Factoring in a sweet tooth

It is lovely weather here in Boston, and we are all enjoying it very much. In fact, a friend of mine recently found a patch of wild blueberries, and so this past weekend I made some blueberry pie. Yum!

This little excursion also got me thinking about pi more generally. In my undergraduate days, my study partners and I really struggled in physical chemistry. We had homework assignments every night (unusual for a class at my university) and, even more strangely, we were given the numerical answers. We just had to figure out how to get them. After many weeks of trying all possible equations that we knew for every problem, one of us had an insight: as long as we used pi somewhere, somehow, we could always get to the right answer – sometimes you had to multiply by pi, sometimes dividing, etc., but always pi. We called this the pi factor. (Then the struggle was to figure out why we needed pi in each case… is this the why factor??)

On a related note, I often see papers where an unexpected increase in binding affinity, or the critical requirement of a phenyl ring on a small molecule inhibitor, or similar, is simply explained by invoking pi-stacking. This is interesting to me: since it is often extremely difficult to provide quantitative (or even qualitative) data to confirm or refute the presence of pi-stacking (especially in large/complex systems), I wonder if some shout-outs to this interaction are just another way that people are using the pi factor? In this case, as something that makes intuitive sense, but will not likely need to be anything more than a vague reference?

Perhaps as we continue to learn about this fundamental intermolecular interaction, and methodologies continue to improve, it will not be so easy to call on pi in any ill-defined way. As long as it doesn’t jeopardize my dessert…

Catherine (associate editor, Nature Chemical Biology)

Journal journeys: Day 179, Picture this…

It’s been a while, I know, I’m sorry…

So, after counting out which day of our journal journey we’re on, number 179 it turns out, here is another entry in the life of setting up a journal.

At the ACS meeting in New Orleans earlier this year (one I will have a hard time forgetting) we gave away Nature Chemistry labcoats – or at any rate we got people to sign up for a couple of e-alerts and then promised to send them a labcoat. Well, we’ve followed through on that promise and if you were one of those who signed up, either your labcoat should have arrived quite recently, or it will be doing so in the next few days. (I’ve had reports of them turning up in some cases – let us know if yours has arrived by commenting on this post..).

We’ve decided to do the same thing again in Philly at the next ACS meeting – sign up for a couple of e-alerts at the Nature Publishing Group stand at the expo (booth 1815/1817) and we’ll give you a Nature Chemistry labcoat for free. Although it is not confirmed yet, we may even have some stock at the booth and so if you are quick, you might not have to wait to have yours mailed.

For a bit of fun we’ve decided to run a competition based on the labcoats… – and full details can be found on the Nature Chemistry Facebook group. We’re asking you send us photos of you (or your friends) in your shiny new Nature Chemistry labcoat (and the logo should be visible so that we know you’re not just using any old labcoat) – and the five most imaginative ones will win a year-long print subscription to the journal. Please keep the contents of the pictures SAFE (no standing next to explosions or flaming bottles of BuLi) and CLEAN (I’m not going to even explain that one…).

The competition will run through until Feb 2009, so you have plenty of time to snap some cool pics and send them to us – please go to the Nature Chemistry Facebook group for details of how to send us the photos – and that is also where we will post any photos (only the clean and safe ones though) that we receive. Feel free to send in as many photos of you (or your friends) in your Nature Chemistry labcoat as you wish (within reason) – and we’ll be writing back to you in March next year if you’ve won!

So as not to discriminate against those who couldn’t make it to New Orleans and won’t be attending the ACS meeting in Philly, feel free to design your own custom Nature Chemistry labcoat and send us your pictures (again, clean and safe please…)

Good luck!

Stuart

Stuart Cantrill (Chief Editor, Nature Chemistry)

NChem Research Highlights: carborane MOFs, metal-ion sensing, and coordination polymers

This week we have covered quite a range of topics in our Research Highlights

First of all we have some nifty metal-ion sensors that are made by attaching different chromophores to 8-hydroxyquinoline – a group that serves as a receptor for various metal ions.

Then, we cover the latest twist on metal-organic frameworks in which simple benzene-based linkers have been replaced with much more funky carboranes – and see how that affects their gas adsorption properties.

