an electron is likely to be found- and [some orbitals do look like spheres. Some, however, look very different](https://en.m.wikipedia.org/wiki/Atomic_orbital). The first two images on the Wikipedia page I linked all show some of the possible orbitals for a hydrogen atom. and that’s just one electron buzzing around the nucleus. For other atoms it quickly gets more complex.
We tend to approximate atoms as spheres. It’s not completely correct, but it’s a model we can wrap our heads around while still being close enough for most purposes. And that’s okay, as long as we remain aware that it doesn’t work all the time, and that sometimes we might have to reach for the more complicated stuff.
[Here’s a stop-motion movie made by moving atoms around with a scanning tunneling microscope](https://youtu.be/oSCX78-8-q0?feature=shared). These aren’t the true colors of the atoms: individual atoms don’t have a color, because visible light doesn’t work at scales this small. But it’s one of the closest things we have to what an atom looks like. [This picture from a couple years ago](https://www.newscientist.com/article/2279115-this-is-the-most-detailed-look-at-individual-atoms-ever-captured/) zooms even closer in, but again, remember that these pictures aren’t using light the way our eyes see it.
This is pretty difficult to talk about with any real accuracy, because existence at these scales is so counter-intuitive. You have to throw away a lot of the ways you commonly think about things to comprehend what’s actually going on.
First of all, the “marbles with sticks” constructions that you see in chemistry class aren’t atoms. Those are *molecules*. One marble represents a single atom, and the sticks represent the ways those atoms are bonded to one another.
Atoms are, at their most basic level, comprised of two things: electrons, and quarks. Quarks come in two flavors that we care about, named “up” and “down” (because scientists are very clever…). These quarks bundle up into sets of three, which will either be a proton or neutron depending on which kind of quarks are in the triplet. 2 up + 1 down = proton, 2 down + 1 up = neutron. 3 quarks of all the same type are, uh, not allowed. Protons and neutrons clump together into a dense little nugget that we call a “nucleus”, and the electrons are… “whizzing around close by”, let’s say. The specific details are *extremely* complicated.
Electrons and quarks tend to be shown in textbooks as little spheres, implying they’re solid objects with volume. But that’s not really the case. Both of them are actually point-like. They have no volume at all. Nothing. So even if you *could* shrink down like Ant Man to try and look at them (and we pretended that light at that size worked the same way it does at regular human size) there would be nothing to see. They would literally be invisible points in space that can move around and just happen to act like tiny magnets and have gravity. Kind of boring, isn’t it?
Entire atoms, though, *do* have volume. They have a size we can measure. And so do protons and neutrons, for that matter. So atoms have volume, but are made entirely of things that *don’t* have volume, how does that work?
Y’know how when you push the north poles of two bar magnets together, you can feel them repel one another? And the closer you bring them together, the more strongly they repel? That’s what quarks and electrons do to one another. Try to push them extremely close together, and they’ll resist your push. The closer you get, the harder the push. Since they have no size, there’s no limit to how close you can get them to one another. But that also means there’s no limit to how hard they can push back.
Realistically, there is a limit to the amount of force you could ever apply to press two particles together. Therefore, they will always be separated by some nonzero amount of distance. We can use this “keep-away” distance between them as the next best thing for “volume”. The space between the particles is completely empty, but since you can’t force them together any closer, then for all serves and purposes they’re *basically* “touching”, right?
The size of a proton and neutron is defined by the “keep-away” distance that the quarks maintain with one another. The size of the nucleus is defined by the “keep-away” distance that the protons and neutrons maintain with one another. And the entire atom’s size is the “keep-away” distance that the electrons of the atom maintain with their nucleus the electrons of other atoms.
All of these “keep-away” distances around these particles and groups of these particles are either perfectly spherical, or very close to spherical most of the time. That’s why textbooks (and your marble-and-stick kits) usually show them as solid spheres, even though they actually aren’t. They “keep-away” distances make them *behave* like spheres in many ways, yes. But they aren’t solid, they are in fact 100% empty. Comprised entirely of invisible points that have no volume, but can still affect one another.
