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I am conducting a synthesis involving Buchwald-Hartwig coupling. The scale is $\approx10^{-4}$ mols of reagents. After running the reaction at 80 ℃ during 24 hours I found that sealing between the 3-neck reaction flask and the reflux condensor became loose, and the reaction flask is somewhat filled up relatively to the start of the reaction (5 mL toluene as solvent) although I did not add additional solvent during the reaction. As I add some toluene, the layer separation was observed and the toluene layer went to the upper layer. Initially I thought that this might be tert-butanol because it is the by-product of the reaction cycle. But I initially added only 0.0426 g of NaOtBu, so formed tBuOH would be very small amounts. In light of the fact that the sealing became loose, is there possibility that water vapor in the air went through the flask and condensed by the reflux condensor, and dropped to the flask? Is there any method to verify whether it is water or not? Ar gas was continuously flowed into the flask during the reaction and an oil bubbler was used.

layer separation

------------ 2022/02/18 edited

My hypothesis is that some water came through the flask from exterior. So I tested some experiments. In this time I added only 10 mL of toluene in the flask and set up the instruments in the same manner. Considering the fact that sealing between the flask and reflux condensor became loose in the previous experiment, I didn't seal that portion intentionally. Below is ordinary instruments setting.

ordinary setting

In the real experiment the portion between the three-necked flask and the reflux condensor is sealed, and the other portions are not sealed. Also the flask is wrapped with Al foils to prevent potential effects of the light. But these procedures were omitted in this time. The result is layer separation again:

layer separation

Based on this result it seems obvious that some water came through the flask. But from where? Is the sealing between the flask and reflux condensor problem? Actually I had same problem with same instruments setting in the past, but the sealing was maintained during the reaction at that time. Then other unsealed portion, for example, the portion between reflux condensor and oil bubbler is the problem? Also I blocked the other open end of the bubbler with just pipette bulb, but can this be a problem too?

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  • $\begingroup$ Seems unlikely, the Ar flow should have given a flow out through the gap stopping any air getting in. Is it possible your bubbler sucked back into the reaction mixture at some point? $\endgroup$
    – Waylander
    Feb 17, 2022 at 7:21
  • $\begingroup$ @Waylander At a glance there seemed to be no change in the level of the oil in the bubbler. And I used silicon oil which is very viscous, but this unknown layer is not viscous. I added the image. I only used 5 mL of toluene at the beginning, but about 20 mL of unknown liquid is newly formed. $\endgroup$
    – Krang Lee
    Feb 17, 2022 at 7:44
  • $\begingroup$ What does analysis of the toluene layer show? Has your reaction worked? $\endgroup$
    – Waylander
    Feb 17, 2022 at 9:00
  • $\begingroup$ @Waylander The MS analysis request is waiting for approval. But from personal experience the color of toluene always turned brown after the reaction, so I presume that the product is formed. However if this unknown layer is formed again in the next synthesis, I think that this layer formation would be prevented. (Actually there was a similar experience in the past) I think the volume of the new layer is too large compared to my reaction scale, so it is hard to say that it is formed from the reaction cycle. So I assume that it may be from the exterior of the reaction. $\endgroup$
    – Krang Lee
    Feb 17, 2022 at 9:12
  • $\begingroup$ On that small scale could you run the reaction in a sealed 20ml microwave reaction vial? $\endgroup$
    – Waylander
    Feb 17, 2022 at 10:53

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I found that inside the reflux condensor water drops are formed continuously and very slowly. Maybe there is very minute crack. Everyone be careful with apparatus...

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