Org Prep Daily

May 21, 2007

On septum bottles

Filed under: procedures — milkshake @ 9:49 pm

I dislike septum bottles of anhydrous solvents from Acros; I found that the integrity of their screw-top cap with wide septa cannot be trusted. I have had a fairly good experience with Aldrich/Fluka. I keep a number of sensitive reagents and anhydrous solvents in SureSeal bottles in humid southern Florida without much problem. 

Couple of comments on keeping the SureSeal-bottled compounds healthy:

1. It helps to pierce the septa only with thin needles (gauge 19, 20) whenever possible. Always put the sure-seal bottles under positive pressure of dry Ar when drawing stuff from them.
2. I use a transparent polyethylene chemical-resistant tape to re-seal the septa crown cap. I cut a 1×1 in square of the tape and affix it over the crown to cover the septa that was pierced and I compress the tape with a thumb to squeeze out air channels. (I replace the tape square with a fresh one whenever I use the bottle.) Then I put the red plastic screw cap on the taped crown and parafilm it around with double-folded parafilm strip. (The parafilm is doubled for better mechanical durability, it is stretch-wrapped and thumb compressed to seal-up tightly.) The parafilming around the bottle red cap is not overly important – but the taping the pierced septa is crucial. A suitable solvent-resistant polyethylene tape is available from VWR (cat# 11211-934).
3. Avoid commercial unstabilized anhydrous ether solvents because they don’t store well – buy the stabilized ones. In medicinal chemistry a trace of BHT is much lesser problem than peroxides. (If one does a very sensitive chemistry where BHT interferes he should not be buying anhydrous solvents anyway but distill his ether solvents from a benzophenone ketyl still)
4. Don’t buy LDA or LiHMDS because these reagents are made very easily, freshly before use – and the quality of their commercial solutions is quite atrocious. Strong bases in THF do not store well. Buy hydrocarbon solutions of NaHMDS and KHMDS. Grignards in THF are usually fine. 
5. BuLi and sec-BuLi solutions in hydrocarbon are stable at RT; the air and moisture is the problem. The same goes for many commercial Grignard reagents. Don’t put stuff in fridge that does not have to be refrigerated – temperature changes cause pressure changes in the bottle and moisture condensation problem. Also, Grignards tend to crystallize in the fridge and are hard to re-dissolve afterwards. A cabinet under hood is where I store most of my organometallics.
6. I don’t like to share my septum bottles (the same goes for the needless and syringes). If there is no other alternative, I hand over my septa bottle allways together with the polyethylene tape and with explicit reminders about what to do. Then quietly watch from distance and yell if necessary.


(Org Prep Daily stats are getting close to 100k total. Thanks for reading this stuff.) 


  1. I’ve always wondered how much money Aldrich and various companies make on folks who purchase things such as LDA, LiHMDS, Dess-Martin, and whatnot which are relatively easy to prep. It’s ridiculous how much is charged for DMP.

    Nice post. Very practical.

    Comment by Totally palytoxined out — May 21, 2007 @ 11:45 pm

  2. (Thanks for posting this stuff!)

    Comment by bad wolf — May 22, 2007 @ 12:04 am

  3. What is your opinion of people who place an inverted 24/40 rubber septum over the Aldrich Sure/Seal cap and secure it with tight copper wire before using the bottle? Effective? Worthless?

    Comment by Paul — May 22, 2007 @ 2:18 am

  4. I don’t know – rubber has a rather high gas permeability and crumbles at the stress-points over time. In theory, it could provide a secondary septa. But piecing through two septas is not fun. I think a new unperforated tape that sticks to the crown is quite a simple alternative.

    Comment by milkshake — May 22, 2007 @ 2:56 am

  5. Regarding statement #5 : Over in our lab, we kinda have temp problem, most of the time, we are at 32-34C. Relative humidity 80-90%. Imagine that, we have no choice but to store some of the more sensitive chemicals in the fridge. Sometime, it gets so hot and stuffy, the reagent bottles popped unexpectedly. Any advice?

    Comment by Taitauwai — May 22, 2007 @ 4:05 am

  6. Regarding point 2.: that’s an excellent trick! I do that too and always have found the lifetime of the sensitive reagent to be much longer than without taping. You should just remember to change the polyethylene film quite often, as the stuff in the bottle can be very aggressive to it and partially destroy it, leaving a kind of gum/glue that will obstruct your needle when you take the reagent (besides being very poor at preventing air to enter the bottle). That happens most often with alkylzinc reagents.

    Regarding point 5.:I agree with that too; I stored my Grignards at RT in a safety closet for many months and they were always fine. BuLi et similia are usually kept in the fridge in the place I am currently working at, but just yesterday I was wandering if this is really necessary.

