I was studying a research paper on DFT calculation for the adsorption of H2S with activated carbon. On two different report, they simulated the carbon using 4 to 7 benzene cluster rings.
I tried doing mine but I found out my Hydrogen counts was more than theirs on both occasion. The second guy used a pyrene as a representation for activated carbon (but his Hydrogen count was 9 instead of 10). I brought up Pyrene from Avogadro and the Hydrogen count was 10.
My question is: how can I make my hydrogen count equal to theirs, to enable me proceed.
I have attached both papers below.
Thanks for your answers.
By hydrogen count, do you mean the number of hydrogen atoms on the carbon cluster or something else? Of course Pyrene as an entity has 10 hydrogen atoms, but as far as I can see, the "activation" in these papers was generated by manually removing the saturating H atoms. Otherwise you would just calculate adsorption of whatever on a way too small graphene slab.
Jürgen Weippert Thanks for you response. Exactly what I was confused about. If they manually removed a (some) hydrogen atom(s), how can I remove mine so that the structure would not change (because, I did try to make my structure to look like theirs by making the number of hydrogen look like theirs, but it was collapsing/distorting)
If you want to remove atoms in Avogadro, just switch it to drawing mode (pencil symbol) and right click all the atoms you want to delete.
Jürgen Weippert and Ahmed Elrashedy
Thank you both. I appreciate your answers.- Badges
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