Monthly Archives: March 2012

Reactions: Andreja Bakac

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Andreja Bakac is at the Ames Laboratory (US DOE)  and the Department of Chemistry, Iowa State University and works on mechanistic chemistry of high-valent metal-oxo complexes and on activation of oxygen and nitrogen oxides.

1. What made you want to be a chemist?

It is true that I was fascinated by chemistry from my first chemistry class in middle school, but I also enjoyed physics and math and literature. In the end, the extra push for chemistry was provided by my chemistry teacher in my senior year in high school. In this man’s outspoken opinion, girls are not meant to do chemistry. Well!

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

I love literature and poetry. If I were not a chemist, I would probably be a starving poet.

3. What are you working on now, and where do you hope it will lead?

Our group is involved in mechanistic chemistry focusing on activation of molecular oxygen, nitrogen and other small molecules with transition metal complexes. The ultimate goal of this work is to design new processes and catalysts that will address the world’s needs in energy, environment and health. We approach this problem by preparing relatively small and simple, typically macrocyclic metal complexes that are capable of mimicking the chemistry believed to take place at the active sites of metalloenzymes. Chemically and spectroscopically simpler mimics facilitate mechanistic studies and provide a wealth of relevant information and important clues about real-life chemistry. The information gained will be used in the next step to develop simpler, better and more durable catalysts for industrial and laboratory reactions. Currently the group’s favorite metals are rhodium and iron, favorite ligands are saturated macrocycles, and favorite small molecules in need of activation or generation are oxygen, molecular nitrogen, and nitrogen oxides.

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

I would love to have dinner with Alexander Borodin, a great chemist and a great composer and musician. In my experience, a lot of chemists enjoy music, but it is quite a feat to excel in both. How did he manage two separate professional lives? And where did he find the time?

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

My most recent adventures in the lab took place a few months ago when I needed some preliminary data for a research proposal. I looked at the reaction of some Rh(II) complexes and chloride ions. The outcome was not what I expected, but it explained a lot of puzzling observations that we made over the years. All in all, it was time well spent.

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

Provided this exodus is safe and temporary, and I do not need a survivor guide to teach me about finding food and shelter, sending smoke signals, or building a boat, I would enjoy a collection of stories by Chekhov while listening to piano concertos by Beethoven or Rachmaninoff.

7. Which chemist would you like to see interviewed on Reactions – and why?

If you could get hold of my senior-year high-school chemistry teacher, that would be great!

We’re (still) hiring

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As pointed out in this blog post, we’re looking for a new Associate Editor here on the journal.

I’d like to take this opportunity to offer some advice to those of you thinking of applying for the job. This all might sound somewhat obvious, but it is very important (and in your best interests) that you include in your application what we ask for in the job advert.

What we need are:

1. An up-to-date CV.

2. A research highlight in Nature Chemistry style that is approximately 250 words long and is about a recent (and relevant, i.e.. chemistry) paper in the literature. Your research highlight doesn’t have to be about a Nature Chemistry paper.

We do not want you to send anything in lieu of the research highlight, such as Thesis chapters, research papers, or other examples of writing you have done for other purposes in the past. If you want to send other (relevant) examples of your writing to demonstrate your experience/skills, that is fine. Nevertheless, so that we can compare across a relatively level playing field, please ensure that you also send in a research highlight following the instructions provided.

3. A cover letter that explains why you are interested in the position and what your salary expectations are. You might also want to use the cover letter to explain why you think you would be a good fit for the position.

Good luck!

Stuart

Stuart Cantrill (Chief Editor, Nature Chemistry)

ACS: Rewind

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Perhaps the biggest difficulty with ACS meetings is the size. There’s a vast amount of good chemistry on show here, and it can be extremely difficult to choose where to go. I’ll tell you a little about what I’ve seen in the last couple of days in a later post, but first I thought I’d talk a little about my strategy for selecting sessions. I think it works quite well – but I’d be interested to hear about other strategies in the comments.

