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September 25, 2006

Better late than never...


I just wanted to write a quick post to let you all know that we've (finally) added a blogroll - it's under 'Related Links' on the left-hand side of the webpage:

Chemistry World Blog
Everyday Scientist
Interfacial Science
In The Pipeline
Molecule Of The Day
Post Doc Ergo Propter Doc
Peter Murray-Rust's Blog
She Blinded Me with Science
Tenderbutton (though Dylan's going to 'turn off the lights' on October 1st)
Totally Synthetic
The Chem Blog
The Endless Frontier
Whistling in the Wind

This is certainly not a complete list of blogs about chemistry/by chemists, so please let us know if there are any excited/interesting chemistry blogs we've missed...

Joshua


Joshua Finkelstein (Associate Editor, Nature)

September 20, 2006

I left my phone in San Francisco

Well, this blog is slightly overdue, since the ACS meeting has been over for nearly a week. But, I think I'm still adjusting back to East Coast time, so clearly I couldn't be expected to muse on all the interesting talks I saw until now?! Also I've been at a loss without my phone, although I have to say, a phone is easier to recover than your heart (but thanks, Tony, for the title suggestion), especially when you just leave it at a friend's house...

Anyway, as a final wrap-up from me on the meeting: I went to the "Biocatalysis in polymer science; New materials" session for the afternoon on Thursday, and I have to say that I was impressed both by the quality of talks and the number of people listening to them, as Thursday at an ACS meeting does have the reputation of being a bit of a ghost town.

Three talks that particularly interested me:

Atanu Biswas (of the USDA), who is studying soybean oil as a source of polymer starting materials and biodegradable synthons. These oils, which contain multiple double bonds, have proven difficult to substitute in the past, as all kinds of polymers and crosslinked species are generated. He and his colleagues previously tackled the problem of creating monomeric, functionalized oils by first creating the epoxidized molecule, and then reacting it with amines. In this talk, he reported the use of DEAD to generate hydrazine-substituted molecules. They then utilized these compounds in further reactions to generate Diels-Alder products and some polymers.

Sabine Wallner (a postdoc in Richard Gross' lab) is studying the metathesis of sophorolipids, natural surfactants consisting of two sugars and a lipid chain that sometimes cyclize spontaneously to form a 26-atom ring. Successful polymerization of these compounds, which are excreted by cells, would result in a biodegradable polymer with many potential uses. What was especially interesting about this talk is that ROMP is normally facilitated by ring strain in the monomeric material. Yet the cyclic sophorolipid is unlikely to be strained because of the very large ring size. In any case, they've gotten polymers of up to 100 kD, indicating that there is a lot to learn about this system.
Finally, HN Cheng (from Hercules Incorporated, also one of the chairs of the session) gave a great talk on the application of lipases to create polyamides. Their rationale for the project was to create nylon with an additional amine in the backbone so that it would be water soluble. This isn't possible with regular polymerization conditions, as the secondary amine would react to form a branch point. He told us that his team had been busy trying to make proteases do this reaction, since it's just the reverse of their normal function, but with no success. When they tried lipases, though, they got nice polymers both because the formation of amide bonds is not so different from ester bonds, and because the cleavage of these bonds is not possible for the lipase. By careful choice of starting materials, they were able to create multiple polymers that just wouldn't be accessible with standard synthetic techniques.

In addition to the good talks of the session, I was impressed with the discussions that ensued - clearly everyone was paying attention and there were some helpful suggestions for the authors. Congrats to the POLY section for an exciting meeting.

Catherine Goodman (Assistant Editor at Nature Chemical Biology)

Grand theft auto: Levinthal paradox city


I doubt many people think about protein folding when shopping for a new video game console, but if you're interested in protein folding and thinking about buying a PlayStation 3 next month, there's an article on CNN.com you should read. Apparently "Sony worked with Stanford University's Folding@home project to harness the PS3's technology to help study how proteins are formed in the human body and how they sometimes form incorrectly."

Folding@home is a distributed computing project, which means you can download a program onto your computer (in this case, your new PS3) that will enable you to donate 'down time' to analyze chunks of data. By dividing the "calculations into smaller packets ... [the computers can] do jobs that would strain the most powerful supercomputers." And since the PS3 has a pretty powerful graphics card, you can apparently "watch the protein as it folds."

