a few of our favourite things
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264 NATURE CHEMISTRY | VOL 6 | APRIL 2014 | www.nature.com/naturechemistry
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A few of our favourite thingsTo celebrate Nature Chemistry turning five years old, editors past and present each share the story of a paper that, for one reason or another, stands out from all the others they have shepherded into the journal.
Steric factors predicting a reaction Dividing vesicles that leap into action Polymer chains made of sulfurous strings These are a few of our favourite things PSII models and calcium in clusters The power to split bonds that hafnium musters Gels stuck together with sugary rings These are a few of our favourite things
Supersized self-assemblyMy own research background in supramolecular chemistry means that I typically handle many of the manuscripts submitted to the journal that involve the formation of host–guest complexes. In June 2010, when a manuscript with the title ‘Macroscopic self-assembly through molecular recognition’ from Akira Harada and co-workers appeared in our submission system, I was intrigued.
Although the title didn’t give much away about the specifics of the work, the idea that it conveyed was certainly interesting and got me thinking about the mesoscale self-assembly work that George Whitesides and colleagues were doing in the late 1990s/early 2000s. Whereas the Whitesides’ approach was a top-down one, in which macroscopic objects made from poly(dimethylsiloxane) assemble into arrays based on the matching of hydrophobic surfaces, Harada’s system (Nature Chem. 3, 34–37; 2011) was designed and built from the bottom up.
The cavity inside ring-shaped cyclodextrins is a well-known host for hydrocarbon groups and so Harada and
co-workers set about using this molecular-level interaction to effect self-assembly at a macroscopic scale. They began by making a range of gels adorned with different host and guest groups. One host gel was functionalized with α-cyclodextrin (α-CD) and another with the slightly larger β-cyclodextrin (β-CD). Three different guest gels were also prepared; one decorated with n-butyl (n-Bu) groups, one with t-butyl (t-Bu) groups and one with much bulkier adamantyl (Ad) groups.
The first self-assembly experiment described in the paper shows that a piece of β-CD-gel (stained red) and a piece of Ad-gel (stained green) stick together in water. When a handful of pieces of β-CD-gel and Ad-gel were agitated in water, a self-assembled structure was formed with alternating red and green pieces. No interactions were observed between gels of the same colour or indeed with a blank acrylamide gel bearing no host or guest groups, suggesting that the specific recognition between β-CD and adamantyl groups is required for self-assembly.
When pieces of the two host gels were mixed together with both n-Bu and t-Bu guest gels, two different assemblies were formed based on the size complementarity of the host and guest groups (pictured). Straight-chain n-Bu groups match the smaller cavity of α-CD better than the branched t-Bu groups, which are themselves a better fit inside the larger β-CD rings. With such visually appealing images that offer a simple — yet powerful — macroscopic manifestation of specific recognition at the molecular scale, it is easy to understand the
comments of one referee: “Simple yet clear and effective. I really enjoyed this work — it’s the first piece of science that’s actually made me smile in a long time.”
Stuart Cantrill is an editor at Nature Chemistry.
The parameters of predictionPredicting which catalyst (or perhaps which ligand) will provide the most selectivity in a given asymmetric transformation is fraught with difficulty, but this doesn’t stifle the desire to try and do so. The problem is rooted in the very small differences in energy (often due to differences in steric interactions) between competing transition states. Predictions are most often made by analogy with the steric interactions in other well-studied systems. ‘A values’ for example — that many will recognize from undergraduate studies — are based on the axial–equatorial preference of substituents in cyclohexanes.
In an Article in 2012, Matthew Sigman and co-workers argued that getting away from such analogies is important because they necessarily require the system under study to be similar to the one from which the parameters are derived (Nature Chem. 4, 366–374; 2012). Instead, they extolled the virtues of the computationally derived Sterimol parameters, which attempt to represent the steric influence of a group based solely on size and shape, rather than on the effect of that group observed in another system. In addition, more than one parameter can be assigned to a particular group — which avoids the often confounding simplification that a substituent can be represented by a sphere. Sigman and co-workers described three case studies to support their claims — carbonyl allylation and propargylation, as well as a mechanistically distinct alcohol acylation, and find striking correlations in each case.
Sigman contacted me directly before submitting this work because its presentation — with a rather long, review-like, introduction — is distinct from many other Nature Chemistry papers and represented something of a special case. As he explained to me, the use of the Sterimol parameters is widely known in the development of
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n-Bu-geln-Bu-gelt-Bu-gel
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quantitative structure–activity relationships (QSAR) in drug discovery, but had not been applied to an understanding of asymmetric catalysis. Cutting across the perceived boundaries of different chemistry specialities is something I have always found appealing as an editor. It also seems to me that this type of physical organic chemistry is, unfairly in my opinion, considered old-fashioned — and I do like to be contrary!
