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Chemistry colouring-in

Posted on September 16, 2012 by Danzig

— 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

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Soft robotics ‘elephant trunk’ with a delicate touch

Posted on September 16, 2012 by Danzig

I picked it for you! © Wiley

Recreating the dexterity and control of an elephant’s trunk is no easy task. However, engineers over the years have risen to the challenge and have developed sophisticated robotic arms. The problem is that they don’t come cheaply. The fine motors and mechanical joints can cost thousands of pounds and could be too valuable to put in risky situations, so what if you could make one for less than $10?

That’s exactly what George Whitesides and his team at Harvard have achieved. By using silicone elastomer tubing and pressurised air, they produced a ‘tentacle’ that can be used for picking up delicate or complicated objects such as flowers or horseshoes. Published in Advanced Materials this month, this is the latest in a series of developments in the ‘pneumatic network’ method over the past few years. Previously, the group developed a starfish-like gripper that could pick up an egg, but the gripping motion was the limit of its movement. Whitesides’ groups have also used this soft robotics technology to develop a crawling robot.

This new tentacular system has hard polymer tubing running through the centre which can bend easily – but resists stretching – surrounded by a highly elastic polymer with channels running through it to allow pressurised air to enter. By controlling which channel the air enters, the tentacle can be manipulated to twist and turn in three dimensions. The construction of the tubing might be simple, but controlling it looks a lot more difficult!

Describing the new system as a tentacle is selling it short — it can do so much more. Just like an elephant’s trunk, it can use the central tubing for suction, either to lift objects or suck up liquids and powders. Just like the best robots (or colonoscopes), it can even have a video camera attached to the end.

As well as being cheaper than conventional ‘hard’ robots, this soft tubing has other advantages. The nature of the system allows for an even pressure spread across the object, rather than the ‘pincer’ method that we use with our fingers and that many robots try to emulate. Also, the stiff links and fixed structure of most robotic arms mean that they have difficulty in situations that they are not specialised for. The flexibility of the tubing allows it to grip in various ways and adapt as is needed.

The long list of innovations coming from the lab of George Whitesides have led to him having his name on nearly 1000 academic papers and over 100 patents. He is a co-founder of a dozen companies, including Genzyme which was the third largest biotech company in the world before it was acquired by Sanofi for $20 billion in 2011. With the level of development in this technology, I imagine it won’t be long before we see these tentacles going commercial.

Ian Le Guillou

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Glassblowing and old newspaper

Posted on September 16, 2012 by Danzig

A Dartington glassblower uses a newspaper paddle to shape a piece of blown glass

A letter in the Financial Times about a month ago piqued my interest. It stated that the characteristic salmon pink pages of the FT play a unique role in producing hand-made crystal glass at Dartington crystal. Since I was about to go on holiday to Devon, and had planned a trip to the Dartington factory anyway, I decided to do a bit of investigating myself.

In the FT letter, the correspondent says that the reason for using the pink pages of the FT is so that no trace elements are transferred to the crystal ‘when the protective newsprint is peeled away’, as they might be with other, bleached, newspaper.

This sounded a little implausible to the chemist in me. If the newspaper was only being used for protection, surely any interaction with the crystal glass would be confined to the ink, or any contaminants left from the paper processing, rubbing off on the surface? The possibility of significant chemical reaction between the glass and the newsprint at room temperature seemed remote at best.

A tour of the factory quickly confirmed my hunch. The role of the newspaper is much more than simply protective, but perhaps quite surprising. It is an integral tool in shaping blown glass. The yellow-handled paddle in the picture is actually made up of a wad of newspaper.

This yellow handled paddle is actually a stack of newspapers

As the glassblower blows and shapes a globule of molten glass into a tumbler (in this case) or any other object, part of the process involves dipping that paddle into a bucket of water and holding it up to the red hot glass. At the same time he rolls the blowpipe backwards and forwards to ensure the glass is the right shape and consistent thickness.

Newspaper is absorbent and cheap to replace, making it ideal for making these paddles. However, being in contact with glass at several hundred degrees means the paper does burn away slowly, so it’s important it doesn’t transfer contaminants to the glass in its semi-molten state, which could then create imperfections in the final product.

So that begs the question, what is it about the FT that makes it the preferred choice of glassblowers? Is it something to do with the chemical processing of the paper? Is the paper bleached less ferociously than its white cousins? Or does the dyeing process mean any residues from the bleaching are washed out more thoroughly? Or is it simply tradition with little scientific backing? Speaking to some of the Dartington staff I got some vague answers about the ‘quality of the paper’, but it would be interesting to know if any of our readers have more insight.

If you have never watched a glassblower at work, it is quite an amazing experience. The apparently effortless skill of a master glassblower is breathtaking. No wonder it takes around 10 years to reach that level. But, as with glassblowing for chemistry equipment, it is a skill that is slowly dying out – Dartington is one of the last commercial-scale producers of hand-blown glass in the UK.