Folding@home isn't the only distributed computing project out there: you've probably heard of SETI@home and there are a number of other projects, including Rosetta@home, the Drug Design and Optimization Lab, and fightAIDS@home.

I think this is a great idea: Sony hopes to sell 2 million PS3s in the United States and Japan in 2006 and 6 million worldwide by March, so using gaming consoles in @home projects could dramatically decrease the time needed to do these computations...

Joshua


Joshua Finkelstein (Associate Editor, Nature)

The Stockholm syndrome

Well, it's that time of year again. In less than a month's time, we'll have a few more Nobel prize winners on our hands - and so the speculation begins...

For the last few years, Thomson Scientific has been predicting who will win the Nobel prize in each of four subjects (Chemistry, Physics, Medicine and Economics*) based upon citations (amongst other things) to their work. Last year, was the first time they correctly predicted the Chemistry prize by naming Grubbs - although, to be honest, the guy from the taco truck in old town Pasadena could have made that pick...

This year, it's out with the old and in with the new. Gone are the usual picks such as Whitesides, Stoddart and Shinkai (also Nicolaou is missing), and we are presented with three possible winning combinations.

1. Tobin Marks (Northwestern) for a mixture of all things organometallicky** and some materials work

2. Dave Evans and Steve Ley (Cambridge, over there and over here) for synthetic organic chemistry

3. Gerald Crabtree (Stanford) and Stuart Schreiber (Harvard) for chemical biology

Let's just say that I would be a little surprised if any of these worthy candidates came out on top this year. And as for pick 2, there's probably a few other synthetic people out there feeling a little left out right about now.

So, who will win. Paul at The Endless Frontier has something to say on the matter - what about you?

* Yes, I know, the Economics prize isn't really a Nobel prize.

** I'm not going to go hunting for it, but I believe this word (or similar) was first used by Dylan at his Tenderbutton blog - or at least by someone posting there. Tenderbutton - RIP - we'll miss you.

Stuart


Stuart Cantrill (Associate Editor, Nature Nanotechnology)

September 14, 2006

ACS: The Rainbow Connection

Well, yet another ACS has come and gone. I leave you with a rainbow of chemistry talks.

"The formation of chromium rich particles by the dissolution of red clays in groundwater monitoring wells." Mysterious chromium in Oklahoma wells found out.

"Identification and characterization of off-flavor aroma impact compounds in canned orange juice"
Canned orange juice's flavor attributes are "tropical fruit, grapefruit, cooked/caramel and medicine." Yum.

"Research on environmental fate of phenanthrene in Lanzhou Reach of Yellow River." Math says the pollutants will be stable in the river sediment in 70,000 hours.

"The Pennsylvania Green fluorophore: A hybrid of Oregon Green and Tokyo Green for the construction of hydrophobic and pH-insensitive molecular probes." The search for the next fluorescent marker. Amazingly, there doesn't seem to be a band called "Tokyo Green."

"Highly efficient fluorene-based UV-blue light-emitting polymers with controlled effective conjugation length." Ah, making things that glow.

"Purple: The dye of dyes" A history lesson with recent archeological findings thrown in. I wish I had seen it.

ACS: Poly want an enzyme?

Polymers and biology, together in perfect harmony. This meeting has intrigued me with a number of sessions about bio-related polymers. Timothy Long's group had two: one about determining which physical properties of polymers make the best vectors for gene therapy, and one about using DNA base pairs to make a polymer with two sets of properties. Heat it to disassociate the base pairs, and you get a flowy substance, cool to clamp them together again, and you've got something strong enough to do something with. Plus, there's bio-inspired dental polymers from Temple University, enzymes in polymers for sensors from Hawaii Natural Energy Institute, and polymers derived from soybean oil, feathers, and rice. Finally, there was a presentation on making better cigarette filters from Salmon sperm, from the Ogata Research Laboratory, Ltd.

