3/3 vs 4/4 gold lattice and (one thiol vs two thiols)

[Ranjana Dangi]

Hello,
I would like to do the transport calculation on a little bit big complex so for that to make a large enough surface for the molecule  I would like to repeat the structure 4*4*2 times instead of 3*3*2(mentioned in the tutorial building a molecular junction). Because in the 3*3*2 my molecule gets connected only on the terminal gold atom.

So I am thinking with 4*4*2, this situation would not occur.My questions are:
1. Does the 4*4*2 repeat gold surface make any change on transport calculation? If yes then would you mind to explain how?
2. What could be the difference in transport properties between the molecule that connected to the gold electrode by using two thiols(in my case I have used 2thiols that connects molecules to the two gold atoms) vs only one thiol(most of the studies have used only one thiol)?

little bit of long questions but I hope you will me on these issues.
Thank you so much in advance,
Ranjana Dangi

[Petr Khomyakov]

1. Does the 4*4*2 repeat gold surface make any change on transport calculation? If yes then would you mind to explain how?

In general, transport calculations should be checked for convergence with respect to the lateral unit cell size. So, doing 4x4 instead of 3x3 makes total sense to verify that the conductance is converged within a given tolerance. If converged, there should be virtually no change in conductance when going to the limit of infinite lateral supercell. Of course, you have to compute the conductance per lateral unit cell  area to able to to compare the conductance values for different lateral unit cells.

2. What could be the difference in transport properties between the molecule that connected to the gold electrode by using two thiols(in my case I have used 2thiols that connects molecules to the two gold atoms) vs only one thiol(most of the studies have used only one thiol)?

I guess this is something you have to study by doing the actual calculations. I assume that this is a part of your research task.

[Ranjana Dangi]

Thank you so much for the response, If you don't mind , could you explain in little bit about  this:
 ''transport calculations should be checked for convergence with respect to the lateral unit cell size'' copied from your response.
How do I do that?

[Petr Khomyakov]

You just have to increase the electrode cross section = lateral unit cell area, e.g., by first doing 3x3 supercell, and then 4x4.