Molecular representation

We will show you different molecule representations. We will take one molecule and see several ways how we can show it.

This lesson is a part of MEL VR Science Simulations. Learn more →

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Have you ever seen a mol­e­cule in real life?

Sure­ly not; they are too small.

Most mol­e­cules can­not be seen even with the best light mi­cro­scope. So what do they re­al­ly look like?

To­day in our lab we have as­pirin pills.

Let's look in­side.

You can see the mol­e­cules, that as­pirin con­sists of.

Let's take one of them and look clos­er. Each ball is an atom and the sticks are the bonds be­tween the atoms that hold them to­geth­er.

But this is not what a real mol­e­cule looks like. It’s just a mod­el that we call a 'ball-and-stick' mod­el.

In fact, the atoms are larg­er in size and in a mol­e­cule, they over­lap each oth­er. So, a more ac­cu­rate mod­el will look like this. We call it a 'space-fill­ing' mod­el.

But this is only a mod­el. In a real mol­e­cule, elec­trons are spread among dif­fer­ent atoms.

So, if you look at the to­tal elec­tron den­si­ty in a mol­e­cule it will look like this.

Since you can­not see mol­e­cules with your eyes, any vis­ual rep­re­sen­ta­tion is just a mod­el. And dif­fer­ent mod­els are more use­ful for dif­fer­ent sit­u­a­tions.

Some­times it’s more con­ve­nient just to use a flat struc­tural for­mu­la. For ex­am­ple, when you write the for­mu­la on a pa­per. Like this.

Also for or­gan­ic com­pounds, you can write a skele­tal for­mu­la. For an as­pirin mol­e­cule, it looks like this.

The skele­tal for­mu­la is a struc­tural for­mu­la in which the hy­dro­gen atoms at­tached to car­bon atoms and car­bon atoms them­selves are not in­di­cat­ed.

Also, we can just write a molec­u­lar for­mu­la. Let's see how to make it.

We sim­ply count the num­bers of each type of atom in a mol­e­cule. So, the as­pirin mol­e­cule con­sists of:

Nine car­bon atoms, Eight hy­dro­gen atoms, Four oxy­gen atoms.

This is the molec­u­lar for­mu­la of as­pirin.

But we have a lit­tle prob­lem with molec­u­lar for­mu­la. Just look!

There is an­oth­er mol­e­cule with for­mu­la C9H8O4: and an­oth­er! and an­oth­er! there are more than 700 mol­e­cules with this molec­u­lar for­mu­la. So, be care­ful us­ing the molec­u­lar for­mu­la when talk­ing about a spe­cif­ic sub­stance.

Look at these mol­e­cules, these are dif­fer­ent rep­re­sen­ta­tions of as­pirin mol­e­cules.

What type of chem­i­cal for­mu­la is it? Cor­rect! The bonds be­tween par­tic­u­lar atoms are shown here, that's why it's a struc­tural for­mu­la.

Teacher's notes


mol­e­cules, atoms, bonds, ball and stick mod­el, space-fill­ing mod­el, elec­tron den­si­ty mod­el, struc­tural mod­el, skele­tal for­mu­la, molec­u­lar for­mu­la

Stu­dents will

  • Learn dif­fer­ent ways to rep­re­sent mol­e­cules
  • Find out which rep­re­sen­ta­tion is suit­able for each pur­pose

Hands-on ac­tiv­i­ties

Af­ter VR

Ask stu­dents to build ball and stick mol­e­cule mod­els.

Top­ics to dis­cuss

  • Tube or rail map anal­o­gy: rep­re­sent­ing real-life ob­jects a cer­tain way, tak­ing into ac­count what in­for­ma­tion we want to de­liv­er. Com­pare two maps: a tube map and a city map with tube sta­tions.
  • Dif­fer­ent ways of rep­re­sen­ta­tion. How to choose the most suit­able rep­re­sen­ta­tion. In­for­ma­tion we can ob­tain from a par­tic­u­lar rep­re­sen­ta­tion.
  • Skele­tal for­mu­la prin­ci­ple, ex­pla­na­tion and ex­am­ples.
  • Why some­times we need 3D mod­els.


  • Which mod­el to choose if you want to see how many bonds are be­tween atoms in a mol­e­cule?
  • Why a molec­u­lar for­mu­la is not a con­ve­nient way to de­scribe a mol­e­cule?


Count how many atoms of each type are in dif­fer­ent mol­e­cules (from struc­tural mod­els).