The general crush on bio-related polymers seems to stem from their ability to acquire reactive, "smart" properties from their biological components, as well as from the environmental advantages of making stuff from things that aren’t petroleum. Now, can they produce the self-drying jacket from Back to the Future II?

September 13, 2006

ACS: Sittin' on the dock of the bay


After the morning session, I jumped in a cab and went to UCSF's Mission Bay campus - it's a 43-acre campus that was acquired at no cost to the university and contains a number of laboratories, centers, and research institutes. It's quite large and is getting bigger: "[a]bout 1,700 faculty, students, scholars and staff already work in the new UCSF Mission Bay campus community. At full build-out, 9,100 people are expected to work and study at the new campus."

I had a meeting with a professor in Genentech Hall, a 434,000 square foot building where many of the chemical biologists work (there are also a number of structural, molecular, and developmental biologists in the building).

It truly is a beautiful building, and the entire campus looks like it'd be a great place to work - none of the grey/dirty walls and strange odors found in older chemistry/biochemistry bulidings... I'd highly recommend checking out the campus next time you're in San Francisco - but security is pretty tight, so you might want to sign up for the tour. In the meantime, click here for the virtual tour...

Joshua


Joshua Finkelstein (Associate Editor, Nature)

ACS: butternut squash soup

J.J. La Clair, the controversial chemist (for background, see http://www.nature.com/news/2006/060731/full/442492c.html) in the mutton chop sideburns, gave a talk today to a packed room. It was hot, stuffy, and young in there, as he talked us, mic-less, through what he called "an approach used in a number of labs that I've developed, optimized and made easier to use." As far as I could tell as a layman, the approach had to do with designing synthesis of natural products with florescent labeling and biological tests in mind. I'll leave an evaluation of the technical content to others more synthesis (or biology)-savvy than I. I'll just mention that his first slide talked about his Xenobe Research Institute (which is pronounced "zen-OH-bee"). His slide said that the company was working on 80 studies with academe, industry and government. He must be a pretty busy man.

He acknowledged the contretemps over his claimed synthesis of hexacyclinol—and even included on his acknowledgement page a shot of the T-shirt being sold which memorializes the controversy, saying that he salutes creativity in all forms. And yes, that was my headline on the shirt, but I didn't write it. Reporters very rarely write our own headlines—but we do get to write our own blog post titles. So I decree that the title of this post shall be: "butternut squash soup", since that is what I am eating right now.

ACS: Conference bon bons

-Our gung-ho enthusiasm for antidepressants mean that there is a certain amount of Prozac in the water these days. Freshwater mussels are less than pleased, though, since Prozac is making them release their larvae before they are viable. Freshwater mussels are sensitive creatures, and 70 percent of the species native to North America are extinct.

-In an irresistible item, a peculiar bird called the Black-Bone Silky Fowl has been found to be packed with carnosine, which has a rep for anti-aging and other positive health effects. The bird is a staple of Chinese medicine, and has soft white feathers over black flesh and bones.

-Check out the brand new Chemical Structure Lookup Service, hosted at NIH,. http://cactus.nci.nih.gov/cgi-bin/lookup/search

-Fucoxanthin, from brown seaweed, is taken up by the fat. It seems to both reduce adipose tissue and turn the fat a bright orange. Anti-obesity clinical trials are in the works.

-Adrienne Kozlowski, retired chemist, and her husband, have taken up hot air ballooning as a hobby. They say it is a perfect diversion for chemists, because manipulating the balloon is all a matter of mastering the laminar flow of the air.

-Peter Murray Rust, of Cambridge, on the future of Chemical information: "We are going to start mashing, and it is going to amaze the world."

ACS: Clicking and beeping

I went to a talk on by UCSB's Robert Vestberg, on "Synthesis of hydrogels with well defined network structure using Click chemistry", because I have been hearing this buzzword floating around – "click chemistry"—and I wanted to figure out what it was.

But first, hydrogels. Hydrogels are polymers all cross-linked together and stuffed with water. They can be useful in medicine, for example, as soft contact lenses. They are biocompatible, key molecules can diffuse through them, and they are tough. Often the crosslinks are induced by a blast of radiation—like UV light, for example.

