Archive for the ‘Piquant Papers’ Category

Some Very Peculiar NMR Spectra in Organic Letters

Monday, August 19th, 2013

A close examination of the Supporting Information attached to this paper from 2011 in Organic Letters reveals some pretty interesting NMR spectra:

compound_5d_hnmr_zoom

(compound 5dfull spectrum)

Hmmmmm. I have collected hundreds of NMR spectra, and I can’t ever recall seeing a spectrum in which intensity was not a reasonably continuous function of chemical shift. That is, values of chemical shifts had only one associated intensity each, and no spectra had missing chunks of signal.

Here are some other interesting pieces of spectra from the same paper:

compound3j_hnmr_zoom(compound 3jfull 1H NMR spectrum)

 

compound3j_cnmr_zoom(compound 3jfull 13C NMR spectrum)

 

compound_7c_zoom  (compound 7cfull spectrum)

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You can check out all of the spectra in the SI for yourself—the file is open access.

So, what is going on here? One explanation is that we’re seeing something very scientifically interesting. I hope this is the case. Another explanation could be user error, or a malfunction on the part of the instrument and/or software used to collect and analyze the data.

Yet another explanation could be that unexpected or undesired peaks (e.g., those corresponding to impurities in the samples) have been erased from the spectra. Some of you might think this suggestion is outlandish—why would a chemical researcher manipulate spectral data in this regard?—but I cannot take credit for conceiving of this idea. I believe the first time I was alerted to this (highly unethical) practice was by the Editor-in-Chief of the journal in which this work appears.

Organic chemists and readers of this blog will recall that earlier this summer, Amos B. Smith III—the Editor-in-Chief of Organic Letters—penned an editorial documenting that he hired a data analyst to examine spectra and other data submitted to the journal for possible manipulation. The editorial included the statement:

I write to alert the organic chemistry community to a serious problem related to the integrity of data being submitted for review and publication by Organic Letters and to outline steps that the Journal is taking to address this concern. Recently, with the addition of a Data Analyst to our staff, Organic Letters has begun checking the submitted Supporting Information more closely. As a result of this increased scrutiny, we have discovered several instances where reported spectra had been edited to remove evidence of impurities. Such acts of data manipulation are unacceptable. Even if the experimental yields and conclusions of a study are not affected, ANY manipulation of research data casts doubts on the overall integrity and validity of the work reported.

I wish to reiterate that I have no definitive idea of what happened in the production of the spectra in this paper; this post only notes that they don’t look normal. In an effort to ascertain more about the spectra, five days ago, I reached out by e-mail to the first author, corresponding author, and Editor-in-Chief of the journal.

Dr. Bruno Anxionnat, the first author of the paper, did not respond. His former PI and the corresponding author on the paper, Professor Janine Cossy, replied with the following statement:

Dear Professor Bracker

There is probably a mistake as I know that the 1st supporting information with some spectra were wrong and I asked an other student to reproduce the experiments and sent back an other SI with the right spectra, may be the 1st SI was not changed by the right one.

Right now, I am abroad and can not check but I am going to check with the Organic Letters editorial office and I will tell theñm to contact you

Sincerely yours
Janine Cossy

I will note that Professor Cossy is an Associate Editor of the journal in addition to being corresponding author on the paper. You may recall that Smith’s editorial in Org. Lett. addressed the responsibilities of corresponding authors quite clearly:

In some of the cases that we have investigated further, the Corresponding Author asserted that a student had edited the spectra without the Corresponding Author’s knowledge. This is not an acceptable excuse! The Corresponding Author (who is typically also the research supervisor of the work performed) is ultimately responsible for warranting the integrity of the content of the submitted manuscript.

The responsibility to foster a research environment where all involved can confidently present their results, even if they are not optimal, resides with each research supervisor and Corresponding Author. At times, the inherent power of a research advisor’s position can create an atmosphere that leads some to embellish results.

