All About Chemistry

Blooger.com

2009-11-28T02:39:00.001-08:00

Nanotechnology Surges Into Health And Fitness Products

2009-02-15T16:46:00.001-08:00

Say "nanotechnology," and geeks imagine iPhones, laptops and flash drives. But more than 60 percent of the 580 products in a newly updated inventory of nanotechnology consumer products are such "un-geeky" items as tennis racquets, clothing, and health products.

A variety of products that contain nanotechnology. There are 356 products in the health and fitness category -- the inventory's largest category -- and 66 products in the food and beverage category of the list prepared by the Project on Emerging Nanotechnologies. (Credit: Photo By David Hawxhurst / Courtesy of Project on Emerging Nanotechnologies)

An updated inventory includes Head® NanoTitanium Tennis Racquets, Eddie Bauer® Water Shorts with Nano-Dry® technology, Nano-In Foot Deodorant Powder/Spray, and Burt's Bees® sunscreen with "natural Titanium Dioxide mineral...micronized into a nano sized particle."

Since the Project on Emerging Nanotechnologies launched the world's first online inventory of manufacturer-identified nanotech goods in March 2006, the number of items has increased 175 percent--from 220 to 580 products. There are 356 products in the health and fitness category--the inventory's largest category--and 66 products in the food and beverage category. One of the largest subcategories is cosmetics with 89 products. All are available in shopping malls or over the Internet. The list includes merchandise from such well-known brands as Samsung, Chanel, Black & Decker, Wilson, L.L. Bean, Lancome and L'Oreal.

The nanomaterial of choice appears to be silver--which manufacturers claim is in 139 products or nearly 25 percent of inventory--far outstripping carbon, gold, or silica.

"The use of nanotechnology and nanomaterials in consumer products and industrial applications is growing rapidly, and the products listed in the inventory are just the tip of the iceberg," said Project on Emerging Nanotechnologies science advisor Andrew Maynard. "How consumers respond to these early products--in food, electronics, health care, clothing and cars--will be a bellwether for broader market acceptance of nanotechnologies in the future. This is especially true given that the Project's recent poll shows seventy percent of the public still knows little or nothing about the technology."

Nanotechnology

Nanotechnology is the ability to measure, see, manipulate and manufacture things usually between 1 and 100 nanometers (nm). A nanometer is one billionth of a meter. A human hair is roughly 100,000 nanometers wide. The limit of the human eye's capacity to see without a microscope is about 10,000 nm. By 2014, a projected $2.6 trillion in global manufactured goods will incorporate nanotech, or about 15 percent of total output.

Full product list available at: http://www.nanotechproject.org/consumerproducts

Adapted from materials provided by Project on Emerging Nanotechnologies, via EurekAlert!, a service of AAAS.

Nanotechnology Now Used In Nearly 500 Everyday Products

2009-02-15T16:44:00.000-08:00

The number of consumer products using nanotechnology has more than doubled, from 212 to 475, in the 14 months since the Project on Emerging Nanotechnologies launched the world’s first online inventory of manufacturer-identified nanotech goods in March 2006. Clothing and cosmetics top the inventory at 77 and 75 products, respectively. A list of nanotechnology products that also includes bedding, jewelry, sporting goods, nutritional and personal care items is available free at http://www.nanotechproject.org/consumerproducts.

A sample of nanotechnology enabled sunscreens. (Credit: Alex Parlini - Project on Emerging Nanotechnologies)

Nanotechnology Consumer Products Inventory Highlights:

The food and beverages category, including containers and dietary supplements, doubled to 61 products since last year.
Nanoscale silver is the most cited nanomaterial used. It is found in 95 products or 20 percent of the inventory. Carbon, including carbon nanotubes and fullerenes, is the second highest nanoscale material cited.
Merchandise from 20 countries is now represented. The United States leads internationally with 52 percent or 247 consumer products that contain nanotechnology. East Asia now boasts 123 products, a 58 percent increase over last year.
New products in the inventory include the Corsa Nanotech Ice Axe which uses an innovative Sandvik Nanoflex® steel alloy that’s 20 percent lighter than normal steel and up to 60 percent stronger. There’s also MaatShop™ Crystal Clear Nano Silver—a clear liquid dietary supplement which peddles protection against colds, flu and hundreds of diseases, even anthrax.

While polls show most Americans know little or nothing about nanotechnology, in 2005 nanotechnology was incorporated into more than $30 billion in manufactured goods. By 2014, Lux Research estimates $2.6 trillion in manufactured goods will incorporate nanotechnology—or about 15 percent of total global output.

“The use of nanotechnology in consumer products and industrial applications is growing rapidly, with the products listed in the inventory showing just the tip of the iceberg,” said Project on Emerging Nanotechnologies science advisor Andrew Maynard. “How consumers respond to these early products—in food, electronics, health care, clothing and cars—will be a litmus test for broader market acceptance of nanotechnologies in the future.”

Adapted from materials provided by Project On Emerging Nanotechnology.

Could Nanotechnology Make An Average Donut Into Health Food?

2009-02-15T16:42:00.000-08:00

ScienceDaily (Feb. 14, 2009) — European food companies already use nanotechnology in consumer products, but few volunteer the information to consumers, said Dutch food scientist Frans Kampers.

Could nanotechnology make donuts into health food? The promise of nanotechnology is that it could allow for re-engineering of ingredients to bring healthy nutrients more efficiently to the body while allowing less-desirable components to pass through, according to a Dutch scientist. (Credit: iStockphoto/Dean Turner)

He is among the panelists gathered in Chicago for the American Association for the Advancement of Science annual meeting symposium "From Donuts to Drugs: Nano-Biotechnology Evolution or Revolution."

Kampers from Wageningen University and Research Center in the Netherlands will take a look at food science issues in his presentation, "What Nanotechnology Can Do for Your Average Donut."

"All of us as scientists are being impacted by nano-bioscience and there are many issues. The interdisciplinary aspect is just one of them," said Rod Hill, a University of Idaho professor and symposium organizer.

The panel includes two graduate students, Jessica Koehne of the University of California, Davis, and Kristina Kriegel of the University of Massachusetts, are working on projects combining, nanotechnology with biology and chemistry.

"On the food side there is greater public resistance to nanomaterials and nanotechnology in food whereas on the biomedical side there is greater public acceptance or less recalcitrance," Hill added.

His focus on applications, products and processes, and on sensors useful for in food safety and food quality monitoring and in packaging, reflects the wide range of nanotechnology's use in the food industry, Kampers said.

"The problem I always face is that people do not understand what we are doing with nanotechnology and food," Kampers said. "Everyone has this vision of nanotechnology being nanoparticles and nanoparticles being risky, so they are very afraid that nanoparticles in food will have an adverse effect on health."

The promise of nanotechnology, the Dutch scientist said, is that it could allow re-engineering ingredients to bring healthy nutrients more efficiently to the body while allowing less-desirable components to pass on through.

European food scientists use nanotechnology to create structures in foods that can deliver nutrients to specific locations in the body for the most beneficial effects, Kampers said.

"We are basically creating nanostructures in food that are designed to fall apart in your body because of digestion so in the end there will not be nanoparticles," Kampers said.

He said there are some researchers studying applications of persistent nanoparticles in food and packaging that he believes could present risks. Use of metal, usually silver, nanoparticles in packaging to slow spoilage could move from the packaging material into the food itself.

"The persistent metal or metal oxide nanoparticles could move into the bloodstream, and research has shown they can migrate into cells or in some cases even into the nucleus of cells," Kampers said.

"These are the more controversial applications of nanotechnology," Kampers added. "More research is necessary to understand the kinetics and dynamics of these particles before large-scale applications in food are developed. At the moment, these types of nanoparticles are rarely used in food products."

Adapted from materials provided by University of Idaho, via EurekAlert!, a service of AAAS.

Making biofuels the chemical way

2009-02-11T17:51:00.001-08:00

US-based researchers have developed the first one-step synthesis of a biofuel precursor from untreated agricultural waste. The work could pave the way to a simple and efficient method of biofuel production.

Biochemist Ron Raines and his team at the University of Wisconsin-Madison have directly converted untreated corn stover - the inedible leaves and stalks of the plant - straight into 5-hydroxymethyl-fufural (HMF); an 'unprecedented' process, says Raines. This compound is a platform for many commodity chemicals, and for the promising potential fuel dimethylfuran (DMF).

HMF can be turned into fuels or chemical feedstocks

Although DMF has yet to be widely adopted as a fuel, advocates argue it has far more potential than ethanol. 'It has the same energy content as gasoline - 40 per cent higher than ethanol,' says Raines. 'It's already been shown to be an effective fuel additive, and it could eventually replace gasoline, and be used with existing infrastructure.'

Since gasoline's power as a fuel is its high carbon content, the aim when converting cellulose into fuel is to make it more carbon-rich. 'Cellulose is a polymer of glucose, and glucose is has a 1:1 ratio of carbons and oxygens,' Raines explains. 'Combustion adds oxygen to the molecule, so we used some simple chemistry to strip away oxygens - to sort of "unburn" it.'

The one-step HMF production process uses N,N-dimethylacetamide (DMA) containing lithium chloride as a solvent, and a chromium catalyst. Once the cellulose is broken down into fructose, three hydroxyl groups are eliminated as water molecules, lowering the oxygen content to give HMF. In a second step, hydrogen gas can then be used to further reduce HMF into DMF.

Tied up in knots

In previous efforts to convert cellulose into useful products, ionic liquids have been used as very effective solvents. But, according to Raines, his team rediscovered a simpler approach - exploiting the ability of chloride ions to dissolve cellulose. 'Cellulose is a recalcitrant material - it ties itself in knots,' says Raines. 'But the chloride ions break up interactions between the cellulose molecules.' Using lithium chloride, with a small amount of ionic liquid to optimise the process, his team was able to obtain a yield of over 50 per cent.

Raines also believes that organic chemistry is a far more feasible approach to biofuel production than fermentation. Small molecular solvents are able to swim around the lignin cage that surrounds the cellulose in untreated plant waste. 'Microorganisms and enzymes can't get access to it. And fermentation is a hugely expensive process - for fuel production you would need fermentation tanks the size of Iowa.'

Stephen del Cardayre is vice president of R&D at LS9, a US-based company that specialises in biofuels, and which plans to develop sustainable industrial chemicals. He points out that DMF still needs to be validated as a suitable fuel before it is widely adopted.

'But if there were an economic and scalable process to produce it, that validation would be pursued, [and this] work is definitely a significant step in that direction,' he says. 'There is still plenty of work to do, but their results certainly suggest that work is worth pursuing.'

Victoria Gill

http://www.rsc.org/chemistryworld/News/2009/February/11020901.asp

(No) twist in the tale for icefish protein

2009-02-11T17:50:00.001-08:00

A cyclic peptide has shattered an established theory about fish antifreeze.

The antifreeze glycoprotein (AFGP) was discovered in the 1960s in the blood and body fluids of the Antarctic icefish. It allows the fish to survive at temperatures as low as -2 °C by binding to small ice crystals and preventing them from growing to a size where they would be fatal.

Antifreeze glycoprotein AFGP allows Antarctic icefish to survive the cold

Shin-Ichiro Nishimura of the Hokkaido University, Sapporo, Japan, designs synthetic analogues of natural AFGPs (syAFGPs) in an effort to understand the connection between their structure and their antifreeze properties. Earlier results from Nishimura's team have implied that the proteins need to contain a helix-type structure to possess antifreeze activity. However, the group has now made cyclic analogues (cyAFGPs) without the helix, which show a significant anti ice-growth effect. The researchers say the finding is the only exception to the established theory that relates the AFGPs' antifreeze activity to their helical structure.

The team made the new peptides using an efficient and facile method which gives only cyAFGPs without contamination of linear glycopeptide intermediates. Peter Davies, an expert in antifreeze proteins, from Queen's University in Kingston, Canada, says: 'This method should eliminate the helical structure of the linear AFGPs. And yet cyclic versions of these glycopeptides, some as small as two repeating tripeptide units, have antifreeze activity.'

"The researchers say the finding is the only exception to the established theory that relates the AFGPs' antifreeze activity to their helical structure"

Nishimura says that further conformational studies of the cyAFGPs will reveal the structural motif required for the peptides' affinity with the ice lattice, helping towards understanding how the compounds exert their antifreeze properties.

'The importance of the novel method for the synthesis of cyclic peptides should also be emphasised,' Nishimura adds, 'because cyclic peptides and cyclic modified-peptides are potent candidates of therapeutic reagents such as anti-virus infection.'

Sandra Fanjul

http://www.rsc.org/Publishing/Journals/cb/Volume/2009/3/icefish_protein.asp

New money for undergraduate research

2009-02-10T18:35:00.000-08:00

By Janet Raloff

Web edition : Wednesday, February 4th, 2009

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GATOR SCIENCESome research really lets undergrads get their hands dirty. Like collecting animals in the wild and then bleeding them to study pollutant loadings in their blood.J. Raloff

Profs who want to push science beyond the classroom have a strong ally: the Tucson, Ariz.-based Research Corporation for Science Advancement. In about a month, it will begin issuing requests for proposals to launch a new type of grants for pre-tenure faculty at predominantly undergraduate institutions, also known as PUIs. The program is open to teams of two or more scientists to mentor cross-disciplinary research.

By undergraduates. We’re talking teenagers, here.

Back in my day, undergrads might contribute some grunt labor to a prof’s project, but we weren’t the principle researchers. And we labored anonymously. The big exception: engineering students doing co-op stints in industry.

But the times, they are a-changin’.

At 19, my daughter was learning lab techniques and doing field work as part of a research team at Florida on gators. A year later, she was doing 95 percent of the research for an inorganic-chemistry project that should yield her first-authorship on a peer-reviewed paper — potentially by the time she graduates.

“Undergraduate research is starting to become almost a staple at many of the better institutions,” notes James M. Gentile, a genetic toxicologist and president of Research Corp. That’s certainly true at a number of research universities. His organization has been sponsoring grants for undergraduate research at much smaller schools since the end of World War II.

That program “was initially chartered by our founder to help young men coming home from war reestablish themselves in the sciences at smaller institutions,” Gentile notes. But for quite a while, now, the program also has been available to female faculty and students — like those at the predominantly undergraduate women’s college my daughter attends.

Predominantly, in this case, refers to schools that don’t have Ph.D. programs in the physical sciences. And Gentile’s organization now offers between 75 and 90 grants at a time to individual young investigators at such schools. Beginning this year, the program will grow to include perhaps another dozen teams of young investigators at these institutions.

Three-year grants will provide $75,000 to pairs of faculty or $100,000 to trios. Where a trio is selected, one scientist may be tenured. In all cases, at least one member of the team must work in physics, chemistry or astronomy. Co-recipients of the grant must work in allied fields, although not necessarily the physical sciences. A partnering researcher could be a mathematician, for instance, or biologist.

The goal is to “fund what we hope will be a young faculty’s entry-level grant into the world of research,” Gentile says, “because we believe that the best educators at PUIs are those who are engaged in the discipline they’re teaching.” Gentile says he witnessed that trend first hand during his years as dean at a PUI — Hope College in Holland, Mich. And soon-to-be unpublished research, he says, will “statistically validate that the students who do undergraduate research are actually your best learners.”

Maybe because their hands-on science — work for which they take ownership of all accomplishments, and failures — cements the scientific method into their skulls. It also teaches them what kinds of questions and criticisms to anticipate from peers and professors — and therefore what kinds of homework and analysis to complete before showcasing their findings.

Research Corp.’s newest program focuses on interdisciplinary research “because increasingly science, particularly complex science, is becoming a tag-team sport,” Gentile says. So is teaching. “There’s not a college or a university that I know that doesn’t boast with justifiable pride that they’re forming or have formed interdisciplinary education programs in the sciences,” he says.

Yet faculty often “aren’t rewarded when they do collaborative research,” he maintains — unless they’re the principal investigator who brought in the funds. That’s one reason why Research Corp. grants money collectively to an entire team. All receive equal credit.

Started in 1912, Research Corporation for Science Advancement is the nation’s first foundation dedicated solely to science and the second oldest of any type. Haven’t heard of it before? “You’re not alone,” Gentile admits: “For a long time, it just conducted quiet philanthropy.”

And that funding will continue, even in this sick economy. “I’ve argued — and our board agrees — this isn’t a time to hunker down. It’s a time to double-down, to get aggressive and help the community,” he told me. So his organization will be upping its spending on research in the coming year, not cutting back.

http://www.sciencenews.org/view/generic/id/40577/title/New_money_for_undergraduate_research

Melamine-tainted infant formula linked to kidney stones

2009-02-10T18:34:00.000-08:00

By Janet Raloff

Web edition : Wednesday, February 4th, 2009

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Last September, Chinese officials acknowledged that months-long illegal use of a fraudulent protein substitute — melamine — had poisoned powdered infant formula that was sold throughout the country. Some 300,000 children are believed to have consumed the tainted product, in some cases for more than a year. Overall, an estimated 1,200 infants and toddlers were sickened. Six died. Today, a Chinese study and two related research letters — all released early by the New England Journal of Medicine — tie infant exposure to melamine with a greatly elevated risk of kidney stones.

An epidemic of kidney stones had been reported previously among these children. Until now, however, the risk of stone formation had not been quantified — nor linked, especially, to consumption of the most-heavily tainted infant formula.

The primary study that was just released involved an examination of nearly 600 children in Beijing. It turned up none of the conventional urinary chemicals that mark stone formation. Sand-size calcifications were only identified in the children through the use of ultrasound. This suggests, the authors say, melamine may trigger the formulation of atypical stones — ones having an unusual chemical recipe.

An accompanying letter by researchers in Taiwan who had screened more than 1,100 children last fall also found that development of kidney stones was "significantly more frequent in the high-exposure group" — children drinking infant formula with the highest concentrations of melamine. However, in this survey, the ostensibly high-exposure group consisted of youngsters drinking formula tainted with anything over 2.5 ppb melamine. In the Beijing population, highly tainted formulas had more than 500 ppb melamine, and even the moderate exposure group was 1 to 500 ppb.

Hong Kong-based researchers performed ultrasound tests looking for evidence of kidney stones in an even larger group of asymptomatic children — 2,140 — and over a broader age range: to age 12. They confirmed the presence of a stone in only one child (age not given), and noted signs of possible stone formation in six additional kids (again, age not given). This group extended its survey to older children since reports emerged of melamine contamination in some milk products. No putative melamine-exposure estimates were reported for any of the children.

“It is remarkable that all three reports describe the absence of conventional symptoms and signs related to [kidney stones],” notes Craig B. Langman of the Northwestern University School of Medicine in an accompanying editorial.

Indeed, authors of the Beijing study observe: "These findings contrast with the present guidelines posted on the Web site of the Ministry of Health of China (www.moh.gov.cn), which suggest that symptoms are useful in diagnosing the presence of stones. Our results indicate that screening for urinary stones should be based on the history of exposure to melamine rather on the symptomatology."

Taken together, the three new reports suggest stone formation rates were generally low, since the majority of youngsters who had consumed even the most tainted formulas failed to develop them. That said, in Beijing-area children exposed to the most contaminated milk, stone formation was roughly seven times higher than in the local children who had been drinking melamine-free infant formula. What’s more, in this Beijing study, infants who had been born prematurely were 4.5 times more likely to develop stones than were babies who had been born full-term.

China, though slow to act in acknowledging the melamine crisis, ultimately responded with stern punishments. According to a New York Times report, on January 22 two people linked to the poisoning incident were sentenced to death. Three more received a life sentence in prison, another received a suspended death sentence, and 15 people ended up with sentences of between 2 and 15 years in jail.

http://www.sciencenews.org/view/generic/id/40591/title/Melamine-tainted_infant_formula_linked_to_kidney_stones

Instant insight: Metal detectors for clean fuel

2009-02-10T18:33:00.001-08:00

Guilhem Caumette, University of Pau - IFP, France, outlines the techniques used to find metal contaminants in petroleum and how they will lead to superior fuels

Petroleum is, and always has been, the primary source of energy on our planet. The shortage of oil reserves, combined with increasing energy demands has brought a surge of interest in revisiting petroleum processing technology in the quest for better performing and cheaper fuels. Oil companies are searching for alternative sources of carbonaceous fuels, such as biofuels and gas condensates, or are trying to improve the efficiency of heavy crude oil (and heavy distillation fractions') conversion to transportation fuels.

"Analysing the elements in petroleum is a nightmare for analysts as the fuel contains thousands of molecules of different sizes and polarities"

Metals and sulfur found in these heavy petroleum fractions can poison the catalysts used during refining processes. They also corrode equipment and contaminate the environment. So investigations focus on detecting metal content in petroleum and petroleum products. The metals' behaviour during the refining processes depends on their speciation - their chemical form. Knowing the size and structure of metal complexes is crucial in choosing catalysts suitable for removing them. Their identity can also give information about the geological origin and migration of oils, and can be used to find new oil fields.

Relatively little is known about the metal species in crude oils

Yet, despite progress in analytical methodology, relatively little is known about the metal species in crude oils. Metalloporphyrin complexes with nickel and vanadium are often cited, but non-porphyrin complexes with molecular weights reaching several thousand Daltons should also be present. More information is available about the forms of sulfur in petroleum or mercury and arsenic in gas condensates but there is no definite agreement on their exact nature.

"Despite progress in analytical methodology, relatively little is known about the metal species in crude oils"

Analysing the elements in petroleum is a nightmare for analysts as the fuel contains thousands of molecules of different sizes and polarities, which interact with different forces. Direct analysis is barely possible and multistep analytical techniques are required to separate and properly identify target metallomolecules. The interest in speciation of metals and other heteroelements in petroleum-related products has led analysts to develop dedicated analytical techniques and methods. They include direct analytical techniques such as x-ray absorption spectroscopy, electron paramagnetic resonance and molecular mass spectrometry (using laser desorption, electrospray and chemical ionisation) as well as hyphenated techniques that combine chromatography's high separation potential (e.g. high performance liquid chromatography or gas chromatography) with an element specific detector's sensitivity (e.g. atomic absorption spectrometry).

As these dedicated techniques become more widely available, identifying metal species in complex organic mixtures such as petroleum becomes easier and meeting the challenge of removing them for cleaner fuels becomes a step away.

Read more in 'Element speciation analysis of petroleum and related materials' in issue 3, 2009 of Journal of Analytical Atomic Spectrometry.

http://www.rsc.org/Publishing/ChemScience/Volume/2009/03/metal_detector_fuel.asp

Interview: Making DNA movies

2009-02-10T18:30:00.000-08:00

Thomas Carell talks to Kathleen Too about epigenetics, DNA lesions, repair and crystallisation

Thomas Carell is a professor for organic chemistry at the Ludwig-Maximilians-University (LMU) in Munich, Germany. His research covers the synthesis of DNA hybrid materials and the study of DNA damage and repair. In 2008, he became an elected member of the Deutsche Akademie der Naturforscher Leopoldina which is the world's oldest continuously existing academy for medicine and natural sciences.

Who or what inspired you to become a scientist?

In both biology and chemistry, I had superb teachers. Then during my studies I always had the privilege to work with very inspiring people, for example Heinz Staab, former head of the Max-Planck Society, and Burchard Franck, a very important natural products researcher at Münster University, Germany. Both were very fine personalities and inspirational to me.

What motivated you to work in the area of nucleic acids?

I started my independent career studying motor compounds for electron transfer studies. We connected electron donors and acceptors to nucleobases to study electron injections and electron abstractions and then we put these building blocks into DNA to study electron transfers through DNA. We decided that we were creating so many lesions that we should look at the lesion repair and lesion tolerance process. So it was a gradual move from physical organic chemistry into nucleic acid research.

How do you think nucleic acid chemistry will be able to solve the biggest challenges in biology?

I really believe that nucleic acid research is fundamentally important, simply because DNA is one of the most important molecules on earth. One can think about some kind of life without proteins but you can't think about life without DNA or RNA. Cancer and all these fundamental diseases have to do with DNA and failures in the information storage and transport system. So I think that with DNA and nucleic acids you work at the most fundamental level of chemistry.

"I really believe that nucleic acid research is fundamentally important, simply because DNA is one of the most important molecules on earth"

So what sort of areas do you think nucleic acids will be able to help in?

First nucleic acid chemistry will help us to better understand life. How did it evolve and from where did we come? I also think it can contribute to finding treatments for diseases. I'm sure that nucleic chemistry will allow us to produce better drugs to fight cancer. Also, if we want to tackle the ageing problem we have to study nucleic acids. I also believe that if you look at the whole new field of RNA interference (RNAi), you will see that a lot of regulations in our cells, at the very fundamental level, are done by small RNAs. Also, if you look into epigenetics then you will discover that there is an information level beyond this sequence information, methylation information, which is very important for the functioning of cells. At the moment, I can see two very hot areas of research: RNAi is one (micro RNAs and small RNAs). The other one is epigenetics. Both areas are linked to nucleic acid chemistry.

