Org Prep Daily

December 26, 2007

The 2007

Filed under: Uncategorized — milkshake @ 3:08 pm

ChemBark is dead.

So is Kinase Pro, Atompusher, Totally Synthetic, Heterocyclic Chemistry, Organometallic Current, Totally Medicinal and Jungfreundlich


Today I settled all family business.

Just don’t tell me you’re innocent.

Come on – you think I’d make my sister a widow? I’m Godfather to your son. Admit what you did.

Update: Turns out Paulie Boy is stil alive. No way we can get to him now. Roth has played this one beautifully.


  1. As I recall, Org Prep Daily was near the brink of extinction several months ago. Glad to see you’re still around when others have passed.

    Comment by Chemgeek — December 26, 2007 @ 4:16 pm

  2. Kinase Pro demise was the real blow – for 12 months I could pretend to be a genius, coming up with all these patent references from KP for our group…

    Comment by milkshake — December 26, 2007 @ 4:42 pm

  3. Is Totally Synthetic really dead? That’s sad.
    At least Ogre Prep Daily is still around. 🙂

    Comment by Ψ*Ψ — December 26, 2007 @ 6:10 pm

  4. Paul Docherty has to write up and graduate – the transformation in which a high-energy grad student decays into a lower-energy postdoc + several papers. We will see afterwards.

    Comment by milkshake — December 26, 2007 @ 6:19 pm

  5. Sad to see ChemBark die. I never blogged before (or even read them), and Paul gave me a widely read forum which I would never have had on my own. I really like the unpompous comments and general irreverant nature of the Blog world. I’d like to continue writing. What do you guys (and psi*psi) suggest?

    Comment by Retread — December 26, 2007 @ 9:29 pm

  6. Retread, you had a long and fairly dramatic career (you served also in a military field hospital, if I remember correctly) so you can sign up with (it is free), chose the name of you page, the theme you like – and start writing whatever comes to your mind, I am sure it will be interesting. The wordpress interface is pretty self-explainatory and no coding skilz are needed

    Comment by milkshake — December 27, 2007 @ 6:11 am

  7. Where else will you find stuff like this?

    Start gnashing your teeth organic synthetists. The humble cyanobacterium Anabaena PCC 7120 makes a C18 fatty acid carboxylic acid methyl ester which contains a bicyclo [1,1,0] butane moiety on the other end. The paper contains no speculation as to what the organism does with it, but lots of hypotheses as to the biosynthesis starting with a linolenic acid hydroperoxide at C9. [ Proc. Natl. Acad. Sci. vol. 104 pp. 18941 – 18945 ’07 ]

    Comment by Retread — December 27, 2007 @ 6:13 am

  8. That’s just the way of blogs. They’re here and gone in a blink of an eye- especially the good ones. The good ones (ie. the real rabble-rousers) that stay tend to lose momentum anyway. In the end, the ones with careers still ahead of them have to deal with bosses and colleagues who think that blogging is a waste of time. That’ll change in the next few years. Maybe.

    Comment by excimer — December 27, 2007 @ 12:12 pm

  9. …now all i want to do is watch the godfather. thanks, m.

    Comment by excimer — December 27, 2007 @ 12:14 pm

  10. “Kinase Pro demise was the real blow – for 12 months I could pretend to be a genius, coming up with all these patent references from KP for our group…”

    Amen to that, but you ought to take some credit too, milkshake. Your contributions – patent refs, other insights – along with some of other regulars added to popularity of KP. Hopefully, there is rebirth in the near future………

    Comment by moody blue — December 27, 2007 @ 1:09 pm

  11. I completely agree. When I saw KP’s demise, I actually said “Ow” loudly. It was like a broadside in my flanks.

    TotSyn and Chembark don’t seem to be officially dead. Just on a break.

    Comment by Wavefunction — December 27, 2007 @ 1:23 pm

  12. ChemBark won’t even let you post now. I tried putting #7 as a comment to Rip Van Winkle #7 (Miles Monroe and Synthesis Bashing) — where it belongs, but was turned away by the site. Hopefully Paul will make a New Year’s resolution to reactivate the site. I’ll wait till then before taking Milkshake’s advice.

    Should I do so, another question arises. Apparently there are zillions of blogs out there. Paul’s site had just the people I want reading my stuff (for which I’m very grateful, and which makes me extremely relutant to leave ChemBark). How do they find out where I am?

