[Pw_forum] Using molecularpdos.x for adsorption on metal-doped graphene

[Rolly Ng]

Dear QE experts,

I am trying to refine computation of 3-NT adsorption on metal doped 
graphene using QE. This is according to our previous work
http://dx.doi.org/10.1016/j.commatsci.2011.07.045

With the help of Dr. Guido Fratesi, I am exploring molecularpdos.x to 
find the change of HOMO and LUMO of the nitrated tyrosine molecule on 
adsorption to metal-doped graphene.

There are my questions and answers, your comments are welcome.

Q1) Spin polarization. The full system contains a metal doped graphene
with single metallic atom of Au and Ni at the center and a 3-NT molecule
adsorbed onto the graphene sheet, so I included nspin=2 for the full
system. But the adsorbate (3-NT) molecule is likely to be nonmagnetic,
so I did nspin=1 for its gas phase. Can molecularpdos.x cope with
different nspin for the full system and adsorbate?
A1) Yes, since nspin=2 can handle a nonmagnetic case
R1) So, I am adding nspin=2 to the 3-NT molecules

Q2) K-points. I used smearing for the full system since it is
semi-metallic. Should I use smearing for the molecule in gas phase? I
believe this is not a good idea but can molecularpdos.x works with
k-point and non k-point?
A2) Smearing: no problem, K-points: should be the same
R2) So, I am using the same K-points for both full system and single 
molecule.

Q3) I would like to evaluate the change of the HOMO-LUMO gap of the
adsorbate (3-NT) on adsorption to the metal-doped graphene. Can
molecularpdos.x do that?
A3) Dr. Fratesi and his team used that code also to study 
molecules/graphene...
http://dx.doi.org/10.1038/srep24603
R3) Very useful and thank you!

Q4) I would like to determine if physisorption or chemisorption occurs as
with DMol3, can molecularpdos.x do the same job? For the physisorption 
vs. chemisorption, the adsorption energy may be a good indicator. 
However, I believe the electronic structure of the bond may also 
indicate which type of adsorption it suppose to be?

With regards,
Rolly

-- 
PhD. Research Fellow,
Dept. of Physics & Materials Science,
City University of Hong Kong
Tel: +852 3442 4000
Fax: +852 3442 0538