Could you explain what you are working on at the moment?

We are working on the degradation processes of DNA. We know that the DNA double strand is a molecule which is not 100 per cent stable. It is degrading and strand breaks can occur causing the loss of nucleic acids and subsequently the loss of genetic information. Looking at the lengths of the molecules needed to encode the genetic information of a human being, it is very clear that we have to deal with 50-80000 lesions per day per cell. We are investigating what causes these lesions and how they can be repaired. The genetic information system is based on two things - one is the DNA molecule itself and the other one is the DNA repair system that keeps it working. The third question we ask is if these DNA lesions cause mutations, what type of mutations are formed in response to each lesion. I believe these are very fundamental problems.

So how are you doing this, how are you going to achieve it?

The strategy is very simple: we synthesise the lesion, put it into a small piece of DNA, add the DNA to a repair protein or polymerase to see how the lesion induces mutation and how it is repaired. We have a strategic advantage as our DNA synthesiser is heavily modified in order to do chemistry that is not possible with a normal DNA synthesiser.

How, in general, has crystallisation helped to speed up the understanding of biological processes?

I think that crystallisation itself is always complicated because it takes time in order to get the full story depending on how well the system crystallises. Very often you need years to obtain the results but new robotic systems have vastly speeded up the crystallisation process making life much easier. This automated high throughput crystallisation technique allows you to get crystals from each step.

How has the advent of new techniques in crystallisation helped?

We have seen a radical change. Today you don't make a single crystal structure as in the past, but a whole series of crystal structures showing the entire process at different stages and then at the end you get movies of the complete process of repair. You can now obtain intermediates of the repair process and see how the repaired DNA is released and so you can really make a movie of the cellular process that is going on. I think the ability to make this movie has changed the crystallographic world.

"We have a strategic advantage as our DNA synthesiser is heavily modified in order to do chemistry that is not possible with a normal DNA synthesiser"

Which scientists do you most admire and why?

During my time at ETH Zurich, I had the privilege to meet Vladimir Prelog, winner of the 1975 Nobel Prize in Chemistry. Vladimir really impressed me as he had a sharp mind, a very good sense of humour and extremely high analytical skills. He always told me 'Thomas, don't fiddle along with small things, go with the most important question.' I must say that I am also impressed by my former advisor François Diederich. He is always so energetic, it is very difficult to stop him and I always feel that in comparison to him I am a lazy scientist. He is truly outstanding in his achievements; it is unbelievable.

What is the most rewarding thing about your career in chemistry?

For a German scientist, the most rewarding thing is to get the Gottfried Wilhem Leibniz Award, which we call the "German Nobel Prize". It is the most prestigious award you can get in Germany and it is extremely competitive. Each year about ten scientists will get this award, which includes all disciplines such as history, language, science, law and business. I received this award very early in my career, when I was 35, so I was one of the youngest Leibniz winners in Germany.

What is the trickiest problem you have had to overcome in your research and how did you solve it or get around it?

In my research there are problems at all stages. The synthesis of these fragile lesions is already tricky and then their incorporation into DNA using non-standard solid phase chemistry conditions is also very challenging. Another problem is that the proteins we are working with are very difficult to handle. These are repair proteins and some exist in only low copy numbers and so they are very difficult to express, particularly if you look at human repair proteins. There are almost no structural studies because of the difficulties in over-expressing the proteins. Therefore, at each step of the research, you have to overcome a challenge. But there is not one thing that is particularly difficult, it is difficult at every stage.

If you weren't a scientist what would you be?

I think I would like to be a medical doctor, a surgeon, because I could help people - that would be my motivation behind it.
http://www.rsc.org/Publishing/Journals/cb/Volume/2009/3/Making_DNA_movies.asp

Molecular thermometer takes cell temperature

2009-02-10T18:29:00.000-08:00

A fluorescent polymer that can accurately measure the temperature inside living cells has been invented by researchers in Japan.

Seiichi Uchiyama and his group at the University of Tokyo have developed the heat-sensitive fluorescent polymer, which they have packaged in a chemically inert polymer gel. The gel can be injected directly into cells and used to detect variations in temperature as small as half a degree, without interfering with cellular functions. The gel's covering of hydrophilic sulfate groups ensures it disperses throughout the cytoplasm rather than sticking to the cell membrane.

'At the moment we can measure the average temperature of the cell as a whole,' explains Uchiyama, 'but we are working on attaching a localising agent (such as a peptide) to the surface so that individual organelles can be targeted more specifically. This will allow us to map the spatial and temporal variations in temperature within the cell.'

Fluorescence reveals temperature changes inside living cells

The thermometer unit works by incorporating a water-sensitive fluorophore inside a thermally-responsive polymer. At low temperature the polymer has an open structure and absorbs water, which quenches the fluorescence. When it is heated, the polymer structure contracts, driving out the water and making the gel fluoresce. The level of fluorescence can be measured, revealing the temperature within the cell.

Previous molecular thermometers, employing europium complexes or green fluorescent protein, were hampered by poor thermal sensitivity, meaning that they couldn't really detect the subtle temperature variation accompanying biological processes. This lack of sensitivity, coupled with the fact that their output could be confused by variations in pH or ionic strength, limited their utility.

Prasanna de Silva from Queen's University in Belfast, UK, says Uchiyama's success in introducing the thermometer gel into living cells sets an excellent precedent for future applications of the technology. 'If you have a thermometer of such a small size, then you can put it into all sorts of interesting places. The demonstration that this gel functions inside a cell means that there's almost nowhere it can't go.

'I think people might have felt before that temperature was not worth measuring,' adds de Silva, 'because we expect it to be held constant most of the time. We are beginning to realise that, while the cell's buffering mechanisms do eventually work, there are short-term local effects. So if you can watch a cell in small spatial detail, with good time resolution then you can pick up on things which wouldn't be seen otherwise.'

The ability to measure variation in cell temperatures accurately will not only give insights into the intimate workings of the complex chemical systems at work within them, but also aid understanding and diagnosis of disease. 'Pathological cells are generally slightly warmer than normal cells because of their enhanced metabolic activity,' says Uchiyama. 'We're working on a way to get cells to absorb the thermometer gel from culture media, which would eliminate the need for microinjection and make it much more useful for diagnosis. We can also tune the solubility and functional temperature range to make the gel suitable for a wide range of cell samples.'

Phillip Broadwith

http://www.rsc.org/chemistryworld/News/2009/February/09020901.asp

Exercise capacity improved with molecules

2009-02-10T18:28:00.001-08:00

Researchers in France and the US have shown how a compound that can be delivered in drinking water can improve the body's capacity for exercise. The molecule, a cyclic pyrophosphate, interacts with haemoglobin, the blood's oxygen carrier, encouraging it to release oxygen more easily. The molecule could provide a new way to help people with heart failure, the researchers suggest.

Jean-Marie Lehn of the Institut Louis Pasteur in Strasbourg and colleagues gave the compound, myo-inositol trysphosphate (ITPP), to both healthy mice and mice that were genetically engineered to have severe heart failure. They showed that the more compound that was delivered, the more both sets of animals could exercise.

Test tube analysis of haemoglobin treated with ITPP showed that haemoglobin releases its oxygen more easily in the presence of the pyrophosphate. It appears that the ITPP binds to the haemoglobin molecule and acts as an allosteric effector - altering the haemoglobin's conformation to ease its grip on oxygen. Haemoglobin has a natural allosteric effector involved in oxygen release called diphosphoglycerate, and it is possible that the ITPP is displacing this molecule, docking onto haemoglobin and exerting a more powerful effect.

ITPP intereacts with haemoglobin to ease its grip on oxygen

'The ITPP makes the affinity for haemoglobin a little bit lower - by about 30 to 40 per cent,' says Lehn. 'This is enough to allow it to release more oxygen in tissues which have a loss of oxygen, called hypoxia, but not enough to cause it to release excess oxygen to healthy tissues.'

This could provide a way of delivering more oxygen in oxygen-starved tissues - for example where a damaged heart is unable to pump sufficient blood deep into muscle tissue around the body. The ITPP could make the smaller volumes of blood reaching the tissues surrender its oxygen more readily.

In their experiments the researchers showed that the biggest effect was achieved when the ITPP was delivered by injection directly into the body; however, it still showed a significant effect when it was ingested in drinking water. 'This is very exciting because if it can be taken orally it would make it much more attractive from a medicinal point of view,' says Lehn.

The molecule could also be used for healthy people who are in extreme physical situations, such as at high altitude. Could it help athletes to cheat? 'This is a question everyone asks,' says Lehn. 'Of course it could be potentially attractive to an athlete, but the molecule would be easy to detect.'

Commenting on the research, Peter Weissberg, medical director of the UK charity the British Heart Foundation, says, 'If a similar effect can be achieved in man it will raise the possibility of a new treatment to improve debilitating heart failure symptoms.'

Simon Hadlington

http://www.rsc.org/chemistryworld/News/2009/February/09020902.asp

Lighting up the active site

2009-02-10T18:27:00.000-08:00

10 February 2009

Belgian scientists have developed a system that could provide information about catalytic cycles at the single molecule level.

Single molecule fluorescence spectroscopy is an important tool for monitoring discrete events in catalytic reactions that would not normally be detected in bulk measurements. Usually this involves attaching a marker to a reactant that fluoresces upon conversion to the product. However, this route offers an indirect approach to obtaining information about the catalytic cycle. Now a team, led by Johan Hofkens and Dirk De Vos at the Catholic University of Leuven, has attached the fluorescent reporter group to the catalyst itself to provide a more direct method for monitoring the cycle.

The reporter fluoresces when a proton or metal ion (X) binds to the amine

The team linked a tertiary amine, the system's catalytic active site, to a perylene-based dye, which acts as the reporter group. They then anchored the dye to a microscope cover slide so they could test the catalyst under different conditions.

"Reporters such as this are certainly important for the development of this field"
- Philip Tinnefeld, Ludwig Maximilian University of Munich, Germany

Electron transfer from the free amine to the reporter quenched the reporter's fluorescence. But when the amine bound to a molecule or ion, such as a proton in a base-catalysed reaction, electron transfer was hindered and the reporter fluoresced. 'This opens perspectives on monitoring complexation by the amine group in a more direct way than present state of the art techniques,' says Hofkens.

'In recent years, beautiful tools have been developed to study catalytic reactions at the single molecule level,' says Philip Tinnefeld, who investigates fluorescence imaging techniques at the Ludwig Maximilian University of Munich, Germany. 'Reporters such as this are certainly important for the development of this field.'

Although the system worked well, Hofkens says that unexpected dark states, where the individual molecules' fluorescence was not detected irrespective of their binding state, could also be seen. The group aim to modify the system, for example by changing the link between the reporter and the cover slide, to eliminate this problem so that the system can be applied to the field of catalysis.

Bailey Fallon

http://www.rsc.org/Publishing/ChemTech/Volume/2009/03/lighting_active_site.asp

Interview: From nano to macro

2009-02-10T18:26:00.001-08:00

10 February 2009

Detlef Günther talks to May Copsey about nanoanalytics, football and measuring the largest crystals in the world

Detlef Günther is professor for trace element and micro analysis at the Swiss Federal Institute of Technology Zurich and chair of the Journal of Analytical Atomic Spectrometry editorial board. His research focuses on fundamental and applied aspects of plasma-based mass spectrometry techniques, ion generation and ion extraction procedures and laser ablation-inductively coupled plasma-mass spectrometry for elemental and isotope analysis.

What inspired you to become a chemist?
I grew up in a little village with a very small school. Our chemistry teacher was also the coach of our football team - so being good at chemistry helped me to get picked for the team. Later on, in high school, I had an excellent teacher who showed us experiments not normally allowed at school. We really had the smell and the taste of chemistry very early on in the classroom.

Did you always want to work in analytical chemistry?
To begin with I was much more interested in organic chemistry. Chemistry was a popular subject because my university (Martin Luther University Halle-Wittenberg) was very close to some of the major chemical companies in East Germany. We had two branches, synthetic chemistry and technical chemistry. However all the places had been filled for synthetic chemistry and I couldn't switch. I went on to pass the major exams in analytical chemistry and it was then I realised that if I couldn't synthesise something new, I might be able to analyse something. So that was the start.

What led you to choose a PhD in analytical chemistry?
Where I did my PhD was very special because we had one of the first inductively coupled plasma-optical emission systems (ICP-OES) in East Germany. That was fantastic because most of our colleagues at other universities had no access to this technology. My PhD supervisor, Professor Moenke, was well known in the field of laser ablation (LA) and she worked very hard to obtain such an instrument for LA-ICP-OES.

"Transferring fundamental understanding from the analytical side [of atomic spectrometry] to clever applications can bring a breakthrough and further recognition"

However, I then realised that chemistry didn't provide any real problems for an analytical chemist to solve. This made me move to study plant biochemistry because I had seen there was a strong need for analytical chemistry in this area. Later on I went to work with geologists as a post-doc in the Earth Science department at Memorial University (Newfoundland, Canada) and Swiss Federal Institute of Technology Zurich (Switzerland).

With the experience of working in other areas of science, do you think chemists have much to learn from other disciplines?
The field of atomic spectrometry involves quite a lot of fundamental work but the highest recognition it receives is always related to application. Transferring fundamental understanding from the analytical side to clever applications can bring a breakthrough and further recognition. The future of our field is somewhere at this interface. We have to take care to maintain our own fundamental interest, but we also have an extremely important task of educating people to go and apply some of these techniques in other fields.

Can you tell us about your current research and collaborations?
The most interesting ongoing research involves the fundamental development of ICP-mass spectrometry (ICP-MS). The project aims to increase the sensitivity of this technique by producing a larger number of ions that can be measured. We hope that this can be done by using a new interface configuration. This research might take us closer to nanoanalytics, which is necessary, particularly for solid analysis using laser ablation.

We are fundamentally interested in mass bias studies on multi-collector ICP-MS. Mass bias is all the processes involved in the change of isotope ratios from the sampling side to the detector. If we have a higher understanding about what is causing mass bias, this will help optimise our instrumentation and that will improve the stability. We might then be able to open up new applications in the future.

"My advice is to search for projects that you are really interested in because fascination and dedication produces the extra energy necessary to carry out a project"

In my field, we have the opportunity to touch many different areas of science. We are currently working with a variety of materials - analysing gold objects from Peru and looking into the authenticity of different gemstones. This research enables us to visit some external sites, and that's the fun part really. We interact with many different people and gain knowledge from them. For example, we are just about to go to Mexico with a colleague from Bologna to look at the Naica crystals. These are the largest gypsum crystals ever found, and there is still a lot of work to do in figuring out how and why they are formed.

We also have some collaboration with industry. The quality control of raw products is becoming more important, as everything that had been at the microgram per gram level a couple of years ago is now reduced to the nanogram per gram level and is harder to detect. So we have the challenge of providing the method to do this.

What's the secret of having a successful research group?
Getting the right people together and always looking for the people who have more knowledge in areas that we are not familiar with. In 2008, my group celebrated our 10th anniversary and it was really nice to reflect on what we had done over the last 10 years. It's been an exciting time and the credit must go to my team. Publications will not make us famous in the future; I simply think our contribution is to generate well-trained PhD students so that they will pass on our intentions and our enthusiasm for research.

What message do you have for someone starting out on a research career?
My advice is to search for projects that you are really interested in because fascination and dedication produces the extra energy necessary to carry out a project. That is the best advice because if you are fascinated then you can do almost everything.

How do you think your family would describe what you do?
My wife works in a nearby nuclear research institute and we are both analytical chemists. Therefore, there is no need to explain my work to her. My daughters know that I am teaching students, that I work with gemstones and that I am always a little late!

What do you like doing when you are not in the lab?
If I'm not talking about lasers, then I talk about football. I am a devoted supporter of Bayern Munich and, of course, the German national team. Since living in Switzerland I have adapted to almost everything, but when it comes to football, I'm German.

Controversial new theory for nanotube growth

2009-02-10T18:24:00.000-08:00

10 February 2009

US scientists have proposed a new theory for how carbon nanotubes grow. If their predictions are borne out experimentally, the theory could have practical implications for researchers trying to control nanotube growth in the lab. But experts say the theory may be unrealistic.

Carbon nanotubes are essentially rolls of graphene - hollow cylinders of carbon in which the atoms are arranged in a hexagonal lattice. But they don't roll up like sheets of paper; they self-assemble or 'grow' in the direction of a tube's length, prompting scientists to wonder how exactly each new layer of carbon is formed.

A new theory for the growth of nanotubes has been put forward

Boris Yakobson and colleagues at Rice University, Houston, and the Honda Research Institute in Ohio have now put forward a formula that they say provides a model for the extension process. Yakobson likens it to weaving a rug - the more atomic kinks or 'threads' are exposed at the growing end, the faster growth proceeds.

'The kinks are an extension of the spiral lines of atoms that make up the tube,' explains Yakobson. 'You can visualise these kinks as the ends of threads, so the more thread ends you have, the faster the tube will grow.'

The number of kinks at the growing edge is ultimately dependent on the tube's chirality, or the angle at which it is 'rolled'. Chiral tubes expose many kinks and so form quickly. A non-chiral tube, by contrast, is not formed by adding to a spiral 'thread' but by the addition of complete rings of carbon atoms. Therefore, explains Yakobson, an energy barrier has to be overcome each and every time a new ring is initiated.

Nicole Grobert, a nanotubes expert based at the University of Oxford, UK, warns that the team's work is purely theoretical and unlikely to explain growth processes in real life systems. 'It has nothing to do with reality, I think, because the conditions in which the tubes grow are very chaotic,' she says. 'You have to look at the different methods that are used to grow nanotubes and I should think all of these have different growth scenarios, so you can't come up with one theory and explain all of them.'

David Tománek, who studies nanostructured materials at Michigan State University, East Lansing, US, says themodel contradicts everything that is known about the formation process of nanotubes in the presence of catalytic particles. 'It also contradicts common sense in claiming that a couple of yarns, representing monoatomic carbon chains, should nicely attach to each other to form a hollow tube,' he says.

'The jury is still out,' admits Yakobson. 'We're going to have to go through never-ending verification processes. 'But he argues that data from previous studies has so far supported his team's findings - for example, data taken from different growth methods shows an abundance of nanotubes with large chiral angles, as predicted by the formula.'

Understanding how nanotubes grow would help scientists gain control over their structure, potentially leading to tubes with predefined properties and applications, says Grobert. But she thinks Yakobson's theory of nanotube growth is too far fetched.

Hayley Birch

http://www.rsc.org/chemistryworld/News/2009/February/10020901.asp

Evonik Medavox to cease production of hydrogen peroxide and sodium percarbonate in Italy

2009-02-09T17:45:00.000-08:00

The management of Evonik Medavox S.p.A., a company belonging to Evonik Industries, has decided to shut down production of hydrogen peroxide and sodium percarbonate in Bussi sul Tirino (Italy) by the end of March 2009. The company is forced to take this step as commercially viable production in Bussi is no longer possible due to altered market conditions. Evonik will actively seek to offer employment opportunities to as many of the affected employees as possible at its other locations in Italy or elsewhere.

Hydrogen peroxide is an oxidizing and bleaching agent used widely in the pulp and paper industry. Italian customers will be supplied in future from Evonik’s production plants in Rheinfelden (Germany), Antwerp (Belgium), and Weissenstein (Austria).

Sodium percarbonate is used primarily as a bleaching component in powdered laundry detergents. In future, Italian customers will be supplied from Evonik’s production plants in Rheinfelden (Germany) and Althofen (Austria).
http://www.chemeurope.com/news/e/96105/

EPC Contract for an Amine Plant Signed With Aker Clean Carbon AS

2009-02-09T17:44:00.001-08:00

On behalf of the future partnership of the European CO2 Technology Centre Mongstad (TCM), StatoilHydro has signed an engineering, procurement and construction (EPC) contract with Aker Clean Carbon AS for an amine plant at TCM. The contract has a value of approximatelyNOK 525 million.

According to plans, TCM shall test two different technologies for capturing CO2 from two flue gas sources with respectively low and high CO2 contents. The contract with Aker Clean Carbon AS for amine technology lasts until the end of 2011. In addition, it is planned that TCM shall also test the "chilled-ammonia" CO2-process. The TCM project is working on putting into place an equivalent contract with another contractor.

"The contract that has been signed with Aker Clean Carbon AS is an important milestone for TCM. The ambitions for TCM as a testing arena are high. Especially, there are expectations that the centre will provide various learning effects regarding technology scale-up, operational conditions, environmental consequences and the testing of sub-contractor deliverables. One of the goals of testing amines is to qualify the technology for the large-scale treatment of exhaust gases, and at the same time develop cost-efficient technologies," saysBjorn-Erik Haugan, the managing director of Gassnova, on behalf of the TCM partnership.
http://www.chemeurope.com/news/e/96466/

Arkema announces the acquisition of American company Oxford Performance Materials

2009-02-09T17:43:00.001-08:00

As part of its strategy to further expand in performance materials, Arkema announced the acquisition of the US company Oxford Performance Materials, Inc. (OPM), maker of polyether ketone ketone ultra-high-performance technical polymers marketed under the brandname OXPEKK®, with sales of the order of $ 2 M.

"Arkema has had a long-standing interest in ultra-high-performance polymers that offer outstanding technical differentiation, opening up the way for major innovations for our customers ", said Thierry Le Hénaff, Arkema Chairman and CEO. " We are delighted to welcome OPM’s teams within Arkema. I firmly believe that this new activity has a huge growth potential. ”

Norner will lead major research project on polymers based on CO2

2009-02-09T17:42:00.001-08:00

Norner Reactor Lab.

Image: Norner Innovation.

10 Feb 2009 - Norner Innovation announced that the company will lead a four years research project with a frame of about 25 million NOK to continue the development of novel plastic materials based on CO2 as a raw material including the process and production technologies. Large companies like Yara and Superfos will join in this industrial R&D project. The project will be supported by the Norwegian Research Council.

”This is a unique possibility to utilise CO2 as a raw material in polymer production and thereby turn the problematic CO2 and environmental issues. Up to 50wt% of the polymer may be CO2. We look forward to this interesting challenge and will work hard to realise this opportunity to establish new and sustainable plastic materials” says Tine Rørvik the Director of Norner.

Norner Innovation has several advanced and industrial laboratory reactors where the polymer is produced for this project with the relevant monomers and process parameters. Together with their plastics processing lab and test centre, this enables Norner to take the lead in the research of both process technology as well as material science. The development process for control of process parameters and material properties of the polymer is going on as a continuous activity in our pilot reactors. This work will now be accelerated by this new funded project.
http://www.chemeurope.com/news/e/96445/

Euro Chlor publishes dossier on biological effects of metallic mercury exposure

2009-02-09T17:40:00.001-08:00

Euro Chlor, representing the European Chlor-Alkali industry, has published a new title in its series of Science Dossiers: "Metallic mercury – The biological effects of long-time, low to moderate exposures”. This publication brings an analysis and synthesis of the most relevant scientific literature on the human health effects of exposure to low to moderate levels of metallic mercury vapour and represents an authoritative reference work on this matter.

The aim of the dossier is to present current knowledge of the effects of exposure to low levels of metallic mercury vapour and to define gaps in knowledge. For the purposes of the report, a "low level” of exposure is considered to be one that gives a kidney burden.

The new Science Dossier collates the findings of more than 120 recent scientific studies on health effects of mercury, which makes it very complete. Areas such as neurotoxicology, renal effects, immunotoxicity, cardio-vascular and cerebro-vascular toxicity, mutagenicity and carcinogenicity, reproduction toxicity and finally endocrine toxicity are explored.
http://www.chemeurope.com/news/e/96406/

Download e-Book : Organic Chemistry

2009-02-09T02:59:00.000-08:00

Organic chemistry

by admin @ 11:34 pm.