Vestberg and his colleagues are using "click chemistry" to do their linking. The click concept was described quickly as a reaction catalyzed by copper (I) that seems to be a one-size-fits-all room temp process that organizes your molecules into a regular structure. Functional groups can be knitted right in.

At least that was the impression I got. The meeting room in the Marriot was next to some sort of noisy kitchen or workroom, and it was hard to concentrate. It sounded like they were banging the lumps out of large cookie sheets on the other side of the wall. The "backing up" beep of some kind of vehicle was also intermittently heard.

Anyway, the hydrogels are made in little Teflon molds. You can make them with other fluids besides water, too. "We've done it in crappy Australian wine that I got from my boss," says Vestberg, who is pleased with his gels, which can be stretched to 1500% their original length before they break, much more than UV crosslinked hydrogels.

After the talk, I did some reading on click chemistry, which was invented by Barry Sharpless. It seems like a kind of Lego chemistry to me. You may be interested to know that searching the program of abstracts for this meeting with the term "click" yields 42 hits.

September 12, 2006

ACS: Sweet surrender

I went to the carbohydrate-protein interactions and glycolipids session this morning (I'm at the ACS, in case you forgot). It was a great session! Even with the best efforts from the session chair, there were so many questions that we got way behind (which unfortunately meant that I missed George Wang's talk due to a previous engagement). One particularly interesting part of the morning was yet another tribute to Emil Fischer, who seems to have done more work in his life than occurs in a year at most universities. In this particular story, Jacqueline Gervay-Hague was discussing the troubles with substituting sugars at the alpha position, and had tried to use trimethylsilyl iodine in combination with an alcohol to activate the center and incorporate the alcohol as a substituent. To her amazement, her student didn't form the ester, but instead purified the iodated sugar. They looked back in the literature for any precedent of stable iodo-substituted sugars, and found that Fischer not only made them, but crystallized them back in 1910. The secret? The alpha-substituted sugar is stable, whereas the beta-functionalized position reacts right away. They have since used this insight to couple unprotected lipids to TMS-protected sugars; with the right purification conditions, they get the unprotected final product in one step.

Catherine Goodman (Assistant Editor, Nature Chemical Biology)

ACS: All that glitters is gold


The morning session of the Arthur C. Cope Award and Arthur C. Cope Scholar Awards just finished - I was really impressed with F. Dean Toste's talk, which was a whirlwind tour of some of the work his group has done involving gold(I)-catalyzed reactions.

There are now a number of groups exploring the chemistry of gold(I) and gold(III) complexes - Toste's group has focused on gold(I) complexes, which are air-/moisture-tolerant and able to catalyze a number of reactions, including the stereoselective cyclopropanation of olefins and intramolecular acetylenic Schmidt reactions (making substituted pyrroles). They've also shown that these reactions can be used to make natural products, recently demonstrating that the gold(I)-catalyzed cyclization of a silyl enol ether onto an alkyne enabled them to rapidly synthesize (+)-lycopladine A (in eight steps with 17% overall yield from the starting enone).

Joshua


Joshua Finkelstein (Associate Editor, Nature)

ACS: I love technology


David Schwartz gave a great talk this afternoon - he's the director of the National Institute of Environmental Health Sciences, which recently created the 'Genes and Environment Initiative,' a five-year research effort that hopes to identify the genetic and environmental causes of asthma, arthritis, and other common diseases.

The initiative has two components: the first involves "efficiently analyzing genetic variation in groups of patients with specific illnesses," and the second involves the development of new devices that can monitor "personal environmental exposures that interact with genetic variations and result in human diseases."

Why - you might ask - is the NIH spending approximately 192 million dollars on this new initiative? Well, we know that "[g]enetic and environmental factors, including diet and life-style, both contribute to cardiovascular disease, cancers, and other major causes of mortality," and there's a growing body of evidence that suggests that environmental factors are responsible for a large percentage of these diseases.

The NIEHS will use a portion of this money to fund grants that involve "innovative new technologies to measure environmental toxins, dietary intake and physical activity, and to determine an individual's biological response to those influences, using new tools of genomics, proteomics and metabolomics," so this looks like an excellent opportunity for chemists interested in complex diseases and human health.

