Author Topic: << Adding H atoms to a Möbius sheet >>  (Read 313 times)

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Offline Camps

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<< Adding H atoms to a Möbius sheet >>
« on: November 25, 2019, 20:08 »
Hello,

I am interested in building Möbius based on graphene sheets.

To do that, I am following the recommendations in this link (https://forum.quantumatk.com/index.php?topic=2752.0).

My issue is that when I add the hydrogen atoms, they are not added homogeneously over the Möbius. There are rings with only 2 hydrogens added where other have 8.

I changed the size of the repeated units of the graphene sheet, but the problem continues.

I am using the Free Academic version of Virtual NanoLab (2017.1).

The images of three Mobius are attached below.

Regards,

Camps

Offline Anders Blom

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Re: << Adding H atoms to a Möbius sheet >>
« Reply #1 on: January 8, 2020, 08:58 »
Try using the more advanced "Custom passivator"  tool under Coordinate tools instead, and make sure to manually specify the hybridization as SP2, because in this geometry the automatic recognition used in the simple passivation tool (the toolbar button) will not identify the C atoms correctly (it looks at bond angles, but the geometry is curved compared to standard SP2, so it will think all C atoms are SP3).