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POLTYPE: AMOEBA parametrization tool
https://pren.github.io/poltype
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Nitrogen is not being added to an adjacent aromatic ring. #39

Closed anessler closed 4 years ago

anessler commented 4 years ago

While parameterizing the structure XAFPAY from the CCDC, I noticed that the experimental structures show the bonds from the nitrogen atom parallel to the bonds of an adjacent aromatic ring. Minimizing the structure with parameters from poltype2 these bonds adjust slightly so they are no longer parallel suggesting that the nitrogen is no longer included in the conjugated system. The attached PNG is an attempt to show an experimental crystal structure overlaid with a minimized parameter structure to juxtapose the nitrogen/ring bonds. CP23_aroma

pren commented 4 years ago

Please check the QM (opt) structure first. POLTYPE may be using the QM structure. If you would like to keep it flat (sp2 like), you can add oop term to the H and C that connects to the N. You can borrow the formamide N OOP parameters in amoeba09.prm.

From: Aaron Nessler notifications@github.com Sent: Monday, August 3, 2020 1:10 PM To: pren/poltype poltype@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: [pren/poltype] Nitrogen is not being added to an adjacent aromatic ring. (#39)

While parameterizing the structure XAFPAY from the CCDC, I noticed that the experimental structures show the bonds from the nitrogen atom parallel to the bonds of an adjacent aromatic ring. Minimizing the structure with parameters from poltype2 these bonds adjust slightly so they are no longer parallel suggesting that the nitrogen is no longer included in the conjugated system. The attached PNG is an attempt to show an experimental crystal structure overlaid with a minimized parameter structure to juxtapose the nitrogen/ring bonds. https://user-images.githubusercontent.com/33242946/89213211-5cf53b80-d58a-11ea-92ff-482176b9097a.png

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anessler commented 4 years ago

Thank you very much for the fix. I had originally tried using a pitor parameter between the nitrogen and the aromatic ring. This also seemed to hold the nitrogen bonds in the same plane as the aromatic ring. Is there a reason to prefer using the OOP parameter over pitor?

pren commented 4 years ago

Pitor does not prevent out-of-plane bending of NH2. It actually does the opposite.

From: Aaron Nessler notifications@github.com Sent: Monday, August 17, 2020 8:40 AM To: pren/poltype poltype@noreply.github.com Cc: Ren, Pengyu pren@utexas.edu; Comment comment@noreply.github.com Subject: Re: [pren/poltype] Nitrogen is not being added to an adjacent aromatic ring. (#39)

Thank you very much for the fix. I had originally tried using a pitor parameter between the nitrogen and the aromatic ring. This also seemed to hold the nitrogen bonds in the same plane as the aromatic ring. Is there a reason to prefer using the OOP parameter over pitor?

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