# NEGF: Create a Molecular Junction¶

In this tutorial we will use the NEGF geometry building tools to create a Au-(4,4’-bipyridine)-Au molecular junction:

## Instructions¶

Start up AMSinput
Switch to DFTB:
Select Model → SCC-DFTB
In the main DFTB panel click on Parameter directory → QUASINANO2013.1
Click on to go to the NEGF panel (or click on Model → NEGF)

Import the leads and fill the central region with 4 layers of lead material:

Click here to download the lead file Au3x3_lead.xyz
Fill the central region with 4 layers of lead material

We now carve two tips out of the central gold wire:

Select the gold atoms as shown in the picture below
Delete the selected atoms by pressing delete on your keyboard

We need to make space in the central region for the 4,4’-bipyridine molecule; to this aim we define a left tip and a right tip:

1. Select the gold atoms on the left-hand side
2. Click on + next to Left Tip in the NEGF panel
Clear the selection by clicking anywhere in the molecule-drawing area
3. Select the gold atoms on the right-hand side
4. Click on + next to Right Tip in the NEGF panel

Your system should now look like this:

Tip

You can remove atoms from a tip by selecting them and clicking on - next to Left/Right Tip in the NEGF panel

The tips are now anchored to their respective leads. If we move the two leads via the Left/Right lead offset, the tips will follow them.

Make space for 4,4’-bipyridine molecule:

Set the Left lead offset to -10.0 Angstrom
Set the Right lead offset to 10.0 Angstrom

and import it:

Click here to download the .xyz file 4_4_bipyridine.xyz
Click on File → Import Coordinates

Your system should now look like this:

Tip

It is good practice to test the convergence of the results with respect to the number of lead repetitions and an amount of buffer lead material in the central region

We are now ready to run the calculation:

Click on File → Save, and name the job “zero_gate”
Run the calculation with File → Run
Wait for the calculation to finish

## Gate potential¶

To include a gate potential for the 4,4’-bipyridine molecule:

In the NEGF panel in AMSinput
1. Select the 4,4’-bipyridine molecule
2. Click on + next to Gate potential region in the NEGF panel
3. Set the Gate Voltage to 0.2 V

We will now run the job and visualize the results:

Click on File → Save as… and save it as gate_0_2
Run the calculation with File → Run
Wait for the calculation to finish
Click on SCM → Spectra…

To better see the effect of the bias potential on the transmission function, we can add the transmission functions at zero gate we computed earlier:

In AMSspectra click on File → Add and select negf.rkf in the gate_zero.results folder