Carbon NMR Fail
by Phil on May 16 2008 (2171 Views)You need to measure a 13C-NMR for all new compounds, that’s a golden rule. But what do you do when you can’t dissolve more than, say, 5 mg, of your stuff? Either you can’t afford to dump more of it in DMSO, never to be seen again*, or it just isn’t soluble enough.
In that case you simply try anyway, run an overnight experiment on a 400 MHz machine, and hope for the best. Sometimes it will work, sometimes it won’t.
What you always get is the massive solvent signal. On the left, there are some tiny bumps in the background noise, mocking me, that might just be the beginnings of real peaks. Of course there should be many more peaks than the three you can hardly see.
What now? I can hand this over to the NMR service. The first thing they will ask is: “Why don’t you give us a more concentrated sample?” In the past, I even had to redo a synthesis in order to get enough material for a missing carbon spec. Naturally, I should have started the synthesis on a larger scale, but somehow I always end up with those ominous 10 mg of end product. I hate sacrificing so much precious product to the DMSO god!
* I know it is possible to evaporate DMSO, but it takes forever. Also, the material I get out of it is usually an ugly, sticky oil instead of the nice solid I started with.
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May 16, 2008 - 04:05:40There are methods to supress Solvent signals. Not that I would know what they are, but my boss does. I have the same problem with one of my compunds. Because of phosphorus interactions my relaxation times on the carbon are rather large. That gives small signals, too.
Good Luck.
My guess at the reason why you are getting crap after removing DMSO is that you are heating it. I have recently come across two (non-heating) ways to remove DMSO that you could try. If you have access to a lyophilizer, freeze your sample and place it in there. I have had quite a bit of success doing this (no bumping even!). The other thing to try is to gently blow argon/nitrogen/air over the sample, oddly enough this seems to do the trick…
If I try this with our lyophilizer, the other users will kill me! Doesn’t the DMSO thaw?
I could try anyway… would be very useful.
How much DMSO are you talking about? I doubt that a little bit of DMSO trapped on the cooling coil would do much harm (as long as you clean it out when you are finished), but some people just get freaked out over the most ridiculous of things. You are right though, it probably will thaw but this method still seems to work and we never observed any bumping. We actually found that adding a small bit of water (if your compound can handle it) kept the entire thing frozen, well at least every time we checked it was frozen.
There are other solvents you can use besides DMSO in NMR; perhaps your compound will be more soluble in one of those?
Also, 5mg in how much volume? 5mg is a freakin huge amount.
The real problem is that I’m working with nitrogen-containing heteroaromatics (guanine analogs) that are bastards to handle. Besides containing lots of tautomers, they are rock-solid. The only other kind of solvent that works for me is acidic D2O, but this specific example is much less soluble in that. Methanol? Forget it.
I’m talking about a “normal” NMR volume of about 0.6 mL. Our institute will get a cryoprobe in the near future, which will hopefully solve my sensitivity problems.
peak irradiation to suppress the solvent signal isn’t a bad idea. I’ve noticed there are many NMR tricks you can turn to before you absolutely need to run a new sample. You need a good NMR guy to show you whats up though if you don’t already know. If you’ve already tried all the deuterated solvents I’ve heard of people using carbon tet for the NMR (mainly for proton though). Are you positive you’re working with the free base? Lyophailizing takes a while and i’m assuming you dont want to deal with that lag. I’m a little surprised no D-solvent has worked. I’ve seen a LOT of solubility issues with these types of heteroaromatics though.
lb=2 wft
check and see if you see peaks that SEEM reasonable (even w/o reasonable S/N), then check your decoupler frequency. maybe you can move the irradiation point so you get better 1H decoupling (a more serious problem w/ 13C peaks at about 200+, though)
adding a relaxation agent can help IMMENSELY eg. Cr(III)acac or whatever floats your boat (and doesn’t kill your stuff).
if the above fails stop making brick dust.
Thanks, I’ll try that!
Shigemi tubes, either 5mm or 3mm, will allow you to easily reduce your required sample volume down to 1/3 the “normal” amount. They are available matched to deuterated DMSO, D2O, CDCl3 and MeOH. Cost is around $100 per tube, but at standard NMR hourly rates they pay for themselves quickly.