Chemistry World Blog

We all love a cartoon. Animation is a fiddly and time consuming but I can remember the fun of making flip books. Taking it up a notch, IBM researchers have some more expensive kit than my notepad and pen, and now they’ve used it to make an ‘atomic movie’.

Scanning tunnelling microscopes can image individual molecules on a metal surface, and drag those same atoms and molecules around to make letters and images. Stop-motion animators today make an image, take a picture, change the image slightly, take another picture, and repeat that cycle until they have enough frames to make a film. Put the two together and you get ‘The boy and his atom’ premièring today on YouTube and certified by Guinness World Records as the smallest ever movie. The cast ? Carbon monoxide molecules.

In total the movie is made of 242 frames and I love how you can see the ripples in electron density that surround ‘Adam’ and his bouncy little friend. I’d love to know how long the entire process took, not just the imaging but the tidying up of the image and the putting it together. Using such big machinery cooled down to low temperatures to keep the molecules where they’re put is pretty expensive and labour intensive, so I’m not sure atomic animation will be taken up by Hollywood just yet. But as a demonstration of the control IBM now has over single atoms and molecules the video is pretty neat. IBM has also released a video with some more behind the scenes detail which you can watch here.

My verdict? Well I just tried to make a flip book of a thumbs up, but I think I’ll leave the animation to the professionals. Good job. What do you think?

Laura Howes

— One of the participating tokay geckos. Photo: Ethan Knapp and Alyssa Stark

I love a good gecko story, and I love how the cute little critters can climb up most things but would apparently struggle with my non-stick frying pan. Now I’ve found out that if my frying pan was still wet from the washing up Mr Gecko would have a better chance of holding on.

There is a serious side to this science. Hundreds of systems have been developed mimicking the adhesive power of gecko toes and all rely on creating a large surface area that can get in contact with whatever surface you want to stick to using van de Waals forces to do the rest. Understanding how different surfaces affect adhesion is obviously important and it’s been anecdotally known for a while that as well as struggling with Teflon, geckos can’t stick to wet glass despite their feet being superhydrophobic. In rainforests, things can get quite wet so how do the geckos manage?

To test this out Alyssa Stark‘s lab at the University of Akron, Ohio, placed geckos on different surfaces to investigate when the geckos slipped and when they stuck. To get more data than slip versus stick, those little geckos were fitted with harnesses and slowly pulled off surfaces using force meters to record the gecko adhesion values. If ever there’s a day you’d have liked to have been in someone’s lab, the day harnessed geckos were slid around for science has got to be up there (at least for me).

The findings are, in part, to be expected. Wetting surfaces usually makes them more slippery for geckos but it’s only wet glass that causes a real problem – hydrophobic surfaces that were wetted could still be clung on to as the lizard’s hydrophobic feet helped get rid of the water and form a contact with the dry surface beneath. So the lab work confirms that wet leaves shouldn’t be a problem. The exception, which also contradicted the Akron group’s modelling, was PTFE, or Teflon. Wet Teflon, it seems, is much easier for the geckos to hold on to. The why is not certain yet though, so I for one am looking forward to more gecko science, ideally with videos…

Laura Howes

— Are you what you eat Mr Gorilla?

It reminds me a little of a certain TV ‘Dr’ obsessed with poo, but US scientists have been busy analysing the faeces of mountain gorillas. So have the gorilla’s been following a healthy diet, are they what they eat and why oh why would you be rummaging around in gorilla poo for your day job?

Well it turns out that tracking and understanding the diets of wild animals can be tricky. You can observe them eating, or rummage around in their poo for what remains, but that will only give you a snap shot: larger trends can be difficult to spot. Scott Blumenthal at the University of New York and his colleagues used isotope ratios to track how the diet of mountain gorilla’s shifts with the seasons. Using the change in ¹³C values the group showed that while gorilla’s usually eat foliage, when fruit is available gorilla’s prefer it and so change their diet. By increasing the amount of fruit they eat the gorillas also increase the amount of ¹³C they ingest because of the fruit’s position in the canopy of the forest. Plants down towards the ground tend to rely on carbon that has been taken up from the soil and has already been metabolised and so lost much of its ¹³C. (more…)

Probably best enjoyed without liquid nitrogen

Reports are coming out that an 18 year old woman has had her stomach removed after drinking a ‘nitro’ cocktail given a smoky effect using liquid nitrogen. It seems that outside of labs liquid nitrogen is proving quite the star turn… from making ice cream in Camden, to being used in cocktails around the country.

These cocktails seem to come in two types, either a small amount of liquid N₂ is used to cool the drink without dilution and with added smoky effect, or much more N₂ is used to whisk up a frozen cocktail, more N₂ is then poured over for, again, that smoky effect. Basically, everyone wants a cocktail that looks like it comes from the set of an Addams family movie. (more…)

— Distortion of the protein

Another nail in the coffin of the arsenic life story has been published suggesting that GFAJ-1 does not in fact metabolise arsenate, but instead is very good at distinguishing the poison from phosphate. Earlier this year, two papers found that despite earlier claims, the bacterium did not in fact take up arsenate, the new paper explains in more detail why.

