In your element catch up

Some of you may have noticed that I haven’t posted about our ‘In your element’ pieces for a couple of months — this is partly because things have been very busy over at the journal [I know I always say that… but it’s because it’s always true!] and also partly because these articles are now freely available online.

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After the New Year, we might stop posting about them altogether and let you go to the articles directly — but we’ll continue to update the periodic table here. And before that happens, let me share with you a few snippets from our three most recent elements.

In our November issue, science writer John Emsley took a detailed look at just how essential manganese is for life. Because the body human needs so little of it (a person contains on average of 12 mg) this only came to our attention in the 1950s, but manganese is present in many enzymes. It is the manganese superoxide dismutase, for example, that protects cells against the superoxide radical O2 (through dismutation into oxygen and hydrogen peroxide). Read the article to find out how manganese also turned up at the bottom of the sea.

In the December piece, geochemist Joel Blum from the University of Michigan, who works on understanding mercury’s behaviour in the environment, discussed why he fell under its spell. The metal that is liquid at room temperature, and particularly dense, has long captivated chemists and before them alchemists. Yet it is notoriously dangerous: mercury is a neurotoxin in most of its form, toxic by ingestion, inhalation and through the skin, both through chronic or acute exposure. It is mercury poisoning that caused hatters to develop dementia, owing to a step in the process of making felt hats that used a mercuric nitrate solution (Hg(NO3)2·2H2O) — their erratic behaviour led to the phrase ‘mad as a hatter’. The risks of mercury exposure were recognized at the end of the 19th century.

And the January article, which went live earlier this week, saw Markku Räsänen from the University of Helsinki reminisce about making the first neutral argon compound, HArF, in 1999 — also just before Christmas —  together with Mika Pettersson and Jan Lundell (now both professors in the University of Jyväskylä) and Leonid Khriachtchev (in the Räsänen group). Argon and the other noble gases have shown over the past several years that they can indeed form compounds, including hydrides. To what extent? We don’t know for sure yet. Theoretists and experimentalists, to your computers and benches!

Blogroll: New thinking

Editor’s note: As we continue to invite bloggers out there in the wild to compose our monthly Blogroll column, Joshua Howgego penned the January 2014 column.

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Mulling over the Mpemba effect, and a call to read more widely.

A recent post at The Physics arXiv Blog tells of a possible explanation for the ‘Mpemba paradox’: the observation, named after a Tanzanian student, that a hot glass of water will freeze more quickly than a cold one. This puzzling and counterintuitive phenomenon seems to fascinate scientists the world over, and was the subject of a 2012 competition run by the Royal Society of Chemistry that garnered more than 20,000 entries.

We learn that, according to a new theory, in warmer water hydrogen bonds expand further and — because of electron-pair repulsions — this compresses the molecules’ covalent bonds, leading to a net cooling effect. The calculated energy changes arising from hydrogen-bond stretching accurately predicts the observed differences in freezing speed for water at different temperatures. Yet the post notes that because the paper makes no new predictions, the researchers will still “probably need to work a little harder to convince everyone”. An interesting — if unproven — idea, nevertheless.

Elsewhere in the blogosphere there’s encouragement to keep reading in unfamiliar places, such as the arXiv blog. A guest post by Nilam Ashra-McGrath at The Thesis Whisperer (a blog encouraging PhD students through their endless toil) has exactly this advice for PhD students: read extensively. Ashra-McGrath says her PhD’s most frequent highs came when she was “devouring books and taking in ideas quickly […] making connections between my emerging data and the theories I was reading”. As one commenter put it “how do we expect ourselves to make new conceptual connections if we follow the same path as everyone else?”.

Written by Joshua Howgego, a science journalist at SciDev.Net, whose work can be found at https://www.joshuahowgego.co.uk/.

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[As mentioned in this post, we’re posting the monthly blogroll column here on the Sceptical Chymist. This is the January 2014 article]

The top 10 chemistry blog posts of 2013

Editor’s note: Jess Breen who blogs at The Organic Solution and Andrew Bissette who blogs at Behind NMR Lines round up the best blog moments of the year. If your favourite chemistry-related blog post doesn’t appear on the list, leave a comment letting us know what it is.

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This year has seen the boundaries between the online and offline chemistry communities continue to blur as chemists writing online react to and influence events in the real world. Particularly notable were editorials in Nature (End harassment) and ACS Nano (Be Critical But fair) which addressed online reactions to, and accusations of, data falsification, harassment or just bad science.

It’s not all so controversial, however. The online chemistry community is ever-growing, as the Nature Chemistry Twittorial demonstrated. The chemistry blogosphere is a vibrant and creative community, as regular readers of Blogroll will have noticed. Here we round up ten of the finest contributions of 2013, from comedic videos to chemical critique. Entries are ordered roughly chronologically.

