how we can calculate streching distance dependence using ATK

[sweta]

Dear all,

I have gone through the paper entitled "conductance of streching oligothiophene single-molecule junctions: A first-principles study", J. Physical Chem C, 115, 25105 (2011).


During streching, I have also calculated the distance between Au-S bond on sandwitching biphenyl dithiol molecule between two Au(111)-(3*3) electrodes. Then reoptimize the structure. But after aptization the breaking distance between Au-S bond that I have calculated is much smaller (~2) than reported value (2.36). Why this difference occurs? How i can calculate streching effect correctly?

[zh]

During the geometry optimization, you may have to fix two atoms, one of which is Au and the other one is S.
For the more details of the calculations step in that paper, you had better try to contact the authors.  That kind of simulation step is designed by them.