In my e-mail to Professor Smith seeking comment, I made sure to mention his recent editorial. He sent back the following note:

Dear Bracher,

Thank you for bringing these discrepancies to my attention. As with any allegation concerning published articles, we have shared your concerns with the author, who is as you note an Associate Editor. Organic Letters has standard procedures for handling inquiries regarding the content reported in published articles, which are in play here.  As you may be aware, COPE (http://publicationethics.org/) provides  journal editors and publishers with guidelines for handling such issues.  Speculation and comment are premature at this time.

ACS and ACS Editors hold the conviction that the observance of high ethical standards is vital to  the entire scientific enterprise. Guidelines for a course of conduct by  those engaged in the publication of chemical research, specifically, editors, authors, and manuscript reviewers are set forth in ACS Ethical Guidelines to Publication of Chemical Research http://pubs.acs.org/userimages/ContentEditor/1218054468605/ethics.pdf.

Amos Smith

So, there you have it. The matter is being examined more closely, and it would appear the ball is in Organic Letters’ court. Interestingly, there are a few more papers (listing Anxionnat as first author and Cossy as corresponding author) where you might notice similar-looking spectra:

Anxionnat, B.; Pardo, D.G.; Ricci, G.; Cossy, J. Eur. J. Org. Chem. 2012, 4453–4456. (paper, SI)

Anxionnat, B.; Robert, B.; George, P.; Ricci, G.; Perrin, M.-A.; Pardo, D.G.; Janine Cossy. J. Org. Chem. 2012, 77, 6087–6099. (paper, SI)

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Go have a look and judge for yourself.

 

Some VERY Suspicious TEM Images in Nano Letters

Wednesday, August 14th, 2013

Mitch at Chemistry-Blog has a new post about a set of very suspicious TEM images that was published recently in the journal Nano Letters.

The associated paper reports the fabrication of pairs of gold nanorods in “chopstick” structures where the two rods touch at their tips and form an angle that the authors say they can tune. Some of the TEM data can be viewed for free in the associated SI file. If you zoom in on the images, it appears that the background immediately around many of the rods is different from the rest of the background field. Hmmm…

from Nano Lett.

from Nano Lett.

 

from Nano Lett.

from Nano Lett.

 

User “spookyjeff” on the chemistry subgroup of Reddit commented:

That is some impressively bad photoshop. Allegedly.

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To which user “FubarFreak” replied:

I’m going to go with MS paint

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Mitch also reports that Leonard Pease, the last author on the paper and an assistant professor at the University of Utah, told Mitch “an investigation [is] underway at the University of Utah into this matter and [he] strongly encouraged [Mitch] not to publish this story until the University completed its investigation.” Pease also “informed [Mitch] that legal action might be pursued by the University of Utah if [he] published this story.”

Longtime readers of ChemBark will recall that Columbia University never explained to the community what happened after it was finished with its investigation of Bengu Sezen. FOIA requests filed by ChemBark and another news organization were required to report the full extent of Sezen’s misconduct to the public. One lesson there [of many] was that you cannot count on universities to investigate or publicize the results of investigations into suspicious data and other possible scientific misconduct. Journalists, sources, blogs, and social media have helped fill this void by making valuable contributions toward identifying suspicious data and ensuring research misconduct is investigated and punished.

Fortunately for Mitch, ensuring that one’s facts are true is an absolute defense against libel in the United States, and the truth is that the above images were published by the authors in Nano Letters.

Finally, if the images in Nano Letters turn out to be manipulated, we should consider the question of “just how lazy/inept was the offender?” Michael on Facebook tried his hand at “fixing” the authors’ figures and produced the following:

michael1  michael2

michael3

Very nice—no more boxy awkwardness and mismatched backgrounds. He reports that “after installing the photoshop trial it took about 5 minutes to do 2 or three images.”

Elsewhere: Chemistry-Blog (original report), Reddit, Chemjobber

Dorta Paper Link Roundup

Tuesday, August 13th, 2013

For chemistry news stories that generate a lot of fragmented discussion online, I like to post a list of links to facilitate keeping track of everything. This post may be updated; I think there’s a good chance we will hear more about this story down the line….

