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Correct bond angles for sp3 hybridized atoms
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simon

Joined: 15 Jul 2016
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Link to postPosted: Fri Jul 15, 2016 11:28 pmPost subject: Correct bond angles for sp3 hybridized atoms Reply with quote

How to you get correct 109 degree angle for sp3 hybridized atoms in your structure?

Bond angle checker marks 109 degree bond angle on sp3 hybridized atoms as "wrong" and the cleaner tool will incorrectly set them to an 90 degree angle.

Zsolt
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Joined: 11 Jan 2006
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Link to postPosted: Mon Jul 18, 2016 1:42 pmPost subject: Re: Correct bond angles for sp3 hybridized atoms Reply with quote

bengtfisk wrote:

How to you get correct 109 degree angle for sp3 hybridized atoms in your structure?

Bond angle checker marks 109 degree bond angle on sp3 hybridized atoms as "wrong" and the cleaner tool will incorrectly set them to an 90 degree angle.

Do you want 109 degree bond angles in 2D or in 3D?

Please review this document and let us know which rules/recommendations are not followed by ChemAxon's depiction.

simon

Joined: 15 Jul 2016
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Link to postPosted: Mon Jul 18, 2016 8:59 pmPost subject: Reply with quote

In 2D.

The rules are followed but the depiction is not ideal when using the "clean structure function". In the file I'm attaching (a picture from the iupac recommendation document) you can see the situation i mean, I'm trying to get the "preferred" structure instead of the "acceptable" one in MarvinSketch.

nmihala
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Joined: 02 Apr 2012
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Link to postPosted: Tue Jul 19, 2016 1:35 pmPost subject: Reply with quote

MarvinSketch draws the structure preferred by you, however that is true that our 2D clean renders them in 90 degree.

We can only suggest you workarounds like clean only a selected part of a molecule or Bond length fixer.

I hope this helps.

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