Phillip Broadwith

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Love Hurts: Brain Chemistry Explains the Pangs of Separation [Excerpt]

Posted on September 15, 2012 by Danzig

Larry Young and Brian Alexander explain how heartache begins in the brain in The Chemistry Between Us

By Larry Young and Brian Alexander

Image: Current, a member of Penguin Group (USA), Inc.

Editor's Note: Neurobiologist Larry Young studies a monogamous species of rodent, the prairie vole, to understand the behavior and chemistry behind relationships. In The Chemistry Between Us, Young teams up with science journalist Brian Alexander to describe science's progress in illuminating the neurochemistry behind our experience of love. In this excerpt, the authors describe the work of neurobiologist Oliver Bosch, a specialist in maternal behavior, who worked with Young's prairie voles to study the bitter price of bonding.

Excerpted from The Chemistry Between Us: Love, Sex and the Science of Attraction, by Larry Young, PhD, and Brian Alexander, by arrangement with Current, a member of Penguin Group (USA), Inc., Copyright Larry J. Young and Brian Alexander, 2012.

To investigate the rodent version of getting hugs, and what happens in the absence of hugs from a bonded partner, Bosch took virgin males and set them up in vole apartments with roommateseither a brother they hadn't seen in a long time or an unfamiliar virgin female. As males and females are wont to do, the boy-girl roommates mated and formed a bond. After five days, he split up half the brother pairs, and half the male-female pairs, creating what amounted to involuntary vole divorce. Then he put the voles through a series of behavioral tests.

The first is called the forced-swim test. Bosch likens it to an old Bavarian proverb about two mice who fall into a bucket of milk. One mouse does nothing and drowns. The other tries to swim so furiously the milk turns into butter and the mouse escapes. Paddling is typically what rodents will do if they find themselves in water; they'll swim like crazy because they think they'll drown if they don't. (Actually, they'll float but apparently no rodent floaters have ever returned to fill in the rest of the tribe.)

The voles that were separated from their brothers paddled manically. So did the voles who stayed with their brothers and the voles who stayed with their female mates. Only the males who'd gone through vole divorce floated listlessly as if they didn't care whether they drowned.

"It was amazing," Bosch recalls. "For minutes, they would just float. You can watch the video and without knowing which group they were in, you can easily tell if it's an animal separated from their partner, or still with their partner." Watching the videos of them bob limply, it's easy to imagine them moaning out "Ain't No Sunshine When She's Gone" with their tiny vole voices.

Next Bosch subjected the voles to a tail-suspension test. This test uses the highly sophisticated technique of duct taping the end of an animal's tail to a stick and suspending it. As in the swim test, a rodent thus suspended will usually flail and spin his legs like a cartoon character who's run off the edge of a cliff. Once again, though, while the other males did just that, the divorced males hung like wet laundry.

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Love Hurts: Brain Chemistry Explains the Pangs of Separation [Excerpt]

Chemistry comes alive at the Botanic Garden

Posted on September 15, 2012 by Danzig

Chemistry comes alive at the Botanic Garden

5:50pm Friday 14th September 2012 in News

VISITORS to the Botanic Garden in Oxford are being invited to listen and learn about the chemistry giving plants flavours, colours and medicinal properties.

A new audio tour features recordings of students and chemistry lecturers at Oxford University who reveal what fascinates them about plants.

As visitors walk around the garden, off High Street, they can use a hand-held device to trigger recordings about the plants around them.

Senior curator Dr Alison Foster said: This audio trail is a fantastic way for research scientists to engage with the public about chemistry.

This trail will show everyone how important chemistry is and how relevant it is to all aspects of our daily lives.

Visitors can discover the way that lotus leaves use microscopic cushions of air to repel raindrops, how ginger gets its many distinctive flavour from a cocktail of molecules, and how the snowdrop is used to treat Alzheimers disease.

Chairman of the Department of Chemistry Prof Tim Softley said: Chemistry is all around us, and we see it as our responsibility, as leading scientists, to make the subject exciting, relevant, approachable and fun.

In March, an audio guide was created at the garden featuring a recording by author Philip Pullman about a bench which featured in the His Dark Materials trilogy.

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Chemistry comes alive at the Botanic Garden

Chemistry renovation could create more labs

Posted on September 11, 2012 by Danzig

Future University of Wisconsin-Madison students may have an easier time registering for introductory chemistry courses and be able to conduct more experiments in new lab facilities if building project plans receive additional funding from the UW System.

The UW System Board of Regents approved the 2013-15 Biennial Capital Budget in their August meeting, but it remains subject to further approval by Gov. Scott Walker and the state legislature.

According to Regent Katherine Pointer, the student representative on the Board, the project focuses on correcting a current lack of general chemistry lab space, which prohibits the university from offering more courses.

Pointer said the extra chemistry building could especially benefit general chemistry classes such as Chemistry 103 and 104, which are the two courses with the highest enrollment during the fall and spring semesters.

The courses currently lack sufficient lab space to accommodate the number of students who wish to enroll, according to Pointer.

Pointer said while the $103.5 million project focuses on increasing lab space, it would also provide additional offices, classrooms and lecture halls.

