Curious Kids: What do molecules look like? | Kiowa County Press

A nanographene molecule imaged by non-contact atomic force microscopy. Patrik Tschudin/gross3HR/Wikimedia Commons, CC BY

Christine Helms, University of Richmond

curious children is a series for children of all ages. If you have a question you’d like an expert to answer, send it to [email protected]


What do molecules look like? – Justice B., 6, Wimberley, Texas


A molecule is a group of atoms bonded together. Molecules make up almost everything around you – your skin, your chair, and even your food.

They vary in size, but are extremely small. You cannot see an individual molecule with your eyes or even a microscope. They are 100,000 times smaller than a hair’s breadth.

The smallest molecule consists of two atoms stuck together, while a large molecule can be a combination of 100,000 or more atoms. A molecule can be a repeat of the same atom, like the oxygen molecules we breathe, or can be made up of a variety of atoms, like a sugar molecule made up of carbon, oxygen, and hydrogen.

But what do molecules look like? It all starts with their building blocks: atoms.

Opposites attract

The particles of matter that make up an atom are not all the same. They can have a positive charge, a negative charge, or no charge. Scientists call them protons, electrons and neutrons.

A gold atom has a dense center composed of 79 protons and 118 neutrons, surrounded by a more spread out cloud of 79 electrons. Illustration created by Galarza Creator.

Neutrons with no charge and protons with a positive charge form the heavy center of the atom. Negatively charged electrons surround this small center.

When atoms approach each other to potentially join and form molecules, the negative electrons of one atom are attracted to the positive protons of the other, and vice versa. The two atoms adjust accordingly.

A diagram showing a single round atom, top.  Below are two atoms stretched into oval shapes, the positive part of one being drawn towards the negative part of the other.
When an atom is alone, the negative electrons surrounding its center are symmetrical. When two atoms approach each other, the negative electrons of one atom move towards the positive center of the other atom. Christine Helms, CC BY-SA

You can compare it to trying to choose a seat in a classroom. There are a few rules. For example, you have to stay in the classroom and you can’t sit on someone. By following these rules, you might try to sit next to your friends and away from your enemies. Finding the perfect position for everyone in the class to be happy is like finding the perfect position for the atoms in a molecule. Sometimes the atoms cannot find a happy arrangement and no molecules are formed.

See the invisible

If the molecules are too small to be seen with your eyes or even with a powerful microscope, how do scientists see them? The answer is that they have developed special tools to do so.

One tool uses x-rays, which you may be familiar with since doctors use them to see the bones of the body. X-rays are a type of light that human eyes cannot see, such as ultraviolet or infrared light.

When scientists shoot x-rays at molecules, some rebound. Scientists can record these bouncing X-rays and use their models to determine what individual molecules look like.

A scattering of black dots on a white background.
X-rays bouncing off atoms of a protein molecule form the black dots in the image above. The location of these points tells scientists how the atoms are arranged in the molecule. Del45/Wikimedia Commons, CC PER

In 1912, one of the first molecules seen this way were salt (NaCl) – the molecule that makes up the ingredient we all know and love on french fries.

Scientists have also invented other methods to see molecules. In the same way that electrons change their behavior when two atoms approach each other, the center of the atom can also change its behavior. A technique called nuclear magnetic resonance detects these changes at the center of the atom and uses them as clues to determine which atoms are nearby.

A atomic force microscope works like a flimsy diving board that shakes when you step on and jump on it. But this diving board is extremely small, so small that a negative charge at its tip will bend it toward the positive center of an atom. Moving this diving board and watching how it bends can show the location of atoms in a molecule.

An animation showing how an atomic force microscope works.

Another technique that scientists have developed to see molecules is called cryo-electron microscopy. First, the scientists freeze the molecules to a much colder temperature than snow or ice. Then they shoot electrons at the molecule and collect those that pass through it to create an image. This technique has won the Nobel Prize in Chemistry in 2017.

All shapes and sizes

So what do molecules look like? They are a grouping of atoms, the center of which contains most of the matter, while the rest is largely empty space. Each atom has a specific position where it is happy, much like the students in this class.

Side by side diagram of a flat molecule and a round molecule.
Diagrams of the atoms composing the molecules of benzene, on the left, and fullerene, on the right. Jynto (left) Benjah-bmm27 (right)/Wikimedia Commons

Every molecule is different – some are really different. For example, benzene is flat like a pancake, while fullerene is round like a ball. Penguin can be drawn to look like a penguin, while other molecules look completely random. But the positions of atoms in a molecule are never random.

While scientists know what many molecules look like, there are some that we are still trying to understand. Knowing these answers can lead to inventions of new materials and medications.


Hello, curious little ones! Do you have a question you would like an expert to answer? Have an adult send your question to [email protected] Please let us know your name, age and the city where you live.

And since curiosity has no age – adults, let us know your questions too. We cannot answer all questions, but we will do our best.

The conversation

Christine Helmsassociate professor of physics, University of Richmond

This article is republished from The conversation under Creative Commons license. Read it original article.

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