    Comment by ZAL — May 22, 2007 @ 6:17 am

  7. With regards to the distillation of solvents: Many universities as well as corporate research facilities are now banning the large scale use of sodium/benzophone for the drying and deoxygenation of solvents, for obvious safety reasons. A useful alternative, which I used routinely on 3-4 L scale when I worked with organoaluminum and organotitanium compounds is to 1) dry with P2O5 then 2) use multiple freeze-pump-thaw cycles to remove the dissolved oxygen.

    Comment by Milo — May 22, 2007 @ 6:59 am

  8. With respect to septum bottles I have the exact opposite experience. I always buy Acros stuff these days because I found that eg n-BuLi lasts at least 5 times as long as the Aldrich stuff. I suspect it is due to the bigger surface of the septum itself – if you have to push a needle through very often this helps as the Aldrich seal is quickly damaged by using the same area again and again. Mind you, I have investigated a lot of other organometallics (just started with Grignards whach appear to be fine as well), but I will certainly give it prioprity over the Aldrich stuff.

    point 2 would certainly help to make Aldrich bottles last longer but I have found that me and my lab associates would be too lazy to make this work. Positive pressure of Argon and Acros stuff is my (convenient) solution.

    Comment by Grubbs the cat — May 22, 2007 @ 7:45 am

  9. For solvents and reagents that are constantly being used in small amounts, I agree with 8 – Acros is superior. However, since the septum top is larger, the tape method (which is awesome) doesn’t work as well, and therefore the shelf-life once punctured is shorter.

    The first lab I ever worked in purchased their LDA, but I remember when I moved on and made my own how surprised I was that the solution was colorless instead of, err, molasses colored!

    Comment by Cat Herder — May 22, 2007 @ 10:47 am

  10. I saw too many Acros septa bottles that came partially unscrewed from Fisher, with the content of the bottle leaking into the box. Use whatever works for you, I just do not trust them.
    P2O5 is great for non-ether solvents but does a slow C-O bond cleavage with Et2O at room temp (you end up with Et ester of polyphosphoric acid).
    With hot and humid environment: doing chemistry at room temp = 33C is kind of difficult and the temperature fluctuation in a lab without AC will ruin your reagents/solvents. I would recommend to buy AC at least for the one storage room and keep things at constant 23C there.

    Comment by milkshake — May 22, 2007 @ 12:08 pm

  11. True about the C-O cleavage, but in the end is not a problem since before the freeze-pump-thaw, you vacuum transfer it to another flask using goo Schlonk techniques, the phospho esters will stay behind.

    Congrats on the hit count, BTW

    Comment by Milo — May 22, 2007 @ 12:16 pm

  12. Yes, the partially unscrewed cap thing can definitely be a problem. I recall getting a bottle of “dry” pyridine like that which had soaked into the vermiculite. Holy jeebus that package stank when opened.

    Comment by Cat Herder — May 22, 2007 @ 2:44 pm

  13. My experience is that *any* organometallic from S-A is really suspect. Their Pd tetrakis is a JOKE. Buy it from Strem and see what it is supposed to look like!

    Comment by Jose — May 22, 2007 @ 3:09 pm

  14. If you pop the cap & pour it realy fast it’s almost still anhydrous.

    Comment by Anon — May 22, 2007 @ 7:49 pm

  15. Jose,

    Make the tetrakis yourself, it takes a half hour and is much cheaper than buying it.

    Comment by Milo — May 22, 2007 @ 7:51 pm

  16. Better still just make your Pd(0)in situ from Pd2(dba)3 and TPP. Within 5 minutes the purple color is replaced with the color that tetrakis is supposed to look like. The only price you pay is a second weighing for the TPP. The only phosphine that is tricky is dppf which doesn’t give you exactly a greenish color when its complexed.

    Comment by TMS — May 22, 2007 @ 10:54 pm

  17. I once made 10 g of tetrakis. I packaged it in 20 little vials under nitrogen, put it in the freezer while I went on sabbatical. When I got back I had 20 different colors which I guess speaks to my lab technique.

    Comment by TMS — May 22, 2007 @ 10:57 pm

  18. Please, a tetrakiss, right now – at 11:20p in the lab, me very lonely.

    Comment by milkshake — May 22, 2007 @ 11:22 pm

  19. Whole-hearted agree with #5.

    I really do not understand why so many people insist that all the Li and Mg reagents should be in the refrig. moisture condensation and frequent temperature change will quickly kill the reagents. I witnessed a big bottle of MeLi crack for this reason. My own experience support the statement that these reagents are usually quite stable at room temperature. There is actually study on how quickly these thing go bad:

    After switch from school to company, I now realize my colleagues have an ultimate solution for this – buy new ones.

