The University of Alabama, Tuscaloosa; Queen's University Belfast, Northern Ireland

A chemist believes that an ionic liquid is the place for a noxious gas.

As a 'green chemist', I worry about the potential dangers of moving toxic and flammable gases around. Most nasty gases are transported in pressurized canisters to save space, posing the risk of hazardous compounds being expressed over people and pleasant greenery on the rare occasions that a container breaks.

Recently, some scientists at Air Products and Chemicals, a chemicals supplier in Allentown, Pennsylvania, found a way to store phosphine (PH3) and boron trifluoride (BF3) — both toxic gases — in ionic liquids, and then recover the gases without introducing impurities (D. J. Tempel et al. J. Am. Chem. Soc. 130, 400–401; 2008).

The advantage of transporting gases in ionic liquids is that many such liquids have no measurable vapour pressure. So were a container to burst, the gases inside it would remain as chemical complexes in a liquid state, making them much easier to mop up. Furthermore, ionic liquids can be recycled in subsequent shipments.

Dan Tempel and his team used a computer model to consider two ionic liquids — the cation 1-butyl-3-methylimidazolium paired with either Al2Cl-7 and Cu2Cl-3 — for phosphine transport. They then tested the latter in the lab; the positively charged copper atoms bound the lone electron pair on phosphine. Similarly, the electron-deficient boron atom in boron trifluoride facilitated the formation of a covalent bond with a fluorine atom in another ionic liquid, in which the same cation is paired with BF-4.

In both cases, more than 90% of the ionic liquid's reactive sites formed complexes at room temperatures. This means that relatively small volumes of ionic liquids could move a lot of toxic gas around. I think this could revolutionize the industry.

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University of Colorado, Boulder

A biologist looks to 'click chemistry' for better three-dimensional tissue models.

A hot topic in organic chemistry is the development of ways to neatly home in on a particular chemical group and cause a reaction to proceed extremely efficiently under mild conditions. Such highly optimized reactions have been grouped under the term 'click chemistry'. A commonly cited example involves functional groups called azides and alkynes, which react to form triazoles with the aid of a copper catalyst.

Click chemistry has all sorts of uses, although few are in biology because the technique relies on toxic metal catalysts. However, Carolyn Bertozzi and her colleagues at the University of California, Berkeley, and the nearby Lawrence Berkeley National Laboratory recently demonstrated copper-free click chemistry in a living system (J. M. Baskin et al. Proc. Natl Acad. Sci. USA 104, 16793–16797; 2007). These authors selectively — and rapidly — labelled cell-surface polysaccharides with with triazole bound to a fluorescent probe. The technique allows real-time imaging of cell surface molecules that are otherwise impossible to achieve.

This research throws open the door for a host of new applications for click chemistry. As a tissue engineer, I am particularly excited about exploiting it to make better gels for three-dimensional cell culture.

Physiological processes are routinely guided by interactions between cells and their tissue environment. Thus, a major hurdle in tissue regeneration is knowing which biochemical signals must be recapitulated in cell culture, and how to present them at the appropriate time and place. Copper-free click chemistry could allow scientists to synthesize materials that deliver these signals at times that are governed by the physiological conditions in which the material resides. Next on my wish list is the ability to control the spatial organization of these reactions.

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Ecole Normale Supérieure de Lyon, France

A geochemist goes à la recherche des climats perdus.

As a young postdoc at the California Institute of Technology (Caltech) in Pasadena I remember glancing through the 1952 logbook of a gas mass spectrometer while the machine readied my samples. In the book, Sam Epstein, one of the founders of modern geochemistry, had scribbled numbers representing the first attempt to determine past temperatures from oxygen-isotope abundances in fossils.

Since Epstein's measurements, the abundance of oxygen-18 in the carbonate skeletons of fossil sea creatures has become a broadly used indicator of past ocean temperatures. Such data are key to understanding modern climate change. But the usefulness of 18O in 'palaeothermometry' is limited by problems including variations in oxygen-isotope levels in sea water and in the way different organisms take up the isotopes.