Publishing in Nature, Dan Tawfik and colleagues decided to investigate how exactly GFAJ-1, and other bacteria that live in arsenic rich environments, survive. Can they distinguish between the two anions, and if so, how?

The trick, suggests Tawfik, is in the peristaltic phosphate binding proteins which are highly tuned in GFAJ-1. Although arsenate ions are only a little larger than phosphate, that size difference is enough to distort a low energy hydrogen bond and stop arsenate uptake (see left).

I can’t help but wonder, have we finally laid this to rest, or will more papers refuting GFAJ-1′s ability to metabolise arsenate keep coming out for a while yet? If they keep getting their authors in high impact journals, you can see why anyone working on applicable research might want to join in.

Laura Howes

— Nanoparticles for colouring

Wondering how to keep yourself amused this weekend, or worried how to keep the kids amused on a rainy day? May I suggest this new colouring-in book full of images from the nanoscale world. If you’ve ever felt that that false colour electron microscope images could really be more eye catching this is the book for you.

Founded perhaps for less suspicious reasons than Terry the Fracosauraus‘ colouring-in book, each image comes with scale bars and a short explanatory paragraph explaining what exactly it is you’re colouring in. The explanations are aimed at a US fifth grader, so about 10 years old, and also asks questions to be filled in along the way.

My only concern, and maybe that’s because I’m a fun killing, literal scientist type, is that rather than use real photographs the book uses line-drawn approximations. That makes sense for DNA perhaps, but wobbly fractals? I think if I were going to lose myself in the crazy complexity I’d want it to be accurate.

However, I applaud the idea of communicating nanoscience early – get them hooked young, I say. And if you’re into stretching yourself, or introducing languages early to your children, the pages are also available in French. Amusez-vous bien!

Laura Howes

Fancy catching up with some of the sights around the Czech Republic, how does Toxic Mountain sound as a field trip? Hmmm, perhaps not so alluring. Toxic Mountain is the translation of Jedovar Har, to the south of Prague, where for 130 years iron and mercury have been mined and smelted. Maria Hojdova from here in Prague, has been analysing mercury levels from the forest floors around Jedovar Har, and another site, Pribram, where lead zinc and silver were mined and lead smelted, leaving mercury behind from the ores.

Hojdova found that most of the inorganic mercury was present as the immobile and water insoluble mercury sulfide, with less than 14% of the mercury in more mobile forms – this was also backed up by showing that most contamination was on the surface of soil, rather than permeating further down. By also analysing the mercury in tree rings Hojdova also showed how the mercury deposition matched the activity of the mining areas, including a secondary peak in the 60s.

However, if that doesn’t put you off, Hojdova did conclude her talk with a recommendation for Pribram and its mining museum. Unfortunately, I don’t think my schedules going to allow such a field trip.

Meanwhile, over in the poster sessions I was treated to a fantastic story of art theft and recovery by a student from Karel Lemr‘s lab, Volodymyr Pauk. The lab were approached when n painting, Crucifixion, stolen from the St Sebestian church on Holy Hill in the Czech Republic, was recovered in Austria. Restorers and conservators obviously wanted to know what they had, both to determine authenticity and to help restoration efforts. Pauk was charged with determining which blue pigment was used – Prussian blue or indigo.

Prussian blue is an inorganic pigment (Fe₄[Fe(CN)₆]₃) and was discovered back in the 18th century in Berlin (hence the name), whereas indigo, an organic dye extracted from plants, has been used since ancient times, until being superceeded by synthetic alternatives. Identifying which has been used can help date painting, but both are insoluble in water or many common organic solvents.

Pauk was tasked with making the pigments soluble so that they could be identified with mass spectrometry rather than traditional methods like HPLC. This was especially important, said Pauk, because when he was finally sent samples ofthe paint, they were so small that to begn with he thought he had been sent empty sample bags.

For Prussian blue, Pauk showed that the pigment could be decomposed with sodium hydroxide to give  Na₄[Fe(CN)₆. Meanwhile, indigo could be reduced with dithionite to give the soluble leucoindigo. That allowed Pauk and his lab to test the tiny samples of paint and identify the paint used. Although the technique was so sensitive that it detected some contamination of Prussian blue, the painting was shown to mainly contain indigo, helping to date the artwork as well as telling conservators what to use.

Restoration of the artwork is still ongoing. Meanwhile Pauk is now trying to do similar work to convert Tyrian, or Royal, purple into a mass spec-able compound. If anyone has any ideas I suggest you get in contact.

— This way for all your chemistry needs

This week, the historic city of Prague is playing host to nearly 1800 chemists for the 4th EuCheMS Chemistry Congress. As you might expect, I’ve been thinking quite a lot about the past over the last day and a half, but not the history that preoccupies the tourists who are sharing my hotel.

