Nature Chemistry, volume 1, issue 1

The first issue is now live, and freely available for everyone to read and (hopefully) enjoy.

Stu and Gav are flying off to Salt Lake City as I type for the Spring ACS Meeting. And tomorrow, Anne goes to Tokyo to work there from now on, and will also be visiting the Japanese Chemical Society Meeting starting next week. Feel free to visit the stand at the ACS exposition or to chat to the editors as they make their jetlagged way around!

I shan’t copy and paste the entire table of contents here, but apart from what will be the usual mix of research articles, reviews, news & views and research highlights, there are a few extras that I’ll draw attention to.

Most apt to The Sceptical Chymist is Blogroll – it’s tucked away in a column next to the Research Highlights and is a quick overview of what’s caught our eye in the blogosphere recently. Who knows, one of your posts or comments could be in there…

One of the most exciting things in the first issue is the feature The future of chemistry. We asked eight leading lights to write about what they see as the future of their discipline and it adds up to a very interesting read.

Finally, as is really well outlined by Egon at Chem-bla-ics, lots of the papers contain data-rich ‘compound pages’. In them you can click on a bold compound number to view a full structure, with InChIs, links to PubChem, etc.

But wait, there’s more! Some of the papers have even more than that. If you click on the ‘Show compounds’ link in the right-hand navigation, compound names in the text will appear highlighted. Clicking on them then reveals links to PubChem and ChemSpider. Thanks to everyone who commented on our previous posts – the feedback was listened to.

So there we are! Almost 14 months since Stu became Chief Ed, ~50 weeks after Gav, Steve and I started, ~6 months after Anne started and at the end of our Technical Editor, Laura’s 3rd week, we have an issue. Apparently, we have to do this EVERY MONTH!

Neil

Neil Withers (Associate Editor, Nature Chemistry)

Reactions – Stuart Cantrill

[To celebrate the first issue, this week our very own Chief Editor answers the questions]

1. What made you want to be a chemist?

Probably the fact that I found physics too boring and maths too easy — neither of which remains the case today. My first stint at university lasted a little less than 2 weeks; I went to do a Physics & Astrophysics degree at Birmingham and when I got there I discovered that I had made a terrible mistake. After a much-needed ‘year out’, during which there was actually very little ‘finding myself’ or indeed soul searching of any kind, I just plumped for one of the other two subjects I had studied at A-level… and the one I found most challenging was chemistry, and so that was that. I was hooked after the first day of class, when a certain (not-then-Sir) Fraser Stoddart ripped up the syllabus and instead of teaching us the basics of stereochemistry, told us all about Olympiadane and other interlocked molecules…

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

Maybe a chef — because that’s essentially chemistry, but you can eat the results. That being said, I’m far too fussy an eater so it probably wouldn’t go well. Obviously in an ideal world I would be a centre-forward playing for Manchester United, but there are many reasons why that never came to pass — mostly because I’m not all that good at football and I have dodgy knees… If I’m being realistic, let’s say an author — I’d quite like to write a book or two.

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

The next issue of Nature Chemistry, and to fame and fortune!

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

This is a tough one — and generally the answer I enjoy reading the most in other Reactions pieces. So, I’m going to cheat, as a few have, and host a dinner party with more than one guest. The first two guests I would invite are Queen Elizabeth I and Queen Elizabeth II — monarchs of England (and other associated lands at various stages). I’d just sit back and let these two remarkable women, who have ruled over this country in times that are roughly four centuries apart, compare notes on their experiences. Oh, and just because I probably won’t get to answer this question again, I’d have to invite along Douglas Adams — a fantastic author with an imagination that is out of this world and a sense of humour beyond compare.

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

Probably at Caltech in early 2003, and I bet it was a ring-closing metathesis reaction, but I can’t be 100% sure… it was also likely done in an NMR tube and led to an Angewandte paper if it’s the one I think it was.

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

Well, assuming I have the standard texts that one is allowed in situations like this, including the first print issue of Nature Chemistry, I’m afraid I’m going to have to cheat again on the book front. I first read Tolkien’s The Lord of the Rings aged 10, and I couldn’t not take my dog-eared copy with me. But, one of the best books I’ve read in recent times — and one I’m still getting my head around — is The Time Traveler’s Wife by Audrey Niffenegger. For reasons I won’t go into, I finished it while sitting in a deck chair outside a beach hut in Mexico as I watched the sun rise — and it just seemed like a wholly appropriate setting.

