When I read papers, I found that the alignment of the fermi level relative to the molecule's HOMO and LUMO in a two probe model is extremely sensitive to charger transfer and conductance.
For example, calculated transmission is strongly dependent on the offset between the HOMO energy level and Fermi level for systems where hole transport dominates. if the Fermi energy lies far from the HOMO energy, the system will have a lower transmission than if the Fermi energy lies close to the HOMO.
This is an illustrative picture to understand the electronic transport properties of molecule coupled with two metal electrodes. It is true in physics.
Can anyone tell me how was the band alignment been tackled in ATK/VNL calculation for two probe systems?
When the molecule is coupled with the metal electrode, the band alignment is automatically and naturally done, and it is not controlled by the code. The code determines the electronic structure of the whole system (i.e., the molecule + metal electrodes) in a self-consistent manner. The band alignment is usually discussed by post-processing the obtained electronic structure, e.g., MPSH.
The key issue is that the absolute value of eigenvalue is meaningless. For example, the absolute values of HOMO and LUMO energy levels of a isolated molecule can not be compared with those of a molecule coupled with metal electrode. Actually, the values of HOMO and LUMO energy levels of a molecule coupled with metal electrode is hard to be determined accurately, because in this case the molecule can not be treated as an isolated system any more.