Chapter 0
Students Guide to Succcess in Organic Chemistry
0.1 What is Organic Chemistry? 4
0.2 Organic Chemistry in the Everyday World 9
0.3 Organic Chemists are People, Too 11
0.4 Learning to Think Like a Chemist 14
0.5 Developing Study Methods for Success 15
Key Ideas from Chapter 0 18

Chapter 1
Atoms, Orbitals, and Bonds
1.1 The Periodic Table 21
1.2 Atomic Structure 22
1.3 Energy Levels and Atomic Orbitals 23
1.4 How Electrons Fill Orbitals 27
1.5 Bond Formation 28
1.6 Molecular Orbitals 30
1.7 Orbital Hybridization 35
1.8 Multiple Bonding 46
1.9 Drawing Lewis Structures 49
1.10 Polar Covalent Bonds 54
1.11 Inductive Effects on Bond Polarity 57
1.12 Formal Charges 58
1.13 Resonance 60
Key Ideas from Chapter 1 66

Chapter 2
Introduction to Organic Nomenclature and Functional Groups
2.1 Drawing Organic Structures 73
2.2 Alkanes 77
2.3 Structural Isomerism 77
2.4 IUPAC Nomenclature 79
2.5 Naming Alkanes 80
2.6 Naming Cycloalkanes 87
2.7 Naming Complex Alkyl Groups 91
2.8 Functional Groups 97
2.9 Naming Alkenes and Alkynes 100
2.10 Naming Alkenes, Part II 108
2.11 Arenes 109
2.12 Organohalogens 113
2.13 Using Molecular Formulas 115
Key Ideas from Chapter 2 117

Chapter 3
Molecular Conformations
3.1 Representing Three-Dimensional Molecules in Two
Dimensions 125
3.2 Dihedral Angles 127
3.3 The Conformations of Ethane 129
3.4 Conformational Analysis of Butane 131
3.5 Angle Strain in Cycloalkanes 134
3.6 Conformations of Cyclohexane 136
3.7 Conformational Inversion of Cyclohexane 142
3.8 Conformational Analysis of Monosubstituted
Cyclohexanes 143
3.9 Naming Stereoisomers 147
3.10 Conformational Analysis of Disubstituted
Cyclohexanes 149
Special Topic – Computer Modeling 155
3.11 Conformations of Other Cycloalkanes 157
3.12 Naming Polycyclic Ring Systems 159
3.13 Polycyclic Ring Systems 164
Sidebar - Higher Polycyclic Structures 166
Key Ideas from Chapter 3 168

Chapter 4
Physical Properties
of Organic Compounds
4.1 Phases of Matter 175
Sidebar - Liquid Crystals 178
4.2 Melting Points 179
4.3 Boiling Points 183
4.4 Solubility 190
Sidebar - Surfactants 194
4.5 Density 197
Key Ideas from Chapter 4 199

Chapter 5
Acid-Base Theory
5.1 Acids and Bases 209
5.2 Acid and Base Strength 215
5.3 Hard and Soft Acids and Bases 222
5.4 Organic Acids and Bases 226
5.5 Relative Acidity and Basicity 231
5.6 Substituent Effects on Acidity and Basicity 235
Key Ideas from Chapter 5 238

Chapter 6
Reaction Mechanisms
An Overview of Organic Chemistry
6.1 Chemical Equilibria and Rates 246
6.2 Equilibrium Thermodynamics 250
6.3 Reaction Kinetics 253
6.4 Reaction Profiles and Mechanisms 255
6.5 Why Reactions Occur 260
6.6 Organic Reaction Terminology 264
6.7 Classification of Reagents in Organic Reactions 270
6.8 Writing Reaction Mechanisms 270
6.9 Substitution Reactions 278
6.10 Addition Reactions 281
6.11 Elimination Reactions 284
Key Ideas from Chapter 6 287

Chapter 7
Nucleophilic Additions to the Carbonyl Group
7.1 Naming Carbon—Oxygen Double Bonds 299
7.2 Reactivity of the Carbonyl Group 304
7.3 Guide for Learning Organic Reactions 307
7.4 The Cyanohydrin Reaction 309
7.5 Addition of Water and Alcohols 311
7.6 Reaction with Nitrogen Nucleophiles 320
Sidebar - Biochemical Transamination 325
7.7 Reaction with Hydride Nucleophiles 326
7.8 Carbon Nucleophiles 331
Synthesis of Triphenylmethanol 336
7.9 Organic Synthesis 339
7.10 The Wittig Reaction 342
Synthesis of Methylene-4-tert-butylcyclohexane 344
Key Ideas from Chapter 7 348

Chapter 8-A
Reaction Summary I
A summary of the reactions learned in Chapters 7-8

Chapter 8
Nucleophilic Substitution on the Carbonyl
Group
8.1 The Acyl Transfer Mechanism 360
8.2 Water and Alcohol Nucleophiles 362
Synthesis of Isoamyl Acetate (Banana Oil) 366
8.3 Halide and Carboxylic Acid Nucleophiles 372
Sidebar - Aspirin and Acetaminophen 376
8.4 Reaction with Nitrogen Nucleophiles 381
8.5 Reaction with the Hydride Nucleophile 384
8.6 Carbon Nucleophiles 392
8.7 Nitriles 401
8.8 The Baeyer-Villiger Oxidation 406
Synthesis of Caprolactone 409
8.9 Solving Mechanistic Problems 410
Key Ideas from Chapter 8 414

Chapter 9
Infrared Spectroscopy
and
Mass Spectrometry
9.1 Electromagnetic Radiation and Spectroscopy 431
9.2 Molecular Vibrations in Infrared Spectroscopy 434
9.3 Introduction to Interpreting Infrared Spectra 436
9.4 Hydrogen Bonded to sp3 Hybrid Atoms 439
9.5 Hydrogen Bonded to sp2 and sp Hybrid Atoms 443
9.6 Carbon—Heteroatom Bonds 448
9.7 Other Bonds 452
9.8 Interpreting Infrared Spectra, Part 2 456
9.9 Mass Spectrometry 459
9.10 The Molecular Ion 463
Key Ideas from Chapter 9 467

Chapter 10
Nuclear Magnetic Resonance
10.1 Theory of Nuclear Magnetic Resonance 475
10.2 Shielding 478
10.3 Chemical Shift and Molecular Structure 480
10.4 Interpreting Proton NMR Spectra 484
10.5 Spin-Spin Splitting 491
10.6 Integration Signals in an NMR Spectrum 501
10.7 Analyzing an NMR Spectrum 503
Sidebar – Magnetic Resonance Imaging 511
10.8 Strategy for Solving Spectral Problems 513
Key Ideas from Chapter 10 519

Chirality
11.1 Symmetry and Asymmetry 532
11.2 Nomenclature of Stereocenters 538
11.3 Properties of Asymmetric Molecules 544
Sidebar - Chiral Recognition 544
11.4 Optical Isomerism 546
11.5 Fisher Projections 549
11.6 Molecules with Two Stereocenters 553
11.7 Resolution of Enantiomers 558
11.8 Stereocenters Other than Carbon 561
Key Ideas from Chapter 11 564

Chapter 12
Aliphatic Nucleophilic Substitution
12.1 Naming Single Bonded Heteroatom Functional
Groups 579
12.2 Comparing Nucleophilic Substitution Reaction
Mechanisms 586
12.3 The SN1 and SN2 Reaction Mechanisms 588
12.4 Stereochemistry of Nucleophilic Substitutions 592
12.5 The Substrate 595
12.6 Nucleophiles and Leaving Groups 601
12.7 Common Nucleophiles 606
12.8 The Reaction Medium 607
12.9 SN1 versus SN2 613
12.10 Halide Nucleophiles 613
Synthesis of 1-Bromobutane 616
12.11 Oxygen Nucleophiles 620
12.12 Nitrogen Nucleophiles 625
Synthesis of 2,5-Diaminoadipic Acid 628
12.13 Carbon Nucleophiles 631
12.14 Neighboring Group Participation 634
Special Topic - SN1 vs. SN2 637
Key Ideas from Chapter 12 641

Chapter 13
Elimination Reactions
13.1 The Elimination Mechanisms 658
13.2 Stereochemistry of Eliminations 660
13.3 Direction of Elimination 663
13.4 E1 vs. E2 670
13.5 Elimination vs. Substitution 671
13.6 Summary of Elimination and Substitution 673
13.7 E & Z Nomenclature 677
13.8 Elimination of Organohalogens 678
13.9 Dehydration of Alcohols 682
Synthesis of Cyclohexene 685
13.10 Pinacol Rearrangement 686
13.11 Hofmann Elimination 691
13.12 Oxidation of Alcohols 694
Synthesis of Citronellal 697
Key Ideas from Chapter 13 698

Chapter 14
Electrophilic Addition to
Unsaturated Carbons
14.1 Addition Reaction Mechanisms 713
14.2 Direction and Stereochemistry of Addition
Reactions 715
14.3 Addition of Hydrogen Halides 718
14.4 Addition of Water and Alcohols 722
14.5 Hydroboration-Oxidation 726
Synthesis of (-)-Isopinocampheol 730
14.6 Electrophilic Addition of Halogens 732
14.7 Addition of Hydrogen 736
14.8 Dihydroxylation Reactions 742
14.9 Addition of Carbenes 745
Synthesis of 7,7-Dichlorobicyclo[4.1.0]heptane 749
14.10 Oxidation of Alkenes 750
Key Ideas from Chapter 14 754

Chapter 15
Organic Synthesis
15.1 Synthesis Design and Strategy 771
15.2 Principles of Retrosynthetic Analysis 774
15.3 Protecting Groups 778
Synthesis of the Ethylene Glycol Acetal of
Cyclohexanone 781
15.4 Lithium Dialkylcuprate Reagents 781
Synthesis of trans-Stilbene 784
15.5 A Synthetic Example 786
15.6 Synthesis of Difunctional Compounds 790
Key Ideas from Chapter 15 795

Chapter 16
Conjugation and Resonance
16.1 Naming Compounds with Multiple Functional
Groups 812
16.2 Conjugated Dienes 816
16.3 The Allyl Group and Resonance 823
16.4 Conjugate Addition Reactions 826
Special Topic - Ultraviolet Spectroscopy 829
16.5 Double Bonds Conjugated With Carbonyl
Groups 832
Sidebar - The Chemistry of Vision 834
16.6 The Diels-Alder Reaction 837
Synthesis of cis-Norbornene-5,6-endo-dicarboxylic
Anhydride 841
16.7 Orbital Symmetry and the Diels-Alder
Reaction 844
16.8 Synthesis with the Diels-Alder Reaction 847
Key Ideas from Chapter 16 852

Chapter 17
Aromaticity
17.1 Benzene 868
Sidebar - Diamond, Graphite, and Buckyballs 872
17.2 The Stability of Benzene 874
17.3 Molecular Orbitals in Benzene 876
17.4 The Molecular Orbitals of Cyclobutadiene 879
17.5 Aromaticity 880
17.6 Hückel’s Rule 882
17.7 Aromatic Ions 887
17.8 Naming Benzene Derivatives 891
17.9 Aromatic Heterocyclic Compounds 895
17.10 Polynuclear Aromatic Hydrocarbons 898
17.11 The Benzyl Group 900
Key Ideas from Chapter 17 901

Chapter 18
Aromatic Substitution Reactions
18.1 Mechanism of Aromatic Electrophilic Substitution 914
18.2 The Nitration of Benzene 917
18.3 Halogenation and Sulfonation of Benzene 920
18.4 Friedel-Crafts Alkylation and Acylation 924
18.5 Effects of Monosubstituted Arenes on Substitution 928
18.6 Rate Effects with Monosubstituted Arenes 932
18.7 Classification of Substituents 935
18.8 Friedel-Crafts Acylation 943
Synthesis of o-Benzoylbenzoic Acid 947
18.9 Multiple Substituent Effects 948
18.10 Substitution on Polycyclic Arenes 951
18.11 Diazotization 954
Synthesis of Methyl Orange 957
Sidebar - Sulfa Drugs 958
18.12 Other Diazonium Salt Reactions 961
18.13 Nucleophilic Aromatic Substitution 963
18.14 Benzyne 965
Synthesis of Trypticene 968
18.15 Synthesis Examples 969
Key Ideas from Chapter 18 975

Chapter 19
a Substitution on Carbonyl Compounds
19.1 Keto-Enol Tautomerism 997
19.2 Enols and Enolate Ions 999
19.3 The Mechanism of a Substitution 1002
19.4 a Halogenations 1003
Synthesis of 2-Bromocholestanone 1005
19.5 Alkylation of Enolate Ions 1009
19.6 Stabilized Enolate Ions 1012
Sidebar - Barbiturates 1020
19.7 Enamine Reaction 1023
Synthesis of 2-Acetylcyclohexanone 1026
19.8 Silyl Enol Ethers 1027
19.9 1,3-Dithianes 1030
Key Ideas from Chapter 19 1033

Chapter 20
Carbonyl Condensation Reactions
20.1 The Carbonyl Condensation Mechanism 1052
20.2 Carbonyl Condensation Vs a Substitution 1054
Sidebar - Borodin and Aldehydes 1056
20.3 Mixed Aldol Condensations 1057
20.4 Intramolecular Aldol Condensations 1061
Synthesis of 1,5-Diphenyl-1,4-pentadien-3-one 1063
20.5 The Claisen Condensation 1064
Sidebar - Biochemical Carbonyl Condensation Reactions 1067
20.6 The Dieckmann Cyclization 1071
20.7 The Michael Addition Reaction 1072
20.8 The Robinson Annulation Reaction 1076
Synthesis of 4,4-Dimethyl-2-cyclohexen-2-one 1079
20.9 Carbonyl Condensations in Synthesis 1080
Key Ideas from Chapter 20 1084

Chapter 21
Radical Reactions
21.1 Radical Structure and Stability 1093
21.2 Halogenation of Alkanes 1095
Sidebar - Atmospheric Ozone Depletion 1099
21.3 Allylic Bromination 1102
21.4 Benzylic Bromination 1105
Synthesis of 1-Bromo-1-phenylethane 1106
21.5 Radical Addition to Alkenes 1107
21.6 Radical Oxidations 1112
21.7 Radical Reductions 1115
Synthesis of 1-Methoxy-1,4-cyclohexadiene 1121
Special Topic - Electron Spin Resonance Spectroscopy 1122
Key Ideas from Chapter 21 1125

Chapter 22
Polymer Chemistry
22.1 Structural Characteristics of Polymers 1138
22.2 Polymer Nomenclature 1141
22.3 Types of Polymerization Reactions 1144
22.4 Chain-Growth Polymerization 1146
Synthesis of Poly(vinyl acetate) 1155
Sidebar - Natural Rubber 1155
22.5 Controlling Stereochemistry in Vinyl Polymers 1157
22.6 Nonvinyl Chain-Growth Polymerization 1160
22.7 Step-Growth Polymerization 1163
Synthesis of Poly(ethylene terephthalate) 1165
Sidebar - Plastic Recycling 1167
22.8 Copolymers 1169
Sidebar - Plasticizers 1172
22.9 Cross-Linked Polymers 1173
Key Ideas from Chapter 22 1178

Chapter 24
Carbohydrates
24.1 Classification of Carbohydrates 1250
24.2 Monosaccharides 1253
24.3 Cyclic Forms of Monosaccharides 1256
Sidebar - The Sweet Taste 1260
24.4 Reactions of Monosaccharides 1263
24.5 Oxidation and Reduction Reactions 1265
24.6 Changing the Chain Length 1268
24.7 Fischer Proof of Glucose Structure 1271
24.8 Glycolysis - I 1275
24.9 Glycolysis - II 1280
Sidebar - Arsenic Poisoning 1285
24.10 Glycoside Formation 1286
24.11 Disaccharides 1291
24.12 Polysaccharides 1291
Key Ideas from Chapter 24 1294

Chapter 25
Nucleic Acids
25.1 Nucleosides and Nucleotides 1306
25.2 Laboratory Synthesis of Nucleotides and Nucleosides 1310
25.3 Nucleic Acids 1314
25.4 Replication of DNA 1317
Sidebar - The Polymerase Chain Reaction 1321
25.5 Structure and Biosynthesis of RNA 1325
25.6 RNA and Peptide Biosynthesis 1328
25.7 Sequencing of DNA 1332
25.8 Laboratory Nucleic Acid Synthesis 1337
Sidebar - Self Replicating Organic Compounds 1343
Key Ideas from Chapter 25 1345

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2009-02-09T02:20:00.000-08:00

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Uranium exposed

2009-02-08T23:59:00.001-08:00

US scientists have developed a way to tell if war veterans have been in contact with depleted uranium.

Exposure to depleted uranium in military equipment may be bad for soldier's health

Depleted uranium is a by-product of uranium enrichment for nuclear power plants. It has less uranium-235 isotope than natural uranium. It is used in a variety of materials, including tank armour and ammunition. There are concerns that it might be bad for the health of soldiers who are exposed to it through, for example, wounds or inhalation.

Todor Todorov, at the US Geological Survey in Denver, and colleagues analysed blood samples from US Gulf War I veterans who had been involved in friendly fire incidents. 'Depleted uranium exposure from the Gulf War and conflicts in the former Yugoslavia has been a health concern in the past decade for military and peace keeping forces,' says Todorov. Using inductively coupled plasma mass spectrometry, he measured the ratio of uranium isotopes in the blood samples. Because the isotope ratios for depleted and natural uranium are different, Todorov was able to work out the source of the uranium.

"Depleted uranium exposure from the Gulf War and conflicts in the former Yugoslavia has been a health concern in the past decade for military and peace keeping forces"

Other methods to identify uranium exposure analyse urine samples. Todorov explains that by using blood, he can gain information on depleted uranium transport rates in the body. 'This can be used to develop biokinetic models for depleted uranium exposure,' he says, adding that the method is simple, rapid and robust.

In the future, the team plans to focus on developing bioassays for measuring the level of uranium in semen so that the effects of depleted uranium exposure on reproductive health can be evaluated.

Madelaine Chapman

http://www.rsc.org/Publishing/ChemTech/Volume/2009/02/uranium_exposed.asp

Microthrusters are go!

2009-02-08T23:57:00.000-08:00

Scientists have developed an efficient propulsion system for microspacecraft.

As satellites become smaller, scientists need more compact propulsion systems to guide microspacecraft through space. Ming-Hsun Wu, at National Cheng Kung University, Tainan, Taiwan, and Richard Yetter, at Pennsylvania State University, University Park, US, have made small propulsion devices called microthrusters that are ignited using electric energy.

Microthrusters ignited with electric energy could be used to maintain satellites in their orbits

Usually microthrusters are ignited by raising the temperature of the propellant using heating elements until it catches fire. But heat energy can be lost from the system, making it inefficient. This is particularly significant on the microscale because of the large surface-to-volume ratios.

Instead, Wu and Yetter put electric energy directly into the liquid propellant, causing it to decompose and ignite at room temperature.

'This is the first time that electrolysis has been used as an ignition mechanism for a microscale liquid monopropellant microthruster,' explains Wu, 'and the results turned out to be pretty exciting.'

"This is truly an excellent demonstration of novel thinking and attention to detail"
- Frederick Dryer, Princeton University, US

Frederick Dryer, an expert on combustion science from Princeton University, US, is impressed by the results. 'This is truly an excellent demonstration of novel thinking and attention to detail. It is a real step forward in fabrication processes, use of novel fuel formulation, and ignition technologies for micropropulsion applications. In my opinion, the paper represents a seminal work in the micropropulsion field,' he enthuses.

While the current microthruster can be fired only once, Wu and Yetter plan to develop a microthruster that can be fired multiple times. Wu says the microthrusters could be used on microsatellites for maintaining spacecraft in assigned orbits and controlling their orientation.

Ruth Doherty

http://www.rsc.org/Publishing/ChemTech/Volume/2009/02/microthrusters.asp

Polymers branch into data storage

2009-02-08T23:55:00.000-08:00

Scientists have harnessed the power of holography to store large amounts of data in a postage stamp-sized disc.

Craig Hawker, at the University of California, Santa Barbara, US, and colleagues designed photopolymers that can store up to 50 times more data than a DVD.

When the highly branched molecules polymerise, the volume change is negligible so data can be stored and retrieved accurately

Unlike a DVD, which only uses a disc's surface, holographic data storage uses the whole volume of the disc. As a result, holography promises terabytes (1000 gigabytes) of storage capacity in a recording disc the size of a postage stamp, says Hawker. A typical DVD holds only 4.7 gigabytes.

Recently, researchers have investigated light-sensitive polymers - which are used to make the holograms seen in driving licences - for data storage. But these photopolymers shrink as the molecules polymerise during the recording process, making it difficult to accurately retrieve the recorded data.

Hawker overcame this problem by making a series of highly branched monomers. He showed that when the molecules polymerised, the volume change was much smaller than for previous photopolymers and so the shrinkage was negligible.

"This work illustrates the power of modern polymer synthesis to custom-design organic materials with advantageous properties"
- Stefan Hecht, Humboldt University, Berlin, Germany

'Of particular note is finding that a holographic media prepared using one of our monomers exhibits 50 times more storage capacity than a conventional DVD,' says Hawker. 'To reach the terabyte goal, you need to have very high efficiency and fidelity during the recording process.'

The polymer's refractive index, which is a measure of how much it reduces the speed of light passing through it, is key to increased storage capacity, explains Hawker. He is working on a system that combines a low refractive index scaffold with ultra-high refractive index monomers, which he expects to show improved results.

'This work illustrates the power of modern polymer synthesis to custom-design organic materials with advantageous properties,' says Stefan Hecht, an expert in organic functional materials at Humboldt University, Berlin, Germany. 'By fine tuning the macromolecular architecture, Hawker and co-workers have created new high performance data storage materials overcoming limitations of conventional polymer chemistry.'

Sarah Corcoran

http://www.rsc.org/Publishing/ChemTech/Volume/2009/03/polymer_data_storage.asp

Instant insight: Scratching at the surface of biosensors

2009-02-08T23:54:00.000-08:00

Justin Gooding, Till Böcking and Kris Kilian of the University of New South Wales discuss how surface chemistry lets porous silicon biosensors fulfil their promise.

Porous silicon photonic crystals can be tuned to reflect different colours of light by altering their periodicity

A biosensor is a device for detecting an analyte that combines biological molecules selective for the analyte with a detector known as a signal transducer. The biological molecules provide the sensor with its selectivity while the transducer determines the extent of the interaction between the biomolecules and the analyte. The transducer converts this information into a signal that a person can read, such as a colour change. Examples of successful biosensors include glucose meters used by diabetics and home pregnancy test kits.

"Examples of successful biosensors include glucose meters used by diabetics and home pregnancy test kits"

Apart from being selective for the target analyte, biosensors should be miniaturisable, portable, robust and sensitive. In vivo biosensors also need to be biocompatible and non-toxic, so ideally a biosensor would not need an implanted power source to operate it. Porous silicon has emerged as an attractive option for biosensors. In fact, it would be the perfect material, in particular for in vivo biosensors, if it could be stabilised against degradation.

Porous silicon is made by electrochemically drilling nanoscale pores into silicon wafers in ethanolic hydrogen fluoride solutions, a process known as etching. The pore size can be adjusted from microporous to macroporous by varying the etching conditions; most biosensing applications use mesoporous materials, which have a pore size between two and 50 nanometres. By varying the current density during etching, the silicon's porosity can be altered to produce 1D periodic structures, known as photonic crystals, that reflect or transmit light at precisely defined wavelengths.

"Absorption or desorption of molecules on to the pore walls in a photonic crystal affects the optical properties of the crystal, making porous silicon an ideal label-free transducer for biosensors"

Absorption or desorption molecules on to the pore walls in a photonic crystal alters the wavelength of light that the crystal reflects, making porous silicon an ideal transducer for biosensors. In addition, the wavelength range can be tuned to the visible or infrared range simply by altering the crystal's periodicity. Porous silicon transducers require no power to operate and, if tuned to reflect near infrared light, which can penetrate living tissues, can be monitored directly through the skin using silicon diode detectors.

Porous silicon has an even more attractive feature over other photonic crystals for biosensing. In the body, mesoporous silicon degrades to orthosilicic acid, the most common naturally occurring form of silicon. Because this product is benign, porous silicon biosensors do not have to be removed from the body. But the degradation of porous silicon also results in a change in optical properties, which of has severely compromised the application of porous silicon in biosensing.

An elegant solution to this hurdle involves using surface chemistry to stabilise the materials. For example, by forming a monolayer of alkyl chains linked to the surface by strong silicon-carbon bonds, scientists have dramatically increased the stability of porous silicon. The same surface chemistry has also allowed researchers to explore a host of strategies for immobilising biological molecules onto the pore surfaces. These advances take us a significant step forward in applying this powerful material to biosensing and revitalise the quest for implantable smart materials.

http://www.rsc.org/Publishing/ChemTech/Volume/2009/02/biosensors.asp

Interview: Mixing it up

2009-02-08T23:53:00.002-08:00

Steven Soper talks to Freya Mearns about interdisciplinary science and a little bit of luck

	Steven Soper is the William L and Patricia Senn, Jr Professor in the department of chemistry at Louisiana State University. He is also a professor of mechanical engineering and an adjunct professor of biological sciences. His research interests include biomicro- and bionanoelectrochemical systems, single molecule detection, and new bioassay developments. He is on the editorial board of Analyst.