Recently, a group at Caltech proposed a measurement that may work better. As before, the carbonates are broken down into carbon dioxide for analysis. Instead of looking only for molecules containing 18O, the Caltech team measures the abundance of molecules that contain both 18O and the uncommon carbon isotope, carbon-13. The excess of this species over what would be expected through random combination of carbon and oxygen atoms indicates the temperature at which the carbonate formed.

Early tests of this 'clumped' thermometer on corals and fish ear bones were promising (P. Ghosh et al. Geochim. Cosmochim. Acta 70, 1439–1456; 2006; and Geochim. Cosmochim. Acta 71, 2736–2744; 2007). Since then, the method has provided a new record of ocean temperature during the Palaeozoic era, which began 543 million years ago (R. E. Came et al. Nature 449, 198–201; 2007).

I believe that clumped isotope thermometry is going to be a valuable new tool for palaeoenvironmental studies.

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Collegium Budapest, Hungary, and The Parmenides Foundation for the Study of Thinking, Munich, Germany

A theoretical biologist recommends thought-provoking reading on the origin of translation and the genetic code.

As Francis Crick and his co-workers once noted, "the origin of protein synthesis is a notoriously difficult problem". Our best hopes of resolving this problem begin, in my opinion, in an RNA world.

The RNA-world hypothesis holds that RNA emerged before DNA and proteins, neatly separating the origin of life from that of the genetic code and its translation. The question then becomes: how did RNA evolve to make proteins?

In a recent paper, Yuri Wolf and Eugene Koonin of the National Institutes of Health in Bethesda, Maryland, present one scenario (Biol. Direct 2, 14; 2007).

They rightly call attention to studies that suggest that protein-based aminoacyl-tRNA synthetases, which are involved in the first steps of assembling amino acids into proteins, are relatively late evolutionary inventions. This forces us to accept the idea that protein synthesis is older than such synthetases.

Before the evolution of synthetases, the only agents that could conceivably have marshalled amino acids are RNA enzymes, or ribozymes. Wolf and Koonin share my view that the recruitment of amino acids was driven by selection for enhanced catalytic activity, and that the ancestor of the large ribosomal RNA that catalyses protein synthesis in today's cells — a molecular 'fossil' — was a catalyst that linked only two amino acids.

I am less happy with these authors' suggestion of a relatively late switch from peptide-specific proto-ribosomes to those that could use an external template such as mRNA to synthesize peptides with arbitrary sequence — but they may well be right.

They lay out an evolutionary sequence that is more complete than the scenario I once proposed. I highly recommend this well-written, thought-provoking paper.

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University of Nottingham, UK

A champion of environmentally friendly chemistry encourages attempts to identify reactions ripe to be turned 'green'.

The aim of 'green chemistry' is to make the design, production and use of chemicals more sustainable. This means that, unusually for an academic discipline, industrial implementation is an inherent goal.

Research groups in this field, including mine, strive to reduce waste by identifying selective catalysts, alternative solvents or renewable feedstocks that could lead to new industrial processes.

But how do we choose which reactions to try to green? Some targets are obvious; the reactions are notoriously inefficient. However, many chemical manufacturers are understandably reticent about the shortcomings of their processes.

It was therefore particularly refreshing to find a paper that results from the collaboration of seven pharmaceutical companies and highlights key research areas for green chemists (D. J. C. Constable et al. Green Chem. 9, 411–420; 2007). The paper describes several classes of reaction that, if 'greened', would significantly lessen the pharmaceutical industry's effect on the environment.

For example, the paper asks that researchers develop methods to carry out oxidations safely in non-chlorinated solvents (chlorinated solvents are non-flammable but toxic); or to find ways to tame the fearsome reactivity of fluorine so that fluorination occurs selectively.

Another clear message is that new strategies for using solvents could lead to substantial reductions in waste. Could reaction vessels be cleaned out at the end of a process without using organic solvents?

This paper is a great start, but I think the authors have been too conservative. They could have asked for more, such as catalysts that can trigger two or more reactions in sequence. We need really tough challenges to intrigue academic chemists and bring new blood to the task of greening chemistry.