Finally, some designer coordination polymers that not only act as hosts for water clusters and nitrate ions, but have an intricate interwoven topology based on the Borromean rings.

Tune in for more this time next week…

Stuart

Stuart Cantrill (Chief Editor, Nature Chemistry)

Reactions – Ronald Breslow

1. What made you want to be a chemist?

Chemistry is both creative and incisive, so it gives us both medicines and biological mechanisms.

2. If you weren’t a chemist and could do any other job, what would it be – and why?

Perhaps a biologist, or if not a scientist then a judge.

3. How can chemists best contribute to the world at large?

Help solve the energy problem, probably with practical photovoltaic devices and batteries.

4. Which historical figure would you most like to have dinner with – and why?

Thomas Jefferson, to convince him that Hamilton was right.

5. When was the last time you did an experiment in the lab – and what was it?

Perhaps 40 years ago, generating a cyclopentadienyl cation and getting its spectrum.

6. If exiled on a desert island, what one book and one CD would you take with you?

The recent biography of George Washington, and Bach’s Goldberg Variations by Glenn Gould.

Ron Breslow is in the Department of Chemistry at Columbia University, and works on biomimetic chemistry, physical organic chemistry and molecular electronics.

ICCC38: Coordination chemistry

Shalom from Jerusalem, where I’m attending the 38th International Conference on Coordination Chemistry (or ICCC38 as it is thankfully abbreviated to).

The conference has only been going for a day, but here’s a thought to keep you going: ENERGY.

Quite a big and important thought, but fortunately for the world, some of the world’s top chemists are thinking about it pretty deeply. In yesterday’s opening plenary lecture, Harry Gray of Caltech talked about his search to find cheaper alternatives to ruthenium-based dye-senstized solar cells. Ending on positive note, he told us he had secured funding for a project involving about 20-30 institutions across America (and BP in the UK). Even more positively, he then told all the young chemists in the audience to go out and make sure that in the future we can make everything we need from nitrogen, carbon dioxide, oxygen and sea-water, using solar power.

And Richard Schrock of MIT (didn’t he win a prize a few years ago…?) finished today by discussing his long-standing battle to make a catalyst that can convert nitrogen to ammonia. But what’s that got to do with energy, I hear you ask. Well, the Haber-Bosch process, developed almost 100 years ago and still used to create a staggering 100 million tons of ammonia a year today, consumes a whopping 1.4% of the world’s energy. He isn’t quite there yet, because the reaction is barely stoichiometric let alone catalytic. But he’s working on it and left the audience thinking on the problems he (or rather his ligands) needs to overcome. Oh, and that’s before you get the necessary hydrogen from splitting water with sunlight…

Don’t hold your breath, but we might get there in the end.

Neil

Neil Withers (Associate Editor, Nature Chemistry)

NChem Research Highlights: Isotopes, proteins and reactive intermediates

Another week and another set of Research Highlights to tell you about…

First up is a report on the conversion of carbon-11 labelled methyl iodide into formaldehyde using a rapid and high-yielding approach, that offers new opportunities for radio-labelling.

Next, we feature a couple of papers in a single highlight, that look at protein synthesis and crystallization. The twist here is that both mirror image forms of a protein are synthesized chemically and then the racemate is crystallized in order to study their structural properties.

Finally, researchers in Japan take a closer look at nucleophilic aromatic substitution reactions and observe an elusive sigma-complex intermediate through which the reactions are thought to proceed.

More next week…

Stuart

Stuart Cantrill (Chief Editor, Nature Chemistry)

Flown the coop

Hi all,

Important news first: Our new issue is out today – including a focus on cooperativity. And in the spirit of cooperativity (or lack of time??? You be the judge), I’ve decided that you all should help me write the rest of the information about the issue. So, please comment and let me know whether you found Jamie Williamson’s Perspective on macromolecular assembly more thought-provoking than Adrian Whitty’s suggestion that cooperativity is the most basic type of emergent property, or vice versa. Or, if reading about Scientists without Borders made you revisit your desire to join the Peace Corps… All kinds of things to think about.

Otherwise, I’m off to a meeting at an undisclosed location. Theoretically it’ll be nice to get out of this Boston heat, but the weather report of my destination sounds just the same… yikes! Silly summer.

