Archive for the 'Hall of Shame' Category

Hello friends.  Remember me?  It’s your ol’ buddy, Paul Bracher.

You’re probably asking yourself, “What brings this guy back from the dead?”  Well, when a postdoc in our lab showed me what arrived in the mail, not only did I roll over in my grave, I decided to resurrect everybody’s favorite chemistry game: “What’s Wrong with this Picture?”

The following 52-page brochure arrived courtesy of Oxford University Press with the following cover.  That’s right…COVER:

Oh. My. God.  The real question is: What’s right with this picture?  Not much.  There are messed up bond angles, aryl Texas carbons, acyl Texas carbons, Rhode-Island carbons, bizzare peroxides, Texas oxygens, Texas nitrogens, and the list goes on.   

What the hell is wrong with these people and why the hell is the ACS logo on this piece of garbage?  The O.U.P. editors should be drawn and quartered, and their heads should be displayed on pikes outside of ACS headquarters in Washington.

As if the front cover didn’t offer enough entertainment, the back cover has the following unintentionally humorous statement:

xford (sic) University Press, Inc. publishes works that further Oxford University’s objective of excellence in research, scholarship, and education.

Hooray for excellence.  Anyway, this weekend I’ll probably post on the upcoming Nobel Prize announcement (Oct. 10th).  After that, I might go back into hibernation.  We’ll see. 

An astute reader passed along the following nomination for the official Chemistry Hall of Shame (accept no imitations).  It’s another chemistry advertisement, published on page 66 in the June 18th edition of C&EN:

Sweet. I guess if you buy two methylene groups, they’ll throw in an extra one for free.  Big props to J. for scanning in the ad and passing it along.

All this succinimide/glutarimide business reminds me of my favorite chemistry mnemonic—the one for remembering the straight-chain diacids (from two carbons to seven):

Oh My, Such Good Apple Pie

(Oxalic Malonic Succinic Glutaric Adipic Pimelic)

Now, I’m not going to do something as hackneyed as ask, “What is your favorite chemistry mnemonic?” Nope. Not going to do it.

Regular commenter CET sent along an interesting picture from a gen-chem textbook at his school. Start the week out right by determining what the chemist below is doing wrong:

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From last week’s Harvard Police log:

6:11 p.m.—A Harvard University Police Department (HUPD) officer was dispatched to a report of a suspicious odor in Jordan Hall South believed to be carbon monoxide in the building. The officer met with the reporting party who stated that while working in the building they smelled a strong odor and began to feel sick so they pulled the fire alarm to evacuate the building. Cambridge Fire Department tested the air quality which came back negative for carbon monoxide and deemed the building safe for re-entry. The reporting individual was treated by EMTs with oxygen on the scene and refused any further medical assistance.

Some people at Harvard are so talented they can smell carbon monoxide, an odorless and tasteless gas.  I’d like to see someone at Free University of Berlin do that.

And pay no attention to the item where an officer caught two guys smoking weed and just let them go.  Carry on, good sirs.

Some commenters in a previous thread took umbrage at the fact that I admit to judging people by their grammar. Well, I do, and I’m not going to change anytime soon. I’ll put poor grammar on par with poor hygiene, dressing like a slob, and bad table manners—while they don’t automatically invalidate a person’s ideas, they will cause me to treat anything the person says with more skepticism than usual. With respect to the four errors I found in the first paragraph of this recent paper from Org. Lett., the misplaced apostrophe in “Evan’s” was the most aggravating. While the chemistry in the paper was good, as The Chem Blog has noted, the authors’ lack of attention to detail was borderline disrespectful. I expected more from one of the most storied labs in synthetic organic chemistry.

A lot of people will complain, “So what if I make a few mistakes? Why don’t you focus on the ideas?” That’s the thing: I want to focus on your ideas, so why don’t you stop whining and learn to write properly? The rules of grammar are not up for discussion—just follow them out of courtesy to your readers. Grammatical errors are distracting and will cause them to lose sight of what you’re writing. If you are someone who has no trouble reading documents riddled with mistakes, that’s great, but when you are writing, you aren’t writing for yourself.

While grammar shouldn’t be the sole criterion for evaluating intelligence, I will admit to judging some things by a relatively obscure set of criteria. For instance, I have a list of favorite subjects for judging textbooks and course packets. One of the first things I do to determine the quality of a sophomore organic textbook is to look in the index for phenol. As you all know, phenol is more acidic than “standard” aliphatic alcohols. If you took a survey, most people would ascribe this fact to a resonance effect by drawing the following structures:

There are a number of variations on this theme, including drawing out all of the unhybridized p orbitals and showing that an orbital on oxygen containing a lone pair can overlap with the pi system, thereby allowing for increased delocalization of the extra negative charge density.