What inspired you to become a scientist?
None of my family went to college or expressed an inclination to participate in any science-related area. So, being a scientist was off base for my entire family and something they did not understand when I first mentioned my professional interests. When I was in high school, I started taking some biology and physics classes and a little bit of chemistry. It was my teachers that set me on the road toward being a scientist and I am grateful for their mentoring and guidance. Many of my undergraduate college professors were also very helpful and encouraging, in particular James Wood and Ted Kuwana.

"I have just been very lucky to have such an understanding and supportive wife!"

When I went to college, my first degree was in psychology - I planned to be a psychiatrist. Then I decided to go back and get a degree in chemistry because I really enjoyed it. Afterwards I went to work in a research laboratory at a local company in Kansas City, Missouri; I was intrigued by some of the problems we were working on, so I decided to go back and get my PhD so that I could more fully understand the underlying chemical phenomena. I was married with a baby and I announced to my wife, 'Guess what: I'm going to go back to graduate school and I'm going to make $800 a month.' Then, I was given the opportunity to do a post doctoral fellowship at Los Alamos National Laboratory, New Mexico, under the direction of Richard Keller, who was doing single molecule detection. Los Alamos is a small isolated city in the mountains of New Mexico, but a great place to do some high-end science. This was a tremendous experience for me, because it gave me the opportunity to do single molecule work, which I am continuing today. After two years at Los Alamos, I decided to interview at a few universities with a view to becoming a college professor. After doing several interviews, I decided on Louisiana State University (LSU). There was never a concise plan - I just made all these decisions as I was moving along. I have just been very lucky to have such an understanding and supportive wife!

Why did you specialise in microfabricating devices for analysing biological molecules?
When I went to LSU in 1992 my intention was to do single molecule detection and ultrasensitive biological fluorescence measurements, especially related to genome analysis (I had done similar work at Los Alamos National Laboratory). But when I arrived, a new facility was opened: the Center for Advanced Microstructures and Devices. It's a synchrotron source where they do X-ray spectroscopy and X-ray lithography, but they also built a clean room to do micro- and nanofabrication. In 1993, when the first microchip electrophoresis paper by Andreas Manz and Jed Harrison appeared in Science, we merged the ideas in that paper with the resources at LSU to forge new ideas in developing microfluidic systems made from polymers. It was a little bit of luck that the resources became available just when the original paper came out.

What projects are you working on at the moment?
We've really spanned out into some intriguing areas. Our original concept was to do genome analysis and we're still doing that, but mostly for DNA sequencing applications. Now we have reached into areas that are still using genomes, but as biomarkers, for some really interesting applications. For example, we have projects in DNA forensics, looking at infectious diseases, and building point-of-care systems for developing and underdeveloped countries. We also have collaborations with people at various medical schools to do diagnostics for cancer-related diseases. We have a new project looking at building systems for doing drug discovery as well that was recently funded by the National Institutes of Health. The interesting aspect of this project is that now we are focused on merging our single molecule detection work with microfluidics and nanofluidics for compelling applications in biology and medicine.

What's going to be the next big thing in your field?

"Now the challenge is to develop integrated systems to carry out fully integrated assays"

People have worked extremely hard at developing microfluidic devices for specific tasks. Now the challenge, at least on the microfabrication side, is to develop integrated systems to carry out fully integrated assays. For example, we've been building devices that do solid phase extraction (to clean up samples), then the polymerase chain reaction (PCR), then a variety of devices on the back-end of the PCR step, for example electrophoresis, microarrays or some spectroscopy readout of PCR reactions. The idea is to build autonomous systems using all of these devices. So the next big challenge will be process integration. The other big project area is nanofabrication - building structures in the nanometre regime. People are starting to get a fairly good grasp on understanding the physics of what happens when you put biomolecules into confined environments that rival their molecular dimensions. Now the challenge is to take those unique opportunities evolving with nanofabrication capabilities and merge them with microfabrication to build logical interfaces between the macro, micro and nano worlds.

What is the secret to being a successful scientist?
I don't care what type of science you do, it's your students that are important - if they don't produce, you are dead in the water. If it was up to me to do all the experiments, I might publish one or two papers a year (if I was lucky). You need a great crop of students who are motivated, creative and intelligent. If students have those attributes, they're going to be successful, your group is going to be successful and you are going to be successful! Students drive the research productivity machinery. I also have a great group of colleagues in areas outside of my expertise that have been instrumental in our research efforts: in mechanical engineering, biological sciences and materials science.

Have your students and post docs primarily trained in chemistry or is there a real mix of backgrounds?
The majority of people coming into my lab do have a chemistry background but when they leave they have fairly good knowledge in biology and engineering as well. Nowadays chemists cannot afford to know only chemistry, especially analytical chemists. When they start working in my group, my students (and even postdocs) will take a class in biology to learn about clinical chemistry and DNA structure, and a class in engineering to learn about lithography (both micro- and nanofabrication techniques) and fluid dynamics. They also learn how to do computational simulations to help guide experimentation. We do a lot of simulations to help guide design before we go into the lab and start building something. That's really helped our productivity immensely.

Are the lines between the traditional sciences blurring now? Is it becoming easier to communicate?
No. Communication across disciplines that haven't been heavily engaged in cross-fertilisation is very difficult to come by. I have been working with people in mechanical engineering for over 10 years and it is only within the last two or three years that we have broken down some of the communication barriers. My students learn their jargon, their students learn chemistry jargon and we now know how to communicate. But these things take time. I still think this is a big problem. Everybody says, 'We're doing interdisciplinary science,' (which everyone should be doing) but I would argue that the only time you can really claim this is when you have joint publications and when your students are conversing with people outside chemistry on a regular basis. That's a great sign of interdisciplinary science.

If you weren't a scientist, what would you be?
This is going to sound mushy, but I couldn't really envision doing anything else. I just love what I do!

Solar power kills bacteria in water

2009-02-08T23:53:00.001-08:00

Scientists have improved solar water decontamination techniques in an attempt to reduce the spread of water borne diseases in developing countries.

Solar water disinfection is a simple way to kill bacteria in water. It is used by households in developing countries where safe drinking water is scarce. People fill plastic bottles with water and leave them in sunlight, where the UV radiation and increased water temperature kill the bacteria within six hours. But the method requires strong sunlight and can only treat limited volumes of water.

Sunlight is used to disinfect water in plastic bottles but can only treat limited volumes

Kevin McGuigan from The Royal College of Surgeons in Ireland, Dublin, and colleagues investigated solar disinfection of Escherichia coli-contaminated water in large volume flow reactors. A pump circulated the water between a holding tank and a glass tube surrounded by solar collectors that focus the sun's energy onto the tube. They found that E. coli inactivation depends on the total dose of sunlight rather than the light's intensity. They also showed that the reactors can be ineffective because the bacteria receive an intermittent dose of radiation as they flow between the dark holding tank and the see-through tube. If the bacteria are not completely inactivated by the sunlight, the dark periods give them time to recover from the radiation damage, making them more resistant when reilluminated.

'For me, the major significance of the research is that these methods can be effective, but recalculating flow through solar disinfection reactors must be carefully designed in order to avoid the possibility of resistant sub-populations of pathogens remaining viable due to incomplete sunlight exposure,' says McGuigan.

"This work is an important contribution which points out potential advantages and limitations of solar disinfection"
- Cesar Pulgarin, Swiss Federal Institute of Technology, Lausanne, Switzerland

'This work is an important contribution which points out potential advantages and limitations of solar disinfection, depending on the type of solar photo reactor and operation mode,' comments Cesar Pulgarin, an expert in biological decontamination processes at the Swiss Federal Institute of Technology in Lausanne, Switzerland. 'It is also the first attempt that assesses the minimal UV dose required for complete bacterial inactivation by solar disinfection.'

The World Health Organization estimates that more than one billion people lack access to safe drinking water, resulting in millions of deaths each year from water-related diseases such as diarrhoea. McGuigan says he plans to introduce the flow reactor technology into developing countries, where he hopes it could provide emergency relief to communities affected by famine, flood and war.

Philippa Ross

http://www.rsc.org/Publishing/ChemTech/Volume/2009/03/solar_power_kills_bacteria.asp

Issue 2 of Chemical Technology now published

2009-02-08T23:51:00.000-08:00

Issue 2 2009 of Chemical Technology is now available online. The complete issue can also be downloaded in pdf format.

Instant insight: Scratching at the surface

Justin Gooding and colleagues discuss how surface chemistry lets porous silicon biosensors fulfil their promise.

Interview: Mixing it up

Steven Soper talks to Freya Mearns about interdisciplinary science and a little bit of luck.

This issue's Application highlights include fluorescent drug delivery vehicles that can be used to monitor drug release.

Chemical Technology is free to view online and news items link directly to the original research articles, which are free to access for a limited period of time.

Issue 2

February

Downloadable Files

Chemical Technology issue 2 2009
PDF (1355k)

PDF files require Adobe Acrobat Reader

http://www.rsc.org/Publishing/ChemTech/News/latest_issue_online.asp

HIV diagnosis improved

2009-02-08T23:50:00.001-08:00

A cheaper and easier way to monitor HIV in patients could revolutionise global health care, according to scientists in the US.

The World Health Organization estimates that more than 33 million people worldwide have HIV. HIV destroys white blood cells called CD4+ T lymphocytes that are crucial for fighting disease. It also reduces the body's ability to replace these cells. Scientists use a technique called flow cytometry to monitor changes in patients' CD4+ levels - when they drop below 200 cells per microlitre, the patient is diagnosed with AIDS and prescribed anti-retroviral drugs. But flow cytometry requires expensive equipment and highly trained scientists to use it.

The microfluidic device separates the monocytes from blood and counts the lymphocytes with high selectivity and sensitivity

Mehmet Toner and colleagues at Massachusetts General Hospital, Boston, have modified a microfluidic device they were previously working on to overcome its major pitfall - sample contamination with another type of white blood cell called monocytes. They developed an upstream monocyte depletion module, which separates monocytes from blood samples before the lymphocytes are counted. Using the module, Toner measured the lymphocyte count with higher selectivity and sensitivity than before. Toner says the device has 'the potential to be one of the holy grails of global health'.

"The device assertively contributes to point of care testing from whole blood and may additionally facilitate other on-chip integrated whole blood-based assays"
- Philip Day, University of Manchester, UK

'The device assertively contributes to point of care testing from whole blood and may additionally facilitate other on-chip integrated whole blood-based assays,' says Philip Day, a expert in tool miniaturisation for quantitative molecular biology from the University of Manchester, UK.

Toner says his device is simpler and cheaper than flow cytometry, meaning it could be used in the resource-scarce settings of developing countries. The method, combined with the recent fall in HIV drug prices, should lead to significant progress in the fight against HIV, he adds.

Jennifer Newton

http://www.rsc.org/Publishing/ChemTech/Volume/2009/03/HIV_diagnosis.asp

Silicate performs strongly at bone regeneration

2009-02-08T23:47:00.001-08:00

Biomaterials scientists in Taiwan have developed a quick-setting cement that could help broken bones to regenerate.

A biocompatible layer of bone-like apatite nodules forms on the cement's surface when it is immersed in a physiological solution

Calcium phosphates were developed over 20 years ago as alternatives to polymer-based cements for mending damaged bones. Their chemical similarity to bone means that they are good repair materials and they are less toxic and more fracture-resistant than polymer cements. However, the absence of silicon - thought to be an important trace element in the early stages of bone formation - means that calcium phosphate cements are not perfect when it comes to integrating with living tissue.

By using silicate rather than phosphate, a team led by Shinn-Jyh Ding at Chung-Shan Medical University, Taichung, has developed a quick-setting cement with promising biological properties. Earlier calcium silicate formulations had setting times of over an hour, which is too long for clinical applications, says Ding, but the new cement sets in just five minutes. It should be a good candidate for bone replacements, he adds, because a biocompatible layer of bone-like apatite nodules forms on the cement's surface when it is immersed in a physiological solution. Ding says that tests in vitro suggest that the cement should encourage the growth of osteoblasts, the cells that are responsible for generating bone tissue, opening up the possibility of its use as an implant material.

"This work broadens our knowledge in this growing field, and I look forward to reading further studies by this group"
- Jake Barralet, McGill University, Montreal, Canada

Future research by the group, says Ding, will focus on improving the injectability and durability of the cement, which he suggests might be achieved by adding natural materials such as gelatin and chitosan.

Jake Barralet, a specialist in bioceramics at McGill University, Montreal, Canada, says that materials that stimulate tissue repair are the 'next big thing' in regenerative medicine. 'It is not yet clear precisely what material parameters cause cell differentiation and tissue regeneration in bone, but this work broadens our knowledge in this growing field, and I look forward to reading further studies by this group,' he says.

David Barden

http://www.rsc.org/Publishing/ChemTech/Volume/2009/03/silicate_cement.asp

China pushes for higher quality patents

2009-02-08T23:46:00.001-08:00

Hepeng Jia and Yue Yuan/Beijing, China

In an effort to boost the quality of patent applications, and encourage Chinese firms to obtain international patents, China has revised its patent law.

The amendment, passed by the standing committee of the National People's Congress on 27 December 2008, will take effect on 1 October 2009. It is intended to encourage independent innovation, said Chen Guangjun, director of the standing committee's science and technology office.

Former patent law revisions in 1992 and 2000 were introduced to enable China to absorb foreign technologies and to abide by international rules.

The new law adopts an international 'absolute standard for novelty' principle for patent authorisation rather than the 'relative novelty' which was previously stipulated. A patent can be approved under relative novelty if the invention or technology is new in China. But with the new 'absolute' principle, a Chinese patent can only be given to an invention or technology that is totally novel worldwide.

Meanwhile, the law now encourages Chinese citizens to obtain international patents by removing the requirement for them to apply first for a Chinese patent. Cao Man, president of new energy company Qingdao Tianren Environmental Technology, predicts that the higher patent standard will drive innovation in low carbon technologies in the long term but will have very limited short-term impact. 'We are still catching up with foreign technologies and most players in the field do not have enough innovative technologies that are ready to be patented,' Cao told Chemistry World.

And because of the high cost of applying for foreign patents, innovators have to consider multiple factors such as the market prospects in other countries before they decide to apply abroad, said Lin Xiaodong, director of Peking University Health Centre's patent management office.

Besides the above amendments, the new law revision also strengthens China's compulsory patent licensing, such as for HIV/AIDS drugs in times of a public health crisis.

http://www.rsc.org/chemistryworld/News/2009/January/26010901.asp

Smoothing the cracks in epoxy resin

2009-02-08T23:45:00.002-08:00

Researchers in China have developed a self-healing epoxy resin which can be repaired by heating when cracks form.

Epoxy resin is a tough polymer with many uses from glues to circuit boards, aerospace engineering to art restoration. Epoxy materials are often used under harsh conditions where long-term service and durability are needed. So, it would be ideal if damaged epoxy resin could self-heal, a property recently developed for other polymers.

Gradual recovery from cracks in cured epoxy due to its remendability

Conventional epoxy resin is based on epoxides to which an additive (or curing agent) is added to form cross-linking between the chains strengthening the polymer. However, these cross-linked bonds are usually irreversible meaning that if cracks form, the bonds cannot be remade to repair the material.

Min Zhi Rong and co-workers from Zhongshan University, Guangzhou, China, have solved this problem by making a new epoxy material which contains both epoxide and furan groups in the same molecule. To this they add a maleimide-based curing agent, as well as the conventional anhydride curing agent.

The anhydride forms irreversible strong bonds with the epoxide groups but the maleimide makes bonds with the furan groups which are reversible at 110 degrees centigrade. So when cracks form in the cured polymer, it is heated to 120 degrees centigrade to break the reversible bonds and then cooled to 80 degrees centigrade so the broken bonds could reform.

'The smart epoxy not only has the superior properties over conventional epoxy', claims Rong, 'but it also exhibits thermal self-healing'. Rong goes on to say that his epoxy 'may prolong the service of the products made from the resin'.

Fred Wudl, a polymer expert from University of California, Los Angeles, US, says Rong's work 'is an interesting step towards creating remendable epoxy resins, following on from previous work in the field.'

Rong says that his group is currently working to make an epoxy resin which will be able to self-heal at lower temperatures.

Ruth Doherty

http://www.rsc.org/Publishing/ChemScience/Volume/2009/03/Smoothing_cracks.asp

Pfizer's Wyeth injection

2009-02-08T23:45:00.001-08:00

Pfizer has agreed to pay $68 billion (£48.3 billion) for rival US biopharmaceutical firm Wyeth, gaining access to its rich product portfolio and promising pipeline of experimental drugs. Pfizer hopes Wyeth's products will fill the financial void that cholesterol drug Lipitor (atorvastatin), which currently brings in $13 billion a year, will leave when it loses patent protection in 2011.

The merged company will boast a product portfolio that includes 17 blockbuster drugs covering a broad range of therapeutic areas, such as cardiovascular, oncology, women's health, central nervous system, and infectious disease. The news of the deal comes after weeks of speculation over who was in Pfizer's sights for a takeover, and has also put an end to Wyeth's takeover talks for Netherlands-based vaccine manufacturer Crucell.

Deals of this size are never without consequences, and in this case, Pfizer has already said it will be looking to cut 15 per cent of the combined company's workforce, as it seeks to save $4 billion from the combined company's annual costs. The extra 19,500 job losses will be on top of the 13,000 jobs the company has cut over the last two years. Even without the deal, Pfizer chief executive Jeffery Kindler said that the firm was planning to shed another 8,000 jobs by 2012.

Jeffery Kindler, Pfizer's CEO, explains the merger

As details of the deal were announced, it emerged that the two companies have been in talks for months. Pfizer's desire to tighten the focus of its research efforts may have played a part in Wyeth's decision in December 2008 to concentrate its drug discovery efforts in just six therapeutic areas - oncology, central nervous system, vaccines, musculoskeletal, metabolism and inflammation.

Bank raid

The cash-and-stock deal will see Wyeth shareholders receive $50.18 per share and will be financed, in part, by loans from a consortium of banks amounting to $22.5 billion - a remarkable amount considering the current reluctance of banks to lend money. The consortium includes Goldman Sachs, JPMorgan Chase, Citigroup and Bank of America, all of which were in the queue for the US Government's $125 billion bail-out package.

Pfizer's shareholders will also pitch in to fund the deal - the company halved its quarterly dividend to just 16 cents a share compared to the last quarter.

According to Kindler, 'the combination of Pfizer and Wyeth provides a powerful opportunity to transform our industry. It will produce a distinct blend of diversification, flexibility, and scale... that positions the combined company for success.'

However, analysts and commentators have questioned whether making such a big company even bigger is the correct way to go. Derek Lowe, US medicinal chemist and Chemistry World's 'In the pipeline' columnist, has taken a dim view of the merger, saying that Pfizer doesn't have a great record of making acquisitions work. 'Pfizer's own labs certainly haven't done a good job producing compounds. Some of that has been sheer bad luck, but some of it may well have been the inertia that happens in a big organisation,' says Lowe.

'I think that the company's size also affects the sorts of products they advance,' he adds. 'A $200 million per year compound does them little or no good at all, whereas a smaller company would be delighted. You end up with fewer programs than you'd think a company of Pfizer's size would have.'

Matt Wilkinson

http://www.rsc.org/chemistryworld/News/2009/January/27010901.asp

Tethered nanocubes seek out analytes

2009-02-08T23:44:00.001-08:00

Giving biosensors room to explore can improve their sensitivity, US scientists have found. The team used tethers to extend the speed and sensitivity of blood glucose detectors, and say they hope the same approach could improve the detection of cancer and Alzheimer's.

A team led by Timothy Fisher at Purdue University have developed a new type of biosensor coined a 'nano-tetherball biosensor' based on nanocube-shaped sensors tethered by conducting carbon nanotubes to electronic circuitry. 'We wanted to test this structure as a biosensor, and used glucose as our first test because the plentiful literature offers a good basis for comparison,' explains Fisher.

Tethered biosensors can reach out into solution

The team built the sensor from the bottom up, starting from a porous alumina support. The team grew individual single-walled carbon nanotubes in the tiny pores of the support, and as these grew they extended out of the pores and formed a loosely interlaced network of nanotubes on the support's surface.

'Each nanotube tends to have a few defects along its length and when we electrodeposit palladium out of solution - in an electroplating-like process - the metal ions come down and find those defect sites on the nanotubes and form little clusters of metal,' explains Fisher. 'We can control the process so we form small cubes rather than clumps of metal by having a moderate rate of metal deposition.'

Biocompatible gold is then electroplated on top of the palladium coating. Finally a linker ligand is coupled to the nanocubes, followed by the glucose oxidase enzyme - an enzyme that couples to D-glucose.

The detector behaves in a standard way, measuring the glucose concentration based on the electrocatalytic detection of hydrogen peroxide produced when glucose binds to the glucose oxidase. What stands this apart from what has come before is that 'the end the sensor itself is flexibly tethered to the support as apposed to being immobilised on a surface,' explains Fisher. 'This means it can actually probe around the medium where you want to sense a target species.' As the sensor can move short distances into the medium being analysed and is somewhat mobile it has increased sensitivity and gives a faster response, he adds.

In terms of sensitivity, it is 'significantly better' than the commercially available sensors, says Fisher. But he did add that 'typical glucose sensing is for diabetes and one does not need an ultrahigh sensitivity most of the time'. This point is also echoed by Michael Strano, from the Massachusetts Institute of Technology, Cambridge, US, who says that increasing the sensitivity is 'not the scientific and engineering challenge in this field as glucose is present in blood at very high concentrations. The challenges are making such sensors biocompatible and long lived in vivo, a subject not addressed in this work.'

Looking to the future, Fisher says he may try to commercialise this sensor - but having proved the concept, he is also keen to explore the device for a wide range of other sensing systems, such as cancer and Alzheimer's, by simply changing the enzyme attached to the nanocube.

Nina Notman

http://www.rsc.org/chemistryworld/News/2009/January/27010902.asp

Plucking proteins from single cells

2009-02-08T23:43:00.002-08:00

As part of a £5 million initiative of the Engineering and Physical Sciences Research Council, scientists in the UK have developed a microfluidic tool to mine proteins from cells.

The system, developed by Mark Neil, Oscar Ces and their colleagues at Imperial College London, uses oil droplets to solubilise and extract proteins from targeted points on a cell's plasma membrane. The spatially selective sampling is done without solubilising the whole membrane and so doesn't destroy the cell, meaning that the scientists can follow single cells to study how protein levels vary in both space and time.

By trapping their microtools with laser beams (red curves) the UK team can target single cells

Ces explains that the initiative, called the Single Cell Proteomics project, is a five and a half year multidisciplinary research collaboration whose aim is to create a suite of technologies to study proteins in single cells. 'Integrating the different technologies required to undertake single cell analysis is challenging,' he says, 'and there are few combinations of researchers with the combined know-how at present.'

"The team plans to look at how changes in protein levels in the plasma membrane affect signalling pathways involved in cancer growth."

The team's droplets are called smart droplet microtools (SDMs). They consist of detergent-coated oil droplets optically trapped, or controlled, using two laser beams. The SDMs can be manipulated using a microfluidic device to enable interactions between the cells and the droplets. Ces explains that protein transfers from a cell to an SDM through interactions with the detergent. It can then be analysed, with the SDM effectively acting as a storage vessel for the protein.

Adam Woolley, an expert in microfluidic systems for bioanalysis, at Brigham Young University in Provo, US, comments: 'This work showcases a clever combination of optical trapping with microfluidic manipulation of droplets and cells. The approach looks to be especially promising for the spatially localised characterisation of cell membrane components, particularly if methods can be developed to enable quantitation of targeted compounds.'

The team now plans to develop the technology for tackling key biological questions, such as how changes in protein levels in the plasma membrane affect signalling pathways involved in cancer growth. Ces suggests that the SDMs could ultimately be used to deliver material to single cells. 'We believe the platform has a great deal of potential,' he says.

Katherine Davies

http://www.rsc.org/Publishing/Journals/cb/Volume/2009/3/plucking_proteins_from_single_cells.asp

Water split with aluminium

2009-02-08T23:43:00.001-08:00

Aluminium clusters' ability to split water molecules and release hydrogen is dictated by the geometric arrangement of active sites on their surface, US scientists have discovered. Many aluminium clusters will absorb water onto their surfaces, but only a few take the reaction a step further, breaking up the water molecules to produce hydrogen. Understanding this relationship might lead to design of new selective catalysts for hydrogen production, or other related applications.

Welford Castleman Jr. and his group from Penn State University make their clusters by vaporising aluminium with a laser. This aluminium plasma is than expanded into a chamber containing a lower pressure gas, which forces it to cool and form the clusters. When the team exposed these clusters to water, they noticed that some of them appeared to release molecular hydrogen.

The interesting factor in these reactions is the selectivity, as Castleman explains: 'When you take sodium and throw it into water, it looks like pretty much every atom is involved in some reaction that will produce hydrogen. In our case only certain aluminium clusters react and others don't, so what we were doing was to try and sort out these unexpected reaction mechanisms.'

