Wednesday, January 16, 2013

Blog Syn #001 - Iron / Sulfur Catalysis

(Disclaimer: The following experiments do not constitute rigorous peer review, but rather illustrate typical yields obtained and observations gleaned by trained synthetic chemists attempting to reproduce literature procedures. We've taken efforts to stay close to the original procedure, using similar glassware, equipment, and reagents wherever possible. Images have been cropped and scaled to fit in the allotted space, but have not been digitally altered otherwise.)

Ref: Nguyen, T.B.; Ermolenko, L.; Al-Mourabit, A. J. Am. Chem. Soc. 2013, 135(1), 118-121.
Previous Analysis: Just Like Cooking: Post 1, Post 2, author response
Experimenters: Three - Matt Katcher (NJ), Organometallica (IL), B.R.S.M. (United Kingdom)

Recommendation: Moderately reproducible - yields much lower than anticipated

Trial 1 - Matt

Scale: 1 mmol
Reaction (table, #): Table 2, entry 2
Reagents: Fe was an old Fisher bottle (40 mesh)

Observations: Tried to keep reaction air-free by setting up with a septum over a pressure tube, but I was not extremely rigorous. Fe stuck to stir bar at end of reaction

Purification: Not attempted
Yield - Published: 83%
Actual: <5% by crude NMR

Advice: I still think the reaction might work, but it may not be a simple "dump and stir". If I did it again, I would run it in a Schlenk tube to minimize exposure to air.

Spectra / Photos:
Reaction setup
LC/MS - Target ion: 246 m/z
Crude NMR

Trial 2 - B.R.S.M.

Scale: 5 mmol
Reaction (table, #): Table 2, entry 1
Reagents: 2-Nitroaniline (Aldrich 98%; of indeterminate age, because I borrowed it), sulfur (Fisher 'lab reagent' grade, fine powder, age unknown), iron (Fisher '97% reduced by hydrogen grade' [no mesh given]), 4-picoline (10 mmol; Aldrich 98%; 1 year old)

Observations: Used 10-mL Schlenk tube that had been dried under vacuum using a heat-gun. The flask was evacuated and back-filled with argon three times. Dark-coloured suspension, agitated at maximum speed by magnetic stir bar.

Purification: Silica gel. Elution with 100:0 - 95:5 CH2Cl2:MeOH gave the product as a beige foam, still containing some impurities (Rf 0.45 in 96:4). Second attempt: Recrystallisation from toluene-hexane (ca 3:1) gave small yellow-golden brown crystals that were dried overnight in vacuo.
Yield - Published: 90%
Actual: before recryst 366 mg (37%); after 241 mg (24%).

Advice: A crude sample of reaction mixture removed at 24 h indicated around 5:1 aniline:product, but this was probably not reliable due to the low solubility of the product in chloroformThe reaction was quite messy, the product streaky and the column non-trivial. 
Spectra / Photos:
400 MHz NMR, after rexstal
Final product
Trial 3 - Organometallica

Scale: 5 mmol
Reaction (table, #): Table 2, entry 3
Reagents: Fe (Aldrich, >99% powder, fine), S (Aldrich, >99.998%, recrystallized)
Observations: Reaction run in inert-atmosphere glovebox in Schlenk bomb. Noted "internet accounts" (trials 1 & 2) before beginning this reaction.

Purification: Pushed through silica pad with DCM, 10%MeOH / DCM. Distilled on bulb-to-bulb apparatus to remove excess picoline.
Yield - Published: 75%
Actual: 35%

Advice: No residual product in picoline distillate or remaining on silica plug. Flask / reaction capable of withstanding increased pressure. Deep brown crude mixture, final product a green powder.
Spectra / Photos:
NMR, post-distillation
TLC, from notebook
Roundup: First, a hearty thanks to all three experimenters for taking time out of their busy schedules to run these reactions. Second, I believe we'd all agree that the reaction works, but in practice we obtain far less material than the original authors. Oxygen contamination plays a major role - note lower yield in Trial 1 - as (we suspect) does mesh size and age of iron and sulfur powders.

Author Response: (When this post goes live, I'll send the link to the corresponding author. Any response will be published in due course)

**Thanks for reading our initial venture into collaborative "crowdsourced reaction validation." We appreciate any comments or suggestions for the next go-around. Want to get involved? Have an idea for another (cheap!) reaction to try? Talk to us in the Comments section!


  1. Testing, testing comments section

    1. Trial 1 should be removed because it's was totally fault. Trials 2 and 3 should be rerun. Glove-box technique is useless if soluble oxygen is not removed from picolines.

