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Designing the structure, such that all the atoms lie in the same plane (without twisting or bending)


#1

I have created a complex chemical structure (Covalent-Organic framework) in Avogadro 1.2.0n. After optimizing the geometry, and applying ‘Auto Optimization’ tool, a final well defined structure has emerged. However, some of the individual structure (like Benzene) were twisted in other direction. This makes my structure to go out of the xy (or yz or zx) plane. I want my structure to be in only one plane, without any twisting. Is it possible?

EDIT-1: Please find below the screenshot of the structure


As you can see, the benzene is twisted into another plane, while other structures are in other direction. I look for a plain structure. Since it is a complex structure it is very difficult to edit the coordinates. Can some one suggest the correct method to solve it?

Thank you


#2

One of the scripts in Avogadro2 is a ‘flatten’ command that I’ve used in my research.

In the meantime, you can go to the Build ⇒ Cartesian Editor… and clean up anything that’s distorted. But I’d be curious to see an example of a distorted benzene - these should definitely be planar.

Can you post a link to a coordinate file (CML, SDF, etc.) or screen-shot?

Thanks!


#4