Archive for the ‘Inorganic’ Category

The OM Paper vs. Drinkel’s PhD Thesis

Friday, August 9th, 2013

ChemBark InvestigatesAs part of our investigation into the controversial paper published by Reto Dorta and coworkers in Organometallics, ChemBark contacted a source in Europe who was able to obtain a copy of the Ph.D. dissertation of the first-author of the paper, Dr. Emma Drinkel. Chapter 4 of the thesis carries the title “Synthesis, Structure and Catalytic Studies of Novel Palladium and Platinum Bissulfoxide Complexes”, and the chapter appears to describe the vast majority of the work reported in the publication in Organometallics.

The entire thesis is 174 pages long. ChemBark has made the editorial decision not to republish Drinkel’s thesis in its entirety, but rather, to provide a set of small excerpts that highlight important information, including a number of discrepancies with the paper in Organometallics. We are also republishing excerpts from the SI of the paper. I believe that this approach constitutes “fair use” with respect to copyright law, because (i) there is a time-sensitive need for the community to be informed about this important case, (ii) these excerpts represent a small fraction of the whole of the published works, and (iii) republication of these excerpts does essentially nothing to deprive Drinkel or ACS Publications of financial gain.

ChemBark’s excerpts from Chapter 4 of Emma Drinkel’s Ph.D. Thesis
ChemBark’s excerpts from the Supporting Information of the OM Paper

Drinkel’s thesis is dated “Zurich 2011”. In her curriculum vitae included at the end of the thesis, Drinkel reports her Ph.D. studies as having spanned “09.2007-09.2011”. Dr. Drinkel’s LinkedIn profile reports that she was at Zurich until December 2011, and she began work as a postdoc at Universidade Federal de Santa Catarina (Brazil) in July 2012. It is worth noting that the Organometallics paper was received by the journal on January 7, 2013—a full year after Drinkel departed from Zurich. This piece of information is interesting when one considers whether “just make up an elemental analysis” could mean “perform an elemental analysis” versus “fabricate the elemental analysis data”. Of course, the (arguably) ambiguous instruction could have been written many months prior to submission of the paper—while Drinkel was still in Zurich—or Drinkel could have carried all of her samples from Switzerland to Brazil.

A brief examination of the dissertation reveals that much of the information published in the supplementary file of the OM paper is identical to the information published in Chapter 4. This includes most of the characterization data and the prose used to describe the experiments. But a rapid comparison is hindered by what appears to be the root cause of the confusion between the main paper in OM and its corresponding supplemental file: Drinkel misnumbered some of the compounds in her thesis. The numbers in the discussion section of chapter 4 are shifted relative to the data reported for the same compounds in her experimental section. For example, compound 14 in the thesis’s experimental corresponds to compound 15 in Figure 13 from the thesis (pasted below). This compound is labeled 14 in Scheme 5 from the OM paper and 154 in the OM supporting information. The same problem goes for compound 16a/15a/15a/165a and others.

Figure 13 from the Thesis

Figure 13 from the Thesis

 

Scheme 5 from the Main Paper

Scheme 5 from the Main Paper

 

The numbering discrepancies in Drinkel’s thesis not only went unnoticed, they were exacerbated when the OM authors built their paper off of the chapter and decided to delete the label from compound 14 in Scheme 5. This is the compound associated with the now-infamous instruction to “just make up an elemental analysis”.

The written response from the editor-in-chief of Organometallics on the SI’s controversial statement regarding compound 14 included the following:

The author has explained to us that the statement pertains to a compound that was “downgraded” from something being isolated to a proposed intermediate. Hence, we have left the ASAP manuscript on the web for now. We are requiring that the author submit originals of the microanalysis data before putting the manuscript back in the print publication queue.

Indeed, there are no data for 14 written in the experimental section of Drinkel’s chapter 4—its preparation occurs as an intermediate in the preparation of 15 (using the numbering from Figure 13). With that said, the discussion section of chapter 4 mentions:

When 5a was treated with only 1 equivalent of AgBF4, unlike in the Pd case, the stable complex 14 was formed. No crystals could be grown to confirm the structure, but the 1H NMR spectrum of the complex shows the ligand is still symmetric. There is precedence for this type of chloro-bridged Pt dimers in the literature with phosphine ligands.