UW-Madison Chemistry professor Fleming Crim said the building is severely out-of-date and has needed improvments for more than a decade.

Crim said lecture halls in the chemistry building are like something out of Dickens and it is challenging to teach 21st century chemistry in a building constructed in 1967.

The laboratories were built at a time when the way you taught chemistry was more like going and turning the crank, Crim said. Now [teaching] is a lot more interactive with people working together, and you want people involved with each other and with teaching assistants.

According to Crim, the physical layout of the labs is inadequate due to insufficient air circulation throughout the labs, which prevents students and professors from conducting most experiments involving hazardous materials.

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Chemistry renovation could create more labs

UGA chemistry discovery could have major medical implications

Posted on September 11, 2012 by Danzig

Public release date: 10-Sep-2012 [ | E-mail | Share ]

Contact: Michael K. Johnson mkj@uga.edu 706-542-9378 University of Georgia

Athens, Ga. The study of an oxygen-sensing bacterial regulatory protein by chemistry researchers at the University of Georgia has provided molecular insight into the oxygen sensing mechanism, which could ultimately lead to a better understanding of the ageing process and new treatments for human diseases such cancer, Parkinson's and Alzheimer's.

Michael Johnson, a distinguished research professor of chemistry in the UGA Franklin College of Arts and Sciences, and Bo Zhang, a UGA chemistry doctoral candidate, have discovered that the fumarate and nitrate reduction regulatory protein, or FNR, in E. coli senses oxygen by a new type of reversible structural change in an iron-sulfur cluster. The work was carried out in collaboration with Nick Le Brun and coworkers from the University of East Anglia. The results were published Sept. 10 in the journal Proceedings of the National Academy of Sciences USA.

Iron-sulfur clusters are abundant biological cofactors that play crucial roles in almost all of fundamental life processes, including respiration, photosynthesis, nitrogen fixation, DNA replication and repair. "Everyone has trillions of iron-sulfur clusters associated with enzymes and proteins in their bodies," Johnson said. "The problem is that they readily degrade in the presence of oxygen and other species that are associated with oxidative stress, leading to loss of protein function."

The research conducted at UGA and UEA focused on FNR, which senses the presence of oxygen in the environment and "switches" off and on specific genes in pathogens, such as E. coli, when there is no oxygen presentconditions often found in the human intestinal tract. Oxygen is sensed by FNR via its iron-sulfur clusterthat undergoes conversion from one form to another, smaller one, thereby causing the protein to change shapethe "switch"and leading to the turning off of genes associated with growth without oxygen.

"E. coli can decide what lifestyle to live, with or without oxygen," said Johnson. "We can't decide to change our need for oxygen, but understanding the mechanisms for reassembly and repair of iron-sulfur clusters in response to oxidative stress is crucial for understanding a host of human diseases as well as the ageing process."

By revealing the structure of the oxygen-damaged cluster in FNR and showing that it can be readily repaired by the addition of iron, this research has discovered a major mechanism for the repair of iron-sulfur clusters. Moreover, preliminary results on other iron-sulfur cluster containing enzymes suggest that this type of iron-sulfur cluster oxygen-damage and repair mechanism is widespread in biology.

Bo Zhang, the lead author on paper said that the iron-sulfur cluster switching mechanism in response to oxygen is smart. "They don't panicthey calmly keep their extra sulfurs and wait to be repaired," said Zhang. She said that any medical applications of the research could take 10 to 20 years for development. The next step is to discover how the repair process works in the cell. Johnson and Zhang are currently working on in vitro models to mimic this biological repair process.

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UGA chemistry discovery could have major medical implications

Oxygen-sensing bacterial regulatory protein: Chemistry discovery could have major medical implications

Posted on September 12, 2012 by Danzig

ScienceDaily (Sep. 10, 2012) The study of an oxygen-sensing bacterial regulatory protein by chemistry researchers at the University of Georgia has provided molecular insight into the oxygen sensing mechanism, which could ultimately lead to a better understanding of the aging process and new treatments for human diseases such cancer, Parkinson's and Alzheimer's.

The research conducted at UGA and UEA focused on FNR, which senses the presence of oxygen in the environment and "switches" off and on specific genes in pathogens, such as E. coli, when there is no oxygen present-conditions often found in the human intestinal tract. Oxygen is sensed by FNR via its iron-sulfur cluster-that undergoes conversion from one form to another, smaller one, thereby causing the protein to change shape-the "switch"-and leading to the turning off of genes associated with growth without oxygen.

Bo Zhang, the lead author on paper said that the iron-sulfur cluster switching mechanism in response to oxygen is smart. "They don't panic-they calmly keep their extra sulfurs and wait to be repaired," said Zhang. She said that any medical applications of the research could take 10 to 20 years for development. The next step is to discover how the repair process works in the cell. Johnson and Zhang are currently working on in vitro models to mimic this biological repair process.

Research reported in this publication was supported by the National Institute of General Medical Sciences at the National Institutes of Health under award number GM62524.