Aluminium clusters react with water to release hydrogen

The team discovered that only clusters of certain sizes and geometries can perform the hydrogen-forming reaction. Previously the reactivity of these clusters was thought to depend solely on the number of electrons in the cluster, but Castleman proposes that it is actually the geometric distribution of electron density on the cluster surface that dictates whether any reaction will occur. The surface of the cluster must have one aluminium atom which can act as a Lewis base in close proximity to a second site acting as a Lewis acid. The Lewis acidic site binds the oxygen atom of a water molecule, allowing abstraction of one of the hydrogen atoms by the adjacent Lewis basic site.

If a second water molecule reacts at another pair of aluminium sites somewhere close by on the cluster surface, then the two bound hydrogen atoms can be released as molecular hydrogen. While several of the clusters studied would adsorb and react with water molecules, only clusters of 16, 17 or 18 aluminium atoms had the appropriate arrangement of active sites to allow the release of hydrogen molecules.

'We are talking about production of hydrogen on a very small scale,' Castleman stresses. 'What we are doing is laying out some fundamental mechanisms by which hydrogen can be generated, perhaps giving people some idea of how they might more effectively make hydrogen in bulk quantities.'

Charles Mims, from the University of Toronto, Canada, agrees that the work is interesting. '[Castleman has shown] clear variation of the reactivity of water with aluminium clusters as a function of the cluster size, and provided insight into which sites on the clusters provide facile activation of water.' However, he is more sceptical about the possible applications of the technology: 'This system should not be viewed as providing a lead for hydrogen generation for hydrogen energy systems, since the aluminium cluster is oxidized in the process. It must be regenerated (at an energy cost higher than that available in the product hydrogen) if it is to produce more than a few hydrogen molecules per cluster.'

Castleman agrees that it will be a challenge to sustain the hydrogen formation, since they will need to work out an effective way of regenerating the clusters by removing the hydroxide groups that end up stuck to the surface after the release of hydrogen. He explains that his group are working on the problem, and that while the technology may not be suitable for bulk production of hydrogen, it could be used to provide controlled local generation of hydrogen on demand at low levels.

Phillip Broadwith

http://www.rsc.org/chemistryworld/News/2009/January/28010901.asp

Ultra-pure boron structure discovered

2009-02-08T23:42:00.001-08:00

Scientists have characterised a new form of elemental boron - a notoriously hard element to synthesise in a pure form - and found that ionic bonding helps hold the structure together.

There are at least 16 known polymorphs of boron, but only three of these are thought to correspond to the pure element. Now Artem Oganov from Stony Brook University, New York, US, and colleagues have made a new structure to add to the list. Termed gamma-boron, their new form of boron is made up of two forms of boron clusters - B₂pairs and B₁₂ icosahedra - arranged in a sodium chloride type structure.

'When I first saw the structure I was very surprised,' says Oganov. B₂ pairs and B₁₂ icosahedra - clusters of twelve boron atoms arranged in a regular 20 sided polyhedron - are well known in boron chemistry, but Oganov's team found that differences in electronegativity between the two forms led to partial ionic bonding. 'It is, say, 90 per cent covalent,' says Oganov. 'But the ionic component is significant and that is something that we really didn't expect.'

The gamma-boron cluster, showing the B2 (yellow) and B12 (purple) clusters

The B₂ pairs and B₁₂ icosahedra act as anions and cations, respectively, affecting other properties of the material such as the IR spectrum and electronic bandgap. Unlike other polymorphs such as alpha- and beta-boron, gamma-boron does not become metallic at increased pressure.

The new form of boron has also shed light on the element's previously unknown phase diagram, helping to map the element's phase changes in response to pressure and temperature. 'We have found a phase which has a gigantic stability field.' Oganov told Chemistry World. Between 19 and 89 GPa the new form of boron is more stable than any other structure, and it also keeps its structure at room temperature and pressure. 'We have been able to find a key to the phase diagram of boron,' says Oganov. 'It has been really embarrassing that boron was the only element for which the phase diagram was simply unknown - now we know a little bit more about how this element works'

The team determined the structure of the new material using a computational technique that allowed them to predict the most favourable positions of the atoms from just the chemical formula.

'It's a big step in understanding the phase diagram of boron,' says Mikhail Eremets at the Max Planck Institute for Chemistry in Germany. He was also impressed by the team's ability to predict and determine such complex structures. 'It's an example of fundamental breakthrough of understanding of quite a complex system.'

Manisha Lalloo

http://www.rsc.org/chemistryworld/News/2009/January/28010902.asp

Iron helps oceans capture more carbon

2009-02-08T23:41:00.001-08:00

A team of international scientists studying the role of iron in the storage of carbon under the ocean have confirmed that natural iron fertilisation increases the rate of carbon capture. However, the group's measurements conflicts with previous studies - and adds to ongoing concerns over planned experiments to artificially fertilise the oceans with iron as a tool to cut carbon dioxide from the atmosphere.

Iron's role in the ocean carbon cycle is to promote the growth of phytoplankton, which remove carbon dioxide from the air through photosynthesis. Whilst most of the carbon in the resulting biomass will re-enter the atmosphere through the carbon cycle, a small amount will fall into the depths of the ocean as the plankton dies, effectively locking away that carbon for up to 300 years. The theory is that the more phytoplankton there are, the more carbon will be stored in the depths of the sea.

The drifting sediment trap that collects samples of sinking material while drifting at 150 m.

Artificial iron-fertilisation to promote phytoplankton growth would involve dumping huge amounts of iron in areas of the ocean deficient in this mineral but having all the other ingredients needed for a phytoplankton bloom to grow. However, the idea remains highly controversial, as the likely effectiveness of the procedure - as well as its wider environmental impact - has been questioned, because the exact relationship between iron and the amount of carbon that is removed for circulation is still unknown. In 2008 the United Nations Convention on Biological Diversity agreed to halt all but small scale coastal iron fertilisation trials over concerns about the potential environmental impact.

Just act natural

The Crozex project led by Raymond Pollard and Richard Saunders from the National Oceanography Centre in Southampton, UK, studied the seas around theCrozet islands in the Southern Ocean in an attempt to confirm exactly how iron levels affect carbon capture. 'Establishing quantitatively the relationship between iron and carbon is a really key thing to do,' says Saunders.

The water around the Crozet islands is naturally supplied with iron from the volcanic islands. 'We know unequivocally that iron comes out of these land masses, enters the surrounding ocean and fertilises plant growth,' Saunders adds.

After measuring the concentrations of total dissolved iron in the ocean, the team used a variety of techniques to measure how much carbon was exported to the ocean depths. They calculated the amount of organic carbon sinking from the surface ocean (the top 100 metres that is mixed by winds and currents) to the ocean interior using ²³²Th-²³⁸U ratios. 'Thorium is a naturally occurring radioactive element with a high affinity for particles, but its parent uranium has a low affinity for particles,' explains Saunders. Thorium particles attach themselves to the carbon particles, and when they sink, change the normally stable ratio of thorium to uranium. 'Because we are dealing with a radioactive element with a defined half life, we can estimate the rate of downwards flux from the surface ocean,' he says.

'Deeper in the ocean we use sediment traps that are analogous to rain gauges. They are funnels that collect the particulate matter and store them in small pots,' Saunders says. One pot is then collected each month over a year long period. The team also took sediment cores to sample deeper sediments.

The team's findings confirm that natural iron fertilisation increases the amount of carbon exported to the ocean interior by two to three fold. However, this amount was 18 times greater than those seen during a 2004 experiment where a phytoplankton bloom was induced by artificially adding iron, but 77 times smaller than that of another bloom initiated by a natural source of iron - studied by another international team led by Stephane Blain, Marseille Centre for Oceanography, France, two years ago. 'We still don't know if the numbers were different because it was a different environment or if there was something fundamentally different,' says Saunders.

But despite the lack of agreement, the figure is still significantly lower than some geoengineering estimates, adds Pollard, which has 'significant implications for proposals to mitigate the effects of climate change through purposeful addition of iron to the ocean'.

'This study gives us a much better idea of what iron fertilisation in the natural sense is doing,' says Michael Behrenfeld, an expert in marine carbon cycling and climate change at Oregon State University, US. 'But why the numbers are so different remains a big question.'

But Behrenfeld is strongly opposed to the idea of artificially spiking the ocean with iron as a way to counter climate change, adding that such a process would trigger large, unpredictable changes to the ecosystem. 'There has been a large amount of discussion in the community as to whether that is a good idea. And generally speaking it is not considered to be an effect way to combat climate change - there are much better ways, with much more predictable outcomes, of dealing with CO₂.'

Nina Notman

http://www.rsc.org/chemistryworld/News/2009/January/28010903.asp

EPA's chemical evaluation process 'high-risk'

2009-02-08T23:39:00.000-08:00

The US government's 32-year-old law regulating chemical safety needs a complete overhaul, according to Congress' investigative arm, known as the Government Accountability Office (GAO). In a 22 January report, GAO says comprehensive reform of the Toxic Substances Control Act (TSCA) - which is administered by the US Environmental Protection Agency (EPA) - should be a top priority.

In GAO's 'High Risk' priority document - which identifies the government programmes, policies, and operations most in need of fixing - the office concludes that EPA's 'inadequate progress' in assessing toxic chemicals significantly hampers its ability to protect human health and the environment.

'The Environmental Protection Agency lacks adequate scientific information on the toxicity of many chemicals that may be found in the environment - as well as on tens of thousands of chemicals used commercially in the United States,' the report concludes. GAO also criticises EPA for failing to routinely assess the risks of the roughly 80,000 industrial chemicals that are already in use in the US.

In addition, the report says action is needed to streamline and increase the transparency of EPA's Integrated Risk Information System (IRIS), a compilation of reports on specific substances and their potential to cause human health effects. GAO notes thatsome of the chemicals most likely to cause significant health problems are among the IRIS assessments that have taken the longest to complete. EPA's assessment of dioxin, for example, has been ongoing for 18 years.

Industry concerns

The American Chemistry Council (ACC), the major trade association for US chemical companies, agrees that improving the quality of EPA's chemical risk assessments is important. 'ACC has been concerned for some time that the IRIS process was moving more slowly than desired, not only in output, but also with incorporating scientific advances in risk assessment,' the group states.

Paul Anastas, the director of Yale University's Center for Green Chemistry and Green Engineering, says an overhaul of TSCA is long overdue. 'A chemicals statue should not facilitate endless review, analysis and characterisation of problems, rather it should facilitate moving toward new classes of substances of less risk to human health and the environment,' he tells Chemistry World. 'Right now, TSCA facilitates paralysis by analysis.'

The GAO report points out that the European Union's Registration, Evaluation and Authorization of Chemicals (Reach) legislation requires companies to provide safety data and risk assessments on the chemicals they produce, but TSCA generally places the onus on EPA to obtain such data. This requirement is costly and time-consuming because it compels EPA to demonstrate that certain health or environmental risks are likely before the agency can require companies to further test their chemicals.

'Without greater attention to EPA's efforts to assess toxic chemicals, the nation lacks assurance that human health and the environment are adequately protected,' GAO warns.

Political power

The new Obama administration does appear to have the political will to rework EPA's system for assessing chemicals. Throughout his campaign, Obama repeatedly discussed the importance of protecting the public and environment from toxic substances. The agency's new administrator - chemical engineer Lisa Jackson - recently listed revising and strengthening EPA's chemical risk management as one of her top priorities.

There is also an expectation on Capitol Hill that members of the Senate Environment and Public Works Committee will use the GAO report to expedite EPA reform in areas like TSCA.

But even if the White House and new Congress actively pursue modifications to TSCA, such efforts will likely face major opposition from chemical companies that have a vested interest in avoiding extra, expensive testing.

'It isn't just one or two studies that will help define the toxicology and exposure of a chemical - it will be many,' says Larry Turner, an ecotoxicologist who worked for EPA for nearly 30 years and served in the agency's toxic substances group during that time. 'This gets very expensive for the chemical companies, and for EPA as well because this extra data has to be processed and assessed,' he adds.

For its part, EPA would not comment on the GAO recommendations. The agency did note, however, that it has a newly confirmed administrator and will review the GAO report and 'respond accordingly'.

Rebecca Trager, US correspondent for Research Day USA

Graphene to graphane by chemical conversion

2009-02-08T23:38:00.001-08:00

An international research team have successfully converted graphene - sheets of carbon just a single layer of atoms thick - into its hydrogenated equivalent, graphane. The scientists, from the UK, Russia, and the Netherlands, say that graphane's electronic insulating properties complement graphene's conductivity, boosting the prospects of graphene-based nanoelectronics and hydrogen-fuel technologies.

The work is the first to show that a chemical approach can be used to tailor the properties of a nano-material like graphene, in order to tune it to a particular application, says Andre Geim, part of the team at the University of Manchester. The team used a stream of hydrogen atoms to reversibly convert graphene into graphane.

Adding hydrogen converts graphene (top) into graphane

Geim and his colleague Kostya Novoselov led the researchers who discovered the first simple approach to make graphene in 2004. Graphene's layer of delocalised electrons gives it remarkable conductive properties, which has since fuelled the idea of creating superfast nano-scale transistors. But one of the biggest obstacles of using it for such applications has been to understand how to control electron flow.

One possibility previously explored by Geim and Novoselov has been to cut graphene into strips only a few nanometres wide. However, 'you can never really stop current flowing when you want to,' says Geim, because graphene lacks the necessary energy gap in its electronic structure.

But graphane offers a possible way around this problem. 'What graphane brings to the game is the possibility of chemically modifiying the structure of graphene to open a gap,' says Jorge Sofo, Professor of Physics at Penn State University, US, who hypothesised the existence of a fully hydrogenated version of graphene in 2007.

'Imagine if you were able to produce a single, transparent plane of graphane - essentially a plastic - and imagine having a magic pencil with which you can remove hydrogen so you will be drawing a channel of graphene.' Sofo says he is now working with colleagues on how to create such a 'pencil', possibly with some kind of scanning tool.

Others think graphane could have applications in new fuel technologies too. Graphane has a huge hydrogen density and Alex Savchenko, who studies graphene at the University of Exeter, believes future research should focus on exploiting this property in order to store hydrogen for hydrogen fuel technologies. Sofo, however, points out that the discovery of graphane is just one small step. 'We are speaking about little atomic flakes. Hydrogenating a little atomic flake is not creating a hydrogen storage tank.'

James Urquhart

http://www.rsc.org/chemistryworld/News/2009/January/29010902.asp

Graphene to graphane by chemical conversion

2009-02-08T23:34:00.000-08:00

Adding hydrogen converts graphene (top) into graphane

James Urquhart

http://www.rsc.org/chemistryworld/News/2009/January/29010902.asp

Making magnetic monopoles, and other exotica, in the lab

2009-02-08T23:33:00.000-08:00

February 5th, 2009 By Lauren Schenkman in Physics / Physics

Enlarge

Physicist Shou-Cheng Zhang. Photo: Lauren Schenkman

Physicist Shou-Cheng Zhang has proposed a way to physically realize the magnetic monopole. In a paper published online in the January 29 issue of Science Express, Zhang and post-doctoral collaborator Xiao-Liang Qi predict the existence of a real-world material that acts as a magic mirror, in which the never-before-observed monopole appears as the image of an ordinary electron. If his prediction is confirmed by experiments, this could mean the opening of condensed matter as a new venue for observing the exotica of high-energy physics.

Zhang is a condensed-matter theorist at the Stanford Institute for Materials and Energy Science (SIMES), a joint institute of SLAC National Accelerator Laboratory and Stanford University. He studies solids that exhibit unusual electromagnetic and quantum behaviors, with an eye towards their use in information storage. But due to his training as a particle physicist, Zhang always keeps the big picture in mind. That’s why it was so easy for him to see that the material he was already working on could behave like what theorists call a magnetic monopole, an isolated north or south magnetic pole.

The monopole is thought of as electric charge’s magnetic cousin, but unlike positive or negative charges, north or south poles always occur together in what’s called a dipole. A lone north or south pole simply doesn’t show up in the real world. Even if you take a bar magnet and cut it in half down the middle, you won’t get a separate north and south pole, but two new dipole magnets instead. For symmetry-minded theorists, however, it’s natural that there should be a magnetic equivalent of charge. String theories and grand unified theories rely on its existence, and its absence undermines the mathematical feng-shui of the otherwise elegant Maxwell’s equations that govern the behavior of electricity and magnetism. What’s more, the existence of a magnetic monopole would explain another mystery of physics: why charge is quantized; that is, why it only seems to come in tidy packets of about 1.602×10^-19 coulombs, the charge of an electron or proton.

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For decades, scientists have kept their eyes peeled for the elusive monopole, but perhaps they were looking in the wrong place. “They were literally hoping it would fall from sky,” Zhang says. The notion isn’t as far-fetched as it seems—our world is constantly bombarded by weird particles showering from far-off cosmic events, and magnetic monopoles could very well show up as part of that rain. Some enterprising physicists installed loops of superconducting material on their rooftops. If anything remotely like a magnetic monopole fell through, the loops, being sensitive to magnetic fluctuations, would register it.

But in more than 30 years of searching, no one’s been able to conclusively detect this particle. Accelerator experiments have been no more successful, leading scientists believe existing monopoles must be far too heavy to create in even the Large Hadron Collider.

Interestingly, Zhang’s magnetic monopole didn’t fall from the heavens; instead, it was leading a quiet life on the other side of a mirror, but a mirror made of a very special type of alloy. What’s more, says Zhang, the math to prove the effect is very clear. “You could give the last part of the mathematical derivation as a final exam in a junior or senior year undergraduate physics class.”

To understand how a material can act like a magnetic monopole, it helps to examine first how an ordinary metal acts when a charge—an electron, say—is brought close to the surface. Because like charges repel, the electrons at the surface retreat to the interior, leaving the previously neutral surface positively charged. The resulting electric field looks exactly like that of a particle with positive charge the same distance below the surface—it’s the positive mirror image of the electron. In fact, from an observer’s point of view, it’s impossible to tell the difference.

The concept of an image charge is something undergraduate physics students encounter in their very first electricity and magnetism class, along with the idea that the magnetic monopole doesn’t exist. But Zhang’s “mirror” alloy is no ordinary material. It’s what’s called a topological insulator, a strange breed of solid Zhang specializes in, in which “the laws of electrodynamics are dramatically altered,” he says. In fact, if an electron was brought close to the surface of a topological insulator, Zhang’s paper demonstrates, something truly eerie would happen. Instead of an ordinary positive charge, Zhang says, “You would get what looks like a magnetic monopole in the ‘mirror.’”

To go back to the example of image charges, it’s important to emphasize that there isn’t actually half of a bar magnet somewhere inside this material. Instead, Zhang discovered, due to a peculiarity of the material called strong spin-orbit coupling, the nearby electron would induce a current in the surface that circulates constantly without dying out. This in turn—undergraduate physics majors, get out your pencils—would create a magnetic field that looks like that of a magnetic monopole. Experimentalists have tried to approximate this field before, for instance by arranging permanent magnets in certain ways. But to an outside observer, Zhang’s material would be completely indistinguishable from the monopole particle that physicists were hoping to catch in their superconducting detectors.

“We like to find things that don’t exist,” says Zhang. His work on the monopole has further ramifications; this could be a way to physically realize a number of particles that, until now, have only existed as mathematical loopholes in high-energy physics theories. For instance, Zhang has shown that the electron and image monopole together would act like a so-called “anyon” located at the solid’s surface. “The ‘any,’ in this case, is as in ‘anything,’” Zhang explains—they are particles that only exist in two dimensions, whose properties straddle those of the two classes of three-dimensional particles, fermions and bosons.

Although Zhang works as a theorist, he has close ties to experimental physics. In 2007, his prediction of the quantum spin Hall effect in mercury telluride was confirmed experimentally, earning his work praise in Science as a runner-up breakthrough of that year. “As a theorist you’re always motivated by the math, but it’s a testament to our understanding that we can predict real-world materials,” Zhang says. “Before, new materials were more or less found by accident.” Now other SIMES researchers will be using the Stanford Synchrotron Radiation Lightsource at SLAC to closely study two specific materials, bismuth selenide and bismuth telluride, that Zhang has predicted will exhibit this strange mirror behavior. They hope to confirm the prediction experimentally some time this year.

“Exotic particles such as the magnetic monopole, dyon, anyon, and the axion have played fundamental roles in our theoretical understanding of quantum physics,” Zhang writes in the paper. “Experimental observation of these exotic particles in table-top condensed matter systems could finally reveal their deep mysteries.” Topological insulators could provide a new experimental outlet for high-energy physicists. “You don’t have to look towards the cosmos,” Zhang says. “I think we’ll see more of the beautiful mathematical structures of high-energy physics become realized in condensed matter physics.”

Provided by SLAC National Accelerator Laboratory, By Lauren Schenkman

Cracking cryptic clues to the plague

2009-02-08T23:32:00.002-08:00

Scientists in the US are modelling the behaviour of the bacteria responsible for bubonic plague to find alternative ways to target the disease. Using a novel approach called CryptFind, Eivind Almaas and Ali Navid from the Lawrence Livermore National Laboratory, US, have found the genes that the bacteria, Yersinia pestis, call upon to survive.

Plague circulates mainly among animals, via fleas

Although the plague is widely considered to be a disease of the past - it has killed 200 million people throughout human history - it still affects thousands of people worldwide. Whilst it can usually be treated using antibiotics, several antibiotic resistant strains have recently been discovered, indicating that new treatments for the plague are needed.

But it is very difficult to study plague behaviour experimentally because of fears over public safety and the need for high-security laboratory conditions (Yersinia pestis, the bacterial cause of the disease, is classed as a potential bioterrorism pathogen by US authorities). Therefore, theoretical models, such as those developed by Almaas and Navid, are used in place of clinical studies.

"By identifying candidate cryptic genes, it is possible to target not only the primary pathway to a compound, but also eliminate dormant alternate pathways."

The US researchers used CryptFind to identify Y. pestis' cryptic genes. These genes are not normally required for cell function, but can ensure cell survival under extreme conditions. Almaas explains that it is Y. pestis' ability to initiate cryptic genes that enables it to survive in hospital environments, and complicates the development of drugs for the plague. 'By identifying candidate cryptic genes,' he says, 'it is possible to target not only the primary pathway to a compound [essential for Y. pestis survival], but also eliminate dormant alternate pathways.'

Bernard Palsson, an expert in mathematical genome modelling from the University of California, San Diego, US, says that 'it is wonderful to see more reconstructions of human pathogens appearing. Hopefully, such reconstructions will open up new dimensions in the fight against infectious disease.'

Almaas is now in the process of modelling other Yersinia variants, including Yersinia pseudotuberculosis, a precursor to Y. pestis which causes tuberculosis-like symptoms in humans.

Hilary Burch

http://www.rsc.org/Publishing/Journals/cb/Volume/2009/3/cracking_cryptic_clues_to_the_plague.asp

Cracking a controversial solid state mystery

2009-02-08T23:32:00.001-08:00

February 6th, 2009 in Physics / Physics

(PhysOrg.com) -- Scientists can easily explain the structural order that makes steel and aluminium out of molten metal. And they have discovered the molecular changes that take place as water turns to ice. But, despite the fact that glass blowers have been plying their trade since the first century BC, we have only just begun to understand what makes molten glass solid.

One hundred and fifty years after the construction of Crystal Palace at the Great Exhibition, scientists at The University of Nottingham and the University of California, Berkeley in collaboration with the University of Bath, have presented an explanation of how atoms behave as glass cools and hardens. Their research has just been published online in Science Express, in advance of publication in Science.

The secret of glass making came to Britain with the Romans in 55 BC. But only now do scientists believe they are a step closer to unravelling the controversy that surrounds the question: what makes solid glass different from the molten liquid from which it is formed?

Juan Garrahan, Professor of Physics, in the School of Physics and Astronomy at Nottingham said: "Snapshots taken with x-rays show that in ice, water molecules fit together in an ordered array, which is called a crystal, while in liquid water, the molecules are jumbled. Scientists can understand why ice is rigid and liquid water is fluid largely from these structural differences. Glass, on the other hand, does not offer this explanation because a snapshot of the molecular structure of solid glass is almost indistinguishable from that of the molten liquid. Both appear to be jumbled random collections of atoms. This observation is at the heart of the problem: if the solid state of glass has a molecular structure just like that of the liquid, how can it be so rigid? Controversy has resulted from the absence of a clear answer to this question."

Using computer simulations, researchers were able to test the theoretical and computational process of melting and hardening glass. They have not yet solved the glass transition problem however they have provided evidence for a new perspective on glassy phenomena which may eventually lead to its solution.