1. Blogs by practicing chemists offer rich commentary on the literature. For example, this year the Baran group started writing at Open Flask, taking us behind the scenes of their cutting-edge chemistry. Our favourite piece of commentary this year was Vinylogousin-depth discussion of a Nature Chemistry article by Paul Hergenrother and co-workers.

2. Over the past year the results of the decade-long ENCODE project were published. Veteran med-chem blogger Derek Lowe covered the project repeatedly, making this complex and interdisciplinary topic accessible to the wider community. His series of posts (here’s one with lots of links to reaction elsewhere), starting in 2012, showcases chemistry blogging at its finest.

3. Videos are becoming ever more popular among chemists, even reaching the hallowed halls of C&EN who now use videos to support their magazine stories. Our hero is Vittorio Saggiomo, who produces amusing and inspiring videos for his blog, Labsolutely. Highlight of the year: turning a chromatography column into a musical instrument.

4. #Realtimechem week in April was a highlight for many a tweeting chemist this year, thanks to Jay. Kat Badiola showed us what #realtimechem is all about with her series of posts on life in the lab as an honours student in Australia. The best of the rest #realtimechem week blog posts are collated by Jess here.

5. Chemophobia is a perennial topic for chemistry bloggers, from critiques of irresponsible reporting to reflections on the ethics of parody. Our favourite was Mark Lorch’s satire published in the Guardian, which created quite the buzz. He discussed this further at Chemistry Blog.

6. For the #chemsummer blog carnival, Lauren Wolf of C&EN asked the timeless question: To pee, or not to pee? In what will surely become a classic of science communications, Wolf covered a simple and universally accessible topic which brings together some fundamental principles of chemistry.

7. This year has been full of drama in the chemistry academic and publishing worlds, from stripy nanoparticles to unreproducible results. Various bloggers have discussed these and other topics but none as well as ChemBark, who shined a light on the now-infamous ‘elemental analysis incident’.

8. Podcasts are becoming popular tools to discuss the latest chemistry news, with Chemjobber, Just Like Cooking, and The Collapsed Wavefunction all hosting interesting podcasts with a variety of guests from across the community. Chad Jones and SeeArrOh joined forces to delve into Bad Science at the Movies as part of the #chemmovies blog carnival.

9. Matthew Hartings, Stu, Chemjobber and SeeArrOh organised an experiment to see if chemists from different backgrounds could agree on which publications in the chemical literature were truly significant. Hartings rounded up the somewhat unexpected but interesting results of The JACS Challenge at ScienceGeist.

10. Finally, we recommend our favourite new blog of 2013. Picture It… Chemistry is a blog from the University of Bristol which combines striking photographs of familiar objects with representations of some of the molecules they contain. The beautiful photography is accompanied by in-depth discussion of the chemistry. A real highlight is their post about aspirin.

Nature Chemistry’s Altmetric top 10 for 2013

Altmetric has released their 2013 Top 100 papers – journal articles that received the most online attention based on their Altmetric score. For more details behind the list, see this blog post. Nature Chemistry managed to get a whopping zero papers in this top 100, so I figured I’d find out what our Altmetric top 10 is for 2013 so that we don’t feel quite so left out. Remember: an Altmetric score doesn’t say anything about the quality of a paper, it’s just a measure of online buzz (which can result for many different reasons…).

And so, here it is (Altmetric scores for this list were retrieved on 10th December 2013).

1. Quantitative visualization of DNA G-quadruplex structures in human cells
Giulia Biffi, David Tannahill, John McCafferty & Shankar Balasubramanian
(Altmetric score for this list = 411)
(Page views as of the date of this list = 93,831)

2. Self-healing chemistry enables the stable operation of silicon microparticle anodes for high-energy lithium-ion batteries
Chao Wang, Hui Wu, Zheng Chen, Matthew T. McDowell, Yi Cui & Zhenan Bao
(Altmetric score for this list = 204)
(Page views as of the date of this list = 4,629)

3. A grossly warped nanographene and the consequences of multiple odd-membered-ring defects
Katsuaki Kawasumi, Qianyan Zhang, Yasutomo Segawa, Lawrence T. Scott & Kenichiro Itami
(Altmetric score for this list = 123)
(Page views as of the date of this list = 12,692)

4. Optical control of antibacterial activity
Willem A. Velema, Jan Pieter van der Berg, Mickel J. Hansen, Wiktor Szymanski, Arnold J. M. Driessen & Ben L. Feringa
(Altmetric score for this list = 96)
(Page views as of the date of this list = 6,698)

