Org Prep Daily

October 4, 2011

A scent of fresh soil

Filed under: Uncategorized — milkshake @ 5:53 pm

Our lab has been smelling a lot like disturbed soil lately, due to my work with 2-ethylfenchol. The flavor and fragrance division of Aldrich is a good place to start when you need highly hindered tertiary alcohols. While many of the low-molecular weight tertiary alcohols are minty and camphor-like, Et-fenchol smells like dirt. Actually in the concentrated state it reeks similar to TBS-silanol, but stronger. In more diluted form though it has a clean smell of freshly dug-up moist earth –  the smell is persistant and very convincing; a colleague asked me if he could wear ethylfenchol on his shroud when he goes to a Halloween party dressed as a mummy.

Turns out, 2-ethylfenchol prepared from (+)-enantiomer of fenchone has been developed with a specific purpose: as a substitute for geosmin – the terpenoid metabolite produced by soil bacteria that makes soil smell earthy. The earthy note is desirable in some compositions, i.e. for pipe tobacco flavoring, and since geosmin is rather hard to make cheaply a semisynthetic substitute was found. (Water utility companies are less fond of geosmin; the odor threshold of geosmin is incredibly low. Together with 2-methylisoborneol – another dirty-smelling terpenoid from soil bacteria/fungi – geosmin lends awful taste to tap water).

Et-fenchol from Aldrich comes in kosher grade, with a large seal from rabbi Gershon Segal on the bottle:


  1. Just what we need. . . .

    Not only is it “artificial dirt” (which is bad enough), it’s KOSHER artificial dirt! To paraphrase a famous Passover line: “But Father, why is *THIS* dirt different from all other dirt?” I guess that makes it OK to eat with your Matzo’s, ‘eh?

    Artificial flowers,
    Artificial fabrics,
    Artificial flavors
    Artificial sugars,
    Artificial sunlight
    Artificial human body-parts,
    Artificial motor oil, . . . . .

    And now, artificial dirt. What’s next? Artificial people? (Just kidding!)

    Seriously now; assuming that this stuff is actually edible – which the kosher seal implies – I can see this becoming an ingredient in a lot of things – BBQ sauce, fake hamburgers to give them that “earthy” flavor-note that is common in charcol or wood cooked meats,, or other fake-grilled foods. Even cheap wines – as there are a lot of expensive wines that are famous for the “earthy note” in the aroma and taste.

    What *I* want to know is how they actually BUILD these beasties – you don’t just stick atoms and molecules together like an Erector Set.

    What say ye?

    Jim (JR)

    Comment by Jim (JR) — October 4, 2011 @ 8:02 pm

  2. Aaah, yes. When I was working with actinomycetes the smell of geosmin was always in the air. Many of the cultures had their own unique smell cycles. There was one culture that sent everyone looking for the dead rat early in its growth cycle, and then it progressed to cooked peaches later (a cyano compound was the ultimate product).

    Comment by Martha Cone — October 4, 2011 @ 10:48 pm

  3. On a related note, norbornene smells like concentrated vomit. Avoid if possible.

    Comment by shoy — October 5, 2011 @ 8:21 am

  4. @Jim probably just like any other molecule that is pumped out of pharma, organic chemistry. F&F companies do the same.
    Depending on your diet, you have probably already eaten it. And it appears to be a nature identical molecule BTW.

    Comment by flavor — October 11, 2011 @ 2:21 pm

  5. Good to see you’re still posting, Milkshake

    Always kind of liked the minty/camphory smell of tert-butyl groups, kind of neat considering how awful n-butyls tend to smell.

    I’ve also worked with actinomycetes, and I’ve got to say, it smells better than E. coli.

    Comment by Honclbrif — October 13, 2011 @ 10:29 am

    • I thought Ninhydrin (from the tlc stain) smelled horrible, until I made the stain solution myself. n-Butanol reeks!!! DITTO for tert-butyl carbonates and light-weight carbamates. Simply love their sweet smell.

      Comment by HPCC — October 14, 2011 @ 6:29 pm

  6. Arachidonic acid, worked with it in multi-gram cGMP scale. The “wet dog” smell lingered all over our clothes and pretty much everything we touched. Managers gave us gift certificates afterward to spend on perfumes.

    Comment by jasonF — January 6, 2012 @ 5:40 pm

  7. – assuming that this stuff is actually edible – which the kosher seal implies –

    Kosher seal itself does not imply edibility.

    Comment by Shimmie — March 5, 2012 @ 6:40 pm

  8. Dear MS,

    I am having problem in preparing DiTMS derivative of tert butyl acetoacetate with good yield. Purification by distillation is also difficult due to thermal instability. Please let me know how this can be generated more efficiently ( I used LDA or NaHMDS but the conversion is only in the range of 50-60%) and isolated efficiently.

    The next stage is to use this compound for the Mukiyama Aldol condensation (Ti (OiPr)4, S-BINOL) with unsaturated aldehydes. This reaction also appears to be problematic with desired peaks are not observed in the HPLC and LC-MS.

    I am not sure about the detection problems in the HPLC. Please suggest me how this can be analyzed by HPLC.

    Since I have tert butyl ester group in the system, I would like to use milder acids for the deprotection of TMS group. Please suggest me the conditions if you have any.



    Comment by marto — June 7, 2012 @ 12:34 am

    • methodology-wise, I suggest that you pull out some papers from D.A. Evans group from 90s – they did lots of asymmetric Mukayama aldols on substrates like yours, with Cu(II) and Sn(II) and Evans is known to be thorough and practically-oriented so procedures from his group tend to work.

      TMS ether deprotection will not be a problem, they fall apart on their own, in aqueous media or on silica (the only stable exception are TMS ethers from tertiary alcohols) and in either case few drop of 40% aqueous HF in acetonitrile or a tip of spatula of ammonium fluoride or K2CO3 slurry in methanol will do the trick, or even a diluted acetic acid.

      Bis-TMS dienoalte: I don’t have much experience. Long time ago (15 years) I made bis-TMS and bis-TES enolate of MeCOCH2COStBu (I prepared the thioester of acetoacetic acid from tBuSH and diketene – it was a quite a nice procedure). The main advantage of these bis enolates-silyl ethers (also called TMS ketene acetals) derived from thioesters is that they have slightly better stability so you can actually do aqueous workup with them (using chilled solution of neutral potassium phosphate buffer, and you have to work fast) and sometimes they also give better ee’s in asymmetric reactions, and the thioester moiety then can be reduced to aldehyde by Fukuyama reduction (Pd-C/Et3SiH/sieves in acetone). I remember I actually did aqueous workup and then distilled the CH2=CH(OTMS)-CH=C(OTMS)StBu. I think the silylation was done in two steps. Check the Evans work, it should be there somewhere/

      Comment by milkshake — June 7, 2012 @ 3:05 am

  9. Dear MS,

    Thanks very much for your suggestions.


    Comment by marto — June 7, 2012 @ 5:31 am

  10. Hi MS,

    I have been trying to derivatize bicarbocyclic ketone derivative (similar to the structures in the above article) to oxime derivative but unable to get good crystalline derivative for single X-ray analysis. Please suggest me any solid derivatives that will have good crystallinity.

    Thanks very much for your help.


    Comment by marto — June 20, 2013 @ 1:12 pm

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