Dr. Robert Jack, from the Department of Physics at the University of Bath, said: "By focusing on the ability or inability of molecules to flow we have provided evidence for a new kind of sudden transition between the flowing liquid and the solid glass. This transformation is apparent only when the system is viewed in both space and time."

Ultimately, the answer is important because the principles that underlie the glass transition can guide scientists and engineers towards methods for producing better glass — stronger and longer lasting. Disordered glassy solids are ubiquitous in everyday materials including ceramics and plastics. For over a century, principles of thermodynamics have aided the design of ordered solids, materials like steel and aluminium alloys. No such principles are yet settled for production of glassy solids. The current work is believed to be a significant step towards these principles.

Provided by University of Nottingham

Toenails reveal arsenic exposure

2009-02-08T23:30:00.000-08:00

UK scientists have finally found a use for toenail cuttings. Mark Button at the British Geological Survey in Nottingham, UK, and colleagues are using the clippings to detect human exposure to elevated environmental levels of arsenic.

Button's group collected toenails from residents living near a former arsenic mine in Devon, UK. They washed and acid digested the samples under microwave irradiation. They then analysed the samples using inductively coupled plasma mass spectrometry. The toenails showed significantly elevated arsenic levels compared to those seen in samples taken from people that had no contact with the element.

The toenails showed significantly elevated arsenic levels

Arsenic occurs naturally in the environment and people can be exposed to it in several ways, for example through contaminated water, food or soil. Chronic exposure is associated with increases in lung, liver, bladder and kidney cancers.

Once ingested, arsenic is absorbed into the bloodstream and then accumulates in several body parts. Evidence disappears from blood and urine after a few days but arsenic accumulates long term in keratin rich materials such as hair and nails. This makes them potentially more useful as biomarkers of chronic arsenic exposure. Toenail samples in particular are an attractive possibility as they are easy to collect, store and transport and are less liable to contamination than hair samples.

'This research', says Button, 'highlights the suitability of toenails as a biomarker of exposure to potentially harmful elements in areas such as the south-west of the UK where more extensive biomonitoring studies are long overdue.'

Richard Kelly

http://www.rsc.org/Publishing/ChemScience/Volume/2009/03/Toenails_reveal_arsenic_exposure.asp

Why do the majority of people never get cancer?

2009-02-08T23:29:00.000-08:00

January 22nd, 2009 By Lisa Zyga in Medicine & Health / Cancer

Enlarge

Dividing Cancer Cells. Image: University of Birmingham

(PhysOrg.com) -- Every year, millions of people are diagnosed with cancer - a remarkably high number. But what about the flipside of those statistics? That is, two out of three people never get cancer, and more than half of heavy smokers don’t get cancer, either. A recent study points out this overlooked fact, and suggests that researchers might discover something by asking why so many people are resistant to the often deadly disease.

George Klein, Professor Emeritus at the Microbiology and Tumor Biology Center at the Karolinska Institute in Stockholm, Sweden, has been teaching and researching since the mid-1940s. In a recent study called “Toward a genetics of cancer resistance” published in the Proceedings of the National Academy of Sciences, Klein highlights evidence of several biological cancer resistance mechanisms that some individuals have that seem to prevent them from developing cancer. Perhaps, Klein says, there are cancer-resistant genotypes that “nip cancer in the bud” and keep most of us healthy.

As Klein explains, the suffering of cancer patients and their families has inspired most cancer researchers to focus on the genetics of cancer susceptibility. On the other hand, the genetics of cancer resistance has been largely unexplored, possibly because it is assumed to be merely the other side of the susceptibility coin. For example, if cancer is caused by mutations in genes that control cell division, then it logically seems that cancer resistance is simply a low occurrence of these mutations.

But, Klein says, maybe there is another alternative to the concept of cancer resistance. Perhaps most people have various protective mechanisms that counteract the development of cancer cells and stop the disease from progressing beyond the earliest stages.

“Cancer resistance must be investigated on its own merits,” Klein told PhysOrg.com. “It is possible and even likely that evolution has provided our species with highly efficient cancer resistance mechanisms. These may be the mechanisms that prevent most circulating, disseminated cancer cells that are found in the blood of all cancer patients to grow into metastasis, and can also nip cancerous foci (islands of cells in, for example, the prostate or the breast) in the bud, so that they do not progress.”

In a previous discussion, Klein and his coauthors identified five kinds of anticancer mechanisms. The first type is immunological, which applies to virus-associated cancers. For instance, researchers have compared the antibody responses of the squirrel monkey and the marmoset when infected with Herpesvirus saimri, a virus that is endogenous to squirrel monkeys but that the marmoset never encounters. When exposed to the virus, the marmosets, but not the squirrel monkeys, develop rapidly growing lymphomas. The researchers found a striking difference in the timing of each animal’s antibody response. In the tumor-resistant squirrel monkeys, the antibodies rose to a high level just three days after the infection, but, for the marmosets, the response took three weeks. By that time, the marmosets already had a rapidly growing virus-driven lymphoma. Research has shown that such immunological responses are influenced by genetic variation.

The second mechanism is genetic, and the most common example is DNA repair mechanisms. Studies have shown that there are individual variations in the efficiency of DNA repair, which is highlighted in cases such as the specific DNA repair deficiency called xeroderma pigmentosum. Individuals with this deficiency are highly sensitive to ultraviolet light, and even with careful protection they develop multiple skin carcinomas due to the genetic deficiency.

The third mechanism is epigenetic, which involve changes in gene expression, rather than changes in the DNA text itself. Studies have shown that when mice that carry a paternal precancerous mutation inherit a maternal imprinting defect, normal parental imprinting is impaired, which can increase the probability of cancerous development. In humans, this same imprinting defect occurs spontaneously and increases tumor incidence, affecting 10% of humans, and increasing their risk of intestinal cancer about threefold.

The last two anticancer mechanisms are intracellular and intercellular. As part of an intracellular defense, a cell can trigger apoptosis, or cell death, if it detects extensive DNA damage, so that the cell doesn’t reproduce and spread the damage. But sometimes, apoptosis isn’t triggered when it should be. For example, individuals who carry the genetically mutated tumor suppressor p53 run an increased risk of inheriting Li-Fraumeni syndrome, a rare disease in which patients develop multiple tumors.

Klein predicts that intercellular surveillance by neighboring cells, the fifth known anticancer mechanism, plays a major role in tumor resistance. Cells that are in direct physical contact with each other can detect precancerous conditions in one another, and together act as a microenvironmental control system to prevent the development and progression of unhealthy cells.

While the first four anticancer mechanisms are known to be influenced by genetic variation, little research has been performed on possible genetic or developmental variations in the efficiency of the intercellular anticancer mechanism. However, Klein mentions a group of largely forgotten experiments from the 1950s and ‘60s, where scientists crossed mouse strains that had a high incidence of cancer in a given tissue (due to inbreeding and selection for that particular type of cancer) with mice from a low incidence strain. In the experiments where they studied mammary cancer, hybrid females were taken from this case. Their own mammary glands were removed surgically. One mammary gland from the high cancer strain parent and one gland from the low cancer strain parent were then transplanted to two opposite flanks of the hybrids. Dealing with two inbred strains and their hybrid progeny, there is no problem with graft rejection, Klein explains.

It turned out that tumor incidence in the normal mammary gland derived from the high cancer parent was tenfold higher than in the mammary gland from the low cancer strain. Since both tissues were in the same host, exposed to the same hormonal and viral influences, it meant that the cancerous propensity of the high cancer strain and/or the resistance of the low cancer strain was at least partly inherited at the level of the tissue itself. This genetic difference could either act at the level of the cancer cells or at the level of their microenvironment.

Klein urges researchers to investigate this intercellular issue, along with the genetics of tumor resistance that act in multiple ways. Evolution seems to have favored some relatively common resistance genes that protect the majority of humans against cancer development. One day, finding out how nature keeps most of us cancer-free could help identify and repair specific genetic mechanisms in the large minority of individuals who do suffer from cancer. However, Klein says that it’s premature to speculate exactly how understanding genetic resistance could help people who are susceptible to cancer.

“First, it has to be shown that such protection mechanisms exist and, if so, what cellular and molecular mechanisms are responsible for them,” he said. “Only after that is clear, is it reasonable to ask whether this knowledge can be applied for the practical purpose of, for example, cancer prevention.”

More information: Klein, George. “Toward a genetics of cancer resistance.” PNAS, January 20, 2009, vol. 106, no. 3, 859-863.

White LEDs to plummet in price

2009-02-08T23:28:00.000-08:00

Home and office lighting using white LEDs is one step closer to becoming reality now that researchers in Cambridge, UK, have developed technology which could slash the cost of their production.

Blue and white LEDs (light emitting diodes) are made from the semiconductor gallium nitride (GaN) and are currently laid on the surface of synthetic sapphire wafers. The two-inch sapphire wafers (made from titanium oxide) are expensive, but Colin Humphreys and his group have found a way of building GaN LEDs on much bigger and cheaper six-inch silicon wafers for approximately the same processing cost.

Colin Humphreys examines a batch of new GaN LEDs

Using bigger wafers reduces the impact of so-called 'edge effects', as Humphreys explains: 'On any wafer there is a ring approximately three millimetres wide around the edge where the LEDs are generally no good. Obviously with a six inch silicon wafer this has a lot smaller impact than on a two-inch sapphire one. Taking into account the increased area of the silicon wafers, it means you get around ten times more LEDs in total from each wafer.'

This corresponds to an overall 90 per cent reduction in production costs, bringing the prospect of cheap LED-based home lighting a significant step closer. Not only are GaN LEDs more energy efficient than fluorescent low-energy bulbs, they are also instantly bright, are compatible with dimmer-switches and contain no mercury, simplifying their disposal.

Power shower

The devices are made by heating the wafer to 1000 °C and then firing a mixture of ammonia and gallium trimethyl (GaMe₃) at it from a 'showerhead'. 'The gases then decompose,' explains Humphreys, 'leaving gallium and nitrogen atoms on the surface, which skate around until they find each other and become bonded into the crystal lattice. The problem is there is about a 50 per cent difference in thermal expansion coefficient between silicon and GaN, so as the wafer cools the gallium nitride tends to crack under the introduced tension. We discovered that if we build up alternating layers of aluminium gallium nitride (AlGaN) and GaN, then this can counteract the tension on cooling and stops the GaN from cracking.'

GaN LED bulbs are already used to illuminate Buckingham Palace and the Severn Bridge, but one of the major problems with earlier generations of blue and white LEDs was their lifetime. Standard red LEDs last around 100,000 hours, but blue and white ones used to be limited to only a few thousand hours. This, explains Humphreys, is all down to the packaging material around the LED chip: 'The epoxy material that was used before could become brittle and discolour over time. These devices do produce a small amount of heat, so the different parts need to be able to move with each other in expansion and contraction. Using a high-grade silicone material more or less completely solves this problem - so the new devices also last 100,000 hours, which at an average use of 4 hours per day is about sixty years.'

While the basic research on the project was funded by the UK Engineering and physical sciences research council (EPSRC), Humphreys and his group are collaborating with several companies, including RF Micro Devices (RFMD), Thomas Swan, QinetiQ and Forge Europa, under the auspices of the UK government's Technology Strategy Board (TSB) electronics and photonics programme, to bring the technology into the marketplace as a high efficiency, low cost lighting system for homes and offices.

Steve Clements from RFMD, who are project leaders for the TSB collaboration, is excited about these developments. 'Our collaboration with [Humphreys] has been immensely successful - but from a commercialisation perspective there is still some way to go,' he adds. RFMD are keen to exploit the technology if it can be translated into a commercially viable business, but Clements explains that the project is still in the early stages. Humphreys is more optimistic, looking forward to the possibility of having a world-leading manufacturer of gallium nitride LED lighting devices based in the UK within the next five years.

Phillip Broadwith

http://www.rsc.org/chemistryworld/News/2009/January/30010901.asp

Nanocrystals get in shape for catalysis

2009-02-08T23:25:00.002-08:00

New research in fine tuning the shape and size of nanoparticles could lead to important advances in catalysis, say scientists. Two independent groups of researchers have shown that the catalytic activities of tiny platinum crystals can be greatly enhanced by tightly controlling their shape and size.

Metallic nanoparticles make powerful catalysts due to their high surface area to volume ratios. But activity also depends on shape and, so far, scientists have struggled to create crystals with well-defined surfaces, or facets, below the 100 nanometre boundary.

Now Matthias Ballauff and colleagues at the University of Bayreuth in Germany and the Israel Institute of Technology (Technion) have developed a method for creating faceted platinum crystals in the range of two to five nanometres.¹ In a separate study, a team at the University of California, Riverside, US, and University of Lyon in France, led by Francisco Zaera, made tetrahedral nanocrystals of a similarly small size and applied them to trans-cis isomerisation reactions.²

High resolution TEM micrograph of a platnium nanocrystal showing well-defined facets

Ballauff's team made their nanocrystals, which are stuck to polymer beads, from gold-platinum alloys, using cyanide to leach out the gold. 'It was a good luck discovery,' says Ballauff. 'If you take the gold atoms out of these nanoalloys, you have these very nice, faceted platinum nanocrystals.'

The discovery, he says, is a good example of how things in the nanoworld may be qualitatively different than in the bulk world - as bulk metals, gold and platinum don't mix. The team used gold to form their nanoalloys, because it can be easily dissolved, but Ballauf hopes their research will encourage others to start working through the rest of the periodic table, trying out different metal combinations.

Taking sides

Using a model reaction - the reduction of p-nitrophenol - the researchers tested their crystals' catalytic activity and found they had some of the highest turnover rates ever shown. But Ballauf thinks their nanocrystals could be used to perform more technically challenging organic reactions, such as the coupling reactions that join together two phenyl rings.

'Most previously published methods for the synthesis of defined nanocrystals unfortunately deliver particles which are too large,' says Edman Tsang, who studies nanocrystals as University of Oxford, UK. 'What's most impressive is that such a simple leaching method works in a controlled manner without small surfactant or stabiliser molecules, so the surfaces of the nanoparticles remain clean from strong adsorbates. Therefore, this new method could allow the production of supported metal particles as real practical catalysts for chemical conversions in aqueous phase.'

YuYe Tong, an expert in nanocrystal catalysis at Georgetown University in Washington, US, says the key to single crystal catalysis at the nanoscale is controlling the precise orientation of the crystals, so that only one type of facet is exposed. In Ballauf's case, he notes, two different types of facet - 002 and 111 facets - are exposed. 'The novelty for me is not the shape or the size,' he says, 'But this kind of heterogeneous catalysis approach where the nanoparticles are on the polymer beads and you can dissolve these in solution.'

Flipping fats

Using a previously reported technique,³ Zaera's team created nanocrystals that self assemble on a silicon surface from colloidal platinum, resulting in only 111 facets being exposed at the surface. But they went further, showing the crystals could selectively drive the isomerisation of olefins in the trans to cis direction. Their work raises the possibility of using nanoparticles to catalyse a wide range of different isomerisation reactions of hydrocarbons, including reactions important in fuel cells and even in minimising the production of the unhealthy trans fats produced in the food manufacture.

According to Zaera, however, the real aim is to demonstrate the potential of new synthetic approaches to catalysis. 'Platinum is expensive so it is conceivable that the food industry would not pick up our way of making the catalyst. But what we are doing is opening up a new approach in general catalysis; using novel synthetic techniques - nanotechnology and self-assembly - and applying them to make these catalysts in a very specific way,' he says.

Tong agrees. He says Zaera's work reflects a push within the field towards a new direction in catalysis. Although, he adds, the researchers aren't the first to show such control over the shape of their crystals.

'They demonstrate an elegant and useful example of catalysis using nanoparticles,' says Ballauf. 'There is a lot of literature on the catalytic activity of metallic nanoparticles, but now people like us are going and pursuing more practical applications, which are more interesting for the organic chemists.'

Hayley Birch

http://www.rsc.org/chemistryworld/News/2009/January/30010903.asp

Food additive promotes tissue regeneration

2009-02-08T23:25:00.001-08:00

Scientists in Singapore have developed an injectable hydrogel that could be used to regenerate cartilage in injured patients.

When the modified gellan gel is loaded with cells it promotes cartilage growth faster than agarose gels

Dong-an Wang and colleagues at Nanyang Technological University modified gellan gum, a widely used polysaccharide food additive, to transform it into a cell-carrying hydrogel. Cell-containing hydrogel solutions can be injected into target sites in the body, where they are cooled to form cell-laden gels that encourage tissue regeneration. But gellan forms a hydrogel at temperatures higher than body temperature and so until now, has been unsuitable for tissue engineering because it can't be injected as a solution.

"One could envisage a cell-carrying gellan solution forming gels in situ that encapsulate therapeutic cells"
- Dong-an Wang, Nanyang Technological University, Singapore

Wang chemically cut gellan molecules to reduce their size. He found that the shorter molecules formed a hydrogel when below body temperature. Wang loaded the gel with cells and monitored its ability to promote tissue regeneration in vitro. The gellan-based gels were faster at promoting cartilage growth than agarose gels, which are widely used in tissue regeneration.

So far, Wang has only tested the gels in vitro but he predicts that the technology will transfer to patients. 'We believe our scaffolding system promises to bridge the gap between bench and bedside,' he says. 'One could envisage a cell-carrying gellan solution being injected into any randomly shaped venues, forming gels in situ that encapsulate therapeutic cells working on tissue regeneration.' Wang says he also plans to investigate the degradation properties of modified gellan.

'Many approaches to regenerate cartilage tissue in the clinic have failed in the past,' comments Matthias Lutolf, who investigates the interface between biomolecular engineering and adult stem cell biology at the Swiss Federal Institute of Technology, Lausanne. 'It will be interesting to see how this technology performs in a more relevant in vivo scenario, for example in a rabbit model.'

Vikki Chapman

http://www.rsc.org/Publishing/ChemTech/Volume/2009/03/food_additive_promotes_tissue_regeneration.asp

Fluorescent tags to see catalysts in action

2009-02-08T23:24:00.001-08:00

German researchers have used a fluorescent tag to monitor the state of a catalyst during a chemical reaction.

Herbert Plenio and colleagues from the Darmstadt University of Technology tagged an N-heterocyclic carbene ligand in a palladium catalyst with a fluorescent dye. They followed the catalyst's progress in a Suzuki cross-coupling reaction using fluorescence spectroscopy. The team found that the fluorescence signal changed at each stage of the reaction. When the catalyst was activated by a base, the signal decreased within a few seconds. It then remained stable until the substrate was added, then decreased gradually until the end of the reaction. The tag also allowed Plenio to see any catalyst impurities left in the product.

The fluorescence signal changes at each stage of the reaction

'Our work provides a highly sensitive tool to monitor catalysts in action in low concentrations,' says Plenio. 'Little is known about the nature of catalyst complexes involved in catalytic transformations. By definition, the amount of a catalyst is small compared to the substrates and, to make things worse, this often acts as only a reservoir for the even smaller amount of active species that is actually doing the work.'

Fluorescence has the high sensitivity required to detect these very small quantities, even with just a few nanograms of palladium. 'This is a nice application of fluorescence that allows a deeper insight into catalytic processes,' says Jay Winkler, an expert in the photochemistry of transition metal complexes at the California Institute of Technology, Pasadena, US.

Plenio says he hopes that in the future, he will have tags that are sensitive enough to reveal the concentration of the active species in the catalytic cycle and the nature of the metal complexes involved. 'We still need to understand so much more about fluorescence dyes and the photophysics behind them,' he says, 'but I am optimistic - Shimomura, Chalfie and Tsien's 2008 Nobel Prize award for the discovery and development of the green fluorescent protein is providing a strong stimulus.'

Michael Spencelayh

http://www.rsc.org/Publishing/ChemScience/Volume/2009/03/Fluorescent_tags_catalysts.asp

Crack-proofing MOF membranes

2009-02-08T23:23:00.001-08:00

Chinese chemists have developed a way to reinforce metal-organic framework-based membranes to toughen them against cracking. The process, which involves growing the porous polycrystalline films onto a wire mesh, could see the membranes used to collect hydrogen from waste gas streams.

MOF(metal organic framework)-based membranes have the potential to be used for a variety of gas separation and sensing purposes. But creating these films on a large scale has been difficult as the crystalline structure is prone to splitting apart.

MOF-based membranes can be used for gas separation

Now, the team lead by Guangshan Zhu, at Jilin University in Changchun, have solved this problem by oxidising the surface of a copper wire mesh to create active copper (II) sites. As the MOF membrane grows on the mesh support, the fixed-copper ions become integrated into the copper-based MOF structure.

'Since the MOF membrane is tightly integrated with the copper net, it provides support in the same way that steel bars are used to make reinforced concrete,' explains Zhu.

Using the net serves another purpose, Zhu adds, as it seeds the growth of the MOF - helping to template an ordered crystal structure across a large area. This ordered structure is crucial for the formation of regular sized pores that allow MOFs to accommodate specific gases.

'Our net-supported membrane shows a high permeability and selectivity for hydrogen gas,' Zhu says - indicating that it could have potential to extract hydrogen from waste gas streams, although further optimisation would be required before this could be commercialised. To demonstrate the material's resilience, the team re-used the membranes over a six month period, showing that they were stable and recyclable.

Zhu is also confident that different metals and other types of framework films - such as zeolitic imidazolate frameworks (ZIFs), which have a high affinity for CO₂ - could benefit from being grown in this way.

'This is very interesting work, as one of the biggest challenges in using microporous solids for gas separations is fashioning membranes that don't have cracks,' says Jeffrey Long, an expert on MOFs at the University of California, Berkeley, US. 'Using a copper wire mesh apparently leads to intimate contacts between the mesh and the dense, polycrystalline framework layer - something that is worth investigating further.'

Lewis Brindley

http://www.rsc.org/chemistryworld/News/2009/February/03020901.asp

GSK targets autoimmune biologics

2009-02-08T23:22:00.000-08:00

UK-based drug maker GlaxoSmithKline (GSK) is making a concerted push to become a world leader in the autoimmune inflammatory disease arena - an area of treatment that has been revolutionised by the emergence of biologic drugs. As well as focusing its internal research on the area, GSK recently signed seven drug development deals that could see the company release a suite of drugs to treat inflammatory diseases ranging from rheumatoid arthritis to lupus.

Doctors treating autoimmune diseases have traditionally had to rely on drugs such as steroids or NSAIDs (non-steroidal anti-inflammatory drugs), which can only reduce inflammation, rather than actually stopping the tissue damage as the body attacked itself.

The introduction of biological drugs that interfere with the disease pathway by binding to proteins involved in the inflammatory cascade, such as tumour necrosis factor (TNF), has in many cases enabled the diseases themselves to be targeted, and the inflammation and tissue damage caused by the diseases to be significantly reduced.

J&J's Infliximab is an antibody-based treatment

Biological therapies such as Johnson & Johnson's Remicade (Infliximab), Amgen and Wyeth's Enbrel (etanercept) and Abbott's Humira (adalimumab) have proven extremely effective. According to Rachel Haynes, director of public affairs at the charity Arthritis Care, these new drugs have made an enormous difference to patients - so much so that people who would have been in wheelchairs without the drugs are able to lead active lives.

Biologic boost

Industry analyst Sylvia Miriyam Findlay from Frost & Sullivan says the number of autoimmune drugs available on the market is growing, and that the entry of biological drugs onto the market has significantly increased revenues in the area.

She estimates that in 2006 the market for rheumatoid arthritis therapies was worth some $36 billion (£25 billion), while the market for inflammatory bowel disease medication reached $16 billion, lupus drugs $12 billion and psoriasis products $6 billion. These markets are likely to continue growing as there is still a large unmet clinical need, and the number of patients with autoimmune diseases is growing.

GSK highlighted the disease area as one of the eight it would focus its research efforts on after Andrew Witty took over as the company's chief executive in May 2008. Since then, GSK's immuno-inflammation CEDD (Centre for Excellence in Drug Discovery) has signed co-development deals with Archemix, Biotica, CellZone, Dynavax, Galapagos, Regulus Therapeutics and Harvard Medical School.

'The strategic intent is to become the world leader in immuno-inflammation through a combination of internal and external research programmes,' says Jose Carlos Gutierrez-Ramos, head of GSK's immuno-inflammation CEDD.

This is an ambitious aim, given that in 2006 GSK did not even feature in the top ten players in the arena, which is currently dominated by Amgen, Johnson & Johnson, Pfizer, Novartis and Wyeth. The company has some catching up to do, as Findlay believes the market will see an influx of new drugs in the next six or seven years if the candidates currently in Phase II clinical trials make it to the market.

According to Gutierrez-Ramos, GSK plans to achieve this rapid growth by conduct around 50 per cent of the research outside of the company - and more deals could well be announced during the coming year.