Coverage of the Dorta-Drinkel paper in Organometallics

12 July 2013 – Organometallics – “Synthesis, Structure, and Catalytic Studies of Palladium and Platinum Bis-Sulfoxide Complexes” – Original published article

6 August 2013 – ChemBark – “A Disturbing Note in a Recent SI File” – Our original report

6 August 2013 – Reddit – “Check out page 12 of the supporting info…”

7 August 2013 – In the Pipeline – “New Frontiers in Analytical Chemistry”

7 August 2013 – Chemistry-Blog – “When Authors Forget to Fake an Elemental Analysis”

8 August 2013 – Reddit – “A Disturbing Note in a Recent Supplemental Information file for a published chemistry paper”

8 August 2013 – Reddit – “Editor-­in­‐Chief of Organometallics Responds to Paper by Reto Dorta”

8 August 2013 – ChemBark – “Organometallics Responds to the Dorta Situation”

8 August 2013 – In the Pipeline – “Make Up the Elemental Analysis: An Update”

8 August 2013 – Retraction Watch – “Insert data here … Did researcher instruct co-author to make up results for chemistry paper?”

8 August 2013 – Science Careers – “Note to Self: NEVER do This”

9 August 2013 – ChemBark – “The OM Paper vs. Drinkel’s PhD Thesis”

9 August 2013 – Slashdot – “Request to Falsify Data Published in Chemistry Journal”

9 August 2013 – Chemical & Engineering News – “Insert Data Here … But Make It Up First”

9 August 2013 – Chemjobber – “The Dorta Affair and others…”

12 August 2013 – Reddit – “[Recap] A failure in peer review enrages /r/chemistry”

16 August 2013 – Synthetic Remarks – “In Defense of Emma” – includes an e-mail from Dr. Drinkel’s mother

16 August 2013 – Reddit – “Emma’s Mother Responds to the Dorta “just make up an analysis” Affair. It’s a reminder that we need to be careful who we criticize in these controversies.”

17 August 2013 – ChemBark – “How Should the Online Community Handle Suspicious Papers?”

20 August 2013 – Der Spiegel Online – “Fälschungsverdacht gegen Schweizer Professor: ‘Erfinde einfach eine Analyse’”

 

Use the comments to call out other links; I’ll add them to the main post.

A HIGHLY Cited Paper

Thursday, February 7th, 2013

Here’s one more piquant paper for the file.

I got into a discussion yesterday about chemistry in PNAS and what important papers had been published in the journal. The best I could do off the top of my head was Lewis and Nocera’s review on powering the planet in 2006. After getting dinged from Science and Nature, most chemists seem to turn to Nature Chemistry, JACS, or Angewandte instead of PNAS.

Figuring there had to be something better, I dropped the question on the Twitter feed, and @josarc came through with this gem—a paper by Fred Sanger on DNA sequencing cited a whopping 64,989 times according to Web of Knowledge.

To put that number in perspective, it is almost 1.4 times the total sum of citations for papers by K.C. Nicolaou over his entire career (47,585).

Hot damn. This has got to be the record for chemistry, right?

Breslow and Dinosaurs in JACS, Oh My

Thursday, April 12th, 2012

You all know that origin-of-life research is near and dear to my heart, and you’re probably sick of how often I lament that the problem has not taken root in chemical academia despite the fact that it almost certainly requires a chemical solution. One of the few PIs at a top university who has dabbled in the field is Ronald Breslow, University Professor at Columbia and a past president of the ACS. Breslow just published this little diddy as a perspective in JACS:

First of all, how often do you see a single-author paper in JACS anymore? It is kind of refreshing. It also means that you can attribute 100% of the content to Breslow, including the ChemDraw structures:

What the hell is that? If I drew that structure on a slide in grad school, my committee would have eviscerated me.