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University of California, Berkeley, USA

A biochemist marvels at a molecule that shares his love of playing with fire.

I like to capture my students' attention by recounting how my early fascination with fire inspired my interest in the stability of sugars.

Glucose will 'burn' to carbon dioxide and water, liberating lots of energy. But it is stable enough that you can stamp on it without triggering the reaction — the energy barrier to the reaction is too high.

In my research, I am interested in how biology harnesses and controls oxygen reactivity. Most reactions, such as burning glucose, are held back by an energy barrier to getting things started. Enzymes can bypass this, finding a lower energy route through some reaction intermediate, to carry out a 'controlled burn'. Their control is not perfect, sometimes causing damage to both themselves and surrounding molecules, but by and large it works.

Typically, these enzymes have metal or organic components, which drive the oxidation. I often tell students that enzymes need their metal and organic cofactors because the 20 naturally occurring amino acids cannot carry out all the chemistry. Two recent papers shake that belief.

The surprise comes from the enzyme DpgC, which is involved in the biosynthesis of the antibiotic vancomycin. The first paper (C. C. Tseng et al. Chem. Biol. 11, 1195–1203; 2004) reports that DpgC uses oxygen in a complex dioxygenase reaction with no bound metal or organic cofactor.

More recently, researchers reported the structure of DpgC and confirmed that it has no cofactor (P. F. Widboom et al. Nature 447, 342–345; 2007). They find that the enzyme has a structure known as an oxyanion hole, which helps to stabilize the reaction intermediate.

I am still amazed that DpgC does oxygen chemistry with no help — and my students should be too.

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University of Hyderabad, India

A chemist applauds an algorithm able to predict crystal structures from chemical composition alone.

I work in crystal engineering, a field that involves designing and constructing crystals with desired physical, chemical or pharmaceutical properties from small organic molecules. It is an experimental science based on pattern recognition and retrosynthetic strategies, in which the structure is considered as the sum of smaller, simpler parts.

Improvements to computational crystal-structure prediction could make design protocols more reliable. But this is such a difficult problem that only a handful of groups in the field work on it. In this context, I found a recent paper presenting a seemingly reliable method to be thought-provoking (A. R. Oganov and C. W. Glass J. Chem. Phys. 124, 244704; 2006).

Typically, crystal-structure prediction involves computer generation of putative crystal structures using a force field, which represents the interactions between atoms in neighbouring molecules. The correct structure is presumed to be that which minimizes the crystal's energy.

The procedure is problematic because the force fields may not be well tailored to the molecules being studied, and because the experimental structure may not be the lowest-energy arrangement. It is also impossible to explore all conceivable structures, which are mind-boggling in number.

Oganov and Glass use an evolutionary algorithm to localize the search to the most promising structures. Their approach is attractive in that it requires no system-specific knowledge — the input is just the molecule's chemical composition, not even its structure — and their ability to predict the unusual tetragonal structure of urea is impressive.

Is this the long-awaited breakthrough in crystal engineering? Perhaps not, but surely it's an important step forward.

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Nagoya University, Japan

A theoretical chemist compares love to hydrogen bonds.

Water molecules assemble into ice "palm to palm", like Romeo and Juliet on their first encounter. Each molecule reaches out to four neighbours, forming hydrogen bonds that lock the molecules into a tetrahedral network. And like the love of Shakespeare's pair, water's hydrogen bonds are resilient. Ice contrives to keep its network, even in the tightest of spaces.

Researchers recently predicted that ice constrained by a carbon nanotube's wall will form either tubular structures or intricate arrangements of double- and quadruple-stranded helices, depending on temperature, pressure and nanotube diameter (J. Bai et al. Proc. Natl Acad. Sci. USA 103, 19664–19667; 2006).

I have spent many years studying the structure and dynamics of water, but am still amazed by these luxuriant ice structures. Had computer simulations not shown how strenuously ice's network can adapt for its molecules to keep their four hands touching, we could hardly have imagined such structures would be possible.

