Crystallography can be really frustrating

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Brownml2
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Crystallography can be really frustrating

Post by Brownml2 » 09 Aug 2016, 23:00

So, I ran crystals from Friday to the end of Monday. I got:

1) Salt that isn't known, but also isn't interesting in any way.
2) Structure that was known, but I got the wrong unit cell at the start so I didn't realize this until the next morning.
3) A potassium nitrate salt
4) Something that I've spent the entire day trying to solve without luck, and I can't figure out why. Good data (out to 0.7 A) and I took the full hemisphere. Twinned of course. I've tried solving using each domain, the first two, all three. Tried doing this in Triclinic and in MonoP (the two possibilities). Tried all the solving programs in Apex3, plus Superflip. Even broke out Crystals and tried it, but didn't seem to make any progress there. So yeah, that is pretty much a whole day gone right there.

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Helge
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Re: Crystallography can be really frustrating

Post by Helge » 11 Aug 2016, 10:50

Welcome to a service crystallographer's every-day-work.
At the moment the control-PC of my instrument drives me mad, although I suspect the problem is rather with the external harddisk onto which I am trying to backup my data. The disk scan is now running for almost 24h, and everything else on the PC is frozen. As the scan is still progressing after having crashed itself a few times I will certainly not interrupt it, but it means that I can do pretty much nothing at present.

And then there are the days when you get completely unexpected jewels. Or the days when you finally get a structure from a sample a student has tried to crystallise for months. Or these moments when a structure which looks inconspicuous on the first glance reveals a completely unexpected, interesting facet. At least I find that rewarding enough to compensate me for days like this (of which I have my fare share as well).

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Brownml2
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Re: Crystallography can be really frustrating

Post by Brownml2 » 11 Aug 2016, 16:19

So far I think my best moment was when I put on a crystal I didn't really expect anything of: it diffracted too well, had a small unit cell, and got a lovely product that would fit perfectly in the paper I was already working on, then later that weekend got an even better structure of something that complemented it perfectly, again from a crystal I was expecting to take off after the first shell.

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Helge
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Re: Crystallography can be really frustrating

Post by Helge » 12 Jul 2017, 15:42

:P I have a crystal running now which I think is jinxed. It keeps moving on the diffractometer. Not the crystal on the needle, but the pin on the goniometer head base (or the goniometer head as a whole? I cannot tell). Weird thing is, this happens with no other crystal.

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Brownml2
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Re: Crystallography can be really frustrating

Post by Brownml2 » 12 Jul 2017, 18:43

I've had that before! Same crystal, remounted it, still moved. Finally took it out and put it in a different pin and that worked. I wonder if the Plasticine goes bad, or got some oil in it or something.

Today's sweet spot: I've had this set of crystals I can't solve. I've gotten identical unit cells with multiple lanthanides, but I can't solve it despite really nice, untwinned data. Today I put a new crystal on, from another one of that reaction series and get the same unit cell, but with one of the lengths being 6.6A instead of 3.3A. I'd suspected that there were spots there, as after the last time I tried really soaking it with x-rays (60s or 120s on Cu microsource, forget which), and saw something there, but hadn't been able to take the time with the xrd was this busy. Today's crystal only needs 30s, and the unit cells seems to be tetragonal, so in another oh, 2 hours I should have a structure I've been wondering about for a month.

It is weird though: All the other spots are really intense. 1s/degree gets me out to 0.83A, but to see these spots well I need 15s/degree. So to see these spots faintly, I'm almost flooding the detector with most of them. Which I've heard of before, but not seen in person.

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Helge
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Re: Crystallography can be really frustrating

Post by Helge » 13 Jul 2017, 10:06

Another example of that sort of thing can be found here:
http://dx.doi.org/10.1016/j.jorganchem.2017.03.050
(the NCO complex); unfortunately the editor banished the crystallographic discussion into the Supplementary Information, and the pictures I had made have disappeared entirely.

I believe I have found the culprit for the crystal movements: The goniometer head. I have replaced it with a stiffer one. Let's see whether that helps.

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