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Sleep deprivation and science

30 October, 2014 - 11:30

Guest post by Heather Cassell

This blog post is inspired by my 3 month old and 6 year old who are both suffering from a cold and not letting me get much sleep.

Over the years I have found sleep deprivation can have a significant impact on my work in the lab. There are many ways to end up overly tired: a child could be keeping you awake, you may be unlucky enough to have insomnia, or you might have been up late doing something much more fun (in which case you get less sympathy). The sensible approach would be to take some time and get some sleep, knowing you will be more productive tomorrow. But often you simply don’t have that luxury, as there is important science to be done.

Sleeping on the job – not a good idea in the lab
©iStock

Sleep deprivation often hits at the least opportune moment, when you most need the sleep. It’s often a deadline that you really need to get results for – be it a conference, a report, or a meeting with your collaborators. ‘If only I can get these experiments finished then my data will be much more convincing! (As long as they agree with the previous results)’. When you have an experiment to do that needs careful set up, has a complicated protocol to follow and many time points to take, or takes many days to run, luck will have it that you will be sleep deprived at the crucial moment.

In situations like this you need to carefully consider what to do – start the experiment now and risk mistakes, or postpone it until you’re less dozy and miss out on the data? If you decide to work through the tiredness, then I recommend you make a detailed, foolproof plan. This will ensure that you don’t need to think, just to do. Also, drink as much tea as you dare before you head to the lab to get started – you’ll need to find your own balance of under-caffeinated versus excessive toilet trips. At times like this, I’m tempted to smuggle a cup of tea into the lab, just to help get through the day.

I’m not proud to say that I have reached the point where I’m so sleep deprived that I go into denial – I believe that I can work normally on a small amount of sleep – and that is when the serious mistakes creep in. My tales of woe include throwing away a solution containing the protein that I had spent two days purifying; or using the wrong antibiotic, and so preventing the growth of my cells. It may have reached my nadir when I only put labels on the lids of a stack of 96 well plates: I put them to one side while adding something to the plates, only to realise that I could no longer tell one plate from another. Analysis of the results was impossible; I had wasted time and resources, all because I refused to acknowledge my limits.

These slip-ups are frustrations, but other mistakes could potentially be much more serious. There are hazards in a lab that we are all trained to understand and risks that we’re equipped with the tools to mitigate. Safe lab work requires each of us to be fully conscious – if we fail to assess risks properly because we’re tired, we put far more than some experimental data at risk. A lab full of zombie-like sleepwalking scientists is not a safe lab to work in.

Every time I’ve made one of these mistakes, I’ve realised that it’s time to get out of the lab and do something else, maybe write up my lab book, skim a few journals or make another cup of tea. But sometimes an extra hour in bed is justified – the results can wait until another day.

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Categories: Education

ISACS winners 2014

24 October, 2014 - 11:11

Congratulations to all of our ISACS Chemistry World poster prize winners this year. Here’s a run-down of the winners:

Katie-Louise Finney receiving her prize from Chemistry World features editor, Neil Withers

Katie-Louise Finney, a second year PhD student in David Parker’s group at the University of Durham, UK, was the winner at ISACS 13 (Challenges in Inorganic and Materials Chemistry), held in Dublin, Ireland. Katie’s poster was titled ‘Development of 1H PARASHIFT probes for magnetic resonance spectroscopy and imaging‘.

Katie explains her work: ‘Our 1H PARASHIFT probes possess a tert-butyl reporter group that can be shifted well away from the water and fat signals at 4.7 and 1.3ppm. We have succeeded in shifting the tert-butyl reporter group as far as +65 and –75ppm. This means that in imaging experiments, we gain two orders of magnitude of sensitivity due to 1) the lack of background signal in vivo and 2) the enhanced reporter group relaxation by the proximal lanthanide ion. As a result, our probes have been imaged in live mice within minutes, at concentrations of 0.1mmol/kg.’

We’ve actually featured Katie’s MRI work in Chemistry World before in our article Moving the goalposts for MRI.

Baihua Ye

Baihua Ye, a doctoral assistant in the laboratory of asymmetric catalysis and synthesis at the Swiss Federal Institute of Technology in Lausanne, was the winner at ISACS 14 (Challenges in Organic Chemistry), held in Shanghai, China.