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Oxygen-sensing bacterial regulatory protein: Chemistry discovery could have major medical implications

Martin Fleischmann

Posted on September 9, 2012 by Danzig

With Martin Fleischmann’s passing on the 3 August, obituaries around the world have revived memories of his notorious association with the cold fusion debacle in the early 1990s. In a letter to Chemistry World, David Williams, a former colleague of Fleischmann’s, attempts to redress the balance, painting an affectionate picture of a brilliant electrochemist, and is careful to convey the importance of Fleischmann’s contributions to science, and his charismatic genius. Williams’ personal account of the episode that led to Fleischmann and Stanley Pons’ Utah press conference and their subsequent pillorying is enlightening.

Science is ruled by the laws of systematic, empirical investigation, where incremental advances and the gradual acquisition of knowledge are the status quo. Truly groundbreaking discoveries are few and far between (but there are just enough to keep our hopes alive). So when such announcements are made, they are of course greeted with the healthy and necessary corrective moderation of scepticism.

And mistakes do happen. Recent examples include the reconstruction of the oxo wall and the withdrawal of record proton conductivity claims. And the retraction watch blog is steadily ticking away, silently intoning its litany of errata.

But once its trust has been betrayed, the science community can be unforgiving, and a reputation damaged is hard to regain, long after the press has emptied the carcass and moved on. Undoubtedly, Fleischmann and Pons tragically mishandled their situation. But where science is ideal, objective and dispassionate, its practitioners are only human and – believer and sceptic alike – they are emotionally responsive. Witness Peter Higgs’ tears at CERN earlier this year. Or the attacks on Felisa Wolfe-Simon’s (now largely discredited) announcement of arsenic life. Or the hostility that followed Fleischmann back to England and sent Pons into isolation.

In his letter, Williams wonders if it was just a single piece of evidence that swayed Fleischmann’s decision to go public. How volatile is temperance in the heat of excitement. One can only imagine how unbearable the tension must have been; how irresistible the lure of proclaiming one’s success; and how crushing the defeat.

Those treacherous imposters triumph and disaster are courted at one’s peril. But it’s often too much for mere mortals to resist.

Philip Robinson

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Heptares Solves First Family B GPCR Structure

Posted on September 10, 2012 by Danzig

WELWYN GARDEN CITY, England and BOSTON, September 10, 2012 /PRNewswire/ --

Update on novel structures and product pipeline to be presented at Biochemical Society and Royal Society of Chemistry meetings

Heptares Therapeutics today announces that it has used its StaR technology to solve entirely in-house the first structure of a Family B sub-class G protein-coupled receptor (GPCR). Chief Scientific Officer, Fiona Marshall and Chief Executive Officer, Malcolm Weir, will present views of a high resolution X-ray crystal structure of the Corticotropin Releasing Factor (CRF-1) receptor, together with information about additional novel in-house GPCR structures and Heptares pipeline programmes, at upcoming scientific conferences.*

CRF-1, a drug target for depression and anxiety, is a member of the Family B sub-class of nearly 50 GPCRs, which includes many targets such as GLP-1 (diabetes), PTH (bone) and CGRP (migraine) that have proven intractable to small molecule chemistry. Novel and unexpected insights into receptor topology, conformation and compound binding have been revealed, showing major differences compared to the many already known Family A structures, such as beta-adrenergic receptor. Owing to the close relationship among Family B GPCRs, these insights from the CRF structure will allow high-quality structural models to be generated to the entire family and provide new avenues for discovery, which are being leveraged by the Company using its proprietary structure-based drug design platform.

Heptares is also reporting the first structure for the Muscarinic M1 receptor in the agonist conformation, and the first structure for the Orexin-2 receptor in an antagonist confirmation. The M1 structure shows conformational and subtype differences in the ligand binding site compared to muscarinic antagonist-bound structures, and is central to Heptares' selective orthosteric agonist programme for the treatment of Alzheimer's disease and other disorders involving cognitive impairment.

The Orexin-2 structure shows substantial topological differences compared to other peptide Family A receptors, and enables selective drug design to both Orexin-2 (chronic insomnia) and Orexin-1 (anti-craving in addiction and compulsive disorders) subtypes, and modelling of receptor activation.

The Heptares platform is nucleated around its unique ability, using its StaR technology, to stabilise GPCRs in precisely defined, biologically-relevant conformations. These StaRs can then be used, based on receptor structural information from X-ray crystallography and Biophysical Mapping, to design and build (atom-by-atom) small molecules with specified drug action and properties, creating an unparalleled medicinal chemistry capability for addressing extremely difficult GPCR targets.

"No Family B GPCR trans-membrane domain structures have been solved until now, highlighting the power of our StaR technology. This is a fundamental discovery for GPCR drug design, and for our understanding of the mechanism of action and function of these biologically important receptors," said Fiona Marshall, CSO of Heptares Therapeutics.

"These exciting new structural insights are allowing Heptares to deliver potentially ground-breaking new medicines, which is our sole focus. We have a robust platform and pipeline, with our industry-first selective Muscarinic M1 agonist expected to enter clinical development next year and further programmes for additional CNS and metabolic disorders advancing well," said Malcolm Weir, CEO of Heptares Therapeutics.