In terms of an album… hmm… ask me on a different day and I’m sure you’d get a different answer. So, I’m going to sort of cheat again… if I’m allowed one CD, I’m going to burn 18 different tracks on it… and it would likely contain some of the following: U2, R.E.M., James, New Order, Depeche Mode, The Cure, Manic Street Preachers, Snow Patrol, Nine Inch Nails — and, for those more thoughtful moments, a little bit of Beethoven, Tchaikovsky and Mozart.

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

Robert Burns Woodward, but since he’s no longer with us, it might be difficult. Living chemists… how about: Barry Sharpless, George Whitesides and E J Corey.

Stuart Cantrill is the Chief Editor for Nature Chemistry.

Chemiotics: Binding physicality rather than chemicality

Posted on behalf of Retread

Organic chemists love mechanism, subtlety and specificity. Books have been written about pushing arrows. Medicinal chemists are always worrying about making molecules which they can dock into either the active site or an allosteric site of a target protein. The fit must be quite close, and a recent post over at In the Pipeline notes that ‘You’ll have whole series of compounds that have to have a methyl group at some position, or they’re all dead. Nothing smaller, nothing larger, nothing with a different electronic flavor: it’s methyl or death.’

So making an organic molecule that responds to the physical properties of its surroundings – rather than the bonding structure of the molecules surrounding it – stands this sort of work on its head. As usual, nature got there first. Here are two examples.

Cells need to respond to the amount of cholesterol they contain, and make more if lacking. Cholesterol is poorly soluble in water, being found mostly in membranes. Here cholesterol functions as a fluidizer, making the long hydrocarbon chains of phospholipids and other lipids more disordered in order to fit around it. So cholesterol doesn’t exist just to make pharmaceutical companies rich. A similar mechanism probably explains why unsaturated fatty acids (such as oleic acid) found in membranes have cis rather than trans double bonds (and in the middle of the chain to boot), making them harder to pack.

So if your membranes have less cholesterol they become stiffer. This stiffness is sensed in some way by several membrane embedded proteins (SCAP, INSIG1). SCAP then moves SREBP, another membrane embedded protein (along with its associated membranes) to another site in the cell where it is cleaved. It took years to figure out how water got inside the hydrophobic environment of the membrane to cleave (hydrolyze a peptide bond) SREBP. One of the SREBP cleavage products is then able to leave the membrane, migrate to the nucleus, bind to DNA and turn on genes in the cholesterol synthesis pathway. Elegant no?

A second example. The DNA in our cells is under constant chemical attack. Ultraviolet light produces cyclobutane dimers of adjacent pyrimidine nucleotides. Nucleotides fall off the backbone or have attached molecular fragments which alter their stereochemistry. Then there are the mismatches (an A or a T pairing with G rather C etc., etc.). Somehow, proteins scan DNA for these lesions (and find them). One such protein complex is DDB1/DDB2 (see here and here) which recognizes a very broad range of DNA lesions which are subsequently targeted for repair. DDB1/DDB2 binds to pyrimidine dimers (which distort the helix) and to DNA with crosslinked bases (e.g., due to cisplatin, psoralen), and also to DNA lacking nucleotide bases (just the opposite of crosslinked DNA).

How can one protein complex do all this? One theory has it that DNA lesions are recognized by their increased flexibility (because of decreased stability of base pairing and stacking in damaged DNA). This enables DNA lesion finding protein complexes such as DDB1/DDB2 to target a broad range of DNA pathologies for repair (without recognizing them specifically). They are binding to the effect of chemistry, rather than the chemistry itself, e.g., they are binding to a physical property of damaged DNA rather than its chemical structure.

Only the chemist can fully appreciate the wonder of what’s going on under the cellular hood. In this we are fortunate, even if regarded as somewhat grubby by everyone else. Pascal’s thinking reed and all that.

Materials Girl: How time flies

Posted on behalf of Materials Girl

So… it has sadly been ages since I wrote a post for TSC. Finals for winter quarter are rapidly approaching, and unlike Stu, I don’t have the legitimate reason of starting up Nature Chemistry. It’s just been long hours in class/lab and late nights spent writing lab reports or essays – nevermind battling senioritis. (The latter is especially difficult these days as my peers on the semester system are preparing for graduation, while the rest of us will be in school through June).