My own research background working on asymmetric catalysis meant that I was also drawn in by the prospect of predicting reaction outcomes. There are, of course, plenty of exceptionally useful catalytic asymmetric reactions that have been discovered and applied without a complete understanding of why a particular ligand or catalyst may be optimal. And it is not my intention to belittle these achievements. The developments in screening technologies mean that it is possible to rapidly identify a ligand or catalyst that can provide the desired outcome for a particular reaction, but I have always found something satisfying about new understanding.
Stephen Davey is an editor at Nature Chemistry.
Vesicle division revisitedOver the past few decades chemists have been delving into a fascinating topic: how life arose and how to build from scratch a ‘minimal cell’ — a system satisfying the minimum requirements to display the characteristics of life. One approach to engineering such a system takes the supramolecular route. Tadashi Sugawara and his group have, for the past ten years or so, been working on giant vesicles that are able to self-reproduce. Their membranes are constructed of lipids and a catalyst, and when specific precursors are added to a vesicle-containing solution, they are converted by the catalyst into lipids and incorporated into the membrane. This makes the vesicles grow and, on reaching a certain size, divide.
In the Article that appeared in the October 2011 issue (Nature Chem. 3, 775–781; 2011) as well as gracing the cover (pictured), Sugawara and colleagues described a related system. But what grabbed my attention was that the division of vesicle compartments had now been combined with the replication of encapsulated DNA — an information-carrying species. To link the two events, the researchers had endowed the membrane with cationic lipids, which interact with polyanionic DNA. The self-reproduction of the vesicle was significantly enhanced by increasing the concentration of DNA within it (through
amplification), however the specifics of the DNA–membrane interactions, and how they lead to the enhancement, are unclear. Notably, the DNA was distributed evenly among the daughter vesicles. As Pier Luigi Luisi and Pasquale Stano put it in their News and Views article that accompanied the study, “By analogy, this orchestrated dynamics can be thought of as effectively modelling one of the intrinsic characteristics of prokaryotic cells — namely, chromosal replication coupled with cell division.”
Another enjoyable, if unrelated, aspect of this manuscript’s life was that the peer-review process it underwent was an editor’s dream. It is gratifying when the process works as it should, that is, when a system or project is developed — and, in turn, a paper improved — based on the helpful advice of the reviewers. In this case, all of the referees agreed on the significance of the study, with one reviewer commenting that “the work is exciting and the submitted movie beautiful”, however, they also took the time throughout three rounds of review to raise points that improved both the researchers’ understanding of their system and the flow of the manuscript — input that Sugawara’s team gratefully acknowledged.
This beautiful system is amenable to improvements, and I look forward to seeing future developments. For example, as Luisi and Stano noted, the vesicle division still requires external action by the researchers (addition of membrane precursors), and the catalysts for DNA amplification and production of membrane lipids do not replicate. As mentioned above, the vesicle division mechanism is also not fully understood; however, when asked about the progress made since this
publication, Sugawara mentioned that his team has gained further insight on the DNA–membrane interactions crucial to the proliferation of the vesicles.
Anne Pichon is an editor at Nature Chemistry.
Two birds with one brimstoneSometimes as an editor you read a newly submitted paper and think ‘this must have been done before’. Mostly it’s because the article is on a current ‘hot topic’ and you’ve recently seen several papers with similar titles — and usually it has been done before (or at least something very similar has). But sometimes it’s because the paper describes an idea, so beautiful in its simplicity, that surely someone must have already thought of it. So you fire up the internet and your favourite scholarly databases, do some digging, and then realize that people have thought about similar things before but they haven’t been able to get ‘it’ to work. But now — with a neat bit of chemistry — they have, and at that point you realize that you might have something very interesting on your hands.
This was the case with an Article published in our June 2013 issue from Jeffrey Pyun, Yung-Eun Sung, Kookheon Char and colleagues (Nature Chem. 5, 518–524; 2013), in which they reported a method for making useful polymeric materials out of sulfur, which they call ‘inverse vulcanization’. Elemental sulfur has several desirable properties — electrochemical activity for example — and is available by the bucket load (Pyun, Sung, Char and co-workers suggest that a surplus of seven million tons is generated annually!). It can also form linear polymers under certain conditions, but they are fragile.
Conventional vulcanization is a process that is more than a century old and it involves making more robust materials from rubber by adding a little sulfur, which creates chemical bridges between the carbon-based polymer chains. So the idea of ‘inverting’ vulcanization and stabilizing chains of sulfur atoms with carbon bridges seems to make some sense. It is, however, not quite that simple and several attempts have been made over the years at creating
OPEN SCIENCEA case study in chemistry
ARTIFICIAL DNA BASESMetal in the middle
BIOMIMETIC MATERIALSCloser to collagen
Protocells proliferate
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sulfur-rich copolymers, but the final products always suffered from low levels of sulfur incorporation or poor properties.
Sulfur is not the most soluble of elements and Pyun, Sung and Char discovered that the key to its copolymerization was to melt it and carry out the chemistry in liquid sulfur — without a solvent. This clever idea allowed them to simply add the divinyl monomer 1,3-diisopropenylbenzene to the sulfur, with the monomer-to-sulfur ratio an important parameter that affected the physical, electronic and optical properties of the final material.