For more information on the NIEHS 2006–2011 Strategic Plan, see "New Frontiers in Environmental Sciences and Human Health."

Joshua


Joshua Finkelstein (Associate Editor, Nature)

September 11, 2006

ACS: Mongolian Licorice

This meeting has it all. Today I caught a wonderful presentation by Frank Lee of Nanchang University about efforts to introduce “Good Agriculture Practice” or GAP (See the FAO’s page on this approach here), on the growing of herbs for traditional medicines. The idea is to make sure the medicines are what they purport to be, are not chock-full of mercury or other toxins, and are being harvested in a sustainable way.

So, field labs have been set up in Inner Mongolia to work of the harvesting of licorice there—used as a medicine to “invigorate the heart, lungs, spleen and stomach,” among other thing. The most interesting challenge they face is supervising the transition from collecting wild plants to growing them as a crop. They are watching to make sure that the domestication process does not affect expression of the active component. Awesome.

ACS: Nobel laureate book club


I only have time for a quick post before I run off to David Schwartz's talk on 'Environmental genomics and human health.' I just left the H.C. Brown Legacy Symposium, where Professor Sharpless talked about 'click' chemistry, azido-phobia, pandas, and Kevin Kelly's Out of Control (which he highly recommended). Needless to say, it was a great talk and I learned a few new things about 'click' chemistry: it turns out that the Huisgen 1,3-dipolar cycloaddition works pretty well in Jack Daniel's whiskey and in human plasma...

I also bumped into Mark Peplow, who used to work at Nature and is now the editor of Chemistry World. He's blogging about the conference, and he's not alone: the ACS, Tenderblog, the Chem Blog, and Chemical Forums are here too... Update: C&EN and Peter Murray-Rust are also blogging from the conference.

Joshua


Joshua Finkelstein (Associate Editor, Nature)

ACS: Against "molecular gastronomy"

The hype-heavy world of haute cuisine has recently been rolling its tongue over the phrase “molecular gastronomy”, said to be practiced by such chefs célèbres as Pierre Gagnaire and Ferran Adrià. The trend is for innovative foods, and new ingredients. Shrimp treated with protein-knitting enzymes, so it can be coaxed into noodle shape, glass-like spheres of isomalt, filled with the smoke from roasting mushrooms, flavored foam.

But On Food and Cooking author Harold McGee, in a session this morning, opined that the term should be ditched. He noted that most chefs labeled as molecular gastronomists rejected the label and say that their experiments rarely take place on the molecular level. Apparently, the phrase came from a workshop about the science of cooking, held in Sicilly in the early 1990s—but the workshop was, according to McGee, was all about the chemical underpinnings of traditional cuisine, and has nothing to do with the Julia Child-meets-Dale Chihuly creations of the new cooking.

These chefs aren’t looking into molecules, says McGee, “they are cooking with ingredients. They are artists, not chemists.”

That said, there are some firm links between the new daring cooks and chemistry. Fat Duck chef Heston Blumenthal questioned the age-old custom of removing the jelly and seeds from tomatoes before cooking with them. To his palate, they were tastier than the flesh. He worked with Don Mottram of the University of Reading to see why, and they found that the jelly has tons more glutamic acid—the source of the famous meaty, nummy umami flavor (See http://www.nature.com/news/2003/030707/full/030707-3.html)--than the flesh.

So, special note to my boyfriend: I now have scientific proof that de-seeding tomatoes is silly.

September 10, 2006

ACS: Ah, high culture

I bet $100 that this is the first ACS meeting where a session has featured a slide of Jesus Christ with an erection.

Yes, you guessed it, it is the presidential session celebrating Carl Djerassi: chemist, novelist, and playwright. He was a top chemist for many years, specializing in synthesis of marine natural products, and collecting awards like pogs. Then, late in his career, he turned to literature. Lately, plays have been his thing, and at the end of the laudatory session, there was a reading of selections from his play "Phallacy". He played the character Prof. Rex Stolzfuss. But it was in a scene where a young art historian chats with a young chemist about the representations of Christ's genitals in art that the image, an engraving from the 1520s called “Man of Sorrows”, according to the online text of the play, appeared. Alas, no amount of googling can summon up an image, but rest easy, Jesus is clothed…but showing.