At this point you are probably wondering how are we able to actually *see* anything, since I’ve been describing everything as completely invisible. *Invisible* might not be the correct word, really. The way you classically think about light is that it heads toward and object like, say, a mirror, and it “bounces off” of that object, like a ricocheting projectile. At the human scale that is accurate enough. But at the atomic scale, that’s not really how it works. Or, maybe it is, depending on how you look at it. But that’s getting into the whole “is light a particle or a wave” thing, which is… uh… complicated!
In addition to all of the topics I completely dodged or brushed away with “it’s complicated”, there’s also a lot of questions that have probably cropped up that I have to leave to keep this answer from becoming even more of a thesis than it already is. Like, “What makes the protons stick together even though they repel each other?”, or “How do neutrons stick to anything if they’re neutral?”, or “Why do quarks like to get together in sets of three?” I’ve already glossed over entire classes worth of physics in this answer, and to answer these questions adequately would need more.
In particle physics nothing has shape as you might think about it. Every particle is a point in space with a repulsion field around it. This repulsion force gets stronger the closer you get. In a sense it creates the shape of the particle, which is a perfect sphere.
Now if we zoom out a bit we can think about protons and neutrons. Each of these is actually created by 3 particles called quarks. So maybe we could think about these as 3 balls stuck together. However, particles are always moving, so the location of any particle can only be thought of as a sphere of possible locations. Effectively a proton or neuron is the combination of the quark particles, resulting in their own repulsive sphere.
Zoom out again and we have the nucleus of an atom made up of neutrons and protons. The fun bit now is that the above explanation applies again, and the nucleus is best thought of as a perfect sphere.
Zoom out again (a lot) and we have electrons. These are negatively charged and attracted to the positively charged protons. However they’re less attracted than the quarks are attracted to each other, so they can go a lot further away from the nucleus. Once again we can’t say exactly where a particle is, but this time the possible locations are much larger, forming this electron cloud everyone is talking about.
Electrons are a lot more tricky than the other particles. They get shared with neighbouring atoms, helping to create molecules, or even wandering off further creating electricity.
However getting back to your original question. Everything is a repulsion sphere, until we get to molecules which are collections of spheres. At which point the concept of shape starts to become relevant. We can observe molecules and see these shapes.
The best way to visualize reality is to think of it like a giant ocean of liquid energy wherein some waves look different from other waves and there are even different types, shapes, and amplitudes of waves. Our brains just say “oh, this wave looks like this and that wave looks like that”, but at the end of the day, it’s all just an ocean of chaotic energy.
Physics, chemistry, and science in general, is the task of coming up with conventions to describe the different types and shapes of waves and to predict how these waves affect and interact with each other. The exact point/moment in which one wave interacts or changes another wave is what we call ‘particles’. They’re less separate ‘things’ and more separate ‘moments’ of that singular same thing (the ocean).
They don’t look like ‘anything’, really. It’s just a vast cosmic ocean of chaos and our brains like to pick out the little pockets of patterns that look ‘ordered’ to our frail and feeble minds.
Your example is a molecule, not an atom.
Atoms are a nucleus with electrons orbiting around it in a cloud.
Molecules are multiple atoms joined together.
Each “marble” is an atom and the “sticks” are the molecular bonds.
We first learned that light could behave like a particle or a wave a long time ago ([19th century](https://en.wikipedia.org/wiki/Wave%E2%80%93particle_duality))
Then we began to see that matter behaves like both wave and particle at the subatomic level.
Then we began do understand the wave as relating to probability equations.
>In 1924 Louis de Broglie in his PhD thesis Recherches sur la théorie des quanta introduced his theory of electron waves.
The big answer is that the method you use to detect them greatly changes what we detect.
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