The concept of the synthesis is neat but the story did not just stop there. The team also demonstrated just how useful the sulfur copolymer could potentially be, by processing it into microstructured films using imprint lithography and showing that it can serve as the electroactive material in cathodes for Li–S batteries. In a world fast running out of resources, new chemistry to make useful materials is extremely important and I am sure that there will be more sulfur-rich copolymers with interesting properties available soon.
Gavin Armstrong is an editor at Nature Chemistry.
So why calcium?I’ve had the privilege to shepherd many papers through peer review but the paper by Theodor Agapie and co-workers (Nature Chem. 5, 293–299; 2013) is memorable, in part, because of the simplicity of the underlying idea, and also because it was the first paper that I sent out to referees while working at Nature Chemistry.
The Article investigates the role of the redox-inactive ion in the oxygen-evolving complex (OEC) of photosystem II. The core of this complex is formed from a cluster of four manganese and five oxygen atoms, and a redox-inactive calcium ion. Although there are a number of different variants of photosystem II, this cluster seems to be conserved in the active sites. Calcium can be replaced in the structure with ions of similar size and charge, but intriguingly only calcium and strontium ions result in a functional complex — posing the question
of what role the calcium plays in the OEC and the water-oxidation reaction it catalyses?
Agapie and co-workers created a series of heterometallic manganese–oxido clusters (one is pictured) that were structural mimics of the OEC. Using a range of experiments they showed that these model systems retained the same structure if the oxidation state of manganese was changed or if the calcium ion was swapped for Na+, Sr2+, Zn2+ or Y3+. After demonstrating this, they compared the properties of the calcium complex to those in which the calcium ion had been replaced with other metal ions. Electrochemical studies revealed a linear dependence between the reduction potential of the complex and the Lewis acidity of the redox-inactive ion — in essence, the choice of redox-inactive ion provides a method to tune the reduction potential of the overall complex.
One of the things that impressed me when I first read the manuscript was the clear and convincing case that was made for the role that the calcium has in modulating the redox properties of the OEC (although it is still possible that the Ca2+ ion plays additional roles in this system). The reviewers were equally supportive and stressed the importance of the modulation of the redox potential in their reports.
The structure and reactions of photo-system II are particularly complicated, but understanding phenomena observed in model complexes is critical to improving our understanding of complex systems such as this, and is a general theme that we see across many of the submissions to the journal. The meticulous design and synthesis of such complexes is certainly not straightforward, but Agapie and co-workers showed that it is worth the effort.
Russell Johnson is an editor at Nature Chemistry.
Breaking and enteringLike all chemists, I learnt at an early stage in my career that nitrogen, N2, is exceptionally stable: the two nitrogen atoms are joined by one of the strongest covalent bonds known. And like many chemists I didn’t, however, learn too much about hafnium, the transition metal below titanium and zirconium in group four of the periodic table. But an Article by Paul Chirik and colleagues in 2010 taught me and chemists across the world that an organometallic hafnium compound could break apart nitrogen — and at the same time activate carbon monoxide, which also has an incredibly strong bond (Nature Chem. 2, 30–35; 2010).
Breaking apart nitrogen is of course done on a vast scale across the globe in the Haber–Bosch process, creating ammonia. This
essential process, developed a century ago, produces the fertilisers critical to modern agriculture and helps to feed billions of people. Almost half of the nitrogen atoms in your body have been through this process, using an iron catalyst at high temperatures and pressures. Of more financial and environmental importance, up to 5% of the world’s supply of natural gas is used to create the hydrogen consumed in the reaction.
A route to making useful compounds that avoids these extreme and energy-intensive conditions could potentially be extremely valuable. And that is what Paul Chirik and colleagues did. They knew from their previous work that a zirconium metallocene complex could activate a dinitrogen ligand and lengthen its N–N bond. The team also knew that using a transition metal from the third row in place of one from the second row would further lengthen that bond.
Putting this knowledge into practice, they prepared a complex with two nitrogen atoms bridging a pair of hafnocene groups. Adding carbon monoxide produced a complex with an unusual (N2C2O2)4– group in between the two metallocene moieties (pictured). This organic core could be released from its metallic prison through treatment with an excess of acid, resulting in oxamide. This compound slowly releases ammonia when it hydrolyses and can be used as an alternative to urea in fertilising crops.
Of course, not even the most ardent advocate of using homogeneous molecular chemistry in preference to heterogeneous processes would suggest using a stoichiometric reaction with hafnium to produce any compounds on a large scale. But as one of the reviewers noted, “These transformations have no precedent in the chemistry of coordinated dinitrogen.” Taking two such simple and abundant compounds and turning them into a useful chemical at mild temperatures and pressures offers a tantalizing glimpse of what future chemists will be capable of — even with the strongest and most stable bonds known to the chemists of today.
Neil Withers was a founding editor at Nature Chemistry and is now Features Editor at Chemistry World.
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