Simulations have also predicted that confined ice can have two symmetrically different phases, which become deformed and indistinguishable when put under pressure (K. Koga et al. Nature 412, 802–805; 2001). So we expect that one type of ice will easily transform into the other through collective motion of its hydrogen bonds.

My prediction is that confined liquid water, which has a disordered network of hydrogen bonds, will undergo similar structural rearrangements. Molecular mechanisms may cause large changes to the network structure of water trapped in proteins or at membrane surfaces, for example. These studies could therefore help us begin to understand another intimate relationship — the relationship between water and life.

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The University of Tokyo, Japan

A chemist sees a commercial future for designer polymers.

Just over a decade ago, a discovery in polymer chemistry triggered explosive progress in macromolecular engineering. A trio of papers published last year will, I think, help to usher the benefits of this development into industry.

The results concern chemists' ability to grow tailored polymers, which have controllable size and architecture. Such polymers are becoming more and more important as major players in the burgeoning field of nanotechnology.

The original breakthrough was the development of a method known as atom-transfer radical polymerization, which made it easy to grow polymers to design.

The method uses a catalyst containing a transition metal, such as copper. The catalyst interacts with the polymer, turning it briefly into a reactive radical that will bind another monomer. Each molecule grows one step at a time, so producing polymers with uniform properties.

A problem with this method has been the large amount of catalyst needed to drive the reaction — leaving residues that are costly to remove. Two recent papers do away with this concern, cutting the concentration of catalyst required by up to 1,000-fold (W. Jakubowski & K. Matyjaszewski Angew. Chem. Int. Edn 45, 4482–4486, 2006; K. Matyjaszewski et al. Proc. Natl. Acad. Sci. USA 103, 15309–15314, 2006).

Another advance, which takes advantage of an unexpectedly active oxidation state of the catalyst's copper, will allow production of polymers with an ultra-high molecular weight and a narrow molecular-weight distribution (V. Percec et al. J. Am. Chem. Soc. 128, 14156–14165, 2006).

Some chemical companies are already setting up industrial plants to make polymers by atom-transfer radical polymerization. These developments mean that more are sure to follow.

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Massachusetts Institute of Technology, Cambridge, USA

A chemist predicts a bright future for sensors based on carbon nanotubes.

I am struck by the parallels between the development of polymer-based chemical sensors and those made from carbon nanotubes.

About ten years ago, I started to develop sensors from conjugated organic polymers, which took advantage of the materials' optical properties, rather than the electrical properties that had been exploited in devices until that time. This work led to fluorescent sensors, which are now being used in Iraq to detect explosives.

As with polymers, early work on nanotube sensors focused on detecting changes in a tube's electrical conduction when it binds to a molecule of interest. But electrical responses are sensitive to stray electric fields, which create interference in the signal.

Now, researchers working with nanotubes are also moving towards optical methods. A demonstration of a biosensor for glucose (P. W. Barone and M. S. Strano Angew. Chem. Int. Edn 45, 8138–8141; 2006) sets the stage.

To make the sensor, the team first attached glucose groups to nanotubes. They then mixed these nanotubes with a large molecule, known as concanavalin A, which can bind to four glucose molecules at once. The glucose-decked nanotubes end up caught in clumps around the concanavalin A, which attenuates their emission. This system is sensitive to glucose because any glucose in solution loosens the nanotube clusters, and so boosts fluorescence.

A significant advantage of nanotubes is that they emit near infrared light, a longer wavelength than that accessible with polymers. And it just happens that human tissue is almost transparent in this spectral region. As a result, sensors based on these materials might be used for in vivo clinical diagnostics.

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Max-Planck Institute for Biogeochemistry, Jena, Germany

A biogeochemist finds inspiration for life on the ocean floor.

My research interests lie in understanding the interplay between the physical and chemical conditions that constrain life, and the feedback processes by which life shapes the Earth's environment.

I want to understand these interactions in terms of a thermodynamic hypothesis that states that systems dissipate as much energy as possible. Can life be seen as an emergent outcome of this tendency for the whole Earth system? To test this, one would need to show that it is possible to predict the emergence of life from the hypothesis, as well as its impact on Earth's early environment.

