Archive for the 'Serial Features' Category

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. 

The Chemmy Award for the Most Outstanding Chemistry Department of 2006 goes to:

Princeton University

In the comments thread announcing the Chemmy Awards, Excimer noted that “although all these awards are subjective as hell, the Outstanding Academic Department is really out there. How can one honestly be 100% objective about such things?”

He’s absolutely right; there’s no way to definitively peg what department had the best year. This award was made to mimic how various sports leagues recognize a general manager or team executive of the year. We’re just asking, “which department made the best personnel moves or exceeded expectations for the past year?” Of course, this is going to make it harder for the “top flight” departments to win this Chemmy. The bar is higher for them, as we’ve come to expect schools like Berkeley, MIT, and Stanford to do amazing things.

So, why Princeton? They’ve made a number of big strides forward in the recent past. Coming on the heels of Sorensen’s arrival from Scripps in 2003, Princeton was able to attract superstar David MacMillan this year. Princeton also gained a resident chemistry blogger in 2006, Carmen Drahl, who’s noted that the school has vastly improved its instrumentation this year. A new chemistry building is also in the works, with completion scheduled for 2010.

In terms of losses, the sophomore organic class at Princeton might suffer with the impending departure of Maitland Jones. He is closing down research operations in preparation for a move to Greenwich Village to teach orgo at NYU. For those interested, The Chem Blog had a post this summer chronicling the movement of some other professors. Yale had a particularly rough year, which included the loss of Hartwig to Illinois.

So, when I think of up-and-coming schools, Princeton is the first that comes to mind. I’ll stand by it as deserving of the award for 2006, but feel free to post your thoughts on other departments that will soon be surging up the rankings.

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 Chemmy for News Story of 2006 goes to:

The Rise of the Chemical Blogosphere

If you think this post is self-congratulatory, you’re damn right. But seriously, what the hell happened in 2006?

A few blogs, like Derek Lowe’s In the Pipeline, have been around for a while, and a few more showed up last year (e.g., Tenderbutton and my old blog). But look at the sidebar on the right. The vast majority of those blogs were born in 2006 and the list continues to grow. Organometallic Current and Levorotation, two blogs that look very promising, were just started in the past two weeks. Even the chemical media establishment is getting into the game with blogs from Nature, Chemistry World, and C&E News all appearing in 2006.

If you’re searching for the catalyst of the rise in blogs, look no farther than the Columbia scandal. After the school went into lock-down and C&E News chose not to cover the story immediately, chemists in search of information about the retractions turned to Google and found chemistry blogs. Communities started to grow around comment threads, and it became obvious to everyone that there are more than a few chemists willing to talk shop on the Internet.

While a lot of people are still wary about obtaining information on blogs, it’s clear that they have a legitimate place in both scientific politics and journalism. As scientists, we must actively seek new ways to improve the operational aspects of our field. An important tool in this plight is to study situations where the system failed. And in any democracy, decisions such as how tax dollars are spent ultimately rest with the electorate. Thus, it is important for the public to stay well-informed of current events. If chemistry blogs hadn’t provided a forum for the dissemination of the Columbia information, many people would never have found out about it.

Of course, this is just one of the many merits of chemistry blogs. You can turn to them to be informed, keep abreast of the latest literature in a niche area, get help with a problem, or be entertained. There’s something for almost everyone, and in cases where there’s not, a new blog is easy to start. While many of the blogs from the Class of 2006 may vanish, the chemical blogosphere is here to stay.

The Chemmy Award for Citizen of Year goes to:

User “V8rik” for his contributions to the chemical content of Wikipedia

I have no idea who this guy is, but he spends an insane amount of time adding chemistry articles to everyone’s favorite online encyclopedia. Just look at his contributions list. Chances are that if you’ve searched for anything chemical on Wikipedia, he’s had something to do with the article.

Cycloadditions? Yup. Ylides? Yup. The Ugi Reaction? That too. The guy is amazing.

