Understand Molecular junctions better.

[Nordland]

Hey everyone.

Apart from Magneto-tunnel junctions, the thing I have spent most of my time modeling is molecular junctions,
and I have build some NL scripts for understanding these better, and try to enable me to speed up the process
of selecting the molecules for creating the molecular junction with the correct properties, and understand how to customize
the molecules to have the properties that I desire.
The idea is too limit the number of twoprobe calculations since they take alot of time, but you can't not leave them out for good.

For this I have written alot of code, and it is a big mesh, but I have tried to clean up in it and I thought I wanted to share the process
with you guys, if you have interest in molecular junctions.

Approach:

• Select the molecule - use the molecular builder in VNL or some other database.
• Perform a calculation of the molecule and store the netcd file
• Calculate the joint density of states to determine the distance between the energies levels in the molecule
• Calculate the susceptibility of the molecule to determine between shich states the electrons couple.
• Compare with transport calculation to see agreement

Tomorrow I will post scripts and a example of the usages of these scripts.

[Nordland]

In order to illustrate how to use this script I have done a little case study of a benzene molecule attached with two sulfur atoms
as bridge in Li-wire. This will be my sample system.

• First take a look at the attachment of the geometry.
  
• Then I calculate the joint density of states to see the possible energy levels. The possible transition energies is 2.77 eV, 3.57 eV, 3.92 eV and so on.
  

  from molecular_optics import *
  scf = restoreSelfConsistentCalculation('c6h4s2.nc')
  calculateJointDensityOfStates(scf)
  
• In order to determine the allowed transition, we calculate the susceptibility of the molecule. However we do it along the z-axis due to the symmetry
  of the system, but in general it should be done along all the axises
  

  from molecular_optics import *
  scf = restoreSelfConsistentCalculation('c6h4s2.nc')
  calculateSusceptibility(scf,axis='z')
  

  As we see from the susceptibility there only energy that is allowed in our energy windows, is the peak around 2.8 eV,
  and therefore we except to see something in the transmission spectrum here.
• Finally we calculate the transmission for the perfect li-wire and then with the molecular junction with the benzene molecule,
  and where are done with the calculations.

When looking at the transmission spectrum we can see that the molecular junction stops all the incomming electrons until they have an energy of rougly 2.9 eV.
The exact energy of this transition state is shifted slighly due to the interacting with the wire, however it is remarkable close. Judging from the joint density of states,
we should have a lot more transmission in the area between 3-6 eV, however the susceptibility shows that these transitions are very unlikely due to the symmetry of the eigenstates/orbitals.
Therefore we know, that if we want to have transmission in the domain from 3-6 eV we need to break the symmetry of these eigenstates, and we can then make a better device. How to break this symmetry is another story, but the idea is to add another chemical group.

Have I lost you or is it plain speak?