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Heptares Solves First Family B GPCR Structure

Chemistry World Entrepreneur of the Year 2013

Posted on September 9, 2012 by Danzig

Do you know an enterprising individual? Do you know anybody who has contributed to the growth of a start-up company that successfully commercialises chemistry-related research? If so, please read on: with your help, that person could become the next winner of the Chemistry World Entrepreneur of the Year award.

This annual award recognises commercial innovation and success and is open to those working in a chemical sciences spin-off or SME anywhere in the world. The award winner receives £4000, a trophy and a certificate plus he or she will be featured in Chemistry World, which is, without a doubt, a great promotional opportunity.

Previous winners include (to name a few): Paul Workman from The Institute of Cancer Research who received the 2012 award and has been profiled in this month’s issue of Chemistry World; Karl Coleman from Durham Graphene Science who became the 2011 winner; and Hagan Bayley from the University of Oxford for his founding role in Oxford Nanopore Technologies.

So how can you help? Well, as candidates are not permitted to nominate themselves we need you to do it. More information and ‘how to apply’ notes are available at http://www.rsc.org/ScienceAndTechnology/Awards/EntrepreneuroftheYear/Index.asp. We are already taking nominations for 2013, but the closing date is 15 January 2013 so there is plenty of time to go… Good luck to all!

Bibiana Campos-Seijo

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Chemistry in its element – coniine

Posted on September 9, 2012 by Danzig

A slow, lingering death – that you’d be conscious to endure. That’s the fate that coniine has in store for anyone unfortunate enough to ingest it. Find out about the poison that killed Socrates in this week’s Chemistry in its element podcast.

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Earth to Mars – Live chat with the driver of Curiosity

Posted on September 9, 2012 by Danzig

In November last year, ahead of Curiosity’s launch, we wrote: ‘This rover – officially named the Mars Science Laboratory, but better known as Curiosity – will carry out the most comprehensive look at Earth’s neighbour to date when it lands on the planet in August 2012.’

When Curiosity safely touched down on Mars in August with its suite of scientific equipment, including a mass spectrometer, a gas chromatograph and a tuneable laser spectrometer, there were still questions as to the ability of the probe to detect signs of habitability. And so we wondered: will Curiosity be searching in vain?

Curiosity is still up there collecting data and what we all want to know is: how is the search going? It occurred to us that the best way to learn how the rover is getting on is by talking to the guys who control it. As it happens, one of our colleagues, Chiara Ceci, got in touch with an old friend and fellow Italian, Paolo Bellutta, who she knew worked at JPL, Nasa’s Jet Propulsion Laboratory, in Pasadena, US. And guess what? He has been handling the Mars rovers Spirit and Opportunity since 2003 and now spends his time driving Curiosity on the surface of Mars. How cool is that!

So she is going to ask him all about it and the interview will be broadcast live on the RSC YouTube channel on Friday 7 September at 1600 BST. Can you ask questions? Of course you can. In fact, we positively encourage it. Send them via the usual channels (see below) or let us know by replying to this post and we’ll pass the questions on.

By the way, before anybody asks: No, we are not allowed to have a go.

Bibiana Campos-Seijo

-Twitter: Questions to @RSC_Comms and follow the live chat using #RSCmars

-Facebook: http://www.facebook.com/royalsocietyofchemistry

-Google+: http://rsc.li/rsc-google-plus

-Email: cecic@rsc.org

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NGCSU professor joins MERCURY Consortium

Posted on September 8, 2012 by Danzig

DAHLONEGA - A chemistry professor at North Georgia College & State University has become one of only 17 professors in the country granted access to the MERCURY Super-Computing Cluster.

Dr. Aime Tomlinson, associate professor of chemistry at North Georgia, has joined MERCURY (Molecular Education and Research Consortium in Undergraduate computational chemistRY), a group of undergraduate institutions that promotes research in computational chemistry. North Georgia is one of only 14 institutions granted access to MERCURYs resources, a cluster of high-performance computers used by chemistry students and researchers at multiple undergraduate institutions across the country.

Our acceptance into the consortium will allow us access to the MERCURY Super-Computing Cluster, said Tomlinson, one of only 17 professors with access to the cluster. The type of calculations we do in computational chemistry could take a month to perform on a normal computer, but the cluster can perform those calculations in about eight hours.

Created and directed by Dr. George Shields, MERCURY holds an annual symposium during which students present research conducted with aid from the super-computing cluster. The first MERCURY symposium was held in 2002. Shields spoke at North Georgia in 2009, and invited Tomlinson to participate in that year's symposium.

Tomlinson was invited to join the consortium in December 2011 and two of her students presented research this summer at the 2012 symposium. Before gaining access to MERCURY, Tomlinsons students had performed their calculations via super-computing clusters in Pittsburgh and San Diego.

Being a part of MERCURY will allow us to run high-power calculations even faster, Tomlinson said. It also makes training students in these calculations much easier.

One of Tomlinsons main projects is developing organic materials for use in solar cells. She and her students use super-computing clusters to perform the calculations for potential structures, and then make recommendations based on these results to Tomlinsons synthetic collaborators at Iowa State University.

