Org Prep Daily

November 21, 2009


Filed under: procedures — milkshake @ 10:27 pm


1,1-dicyano-2-methoxy-2-(1′-naphtylmethyl)-ethylene 9.175g (36.95 mmol) and t-Bu-hydrazine hydrochloride 4.65g (37.3 mmol) was suspended in absolute ethanol 0.25L and triethylamine 5.3mL was added dropwise over 7 min period. After stirring at RT for extra 10 min, the mixture was placed on oil bath (90C) and refluxed overnight (18 hours).  The cooled reaction mix was evaporated and the residue was portioned between DCM 150mL and water 100mL. The aqueous phase was re-extracted twice with DCM (2x100mL), the combined extracts were dried (Na2SO4) and evaporated. The residue was purified on a column of silica (250g) in DCM, eluted with straight DCM 0.3L and then 20:1 DCM+EtOAc (v/v; 2L).

The obtained 5-amino-1-tert-butyl-4-cyano-3-(1′-naphtylmethy)-pyrazole (cream-colored crystalline solid, 7.15g, 63.5%Y) was flushed with Ar in a 1L flask, formamide 100mL was added, the flask was equipped with a straight glass tube as air-cooled condenser and the mixture was deoxygenated by a highvac/Ar purge. The mixture was stirred on a 180C oil bath under Ar for 7 hours. The mixture was allowed to cool to R.T., the formed slurry was gradually diluted with water (60mL) and the mix was stirred for additional 30 min. The precipitated product was collected by filtration, thoroughly washed with water, dried by suction and on highvac. The crude product (7.05g) was dissolved in ethanol 0.5L at reflux. One spoon of charcoal was added, the mix was stirred at reflux for additional 10 min then filtered while still warm (the charcoal was washed with additional ethanol) and the filtrate was evaporated to dryness. The obtained foamy residue was re-crystallized from a mix of benzene 30mL and cyclohexane 20mL (RT, overnight). The crystallized product was collected by filtration, washed with 1:1 benzene-cyclohexane mix and then with hexanes, dried by suction and on highvac.
Y=7.788g (57% overall Y) of a cream-colored crystalline solid as a 2:1 co-crystal with benzene.

1H(d6-DMSO, 400MHz): 8.905(very br s, 2H), 8.473(s, 1H), 8.249(m, 1H), 7.936(m, 1H), 7.816(d, 8.2Hz, 1H), 7.555(m, 2H), 7.395(dd, 8.1Hz, 7.2Hz, 1H), 7.153(d, 7.0Hz, 1H), 4.873(s, 2H), 1.654(s, 9H); LC/MS(+ESI): 332(M+1)

Note 1:  1NMPP1 is commercially available but very dear

Note 2:  To remove the benzene trace (the compound is intended for biology use) the purified material was re-dissolved in ethanol 150mL, the solution was carefully concentrated on rotovap from a 50C bath down to about 1/3 volume and the remaining solution was slowly diluted down with water – about 200mL – until cloudy, the crystallization was then induced mechanically (by scratching the solution against the flask joint). The resulting slurry was stirred on ice bath for 1 hour. The precipitate was collected by filtration, washed with ice water, dried by suction and on highvac. This provided 6.012g of pure product free of benzene (Y=49% overall). 1H(d6-DMSO, 400MHz): 8.319(m, 1H), 8.141 (s, 1H), 7.921(m, 1H), 7.793(d, 8.2Hz, 1H), 7.541(m, 2H), 7.391(dd, 8.1Hz, 7.3Hz, 1H), 7.145(d, 7.0Hz, 1H), 7.027(very br s, 2H), 4.875(s, 2H), 1.662(s, 9H)


  1. Seems surprising that the trace of benzene has such a big effect on the NMR.

    Comment by dan — November 23, 2009 @ 3:41 am

  2. Sorry off-topic question. I have some 1,10-phenanthroline monohydrate that I need to react with phenyllithium (made in situ). Do I need to dehydrate the phenanthroline first, and if so, how? Thanks very much!

    Comment by Daniel — November 23, 2009 @ 3:52 am

  3. Phenanthroline hydrate: You should use anhydrous stuff. Do recrystallization from a solvent that makes an azeotroph, like toluene or benzene, and distill some of it off to dry it up.

    NMR: Its not benzene. Actually, the first sample got about 3-times more concentrated than the second one (I thought originally that I should run C13 on it too – but both our instruments were too busy at the time for taking an unnecessary carbon spectra). I puzzled also over those aminopyrimidine signals – both the amino and the ring CH – which were significantly shifted between the two proton spectra, the rest was fairly similar. My guess is that there is a strong intrermolecular H-bonding even in DMSO as a solvent so the aminopyrimidine signals depend on the concentration a lot.

