Is it necessary to satisfy the dangling bonds?

[swap700]

Hi,

I want to know if it is necessary to satisfy C dangling bonds, I am trying to create a defect in graphene system by deleting certain atoms, do I need to passivate the structure before proceeding or I can proceed with passivating the dangling bonds?

[Anders Blom]

You should passivate them for sure, or else the Fermi level has a tendency to wander into places it doesn't belong. For sp2 you can find a Custom Builder that does the passivation in the tutorial on transport in graphene nanoribbons.

[swap700]

What if the graphene structure rearranges it self to give some other structure, like an example below.

[Anders Blom]

The important thing is to count the number of bonds for each C atom (which is actually what the script I mentioned does). The H atoms are supposed to go in and add a 3rd bond to C atoms which only have 2 C neighbors.

[swap700]

Thanks for the prompt reply, I had the doubt cause, I use the file attached below, i let it relax to get the image posted above, in which the bonds rearrange such that there is no need of passivation. So i wanted to know if I use the structure above, which i get from relaxing the one below, is it ok? or I am making an error cause I dint passivate before relaxing?

[zh]

The di-vacancy in graphene is more stable than the single vacancy, because in the former case the dangling sigma bonds of carbon atoms next to vacancy site can be passivated by themselves. So it is reasonable that you just do the geometry optimization for the di-vacancy without hydrogen passivation. However in the latter case, two of the three carbon atoms next to vacancy site will form a new bond and the remaining third carbon atom has a dangling sigma state, and hence the passivation of the dangling sigma state by hydrogen is quite favorable in the energetics.

The stabilities of single vacancy and di-vacancies in graphene were well studied in literature, please did a literature survey.