The research focuses on benzobisazoles, a synthetic compound that we manipulate the core of to make it more conducive to collecting and storing solar energy, Tomlinson said.

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NGCSU professor joins MERCURY Consortium

Sweden’s 400-year old warship gets a checkup

Posted on September 9, 2012 by Danzig

The remains of the warship Vasa, which is around 400-years old – one of Sweden’s most popular tourist attractions with over 1 million visitors a year – could be significantly weaker than previously thought. But if you’re planning a trip to Stockholm in the near future, don’t worry: the ship isn’t in immediate danger.

The Vasa was built in 1628 during Sweden’s golden age for King Gustavus Adolphus and sank on its maiden voyage, just 2km from its dock. For the time, it was an enormous ship, capable of carrying 300 soldiers and firing a broadside of almost 600 pounds. But its construction seems to have been dogged by too many political considerations meaning it was built top-heavy. When the wind blew above a light breeze as it was manoeuvring in Stockholm harbour, that was it.

The Vasa was sprayed with polyethylene glycol to preserve the oak timbers. Credit: Ingela Bjurhager

For more than 300 years, the Vasa lay under the cool waters of the Baltic, until she was raised in 1961 to widespread media interest. Those cool waters are believed to have helped keep the oak timbers intact. Since then, the Vasa has been dried out, sprayed with polyethylene glycol (PEG) and housed in a museum.

PEG replaces water in the cells of the wood, strengthening it and stopping the shrinkage that would occur while it was drying. Now, a team of researchers from institutions in Stockholm and Uppsala have measured the tensile strength of portions of the wood taken from different parts of the ship. They found that the strength is roughly proportional to the molecular weight of PEG – the longer the polymer chains the better preserved that portion of the ship is likely to be. But the molecular weight of the polymer – and thus strength – is inversely proportional to the amount of iron present in the wood. The iron, in case you were wondering, comes from the iron nails and rivets that held the ship together.

So what’s going on between the iron and PEG? Ingela Bjurhager and colleagues suggest that, while the ship was drying out, iron and oxygen reacted with cellulose and lignin in the wood to produce an acid. The acid, they think, is responsible for the degradation of the polymer and the weakening of the wood – by up to 80% in some areas. Although the Vasa isn’t about to fall apart, the researchers do caution that the ‘risk of failure cannot be disregarded’.

UK readers may be thinking about our own salvaged historical wooden museum ship, the Mary Rose. She sank during the Battle of the Solent in 1545 after over 30 years’ service as Henry VIII’s favourite, only to rise again in 1982 – another televised salvage (which I remember watching as a child!). PEG was also used in treating the timbers, but from what Wikipedia tells me, they were not allowed to dry out beforehand, so it may retain such strength as it now has for longer. Neatly, I see that the Mary Rose will be unveiled in a new museum later this year – I’ll report back after a visit! (Full disclosure: my father-in-law is involved in the Mary Rose Trust.) Hopefully, my adult self will be more impressed seeing it than I was during a previous visit as a child seeing the hull being showered with water or PEG…

Neil Withers

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Changes in water chemistry leave lake critters defenseless

Posted on September 7, 2012 by Danzig

Public release date: 6-Sep-2012 [ | E-mail | Share ]

Contact: Janice Walls wallsj@yorku.ca 416-736-2100 x22101 York University

TORONTO, Sept. 6, 2012 Imagine that the players on your favourite football team were smaller than their opponents, and had to play without helmets or pads. Left defenseless, they would become easy prey for other teams. Similarly, changes in Canadian lake water chemistry have left small water organisms vulnerable to their predators, which may pose a serious environmental threat, according to a new study.

"At low calcium levels the organisms grow slower and cannot build their armour," says study lead author Howard Riessen, professor of biology, SUNY College at Buffalo. "Without suitable armour, they are vulnerable to ambush by predators," he says.

Riessen and colleagues, including York University biology Professor Norman Yan, studied the effect of changes in water chemistry on plankton prey defenses. Specifically, they examined how lower calcium concentrations affect Daphnia (water flea) exoskeleton development. These low calcium levels are caused by loss of calcium from forest soils, a consequence of decades of acid rain and multiple cycles of logging and forest growth. The results are published this week in the Proceedings of the National Academy of Sciences.

"Calcium is a critical element for Daphnia and many other crustaceans," Riessen says. "Daphnia build their exoskeletons, which include some defensive spines, with calcium to protect themselves from predators. Where calcium levels are low, the Daphnia have softer, smaller, exoskeletons with fewer defensive spines, making them an easy snack."

Why do plankton matter? Yan, the study's senior author and a Fellow of the Royal Society of Canada, emphasizes that the tiny creatures are critical to our survival. "Without plankton, humans would be quite hungry, and perhaps even dead. Much of the world's photosynthesis, the basis of all of our food, comes from the ocean's plankton. The oxygen in every other breath we take is a product of phytoplankton photosynthesis," says Yan.