    Comment by diketene — May 23, 2007 @ 1:12 am

  20. Definitely make your own tetrakis. It’s such a fun little reaction.

    Comment by Ψ*Ψ — May 23, 2007 @ 1:14 am

  21. #18 – Muah! Muah! Muah! Muah! Feel better?

    Comment by Taitauwai — May 23, 2007 @ 3:13 am

  22. thank you, it’s much better now

    Comment by milkshake — May 23, 2007 @ 10:56 am

  23. What about alumina columns for drying solvents?

    Comment by liquidcarbon — May 23, 2007 @ 1:27 pm

  24. We do the tape trick as well, and it works wonders. I was wondering about MeLi storage. We store our BuLi at room temp, but the methyl lithium at -20C. It definitely seems to me that room temp would be better, but was worried about stability. Is there a problem with MeLi at room temp? Also, that link from #19 appears to be broken. I seem to remember seeing that handout at some point, but does anyone have a copy of it?

    Comment by carbazole — May 23, 2007 @ 2:23 pm

  25. The previous link was from “my favorites”. It is not up-to-date. Now the link is:

    Click to access 8_Organolithium.pdf

    Hope it works this time.

    Comment by diketene — May 23, 2007 @ 5:03 pm

  26. By the way, nice kitten 🙂

    Comment by Ψ*Ψ — May 24, 2007 @ 1:39 am

  27. Is the DessMartin Reagent really easy to prepare? How is it done?



    Comment by Javaslinger — May 24, 2007 @ 3:42 pm

  28. For #3, buying large jugs of uninhibited THF is a must for polymer research people, as our GPC drinks it like a Russian with vodka. If you go through it fast, it’s not a big deal, though.

    Comment by excimer — May 24, 2007 @ 7:11 pm

  29. The DMP procedure was posted here on Sept 5 and 6. There is an improved procedure for the IBX intemediate, using Oxone, the reference is there in the comment section.

    Comment by milkshake — May 25, 2007 @ 10:04 am

  30. Use the new Oxone one, it is much safer than the old one. BTW, you’d be suprised how well IBX works for many things and you don’t always need to make the actual periodinane. For 2,3-epoxy aldehydes we get much better results with IBX.

    Comment by Watson — May 26, 2007 @ 2:58 am

  31. By the way, I can’t stand any of the sure seals. The alfa aesar melting wax ones are the worst. This time we got BuLi with no septa, and as long as I use the right sized septum with a balloon through it, I can swap it on in a flash and keep things dry. Then just pop off and seal with the good sealing teflon cap and the stuff doesn’t degrade on the shelf. Note, this doesn’t work with tBuLi or Et2Zn or other highly reactive things.

    Comment by Watson — May 26, 2007 @ 3:00 am

  32. The alfa aesar melting wax ones are the worst.

    Alfa Aesar has a sure seal? Then it must have melted by the time I got my bottle of BuLi. That was not a very pleasant experience. Also, I made LDA last week and was please to find that it is a white, fluffy powder that is easy to measure out and use and not the black solution that we have sitting in our fridge.

    Comment by blatnoi — June 2, 2007 @ 11:04 am

  33. Alfa Aesar’s BuLi is actually my favorite. They last longer than Aldrich ones. You just need to remove the sticker on the top to reveal the sure seal. Many of my colleagues made the mistakes by directly unscrewing the cap.

    Comment by leo — June 6, 2007 @ 3:31 pm

  34. i like alfa aesar’s BuLi, too…suum quique, i guess. in my book, acros’ suck and aldrich’s are so-so.

    totally agree about the refrigerator/freezer issue. i just can’t help imagining water being sucked in by cooling down the bottle like that and i’ve definitely seen grignard’s come out of solution.

    i don’t have the VWR tape, but i cover the septa with a couple pieces of teflon tape and put some normal tape over it to keep it on.

    Comment by squirmy — July 18, 2007 @ 11:52 pm

  35. How can we make sure that anhydrous DMF with Aldrich Sure Seal bottle remains anhydrous?

    Comment by pmgb — June 9, 2008 @ 5:04 am

  36. Regarding comment # 3, I used to use the double septum / copper wire trick everytime I dried DMF. Worked like a charm, though I was using only half liter bottles.

    Comment by Vinod Jairaj — March 31, 2009 @ 7:37 am

  37. […] liked to think that it offered at least some added protection from atmospheric moisture. Milkshake likes to tape the tops of his Sure/Seals after use, and that seems like a simple alternative. I’d […]

    Pingback by Hacks for Septa | ChemBark — August 5, 2013 @ 1:52 am

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