It turns out that an inductive effect—not a resonance effect—is the predominant reason for the increased acidity of phenol relative to aliphatic alcohols. Whereas aliphatic alcohols have a C(sp³)—O bond, the carbon to which the hydroxyl group is bonded in phenol is sp² hybridized. The increased s-character of the carbon orbital used to form the C—O bond makes it more electron withdrawing, which leads to greater stabilization of the conjugate base of the alcohol. For the purpose of comparison, look at the pK_a of phenol compared to that of enol tautomer of acetone:

Even though you can only draw two resonance forms showing delocalization of the extra negative charge in the conjugate base of the enol (vs. four for phenol), the acidities of the two protons differ by less than an order of magnitude. For those interested, these data come from Evans’ Chem 206 lecture notes (Lecture 20, restricted access), where the point is hammered home in glorious detail. Professor Evans’ PowerPoint slides should be framed and displayed in the Smithsonian.

While we’re discussing phenol and errors, let me also use this example to illustrate one of the main problems with Wikipedia. Wikipedia is great, but it is home to a number of edit-happy users who think they know more than they actually do. If you look at the discussion page for phenol, someone actually addressed the resonance vs. inductive effect argument, but was unceremoniously (mis)corrected by another user, who references an incorrect explanation on the Internet. Thus, the main article (as of today) gives the incorrect (resonance > inductive) explanation:

Phenol has a limited solubility in water (8.3 g/100 ml). It is slightly acidic: the phenol molecule has weak tendencies to lose the H⁺ ion from the hydroxyl group, resulting in the highly water-soluble phenoxide anion C₆H₅O⁻. Compared to aliphatic alcohols, phenol shows much higher acidity; it even reacts with NaOH to lose H⁺ whereas aliphatic alcohols do not. This is due to orbital overlap between the oxygen’s lone pairs and the aromatic system, which delocalizes the negative charge throughout the ring and stabilizes the anion. This effect is attenuated, however, due to oxygen’s relatively high electronegativity. ^[1]

God knows that we in the chemical blogosphere love the Wikipedia, but read it with skepticism.

This concludes today’s lesson. Your homework for the weekend is to find all of the grammatical errors in this post. For extra credit, find an error in a chemistry article on Wikipedia, fix it, and brag about having done so in the comments. Class dismissed.

Ready for another round of what’s wrong with this picture?  Good.  Take a look at this ad for ACS Publications that ran in the last edition of C&EN (Feb. 19, p. 33, click for full image):

I’m not particularly upset that Dr. Julian isn’t wearing gloves, and I’m not going to whine about the bright sources of light in the background that make this an awful photograph.  This time, my beef is with the caption:

In 1948, Percy Julian developed a new way to synthesize hydrocortisone, which is still used to treat rheumatoid arthritis; 45 articles published by Julian are in the ACS Legacy Archives. 

As far as I know, Julian never came up with an original synthesis of hydrocortisone (or cortisone, for that matter).  What Julian is famous for making is Reichstein’s Compound S, which Upjohn later found a way to oxidize to cortisone using a microorganism.  In fact, once Upjohn discovered the process for selective oxidation at the 11-position, there were many routes to cortisone, not just through compound S.  Julian’s route through steroids isolated from soybeans was not as effective as Syntex’s route through the Mexican Yam, since this species of yam produced a greater yield of the steroid precursors.  Julian eventually quit his job as director of the Soya Products Division at Glidden so that he could work with the Mexican Yam.

While we’re busy correcting things, the 45 articles by Julian that the ACS claims to have in its “Legacy Archives” include two addition/correction notices.  Thus, the correct value for the number of articles he published with the ACS is 43, two of which he later amended.  Feel free to check my math.

So, let’s recap:

1.  Julian did not make hydrocortisone in 1948.   He reported the partial synthesis of Compound S in 1951 (submitted to JACS in 1950).  I don’t know what 1948 has to do with anything.

2.  Julian never came up with an original, complete route to hydrocortisone.  Upjohn’s fermentive oxidation of the 11-position of steroids made it possible to take Julian’s route to Compound S all the way to cortisone.  This process was developed in 1951/2.  (Although he did not make the key discovery, Julian should be praised for predicting that this amazing transformation would eventually be discovered.)

3.  Julian/Glidden applied for a patent on the “Preparation of Cortisone” on September 9, 1950, but it was one of those pie-in-the-sky deals.  They never actually made the key transformation, and basically said so in the patent: “The present invention is not concerned with the introduction of the 11-keto group, nor with the formation of the acetyl group in the 17-position of the molecule, but is concerned with the other conversions and reactions mentioned.”

3b.  In light of this important fact, it is amazing that Julian was inducted into the Inventor’s Hall of Fame for this particular patent.  Why not choose one of his many other inventions?

