Au-(4,4’-bipyridine)-Au molecular junction¶

Instructions¶

: Start up AMSinput

Switch to DFTB: →

Select Task → NEGF

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

Import the lead file Au3x3_lead.xyz by clicking on the folder icon next to Lead

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

Open 4_4_bipyridine.xyz (the .xyz file you just downloaded)

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