I am no theater critic, so I won’t say anything more about the play. I will say, though, as a feminist, it is fun to see the man who first synthesized progesterone—which led to the birth control pill.

ACS: Fuelmen

Went to some sessions on hydrogen storage (you know, so that cars can run around emitting just clean, pure water vapor, and so that we can enter the "hydrogen economy") today and was introduced to ammonia borate by Bill Tumas of Los Alamos. I liked him, because he kept telling us "the hard cold facts". I've heard people talk about the "cold hard facts," but somehow, the "hard cold facts" seem even more bitterly inevitable. One of these was that no one has found a solution to storing hydrogen. The other is that his favorite candidate—ammonia borate—is not going to slot neatly into the current infrastructure.

The stuff may be good at holding onto hydrogen until you want to go vroom, and then letting it go, and it has a glimmer of a hope of getting the hydrogen compact enough so that one can drive 300 miles on a full cell—the standard measure of success—but it isn't possible to just shoot more hydrogen into it when it's gone "dry". So in this version of the hydrogen economy, one would buy a fuel cell, drive until it was used up, then return it to the fuel station for a full one. The old one would have to go back to the plant for some more complex chemical treatments. For some reason, everyone seems to think that this makes the technology completely impractical, but I don't see why. Everyone used to return their empty milk bottles when they picked up a full one. Maybe we can even take a page from the golden age of dairy and hire fuelmen, who will take the empty fuel cells from your front porch and leave full ones. They can even wear those swell hats.

Well, I suppose we ought to work out whether ammonia borate will even work before we start designing uniforms. In the meantime, I suggest Tumas get his own show on cable news called "The Hard Cold Facts with Bill Tumas."

ACS: Big in America

The conference gets underway even before my plane lands. A fellow from a microscopy concern is leaning across the aisle chatting to a chemist about his latest model. In the airport shuttle to downtown, chemists wedge inside the van, their poster tubes making the whole process seems like some complex protein folding problem. And today the streets of downtown San Francisco are alive with chemists--teeming with badged hordes looking for a cup of coffee between sessions.

The ACS meeting is big. It has strong points and weak points, but most of all, it is big. This year sees the innovation of satellite registration desks in hotels throughout downtown, and a mind-boggling number of papers—almost 10,000. And I am going to "cover" the meeting. Ha ha ha.

Catherine Goodman, below, says she ends up more or less walking the poster sessions as her fancy takes her. This is perhaps the perfect way to approach a meeting of this size—both posters and talks. Why see all the talks in your own field, when half of it will be old news? Why not stab a pin into the program or just amble into any old session? I pledge to spin the wheel of fate at least once this time—stay tuned for some chemical Kismet.

September 08, 2006

Goin' back to Cali

After my recent trip to San Diego, I'm heading back to California for the ACS meeting in San Francisco. The meeting looks great (especially for us chemical biology types); if you want to see what I'll be up to (and some of the other NPG editors), check out our editor's choice site (I know, Josh already told you that).

What's on my mind at the moment, though, is the overall organization of the meeting.

Can we make any sense out of the variation in assigning anything from 20-45 minutes to each speaker? Is it the ongoing conflict of wanting to accommodate more speakers versus really giving them the chance to say something? Is it a statement on the standards of behavior for the different subsections? Or is it all about the seniority of the speaker? Of course we wouldn't see graduate students giving plenary lectures, but I have seen some pretty established/respected professors lined up for 20 minute slots.

As a side note: The bonus of finding a session filled with 20-minute talks by professors is that it's likely that you will come out of the session with 8 times more information in your head than was there going in. The bad part about risking your time on a session without professors is that information may have actually leaked out of your head by the time you can gather your wits enough to leave. (Please note that I say this as one who gave a student seminar not that long ago...)


How can graduate students get more out of the meeting than just a rambling haze of science, intermingled with rambling hazes revolving around drink tickets redeemed at their friends' poster sessions? Certainly my first ACS meetings were overwhelming, with the number of talks that I 'must see' filling more hours than I had and the uptake on new scientific information limited to the first day or two before my brain got full. Students and postdocs on the job hunt seem to be much more focused and calm. Perhaps the secret is going in on a mission?