    2. Well, hello there, person with obvious knowledge of the reaction! May I ask where the supporting information says to do that? IT reads: "Reagents were obtained from commercial supplier and used without further purification"

    3. This comment has been removed by the author.

  2. Organometallica (and all, really) — Would you attribute the green color of the purified product from Trial 3 to its propensity to bind to trace metals in the eluting solvents?

    Love the idea of this blog! Can't wait to see where this goes from here.

    1. I thought the same thing when I read about the green powder...

  3. Great job, guys! I loved the real-life experimentation and am looking forward to more!

  4. This is awesome you guys. I will join in, where I can.

  5. Great post. No comment on above except authors have some explaining to do on reagents used and technique. Keep up the great work, cant wait to see future posts.

  6. This comment has been removed by the author.

  7. Great stuff can't wait to read another entry.

  8. Blog Syn... Peer tested, chemist approved!

    This is great stuff, keep it up

  9. Great idea, I hope you can keep it up.

  10. Do you have your own lab space? Just wondering where'd you get funding to keep this up.

    1. This comment has been removed by the author.

    2. The idea's certainly been pitched around. Kickstarter doesn't usually like basic research, so I'd have to speak to E. Perlstein about RocketHub.

      Keeping it in mind...

    3. Abs. brilliant initiative. I'm looking forward to contribute on RocketHub and very soon a much MUCH bigger crowdsourcing platform ;). Meanwhile I would humbly recommend if 1- "Big" labs go first under the magnifying glass. 2- Creative original research comes out as a side-reaction. After all, if you are going to get funded why not do whatever young researcher dreams about and... well +Explore+Learn+Create (P).

  11. This blog is a terrific idea. I hope to pitch in whenever I can.


  12. Replies
    1. Hope I gave you enough due credit. Your post helped me move forward...

  13. Thoughts on including attached files -- specifically NMR fids, GC-MS, LC-MS traces, etc? That kind of stuff might allow for some interesting crowdsourcing of data interpretation.

    1. Honestly? Files like those are best done "on request." Org Syn, around for nearly a century, only offers a few select NMRs per prep, partially to keep down server space and reduce load time, I'm sure. Supp Info in mainline journals rarely offers FIDs, either.

      If we were (gasp!) already a small company with a BUDGET - and our own servers - I'd say full speed ahead...Since, though, we're mixing data from various institutions, who all have their own digital information policies, it may be too tough an egg to crack at present.

    2. To some extent, I think you have to trust that the majority of the results you find in the literature are basically correct (with some skepticism and an understanding that sometimes people get it wrong), and you already get tabulated spectral data with the experimental in most journals, so I don't see a lot of value in examining the raw data, except in exceptional cases.

      I do see value in testing certain reactions, because there are always little things that you learn by experience with different kinds of chemistry or just idiosyncrasies peculiar to certain people or groups, that you don't always identify or test but which can have a big impact on how a reaction works. This sort of testing reveals those things and could help make those reactions more robust and the reported yields more reproducible. Although, if I were developing a methodology, I would try to identify any of those factors myself and include them in the report, but I know that doesn't usually happen. So if this blog takes off, it might help raise awareness and make people more thoroughly test things in the first place, and make overall improvements in the literature.

  14. I think you folks have an official request:

  15. I just blogged about your efforts online here: . It looks like a parallel effort to the ChemSpider SyntheticPages effort that we have. Not sure if you've seen it???

  16. Couple months ago I had to follow a recipe and it was really difficult, because they were lying and was very frustrating because it was a long time synthesis and pretty expensive.

    Even I have already fixed the problems and I achived to obtain the desired product making some changes, I still quite upset with them xD

    I think your idea is really good, and I just wanted to say you good luck!!!

    Best regards,


  17. Feel free to drop me a line (my name, we would love to help and can run searches on reagents to help save you funds.

  18. Would be great to see a summary of your findings here: It could potentially open a nice dialog with the authors on a non-confrontational platform.

  19. Barely started and already praisingly mentioned in the Nature podcast. Good job!

  20. As an idea for a next one- A few years ago I tried to access the starting materials prepared in Angew. Chem. Int. Ed. 2008, 5049 (the alpha-beta unsaturated dicarbonyls). This prep had been reported in multiple different articles such as Tet Lett. 1981, 3043, and J. Org. Chem. 1981, 2920.
    I never managed to get product. The selenation after the deprotonation to form the enolate worked fine. However, the elimination to form the unsaturation never worked. I must have tried the reaction ~10 times. My lab mate had wanted the product for a different reaction a year earlier and had also tried but had failed to get product also.

  21. You could have a whole section on t-butyl ester formation from corresponding acids!!

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