Catherine

Reactions – Gavin Armstrong

1. What made you want to be a chemist?

It’s certainly not a career you just fall into to but there was certainly no point at school at which I thought “I want to be a chemist”. I enjoyed chemistry at school so I continued doing it at university. As the physical side of it got more complex I got more and more immersed in it and couldn’t get out!

The move to publishing came when I realized that I couldn’t see myself spending any more time in the lab. I enjoyed reading other people’s research more than I did doing my own. I also realized that I’d like to spend more time reading more diverse science than what I could when doing fairly specialist projects.

2. If you weren’t a chemist and could do any other job, what would it be – and why?

I think I’d always have ended up in publishing but if I was to choose what I could write about it would be sports. I love football (soccer) and cricket and being able to watch it and get paid for it would be great!

3. How can chemists best contribute to the world at large?

There are two things that I think are very important. The first one is for chemists to not only address the major problems that are facing civilization currently, such as energy and sustainability, but to continue to work on fundamental problems still not fully understood. The second thing is to teach and discuss science with enthusiasm. Interest from non-specialists and students is fostered through passionate teachers. So many chemists tell stories about great teachers inspiring them to work in science and this is a responsibility that shouldn’t be taken lightly.

4. Which historical figure would you most like to have dinner with – and why?

I have a real answer and a “professional” answer. My real answer is Brian Clough. For those of you who were not big football (soccer) fans in the 70’s and 80’s he was a manager (coach) for several English teams. During his career he won everything (English and European competitions) basically through great man management. He trusted his team and they trusted him. He would ask them to do something and even though they might not have understood why (any grad students know that feeling?) they would do it anyway (any grad students know that one?).

My professional answer is Ed Lorenz. Sadly, he died very recently but his legacy will live forever. His discovery of deterministic chaos in weather systems sounds like it could be interesting to only a select group of meteorologists, but the intrinsic mathematics behind those systems are important to so many researchers, from biologists to economists, that it started a new way of looking at deterministic systems. He had one of those “eureka” moments and it would be great to hear him talk about it!

5. When was the last time you did an experiment in the lab – and what was it?

I really can’t remember the last actual lab experiment I did. I left the lab to carry out some computational work half way through my PhD and I forgot to go back! So if simulations count then the last batch I ran were related to a kind of spiral pattern that I’d previously observed in the Belousov-Zhabotinsky reaction. In the experiments it behaved in a way that had never been reported before that we couldn’t obviously explain. We couldn’t reproduce its behaviour in the simulations no matter what we tried!

6. If exiled on a desert island, what one book, and one CD would you take with you?

My book choice is High Fidelity by Nick Hornby. It introduced me to the concept of “Top 5s”, the greatest pub game ever (if it needs explanation it’s basically just listing your top 5 songs, films, papers in Nature this year, 1970 cop shows, etc.). As for music, it would be Definitely Maybe by Oasis; a classic.

Gavin Armstrong is an Associate Editor for Nature Chemistry.

Who’s the greatest Russian (scientist)?

Cross-posted from here

There are two clear front runners in Russian state TV’s ‘greatest Russian’ contest. So far Josef Stalin and Tsar Nicholas II are way ahead in the poll, which is being decided by that arbiter of our age: online voting.

But what about Russia’s great scientists? How are they faring? It is quite impressive how many scientists have actually made the voting shortlist.

Cosmonaut and first man in space Yury Alekseyevich Gagarin is currently in tenth place with 96,000 votes. Although far behind the 280,000-odd of the two leaders this still puts him ahead of Boris Yeltsin.

Slightly further down in 14 with 81,000 is Mikhail Lomonosov, scientist and the man who gave his name to that troublesome ridge in the Arctic. Nuclear physicist Andrei Sakharov is in 18th place with 38,000 votes and aeronautics expert Konstantin Tsiolkovsky polls 13,000, putting him in 28th place.

Not so popular is the great chemist Dmitri Mendeleev, inventor of the periodic table. He’s stuck down in 33rd place with a shockingly paltry 8,000 votes. This is possibly because of the hugely unflattering photograph used, which makes him look like a slightly elderly Rasputin or Alan Moore on a bad day.

Come on chemists! Vote him up! With 4,000 votes we can get him above both Tolstoy and Bulgakov…

Daniel Cressey