The ACS helpfully provides a planner that allows you to create a schedule of talks you want to attend. You select the talks, and it will alert you if there are conflicts. What it doesn’t (and to be fair probably can’t do) is tell you that you’ll never be able to go to talk X and then move on to talk Y (scheduled to start immediately after the end of X) because they are approximately a 0.5 miles apart – that’s as the crow flies — and in different hotels. So you have to be a little more selective. Add to that the fact that whichever talk you select, a later conversation with friends will invariably start with ‘Did you see the talk by Prof. Bigshot? It was amazing/terrible/I can’t believe he said….’. To cut a long story short, you will have missed that talk, because you were 0.5 miles away in a…you get the picture.

So, I’ve started using a slightly more random approach to selecting which talks to attend. I pick a talk that I’ve seen before and enjoyed — there is always a chance that there will be some updates on progress — then I’ll stick with that session. So I use the scheduler to select around 3 talks a day but get to see plenty that I wouldn’t necessarily have selected otherwise.

And, come the next big multi-session meeting, I will hopefully have some new choices to ‘rewind’ and act as the seed for my discovery of some new chemistry.

Steve

Stephen Davey (Senior Editor, Nature Chemistry)

Element of the month: Counting on copper

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Readers of this blog will be familiar with last year’s essay competition — as Stuart mentioned here a few days ago, the winning  essay on copper, written by Tiberiu Moga, appears in this month’s ‘in your element’ feature.

Copper has been part of our lives pretty much for ever — the Copper Age started around 5,000 BC (give or take a couple of thousand years depending on whether you count the Copper–Stone Age or not), made its way into epic poetry (read the article to find out how it features in the Kalevala) and copper-based materials are still virtually everywhere, from the humble penny to electrical wiring. So what exactly does copper do, apart from giving her copper(II) carbonate-green colour to the Statue of Liberty? Scientifically speaking, lots of things.

Moga is a Medical Doctor student at the University of Toronto, and previously studied both chemistry and biology at Dartmouth College — he is thus particularly interested in copper’s biological functions and catalytic role in the synthesis of new medicines. He identifies three processes that cover most of its abilities: Lewis-acid catalysis, single-electron-transfer processes, and two-electron-transfer reactions.

One of the best-known reactions involving copper as a Lewis acid is the popular ‘click’ azide–alkyne cycloaddition that connects the two groups to form an azole ring. This fast, reliable reaction is generally easy to carry out and makes for a highly efficient step in a wide variety of processes including, for example, natural product total syntheses.

Single-electron-transfer processes where copper adopts either a Cu+ or Cu2+ form are widespread in biosystems. Cellular respiration in organisms, for example, relies on a succession of these steps carried out by copper-containing enzymes to oxidize glucose, and extract its energy. Two-electron transfer reactions are also common — they go through a slightly more complex mechanism involving a halide ion.

Of course, this is by no means an exhaustive list. Copper is looking increasingly like a good alternative to palladium catalysts, and it’s also a useful building block — remember the copper nanotubes?

As it turns out, we’re still very much in a copper age, and it looks all set for the duration.

Anne

 

Anne Pichon (Associate Editor, Nature Chemistry)

Materials Girl: Beginning of the end

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[Posted on behalf of Materials Girl]

Late last year during the fall term, YouKnowWho dropped a small bomb on my plans: I could write a dissertation using the work for my intended Master’s thesis. What?! In previous bids he had simply asked me to stay for a PhD to work on some project, whereas now there was the claim that I could finish in just another year. (I assume this means two more, bringing the total to a reasonable five years.) It was then the time for waffling. On one hand, staying would save a large amount of time and effort – no need to retake classes, create new networks, and familiarize myself with a different academic system. On the other hand, I had always planned to relocate sometime in the future to do my PhD. Also, although my search for specific jobs was coming up nil, a [very big] company had found my resume in their online bank and decided that I should work for them (after flying me in for some quick interviews) – but their tempting offer was contingent on graduating in the spring. I was conflicted.

Now that I think about it, turning down the job would feel akin to breaking up with a serious boyfriend. Would I ever get another offer or would I be reduced to a penniless, lonely miscreant forced to move into my parents’ basement while honing my skills as a barista? Was anyone else going to pick me from the sizable crowd of contenders? Did I actually possess the skill for a good position or was I deluding myself in assessing my value? The potential outcomes plagued me for months, during which time I turned down [very big company’s] offer in order to ruminate further. This should’ve been a hint that deep down I had already made up my mind, but it wasn’t until the end of winter break that I steeled myself for the long haul. I was going to stay.