Yesterday at the opening ceremony, several of the speakers were keen to talk about their links with Prague – how they had visited before and were pleased to come back, or to highlight a longer standing connection with the city. President of Iupac Kazuyuki Tatsumi, used the opportunity to share some snaps from his previous visit back in 1982, with a familiar physical chemist stood in the picture with Tatsumi and  common mentor Rudolf Zahradnik – a young Angela Merkel. Meanwhile, Jean-Marie Lehn claims links to Prague back to 1963, and a paper co-authored with a Czech chemist. Lehn has now set up a prize, in collaboration with the French Embassy in Prague, a prize to help support Czech chemistry and young Czech researchers. This year, the winner was Michal Kolar from Charles University here in Prague for his work on halogen bonds. As part of his prize, Konar will be sponsored for a month’s study visit to France.

However, after the opening ceremony and beer on Sunday, Monday started bright and early with a full scientific programme with 12 parallel sessions. The topics that caught my attention all had a common theme – history.

One talk that stood out was in the Environmental and Radiochemistry section. This morning, Tarja Ikaheimonen of Finland’s Radiation and Nuclear Safety Authority compared the Fukushima accident to Chernobyl, and as someone who doesn’t remember the 1986 event, some of the facts and stats she reported were incredibly sobering. Forests are apparently very susceptible to nuclear contamination because the plants take up caesium instead of potassium and the Fukushima fallout was mainly over Japanese forests. In Finland the post-Chernobyl contamination is still 40% of the maximum, says Ikaheimonen, showing how long lasting that contamination can be. And of course, that then concentrates up the food chain. Butterflies in the forests near Fukushima are now showing morphological variability, just as in Finland’s forests

However, the Fukushima disaster, while obviously awful, was no where near as bad as Chernobyl, says Ikaheimonen. Caesium discharge in Japan was about 20-30% that of Chernobyl, and the fall out was mainly local, rather than contaminating vast portions of northern Europe, as Chernobyl has. And perhaps, just as the Chernobyl site is now an incredibly diverse nature reserve, the same could happen for the forests in Japan says Ikaheimonen. I have to say though, I don’t think I’d recommend that as a general strategy for improving environmental diversity.

We realise that gold means only one thing to most people at the moment (and believe you me Chemistry World towers has been as gripped by the Olympics as everyone else) but we also need to congratulate the University of Edinburgh’s school of chemistry for getting a gold Athena SWAN Charter award. That’s the UK’s top accolade for good practice in recruiting, retaining and promoting women in science, engineering, technology, maths and medicine in higher education. Only two departments in the country have been judged to be gold standard: Edinburgh’s chemistry department and the University of York’s chemistry department (yay chemistry, etc).

This is especially relevant as Lesley Yellowlees, of the University of Edinburgh, begins her term as RSC President, pledging to identify and remove the barriers that prevent women from staying in chemistry. Hopefully more chemistry departments (as well as those in other disciplines) can rise up the ranks. And then, maybe one day, these sorts of awards won’t be needed at all.

Laura Howes

There’s something very summery about building a sandcastle. From my first attempts with a simple bucket, and my Dad hydro-engineering sea-filled moats, I was hooked and these days no trip to the beach is complete without some sort of sand sculpture. From those early days and experiments I learnt how the sand had to be wet, but not too wet. Goldilocks sandcastle sand is wet enough to hold the grains of sand together but not so wet as to cause the walls to become unstable, crumbling to the ground and leaving you with a sand ruin. But how was I to know you could pursue a scientific career in sandcastle science?

— Not one of mine

Daniel Boon from the University of Amsterdam in the Netherlands, and colleagues, has shown that the Goldilocks recipes for sandcastle uses just 1% water (however, he investigated this with beach sand and deionized water, I do wonder if the saltiness of sea water makes a noticeable difference). This is enough water to form the capillary bridges between grains of sand, pulling them together and making wet sand such a good building material for complex structures.

As Boon notes in his paper (Scientific Reports, DOI: 10.1038/srep00549), the literature has previously claimed that sandcastles can only be built to around 20 cm, due to the capillary rise of the sand, but you can get much bigger sand structures than that so what’s going on? Well, more painstaking research building sandcastles, or rather sandcylinders, showed that sand buckles under its own weight at a critical height which is proportional to the cylinder’s radius to the power of two thirds. Using his calculations, with the best sand-water mix, a castle with a base with a radius of 20 cm should be as tall as 2.5 m. Compacting the mix (or tapping the sand with the back of the spade, as my Dad calls it) also helps, according to Boon.

Of course, these findings can be used by civil engineers and people working in soil mechanics, but will you be taking your calculator to the beach this summer? I think I’ll just stick with guesstimates, but might see if a drier sand than I expect will give better results.

Laura Howes