Reactions – Dongyuan Zhao

1. What made you want to be a chemist?

When I was an undergraduate, I spent much of my leisure time in a chemistry lab because of my great interest in various fantastic chemical reactions. In my Ph.D. studies, I began research work on molecular sieves due to my supervisor’s suggestion. At that time, I was attracted by the magical porous materials which made me go further along this way.

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

I like the kind of work where I can invent and create with my head and hand, and enjoy the whole process from raising ideas, to drawing papers, and to making the final objects. Indeed, if I wasn’t a chemist, I have a dream to do detective work like a policeman, because investigating and solving a law case is similar to scientific research. I like to ask myself questions and understand why.

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

Generally, there are two points: vision and ability. A chemist must stand higher to have a panoramic view of the world and make some judgments and predictions. At the same time, he should have certain abilities to realize those ideas.

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

It must be Edison, my idol, the most outstanding inventor in the world. I wish we could share some ideas and opinions with each other, especially the unsuccessful experiences in our careers. I wonder if I am similar to him…

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

In 2007, I made some attepmts to scale up the production of FDU-15 by myself. After so many years of experience of small-scale laboratory syntheses, I am now paying more attention to the production of new materials on a large scale, which is the prerequisite to their real applications.

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

The book, Advanced Inorganic Chemistry, by F. A. Cotton and G. Wilkinson should be with me all time, which would take me far from loneliness and sadness, and bring the happiest time with me. The symphonies of Beethoven, the greatest German composer, would always encourage me to face and overcome the difficulties encountered.

Dongyuan Zhao is in the Department of Chemistry at Fudan University, and works on the development of novel synthesis/assembly methods for microporous molecular sieves and mesoporous materials, and the exploration of their properties and applications.

Chemiotics: Sherlock Holmes and the Green Fluorescent Protein

Posted on behalf of Retread

Gregory (Scotland Yard): “Is there any other point to which you would wish to draw my attention?”

Holmes: “To the curious incident of the dog in the night-time.”

Gregory: “The dog did nothing in the night-time.”

Holmes: “That was the curious incident.”

The chromophore of green fluorescent protein (GFP) is para-hydroxybenzylidene imidazolinone. It is formed by cyclization of a serine (#65) tyrosine (#66) glycine (#67) sequential tripeptide. It is found in the center of a beta barrel formed by the 238 amino acids of GFP.

What is so curious about this?

Simply put, why don’t things like this happen all the time? Perhaps nothing quite this fancy, but on a more plebeian level consider this: of the twenty amino acids, 2 are carboxylic acids, 2 are amides, 1 is an amine, 3 are alcohols and one is a thiol. One might expect esters, amides, thioesters and sulfides to be formed deep inside proteins. Why deep inside? On the surface of the protein, there is water at 55 molar around to hydrolyze them purely by the law of mass action (releasing about 10 kJ/Avogadro’s number per bond in the process). Some water is present in the X-ray crystallographic structure of proteins, but nothing this concentrated.

The presence of 55 M water bathing the protein surface leads to an even more curious incident, namely why proteins exist at all given that amide hydrolysis is exothermic (as well as entropically favorable). Perhaps this is why proteins contain so many alpha helices and beta sheets — as well as functioning as structural elements they may also serve to hide the amides from water by hydrogen bonding them to each other. Along this line, could this be why the hydrophilic side chains of proteins (arginine, lysine, the acids and the amides) are rather bulky? Perhaps they also function to sterically shield the adjacent amides. After all, why should lysine have 4 methylene groups rather than just one or two?

Now the serine-tyrosine-glycine tripeptide should occur by chance once in every 8000 tripeptides. The SwissProt database of proteins contains 144,041,553 amino acids in 399,749 proteins as of 14 October. Does this tripeptide occur 18,805 times in the database as it should? If it doesn’t, is negative selection preventing it? If it does occur this often, have we missed other chromophores? Are there other tripeptides missing from SwissProt? If there are, does this tell us how to build other chromophores? Or does it tell us something important about protein structure?

I don’t have the skills to properly interrogate SwissProt or the Protein Data Bank, but I imagine that some of the readership does. Go to it. These are curious incidents indeed.

Hic!

Thanks to a comment by John Brockley on a New Scientist story about hoaxes, I’ve just discovered a fascinating paper. I’ve only got an abstract of it, published in The Analyst in 1944 (vol. 69, p. 97 – possibly free access thanks to the RSC’s archive), because the original work was published in Bull. Bureau Chemical Investigation (New York State Police, Dec. 1943, 8). I don’t think we subscribe!

Anyway, the article: Toxicological Significance of Laevorotatory Ice Crystals. The researcher, J. Beeman, isolates laevorotatory (left-handed) ice crystals from the right-handed by dissolving them in alcohol. “Quantitative toxicity studies showed that laevorotatory ice had a toxic index of +3.45 and the dextrorotatory ice an index of -3.45.” The left-handed crystals were injected into animal subjects, and they showed some quite unpleasant symptons: “diarrhoea, foul breath, rapid pulse and bulging eyes”, as well as being ‘extremely irritable’.