At the beginning of my undergraduate studies, the difference in academic standards between high school and university came as an unexpected shock. It felt as though that nothing could upstage the difficulties of earning all As instead of A-minuses. Now, those gruelling undergrad o-chem labs seem trivial and writing a 10-page paper in any subject is more of an extended frustration than a hair-ripping horror (although theses still scare me). With whatever wisdom my 3.5 undergraduate years have imparted, I have: 1) discovered that constantly working hard is a given, 2) come to terms with “bad” grades, and 3) learned the importance of higher education in the sciences.

This raises a subject that has lately piqued my curiosity: It comes without saying that a majority of chemists need graduate degrees, but how important is it to have them from a top university, renowned advisor, or an especially demanding program? It’s been said that the undergraduate institution attended is of relatively little consequence, but will the name of my graduate school make a real impact on my future prospects?

Reactions – Jacob Klein

1. What made you want to be a chemist?

I am not “really” a chemist, since I both read for my first degree and carried out my PhD in the Cavendish, the University of Cambridge’s physics department, where I was later on the faculty. And what made me want to be a physicist was an inspiring high-school teacher. But the beauty of modern scientific research is that traditional areas overlap and have merged fruitfully; so that despite my physics background, I work in a department of materials research in a chemistry faculty at the Weizmann Institute, and was for many years the Dr. Lee’s Professor of Chemistry at Oxford University, as well as being head of Oxford’s Physical Chemistry Department.

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

I very much enjoy explaining to young people and making them aware of the physical world – which I had opportunity to do through my own children in their schools. I would be a teacher.

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

Many of the world’s really large problems – clean energy shortages, global warming (related of course), prolonging and improving people’s health, and others, are already being addressed by chemists in the broader sense.

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

If the sky is the limit (as it were): Jesus of Nazareth. I would like to discuss directly with him what his views were, in the light of later interpretations…

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

In the mid-1990’s, many years after being promoted full professor and heading a relatively large research group, I was still doing my own all-night (surface-forces) experiments with a student or a postdoc for company (night is the best time as ambient vibrations are at a minimum). More recently I go into the lab frequently to look at the experiments, twiddle the knobs (mandatory!), and look through the eyepiece at moving optical fringes…

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

Tolkien’s Lord of the Rings. I read it page by page to each of my children in turn when they were young, and a few times on my own account, and the world it creates is still vibrant. For music – Vivaldi’s Four Seasons, especially useful for a desert island.

Jacob Klein is in the Department of Materials and Interfaces at the Weizmann Institute, and a Professorial Research Fellow at Oxford University. He researches the properties soft matter, in recent years especially the behaviour of highly confined complex fluids and the molecular basis of biological lubrication.

It’s all going on…

Following the lead of Nature Materials, we’ve gone and got a Twitter feed. I don’t know if we really know what to do with it yet though! Feel free to follow us, and suggest what we should use it for. Maybe when we’re all out and about at conferences later in the year it’ll be more useful.

Meanwhile, our latest paper published online has received a pleasing amount of coverage in the wider press, including C&EN, Chemistry World, the MIT Tech Review and even the New York Times. Now you’ve read the journalists’ take, make up your own mind about attolitre reaction vessels from polymer nanofibres.

Even with all this going on we certainly haven’t forgotten to bring you our latest picks of the pops in the form of Research Highlights. This week we feature five-fold symmetric corannulenes forming 2D crystals, how the surface oxygen coverage of gold catalysts influences their selectivity and how polymers can act as a TLC-like ‘stationary phase’ and separate NMR spectra of mixtures.

Phew. Easily sailing into this week’s ‘And finally…’ section is the Nano Song. This simply wonderful music video is an entry for the ACS Nanotation ‘What is “nano”?’ competition. Go and vote now!

Neil

Neil Withers (Associate Editor, Nature Chemistry)

Reactions – Xueming Yang

1. What made you want to be a chemist?

I was really lucky to have an outstanding chemistry teacher during my high school years. Her name is Yueming Chen. High school time was pretty tough for because of my family background during the period of cultural revolution, Mrs. Chen was a very good chemistry teacher and also very caring. I just fell in love with chemistry. Even though I got my bachelor degree in physics, eventually I found my way back to chemistry.

