Simulation of stocking different molecules in a nanotube


The carbon nanotube (CNT) has many applications, and we are going to demonstrate some of them in this tutorial. 

A CNT is a stable structure, consisting of carbon atoms only, that are twisted into a cylinder and held together by convalent bonds. It has some interesting properties, such as electrical conduction and hydrophobic walls which we are going to discover together in this tutorial.

Creating a nanotube:

First of all, we create a dihydrogen (H) by combining two hydrogen atoms. Be careful not to place the hydrogen atoms too far from eachother, otherwise the bond between them will dissappear. 

Secondly, we need to create our nanotube. This is easily done with the element Nanotube creator . The hydrogen molecule should now be placed in the middle of (inside of) the CNT, which we can quickly verify by moving the camera.


figure1: Creating an H2 molecule inside of a CNT

Now launch a simulation (Universal force field – Interactive modelling) and set the step size to 0.5 fs and 10 steps.

If you weren’t careful enough (despite the warning) and the H bond dissappeared, don’t worry, there’s a simple solution. You will need to delete one of the hydrogen atoms with the ereaser  and then add another one (as well as forming the bond between the two). Now launch the simulation and everything should work as intended.

figure2: Simulating a H2 molecule inside of a CNT

Alright, it’s time to play with the dihydrogen. To get a good view of the molecule, use this button  to move the camera, or use the different viewing angles available in the upper toolbar . Use the rectangle selection  and select both the hydrogen atoms forming the H₂ molecule and try to slowly move it through the nanotube wall. Let go of it when it is close to the wall, and watch what happens (see GIF below).

figure3: Moving the H2 molecule towards the CNT wall and then letting go of it. This will cause the tube to repell the hydrogen molecule and keep it confined inside the CNT


The H₂ should rest inside the CNT, not being able to easily escape it. The dimensions of the CNT, such as its diameter and length, as well as the different structures (multi-walled or single-walled etc.) play an important role and determine how good the nanotube is stocking the dihydrogen. For those interested we leave a link to a simulation of a similar problem using the Monte-Carlo principle.

One important feature of this CNT property is the ability to stock H₂-molecules inside the tube. This could be useful in the future when the hydrogen fuel-cell cars have been properly developped.


Water molecule in the nanotube:


We are now going to perform a similar experiment as the dihydrogen one. This time we are also adding an oxygen molecule in the mix, creating H₂O, known in everyday-life as water.

Before we start, we could have some residues (an H2 molecule and a CNT) left from the previous exercise. To remove these, we stop the current simulation (red stop button), click on “Document 1” in the Document View and then press Delete on your keyboard. We are now ready to start our next experiment.

The process is almost identical, only that this time we create a water molecule by adding two hydrogen molecules to a single oxygen atom.

Around this water molecule, a carbon nanotube is created in the same way as the last time. Subsequently launch a simulation with the same parameters as previously (step size = 0.5 fs and 10 steps) and watch what happens when you try to move the water molecule outside of the CNT in a similar manner as we did with the hydrogen molecule.

This time we observe another interesting property of the CNT, its hydrophobic and hydrophilic abilities. The walls of the nanotube are hydrophobic (meaning that they will repel water – Hydro is latin for water and phobic comes from the greek word phóbos meaning “fear“) so the water is always repelled from the inner tube surface and will therefore be contained within the CNT.

figure4: Droplet of water being held together by hydrophilic forces 

When performing these simulations, it could be useful to know that you can in fact place (almost) any molecule inside the carbon nanotube and still obtain the same results. This is due to the fact that the choice of simulator (Universal Force Field) works on the basis of quantum physics, but does not account for any electric polarization or any hydrophobic/hydrophilic properties of the molecules. It is however a good way to simulate our reality, more or less accurate depending on how many different parameters and molecular properties you give it.



So that was a quick demonstation of the countless properties of the carbon nanotubes. Of course, these are not the only applications out there, and seeing how new discoveries within the field are made everyday, the number of applications will continue to grow. Here are some other interesting applications along with their sources (if you find a particularly interesting one you would like to know more about):

Filtering water with nanotubes:

Scientists have discovered a new way to make reusable waterfilters, using multi-walled carbon nanotubes (MWCNT) that absorb organic contaminants in the water such as pharmaceuticals or coloured dyes. The filtering process is based on the hydrophobic principle, allowing water to pass the tubes, while organic particles are being absorbed by the CNTs by forming bonds with them. This behavior is exploited in products such as the LifeStraw.

Increasing the freezing point of water:

A counterintuitive property of water confined in a CNT is that the temperature where ice is melting, or being liquified, into water is increased to over 100°C (the temperature where water normally boils and forms steam).



Home page




Monte Carlo-simulation:

Different CNT structures and hydrogen stocking:

Hydrogen fuel-cell cars:’

Hydrophobic and hydrophilic properties:

UFF simulation:

Studies on water filtration with CNT:

Brief description of the LifeStraw filtering technology:

Another similar filtering technique: Water Purification using Carbon Nanotubes – A. Cummings

Increasing the freezing point of water inside a CNT:



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