2 probe geometry problem

[sweta]

Dear everyone,

There have been lots of work been done using dithiocarboxylate (-CS2) anchoring group in 2-probe system using ATK. Some of the articles I have mentioned here for your reference:

1. Torsion angle dependence of the rectifying performance in molecular device with asymmetrical anchoring group; Physics Letter A 374 (2010) 4876-4879

2. Negative differential resistance and rectifying behavior in atomic molecular device with different anchoring groups; Physica E 43 (2010) 524-528

I want to work with (-CS2) anchoring group and my problem is that when I make geometry by connecting (-CS2) group and then drop to molecular junction (custum builder) and then optimize the geometry. After optimization get changed.

 Please anyone help me how to make simple carbon dimmer geometry using dithiocarboxylate group properly so that both sulphur atom of CS2 will remain connected to AU electrode properly after optimization  

[zh]

Whether the S atoms of CS2 in the dithiocarboxylate group can be chemically bonded with Au electrode or not? It is a chemical and physics problem. One cannot  make a simple geometry as you mentioned. A simple test to solve the aforementioned problem is first optimize the adsorption of dithiocarboxylate group on a Au surface. The geometry optimization of such case is much easier than those in the geometry optimization of a two-probe system.

[sweta]

Thanx for your help sir.

What is the role of allignment layer 0-0,1-1, 2-2 of electrodes in two probe system. Is it related to top & hollow site of AU electrode.
How to measure distance between AU and anchoring group (say Sulphur) in above 3 allignment layer cases

[zh]

1). Au has the stacking sequence of ABCABC... along the [111] direction. I guess that the "0", "1", and "2" in your question may corresponding the different atomic layers of Au along the [111] direction.

2). There are some discussions on the measurement of distance between atoms. Please check them on this forum.