Question on the alignment of Fermi energy

[kaypu]

Dear everyone
    i want to study the transport properties in molecular devices with different orientation, When the  molecule is contacted by two Au (111) electrodes in different orientation, the Fermi energy of isolated molecule can be set to the electrochemical potential of the electrode. In the process, our calculation indicates that there is a tiny charge transfer between the gold electrode and the molecules. For one orientation, the charge transfer is 0.22e, for another is 0.07e. The Fermi energy of the isolated molecule in different orientation is the same. why the charge transfer is different in the process of alignment?

[zh]

When a molecule contacts with Au(111) in different orientation, the charge transfer between molecule and Au substrate may be different. This is reasonable in physics. The followings claimed by you are problematic: "The Fermi energy of the isolated molecule in different orientation is the same. ".

[kaypu]

Maybe I didn't express clearly,  i optimize the isolated molecule in Dmol3, and get the fermi level. When i rotate the isolate molecule along the X axis and then optimize it, i will get the same fermi level.

[Anders Blom]

Of course a molecule in free space has no preference for the orientation, so you get the same value. When the molecule is contacted to the surface, however, the orientation of the molecule relative to the Au atoms plays a role (a small one, probably, but some). Note that in ATK you simulate an open system where charge flows, and so the total number of electrons in the system will adjust itself self-consistently to the solution.

[kaypu]

thank you very much