Baihua’s poster was titled ‘Development of chiral cyclopentadienyl ligands for Rh(III)-catalysed asymmetric C-H functionalisations‘.

Baihua explains his poster: ‘My PhD thesis under the supervision of Nicolai Cramer was devoted to the investigation of novel cyclopentadienyl (Cp) ligand as a stepping stone for the asymmetric rhodium(III)-catalyzed C-H functionalizations. The challenge to achieve the high level of enantioselectivity basically stems from the spatial arrangement of the three coordinating components around the metal center. The Cp derivative, thus, acts as the sole source of chirality. From the year of 2012, we have pioneered on the design of chiral Cp ligands and elaborated two complementary families of the CpRh(I) complexes. Upon the facile oxidation in situ of the Rh(I) species, the resulting chiral CpRh(III) have been successfully applied in the C-H functionalizations of aryl hydroxamates coupled with olefins, allenes as well as diazo esters. The corresponding heterocyclic products are generally obtained in good yields with high levels of regio- and stereo-selectivity. In the future, we believe that our effort would provide more variant on enantioselective Cp-based metal catalysis.’

David Ordinario

David Ordinario, a graduate research assistant in Alon Gorodetsky’s group at the University of California at Irvine, was the winner at ISACS 15 (Challenges in Nanoscience), held in San Diego, US. David’s poster was titled ‘Protonic devices from a cephalopod structural protein‘.

David explains his poster: ‘In my poster, I first introduced the reflectin protein, explained where it comes from, and described some of its unusual but interesting properties. Next, I explained our electrical characterisation work on thin films from the reflectin protein. We performed tests such as two- and three-terminal IV measurements and electrochemical impedance spectroscopy (EIS). Finally, I showed and explained the protonic transistor devices we fabricated which uses reflectin as the active material. I focused on explaining the underlying mechanisms by which the reflectin-based protonic transistors function, as well as a couple of methods we developed to optimise the performance of the transistors.’

The next ISACS, ISACS 16: Challenges in Chemical Biology, will held be in Zurich, Switzerland, from 15–18 June 2014. See the Royal Society of Chemistry’s ISACS 16 event page for details.

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Categories: Education

The Devil’s Element

23 October, 2014 - 16:05

Guest post by Rowena Fletcher-Wood

‘The Alchymist, in Search of the Philosopher’s Stone, Discovers Phosphorus, and prays for the successful Conclusion of his operation, as was the custom of the Ancient Chymical Astrologers’ – Joseph Wright of Derby

Hennig Brand was known as ‘the last of the alchemists’, even though Isaac Newton, possibly the most famous alchemist, outlived him by between 17 and 35 years. This number is vague for a reason: strangely enough for a man who spent his time searching for eternal life, there is no record of when or how Brand died. Like his alchemy, he appears to have disappeared into a puff of mysticism.

Although alchemy had been around since at least 500BC, it had never had any luck with its most famous quests: transmutation of metals and the hunt for the elixir of life, both thought to be capacities of the mysterious philosopher’s stone. A secretive practice, (alchemists often wrote their recipes in arcane code) it seems ironic that its last legacy was illumination: the unnatural glow of a strange, white, waxy and translucent material, the first element to be chemically discovered, and the 13th known to man. It was called the Devil’s element. And its method of discovery in 1669 is certainly something best reserved for horror stories. Brand wasn’t trying to make the luminous substance he originally dubbed ‘cold fire’, of course: he was trying to turn lead into gold.

Using valuable techniques later appropriated into modern science, he followed a procedure typical of alchemy. This involved boiling, filtering and purifying as many as 60 buckets of bodily fluids in attempts to understand the ‘essence’ of living things. His fluid of choice was urine, which he allowed to rot for several days until it became powerfully pungent. Just as the smell became unbearable, Brand distilled his urine down to a black paste and left it to fester for months. Later, he heated it with sand to vaporise off the oily components, which he trapped and condensed with water to give the material he hoped was gold.

It wasn’t. But it did have some unusual properties. It glowed an eerie green in the dark but, left in a stoppered jar, eventually extinguished. In open air, it would ignite spontaneously, producing acrid flames and a brilliant light; under vacuum, it sublimed to a gas upon light exposure. It melted at just 44°C and was highly toxic, burning skin upon contact. Brand had accidentally discovered white phosphorus, and two other allotropic forms, red and black, would later be identified.