So in January, I found myself on the road to oral preliminary exams in the materials science & engineering department – something mere months prior I had never dreamed of (and had gleefully ignored every term as a Master’s student). The pressure for me to pass was enormous, more so than the inherent nature of the exams. Not only did I want to avoid the mortification of retaking them, but also the required time to finish a Master’s was running dangerously low. If I spent the rest of the school year studying for the maximum two attempts at prelims, no time would be left to graduate if I failed both – thus leaving me in some horrible purgatory of no degree after three years laboring in grad school. To say the least, it was a very sobering thought and serious business.

The other major hurdle to prelims was my undergraduate background. (In)organic chemistry has distinctly different curricula from that of any engineering major. Being in materials eased the pain to a degree, although topics such as mechanical properties and diffusion were still foreign to me. Between TAing, classes, and Lab Mom duties, I stayed buried [or at least attempted to] in heavy textbooks.* Never before had I experienced such prolonged, excruciating pain in the form of studying. (Call me a bad student with no attention span, but despite sleeping through most classes I’ve learned to earn good grades after studying only days before tests. Blame the apnea?) I formed a study group with other prelim-takers from a hodgepodge of backgrounds: the physics guy knew his electrical properties beautifully, the two from chemical engineering were comfortable with thermodynamics & diffusion, the one from materials had already learned everything, etc. The group helped a bit despite our sessions being exhausting and relatively short – and sometimes spent pondering how to bribe each professor to pass us, or if it’d help to bring a bottle of vodka (or a revolver) during the actual exams. Our weekly sessions of questions, griping, and even laughter were a little reminder that I wasn’t alone in a traumatic world of stress and cramming. As it is with the rest of my grad student family, we ultimately helped each other through the blood, sweat, and tears.

*Countless thanks goes to the friends who lent me their books and support. Hopefully the cookies I’ve baked have repaid them.

To cut a long story short, after two months of studying I took prelims and PASSED. (!!!) No second attempt, no earth-shattering reprimands from professors who find me an inadequate candidate, and just about no dishonor. I am officially on the road to being Dr. MG, as well as starting to act somewhat human again. So it’s probably a good time to get back to writing those papers for YKW (which will eventually turn into the dreaded dissertation)… Gulp.

Thomas Hager – a chronicler of chemistry

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The April issue of Nature Chemistry sees the publication of our first-ever interview in the journal. I was delighted when Thomas Hager, author of books such as ‘The Alchemy of Air‘ and ‘The Demon Under the Microscope‘ agreed to field some questions from me. For the full interview, you’ll need to be a subscriber, but here are some snippets from the piece.

Thomas_Hager

Image courtesy of Thomas Hager

Is the chemistry theme in many of your books simply a by-product of your interest in food and medicine or is there an underlying fascination with chemistry, too?

I was not a chemistry fan. I majored in biology as an undergraduate, and then did my graduate work in medical microbiology, molecular biology and immunology. Along the way I took the standard slate of chemistry courses, but didn’t really take to them. Organic chemistry was torture. Then I took a class on molecular orbital theory that was close to incomprehensible — it might as well have been Sanskrit. I was clever enough to pass the course, but I learned nothing. I appreciated the field only later, while working with Linus Pauling on his biography. Interviewing Pauling was like taking the world’s best class on the development of twentieth-century chemistry. I’ve been hooked ever since.

In both The Demon Under The Microscope and The Alchemy of Air you don’t shy away from the fundamental chemistry that underpins the story in each case. Did this make it harder to write the books for a general audience?

The short answer is yes. The challenge comes from the fact that the typical non-specialist reader has close to zero chemical knowledge. The trick is to find a structure for the book that will introduce the reader first to a compelling story, then move them through the often-difficult science from square one, along with the story, carefully and progressively, not overwhelming the reader with too much at once, giving them time to digest the science by embedding it in a dramatic narrative with strong characters, challenges, mystery and so on.

You’ve written about sulfa drugs and ammonia synthesis — arguably two of the most significant breakthroughs of the twentieth century underpinned by chemistry. If you had to pick just one of these, which would you say had had the greatest impact on society, and why?