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

I think I would become an mechnical engineer. I really love designing and building machines, and I feel I am pretty good at this. This ability and interest actually help me greatly in doing my own chemistry research.

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

I think chemistry is a very unique field that could make fundamental impacts on our everyday life. I believe that chemistry has also a unique position in solving our most urgent problems in the world, such as energy shortage and environmental problems because chemists have the tools and ability to understand these processes at the most fundamental levels as well as to create new materials that are often required in solving problems. However, we do need to avoid creating more long term problems in solving the most urgent problems.

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

I would really love to meet Deng Xiaoping. I think he is a great man that has changed many people’s life including mine in a fundamental way. I would want to thank him personally for what he has done for China and its people.

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

I really don’t like to answer this question because this question reminds that I have not done a whole experiment for a long time. I think the last time I did a whole experiment was about 9 years ago. The experiment was water photodissociation. But to be fair, my best time at work even now is with those students who are doing experiments.

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

I would like to bring a big book of papers with nothing on it so I can make drawings or write something everyday for a long time. A CD of Erhu (Chinese violin) music by the famous blind musician Ah Bing, Reflections of the Moon on the Water of Erquan. A beautiful sad and peaceful music. You will never be really tired of this music when you are alone.

Xueming Yang is in the State Key Laboratory of Molecular Reaction Dynamics at the Dalian Institute of Chemical Physics and works on spectroscpopy and chemical dyanmics in the gas phase as well as on surfaces.

Chemist challenged

It probably hasn’t escaped the notice of UK-based readers that the winners of University Challenge, Corpus Christi College, Oxford, have been stripped of their crown, after it turned out that one of the team was no longer a student when the final rounds were filmed.

The guilty party was studying chemistry (I read somewhere that he got a first) and graduated after the first two rounds had been recorded. This has attracted vast swathes of media attention, partly because the final itself was jolly exciting and partly because of the media coverage of the vastly intelligent love/hate figure, Corpus Christi captain Gail Trimble. Check out some of the clips on YouTube.

Apart from the reasonably tenuous link to chemistry, I thought this needed blogging about (not just because I was once on the show – and I managed to read and understand the rules) because it reminded me of the host, Jeremy Paxman, and his generally poor knowledge of science (compared to his impressive knowledge of other areas).

Some lapses, like the 2 or 3 takes pronouncing ‘superfluidity’, I can forgive, but all too often he gives teams the points for science answers that are just wrong, but sound a bit similar. Such as ‘momentum’, when the answer was ‘angular momentum’. He’d never let them get away with saying Anne Brontë, not Emily, wrote Wuthering Heights. I suppose it’s another reflection of The Two Cultures – but that doesn’t mean to say I have to like it!

Other angles you might like to discuss amongst yourselves: someone with a first in chemistry from Oxford goes to work for PWC, even in today’s credit-crunched climate, happily abandoning science for accountancy. Oxbridge colleges getting separate entry into University Challenge. Would the media whirlwind around ‘cleverest ever contestant’ Gail Trimble have been so frenzied had she been male? I can practically hear the dissertations being written across the country!

To shoe-horn in some proper chemistry, I’ve noticed that both Chemistry World and Angewandte Chemie have articles about the periodic table (subscriptions required for both). The CW one is slightly lighter reading, so I haven’t got through the Angewandte one just yet. But it’s interesting to see slightly different takes on this icon of chemistry. Here’s a trivia snippet to whet your appetite: it was only in the 1940s that Glenn Seaborg rescued the actinides from being ‘inner transition elements’.

Neil

Neil Withers (Associate Editor, Nature Chemistry)

Microtubes on YouTube

Our second research article went live yesterday evening – this one about how you can grow microtubes from polyoxometalate crystals. You can control the direction in which the tubes grow and also how big their diameters are – and to show they are structurally sound, you can flow fluorescent dye through them.

Lee Cronin and colleagues have put up a video on YouTube showing how the tubes can be grown – have a look if you get the chance… there are also a collection of videos associated with the paper as part of the Supplementary Information.

Stuart

Stuart Cantrill (Chief Editor, Nature Chemistry)