'This business model adopted by GSK is sound and shows good foresight into the future dynamics of the autoimmune/inflammatory disease areas,' Findlay told Chemistry World. 'GSK is likely to emerge as a leader in the inflammatory diseases market in the next eight to ten years,' she adds.

Gutierrez-Ramos is certainly buoyant about GSKs prospects, and believes the company is entering the arena at just the right time. 'Immuno-inflammation is in a similar place to where oncology was five or six years ago; certain biological drugs have really opened up a way to increase our understanding of the key pathways - much like the biologics that told us that EGF [epidermal growth factor] pathways were important in oncology,' says Gutierrez-Ramos.

On trial

Pharmaceutical firms continue to be frustrated by the large number of drugs that fail during late stage clinical trials - after lots of time and money has already been spent developing them. Gutierrez-Ramos is looking to tackle this problem head-on by conducting more thorough Phase I trials that will gather more pharmacological data than is currently being collected.

Rather than looking for the next blockbuster by targeting only the most common illnesses, these trials will be designed to test each drug's mode of action, from which the disease each is best suited to treat will be identified.

'We are actually disease agnostic and have decided to focus on certain mechanisms that regulate the immune system that we believe are fundamental, and we will follow those mechanisms through molecular medicine studies into the indications that suit the mechanism best,' says Gutierrez-Ramos.

'We will not shy away from the smaller indications like sub-types of lupus or malignant autoimmune orphan disease - which traditionally are not a space that big pharmaceutical firms have focussed on,' he concludes.

Matt Wilkinson

http://www.rsc.org/chemistryworld/News/2009/February/04020901.asp

BASF seeks GM alternative

2009-02-08T23:21:00.000-08:00

Ned Stafford / Hamburg, Germany

German chemical giant BASF has applied directed mutagenesis to develop crop plants that are tolerant to specific pesticides. Unlike traditional genetic modification methods, which introduce genes from foreign species, directed mutagenesis alters the genetic makeup of the plant through the natural process of gene repair - and so is less likely to meet resistance from regulators and environmental groups.

Working in collaboration with Cibus, a plant trait development company based in San Diego, BASF has used directed mutagenesis to develop Brassica winter rapeseed and spring canola plants that are resistant to BASF's 'Clearfield' herbicides.

Fields of canola growing weed free

According to Dwight More, global marketing manager for Clearfield oilseed rape/canola, the BASF Clearfield production system has been used extensively since 1993 - but traditionally bred seeds required custom-designed imidazolinone herbicides. More told Chemistry World that winter rapeseed and spring canola seemed the most suitable crops to develop using Cibus' directed mutagenesis breeding technique, which improved the crops' resistance to the herbicide.

Dale Carlson, senior global product manager of herbicide tolerant crops at BASF Plant Science in Research Triangle Park, North Carolina, told Chemistry World that BASF started working with Cibus in 2006. Whereas GM (genetically modified) plants take about 10 years to develop, directed mutagenesis can be accomplished in six to seven years, he says, adding that BASF could commercialise the new spring canola by 2013.

Guru Rao, a directed mutagenesis expert and chairman of the Department of Biochemistry, Biophysics and Molecular Biology at Iowa State University in Ames, Iowa, says that the major disadvantage of transforming an organism, plant or animal, with genetic modification is that 'one has little or no control over where the gene gets incorporated in the genome of the host. Thus, the gene may be inserted in a region of the DNA that affects other functions.'

But directed mutagenesis 'allows one to make precise changes in the DNA sequence of the native gene that alters its function to achieve the desired trait, [and is capable of introducing any trait] as long as one knows the target gene associated with the particular trait of interest,' says Rao.

However, BASF's Carlson says directed mutagenesis would not be as effective as GM techniques to develop drought tolerance or yield enhancement. 'These traits would likely rely on a gene from another plant species,' he says, adding that BASF are using both directed mutagenesis and GM techniques as they have different characteristics and benefits.

Rao believes that although the foreign genes in GM crops can confer beneficial properties, they also can introduce concomitant undesirable and unpredictable properties, saying that: 'targeted [directed] mutagenesis technology is exciting and offers the best path forward.'

Alexander Hissting, agricultural expert for Greenpeace Germany, which is vehemently opposed to GM crops, says the organisation is not opposed to plants developed using directed mutagenesis, but will not promote it. 'It is not going in the direction we favour for sustainable agriculture, [we believe] the future of agriculture is not industrial agriculture, but local, small-scale agriculture,' he says.

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Marine sponges show their age

2009-02-08T23:20:00.000-08:00

Whilst searching for oil, a team of international scientists have found something completely different -proof that animal life existed more than 635 million years ago. That's at least 40 million years earlier than previous discoveries had shown.

The team led by Gordon Love at University of California, Riverside, US, analysed extractable hydrocarbons in the South Oman Salt Basin and found a 30-carbon (C₃₀) sterol biomarker, confirming that sponges existed in this area during the late cryogenian period.

Chemical fossils have confirmed that marine sponges have existed on Earth for more than 635 million years

The South Oman Salt Basin contains one of the world's oldest deposits of oil. 'We were there to make up molecular fingerprints to find oil for the oil companies,' explains Love. 'They wanted to get a better handle on the rocks they were drilling their oil out from, and C₃₀ was just one of many hydrocarbons we were looking at.'

The team first drilled a sediment core. 'We then dated parts of the core using uranium-lead isotope dating,' says Love. Next, for each layer of interest they took samples, and extracted out the organic compounds, resolved them using gas chromatography, and then used mass spectrometry to detect the fragments of interest (even though they were only a very small percentage of all the compounds present).

In the oldest sample from the core, dated as being more than 635 million years old, the team located the C₃₀ chemical biomarker 24-isopropylcholestane -known to only originate from the lipid membranes of marine sponges.Love was also able to confirm that the biomarker had not migrated from the younger rocks.

This is '40 to 50 million years earlier that any fossil sterols seen before', says Love. Kevin Peterson, Dartmouth College, Hanover, US, had previously predicted that animal life started at this earlier date, but this is the first time any proof had been found, Love explains.

Peterson says that these findings are 'very exciting' as they provide the first direct evidence that his predictions were correct. 'Love's findings have the gee wiz factor that these are actual chemical remnants of animals that live in that time period.'

Love now wants to see if proof of animal life can be found even earlier. And in order to do this they have had to relocate to south China. 'We are now looking at basins where the sediment is 1000 to 1800 million years old,' says Love. 'We are particularly interested in when algae first appeared,' he adds.

Nina Notman

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Instant insight: Sorting perturbed proteins

2009-02-08T23:19:00.001-08:00

Ruth Nussinov of the National Cancer Institute at Frederick, US, and colleagues put their case for a more organised way of looking at protein allostery

Allostery is a universal phenomenon: all dynamic proteins are potentially allosteric. Crucial in all cellular pathways, it comes about when a perturbation by a molecule called an effector alters a protein's shape and/or dynamics and leads to a functional change at the substrate binding site. Allosteric perturbation can arise due to small or large molecule binding; changes in pH, temperature, ionic strength, or concentration; or from covalent modifications such as sugar or phosphoryl group linking. Yet, despite how much we know about how allostery occurs, how signals initiating at a perturbation site transmit through a protein is still an open question.

In seven-helix receptor enzymes GDP replacement by GTP involves two allosteric steps

The number, breadth and functional roles of documented protein allostery cases are rising quickly, creating a need to arrange the information into a logical order. Sorting and classifying allosteric mechanisms in this way should be extremely useful in understanding and predicting how the signals are regulated and transmitted in proteins.

Classification assists us in making sense of observations. What are the differences between plants and animals; between mammals, birds, reptiles, fish, and amphibians; between classes of protein structures; drugs; types of interactions and chemical reactions? Sorting objects into distinct categories organises the information, revealing patterns and relationships, and so provides insight. While the importance of classification is clear, how to classify and into which categories is less obvious.

"Our framework is based on six properties, including whether there is conformational change at the substrate site and whether the effector perturbation increases or decreases the affinity of the substrate"

Current classification schemes in signalling class molecules according to their functions. For example, epinephrine - secreted by the central nervous system - is classified as a neurotransmitter; or, when the same molecule is secreted instead by the adrenal medulla in the adrenal gland, as hormone-like. Yet, such classifications account for the molecule's function, not for the molecular mechanism of how the signal transmission initiates and how it is transmitted.

We have presented a unified view of allostery and the first classification framework for allostery mechanisms. Allostery is a vehicle through which function is exerted so the logical approach was to organise mechanisms from a cellular function standpoint. Our framework is based on six properties, including whether there is conformational change at the substrate site and whether the effector perturbation increases or decreases the affinity of the substrate (positive or negative cooperativity respectively).

To illustrate this with an example, consider a textbook mechanism: GDP (guanosine diphosphate) replacement by GTP (guanosine triphosphate) in seven-helix receptor enzymes (see figure). Here classification indicates that two different types of allosteric step are involved. In the first (top), an extracellular ligand binds at an allosteric site causing a conformational change at the GDP binding site (the substrate site) leading to GDP's release. In the second allosteric step (bottom), the empty GDP binding site becomes an allosteric site for GTP binding. GTP binding then causes a protein to dissociate from the system - a negative cooperativity step.

"The aim is to provide a tool to help scientists place allosteric mechanisms in context, allowing a better comprehension of the signalling pathways they affect and how these pathways are regulated."

Textbooks describe series of events, not mechanisms. They cite the event and its consequences: a certain gene knock-out will lead to a certain loss of function. Yet, in disease our goal is to be able to trace back to a particular signalling checkpoint; to identify the source of the functional loss. Further, a disease-related mutation does not have to be in the substrate or the functional sites; but it may block signal propagation. Classifying allostery helps here, since a change in any of the six properties defined in our classification framework could conceivably affect function. A key question is which property would affect it the most.

Eventually, a classification scheme along the lines we propose could allow a systematic compilation and organisation of available allostery cases. The aim is to provide a tool to help scientists place allosteric mechanisms in context, allowing a better comprehension of the signalling pathways they affect and how these pathways are regulated. Ultimately, scientists would be able to predict signalling at the molecular level; it should also be useful for allosteric drug design.

Read more in the opinion article 'Protein allostery, signal transmission and dynamics: a classification scheme of allosteric mechanisms' in Molecular BioSystems.

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Toxicologist assumes leadership of key NIH institute

2009-02-08T23:17:00.000-08:00

The woman who took the helm of the US National Institutes of Health's environmental science agency in January has spent the bulk of her three-decade career researching the health effects of environmental pollutants. Linda Birnbaum, who is the first toxicologist to head NIEHS, hopes her expertise will help inform US policy.

Birnbaum's return to the National Institute of Environmental Health Sciences (NIEHS) comes after working there for nearly 10 years in the 1980s. In 1989 she headed to the US Environmental Protection Agency (EPA) and spent 16 years as director of their experimental toxicology division, which carries out multidisciplinary research to improve the scientific basis of chemical risk assessment.

She also had a temporary stint as the director of EPA's human studies division, which conducts research into human health risks associated with environmental pollution.

At NIEHS Birnbaum oversees an annual budget of $730 million (£500 million), which funds multidisciplinary biomedical research programmes and supports more than 1200 research grants. She emphasises that her institute's purview is science, not politics.

Regulatory connections

In her new position, Birnbaum aims to have greater contact than her predecessors did with EPA and other regulatory agencies. 'I hope that we can dramatically increase those interactions,' she says. 'Work funded by NIEHS may help address some of the issues that confront EPA, for example.'

Under the former Bush administration, federal agencies like EPA were accused of allowing the chemical industry to have too much influence over regulatory decision-making. The allegations included inappropriate and disproportionate representation of corporate interests on government science advisory committees. Although Birnbaum shares these concerns, she is quick to point out that one cannot simply discredit industry scientists.

'Full disclosure and balanced panels are what we need, but I don't think we should ignore people because of who they work for,' she tells Chemistry World.

Birnbaum's goal of fostering enhanced coordination between NIEHS and regulatory agencies is interesting in light of her stance on the controversial chemicals like Bisphenol A (BPA). The compound - a common ingredient in plastic baby bottles and food storage containers - has been linked with serious reproductive and developmental problems like breast cancer, and more recently it has been associated with heart disease as well as diabetes.

As director of NIEHS, Birnbaum also heads the US government's National Toxicology Program (NTP), which is an interagency programme charged with evaluating agents of public health concern. Last year, an NTP panel concluded that there was 'minimal concern' about the reproductive and developmental effects of BPA. Following the report, NTP's associate director, John Bucher, said there is 'considerable uncertainty' about whether the harmful effects of BPA seen in the animal studies are directly applicable to humans.

Birnbaum herself takes a pragmatic approach to BPA safety. 'There is enough information to say that [BPA] levels that have been reported in the American public are similar to levels that have been reported in experimental animals where effects have been seen,' she tells Chemistry World. 'To me that is important, but we have to be very careful that we don't jump from proverbial frying pans into proverbial fires.'

Controversial chemicals

Beyond BPA, Birnbaum is also an expert on another contentious type of chemical - dioxins. Labelled a 'known human carcinogen', dioxins have been linked with health problems involving reproduction, sexual development, and the immune system.

The Obama administration is currently being lobbied by a coalition of over 100 environmental health and social justice groups to release EPA's decades-long study of the toxicity of dioxin, and to withdraw a dioxin reassessment that was ordered in the last days of the Bush administration. Although EPA has been studying dioxins since the 1980s, the agency has issued no safety assessment. In a 16 January letter, the 100 associations request that Obamadirect EPA to cancel the 'unnecessary review' and make public its unfolding research so that 'protective dioxin policies and standards' can be pursued.

Birnbaum has authored papers linking dioxin exposure with mortality from both ischemic heart disease and all cardiovascular disease. She has called dioxin 'a very potent growth dysregulator.'

At NIEHS, Birnbaum expects to have to be mired in controversy and claims to be up to the challenge. But, she is also hopeful about the Obama administration and EPA's new director, chemical engineer Lisa Jackson.

'Many of us are anticipating that the tone of government is going to change,' Birnbaum states, pointing out that Obama and his team have identified the environment and health as top priorities. 'Many of us hope that the slowdown or blockage of regulations will change,' she says.

She succeeds David Schwartz, whose leadership of the NIEHS was tarnished by allegations of overspending, mismanagement, and alleged conflicts of interest. He left NIEHS in May 2008 to assume a research position with the National Jewish

Medical and Research Centre in Denver, Colorado, US. The accusations against him, which included disregarding established extramural grant approval policies and procedures, were the subject of congressional investigation.

Rebecca Trager, US correspondent for Research Day USA

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Carbon nanotube catalysts 'better than platinum'

2009-02-08T23:16:00.001-08:00

Researchers in the US have developed a novel catalyst based on carbon nanotubes for the electrochemical reduction of oxygen. The new material, they say, could be an effective and cheaper substitute for platinum in certain types of fuel cell.

The team, led by Liming Dai of the University of Dayton, created tightly packed, vertically aligned carbon nanotubes that were doped with nitrogen atoms. When these nanotube arrays were used as cathodes in highly alkaline solution, they were able to catalyse the reduction of oxygen more efficiently than platinum.

The researchers suggest that the nanotubes could be useful in alkaline fuel cells, which were developed decades ago but for a number of reasons have remained commercially unviable. One reason, Dai suggests, is the high cost of platinum which is used as a catalyst in the fuel cells' electrodes.

Vertically aligned nitrogen-doped carbon nanotubes have been used as catalysts for oxygen reduction

It was already known that carbon nanotubes containing iron were effective catalysts for oxygen reduction, with the iron-carbon centres forming the catalytic active site. Dai's team, however, has shown that efficient catalysts can be made from a carbon nanotube scaffold without the need for metals, demonstrating a novel mechanism for the catalysis. They suggest that this new catalytic mechanism could be incorporated in other materials or used for other applications where the reduction of oxygen is required.

The presence of a small amount of nitrogen in the walls of the nanotube - typically around four or six atoms of nitrogen for every 100 of carbon - has the effect of drawing electrons away from neighbouring carbons giving them a net positive charge. When an electrochemical potential is applied to the electrode, these carbons become reduced, becoming negative or neutral. When oxygen is presented to the electrode's surface, the carbons readily donate electrons to revert to their preferred positive status. 'This is the mechanism we believe is operating to provide a metal-free active site for the electrochemical reduction of oxygen,' Dai says.

Precisely how expensive the new catalyst would be to produce commercially is not possible to calculate yet, says Dai. However, he adds, 'Since 1990 the cost of producing carbon nanotubes has fallen 100-fold and can be expected to fall further. Platinum on the other hand is a finite resource - there are limited reserves in nature.'

Fuel cell experts, however, are not convinced that the new work will make alkaline fuel cells viable. Paul Christensen of the University of Newcastle in the UK -who has been working on fuel cells for many years -says the nanotubes have interesting properties, but disagrees with Dai that the expense of the electrode is what has held back the take-up of these alkaline fuel cells. 'The big problem with alkaline fuel cells is not the expense of the electrode material, but the failure to date to develop an alkaline version of the solid polymer electrolyte employed in acidic fuel cells, such as Nafion. This has made alkaline fuel cells impractical in terms of size and complexity, and ruled out the use of liquid fuels such as methanol. Electrode materials are not that relevant,' he told Chemistry World.

Simon Hadlington

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Crystalline polymers make airtight films

2009-02-08T23:12:00.001-08:00

Squeezing polymers into extremely thin layers can make them a whole lot less gas-permeable, US scientists have shown. The constrained polymer films are forced to grow as ordered crystallites, forming an effective barrier against diffusing gases.

Anne Hiltner and Eric Baer from Case Western Reserve University in Cleveland, Ohio, were actually trying to develop a selectively permeable polymer when they made their discovery. The team found that sandwiching very thin layers of polyethylene oxide (PEO) between layers of poly(ethylene-co-acrylic acid) (EAA) forces the PEO to form large, crystalline plates that are essentially impermeable to both oxygen and carbon dioxide.

'We were originally trying to modify EAA, which is a typical packaging film resin, with PEO, which has an unusual selectivity for transporting oxygen and carbon dioxide, to try and make a film which could separate the two gases,' says Hiltner. 'What we came up with was something totally different - an exceptional change in the overall permeability and a whole new structure.'

Crystalline nano-layers of polyethylene oxide (PEO) within poly(ethylene-co-acetic acid) (EAA) obstruct diffusion of gas through packaging films.

The team modified a well-established polymer processing technique known as co-extrusion, in which two or more molten polymers are extruded through a special die, to make the films. The crucial modification was to take the extruded molten polymer, divide it in half, and then recombine the two halves, doubling the number of layers in a manner akin to making puff pastry.

This process is then repeated until there are about 1,000 individual layers in a film about 25 microns thick, typical of commonly used packaging films. And the thinner they made the PEO layers, the more crystalline they became - until at 20nm the layers were almost completely made up of large, plate-like crystallites. As the polymers solidify from the molten state, the confined PEO layers are forced to form a more ordered, space-filling crystalline solid, rather than the amorphous solid which would normally form when the melt is cooled.

'I was really surprised to see this unique morphology,' says Piet Lemstra, professor of polymer technology at Eindhoven University of Technology in the Netherlands. 'To grow single crystals from the melt is normally impossible, they were only really grown out of very dilute solutions before.'

By forming tightly-packed crystals, rather than an amorphous spaghetti-like mass of tangled polymer chains, the PEO layers block diffusion of gas molecules through the film, as they can only pass through at the boundaries between crystals. By having lots of layers, the path a molecule would have to take to diffuse through the film becomes extremely tortuous, making it almost impermeable.

'This is also a continuous process - we can already make miles and miles of these micro- or nano-layered films, so it should be easy to transfer to an industrial scale,' adds Baer. However, Lemstra is a little less certain: 'The technology for making thin films with multi-layer arrangements is available, but in this case the layers are very, very thin, which is not so easy. The beauty of this work is that it's already on a reasonably large scale, but whether it can be translated into technology depends on it being picked up by an industrial company.'

These kinds of layered polymers have all sorts of potential applications, Baer told Chemistry World. 'Using different polymers and size scales we can make light filters, we can put dyes in the layers to make all-plastic lasers, and we're also working on dielectric materials for energy storage.'

Phillip Broadwith

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EU clash over pollution permits

2009-02-08T23:11:00.001-08:00

The European Parliament and the Council of Ministers - the two arms of the European Union's legislature - appear to be heading towards a confrontation over a proposed law to further cut emissions from chemical and other plants.

The new directive, drawn up by the European Commission, aims to make more effective the EU's existing system for giving operating permits for chemical and other plants, a key issue being the introduction of more uniform emissions standards which would set centrally by the Commission.

And the proposed legislation could be tightened still further, after parliament's environment committee debated 533 tabled amendments. The committee's redrafted text now looks likely to be backed by the full parliament in the first reading of the legislation in March.

But the Council of Ministers, representing the governments of the EU member states, will almost certainly want less stringent and more flexible controls on emissions when it debates the directive in June. The revised draft will have to go back to parliament for a second reading before possibly continuing into a conciliation procedure to thrash out legislative compromises between the two bodies

BAT controls

Under the present 12-year-old system, which is part of the EU's scheme for Integrated Pollution Prevention and Control (IPPC), permits are given on the basis of Best Available Techniques (BATs), or the most cost-effective techniques for achieve high levels of environmental protection. But authorities in member states are allowed to make exceptions to take into account local environmental conditions and different plant designs.

The Commission decided to bring in new legislation because it claims the IPPC derogations are being abused. So far, only 50 per cent of chemical and other plants operate under the strictest BAT-based permits. The parliament's environment committee wants deviations from the Commission's minimum standards to be made even more difficult so there is less room for adapting BATs to local conditions.

'We believe that this new principle of "one size fits all" is not practical,' says an official at the European Chemical Industry Council (Cefic), the chemical industry's trade association. 'Local environment conditions and the specific technologies of installations must be taken into account if the permit system is to work properly.'

Carbon considered

The chemical industry is also concerned about possible moves by MEPs in the parliament's plenary session in March to include plant-specific standards in the legislation for reducing emissions of carbon dioxide and other greenhouse gases. These emission performance standards (EPS) - which would be another source of friction with the Council of Ministers - would initially apply only to power plants. But one worry for industry is that the limits on CO₂ emissions from power generation would raise electricity prices for energy-intensive plants, such as petrochemical facilities, as well as push up the cost of ETS emission allowances.

'We think it inappropriate to have a second piece of legislation imposing limits on CO₂ emissions when the EU has only just approved regulations for a new emission trading system (ETS) for greenhouse gases,' says the Cefic official.

But environmental groups are already pressing for stricter limits on CO₂ emissions once an EPS system is introduced. 'The introduction of EPS into power plants will mean fewer emissions from electricity generation - so more allowances available on the ETS market, which would lower their cost for other sectors like steel, cement and chemicals,' says Einvind Hoff, director of Bellona Europa, a Brussels-based environmental NGO. 'We want ETS limits to be tightened up once EPS is introduced in the power sector so that this doesn't happen,' he adds.

However, NGOs like Bellona Europa are not yet campaigning for emissions performance standards to be laid down in sectors like bulk chemicals. 'We think that the most obvious candidate for EPS to be introduced outside power generation would be the cement sector because, as with power generation, the production technologies in plants are similar,' Mr Hoff explains. 'But it would be difficult to have EPS in petrochemicals. There are so many different production technologies that it would be too complicated.'

Sean Milmo

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How to create less selfish societies?

2009-02-08T23:09:00.001-08:00

February 6th, 2009 in Physics / Physics

(GPEARI, Portugal) -- Cooperation, despite being now considered the third force of evolution, just behind mutation and natural selection, is difficult to explain in the context of an evolutionary process based on competition between individuals and selfish behaviour. But this puzzle, that has haunted scientists for decades, is now a little closer to be solved by research about to be published in the journal Physical Review Letters.

The work, by scientists in Portugal and Belgium, reveals that an increasing range of behaviours among the individuals of a population leads to cooperation, supporting the idea that democracy - where individuals are free to act as they wish - is in fact the path for better societies. Jorge Pacheco one of the authors of the study says: "The results support the idea that behavioral differences, on a grand scale, are instrumental in shaping us as the most sophisticated cooperating machines on this planet what is particularly interesting as it contradicts some social and political dogmas - such as Maoism and Stalinism - which, sometimes with rather unfortunate outcomes, have tried to enforce reduced behavioral diversity, supposedly with an aim to improve society."

Richard Dawkins never gets tired of reminding us that evolution is based on the survival of the fittest and on selfishness. Every cell, every living thing is designed to promote its own survival, if necessary at the expense of everything else. Still, cooperation is very much alive, and more, is widespread, being found in a multitude of living beings from the cells of a multicellular organism to insects and of course humans - the “big cooperators”. Some examples are easy to understand, like those among family members, but those are not enough to explain how an apparently disadvantageous behaviour is, nevertheless, so common.