Anyway, let’s get down to the science. Breslow’s premise is that you can take alpha-methyl amino acids found in non-racemic mixtures in meteorites—generated by selective destruction of one enantiomer by circularly polarized UV light—and “use” these compounds to generate non-racemic mixtures of sugars (which are also found as moieties in nucleic acids). Since meteors hit the early Earth with great frequency, maybe one or more of these chiral amino acids was the origin of life’s homochirality. It is an interesting idea and one worth keeping in mind. We could argue all day about how unlikely the scenario is, but this field needs to collect more neat ideas accompanied by simple demonstrations. That said, I take issue with the premise of the paper as outlined in the Introduction:

In 1969 a carbonaceous chondritic meteorite landed in Murchison Australia carrying many organic compounds. These compounds were apparently able to survive the frictional heating as the meteorite passed through our atmosphere since they were initially at ca. 10K, and chondritic meteorites are pieces of rock, with low thermal conductivity, from the asteroid belts that surround the sun. When the meteorite was split open the interior was still cold enough to freeze water.

Among the compounds identified were the amino acids alanine, valine, aspartic acid, glutamic acid, proline, and leucine, which were racemic, with equal mixtures of the L and D forms, along with achiral glycine. However, five amino acids were found that had methyl groups instead of hydrogens on their alpha positions (Figure 1), and these had a range of small excesses of the enantiomers originally described as the L amino acids (in modern terminology they are the S enantiomers). Since that time, these and other α‐methyl amino acids with small excesses of the S enantiomer have been found in the Murchison, Murray, and Orgueil meteorites (ref 1).

The whole point of why the Murchison meteorite is so interesting is that while the “natural” amino acids in it were initially thought to be racemic, subsequent analyses revealed them to have enantiomeric excesses.  I could be missing more recent analyses, but I don’t think so. Breslow should check out these seminal papers (1 2) and revise his background before the paper is “truly” published in JACS.

It is things like the odd ChemDraw structures and completely wrong information in the background that make me question the quality of peer review in JACS (and in all of chemistry, for that matter). I think one should also question the fairness of the editors, for I cannot imagine that this paper would have made it anywhere near publication in JACS if the author were Assistant Professor Joe Schmoe from Sunny Valley Technical College. But that said, the editors of JACS are the sole arbiters of what is “worthy” of publication in JACS, so I’ll just accept it and move on.

Normally, I wouldn’t blog about an otherwise run-of-the-mill paper about the origin of life, but this paper has really taken off in the world of popular science thanks to what amounts to a poetic thought by Breslow used to close the paper:

An implication from this work is that elsewhere in the universe there could be life forms based on D amino acids and L sugars, depending on the chirality of circular polarized light in that sector of the universe or whatever other process operated to favor the L α‐methyl amino acids in the meteorites that have landed on Earth. Such life forms could well be advanced versions of dinosaurs, if mammals did not have the good fortune to have the dinosaurs wiped out by an asteroidal collision, as on Earth. We would be better off not meeting them.

Since you are a reader of blogs, you will recognize this paragraph for what it is: a silly piece of fluff meant to close an otherwise esoteric piece on a humorous note. I’ve got no problem with that. We can argue over whether the joke is funny, but the attempt at humor is obvious…

…except to the staff in the ACS Pressroom, for they issued the following press release to promote the paper. I am copying it here verbatim because these things are intended for distribution—and because it is ridiculous.

Could “advanced” dinosaurs rule other planets?

Evidence for the Likely Origin of Homochirality in Amino Acids, Sugars, and Nucleosides on Prebiotic Earth
Journal of the American Chemical Society

New scientific research raises the possibility that advanced versions of T. rex and other dinosaurs — monstrous creatures with the intelligence and cunning of humans — may be the life forms that evolved on other planets in the universe. “We would be better off not meeting them,” concludes the study, which appears in the Journal of the American Chemical Society.

In the report, noted scientist Ronald Breslow, Ph.D., discusses the century-old mystery of why the building blocks of terrestrial amino acids (which make up proteins), sugars, and the genetic materials DNA and RNA exist mainly in one orientation or shape. There are two possible orientations, left and right, which mirror each other in the same way as hands. This is known as “chirality.” In order for life to arise, proteins, for instance, must contain only one chiral form of amino acids, left or right. With the exception of a few bacteria, amino acids in all life on Earth have the left-handed orientation. Most sugars have a right-handed orientation. How did that so-called homochirality, the predominance of one chiral form, happen?