How can everyone get more out of the poster sessions? These events have become so huge that it's almost impossible to find anyone or anything on purpose. My recent experiences have pretty much relied on wandering around and looking for interesting stuff, regardless of whether it's related to my work at all. To be fair, I've met some great people and found out about amazing work that way, but theoretically poster sessions could serve a much more important function of meeting people in your field to share ideas and experimental advice.

What are your thoughts on ACS meetings? How do you get the most out of them? What, in fact, does it mean to 'get the most out of them' when there are talks to be listened to, jobs to be interviewed for, free pens to be accepted, a new city to be seen...? Let me know, and I'll try to put your advice into practice. Alternatively, you can wait for the meeting updates and see how my new secret plan works.

Catherine Goodman (Assistant Editor, Nature Chemical Biology)

It's not easy being green


In yesterday's issue of Nature, we published a paper from Amir Hoveyda's and Mark Snapper's groups at Boston College. The paper describes a simple metal-free catalyst that can perform enantioselective catalytic silylations on a variety of meso 1,2-diols, obtaining mono-protected chiral diols.

In the accompanying News & Views article, Scott Denmark wrote

The chemical yields and enantiomeric selectivities of the reactions are very good - in some cases, excellent - although the reaction times are long (2-3 days). Relatively large amounts of the catalyst are required, but this is not a problem as the catalyst is simple to prepare from inexpensive starting materials. Clearly this is just the beginning of a development process and more active catalysts will be forthcoming.

These kinds of catalysts could shave several steps off synthetic routes to prostaglandin analogues, unnatural nucleosides, and neocarzinostatin analogues, which currently require a number of chemical transformations and an enzymatic de-acylation to obtain a key building block. By shortening the synthetic route, the amount of chemical waste produced can be minimized and the amount of time needed to make the molecule can be dramatically reduced. Denmark concludes the News & Views article by saying that

this procedure is likely to have a significant impact on the efficiency and cost of constructing single-enantiomer products. Most importantly, however, this report demonstrates the creative power of synthetic chemistry to build simple organic catalysts that mimic and ultimately surpass, biological catalysts - especially for non-biological transformations.

Collaborations between two well-known organic chemistry labs aren't extremely common, and Hoveyda talked about this phenomenon on our 'Authors' page:

Hoveyda says the synthetic organic chemistry field has traditionally been wary of two principal investigators sharing credit on single papers. "The culture almost discourages it," he says. Early on, colleagues warned Snapper that working with a more senior researcher could hurt his career. But their partnership has been fruitful; the two have received joint grants from the National Institutes of Health since 1997 and have published about 20 papers together. "The reason this collaboration has been so successful is that neither of us cares who gets the credit," Hoveyda adds.

If you’d like to learn more about the research, Hoveyda was interviewed on this week’s Nature Podcast (he also appears on the recent chemistry podcast). And if you're in San Francisco at the Fall ACS Meeting next week, you can see Yu Zhao talk about the work on Monday afternoon.

Joshua


Joshua Finkelstein (Associate Editor, Nature)

NPG at the 2006 Fall ACS meeting


As I mentioned yesterday, I'll be attending the ACS meeting next week... You might remember that we created a special conference website for the Spring ACS meeting - well, we've updated the conference website for this ACS meeting:

- once again, there is a list of some of the sessions the editors will be attending.

- there is a special edition of the Nature Podcast, in which Dr. Simon Frantz talks with the authors of several recent chemistry papers from Nature, Nature Reviews Drug Discovery, Nature Chemical Biology, Nature Materials, and Nature Methods. The five papers featured on this podcast are:

Enantioselective silyl protection of alcohols catalysed by an amino-acid-based small molecule by Zhao et al. (Nature)
Targeting proteases: successes, failures and future prospects by Turk (Nature Reviews Drug Discovery)
Small-molecule activation of procaspase-3 to caspase-3 as a personalized anticancer strategy by Putt et al. (Nature Chemical Biology)
Molecular computational elements encode large populations of small objects by de Silva et al. (Nature Materials)
An unnatural hydrophobic base pair system: site-specific incorporation of nucleotide analogs into DNA and RNA by Hirao et al. (Nature Methods)


We've also added a few recently published papers to the list of exciting chemistry papers from Nature, Nature Chemical Biology, Nature Materials, and Nature Methods - some of these papers can be downloaded for free during the ACS meeting. We hope you enjoy reading these papers as much as we did, and would love to hear what you think about them...