The name phosphorus derives from phosphoros mirabilis – ‘miraculous bearer of light’.

Always a good alchemist, Brand originally tried to keep his discovery a secret, although he readily gave away his supplies of phosphorus. He finally sold the secret of his synthesis to three alchemists, including Johann Daniel Kraft, who toured much of Europe with it. The secret escaped – first it leaked from Johann Kunckel in Sweden, and two years later from Robert Boyle in England, who had met with Kraft during his travels and heard how phosphorus was derived from ‘somewhat that belonged to the body of man’. Boyle followed the clues, synthesised and published on phosphorus (discovering meanwhile that the urine didn’t need to rot at all), and became the first person to use it to ignite sulfur-tipped wooden splints.

In later years, the ‘unnatural’ glow of phosphorus was explained by an excruciatingly slow surface reaction with oxygen, producing short-lived HPO and P2O2 emitters of visible light.

In the 1770s, Carl Wilhelm Scheele procured phosphorus from bone. Today, it is mostly prepared from calcium phosphate rock and used in the manufacture of phosphoric acid for fertilizers. It is also used for cleaning agents, water softeners, baking powder and fluorescent light bulbs. Red phosphorus is a starting material for safety matches, explosives, poisons and pyrotechnics. If you like, Brand’s alchemy has gone up in flames.

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Categories: Education

What can Sugru do for scientists?

20 October, 2014 - 12:33

Looking around Form Form Form’s laboratory in Hackney, London, you can’t help but notice that the standard lab equipment has been modified, tweaked, personalised and adjusted using Sugru – the mouldable silicone rubber adhesive they manufacture. When I went to visit them with Phillip Broadwith, Chemistry World‘s business editor, to learn about the history and chemistry of Sugru, we asked a simple question: ‘what can Sugru do for scientists?’

Jude Pullen, head of R&D, took us through a handful of ‘lab hacks’ – quick and simple ways to make lab equipment safer, more efficient and easier to use:

Can you think of a way to use Sugru in the lab? Let us know by commenting below, or find us on Twitter: @ChemistryWorld

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Categories: Education

Is it a bird? Is it a plane? No, it’s Raney Cobalt-man!

16 October, 2014 - 15:46

Guest post from Tom Branson

In a bold move by Organic and Biomolecular Chemistry, the journal has unveiled the latest superhero in the fight to save the common scientist from the ruthlessness of today’s laboratories.

With great power comes great selectivity

Standing firm with test tube in hand, Raney Cobalt-man is a new character from Catalyst Comics. The star wears a rather tight, bright cobalt blue coloured outfit, reflecting one of the element’s most notorious uses. How Raney Cobalt-man gained his powers, we will never know. But perhaps it was in a careless lab accident, and if so, he has certainly learnt his lesson. Now with goggles and elbow-length gloves (not to mention a full body suit and special groin area protection), Raney Cobalt-man is a true ambassador for PPE.

This first adventure takes our hero into the domain of the domino reaction where he’s be helped by his trusty sidekick, Dihydrogen Boy. The young assistant plays an essential role in their joint mission to catalyse peace and his support is needed even more as the hero ages. Here in the domino reaction, they join forces to selectively bring harmony cascading through the scientific community.

But where are the other great chemical heroes of today? Well, I suppose there is the elementally named Iron Man – a brilliant scientist, although he was actually more of an engineer. The Flash was first a forensic scientist who came by his powers after a lightning bolt hit his lab. This mishap is, of course, one of the many dangers of working alone late at night. The lovable Chemist Hulk may also be familiar to those folks on Twitter, this mean green scientist likes nothing better than to tweet about ‘SMASHING PUNY MOLECULES’.

Raney Cobalt-man is the hero that chemists deserve, but is it the one they need right now?

In this edition of the Raney Cobalt-man comics, the eponymous hero is helped by Martin Banwell and colleagues from the Australian National University. Together they review an underappreciated reagent and compare its powers to that of its nemesis, Raney Nickel-man. The story tells that high pressure from Dihydrogen Boy can often be off-putting for those wanting to call upon Raney Cobalt-man’s selective powers. But these drawbacks are simply overcome by using a larger amount of Raney Cobalt-man and therefore less of his annoying sidekick.