This statement from the thesis might appear to refute the claim in the letter that the authors could not isolate 14 and that it was simply a proposed intermediate, but the text of the main paper states that NMR was taken “in situ” after the first reaction. With that said, no NMR data are provided for compound 14 in the Supporting Information file, and an instruction is given to Emma (Drinkel) to insert these data. Perhaps the instruction to “insert” was given because the instructor already knew the data existed (based on what was written in the discussion section of the thesis)?

Beyond the problems associated with misnumbering, there are several discrepancies between the data reported in the thesis and the data reported in the SI of the Organometallics paper. All of the examples that I could find related to elemental analyses. Specifically:

SI-5b vs Thesis-5b

Compound 5b from the SI

Compound 5b from the SI

 

Compound 5b from the Thesis

Compound 5b from the Thesis

 

SI 11a vs Thesis 9a

Compound 11a from the SI

Compound 11a from the SI

 

Compound 9a from the Thesis

Compound 9a from the Thesis

 

SI 12 vs. Thesis 12

Compound 12 from the SI

Compound 12 from the SI

 

Compound 12 from the Thesis

Compound 12 from the Thesis

SI 165b vs. Thesis 15b

Compound 165b from the SI

Compound 165b from the SI

 

Compound 15b from the Thesis

Compound 15b from the Thesis

 

You can see that the authors chose to “count” different associated solvents when calculating the expected values for the elemental analyses, and they reported different observed results in the paper vs. the thesis for some compounds. Were these samples run multiple times? Since the original data have been demanded by the journal, I guess we’ll find out.

 

Stay tuned for continuing coverage…

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Note: In the reporting of this story, we wanted to give both the first author of the paper (Emma Drinkel) and the corresponding author (Reto Dorta) the chance to comment on the discrepancies we found in the data prior to the publication of this post. ChemBark first attempted to contact Professor Dorta by e-mail on Tuesday night (St. Louis time) and received no response. Dorta also has yet to respond to a second message, sent Thursday afternoon, that sought comment on the discrepancies reported in this story. A message seeking comment was also sent to Dr. Drinkel, at the same time, through her Facebook account. Should either author respond to our requests for comment, the responses will be posted in their entirety.

A Disturbing Note in a Recent SI File

Tuesday, August 6th, 2013

ChemBark InvestigatesA recently published ASAP article in the journal Organometallics is sure to raise some eyebrows in the chemical community. While the paper itself is a straightforward study of palladium and platinum bis-sulfoxide complexes, page 12 of the corresponding Supporting Information file contains what appears to be an editorial note that was inadvertently left in the published document:

Emma, please insert NMR data here! where are they? and for this compound, just make up an elemental analysis…

This statement goes beyond a simple embarrassing failure to properly edit the manuscript, as it appears the first author is being instructed to fabricate data. Elemental analyses would be very easy to fabricate, and long-time readers of this blog will recall how fake elemental analyses were pivotal to Bengu Sezen’s campaign of fraud in the work she published from 2002 to 2005 out of Dalibor Sames’ lab at Columbia.

The compound labeled 14 (an acac complex) in the main paper does not appear to correspond to compound 14 in the SI. In fact, the bridged-dichloride compound appears to be listed an as unlabeled intermediate in Scheme 5, which should raise more eyebrows. Did the authors unlist the compound in order to avoid having to provide robust characterization for it?

ChemBark is contacting the corresponding author for comment, and his response will be posted in full when we receive it.

This story points to very real concerns that young researchers can be instructed and pressured to fabricate data. Would a scientist be so concerned that a journal would reject his manuscript over a piece of missing characterization data that he’d feel pressure to make something up?

Expect more as this story develops…

Quiz: Named Chemical Reagents and Catalysts

Sunday, May 26th, 2013

I made this little ditty on Sporcle. Given a systematic name of a molecule, provide the last name of the chemist for whom the reagent or catalyst is named…

Nocera to Harvard!

Wednesday, February 22nd, 2012

ChemBark has learned that superstar inorganic chemist Daniel Nocera is moving from MIT to Harvard. Eric Jacobsen, chairman of the Department of Chemistry and Chemical Biology at Harvard, announced the news today by e-mail:

Dear Members of the CCB Community,

I am very pleased to share some very good news: Dan Nocera, one of the world’s leading inorganic chemists and a major figure in energy-related research, will be moving with his group to our department this Fall.