5. A missing link in the transformation from asymmetric to symmetric metallofullerene cages implies a top-down fullerene formation mechanism
Jianyuan Zhang, Faye L. Bowles, Daniel W. Bearden, W. Keith Ray, Tim Fuhrer, Youqing Ye, Caitlyn Dixon, Kim Harich, Richard F. Helm, Marilyn M. Olmstead, Alan L. Balch & Harry C. Dorn
(Altmetric score for this list = 92)
(Page views as of the date of this list = 2,097)

6. Layer-by-layer cell membrane assembly
Sandro Matosevic & Brian M. Paegel
(Altmetric score for this list = 91)
(Page views as of the date of this list = 2,821)

7. Accelerated chemistry in the reaction between the hydroxyl radical and methanol at interstellar temperatures facilitated by tunnelling
Robin J. Shannon, Mark A. Blitz, Andrew Goddard & Dwayne E. Heard
(Altmetric score for this list = 76)
(Page views as of the date of this list = 3,532)

8=. Site-specific positioning of dendritic alkyl chains on DNA cages enables their geometry-dependent self-assembly
Thomas G. W. Edwardson, Karina M. M. Carneiro, Christopher K. McLaughlin, Christopher J. Serpell & Hanadi F. Sleiman
(Altmetric score for this list = 69)
(Page views as of the date of this list = 5,461)

8=. Fluctuating exciton localization in giant π-conjugated spoked-wheel macrocycles
A. Vikas Aggarwal, Alexander Thiessen, Alissa Idelson, Daniel Kalle, Dominik Würsch, Thomas Stangl, Florian Steiner, Stefan-S. Jester, Jan Vogelsang, Sigurd Höger & John M. Lupton
(Altmetric score for this list = 69)
(Page views as of the date of this list = 4,105)

10. The use of elemental sulfur as an alternative feedstock for polymeric materials
Woo Jin Chung, Jared J. Griebel, Eui Tae Kim, Hyunsik Yoon, Adam G. Simmonds, Hyun Jun Ji, Philip T. Dirlam, Richard S. Glass, Jeong Jae Wie, Ngoc A. Nguyen, Brett W. Guralnick, Jungjin Park, Árpád Somogyi, Patrick Theato, Michael E. Mackay, Yung-Eun Sung, Kookheon Char & Jeffrey Pyun
(Altmetric score for this list = 63)
(Page views as of the date of this list = 10,450)

These are the top 10 research Articles. If you include other content from the journal, the list would look very similar, but this Editorial from the April 2013 issue would shoot into the chart at the number 2 position (Altmetric score = 206).

A letter about ‘Neon behind the signs’

Editor’s note: Earlier this year our ‘In your element’ section featured an article about neon written by Felice Grandinetti from the University of Tuscia (you can also find a write-up here by yours truly). We recently received a letter from Roald Hoffmann from Cornell University, which we are publishing here on the blog, with a reply from Felice Grandinetti. Feel free to add your own thoughts in the comments section below.

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To the Editor:

Felice Grandinetti’s comment on the singularity of supremely inert Ne, and his suggestion of having He head group 2 of Mendeleyev’s Table are on the mark1. But he should have mentioned the people who suggested that before him — Henry Bent2 and Eric Scerri3 have argued over the years for this placement. And Wojciech Grochala likewise, supporting his argument with detailed quantum mechanical calculations on diverse He and Ne containing molecules4,5. Their well-thought-through arguments deserve reference.

Roald Hoffmann, Cornell University

References

1. Grandinetti, F. Nature Chem. 5, 438 (2013). [Link]

2. Bent, H. New Ideas in Chemistry from Fresh Energy for the Periodic Law (AuthorHouse, 2006). [Link]

3. Scerri, E. R. The Periodic Table: Its Story and Its Significance (Oxford University Press, 2007). [Link]

4. Grochala, W. Pol. J. Chem. 83, 87–122 (2009). [Link to journal website]

5. Grochala, W. Phys. Chem. Chem. Phys. 14, 14860–14868 (2012). [Link]

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Felice Grandinetti replies:

In reply to the letter by Roald Hoffmann:

My essay on neon chemistry intended to be an entertaining recognition of salient facts, systems, and concepts. The supreme inertness of Ne and the actual position of He in the periodic table are, in particular, “hot” topics, well highlighted before me by the scientists mentioned by Roald Hoffmann in his comment. I at present share the suggestion that neon is the most inert element, based also on my own experience in the theoretical investigation of noble gas compounds. The competition between He and Ne as the most inert element certainly invites further investigation, and I hope that this blog may be the place for future debate.

Felice Grandinetti, University of Tuscia