I am drawn to discoveries that have enormous direct impact. We increasingly live in a world that is as much technological as it is natural — often more so. We swim through technology all day, yet most people do not appreciate or understand the science that made it all possible, any more than we appreciate the atmosphere every time we take a breath. We take it for granted that we can flip a switch and make it as bright as day all night long, or get a shot for a disease that would have killed us (and most of our family, and maybe our town) a century ago, or fly through the air like gods. We accept these miracles as commonplace and have lost the exhilaration of that moment of first appearance, when these discoveries were seen for what they were: life-altering breakthroughs, watersheds in history. The Haber–Bosch method of nitrogen fixation, on the other hand, remains after 100 years the world’s major way of making nitrogen fertilizer; the products made by this method consume more than 1 per cent of all the energy on earth and feed around 40 per cent of the world’s population. I would argue that Haber–Bosch is, in terms of direct societal impact, the most important chemical discovery ever made.

Why is it important to tell story of the history of the science that is now part of our everyday lives?

Without understanding the history of science, it is difficult to fully understand the beneficial and not-so-beneficial roles it plays in modern life, the things it might do (and might not do) in the future, and why supporting it is so important. Science history tells scientists where they came from and who they are; and tells the general public important things about how the modern world came to be.

———-

To find out more about why Hager became a writer, how he views Pauling’s legacy, and what projects are potentially in the works, the full interview can be found here ($).

Stuart

Stuart Cantrill (Chief Editor, Nature Chemistry)

Reactions: Simon Friedman

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Simon H. Friedman is in the division of Pharmaceutical Sciences at the University of Missouri Kansas City  School of Pharmacy  and works at the interface of chemistry and biology, building chemical tools for understanding and altering biology.

1. What made you want to be a chemist?

A childhood building things from legos. A love of machines and contraptions. A love of shapes and symmetry. The hope of making something useful and having fun while doing it.

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

Filmmaking, music, or design. I enjoy creative self expression. The Muse at times seems like a less harsh mistress than does Nature.

3. What are you working on now, and where do you hope it will lead?

Multiple things including: 1) Developing and applying light activated RNA interference to control gene expression spatio-temporally and in so doing understand fundamental biological processes, and 2) Super-secret project Omega. Hopefully you will hear about it sometime soon.

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

The progenote, so I could ask it what makes it tick.

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

I tend to be a designated hitter in the lab, meaning I work with individual students on their experiments, in particular making and using new apparatus for specific projects. The last apparatus I made was a high intensity UV point source.

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

Book: FM3-05.70 US Army Survival Manual (non-electronic version). Album: Probably the White album. I hope that they don’t notice that it is a two disk set.

7. Which chemist would you like to see interviewed on Reactions – and why?

Steven A. Benner. He just seems like a very philosophical and contemplative guy. It would be interesting to get that eight miles high perspective.

April 2012 issue

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April 2012 cover

Another month goes by and so we have another issue of Nature Chemistry to share with you. Quite a striking (and colourful) cover on this one! Clashes a bit with Nature Chemistry-purple, but you can’t have everything! You’ll find all the usual good stuff in the issue: research highlights, News & Views pieces, and research Articles that we hope you will find interesting.

A few things do stand out from the usual crowd. We have published our first ever interview ($) — with author Thomas Hager. Last year someone tipped me off to ‘The Alchemy of Air‘ (I think it was @biochembelle) – and I really enjoyed reading it. So much so, that I looked around to see what else Hager had written about, and that prompted me to read ‘The Demon Under the Microscope‘. I thoroughly recommend these books to any chemists out there, but more than that, they are written in such an accessible style that you don’t need to be a chemist to get maximum enjoyment out of them. I’ll post excerpts from the interview here on the blog in a day or two.

We also have another winning entry from the In Your Element essay competition, this one all about copper (this is free to access if you’re registered on nature.com). The Thesis article this month ($) is from Bruce Gibb — one of our regular columnists — and he takes exception to the notion of enantiomeric excess (e.e.), suggesting that it is counter-intuitive and should be ditched for enantiomeric ratio (e.r.) as a better measure. And the book review ($) was kindly written by David Kroll, who considers ‘The Quest for the Cure‘ by Brent Stockwell.