And finally, I'd like to mention that this happens to be our 100th blog entry - on behalf of all of us, I'd like to thank you for coming back here week after week...

We'll be adding blog entries throughout the conference, so please check back frequently to see what we’re writing about...

See you at the meeting!

Joshua


Joshua Finkelstein (Associate Editor, Nature)

September 07, 2006

Sympathy for the chemist


For some reason, many non-scientists (and even some scientists) see chemists as "nefarious creators of toxic pollutants ... [or] mad scientists brewing up Love Potion #9 in ... [a] cluttered and archaic laboratory." Or worse yet, they think chemistry is boring and/or useless...

The editorial in the September 7th issue of Nature tries to capture why organic chemistry is interesting and attempts to explain some of the things that excite the 'average' organic chemist. (Though the editorial is mainly about organic chemistry, I think many of the statements in the editorial are true for other areas of chemistry...)

Many organic chemists spend their days searching for creative solutions to real-world problems, yet the media pays them just a fraction of the attention devoted to physicists or biologists. Even fellow scientists think organic chemistry is esoteric ... [But a]sk a group of organic chemists why they love their work ... and most will tell you that it enables them to make things that no one else has made before ... [C]hemists are frequently drawn to the field because there is not just one way to solve the problem, and the search can reveal a bit more about how the world works.

When people ask me why I like being an editor, I often tell them that it's like being a first year graduate student again: every day I get to read exciting chemistry papers and often feel like that "child in a sweetshop" - there are so many interesting discoveries out there, and countless problems that still need to be solved. The excitement peaks when I'm at a meeting - I love going to sessions and hearing people talk about their unpublished/newly published work, meeting students and post-docs at the poster sessions, and chatting with speakers after the talks about their future plans...

With that in mind, I hope to bump into you at the ACS meeting next week - keep an eye out for Catherine Goodman (from Nature Chemical Biology), Mirella Bucci (from Nature Chemical Biology), and Emma Marris (from the Nature news team) who are also in town for the meeting. And don't forget to check back here regularly, as we'll be blogging throughout the meeting...

Hope to see you there,

Joshua


Joshua Finkelstein (Associate Editor, Nature)

September 05, 2006

I still haven't found what I'm looking for


In this month's issue of Nature Reviews Drug Discovery, Monya Baker wrote a 'News & Analysis' piece about open access chemistry databases: though there are a number of free chemical databases (including PubChem, which I blogged about last spring), "the chemical data [in these open access databases] still pale in comparison to what already exists in other databases and the published literature."

One problem is that it takes a great deal of time to collect data for these large databases: "PubChem's director, Stephen Bryant, says he lacks the staff and mandate to collect data from published literature and patents." So it's not surprising that the Chemical Abstracts Service (CAS) database contains more chemical information than PubChem: whereas PubChem has about eight million unique structures, CAS contains nearly 30 million organic and inorganic substances.

In addition, there are some concerns about quality control in these open access databases: "[t]he screening data [in PubChem] are less rigorous than those in peer-reviewed articles, and contain many false positives. Deposited data aren't curated, and so mistakes in structures, units and other characteristics can and do occur." I can't imagine how frustrating it would be to synthesize a molecule that was listed as a 'hit' in one of those databases just to find out that it was inactive because someone mixed up the stereochemistry (or omitted a double bond)...

What are your experiences with these databases? Have you used them in your own work? If so, were they useful? What would you do to make them better? Do you think that the problems with these open access databases are the sort of 'growing pains' that happen for any new technology/database, or is there something special/unique about developing open access chemistry databases?

Joshua


Joshua Finkelstein (Associate Editor, Nature)

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