Now for the fun part: human subjects! “In human expts. 1 litre of commercial brandy was ingested in 3 hr. in 60-ml doses with a 2.5-cm cube of [left-handed] ice.” Perhaps unsuprisingly, the subjects showed some pretty extreme symptoms! “In the acutely poisoned subject, the sight and odour of an alcoholic beverage produced reflex nausea; in some cases the subject developed a split personality.” Fortunately, “Relief was afforded by cold milk and by aspirin (0.3g every 30min.).”

One litre of brandy! Can you imagine doing that experiment?! My mind is boggling. So next time you’ve got a hangover, blame the ice cubes…

Neil

Neil Withers (Associate Editor, Nature Chemistry)

Materials Girl: Scientific debate

Posted on behalf of Materials Girl

It’s late October, I’m running on ~7 hours sleep for the last 48 hours, and deadlines are fast approaching (not to mention my quantum midterm in 2.5 hours)! Must… sleep… study…

My original intent – up until yesterday when my parents offered a “bribe” for staying in school – was to get a job after I graduate next June. After getting that “break” for a year or two, I could head off to grad school. I’ve already started sending off resumes to big companies… Considering the new aforementioned development, however, I’m considering staying at my university for a Master’s in materials science & engineering – possibly ceramics, in which case I have to study for the GRE and write essays now!

So the debate in question is: break to work or grad school ASAP? I’ve heard a few arguments, but not much from scientists. Go!

NChem Research Highlights: Bimetallic nanoparticles, oxo complexes and those blue bananas

Greetings blogateers, welcome to another batch of Research Highlights.

Busy week for Gabor Somorjai: paper in Science, featured in C+E News editorial, now a Nature Chemistry Research Highlight! Gav covers the work, which used ambient-pressure XPS to discover that bimetallic nanoparticles essentially turn inside out in different conditions.

Someone else with a busy week was David Milstein, who had a paper in Big Nature, features in this week’s ChemPod (which itself features in C+E News) and now in a Research Highlight. Oxo complexes are believed to intermediates in lots of crucial catalytic processes, but isolating complexes has been extremeley difficult – find out how here.

Picking up almost as much attention is our final piece: did YOU know that bananas fluoresce blue under UV light – but only when they’re ripe?? It’s quite amazing to think that in all the years that humans have had UV lights no-one’s noticed this before!

And in this week’s prize for Press Releases with Staggeringly Tenous Links to Chemistry, the RSC win again! To add to the annals of cringe (Sherlock Holmes, ‘on-screen chemistry’, football managers chewing gum, Carol Vorderman in mauve…), there’s a competition that manages to shoehorn chemistry into the Italian Job. You can win a trip to Turin, so it’s almost worth gritting your teeth and having a go. Do remember that submissions must “be based upon the principles of serious scientific rigour” (whatever that means), helicopters aren’t allowed, and you can’t use what Michael Caine has revealed would have been the real ending. And they got the quote wrong – spotter’s badge to film-boy Ed.

Neil

Neil Withers (Associate Editor, Nature Chemistry)

Bumper ChemPod edition

The latest edition of the ChemPod is now live and can be found here.

In the main show we meet the researchers who’ve created a colour-changing polymer that could be used in electronic books, celebrate the extraordinary life and work of ‘Mr Stereochemistry’, survey the organo-catalysis landscape, and find out what’s been reinvigorating the field of metabolomics. Plus we hear from one of this year’s Nobel Prize winners.

In a bonus ChemPod Extra, you can hear the full interview with Martin Chalfie – who has just been awarded a Nobel Prize for the discovery and development of GFP – in which he tells us how he found out that he’d won the Prize, how he first came across the protein and what a fantastic tool it has become, with new applications still being invented today.

Enjoy!

Stuart

Stuart Cantrill (Chief Editor, Nature Chemistry)

Reactions – Daniel O’Leary

1. What made you want to be a chemist?

I entered college wanting to be a biology major and took two years of introductory chemistry to satisfy the biology degree requirements. I then had a fantastic summer undergraduate research experience and learned how to study a biological system with nuclear magnetic resonance. That project solidified my interest in biology and showed me that if you really want to get to the bottom of a biological process, then you had to understand the chemical factors at play. Majoring in chemistry was a logical next step.

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

I have a cousin who works for the Alaska department of fish and game. He spends many of his days outdoors and on the water, conducting surveys of fish and shellfish populations. For a person with my eating habits, this job would be the equivalent of a kid working in a candy store-except that it involves SCUBA diving, so you get to stay in shape and see beautiful sights!

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

This is a no-brainer-we need to figure out how to power the planet with processes that don’t use fossil fuels. As this problem won’t be solved overnight, chemical educators need to realize that it’s the kids sitting in the lecture hall who will solve this problem, not us. We need to inspire them to join the effort.

