Why the MPSH spectrum does not aggree with the transmission spectrum

[zhangguangping]

Hi,all:
I have calculate a molecule sandwiched between two Au electrodes.And I found the MPSH spectrum of the bare molecular do not aggree with the transmission spectrum at some place(as shown in FIG1) though some aggree.There is a transmission peak at -1eV,while no MPSH.MPSH of FIG1 is for the bare molecular without any Au atoms.As I know the transmission spectrum is for the whole system including the bulk electrode and surface atoms.So I guess the transmission peak at -1eV maybe from the surface.So I recalculate the MPSH for bare molecule and the neighouring 3 Au atoms at each side (so 6 Au atoms in all)which connect the molecule to the surface.And the MPSH is in FIG2.But this time the aggreement is yet not good.
I think if there is a peak in the transmission spectrum, there should a corresponding MPSH state for the bare molecule,for the molecule connect the left and right electrodes.(Am I right?)
So who can tell me the reasion?

[zhangguangping]

Can anyone give some advice!

[zh]

I think if there is a peak in the transmission spectrum, there should a corresponding MPSH state for the bare molecule,for the molecule connect the left and right electrodes.(Am I right?)

This may not always true. When a molecule is chemically connected with the left and right electrodes in absence of bias voltage, the HOMO (highest occupied molecular orbit) of molecule and the Fermi level of electrodes will be aligned automatically, and hence charge transfer between molecule and the surface of electrode occurs. In other words, the orbitals of molecule may be strongly hybridized with the electronic states of electrodes.

[zhangguangping]

I think if there is a peak in the transmission spectrum, there should a corresponding MPSH state for the bare molecule,for the molecule connect the left and right electrodes.(Am I right?)

This may not always true. When a molecule is chemically connected with the left and right electrodes in absence of bias voltage, the HOMO (highest occupied molecular orbit) of molecule and the Fermi level of electrodes will be aligned automatically, and hence charge transfer between molecule and the surface of electrode occurs. In other words, the orbitals of molecule may be strongly hybridized with the electronic states of electrodes.

Dear zh,
I have been waiting for your reply all the time.Thanks for your reply very much.
My opinion aggrees yours.
But in order to analysis using MPSH,is it need to do the MPSH including some more Au atoms?
Or at this situation,MPSH analysis is not valid?
Thanks again.

[zh]

In MPSH analysis, you may need to include two Au atoms that are bonded with molecule. Alternatively, the projected DOS may be more helpful  to understand the features in the transmission spectrum.

[zhangguangping]

In MPSH analysis, you may need to include two Au atoms that are bonded with molecule. Alternatively, the projected DOS may be more helpful  to understand the features in the transmission spectrum.

Thanks for your reply dear zh.
Can you describe in detail how to use the PDOS to understand the features in the transmission spectrum?
Or can you give me some clues?
Thanks in advance!

[zh]

It cannot be described simply using text. An example of projected DOS (PDOS) is demonstrated  in the manual. Please check it first: http://quantumwise.com/documents/manuals/latest/ReferenceManual/XHTML/ref.devicedensityofstates.html, and then do a test on a simple case to check the correspondence between the features in transmission and those in PDOS.

[zhangguangping]

It cannot be described simply using text. An example of projected DOS (PDOS) is demonstrated  in the manual. Please check it first: http://quantumwise.com/documents/manuals/latest/ReferenceManual/XHTML/ref.devicedensityofstates.html, and then do a test on a simple case to check the correspondence between the features in transmission and those in PDOS.

Thanks I will do as your instruction.