Comic book and science fans alike may be waiting a while before Raney Cobalt-man’s next adventure hits our book shelves, but be sure to pick up the first edition over at OBC.

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Categories: Education

With this ring…

16 October, 2014 - 10:22

Guest post by Jen Dougan

I attended five weddings this year, between February and October, making 2014 most definitely the Year of the Wedding. Each day was unique and reflected closely the couple, their relationship, vision and hopes for the future.  And while there was a broad range of traditions at each, whether religious or humanist approaches, one tradition – the exchange of rings – provided a common element throughout.

The element is, of course, gold. But what is the chemistry of this symbol that is ritually shared as a sign of commitment and lasting love?

© Murray Robertson / Visual Elements

Gold is the most noble of metals, it doesn’t corrode or oxidise in the Earth’s moist, oxygen-rich atmosphere. Ductile and malleable, it can be fashioned at will and, since it doesn’t tarnish, is an ideal material for producing jewellery. The decorative attributes of gold have long been coveted – examples of gold jewellery have been found in the tombs of the Queens of Egypt and Sumeria, 3000 years BC.

Gold is one of only three coloured elemental metals (the others being copper and caesium). Most metals appear whitish-grey as they reflect all wavelengths of visible light. Gold, on the other hand, due to its electronic configuration exhibits a reduction in reflectivity efficiency in the blue region of the visible spectrum. It has, in the pure form, a striking yellow colour and brilliant lustre for which it became known by the latin Aurum, meaning ‘shining dawn’ (depicted by artist Murray Robertson in the image above).

Today the purity of gold jewellery is expressed in terms of ‘karat’. Pure gold is 24 karat, where, K = 24(Masspure/Masstotal), meaning 24/24 parts of the material are gold, by weight. In practice, even 24K gold is often stated as 99.99% pure due to residual impurities from the extraction process. Although 24K gold can be used for jewellery, the softness of pure gold means that alloying the metal to improve its physical properties or to design colour variants is a popular approach. The European standard, for instance, is 18 karat, meaning 18/24 parts are gold (75% pure by weight). The other 25 % of the weight is made up of another material (in the case of jewellery, a second metal) to make an alloy, which is typically stronger than the pure metal.

The improved strength of gold alloys occurs when, having melted two or more metals together, a new structural phase is formed on cooling. The precipitation of the added metal atoms reduces slippage of the original atoms across one another.

Ternary plot of approximate colours of Ag–Au–Cu alloys, which are commonly used in jewellery making.
Original image: Metallos [CC-BY-SA-3.0-2.5-2.0-1.0 (http://creativecommons.org/licenses/by-sa/3.0)], via Wikimedia Commons

Common alloys of gold for jewellery fall into the yellow gold or white gold categories. Most jewellery alloys of yellow gold, including that of rose and green-shade gold, fall within the Au-Ag-Cu system (see image above). Zn is sometimes added to further increase the alloy strength and to change the red colour of high Cu alloys to a paler rose.

For white gold, Au-Pd-Ag is a common alloy system, where Pd is used as a bleaching agent. Nickel, another metal capable of producing the desired bleaching effect to produce white gold, is a known skin sensitiser and has become less popular in jewellery making.

The bleaching effect occurs due to the added material changing the reflectivity of the alloy in the low energy part of the visible spectrum. In all cases, the relative ratio of the alloy’s components dictate the resulting hue and mechanical characteristics.  The alloy systems allow the characteristics to be achieved such that the design lasts the length of a marriage and beyond.

A word of warning/advice to the newlyweds: although your gold is stable, it is not chemically inert. Avoid exposure to mercury, with which the gold will form an amalgam; cyanide salts, which will react with your band; and aqua regia* in which it will dissolve. Of course, if you encounter any of these three materials by accident, you have greater worries than the integrity of your wedding ring!

The chemical susceptibility of gold for these reagents has proven useful. Mercury and cyanide salts have been used to extract gold from its ore. In fact, gold cyanidation, developed industrially in the 1880s by Glaswegian chemists John Stewart McArthur and Robert and William Forrest is still the main method of gold extraction – and the biggest use of sodium cyanide – globally. The ability of aqua regia to dissolve gold helped foil the Nazis during World War II. Two German Nobel laureates had placed their medals (23K gold) at the Niels Bohr Institute in Copenhagen for safe-keeping. But removing gold from Nazi Germany was a grievous offense and with the laureates names inscribed on the medal, this was an incriminating piece of evidence. ‘While the invading forces marched in the streets’, George de Hevesy – a (future) Nobel laureate himself – dissolved the medals in aqua regia. While the laboratories were laboriously searched by the Nazis, the medals remained dissolved, but undiscovered, on the bench. The metal was recovered after the war and the medals recast and returned to the laureates.