    Comment by Retread — December 27, 2007 @ 3:06 pm

  13. as a fallout, the progress of Paul’s thesis work is probably watched more closely by his boss

    My guess is that the cyanobacteria make these ladder-like cyclobutanes instead of cholesterol as a rigid building block for their membranes. (Less rigid analogs are relatively easy – just adding cis double bonds to glycerides – but quite elaborate synthetic apparatus is needed to transform cycloprenoids into steroids. So maybe cyanobacteria found this alternative). There is lots of weird stuff in evolutionary-old organism – some thermophilic archaea have branched ether lipids…

    Comment by milkshake — December 27, 2007 @ 7:30 pm

  14. Milkshake #13 — Interesting point. Have a look at the structure. It isn’t a ladderlike cyclobutane as there is only one such moiety in the molecule. The end away from the carboxyester is likely to be fairly rigid as you suggest, as there is an omega methyl group hanging off the bicyclobutane which is linked to a trans double bond which is linked to an epoxide, so there are only two points of rotation in the last 9 carbons. However between these 9 carbons and the carboxylic acid lie 7 methylene groups.

    Also no one is quite sure just what cholesterol is doing in cellular membranes. Imparting rigidity is certainly one possibility. In the membrane surrounding the eukaryotic cell (plasma membrane) cholesterol is present in equimolar amounts to all the other lipids (according to a rather old reference [ Science vol. 261 pp. 1280 – 1281 ’93 ]). In other cellular membranes (endoplasmic reticulum, Golgi apparatus) cholesterol is barely present at all.

    Also there is a huge controversy as to the existence of lipid rafts (high in sphingolipids and cholesterol) in the outer leaflet of plasma membranes. Thermodynamically its hard to see how two such phases could coexist in the rather formless lipid bilayer of the cell membrane. Where is Irving Langmuir when you really need him?

    Comment by Retread — December 27, 2007 @ 11:20 pm

  15. “Don’t it always seem to go that you don’t know what you’ve got til’ it’s gone?” Sic transit gloria mundi

    Comment by Uncle Al — December 28, 2007 @ 2:46 pm

  16. retread–maybe we could use a guest post every now and then, if excimer is up for it? CBC is not dead, but is “sleeping” over the holidays. I’m fairly sure we can keep it alive, even if it turns out less-than-awesome (a picture maybe once a week? minimal effort required). but be forewarned…we don’t do bio-anything.
    alternatively, you could start your own. it’s harder to go at it alone–having a coauthor makes things much better (especially if said coauthor is as entertaining as excimer).

    Comment by Ψ*Ψ — December 28, 2007 @ 4:29 pm

  17. It is simply amazing how much time a proper career takes up. Whilst a postdoc, I had lots of energy and topics to blog about, now, I only really write when time allows (which aint that often…)

    Comment by Milo — December 29, 2007 @ 12:31 am

  18. Whats the basis for the strict addition sequence followed during all of the sonogashira reaction preps I have found? It seems like the CuI is always added last? Not sure why it makes any difference as long as you add the alkyne as the very final thing?

    Comment by Tom — December 29, 2007 @ 3:06 am

  19. I don’t really know but the authors of the published procedure insisted the order of addition was important. I noticed that the color of reaction mixture started changing immediately after the CuI addition (orange to gray, then to pale yellow) and the pre-catalyst that I was using (PdCl2.Dppf) was dissolving. My best guess is that Cu-acetylide formation happens very fast and brings about the reduction of Pd(II) to Pd(0). In that case it would make sense to add CuI last and cap the vial immediately, as both Pd(0) and Cu(I) acetylide are air sensitive.

    Comment by milkshake — December 29, 2007 @ 3:26 am

  20. I too have noticed the color changes… but I haven’t tried myself to figure out if it makes a difference… perhaps some process type chemist could chime in.

    Comment by Tom — December 30, 2007 @ 3:16 am

  21. Tom: on a small scale a tiny amount of CuI or CuBr is difficult to add last – 2mg of CuI is just a tiny amount of heavy solid that tends to stick to glass/ But you don’t want to overload your reactions with Cu nevertheless/

    Some people have been using CuI solidified slurry in molten paraffin, to bulk up the volume.
    What I do instead is to cut a Pasteur pipette or NMR tube into a short glass tube, weigh the CuI in there, then use a small amount of solvent (anh THF) to wash it down into the reaction mix

    Comment by milkshake — December 30, 2007 @ 11:02 am

  22. Pipeline is dead, too! What did you do?

    Comment by Klug — December 30, 2007 @ 3:40 pm

  23. Derek got an offer he couldn’t refuse – to take couple days off. A family business, you know. But don’t worry, he’s gonna be alright.

