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DBL%20Hendrix%20small.png College chemistry, 1983

Derek Lowe The 2002 Model

Dbl%20new%20portrait%20B%26W.png After 10 years of blogging. . .

Derek Lowe, an Arkansan by birth, got his BA from Hendrix College and his PhD in organic chemistry from Duke before spending time in Germany on a Humboldt Fellowship on his post-doc. He's worked for several major pharmaceutical companies since 1989 on drug discovery projects against schizophrenia, Alzheimer's, diabetes, osteoporosis and other diseases. To contact Derek email him directly: derekb.lowe@gmail.com Twitter: Dereklowe

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February 8, 2012

Every Methods Paper Has a Table

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Posted by Derek

Here's a helpful translation, and there's more truth in it than there should be. My rule of thumb is to be extremely suspicious of a methods paper that doesn't have at least a couple of low-yielding or "NR" entries. If they aren't there, it means that someone didn't do enough experiments (or, worse, that they're not telling you about those little details).

Comments (21) + TrackBacks (0) | Category: The Scientific Literature


COMMENTS

1. Anonymous on February 8, 2012 1:58 PM writes...

Yes, but if you don't exaggerate your yield or if you include bad ones, you'll be rejected from JACS. That sword cuts both ways.

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2. OldLabRat on February 8, 2012 4:01 PM writes...

#1, Are you kidding? JACS doesn't care about science? I'd sure like to know when not to use a method just as much as I'd like to know when to use it. Perhaps that's why I don't trust new synthetic methods until it's in Org Syn. At least then, it might be a real reaction.

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3. canchem on February 8, 2012 4:52 PM writes...

I never trust a synthetic paper that doesn't have at least a couple of "odd" reaction times, like 11-14 hours. Ie. longer than a normal work day, and less than an overnight. It means the grad student was actually working hard when the work came out, not just fudging up the work while the boss was away.

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4. Anonymous on February 8, 2012 6:02 PM writes...

No OldLabRat, I'm not kidding. There's been many a discussion here about how reliable these papers are and how common yield/ee/de/selectivity inflation is. If you don't make it sound like your method is going to cure cancer RIGHT NOW you're probably going to get bounced straight out of JACS. In that respect, no, they don't care about all science. Only the stuff that sounds great, which means no bad yields or low diastereoselectivities.

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5. Anonymous2 on February 8, 2012 8:27 PM writes...

*not good science

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6. Diffraction on February 8, 2012 8:41 PM writes...

#3 (canchem): I also tend to be more inclined to trust a paper if conditions, e.g. time, vary between entries, but I don't think the grad student working hard has much to do with it. Doing one or two reactions and checking them every hour still allows ample time for being lazy. Also, at least in my grad student world, 12-14 hours is right in the overnight range (21:00-09::00).

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7. Anonymous on February 9, 2012 2:49 AM writes...

to 3 and 6

Are you serious????
So you judge the value of the paper by how much time a student spent (wasted) on it????

I cannot believe you mean it.

Science should be about having ideas, solving problems, asking questions.

If you want just some hands mixing reagents...buy a robot!

And even in the case they write 13h reaction time, what do you now?
Tell the wife and 9 in the evening that you shoulg get back to work to make a TLC??
Or you tell the process chemists that reaction should be REALLY 13 hours and not 12 or 14h??

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8. petros on February 9, 2012 3:19 AM writes...

I remember a paper from Merck in Tet Letts where they used a silyl protecting group but didn;t bother to mention the reaction time.

When I inquired after failing several times I was told they had used 7 days- for a fairly simple secondary alcohol!

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9. irii on February 9, 2012 4:50 AM writes...

sorry petros, i am being dense, but what's the point?

did the protecting group really take 7 days to go on, and you were seeing no reaction because you were not leaving it that long, or what?

or is 7 days too ridiculous a time to quote. or are previous posters (and you??) thinking the time quoted for complete protection of the secondary alcohol with the silyl group should be 6 days, 20 hours and 4 mins and if the student (in this case employee of course) failed to nail the "completion time" of the reaction, she should be fired?

or did it not really take 7 days? I am just not sure what you are saying is quite clear. maybe just me though.