During his career at Michigan State University and more recently at MIT, Prof. Nocera has done ground-breaking work in the activation of small molecules such as oxygen and water by designed inorganic complexes.  He and his group are particularly interested in finding practical ways to harness the sun’s energy, with obvious implications for global energy production and storage.  The following press release describes some of his most recent work: http://web.mit.edu/newsoffice/2011/artificial-leaf-0930.html

The new Nocera labs will be located on the third floor of Conant, and a major renovation of that space will be taking place between now and the expected arrival of the group in the Fall.  I hope you will join me in doing everything possible to welcome the Nocera group when they arrive, and to make their move down Mass Ave as pleasant as possible.

Sincerely,

Eric Jacobsen

For many years, inorganic chemistry at Harvard began and ended with the magnificent Dick Holm. There simply were no other true inorganic professors, and when he semi-retired, Harvard was left with a gaping hole in its faculty. For years, rumors swirled that several lucrative overtures made to inorganic professors at MIT were rebuffed. In fact, the pendulum swung so far the other way that MIT nearly poached Jacobsen from Harvard. Questions still linger over how MIT was left standing at the altar.

Nocera positions himself within a herd of inorganic chemists, possibly to avoid capture by poachers from Harvard. January 2012 – Huntington Beach, California

In Nocera, Harvard has finally purchased a star. He instantly elevates inorganic chemistry on Oxford Street to a top or second-tier program. The school also now seems in a much stronger position to solidify its program from both the top (with other senior hires like Nocera) and bottom (with junior-faculty searches specifically targeted at making inorganic hires like young star Ted Betley). It will be interesting to see how Nocera and Betley work together; Betley was a postdoc under Nocera at MIT.

So, score one for the Crimson. I hope the Nocera Group enjoys its shiny new (and historic) lab space.

 

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Organic Achievement of 2006: Pd(IV) Intermediates Might Not Be That Rare

Friday, April 27th, 2007

The Chemmy Award for Organic Achievement of the Year goes to:

Melanie Sanford (Michigan) for establishing that Pd(IV) intermediates are important in at least one class of catalytic C–H bond activation reactions

I had decided on the recipient of this Chemmy a long time ago but procrastinated on writing the citation. This weekend, commenter “tuna fish” mentioned that Dr. Sanford might be moving to Yale or Caltech, and while I have no idea if this is true, the comment reminded me of my fondness for her work and that now is as good a time as any to write about it.

First off, trying to “contain” the Chemmy achievement awards in the various chemical disciplines to one year (here: 2006) is going to be difficult, because cool discoveries often take time to develop and get noticed. In this case, Sanford’s C–H activation work can be traced back to 2004. It was only last year, however, that the picture became clear (at least, clear to me).

When I learned organometallic chemistry—way back in 2002—we were essentially taught never to invoke Pd(IV) intermediates in our mechanisms.  Pd(IV) was simply too energetically-inaccessible to be relevant in most cases. Along these lines, I witnessed the merciless ridicule of more than one student by the teaching staff for using Pd(IV). Instead, good boys and girls used the Pd(0)/Pd(II) couple in their mechanisms.

In 2004, Sanford came along and published a simple case of catalytic, chelate-directed C–H bond oxidation:

Instead of outlining a mechanism that shuttled back and forth between Pd(0) and Pd(II), Sanford proposed a mechanism involving Pd(IV):

Naughty!  Or so I thought.  A subsequent study essentially extinguished all doubt that the Pd(IV) mechanism was correct. In this 2005 JACS comm., the Sanford crew hypothesized they could change the system to stabilize the Pd(IV) intermediate, found they could actually isolate it, got a crystal structure showing that it was indeed a Pd(IV) species, and then showed that heating it gave the same types of products that they saw in reactions where the intermediate could not be isolated. Crystal structures are the closest thing we can get to having incontrovertible photographic evidence of what molecules are actually doing, so you can’t really argue this one.  Score one for Pd(IV).

I know a lot of the hardcore synthesis crowd isn’t enamored with this sort of C–H activation chemistry because it is chelate-directed, which limits the scope of the reaction. That’s true, but what makes this batch of work so interesting is not the synthetic utility as much as the scientific value. We gained a new appreciation for the mechanism at play in these reactions and had to reassess a long-held notion of what isn’t reasonable.

So, congratulations to Dr. Sanford and coworkers. Enjoy your Chemmy and keep the good work coming.  And if any of you donkeys out there thinks there was someone else more deserving of this award, feel free to register chemmeow.com and start your own damn blog.

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