Finally, the Review article, which is free until the May issue goes live in a month’s time, is all about dendrimers (and was written by Didier Astruc). Lovely compounds, but a bit of a pain to draw nicely…

Stuart

Stuart Cantrill (Chief Editor, Nature Chemistry)

 

IMAGE: DANIELA WILSON

COVER DESIGN: ALEX WING

We’re hiring!

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The founding editorial team at Nature Chemistry was assembled back in 2008 and has stuck together since then, providing a solid foundation for the launch of the journal and its growth in these early years. But it’s time for a change and now Neil is (back) off to the Royal Society of Chemistry to take up the position of Features Editor at Chemistry World. We wish him well (really, we do), but now we need someone to fill his shoes. So, we’re looking for a new Associate Editor here on Nature Chemistry.

Enjoy reading papers and fancy a move away from the bench? Enjoy reading the latest hits in the chemistry literature and would like to write about them for Nature Chemistry? Want to attend conferences to see what the latest and greatest developments are (at least at the conferences where such things are aired)? Want to blog and tweet about cool and creative chemistry (we know a lot of you do that already, but this is part of a job that you get paid to do!)? Well, if the answers to those questions are ‘yes’, have a look at the advert and give it some thought. Applications need to be made through the website, but informal queries can be directed to our journal inbox (you can find the address on our website).

Stuart

Stuart Cantrill (Chief Editor, Nature Chemistry)

DNA nanotechnology workshop: Unnatural assemblies

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I’m just back from Shanghai, where I attended the 2nd DNA nanotechnology workshop, a very exciting meeting at which we also celebrated the prestigious Albert Einstein professorship of the Chinese Academy of Sciences being awarded to Ned Seeman, often called ‘the father of DNA nanotechnology’. The story goes that as a young crystallographer, worried about getting tenure, he went to the campus bar to have a few beers and mull things over. Seeman found inspiration in the Escher woodcut Depth to make crystals using DNA, so as to avoid the guessing game (and potentially praying)­ that everyone who ever tried to crystallize anything is only too familiar with. The rest, as they say, is DNA nanotechnology.

The idea of hybridization — mixing two separate DNA strands to make a double helix — was reported in 1956 by Alex Rich, in a paper that incidentally very nearly fitted into a single column (half a page) of the journal! The beauty of the assembly lies in the precisely controlled positioning it enables at the nanoscale, and by carefully designing strands you can fold them up into increasingly complex designer structures (origami).

The meeting — whose theme was “From structure to function” — undeniably showed that DNA nanotechnology now branches out in many directions. We saw a wide variety of DNA items, triangle, cube, tetrahedron, octahedron, and even curved architectures; used for example to position other species (from gold nanoparticles to proteins); or manipulated to form nanomechanical devices such as tweezers, chopsticks-renamed-pliers, or walkers. These behaviours can in turn be used for example for guest recognition, detection, or to construct logic gates; make up DNAzymes (single-stranded DNA sequences that act as enzymes). It would be impossible to try and discuss here all the elegant structures and systems presented at the workshop, but I would like to mention an unusual one. Fritz Simmel from Munich looked into autonomous behaviours, and coupled DNA tweezers with oscillating systems. You will find more details at PNAS, 108, E784-E793 (2011) but essentially, they used transcription and RNA degradation reactions to induce, under the right conditions, the periodic opening and closing of DNA tweezers, making for a synthetic transcriptional clock.

There was also quite a lot of talk of cell studies — which perhaps shouldn’t be surprising as we are, after all, discussing DNA here. When it comes to therapeutic applications though, as William Shih mentioned, it is great to have new drugs but the hurdle we need to get passed is their delivery — how to get them in the cells? And so he’s exploring how the shape, size and function of DNA items affects the rate at which they are internalized.

The wide variety of DNA assemblies presented leaves no doubt that the field will only continue to get more exciting, and I look forward to seeing these developments and further branching out. I have to say as well that, for me, all of this made all the more exciting by being hosted at the Shanghai synchrotron facility!

Anne

 

Anne Pichon (Associate Editor, Nature Chemistry)