4.  The ACS Legacy Archives contain 43 (not 45) articles by Percy Julian.

Do not leave with the wrong impression; Percy Julian was a truly excellent chemist.  But the fact that the ACS didn’t even bother to get its facts right suggests that this full-page ad was more about pandering to a perceived need to participate in Black History Month than about honoring an excellent chemist.  In the future, I hope that the ACS publishes an ad that accurately reflects Julian’s wonderful contributions to our field, and I hope it doesn’t wait until next February to do so.

After thorough examination, the Chemmy “Award” for Villain of the Year goes to:

Prof. Dr. Dalibor Sames for the Columbia C-H Activation Fiasco

The sad part of this post is not that Sames won, but that there were other legitimate contenders. The strongest cases could be made for Dalibor Sames, Bengu Sezen, and JJ La Clair. Some people might have also thrown R&D at Pfizer into the mix for ruining our stock portfolios, but that’s not really fair. The fact of the matter is that the system seems to have worked in the case of Torcetrapib—the drug’s danger was discovered in clinical trials and the project died. That’s life.

So, why not La Clair? Any other year he probably would have won, but in the end: 1) the hexacyclinol story was not as disgusting as the Columbia case, and 2) hexacyclinol has locked up the Chemmy in a different category.

The decision between Sames and Sezen was a tough call. If Columbia’s investigation shows that Dr. Ms. Dr. Sezen did naughty things with her data, you can bet that she’ll will run away with the Chemmy next year. For now—as is the custom in academia—the advisor takes home the award.

And I really think that Sames deserves it. Let’s review his credentials:

1. He retracted six papers and a significant part of a seventh. What chemist (besides Sezen) has ever had to do anything like this?

1a. If you think that Sames might be an “innocent victim,” please refer to Columbia’s policy on professional misconduct:

In modern collaborative research, the implications of academic misconduct or fraud go far beyond the individual; they also affect collaborators whose own work has been committed to objective search for truth. The specter of guilt by association may lurk in the background for many years to come. Therefore, joint authorship requires joint responsibility; each author claiming credit for the entire work must also be aware of joint discredit. Investigators in collaborative research projects each must make reasonable and periodic inquiry as to the integrity of and processes involved in gathering and evaluating data. It should be understood that overall responsibility for the integrity of collaborative research rests with the principal investigator. Senior investigators cannot be allowed to escape the consequences of the discovery of misconduct or fraud committed under their supervision.

2. The first round of retractions submitted by Sames had Sezen’s name on them without her approval or any indication that he was acting without her consent. (Note that JACS changed the wording of these retractions after publishing them—without making note of the edits).

3. While it has yet to be confirmed by Columbia, a lot of people have said that one or more students were essentially encouraged to leave (a.k.a. fired from) the Sames Lab for incompetence, at least in part because they could not reproduce the results that were eventually retracted. If someone in your lab raised questions about the reproducibility of an experiment, wouldn’t you feel obligated to check the procedure out for yourself? It’s not like Sames was that far removed from bench work; he easily could have run these reactions. Doing so probably would have prevented a lot of the subsequent mess.

4. When it became clear that something was wrong, Sames waited at least six months before publishing the retractions. Why did he wait if it wasn’t for her approval? Taking so much time was inconsiderate, as other chemists in the area of C-H activation wasted time trying to use Sames’ reactions (for example: Bellina, et al. Eur. J. Org. Chem. 2006, 1379).

5. Sames has publicly blamed Sezen in a variety of ways, such as in his wording of the retractions, in statements to news organizations, and by removing her from his lab’s Web page. While he was willing to fire these shots at her, when the press came calling to question him, he threw up his hands up and claimed that he’s not allowed to comment on the case due to the ongoing investigation. Either talk or shut up. Pick one. To do otherwise is unfair and cowardly.

There’s more, as you know, but you can use Google to refresh your memory. And if anyone thinks that this wasn’t a significant story, feel free to go crying to the editors of C&EN, Science, Nature, and the NY Times, too. The story is legitimate and newsworthy. If you don’t want to hear people talk about it, go somewhere else.

In fact, given the gravity of this particular story, I think we should consider including an actual prize with the Chemmy. Perhaps we can put Ed the Dog in charge of raising funds for an all-expenses-paid trip to Circle 8, Bolgia 8.

Who’s willing to chip in?

The following picture accompanies the story titled “Women in Science” in this week’s C&E News (Nov. 27th, p. 34):

I bet the layout editor was quite pleased with himself after picking this image out of the database:  Woman doing science?  Check.  Obligatory chemistry glassware?  Check.  Pretty colors? Check.

Now, what the hell is she going to do with all of these solutions?  Isn’t it a little early to be dyeing Easter eggs? Anyway, while admiring this “scientist” doing “research,” I noticed something truly disturbing. Take a closer look and see if you see it too…

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