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 Post subject: Unwanted hydrogen on azide group in ligand
PostPosted: Tue Mar 28, 2017 7:53 pm 

Joined: Sun Mar 19, 2017 4:25 pm
Posts: 2
Hi all,
I have a ligand with azide group. Every time I draw or upload the ligand, after computing it is taking itself one hydrogen at the negative end of azide group. According to the resonance forms of azide group, there must be one negatively charged and another positively charged nitrogen but I don't want hydrogen on the negatively charged nitrogen.

Can anyone help me why it is happening and how to fix this problem?

Thanks in advance.


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 Post subject: Re: Unwanted hydrogen on azide group in ligand
PostPosted: Wed Mar 29, 2017 8:57 pm 

Joined: Wed Oct 29, 2008 2:24 pm
Posts: 204
You can uncheck the pH button or change the pH


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 Post subject: Re: Unwanted hydrogen on azide group in ligand
PostPosted: Thu Mar 30, 2017 1:10 pm 

Joined: Sun Mar 19, 2017 4:25 pm
Posts: 2
bikadi wrote:
You can uncheck the pH button or change the pH

It didn't help. It is protonated irrespective of the pH value. Also did by unchecking the pH button.


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 Post subject: Re: Unwanted hydrogen on azide group in ligand
PostPosted: Mon Apr 03, 2017 7:17 pm 

Joined: Wed Oct 29, 2008 2:24 pm
Posts: 204
Try uploading an optimized ligand and choose optimization none option.


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