This phenomenon of reduced calcium is also playing out on a much larger scale in the world's oceans, he notes. "Increases in ocean acidity are complicating calcium acquisition by marine life, which is an under-reported effect of global carbon dioxide emissions. Thus marine plankton may also find themselves more vulnerable to predators," he says.

The public is used to stories about changes in water chemistry that lead to large-scale fish kills, says Riessen. "These changes are more insidious. Daphnia might not be a household name, but they are food for fish, and they help keep our lakes clean. Changing the balance between Daphnia and their predators marks a major change in lake systems."

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Changes in water chemistry leave lake critters defenseless

Undergraduates Aid Millsaps College Chemists In Analysis Of 'Black Drink' Residue For Study Published In NAS Proceedings

Posted on September 7, 2012 by Danzig

JACKSON, Miss., Sept. 6, 2012 /PRNewswire/ --Researchers from across the United States, including Millsaps College Professor of Chemistry Timothy Ward, Ph.D., and Research Fellow Jiyan Gu, Ph.D., have analyzed chemical residues in prehistoric Native American ceramic vessels that are believed to offer the earliest known evidence for black drink consumption. Their findings were published in the on-line Proceedings of the National Academy of Sciences in August.

Black drink is a caffeinated tea-like beverage brewed from holly leaves and stems that was used during cleansing rituals and religious ceremonies. The ceramic vessels tested date to approximately 1050-1250 A.D. and are associated with the prehistoric Native American civilization of Cahokia, once located near present-day St. Louis.

Chemists at Millsaps College's W.M. Keck Center for Instrumental and Biochemical Comparative Archaeology in Jackson, Miss. designed and developed the methods to identify the chemical compounds found in residue from porous, unglazed mug-shaped ceramic containers excavated from sites in Missouri and Illinois. Ward and Gu led the development of the chemical methods and oversaw the chemical analysis and data generation. The chemists differentiated between the presences of several substances to identify a chemical signature, or bio-marker, for the holly species Ilex. The work was funded in part by the W.M. Keck Foundation.

A remarkable aspect of the research project is that undergraduate students from Millsaps College conducted the chemical analysis, working under the direction of Ward and Gu.

"At Millsaps, students in the sciences learn to operate sophisticated instruments and participate in research normally reserved for graduate students in the latter years of graduate study," Ward said. "Such notable experiences build the resumes of Millsaps graduates in ways that make our students sought after by graduate research programs and medical schools. Interestingly, the most often asked question of our students at the various national and international meetings where we present is always, 'Did you really do that work yourself?'"

Millsaps students, Syed Ali of Madison, Miss., Marlaina Berch of Sturgis, Miss., and Erin Redman of Carrboro, N. C., are acknowledged in the published article of the findings, "Ritual Black Drink consumption at Cahokia."

Since conducting the research, Berch and Redman graduated from Millsaps with bachelor's degrees in chemistry. Berch is a medical student in the Rural Physicians Program at the University of Mississippi School of Medicine, and Redman is studying analytical chemistry at the graduate level at the University of North Carolina. Ali, a biochemistry major, is a junior at Millsaps College.

"One thing impressive and interesting about the Keck Center at Millsaps is that it is staffed with a diverse group of undergraduates with unique backgrounds," Gu said. "We have students born in America, Vietnam and Pakistan as well as international students that have come from China and Rwanda. Students not only work together in the lab, but they build friendships and learn from each other's unique perspectives, exchanging their favorite music, stories from their native country, ideologies and their dreams.

"The Keck Lab is a small reflection of Millsaps culture, a culture that will prepare students for a world full of diversity, a world in which the great things can only be achieved by working with people from different background and perspective."

Sociologists and chemists cited equally as authors in the study are Gu; Ward; University of New Mexico Distinguished Professor of Anthropology Patricia Crown, working with Thomas E. Emerson from the Illinois State Archeological Survey, Prairie Research Institute and University of Illinois, Champaign; W. Jeffrey Hurst at the Hershey Technical Center in Hershey, Penn.; and Timothy R. Pauketat from the Department of Anthropology at the University of Illinois at Urbana-Champaign, Urbana.

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Undergraduates Aid Millsaps College Chemists In Analysis Of 'Black Drink' Residue For Study Published In NAS Proceedings

U receives $13M for 2 campus chemistry centers

Posted on September 3, 2012 by Danzig

The University of Minnesota is now home to two new centers that could potentially reduce carbon emissions and make solar energy more efficient.

The Department of Chemistry received $13.1 million from the U.S. Department of Energy to fund the centers, which officially began research Saturday.

Its kind of a tribute to the science [here] that for both centers they chose Minnesota, said Christopher Cramer, director of the new Center for the Study of Charge Transfer and Charge Transport in Photoactivated Systems.

Both centers focus on theoretical chemistry and will use the Minnesota Supercomputing Institute to test models and programs.

Because the University already has this hardware, most of the grant money for both centers will be used to hire more researchers.

The Nanoporous Materials Genome Center will receive $8.1 million and partner with six other institutions.

