Creating a capped nanotube is an easy task to perform using the Builder, but it's perhaps not entirely obvious

how to do it. This tutorial teaches you the necessary steps!

Introduction
This tutorial consists of four steps, each involving just a few operations:

Create a nanotube Cut a C60 fullerene in half (in a clever way) - this will be the cap Attach the cap to the nanotube Clean up a bit

In this tutorial we will build a (5,5) nanotube capped by a C60 hemisphere. There are however multiple other combinations of nanotubes and fullerenes that match, and such capped tubes can be constructed using the same approach as here.

Step 1: Build an extended (5,5) carbon nanotube

1. 2.

Start VNL and open the Builder

Click Add>Add Custom>Nanotube. Set N=M=5 and click Build.

3.

Use Bulk Tools>Repeat to extend the structure 10 times in the C-direction. Press Crtl+R to see the whole structure properly.

4.

Finally, remove the unit cell by clicking

. The capped tube is anyway not periodic, so we build it as a

molecule.

Step 2: Cut the fullerene in half

1. 2. Insert a C60 molecule by clicking Add>Add From Database, and choose Databases>Fullerenes from the menu. Locate C60 in the list and add it to the stash. In the C60-CNT (5,5) system the tip of the cap is a pentagon. Imagine now a coordinate system in the screen plane where east is right, north up, south down, and west left. Then rotate the fullerene so that the western face of the system is a pentagon, while keeping the Z axis pointing to the "east" and the X axis roughly to the "north".

3.

The cap is made from 30 carbon atoms, corresponding to half the C60. If, however, you cut the molecule in half, it becomes very difficult to attach it to the nanotube. The trick is instead to leave one extra "layer" of atoms, which match almost perfectly the edge of the nanotube. Therefore, select the atoms as shown in the picture above, and delete them.

4.

The edge of the cap consists of pairs of atoms - just like the edge of the tube. Thus, select 3 atoms as shown in the picture below - two in a pair and one more in the neighboring pair - and change them to Nitrogen. This is just to make it easier to identify them in the next step.

Step 3: Capping the tube

1. 2. Go back to the "(5,5) Carbon Nanotube" stash item by double-clicking it. Select three equivalent atoms in the tube, as you did in the cap. By equivalent is meant that the edge of the tube looks just like the edge of the cap, with pairs of atoms, and the goal is to match up these pairs. Change these three atoms to oxygen, again to make them easy to identify.

3.

Then drag the C60 stash item onto the 3D window to import the cap. The next few steps may differ slightly in precise detail from the images, depending on which precise atoms you changed to nitrogen.

4.

When the cap was imported, the Move tool

was automatically activated. Select one of the nitrogen

atoms (as shown in the picture, the first atom in the pair which is not next to the lone nitrogen atom) its selection marker turns red and the atom is labeled "0". Then drag it so that it ends up on top of the equivalent oxygen atom in the tube.

5.

Then select the second nitrogen atom in the pair. When you now drag this atom (red selection marker,

and labeled "1"), the cap will not move, it will rotate around the bond between atoms "0" and "1". Rotate the cap in place by making atom "1" overlap the next oxygen atom in the pair on the tube edge. You may need to rotate the view to get a clear aim. 6. Finally, select the third nitrogen atom, and move it on top of the third oxygen atom (dihedral rotation). The final structure is shown below.

In case you didn't succeed (sometimes the cap becomes inverted), undo the last two steps, unselect all anchor atoms by clicking the background, select only one atom and move the cap out a bit from the tube, and try again from 4. It can also be a good idea to pre-align the cap with the tube - see the video for details!

Step 4: Finalizing the geometry

At this point there are overlapping atoms - in fact we utilized this to construct the geometry. You could use "Fuse" in the Move tool, but there are atoms which are only almost overlapping, which are not detected. 1. 2. 3. Instead, close the Move tool, and open Select>Close Neighbors, enter a distance of 0.7 and press Select (10 atoms should be selected) and then press Delete. Change all atoms back to carbon. The final touch to the structure is to optimize the cap, since the radius of the fullerene is slightly different from the naontube. You will however at the same time want to keep the other end of the nanotube as it is (perfectly periodic) so that we can later extend it, if necessary. Therefore, first select the cap and a few more layers of atoms in nanotube (about half of the tube should be fine). Then, open Coordinate Tools>Quick Optimizer, set the maximum number of iterations to 100, and click Run. The tool uses the classical Brenner potential (available for C, H, Si, Ge) so the optimization only takes a few seconds.

Notes
Of course, building this structure just by itself is not very meaningful - you will want to connect it to something, like a surface or molecule. This will be covered by other tutorials, where you will learn how to build structures like those in the pictures below.

Below is selection of other capped nanotubes that can be built with a very similar approach. These system are slightly more difficult to build, and require some hand tuning.

(9,0) CNT + C60 - in this case the cap tip a hexagon and the edge of the tube is zigzag.

(6,6) CNT + fullerene No. 134 (C3v symmetry) from the database

Last Updated on Wednesday, 31 October 2012 12:54