Isolated Oxygen Atom (H-atoms Missing

[ylidcrystal]

Hello
I couldnt add to O6 atom hydrogen atom from fourier map, which causes alet A in check cif. Do you have an idea for this reason?


Principal mean square atomic displacements U

0.0182 0.0152 0.0133 N3
0.0253 0.0210 0.0087 Ag1
0.0318 0.0278 0.0188 O1
0.0382 0.0291 0.0153 O4
0.0436 0.0265 0.0184 O3
0.0344 0.0252 0.0221 O2
0.0377 0.0169 0.0061 C6
0.0359 0.0186 0.0141 C1
0.0347 0.0185 0.0156 C5
0.0307 0.0236 0.0128 C4
0.0367 0.0194 0.0078 C2
0.0292 0.0213 0.0144 C7
0.0278 0.0185 0.0126 C3
0.0184 0.0144 0.0129 N1
0.0239 0.0185 0.0134 C8
0.0213 0.0185 0.0113 C10
0.0235 0.0141 0.0098 N4
0.0258 0.0172 0.0138 N2
0.0388 0.0336 0.0194 O5
0.0236 0.0170 0.0088 C11
0.0281 0.0190 0.0097 C13
0.0204 0.0180 0.0111 C9
0.0220 0.0178 0.0140 C12
0.1152 0.0341 0.0229 O6

[Marc]

Hi,

if you cannot see the H atoms in the difference Fourier, don't worry. Missing H atoms for water molecules isn't exactly unheard of, and nobody (human) will complain. That should never be a 'serious category' A level alert. It shouldn't be an alert at all.


Marc

[johnewarren]

Yeah there is a thread about this here:
viewtopic.php?f=11&t=878&hilit=hfix+water

But as Marc says if you can't see it don't bother.

If they do then also quote this reference from the FAQ back to them:

Q2: When I start SHELXL on my PC the disk rattles loudly for several hours and smoke comes out of the back. Is this a bug?

A: You must be trying to run SHELX under some version of Windows! The best solution is to reformat the hard disk and install Linux. However the current release should produce less smoke.

[HorstPuschmann]

Of course this is a matter of debate. Personally I think that if you can add hydrogen atoms geometrically, then you should do so. They are present. We know they are. Often it is possible to 'build up' a sensible hydrogen bonding network (starting from a water molecule where you can see they hydrogen atoms. Tools like HADD in Olex2 can be quite successful in providing many sensible H positions. This way, you will fully account for all scatters present in your structure and your final sum formula will be correct (avoiding an otherwise unavoidable CIF ALERT: even if you don't have the hydrogen in your atom list, they must appear in the sum formula, causing a discrepancy which CheckCif will complain about).

[johnewarren]

I disagree with you Horst. I think that you can not be certain that the hydrogen is located where you are putting them. You are may not see anything in terms of sensible hydrogen bonding. Then again the term of hydrogen bonding is another debate what the parameters are do change, have changed in the past. At some point you can say that you can computationally model everything and then use that model to fix all the atoms in your refinement.Just because we can do something and know that something should be there the absence of it in a crystal structure does not mean we need to force it to be there.

And does it matter if CheckCif gives you an alert? It is a tool for validation not the law or some supreme being. You can deviate from it. I think we are all getting caught up if this checkcif red tape a bit too much sometimes.

ylidcrystal - stick to your gut add hydrogens if you want or don't add hydrogens on an isolated oxygen either why don't let yourself be bullied into anything you are uncertain about.

[HorstPuschmann]

As I said, this is a matter of debate. I have carefully chosen my words, and am not advocating adding hydrogen atoms regardless. And while, indeed, in some cases we really can't be certain that the hydrogen atoms are located where we put them, we can certain that a water molecule without hydrogen atoms is wrong. Unless it isn't a water molecule, but an OH^- or an O^2-, of course, but then this should be known from other analytical techniques and the crystallisation conditions.

From the chemist's point of view, I'd rather have all hydrogen atoms present in a chemically plausible position and end up with a structure that resembles chemical reality, even if the actual position of the hydrogen atoms could not be determined by the x-ray diffraction experiment.

[Marc]

If you know where the H atoms are, go ahead and add them. In case of water molecules, most of times you might have some indication but if you see no H atom electron density whatsoever, I'd prefer some honesty and leave them out rather than fix them to probable but still potentially wrong positions. Do not want to give the impression that I have located H atoms if I have not.

Marc

[HorstPuschmann]

I am all for honesty. I'd add the hydrogen atoms in chemically sensible positions and then tell the _refine_special_details that I've done so. I don't want to pretend that I've got a whole lot of O^2- ions about the place.