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10. irii on February 9, 2012 4:52 AM writes...

or maybe just to diss tet lett???

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11. anchor on February 9, 2012 8:36 AM writes...

As a practicing organic chemist with 20+ years, I utilize literature procedure as a road map and not a gospel truth. I start the reaction and track the same by HPLC or TLC. Translation-do not wait for 7 days. It is possible that this gentleman started the reaction and went to vacation.

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12. Fluorine on February 9, 2012 8:38 AM writes...

I feel that this is the major flaw of most method papers, pointless substrate ranges combined with ridiculously high yields. Knowing the limitations of a published procedure is much more useful than knowing that it works well for closely related starting materials.
Seems like the content of a high profile publication is less important than the overall impression an article gives the reader on a superficial glimpse...

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13. Morten G on February 9, 2012 9:19 AM writes...

No standard deviations of yield suggests to a biologist that you were only able to get the reaction to work once.

@7 Right on! I was upset by those comments too.

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14. Diffraction on February 9, 2012 10:04 AM writes...

#7: no, I don't judge a paper by how much time a student spent on it. My point was this: when judging a paper I don't care if it took someone 2 years working 3 hours a day or 2 months working 12 hours a day, I just care that the work was done with reasonable care. Tables with some variation in yields, conditions, etc. are one indicator of this (but by no means proof positive).

With regards to #9, I don't expect reaction times to be quoted to the minute. If a reaction actually takes 6.4 days, saying 7 days is fine. But if a reaction actually is complete after 4 days, saying 7 days isn't great. Similarly, if a reaction takes 3 hours, listing the time as 4 hours is fine, but listing it as overnight isn't as good. With my reactions (which are often, but not always, slow), I typically check after 10 min, 1h, 2h, 4h, 8h, overnight, then 1d, 2d, 3d, etc., adjusting as necessary.

My other point was a minor one: basically, I'm a grad student and 12-14 hours is a typical "overnight" for me (19:00 or 21:00 to 09:00).

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15. InfMP on February 9, 2012 11:54 AM writes...

for the worst looking scope table, please see:
10.1021/ol102029u
The bond angles are legendary.

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16. Mmol on February 9, 2012 1:38 PM writes...

I just recall, albeit a few years ago, an Associate Editor for “a well-known (and very good) ACS journal”, suggesting that "the readership would be more impressed if we quoted higher yields for two entries". In response to my somewhat incredulous retort of “well, what do you suggest I put in!” (followed up by the comment that the purpose of those two specific entries was to indicate clearly the limits of the chemistry), the Editor intervened and the Assoc. Ed. sought to pursue his floundering editorial career in pastures new ………… There is far too much sanitisation and the problem, frequent with organic synthesis types, is that one’s yields to often reflect on one’s manhood……….

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17. Anonymous on February 9, 2012 5:45 PM writes...

JACS doesn't even care if you cant count bonds:
10.1021/ja209068z

Five bonds to carbon, yup, that happens all the time in the real world.

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18. sepisp on February 10, 2012 5:00 AM writes...

#17, it's a radical. It's supposed to have three bonds and an unpaired electron. There's no implicit hydrogen if you draw a radical dot.

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19. Anonymous on February 10, 2012 4:47 PM writes...

#18, look at figures in the paper, ie. structure 8 or 11. I don't see radicals, I see 5 bonds!

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20. Secondaire on February 12, 2012 1:00 AM writes...

#13. I agree. I'm a post-doc and people frequently make comments about how I'm expendable, worth nothing, etc. to my face, and the comments by #3,5,7 really hit a bit too close to home..

#12. Seriously. You won't believe how many times it's a case of "We tried [New Method X] on every methoxybenzaldehyde we have". I then try it with p-chloro, and it doesn't work at all.

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21. newnickname on February 14, 2012 11:15 AM writes...

Even though I do it and understand it and the reasons for it, it is rather amazing that even the best synthetic organic chemistry is reported as singletons. No multiple runs, no error bars, no SDs.

There just aren't enough resources or time. It can take months to optimize a reaction after dozens of variations but we only report the best one. Sometimes, the reported specs may not even be due to the best set of conditions but due to the improved technique and skills applied to the later occurring examples.

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