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

[Максим Арсентьев]

Hi, I worked at the same field, to find out which atoms could be doped with
look
https://www.researchgate.net/publication/285619763_Doping_graphene_with_a_monovacancy_bonding_and_magnetism
You can use faster codes loke SIESTA to find most stable configurations of
the molecule on the graphene surface, and then use QE for refined calcs

2016-08-09 20:46 GMT+04:00 Rolly Ng <rollyng at gmail.com>:

> 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
>
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-- 
Best wishes,
Maxim Arsent'ev, Ph.D. (Chemistry)
Laboratory of research of nanostructures
Institute of Silicate Chemistry of RAS
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