Model an NH4 ion

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Spacebat_1
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Model an NH4 ion

Post by Spacebat_1 » 26 Sep 2020, 15:38

I'm trying to model an NH4+ ion and I can't seem to figure out how to do it. There are no obvious hydrogen positions or I would have just added hydrogens around an N atom as usual.

I found a mention of predefined SFAC parameters for "NH+1" on the internet but I can't get it to work. If someone can help me with the syntax or if there are other ways to deal with these ions like an AFIX command, I would be most grateful.

Thanks!

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Helge
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Re: Model an NH4 ion

Post by Helge » 30 Sep 2020, 17:07

Right, second attempt:

In order to fix hydrogen atoms via AFIX to a parent atom you need non-hydrogen bonding partners to this parent atom to fix the H positions to. As these are absent in an NH4+ you cannot use AFIX here. The same problem occurs for water.
Do you see the H atoms in the difference fourier, at least vaguely? If so, you can use DFIX and SADI: Assign the four electron density peaks around the nitrogen. Then use DFIX to restrain the N-H bond lengths to the default value (I believe 0.91 angstroem, but I am not sure; this should be listed in the LST file from SHELXL if any fixed hydrogen atoms are present: sp3 nitrogen) and use SADI for all six H...H distances. I suggest to make both restraints quite hard, i.e. a low standard deviation. I usually use 0.001. In my experience anything below that switches the restraint off, but this is an experience from SHELXL97.

Spacebat_1
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Re: Model an NH4 ion

Post by Spacebat_1 » 20 Oct 2020, 17:13

Thank you so much for you answer Helge! I apologize for not following up earlier!

Unfortunately I cannot see the H-atoms so this particular strategy does not work.

//d

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