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

The Oregon distance runner Steve Prefontaine. Why? He was all about hard work, dedication to the cause, mental and physical toughness, teamwork, and friendship. His talent electrified the nation and helped inspire the running boom of the 1970’s. The evening would start off with 400 repeats on Hayward Field and be followed with a nice meal and quite a few beers. I’ve been searching for a good reason to get back in shape, and this would probably do it.

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

Just this past week, I spent some time working with a student on the NMR spectrometer. In a collaboration with Scott Miller’s group at Yale, we are trying to determine the solution conformation of a peptide with interesting catalytic activities. One of the reasons why I decided to teach and do research at a primarily undergraduate college is that I enjoy being in the lab and work closely with students.

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

I’d want to start my exile with some laughs and memories from a prior life, so the book would be Richard Russo’s Straight Man. The CD would be recordings of the collected speeches of John F. Kennedy. I figure that getting out of exile would quickly rise to the top of my ‘to do’ list, so I would not want to sit around listening to music. Kennedy’s speeches get my adrenaline flowing and I would need bursts of energy to live my new life in a Bear Gryllsian manner. If my attempts to get off the island fail, then I would sit on a rock and repeat, from memory, Kennedy’s “Radio and Television Report to the American People on the Soviet Arms Buildup in Cuba.” There’s a lot of good scolding in that speech, and something tells me that I would be in a scolding mood if I couldn’t get off the island!

Daniel O’Leary is in the Department of Chemistry at Bowdoin College and uses NMR spectroscopy and synthetic organic chemistry to study hydrogen bonding and aspects of peptide conformation.

Journal journeys: Day 266, We’re hiring!

So, we’re 266 days in. Or at least Stu is – Steve, Gav and I are just over the 6 months mark (crucially past our “probation” period, which means we’ve got to screw up REALLY REALLY badly for Stu to sack us!). How do you think we’re doing?

So far we’ve: racked up a lot of airmiles, enthused about the journal to lots of people, argued among ourselves (and yourselves) about what we want the articles to look like, welcomed the fifth editor and most importantly opened the doors to papers.

As the papers walk the tightrope of peer review and we get closer to our first issue, we need people to handle the papers once we’ve accepted them. Specifically, an Art Editor and a Technical Editor (oddly, I can only find the job at the Guardian, but I assure you we really do need one).

The Art Editor will ‘liaise constructively with editorial colleagues [us!] and suppliers to produce striking and attractive artwork for the journal’. As you might expect, ‘They must also be highly proficient in Illustrator, Photoshop and InDesign/QuarkXPress. Two years’ experience in magazine publishing is essential [… and k]nowledge of Chemdraw and/or prior experience on chemistry publications would be an advantage.’

The Technical Editor ‘will be responsible, with other parts of the company, for developing our technical editing tools and workflows, as well as ensuring published manuscripts ‘lead the way’ in chemistry publishing’. So do you ‘have a good degree in a chemistry related subject and enjoy attention to detail.’? Relevant experience would be an advantage. The post isn’t just Nature Chemistry either, it’s for a range of Nature journals.

The deadlines are pretty soon, but dust off those CVs and get applying! One thing that isn’t mentioned in the job ads is the free canteen, or the weekly cake competition. How can you say no?

Neil

Neil Withers (Associate Editor, Nature Chemistry)

System requirements

Our November issue is out, and it’s a focus on chemical systems biology. My colleague Joanne points out that, from cell phones to social networking and even to Nature Network, life is increasingly interconnected. Thus, this focus issue highlights how networks are coming to chemical biology – and chemists to systems biology.

Do you think, as Randy Peterson suggests, that chemical biologists have reductionist tendencies? As Andrew Hopkins writes, is network pharmacology going to be the next era in drug discovery? What systems are you interested in, and more broadly, how do you define a systems approach? Finally, what do you think of our new term (chemical systems biology)? What terms have you coined, or would like to?

All this reminds me that I’ve still got to figure out a system for organizing the papers on my desk. So, I’d better get to it!

Catheirne (associate editor, Nature Chemical Biology)

NChem Research Highlights: Bidentate ligands, squares and chirality

Monday morning usually means a big jug of coffee, discussions about points accrued over the weekend in the Nature fantasy football league and of course… Nature Chemistry Research Highlights.

First up, Steve discusses studies on the unexpected reactivity of bidentate ligands, carried out in my beautiful hometown of Durham.

Neil writes about a technique for creating nanoscale square patterns using the supramolecular assembly and controlled phase separation of diblock copolymers.

And Anne describes research that shows the transmission of chirality from a monomer to a solid mesoporous material during its polymeric synthesis.

And finally, since the closest I get to doing experiments these days is playing around in my kitchen (and as announced on the last ChemPod, I honestly do wear my Nature Chemistry lab coat when cooking) an interesting “”https://www.wired.com/techbiz/startups/magazine/16-10/pl_create">taster" for a book called “The Hungry Scientist Handbook” caught my eye in Wired magazine.

Using kitchen equipment for science seems to be the order of the day. Over at Chemical Technology (once edited by our very own Dr. Withers) they’ve just published a story called “Lab-on-an-egg-beater”.

Gav

Gavin Armstrong (Associate Editor, Nature Chemistry)