graphene sheet defect

[yogita taluja]

 I want to create pyrollic defect in a graphene sheet . In pyrollic defect I doped one  nitrogen atom  and deleted one atom  and change there coordinate of doped  atom , but when i perform optimization through optimizegeometry option . In my my stabilized bulk configuration  whose atom  coordinate I changed return back to there original position. i don't want it to return back it's original postion . Both before and after optimization bulk configuration i attached  1 ) without optimization 2) with optimization. kindly suggest a way ......

[Jess Wellendorff]

From your calculations it appears that your initial guess for the position of the N atom is simply not stable; the N atom moves to a different site and thereby "repairs" the carbon lattice. Did you consider Hydrogen-terminations for the unsaturated carbon bonds? Perhaps that will help to stabilize the N atom in the original position.

[zh]

This suggests that the initial position of of doped N atom is quite unstable. You may refer to the  following paper (particularly look at Figure 11 ):
http://pubs.acs.org/doi/full/10.1021/jp512886t
The pyrollic N at monovacancy is a saddle point for the migration of a pyridinic N around vacancy site of monovacancy. That is say, a pyrollic N at monovacancy is much unstable, compared with a pyridinic N at monovacancy.

The way in my experience to generate the atomic structure of a pyrollic N  at monovacancy in graphene:
1) replace one of carbon atom in graphene by a nitrogen atom and optimize the structure;
2) rotate one N-C bond in the optimized structure of 1st step by 90 degree (in plane) and optimize it to get the structure of N-doped Stone-Wales defect
3) remove the C atom in rotated N-C bond in the optimized structure of 2nd step and optimize it.
In such way, the initial position of pyrollic N will be placed in high symmetry position, which is better than the one generated by hand as you have done. And so you may have chance to get the optimized structure of a pyrollic N at monovacancy in graphene.

[zh]

If hydrogen atom appears around doped N at vacancy, the hydrogen atom will be favourable to bind with the doped nitrogen rather than carbon atom to make it pyridinium-like N. (http://pubs.acs.org/doi/full/10.1021/jp512886t)

[yogita taluja]

dr. zh..... i tried as per u said but its not working after stonewales when i remove one atom and optimized  it nitrogen atom again back to there original position . i don't want to use hydrogen atom in my defect .    plz give me another suggestion to tackle this problem... as soon as plz.........

    yogita