Impure 9-bromofluorene from Sigma, but issues purifying

[Spezialemic]

So I had a stock of Sigma 9-bromofluorene I planned to use to generate some new chemical antagonists. Problem is that the TLC showed 4 spots. Ordered fresh stock, still came impure. Issues with Sigma aside, I need the compound so I just ran it through the biotage...TWICE...and it’s still not completely pure. The second purification did yield only one spot, but the NMR was not clean and being a student I’m not familiar enough with spectroscopy to determine where these peaks upfield are coming from. I’ve included the NMR (CDCl3) and maximization of the troubling peaks at 1.25 and 1.5. Though I’d usually assume 1.5 to be water, this was after a flash purification in 1% EtOAc:Hex, and a nice long rotovap, so I don’t buy that it’s a water peak since it’s so intense. I’m thinking everything upfield of 1 is just hexane. The TLC still shows only one spot and most of the impurities (if not all) are gone, but I’m hoping someone can help.

Edited April 3, 2019 by Spezialemic
Typo

[hypervalent_iodine]

A rot evap won’t get rid of trace water, not to mention you likely have some water in your NMR solvent. I would suspect water and hexane or grease are the culprits here, based on chemical shifts. You need high vac and very dry NMR solvent to completely eliminate the water peaks. Have you run anything else? GCMS? 13C NMR?

(edited)

[Spezialemic]

I haven’t done a 13C yet because there hasn’t been a long enough block of time I could grab. Our LCMS is also down until the new column comes in cause someone just ran a really concentrated sample the other day.

I wouldn’t be surprised if those are from other solvents, though. My vacuum pump needs to be opened and cleaned, so I’ve been using the hood vac. 

Edited April 3, 2019 by Spezialemic

[hypervalent_iodine]

15 minutes ago, Spezialemic said:

I haven’t done a 13C yet because there hasn’t been a long enough block of time I could grab. Our LCMS is also down until the new column comes in cause someone just ran a really concentrated sample the other day.

If your NMR matches literature besides those two peaks (that I am fairly sure are residual solvent / grease peaks), I would proceed with whatever you’re using it in. Go small scale first so you don’t blow all your compound (just in case). 

For future, try and source the compound from another company if Sigma is giving you bad stock. We’ve had to do this on several occasions, with the added bonus that it’s often cheaper. If you’re in the US, I’ve always been fond of Oakwood Chemicals. 

Edit:

For the record, you will sometimes find that your NMR solvent has a grease contaminant in that pops up at about 1.25 ppm or so. Some years ago my lab had a problem where every bottle of CDCl3 we got from Sigma had this peak, and it didn’t go away until we switched back to Cambridge Isotopes. What you may like to try is to run an NMR of just your solvent, to see whether or not those peaks come from there or from your compound. 

[Sensei]

33 minutes ago, hypervalent_iodine said:

For the record, you will sometimes find that your NMR solvent has a grease contaminant in that pops up at about 1.25 ppm or so. Some years ago my lab had a problem where every bottle of CDCl3 we got from Sigma had this peak, and it didn’t go away until we switched back to Cambridge Isotopes. What you may like to try is to run an NMR of just your solvent, to see whether or not those peaks come from there or from your compound.  

Chlorine-37 + Ve + 814 keV -> Argon-37 + e-

This reaction is used in Chlorine-based neutrino detector.

"Chlorine detectors, based on the method suggested by Bruno Pontecorvo, consist of a tank filled with a chlorine containing fluid such as tetrachloroethylene. A neutrino converts a chlorine-37 atom into one of argon-37 via the charged current interaction. The threshold neutrino energy for this reaction is 0.814 MeV."

https://en.wikipedia.org/wiki/Neutrino_detector

Check if your peak matches Argon..

 

[Spezialemic]

So I re-ran the NMR in acetone-D6 1% (v/v) TME and those peaks disappeared, replaced by the acetone, HOH, and HOD peaks, I presume. I think my CDCl3 might be contaminated. I also notice that the expected peaks are shifted more downfield in acetone. 

[John Cuthber]

4 hours ago, Spezialemic said:

. Problem is that the TLC showed 4 spots

What  conditions?

( in particular, what solvent?)

 

[Spezialemic]

10 minutes ago, John Cuthber said:

What  conditions?

( in particular, what solvent?)

 

EtOAc and Hexane 

[John Cuthber]

Do you have hydroxy-, ethoxy- and acetoxy- fluorene to use as comparisons?
Silica gel can be annoyingly good at catalysing reactions you didn't expect- especially in the presence of HBr etc.

[Spezialemic]

What do you think of the most recent NMR, though? It seems like the problem resolved itself. I wonder if my chloroform D was contaminated

[hypervalent_iodine]

3 hours ago, Spezialemic said:

What do you think of the most recent NMR, though? It seems like the problem resolved itself. I wonder if my chloroform D was contaminated

 

Have you looked at literature NMR?

[John Cuthber]

On 4/3/2019 at 3:01 PM, Sensei said:

Chlorine-37 + Ve + 814 keV -> Argon-37 + e-

This reaction is used in Chlorine-based neutrino detector.

"Chlorine detectors, based on the method suggested by Bruno Pontecorvo, consist of a tank filled with a chlorine containing fluid such as tetrachloroethylene. A neutrino converts a chlorine-37 atom into one of argon-37 via the charged current interaction. The threshold neutrino energy for this reaction is 0.814 MeV."

https://en.wikipedia.org/wiki/Neutrino_detector

Check if your peak matches Argon..

 

A bit late for April fool's day, isn't it?