    Comment by milkshake — November 23, 2009 @ 4:28 am

  4. Greetings MS,

    I am doing cyclization reaction of 1,3 diketones (both keto group have got similar reactivities ) with methyl hydrazine. I get both regiosomers with equal amount. Its difficult to characterize the two regisomers. Is it worth doing 1H – 13 C correlation ..If you can suggest any other NMR/analytical techniques would be really helpful.



    Comment by marto — November 24, 2009 @ 8:03 am

  5. If 1NMPP1 is so expensive, have you considered selling some of those 6g? Could raise some funds for the Christmas party!

    Comment by Ed — November 24, 2009 @ 10:53 am

  6. Its for a friend of my friend who even does not work here, so I don’t know all the details. If I understand it correctly it is used for a very specialized assay that requires mutant animals/mutant cell lines. The compound hits only the mutant – it does nothing to normal cells. Not too many people run this assay because the engineered animal stuff is hard to get, and it is good only for one particular signaling pathway. I suppose the worldwide consumption can be like 1 g a year, which is only few thousand USD (I think the lowest price I saw online was $880/100mg)

    Comment by milkshake — November 24, 2009 @ 1:41 pm

  7. Thank you very much Milkshake, worked perfectly. I’m now trying to react it with phenyllithium, made in situ from decades-old lithium block and decades-old bromobenzene, using non-distilled, non-dry ether, in air. Am I wasting my time? It’s truly hard to do chemistry in a biology lab!

    Comment by Daniel — November 25, 2009 @ 11:38 am

  8. Milkshake:

    Did you envision this synthesis yourself?

    Comment by Jonez — November 25, 2009 @ 12:38 pm

    • Its from a JACS paper that deals with animal biology. The paper does not contain any synthetic experimentals, only a scheme (without yields and without reaction condition details) but provides a reference to J. Chem. Soc. Perkin 1 paper – which does not have this particular compound either. Then there is a recent patent which does describe similar compounds but again not this one. My problem was that all detailed procedure precedents in the literature have aryl directly linked, there were no examples with benzylic substituents so I worried about the regiochemistry a bit. The main change is using MeOTf in MeCN – I knew from another example (2-acetyl-Et-acetoacetate O-methylation) that this shoudl work. I don’t like dimethyl sulfate 5 eq. reflux which they used in the Perkin paper, and we did not have tons of TMS-diazomethane at hand, the reagent they used in the patent.

      Daniel: you are wasting your time by using wet ether, ether distills very nicely, just add a spoon of LiAlH4 to your old stuff and distill it over from a warm bath under Ar for your purpose. Old Li crust can be scraped off or cleaned by dipping it in methanol and drying. It darkens fast because of the reaction with air. Use Ar, not nitrogen. Old bromobenzene should be fine but it won’t hurt you to re-distill it – it builds your backbone. If you want to be sloppy go to peptide chemistry.

      Comment by milkshake — November 25, 2009 @ 6:25 pm

  9. One of my frnd (sr. research colleague), did prepare some derivatives of allopurinol and I think he did prepare so many derivatives of pyrazolopyrimidines starting from 2-cyanoacetamide…

    Comment by umesh — November 28, 2009 @ 1:15 am

  10. Hey! That compound’s from our lab (Kevan Shokat at UCSF)!

    Your synthesis is actually a lot more elegant and convenient than the way we make it (which doesn’t involve methyl triflate).

    Comment by Brandon T — December 4, 2009 @ 4:02 pm

  11. Ehh, actually, it seems like it’s pretty similar yieldwise. You’re more comfortable using methyl triflate than dimethyl sulfate though?

    Comment by Brandon T — December 4, 2009 @ 4:10 pm

    • I did not want to use 5 equivs of dimethyl sulfate. The other option was TMS-diazomethane or diazomethane but we would need a boatload of it. I had a bottle of Me-triflate and no use for it, and previously worked with it for a similar O-alkylation so I gave it a try.

      This was a first attempt done in a great hurry, I think on second run one could do little better and telescope it by using glyme as a solvent, to do both the acylation of malononitrile and O-alkylation in one pot. I can re-make some more if anybody needs – or if they write a biology paper and need a decent procedure for the supplementary, but it takes few days of work…

      Comment by milkshake — December 4, 2009 @ 4:26 pm

  12. It’s a protein kinase inhibitor designed to inhibit only protein kinases with an unnatural space-creating mutation. It has really low affinity for natural kinases (you could almost eat it, I think), which is a bit surprising because pyrazolopyrimidine derivatives can be made to inhibit a pretty wide variety of protein and lipid kinases.

    Comment by Brandon T — December 4, 2009 @ 5:03 pm

  13. It inhibits YANK subfamily (Ala as gatekeeper), not published yet. What effect it might has on human health – no idea.

    Comment by fromsgc — January 5, 2010 @ 6:28 am

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