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Offline paramjot

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Regarding Bonding
« on: November 3, 2020, 18:48 »
Hi,
I  run DFT-optimization between a molecule and graphene crystal. In the attached figure, After optimization, Oxygen (red ball) of molecule form a bond with Pt (purple ball) atom on graphene but oxygen already has two other bonds. How this can be possible for oxygen to form three bonds as oxygen have valency 2. Does that stick signifying a covalent bond or not??
« Last Edit: November 3, 2020, 18:50 by paramjot »
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Offline mlee

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Re: Regarding Bonding
« Reply #1 on: November 4, 2020, 12:53 »
Tune the Fuzz Factor in the Graphics properties of builder.
It just allows tuning threshold for maximum bond distance visualized with sticks  in the Builder. 
Note that the Builder does not know anything about the chemistry of your material. It means that having two atoms geometrically connected or not is just visual thing. Concluding on whether two atoms chemically connected can be done only after analysis of the actual electronic structure.

Refer to https://forum.quantumatk.com/index.php?topic=5887.0
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