Two articles (M. J. Russell & A. J. Hall GSA Memoir 198, 1–32; 2006, and M. J. Russell Am. Sci. 94, 32–39; 2006) could provide a starting point. The authors give a detailed picture of the thermodynamics of life emerging at hydrothermal mounds on the ocean floor.

One of the earliest metabolic reactions would have involved the conversion of hydrogen, carbon dioxide and sulphur compounds into organic carbon, acetate and water. This would have happened in the hot, mineral-rich spring water seeping into the hollow mound.

But its influence would have been felt more widely. Removing sulphur from the environment would have changed atmospheric composition and cloud cover, affecting the amount of sunlight reaching the ground. And acetate may have served as fuel for methanogens, methane-producing organisms known to live in vents. Increased methane production would have raised its levels in the atmosphere, resulting in higher surface temperatures on Earth.

Quantifying these interactions should help us to understand whether the evolution of our planet emerged from general thermodynamic trends.

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University of Toronto, Canada

The molecular dance of a protein allows a chemist's secret wish to come true.

One fascinating aspect of molecular function is the way information propagates between parts of a molecule that can be many tens of angstroms apart.

Our understanding of how proteins do this, a process termed allostery, emerged from Max Perutz's pioneering studies of oxygen-carrying haemoglobin. Three-dimensional images show that when a ligand binds to part of the molecule, a discrete set of structural changes take place at distinct sites. This, in turn, influences the ease with which subsequent ligands bind.

Nature has chosen this model in designing many allosteric proteins. However, as a practising nuclear magnetic resonance (NMR) spectroscopist with a strong interest in protein dynamics, I was secretly hoping she might design proteins in which information is communicated through changes in the dynamics between distal sites, with little or no change in overall structure. Moreover, I was rooting for NMR to play a major role in characterizing such a system.

How exciting it was, therefore, to read that Charalampos Kalodimos and his co-workers recently found such a case by studying the motional properties of a protein in different ligated states (N. Popovych et al. Nature Struct. Mol. Biol. 13, 831; 2006). Using NMR spectroscopy, the team quantified protein dynamics for a wide range of timescales. Remarkably, ligand binding at one site is linked to changes in motion far removed, over the complete set of timescales, while a corresponding propagation of structural changes does not occur.

The work of Popovych et al. provides a striking example of the importance of protein dynamics to information transfer. I eagerly await the discovery of more molecular dances and of how they, too, will relate to biological function.

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Scripps Institution of Oceanography, La Jolla, California, USA

A marine biologist sees the potential of cyanobacteria, and the benefits of their renaming.

Let's start with a false syllogism: bacteria are prokaryotes, blue-green algae are prokaryotes, and therefore blue-green algae are bacteria. All other algae are eukaryotes and so, the argument went, we should reclassify the Cyanophyta as cyanobacteria.

I was never in favour of this renaming, but it may have been good for funding. I've heard that grant applications for research on bacteria have better chances of success than those for research on blue-green algae.

And these oft-neglected organisms have a lot to offer. A recent paper on Lyngbya majuscula from Bill Gerwick, now at the Scripps Institution of Oceanography in La Jolla, California, and his colleagues (B. Han et al. J. Nat. Prod. 69, 572–575; 2006), for example, reveals some interesting new compounds.

L. majuscula grows on warm seashores as tufts, which, when they come loose and float away, can stick to swimmers' skin and cause a rash — known as swimmers' itch or seaweed dermatitis.

Gerwick and his team extracted from dried L. majuscula two compounds that may explain its irritant effect. The compounds, aurilide B and aurilide C, are hugely complicated ring-shaped molecules that resemble a toxin previously isolated from sea slugs.

In tissue culture assays, the compounds proved toxic to human and mouse cancer cells. Such natural products can act as starting points for pharmaceutical chemists.

Gerwick's paper refers to L. majuscula as a cyanobacterium in its title and as an alga elswhere in its text, but what's important is the science, not the names.

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