QuantumATK Forum
QuantumATK => General Questions and Answers => Topic started by: majeedqau on May 29, 2018, 17:02
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Hi all,
As you know that to simulate the surface we use slab model. In order to avoid the states originating from dangling bonds from the bottom surface, we use passivation techniques i.e we passivate these dangling bonds with hydrogen atoms. The procedure to passivate dangling bonds with hydrogen atoms, the procedure using VNL is as follows:
(1) Open Coordinate Tools → Custom Passivator.
(2) Set Hybridization such as Sp,SP2 etc.
(3)Adjust the bond distance among the hydrogen atoms
(4) Press the “Passivate” button.
My question is related to the step no.2 i.e to chose the relevant hybridization for my system. How can I find the exact hybridization for my system using VNL? In other words, as to passivate dangling bonds we need exact information about the hybridization of our system/structure so how can I find that which hybridization is following my structure using VNL? I need your help and suggestion in this regard. Your help would be highly appreciated.
Thank You and looking forward for your nice comments.
Using VNL, how can i find the hybridization of my strucutre?
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The simple answer, as a rule of thumb, is to count the number of bonds on the atoms you need to passivate. A carbon atom wants to have 4 neighbors, so if it only has 3, then you need to add 1 Hydrogen atom (sp3), if it has 2 then you need 2 H (sp2), and so on. This rule is however only for carbon, and will be different for other elements (outside group IV).