This year, I finally made the leap and starting editing Wikipedia. It takes a while to get a hang of the Wiki code, and the style guidelines are even less fun to deal with. Finally, after you’ve learned the code and the style, what you write is forever subject to being changed by any random person on the Internet. So not only are Wikipedia users not paid for their contributions, they have zero editorial control over what they’ve written.

That’s what makes V8rik’s contributions all the more amazing. Sadly, he’ll probably never find out that he’s been awarded a Chemmy, but if he does, he has my sincere appreciation for his hard work. The world of chemistry could use more people like V8rik.

Next post: Top Chemical News Story of 2006

As discussed in an earlier comments thread, this award was never intended to tag the accident with the most tragic outcome. If that were the case, we would have picked the explosion of ethene that destroyed a French research lab in March, killing a professor that wasn’t even working on the botched experiment. Instead, we’ll use this award to (dis)honor the most avoidable or bone-headed accident of the year. Correspondingly, the Chemmy for the Worst Accident of 2006 goes to:

The undergraduate student at Berkeley who tried to move a 400-lb.
dewar of liquid nitrogen down a flight of stairs

As chronicled on another blog:

Condensed matter labs such as ours receive frequent deliveries of liquid nitrogen in one- or two-hundred liter dewars. Unfortunately, most of the Berkeley cond-mat labs are in Birge Hall, which has no loading dock, so that the LN2 dewars arrive on the first floor of neighboring LeConte where they must be wheeled over to their destination by some low-seniority student. Since the Berkeley campus is on a hill, the loading dock at the back of the building is one floor higher than the other entrances to LeConte and all the entrances to Birge. One can push the dewar around the outside of LeConte, but a shorter route is to take the elevator down one floor and go out the side door.

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Yesterday the LeConte elevator was out of order, which for most of us would have meant taking the long way around. However, one undergrad, tasked with transporting a full 230L dewar, simply decided to take the stairs.

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At about 80% the density of water, 230 liters of liquid nitrogen weighs about 400 pounds, not counting the additional weight of the steel vessel containing it. When rolled onto the stairs, the dewar promptly tipped over and plummeted downward on its side, knocking deep gouges in the marble steps and dragging along the unfortunate student, who inexplicably held on as his cargo began to tumble. Miraculously both student and dewar arrived at the landing without rupturing…

The nameless student is lucky that his Chemmy wasn’t awarded posthumously; the outcome could have been a lot worse. As for the people who agreed to go back into the staircase to right the tipped dewar, I don’t know whether they deserve an award for bravery or stupidity. It’s safe to say that I would have left the vicinity as quickly as possible.

On a related note, anyone with a tale of an unsecured gas cylinder becoming a torpedo should share it in the comments. I’ve heard plenty of stories, both in real life and on the Internet, but it’d be nice to see some legitimate evidence. For instance, this story has several hallmarks of an urban legend: no source, no specific subject, and no photographs. My instincts say that there are a few safety officers out there who enjoy writing ghastly reports of fictional accidents.

Next post: Citizen of the Year (for service to the chemistry community)

The First Annual Chemmy Awards will be announced here on ChemBark at a special ceremony on Boxing Day.  To supplement our undisclosed nominees, please use the comments to submit nominations in the following categories:

Best Organic Paper/Achievement
Best Physical Paper/Achievement
Best Inorganic Paper/Achievement
Best Biological Paper/Achievement
News Story of the Year
Comeback of the Year
Molecule of the Year
Villain of the Year
Worst Accident
Outstanding Academic Department
Good Citizenship Award
Lifetime Achievement Award

People interested in voting for the Best Chemistry Blog of the Year should visit Mitch at ChemicalForums.  My vote goes to Tenderbutton, even though it’s dead.  I also hope that Paul at TotallySynthetic is going to post a poll for Total Synthesis of the Year, but I’ve got no idea who should win that one.

Part of the fun of being a teaching assistant is getting to mess with undergrads’ heads. It’s more fun when the undergrads are pre-meds, and even more fun when they’re in the middle of their hardest course, organic chemistry. I was cleaning up my hard drive and came across three of my favorite trick questions, shown below. For best results, use them on exams rather than practice tests or problem sets.

Posted in Education, College, Problem Sets | 21 Comments »