    Comment by milkshake — December 30, 2007 @ 4:42 pm

  24. Woah, I wasn’t aware that these blogs were already dead. I suppose I’ve shown up too late on the scene. However, I have been reading my backlog of posts from Saturday Night Synthesis. Maybe we should start making archives of these dead blogs before they truly vanish?

    – Bryan

    Comment by Bryan Bishop — December 31, 2007 @ 11:58 pm

  25. Moonlight Serenade reminds me on the great Jet Set Willi 1980s arcade game.

    Comment by ASDF — January 2, 2008 @ 3:17 am

  26. I think it also featured in the Resident Evil IV game. This particular recording is played in a subtle way and I am very fond of it: almost anyone can manage the first movemet – to some jarring dramatic effect – but only few actually play it delicately, with the right tempo, grace and balance.

    Comment by milkshake — January 2, 2008 @ 3:47 am

  27. Interesting that you guys are interested in classical music. The chemists I knew back in the 60s were not. As an amateur chamber musician who has gone to amateur chamber music festivals for 30+ years where we do the best we can with help by the professional musicians running the show, I’d estimate that 20% of the attendees are either (1) mathematicians or (2) physicists or (3) computer scientists at most festivals. There were no chemists with one great exception: Edwin Gould who wrote what we considered the bible of physical organic chemistry back then “Mechanism and Structure in Organic Chemistry”. He is an excellent amateur violinst, and I had the pleasure of playing with him at Interlaken in Michigan a few years ago.

    Any chemists out there who play (not just listen to) chamber music for fun?

    Comment by Retread — January 2, 2008 @ 9:04 am

  28. Not me: I was terrible at the piano lessons (for complete lack of discipline, I hated to practice) and I remember my old teacher, reaching with a shaking hand for yet another cigarette and lighting up as soon as I started playing…

    But I got something out of her lessons – I inherited her guinea pig that was in the acute danger of being eaten by her dog. This was a wonderful going-away present for me, at the age 11, and she solved two problems in one stroke.

    (Soon after I had a productive guinea pig breeding program in the kitchen of our flat – I got another one to make a pair; they eat almost anything – and the sale of the cute guiney ofspring provided a supplement to my alowance. The chorus of excited squeals from the kitchen welcoming my arrival and the comencing feeding time was more sweet than the Bach etudes).

    Comment by milkshake — January 2, 2008 @ 10:31 am

  29. Chessmaster series would play Moonlight Serenade by default.

    Comment by liquidcarbon — January 7, 2008 @ 2:47 pm

  30. I think I might start my own Organometallics blog, although I did enjoy contributing to the Organometallic Current. There will be more freedom to put up content that I want to write about… sometimes at length.

    I will probably try WordPress since everyone likes that format. The biggest stumbling block however, is the name. ‘Organometallic Advocate’? ‘Organometallic Comment’? Oh for the love of… I really need help on this one.

    Comment by blatnoi — January 9, 2008 @ 2:40 pm

  31. try something silly & memorable, like “The Transition-Metal Hustle” or “Carbon-Metal Monstrosities”

    Comment by milkshake — January 9, 2008 @ 7:25 pm

  32. Can we go back to view the old stuff on Kinasepro? It is password protected. But even after I registered on WordPress, I still could not find it.

    Comment by diketene — January 17, 2008 @ 9:12 pm

  33. I don’t know what’s happening: KP mentioned his upcoming projects in his last post (I would love to hear more on those) and the lack of time to continue the KinasePro site. Let’s hope he is not in some kind of trouble as industry bosses can be complete dicks.

    My guess is that maybe KinasePro, being succesful, is now trying to set up some kind of a patent analysis business – in which case he would want to include the current material at KinasePro into his offerings. So maybe we will hear from him once he puts his plans into action.

    Comment by milkshake — January 17, 2008 @ 10:07 pm

  34. Not reading 95% of other scientist’s blogs, I only knew about Paul’s. Eh, eh! Great news for those which have survived! (to be read with an evil, creepy voice)

    Comment by albert — January 19, 2008 @ 11:14 am

  35. …is not dead!

    Comment by Tot. Syn. — January 21, 2008 @ 7:22 pm

  36. Milkshake and Psi*Psi

    Thanks for help about blogging. Starting today I can be found at “Chemiotics” on the Skeptical Chymist website

    Comment by Retread — February 14, 2008 @ 2:16 pm

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