ChemBark

First they ignore you,
then they laugh at you,
then they fight you,
then they join you,
then everybody wins.

Mahatma Gandhi posted that piece of advice on his blog shortly before his death in 1948, and it still holds true today.

After admitting that chemistry faculty typically roll their eyes at blogs and that he personally doesn’t have time for them, Phil Baran—or, more precisely, the Baran Lab at Scripps—has established the newest chemistry blog on the Internet. Baran and his lab are at the top of the game of organic synthesis, so this is a major development for academic chemistry. Their participation can do nothing but lend legitimacy to an activity that has been robustly and repeatedly poo-pooed by the respected Old School of our field.

The establishment of the Baran Lab’s blog fell out of the ongoing post-publication review of IBX-promoted benzylic oxidation at Blog Syn, a relatively new site that focuses on checking synthetic procedures in the vein of Organic Syntheses. Post-publication peer review is something familiar to the chemical blogopshere. Previous examples include the questioning of the science in the “Arsenic Life” paper, the exposure of duplication by Breslow in the “Space Dinosaur” saga, and the experimental investigation into the oxidation-by-NaH paper in JACS. Blog Syn takes post-publication review of synthetic procedures to the next level by coordinating replication of the procedures among a group of bloggers who compile and compare their results for all to see and discuss.

Last month, Blog Syn decided to examine a method for IBX-promoted benzylic oxidation published as part of Baran’s graduate work in K.C. Nicolaou’s lab. What started as a straightforward effort to test the (questioned) reproducibility of the reaction quickly evolved into a vigorous and thoughtful discussion of both the merits of anonymous bloggers’ questioning peer-reviewed research and of the reaction itself. Baran and the first author of the paper have participated actively in the generation of data and its analysis, and the most recent development appears to be improved mechanistic insight as to how the reaction might work.

Those interested in this specific reaction can check out the discussion for themselves, but all chemists can appreciate the value that blogs and other Web 2.0 venues offer in terms of advancing scientific knowledge and enriching our understanding of chemistry. While blogs may often engage in journalism that is a little rough at the edges, the ease of online publishing has helped to provide open venues for meaningful discussion, to give voice to important ideas, and to democratize power in a field where many grumble that power is overly centralized. What Blog Syn has started is a great service to the field of organic chemistry, and I look forward to the wealth of material that the Baran Lab can bring to the table in its own addition to the blogosphere.

Great stuff!

Edit to add: This great post by Rich Apodaca at Depth First places Blog Syn in historical context among similar experiment-based efforts in the chemical blogosphere. The post also offers an interesting analysis of the role that blogger anonymity plays.

Edit: Another (similar) great analysis and comment thread in this post by DrFreddy at C&EN‘s blog.

I enjoy watching the field of supramolecular chemistry just about as much as I enjoy following the movement of professors among chemistry departments. Thus, it should come as no surprise that J. Fraser Stoddart is someone who passes across my radar with some degree of regularity. Sir Fraser has been a pioneer in using organic chemistry to build supramolecular structures that can function as rudimentary devices, and many of the systems developed by his lab are impressive synthetic feats.

While it is not uncommon for big-named professors to jump from one school to another, it is less common to find full news stories that cover these events. In the case of Stoddart, he seems to have a precise method for deciding where to migrate:

Here’s what Stoddart said in 2000 regarding his move from Birmingham to UCLA:

Stoddart came to UCLA from England’s University of Birmingham, where he was head of the school of chemistry and professor of organic chemistry.

“I tried to get collaborators to work on a molecular computer in Europe, but I drew a blank,” Stoddart said. “It was all a dream until I came to UCLA.”

“I liken Southern California today to Paris in 1900, which was the place to go if you were an artist,” Stoddart said. “When I was working in England in the ’90s, I felt that the place to make things happen as a scientist was Southern California, and I have been proved right.”

And here’s what he said in 2007 regarding his move from UCLA to Northwestern:

I have had the opportunity to visit both Southern California and Chicago in this century. While I cannot comment on their resemblance to Paris in 1900, these cities and the science they foster appear quite different to me. I wonder where the next Paris of Nanotech will be?

Una cuestión muy importante cuando usted está enseñando a la química orgánica es la manera de dibujar estructuras químicas correctamente. Es muy fácil. Todo lo que tienes que hacer es tomar la estructura ChemDraw y añade un montón de acentos al azar. Por ejemplo:

Siguiente lección: cómo traducir recetas sintéticas

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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Princeton University took home the Chemmy for Outstanding Department of 2006, and it looks like they’re going to make a run at defending the title in 2007. Valued sources recently told the ChemBark News Network that the Ivy League school has made generous offers to a number of outstanding young organic chemists who are already tenured in top-five departments. Fresh on the heels of adding Sorensen and MacMillan, Princeton is looking to firmly establish itself as a hotbed of organic chemistry for years to come.

Raiding other schools’ faculties has long been a strategy for building departmental strength. Where the Yankees and Red Sox are the baseball teams most willing to reach deep into their pockets for big-name talent, Harvard is the school most famous for doing so in chemistry. Most of the department’s big guns were hired as tenured professors from other schools: Corey and Jacobsen from Illinois, Whitesides from MIT, Evans and Myers from Caltech, Lieber from Columbia, Schreiber from Yale, and Kahne from Princeton. On the flip side, assistant professors have had a miserable record of gaining tenure in the department (until recently).

While pursuing the free agent market at the expense of decimating your farm system is generally a poor idea in baseball, it is a viable strategy in the world of chemistry. Granting someone tenure equates to giving them a contract for life, something unheard of in the sports world. Unfortunately for universities, it often takes more than seven years to get a handle on the quality of an assistant professor. Hiring a proven forty-year-old is a much safer bet. And unlike in sports, there are no salary caps or luxury taxes in academia, so there are no limits to the amount of money you can spend.

Of course, the strategy of buying talent is contingent on being rich—the more money a school has, the better it can play the game. Schools with less funding not only have a harder time reeling in heavy hitters, they have a harder time retaining members of their faculty who’ve attracted the interest of other schools. Money doesn’t just factor into salary, but also into expanding lab space and improving instrumentation. Ambitious professors want to improve the efficiency of their research and have the flexibility to expand their labs and their programs.

There are some factors that money can’t help.  Geographic location is often important, as it influences features such as the local culture and the employment market for professors’ significant others. And as with anything related to academia, politics can play a big role. If the deans at a school get on an interdisciplinary kick, there many be money available for a nanobiophysical chemist but not for a synthetic one. An aspect that is particularly intriguing about the Princeton move is that it is geared towards pure chemistry instead of the interdisciplinary flavor of the month. That’s rare nowadays.

Of course, this story is still developing and nothing has been set in stone, but things are looking mighty exciting if you’re an organic chemist at Princeton.

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