Breslow describes evidence supporting the idea that the unusual amino acids carried to a lifeless Earth by meteorites about 4 billion years ago set the pattern for normal amino acids with the L-geometry, the kind in terrestial proteins, and how those could lead to D-sugars of the kind in DNA.

“Of course,” Breslow says, “showing that it could have happened this way is not the same as showing that it did.” He adds: “An implication from this work is that elsewhere in the universe there could be life forms based on D-amino acids and L-sugars. Such life forms could well be advanced versions of dinosaurs, if mammals did not have the good fortune to have the dinosaurs wiped out by an asteroidal collision, as on Earth. We would be better off not meeting them.”

What. The. Hell. Some booger-eating PR guy on 16th Street jumped to the end of the manuscript and took Breslow’s joke at face value. Then, his/her editor never thought to question the idea, and sent the press release out in the weekly PressPac. Now, the ACS is the laughing stock of the world of scientific publishing and popular science writing.

I guess we’ve learned nothing from the NASA/Wolfe-Simon/Arsenic Life episode. Why the hell do these things always seem to happen to origin-of-life chemistry?

:/

See also:

Just Like Cooking
Chemistry-Blog
Pharyngula
David Bradley’s Sciencebase
The Awl

Armpitin – “A Peerless Contraceptive”

Wednesday, March 21st, 2012

This article from 1965 might be the first example of the publication of a purely farcical chemistry paper in a respectable journal. This article also appears to have completely eluded the attention of blogs, most likely because bloggers were especially lazy in the 60s. The unmistakable quality of the paper is certified by a consequent letter to the editor, in which a concerned member of the Canadian Medical Association wrote:

I was appalled to read J.S. Greenstein’s Very Original Article on “Armpitin”…I am very sorry to observe that the official journal of Canadian doctors has published this article.

The paper describes the development of armpitin as a powerful contraceptive agent. While the author provides a structure for a portion of the molecule, he refuses to provide the full details of its synthesis because he “intends to make a fortune.”

The results seem unsurprising. I would wager that a majority of us have collected anecdotal evidence that a repetitive string of NOs can be very effective at preventing pregnancy. The author reports he serendipitously stumbled into the field of contraceptives while designing deodorants. One deodorant led to a noticeable increase in libido without concomitant increase in pregnancy. His initial studies proceeded from there:

With typical male self-assurance, we undertook to examine the females for the causative factors leading to their infertility. We employed every known gross anatomical, histological, histochemical, biochemical, endocrinological, physiological and psychological test of reproductive capacity and could find no evidence of malfunctioning of the female reproductive systems and accessory structures. We could only conclude, reluctantly, after months of exhaustive investigation, that the females were normal in all respects, and that we should turn our attention to the males.

When we took the trouble to examine the ejaculates obtained by masturbation, artificial vagina, or by post-coital recovery from the site of deposition, the answer to the enigma stared back at us through the narrow barrel of the microscope tube: THERE WERE NO SPERMATOZOA IN ANY OF THE SEMEN SAMPLES.

Yeah, this paper was actually published in a respectable journal—and in 1965, when by all accounts, people were humorless. (There is simply no other rational explanation for the popularity of Jerry Lewis.) What shocks me more than anything is that the content of the paper is 98% pseudo-legitimate technobabble and only 2% punchlines, yet the editor allows the damn thing to go on for 5 pages. That said, the list of references is particularly amusing. The author acknowledges “A. Gabriel” for divine inspiration in the form of a personal communication, and also cites a paper on orgasm by C. Men as well as a child’s guide to erotica by M. Goose.

While I regularly advocate that Carl Djerassi should be recognized by the Nobel Committee, I don’t think that Dr. Greenstein’s seminal contribution rises to the same level.