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Welcome to ATK, my name is Nanna. In this video I will show you how to build
a pentacene molecule.
A pentacene molecule is five benzene rings merged together, so we will start by
locating the benzene molecule from the database.
Open the Builder.
Go to stash, click Add>
From Database.
Go to the menu bar. Click Databases and choose Molecules.
Locate benzene.
Add it to the Stash.
You can turn the benzene molecule in the 3D window by holding down the right
mouse button.
We need some more benzene molecules in order to make the pentacene.
So go to Stash.
Click on the benzene molecule stash item, and press Copy twice.
Then go to the first Stash item.
Remove two hydrogen atoms
from the first stash item. This will be the left unit.
Then select the second Stash item
and remove
four hydrogen atoms from this molecule.
Then go to the third Stash item
and remove two hydrogen atoms from the left side
this will be the right unit.
Then open unit one
and open the move tool. Here can be a good idea to zoom out a bit. You can do this
by scrolling with the wheel on the mouse. Then select the molecule and drag it
vertically in the 3D window.
This is to distinguish it from the others. Then close the Move Tool widget,
Because otherwise you won't be able to select the next stash item
which we're going to do now. So drag the second stash item to the 3D
window.
It's already selected and Move Tool is activated
select an anchor atom
and merge it to the right edge of unit one.
Repeat this two times.
Close move tool widget. Drag.
Select an anchor atom.
Merge.
Until you have four rings in total.
Like this.
Then drag unit three into the scene and put it on the end ring.
Like this.
Close the move tool widget.
Now go to Select>
Close Neighbors.
And select and delete overlapping atoms.
Finally we need to optimize the structure.
Go to Coordinate Tools>
Quick Optimizer.
Increase the maximum steps to a hundred.
Then click Run. Press Ctrl+R
to center the view.
The pentacene molecule is now ready,
so make sure to save it
This tutorial is the first part of a longer tutorial on on how to create
metal-organic interfaces. Thank you for watching!