Whatever gold you choose for your wedding band, you add to a rich history of human civilisation fascinated by and adorned with gold. And to the newlywed class of 2014, congratulations!

 

 

* Note: Aqua regia is latin for ‘King’s water’, a 1:3 nitric:hydrochloric acid solution, it is known in Russia as Tsar’s vodka and its ability to dissolve gold is shown wonderfully in this Periodic Table of Videos.

References:

 

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Categories: Education

Academic family: the Nobel prize in Chemistry 2014

14 October, 2014 - 13:29

Guest post by JessTheChemist

‘Where the telescope ends, the microscope begins. Which of the two has a grander view?’ – Victor Hugo

In 1873, German physicist Ernst Abbe reported that the resolution limit of the optical microscope was 0.2 micrometres. Although this still remains true, recent work in the field of microscopy – specifically Stimulated Emission Depletion (STED) microscopy and single-molecule microscopy – has allowed scientists to visualise molecules smaller than this limit. This is accomplished by tagging molecules with fluorescent labels, which allows a more detailed picture to be visualised. On Wednesday 8th October 2014 Eric Betzig, Stefan Hell and William Moerner were awarded the Nobel prize in chemistry for their ground-breaking work in ‘the development of super-resolved fluorescence microscopy’. You can learn more about the ins and outs of the Nobel prize winners’ work by reading the recent Chemistry World article.

I am interested in finding out how chemists are connected to each other, and in particular, investigating whether your likelihood of winning a Nobel prize is increased by having a high number of laureates in your family tree.  It is also interesting to see how closely related, if at all, are the scientists that share a prize.

If we consider his academic pedigree, one might say that Eric Betzig was destined to become a Nobel prize winner. He is connected to a number of notable laureates, including the father of nuclear physics, Ernest Rutherford. Rutherford won the Nobel prize for chemistry in 1908 ‘for his investigations into the disintegration of the elements, and the chemistry of radioactive substances’. Through Rutherford, Betzig is also connected to Niels Bohr, who won the Nobel prize for physics in 1922 for ‘his services in the investigation of the structure of atoms and of the radiation emanating from them’.

Additionally, Betzig is academically related to John William Strutt (Lord Rayleigh) who won the prize for physics for the discovery of argon in 1904, along with his collaborator Sir William Ramsay, who won the 1904 chemistry prize for the same discovery. With ancestry like that, Betzig was always destined for greatness.

Alternatively, William Moerner is closely linked to Dudley Herschbach and Yuan T. Lee, who won the 1986 Nobel prize in chemistry ‘for their contributions to the dynamics of chemical elementary processes’. To find out more about Herschbach and Lee’s academic family connections, check out last month’s blog post about one of their connections, Sir Harry Kroto.

Although Eric Betzig and William Moerner worked independently from one another, they both developed single-molecule microscopy, so it is not a surprise that their lineage is intertwined. As you can see from the tree, they are connected via some of the science greats such as Linus Pauling.

Stefan Hell worked in a slightly different field to Betzig and Moerner and, amongst others, is connected to biochemists Robert Huber and Johann Deisenhofer, who won the 1988 Nobel prize for chemistry ‘for the determination of the three-dimensional structure of a photosynthetic reaction centre’.  As predicted, however, all three of the prize winners can be connected through their academic relations – via Deisenhofer, Hell can be connected to Moerner and, therefore, Betzig.

As you can see, all three winners have a rich Nobel history but what I found particularly interesting about this academic family tree is that it contains scientists from all sorts of backgrounds – from nuclear physics to biochemistry to organic chemistry. This led me to think, what kind of scientists am I connected to? To find out what kind of scientists you are connected to, head to academictree.org, where you can add yourself to the website and start creating your very own tree.  You never know who you may be connected to.

And don’t forget to tweet me (@Jessthechemist) with suggestions for the focus of next month’s blog post!

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Categories: Education

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