Laura Gagliardi, director of the center, said the goal will be to create a database, or genome, of nanoporous materials in order to have a standard way of reporting the properties of these materials. This will allow researchers to make faster advances in the field because theyll have a reference guide, she said.

Nanoporous materials can be used in carbon capture, for example, to sequester carbon dioxide and reduce pollution. Gagliardi said they will evaluate which materials could be best suited for this.

This center will also house experiments to develop and test nanoporous materials to confirm theorists predictions.

Its really about the interplay between modeling and experiment that we hope the most exciting results will arise, Gagliardi said.

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U receives $13M for 2 campus chemistry centers

Non-equilibrium quantum states in atmospheric chemistry

Posted on September 3, 2012 by Danzig

An artist's impression of O2 'intercepting' the beta-hydroxy vinyl (BHV) radical. The hot orange colours represent non-equilibrium quantum states, while the cooler blue colours represent equilibrium quantum states.

(Phys.org)Research that sheds new light on the microscopic chemical physics driving one of the most important reaction sequences in atmospheric chemistry is published in Science today by Dr David Glowacki from the University of Bristol's School of Chemistry, in collaboration with an international team including experimentalists and theoreticians based in Leeds, Cambridge, and Chicago.

The Earth's atmosphere is a huge chemical reactor where sunlight (rather than heat) starts off chemical chain reactions that ultimately control the fate of greenhouse gases and atmospheric pollutants. Within the Earth's atmosphere (and more generally), one of the most important classes of chemical reactions are so-called 'association reactions', where one molecule (call it A) reacts with another molecule (call it B).

Chemical physicists have known for a long time that molecules can exist in both high energy and low energy quantum states, often referred to as 'equilibrium' and 'non-equilibrium' states, respectively. For arbitrary A + B reactions taking place in the Earth's atmosphere, the nearly universal assumption is that, prior to reaction, both A and B are in their equilibrium states.

Earth's atmosphere is composed of 20 per cent O2, meaning that O2 is a participant in most atmospheric reaction sequences. Contrary to the assumption that atmospheric association reactions always involve reactants in equilibrium states, Dr Glowacki and colleagues show that, for association reactions of the type O2 + B, there is a high probability that O2 'intercepts' B before its non-equilibrium quantum states have relaxed to equilibrium.

The authors present compelling experimental and computational evidence showing that this occurs during the atmospheric degradation of acetylene, which is an important tracer of atmospheric pollution and also plays an important role in the formation of atmospheric particulates.

Furthermore, Dr Glowacki and colleagues show that that the products produced when O2 intercepts another molecule's non-equilibrium quantum states are different from those produced when the states are in equilibrium.

Using detailed mathematical models to unravel the timescales of non-equilibrium quantum state relaxation, the researchers speculate that the interception of non-equilibrium quantum states by O2 is likely to be important for a range of chemical reactions in Earth's atmosphere, with possibly unexpected chemical reaction outcomes.

Dr Glowacki said: "Ultimately, this work improves our fundamental understanding of the microscopic chemical physics driving one of the most important reaction sequences in atmospheric chemistry, and paves the way for further studies of non-equilibrium systems within nature."

More information: 'Interception of excited vibrational quantum states by O2 in atmospheric association reactions' by D. R. Glowacki et al in Science.

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Non-equilibrium quantum states in atmospheric chemistry

Research and Markets: Comprehensive Organometallic Chemistry III, 13-Volume Set. From Fundamentals to Applications

Posted on September 7, 2012 by Danzig

DUBLIN--(BUSINESS WIRE)--

Research and Markets (http://www.researchandmarkets.com/research/kbpwhf/comprehensive_orga) has announced the addition of Elsevier Science and Technology's new report "Comprehensive Organometallic Chemistry III, 13-Volume Set. From Fundamentals to Applications" to their offering.

Comprehensive Organometallic Chemistry, 3rd Edition (COMC-III), is aimed at the specialist and non-specialist alike. It covers the major developments in the field in a carefully presented way with extensive cross-references. COMC-III provides a clear and comprehensive overview of developments since 1993 and attempts to predict trends in the field over the next ten years. Applications of organometallic chemistry continue to expand and this has been reflected by the significant increase in the number of volumes devoted to applications in COMC-III. Organic chemists have edited the volumes on organometallic chemistry towards organic synthesis - this is now organized by reaction type so as to be readily accessible to the organic community. Like its predecessors, COMC (1982) and COMC-II (1995), this new work is the essential reference text for any chemist or technologist who needs to use or apply organometallic compounds.

- Presents a comprehensive overview of the major developments in the field since 1993 providing general and significant insights.

- Highlights the expansion of applications in organometallic chemistry with a strong organic synthesis focus.

- Provides a structured first point of entry to the key literature and background material for those planning research, teaching and writing about the area.

Key Topics Covered:

Volume 1. Fundamentals (G. Parkin).

Volume 2. Compounds of Groups 1 to 2 and 11 to 12 (K. Meyer).

Volume 3. Compounds of Groups 13 to 15 (C.E. Housecroft).

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Research and Markets: Comprehensive Organometallic Chemistry III, 13-Volume Set. From Fundamentals to Applications

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