The key, it seems, lies on specific conditions in which cooperators become the individuals with highest fitness, allowing their expansion within the populations. Very few examples have been found so far, however, and the simple observation of biological processes does not seem to be able to provide many more answers. An alternative is to use mathematical models to look for those conditions that allow cooperators to thrive.

With this in mind S. Van Segbroeck, J.M. Pacheco and colleagues from the University of Lisbon, Portugal and the Vrije Universiteit Brussel and the Universite Libre de Bruxelles in Belgium developed an artificial society in which individuals engage in a mathematical game called the “prisoner’s dilemma” (or PD). In PD individuals interact with the choice of cooperating or defecting (not cooperate) and while cooperators provide a benefit to their partners (and pay a cost for that) defectors, not only have no costs, but also rip the benefits given by the cooperators. In the basic version of PD defectors “win” and cooperators gradually disappear. But recently it has been found that adaptive social networks - like human populations where individuals change behaviour all the time making new acquaintances and breaking others, continuously shaping and reshaping the social network structure - supported cooperation. This led Pacheco and colleagues to ask if specific behavioural diversity within this dynamic world could be linked to cooperators emergence.

To answer that they adapted PD to take into account the adaptive social dynamics of human populations, while also introducing behavioural diversity to test if this last parameter affected the viability (and consequently the emergence) of cooperators. As an example of behaviour variability they analysed partner fidelity. In fact, when a social connection is established, it is rapidly evaluated and, if disadvantageous - like when one of the partners is a defector - it is broken but while some discontented individuals try to break contact (defect) very rapidly, others take much longer and it is this “time taken to defect unwanted links” that Pacheco and colleagues used as an example of behaviour variability to look for cooperation emergence.

The group started by considering a situation where only two break-up velocities existed - fast and slow - with the population, as a result, being constituted by fast and slow defectors - respectively FD and SD - and fast and slow cooperators (FC and SC) all depending how long the individuals took to break unwanted ties (although the time of a connection depends on both partners). In this situation they found that most of the population turns into SD because these would be the ones with higher gains/higher fitness, as their interactions with cooperators would last longer In the same way, most of the few cooperators surviving will be FC since they are the ones, among cooperators, losing less, as they spend less time interacting with defectors. So in this example, again, the model predicts that defectors will be the ones predominant in the population.

Next, the researchers increased the number of possible defecting speeds to an almost continuum of values between fast and slow, and, to their surprise, many Cs are now capable of surviving and even thrive in the population. The reason for that resides in the fact that many more types of defectors, and not only SD, are able to survive, and those faster Ds will provide an escape hatch for cooperators, which, by interacting mostly with cooperators and preferentially with the faster defectors, now manage, not only to survive, but also to dominate in the population. So in this case cooperators thrive and “invade” the population.

Van Segbroeck, Pacheco and colleagues’ model reveals that populations in which individuals exhibit higher diversity when handling their social contacts end up being much more cooperative, than those where no such diversity exists. This is particularly interesting if we consider that individuals always behave according to their own narrow-minded preferences and still, despite of this, cooperation blooms.

There are several interesting aspects to this work, and not the least because it helps to understand better the emergence of cooperation, a crucial force for better human societies. But like Pacheco says: “The results are even more exciting, if we take into account that diversity in individual behavior is on the basis of this result. Hence, we expect that societies in which individuals are free to express their inherent differences will be more cooperative than those in which individuals are constrained to exhibit very similar behavior. Of course, to extrapolate from such a simple model into complex Human Societies is both unreasonable and inescapable. In this respect, we may contrast democracies with dictatorships, religious freedom with religious indoctrination, and so on.”

Another important aspect of the research is the flexibility of the model developed by the team of researchers that can now be used to answer other questions like Pacheco explains: a great example is epidemics. There the dynamical process between individuals is the contagion due to a biological virus, and the model allows now to determine how the evolution of the number of infected individuals in the community affects and is affected by the dynamical network that supports the individuals.

More information: Physical Review Letters, 06 February 2009 online Early Edition, “Reacting differently to adverse ties promotes cooperation in social networks”

Source: GPEARI, Portugal

New Smart Material Bends Under Internal Heat Source

2009-02-08T23:07:00.000-08:00

February 6th, 2009 By Lisa Zyga in Physics / Materials

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A prototype of an aerodynamic flap made of the new smart material. The smart material consists of thin plates containing carbon yarns that can carry a current, which heats and bends the material. Image credit: H. Drobez, et al.

(PhysOrg.com) -- Scientists have developed a new smart material that can bend under the influence of an internal heat source. The material could be used as an aerodynamic flap in cars, in order to stabilize the vehicles at high speeds. Because the entire structure actively bends, the material could have advantages over actuators that need to be externally fixed to a structure.

A team of scientists from CETIM CERMAT and the Laboratoire de Physique et de Mécanique Textiles (LPMT), both in Mulhouse, France, have been working on the active structure for the past few years. In a recent study published in Smart Materials and Structures, they present the material called CBCM (controlled behavior composite material), which can bend when heated.

“The main advantage of the CBCM is that the entire structure is active, compared to classical actuators used in this kind of structures, such as shape memory alloys (SMA) or piezoelectric materials, so there is no problem of junction and connection between the actuator and the structure,” coauthor Gildas L'Hostis of LPMT told PhysOrg.com. “Moreover, the load that can carry the structure is much greater than the one carried by an SMA or piezoelectric material because the performances are not as limited by the rigidity of the composite structure. A third advantage is the simplicity of use - directly on DC current with a variator.”

The CBCM consists of thin laminate plates, inside of which are highly conductive carbon yarns that are connected to a generator and serve as the internal heating source. When the power is turned on, the current circulates in the carbon yarns and the temperature rises in the plates. The increased temperature causes the plates to bend, and the deformation can be controlled by controlling the amount of current.

The researchers experimented with two kinds of plates: “single effect” plates that can bend in one direction, and “double effect” plates that can bend in two directions. In the thin single effect plates, the temperature reached 57°C (135°F) and the structure deflected up to 15 mm. In the double effect plates (which consist of a conductive layer on one side and insulating layer on the other), the temperature reached 70°C (158°F) on the conductive side and 42°C (108°F) on the insulated side, and deflected up to 3.7 mm. While the single effect plates could deflect more, the double effect plates could lift a heavier load.

The scientists also discussed incorporating a control system into the material. By adding temperature and strain sensors to the CBCM, such a system could detect variations in its background and then adapt to the new context.

To demonstrate the new material, the researchers built a prototype of a 4-mm-thick retractable aerodynamic flap that could be used on cars for stabilization at high speeds. Unlike the existing flap, which has three joints and is moved with a jack, the smart material structure could move simply due to its thermomechanical properties.

With its advantages over other actuators and moving components, the CBCM smart material could be useful for a variety of applications. However, more research is needed to overcome some difficulties, which the scientists highlighted in their study. For instance, future research could include testing the rigidity of the plates and minimizing local overheating, possibly with the use of carbon nanotubes.

“The CBCM has already been used to manufacture an active binder for pipes,” said coauthor Karine Buet-Gautier of LPMT. “Today, some other active connectors are under study.”

More information: Drobez, H.; L’Hostis, G.; Buet Gautier, K; Laurent, F.; and Durand, B. “A new active composite.” Smart Materials and Structures 18 (2009) 205020 (7pp).

New Data Suggests We Don’t Live in a Void, and Supports Dark Energy

2009-02-08T23:03:00.000-08:00

January 28th, 2009 By Lisa Zyga in Physics / Physics

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Temperature fluctuations in the cosmic microwave background, among other data, are helping researchers better understand the accelerating expansion of the universe. Image credit: NASA.

(PhysOrg.com) -- An alternative proposal to dark energy in which the Earth sits near the center of a large void is undergoing scrutiny, and the results show that void models fit poorly with observed data. Nevertheless, scientists say that more research will be needed to determine if void models, dark energy, or something else can accurately explain how the universe is expanding at an accelerating rate.

Almost a decade ago, theorists proposed a void model as an alternative to the repulsive force of dark energy, an unknown force that is not well understood. According to the void model, much of the visible universe lies in a giant void that contains very little matter compared to the matter density outside the void, which is difficult to observe. The void’s low density means the gravitational “braking” force is weak in the void. This creates the illusion that the visible universe is expanding faster than it used to; however, the actual change is not a change over time, but over space.

Scientific data aside, void models have an important philosophical implication: that the Earth occupies a special place at the center of the visible universe. This contradicts the Copernican principle, which says that we should not be at a special place, and has been extended to state that the universe is homogenous. The Copernican principle has served as a pillar for modern astronomy, and if it weren’t true, then astronomers could not rely on local measurements to learn about universal properties.

Now a team of researchers from the University of British Columbia has compared new data with the predictions of various void models and standard dark energy models. Post-doctoral fellows Jim Zibin and Adam Moss, along with Professor Douglas Scott, studied supernova, cosmic microwave background, and baryon acoustic data from the early universe, and found that altogether the data fits standard dark energy models much more closely than void models. Their study is published in a recent issue of Physical Review Letters.

“Our study addresses one of the greatest mysteries in cosmology today - the apparent acceleration of the Universe's expansion,” Zibin told PhysOrg.com. “The standard explanation, dark energy, is itself so puzzling that researchers have tried hard to find viable alternatives, but with very few successes. Our study shows that it is extremely unlikely that one such alternative, void models, can be made to work. This strengthens the case that the acceleration is real and is due to dark energy.”

The researchers examined two kinds of void models: unconstrained and constrained (in which the density distribution is limited). They found that unconstrained voids can fit the CMB and supernova data, although this comes at a price of requiring a very low Hubble constant - which ultimately rules out the unconstrained voids. Constrained voids also run into problems, as they require finely-tuned features in order to fit the CMB data. However, standard dark energy models closely match the CMB data. Further, the baryon acoustic data is at odds with the likeliest void models, but agrees very well with standard dark energy models. As Zibin explained, this type of analysis is only possible with the ability to gather very precise data, as in the current era of “precision cosmology.”

“More than about a decade ago, the fundamental parameters that describe the Universe on the largest scales, such as the expansion rate and the amount of spatial curvature, were only known with poor accuracy,” he said. “Since then, precision measurements of the CMB by satellite and massive automated sky surveys on the ground have revolutionized cosmology by pinning those parameters down with high precision. It seemed very surprising to us that cosmological models such as the void models, which are so drastically different from standard dark energy models, could still fit all of this precision data.”

The scientists conclude that it is quite extraordinary that standard dark energy models can describe a wide variety of observations so well, without requiring finely tuned parameters. In investigating the robustness of void models, the researchers have in fact solidified the conventional view that dark energy causes the acceleration of the universe.

“Further refinements in measurements of the CMB and even bigger sky surveys are planned, and will help us to understand the acceleration better,” Zibin said. “It may turn out that even the improvements planned in the next decade or so won't distinguish the simplest form of dark energy, the cosmological constant, from other forms. On the other hand, we may be fortunate and learn soon what dark energy really is.”

More information: Zibin, James P.; Moss, Adam; and Scott, Douglas. “Can We Avoid Dark Energy?” Physical Review Letters 101, 251303 (2008).

Shocking: Environmental chemistry affects ferroelectric film polarity the same way electric voltage does

2009-02-08T23:01:00.000-08:00

February 2nd, 2009 By Miranda Marquit in Physics / Physics

(PhysOrg.com) -- “Ferroelectric materials are interesting scientifically, and, while they are used for some things now, they are potentially useful for even more applications in the future,” Brian Stephenson tells PhysOrg.com. Stephenson is a scientist at Argonne National Laboratory in Argonne, Illinois. He has been working on a project to study chemical switching in a ferroelectric film.

“Normally,” Stephenson continues, “voltage is applied to change the internal structure in ferroelectric materials. You can turn the crystal upside down from the internal point of view. We have shown, I think for the first time, that this can also be done chemically by changing the chemistry of the environment.” The results of the work, which includes scientists from Northern Illinois University and the University of Pennsylvania as well as Argonne, can be found in Physical Review Letters: “Reversible Chemical Switching of a Ferroelectric Film.”

In order to test the process of chemical switching by changing the environment of the ferroelectric film, Stephenson and his colleagues varied the oxygen partial pressure. In situ x-ray scattering was used to “see” the changes in the polarization of the material. The specific ferroelectric material used for the experiment was lead titanate (PbTiO₃). The group found that changing the oxygen pressure switched the polarization of the PbTiO₃ film in much the same way as the conventional practice of using electrodes and voltage.

The use of x-rays is important, since it allows scientists a peek at what is actually happening inside these materials. “The challenge has been to measure what is going on,” Stephenson admits. “With these thin films, external voltage measurements become more ambiguous. With our x-ray technique, we are able to watch the atomic-scale structure inside these systems.”

“Up until now,” he continues, “we didn’t really think that the environment these ferroelectric materials were in could be just as important as the voltage applied. Fundamentally, we didn’t realize that extra oxygen or missing oxygen at the surface could produce an electric field big enough to affect properties.”

This knowledge will become more important, Stephenson explains, as the demand for smaller devices made from new materials increases. Infrared and terahertz technology, controllable catalysts and chemistry applications on chips represent some of the areas that might benefit from a better knowledge of how switching works with PbTiO₃ films.

“Already there are ferroelectric materials used for non-volatile computer memory devices,” Stephenson points out. “But the holy grail of these is a memory element the size of an atom. As films get thinner, understanding the interfacial properties of these materials makes a difference. If the chemistry of the environment can change the polarization, we need to harness this to create new types of devices.”

“The big picture is that we are trying to create new functional materials with interesting properties. We want to understand the way interfaces between different materials work. Ferroelectrics provide a model system where we can produce and measure large effects of the electric fields from the interfaces.”

Additional information: Wang, et. al. “Reversible Chemical Switching of a Ferroelectric Film.” Physical Review Letters (2008). Available online: http://link.aps.org/doi/10.1103/PhysRevLett.102.047601

Global warming threatens Antarctic sea life

2009-02-08T23:00:00.000-08:00

February 5th, 2009 in Space & Earth science / Environment

Climate change is about to cause a major upheaval in the shallow marine waters of Antarctica. Predatory crabs are poised to return to warming Antarctic waters and disrupt the primeval marine communities.

"Nowhere else than in these ecosystems do giant sea spiders and marine pillbugs share the ocean bottom with fish that have antifreeze proteins in their blood," says Rich Aronson, professor of biological sciences at Florida Institute of Technology in Melbourne, Fla. "The shell-cracking crabs, fish, sharks and rays that dominate bottom communities in temperate and tropical zones have been shut out of Antarctica for millions of years because it is simply too cold for them."

But this situation is about to change. "Populations of predatory king crabs are already living in deeper, slightly warmer water," says Aronson. "And increasing ship traffic is introducing exotic crab invaders. When ships dump their ballast water in the Antarctic seas, marine larvae from as far away as the Arctic are injected into the system."

Aronson and his colleagues published their results in the electronic journal PLoS ONE to coincide with the U.S. National Teach-In on Global Warming Solutions on Feb. 5.

Fast-moving, shell-crushing predators, dominant in most places, cannot operate in the icy waters of Antarctica. The only fish there—the ones with the antifreeze proteins—eat small, shrimp-like crustaceans and other soft foods. The main bottom dwelling predators are slow-moving sea stars and giant, floppy ribbon worms.

To understand their history, Aronson and a team of paleontologists collected marine fossils at Seymour Island off the Antarctic Peninsula. Linda Ivany of Syracuse University reconstructed changes in the Antarctic climate from chemical signals preserved in ancient clamshells. As temperatures dropped about 41 million years ago and crabs and fish were frozen out, the slow-moving predators that remained could not keep up with their prey. Snails, once out of danger, gradually lost the spines and other shell armor they had evolved against crushing predators.

Antarctica's coastal waters are warming rapidly. Temperatures at the sea surface off the western Antarctic Peninsula went up 1°C in the last 50 years, making it one of the fastest-warming regions of the World Ocean.

If the crab invasion succeeds, it will devastate Antarctica's spectacular fauna and fundamentally alter its ecological relationships. "That would be a tragic loss for biodiversity in one of the last truly wild places on earth," says Aronson. "Unless we can get control of ship traffic and greenhouse-gas emissions, climate change will ruin marine communities in Antarctica and make the world a sadder, duller place."

Source: Florida Institute of Technology

Internal clocks keep all living things ticking -- even you

2009-02-08T22:58:00.000-08:00

February 8th, 2009 By Robert S. Boyd in General Science / Biology

Like kids taking apart a fine Swiss watch, scientists are laboring to understand what makes the biological clock that's inside every living creature tick.

Researchers have long known that bacteria, flies, worms, flowers, oak trees and human beings all have tiny internal timepieces that keep them on a roughly 24-hour cycle, the time it takes the Earth to spin once on its axis.

"Living cells can actually tell the time and use this information to control their behavior," said Hugh Nimmo, a plant biologist at the University of Glasgow, Scotland.

Many questions remain to be answered, however, such as how the clocks work at the level of individual molecules. To find out, some scientists are building simple biological clocks in a test tube.

"If you can build it, you really understand it," said Jonathan Arnold, a geneticist at the University of Georgia in Athens. "It's very important that we know how the clock works at the molecular level."

"Biological timekeeping is a core property of life on a revolving planet," said Jay Dunlap, a biochemist at Dartmouth College in Hanover, N.H., and the author of a book on the subject. "Time organization is a vital part of the survival and normal functioning of every species."

These living pacemakers keep running whether it's light or dark. Creatures that live underground or at the bottom of the ocean continue to have timers that they inherited from their ancestors, even though they no longer see the sun shine.

Inner clocks tell people when to wake up and plants when to unfurl their leaves. For small nocturnal mammals, knowing when dawn is coming can mean life or death from a predator. Contrariwise, a fungus may wait to send up its reproductive stalks until after dark to avoid dangerous ultraviolet light.

When clocks go awry, they contribute to miseries such as insomnia, liver disease and cancer, Arnold said. In humans, a gene that the biological clock controls is involved with early-morning heart attacks.

Organic timing mechanisms are governed by one or more clock genes in a cell's DNA. The genes produce specialized proteins - long strings of organic molecules - that control the sequence of bodily functions.

Taken together, the genes and proteins make up a complex regulatory network that fits together like the gears in a watch. As in a clock, the timing can be reset to compensate for daylight saving time, night work, jet lag and even a slightly longer day-night cycle on Mars, if humans ever land there.
People's clock genes may set their sleep patterns. Last summer, Sarah Forbes-Robertson, a British researcher at the Swansea University School of Medicine in Wales, reported that she can tell whether a person is an early riser or a night owl by inspecting a gene called REV-ERB in his or her DNA, taken from a swab on the cheek. A low level of gene activity is associated with sleep, a high level with wakefulness, she said.

"If your peak is earlier than 4 p.m. it would indicate that you are a natural early bird," she said. "If you peak later than 5 p.m., then you are more of a night owl."

The first clock gene - named "period" - was discovered in 1971. Others followed, with names such as "timeless," "frequency" and, naturally, "clock." Dozens of genes have been identified since then and their elaborate biochemical structures unraveled.

The simplest biological clock is probably the most ancient. It's found in blue-green algae, also known as cyanobacteria, the one-celled creatures that create pond scum. This clock started keeping time about 3.5 billion years ago, when the world was young.

The cyanobacteria clock consists of just three proteins. One of them, shaped like a six-sided ring, looks surprisingly like a cog, or escape wheel, in a mechanical watch, according to Susan Golden, a biologist at Texas A&M University in College Station.

"The gears mesh and turn to crank out a 24-hour timing circuit," Golden reported in the journal Proceedings of the National Academy of Sciences.

As organisms grew increasingly complex over millions of years, so did their timing mechanisms.

"In flies, worms and mice, the clock has become more elaborate," said Arnold of the University of Georgia. "Functions once found in one protein have been separated into multiple proteins."

For example, the frequency gene in bread mold, a common fungus, controls 295 other genes, Arnold said.

Humans and other mammals have "master clocks" buried deep inside their brains in bundles of cells called the suprachiasmatic nucleus. The suprachiasmatic nucleus coordinates peripheral clocks in other organs, including the lungs, liver and kidneys.

According to Nimmo, the Scottish expert, biological clocks evolved separately on four occasions: first in cyanobacteria and later in funguses, plants and animals.

"The essential nature of a clock has led to its arising more than once in the evolution of life," Arnold said.

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ON THE WEB

• "The Biological Clock's Incredible Influence Revealed" (National Science Foundation): http://tinyurl.com/bdfgm7

• Circadian clocks go in vitro: http://www.nature.com/msb/journal/v1/n1/full/msb4100027.html

• Circadian rhythms: http://template.bio.warwick.ac.uk/Staff/amillar/circad.html

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(c) 2009, McClatchy-Tribune Information Services.
Visit the McClatchy Washington Bureau on the World Wide Web at http://www.mcclatchydc.com

How Darwin's ideas were twisted into 'social Darwinism'

2009-02-08T22:55:00.000-08:00

February 8th, 2009 by Boris Cambreleng in General Science / Biology

Charles Darwin, born 200 years ago on Thursday, upended our conception of humanity's place in Nature but also unleashed a pernicious justification of social and racial inequality.

At its most extreme, what came to be known as "social Darwinism" was invoked to defend the practice of eugenics: enhancing the "quality" of the human race by weeding out -- through sterilisation, even extermination -- persons deemed feeble of mind, body or both.

Darwin, a Christian, a Victorian liberal and opponent of slavery, rejected these ideas as not only scientifically unsound but also morally repugnant.

But that did not stop them from spreading and persisting in one form or another up to the present day.

Adding insult to injury, the person who first sketched a theory of eugenics, Francis Galton, was a second cousin of Darwin.

Unaware of the influence of genes, Galton and most of his scientific contemporaries were convinced that traits acquired over a lifetime could be passed on to one's offspring.

He also assumed that some races were innately superior, giving comfort to racist theories that placed white Europeans at the pinnacle of evolution.

His claims were supported in the late 19th century by the pseudo-science of anthropometrics, which equated facial structure and skull capacity with intelligence.

Italian criminologist Cesare Lombroso went so far as to conclude that some individuals were born criminals -- "uomo delinquente," he dubbed them -- who could be unmasked through their physiognomy.

The use of slang, and ape-like features such as a narrow skull and an unusually mobile big toe, were brandished as proof that these irredeemable specimens were in fact a human sub-species.

"They speak like savages because they are true savages in the midst of our brilliant European civilisation," Lombroso wrote.

But it was British sociologist Herbert Spencer who coined the concept of social Darwinism, arguing that the same forces of natural selection guiding evolution applied -- and should apply -- to human society too.

Spencer summed up his philosophy with a phrase, later used by Darwin himself, that was to become a watchword for libertarians and laissez-faire economists for decades to come: "survival of the fittest."

When champions of the free-market system "justify the economic status quo as a struggle for life, they are reducing Darwin to a slogan," said Guillaume Lecointre, a professor at France's National Museum of Natural History.

At the end of the 19th century, a number of thinkers turned to Darwin and his insights about the natural world to justify different social and economic hierarchies, he said.

It was not hard to do. "In nature, one can find anything: the mirror image of democracy, a dictatorship, or a libertarian world," Lecointre said.

A poor understanding of genetic inheritance bolstered by dodgy intelligence tests, for example, were used to support a 1924 law in the United States severely restricting immigration from eastern and southern Europe, as well as non-European countries.

The historical abuse of Darwin's ideas has helped provoke a hostile reaction even to legitimate science that hits on a raw nerve.

When American biologist Edward O. Wilson in the mid-1970s created the discipline of sociobiology, whose central tenet is that human behaviour is largely determined by our genetic endowment, he was engulfed in controversy.

"Genes hold culture on a leash," he famously said.

More recently, the "nature before nurture" flame has been taken up by evolutionary psychologists, whose argue that even the most intimate choices we make in love and friendship are shaped by genetic imperatives.

Scientists create first crystal structure of an intermediate particle in virus assembly

2009-02-08T22:53:00.000-08:00

February 8th, 2009 in General Science / Biology

The structure, described February 8 in an advance online publication of the journal Nature, provides fresh insights into the elegant dance that viral proteins perform to create the infectious structure that causes all manner of misery and disease, say researchers. While the virus they studied, HK97, only infects bacteria, well-known viruses such as herpes and HIV are also known to assemble an "intermediary" structure before morphing into its final assault-proof, infectious form.
"The principles of this multi-stage protein coat assembly will likely be similar across all complex viruses," says the study's senior author, Scripps Research Professor John E. Johnson. "But this process has never been seen before at this resolution, and now we known that what we thought happens, doesn't."

That's important, Johnson says, because if scientists understand how a virus builds its protective coat, they may be able to medically target vulnerabilities in the first stage of that assembly. "We believe that without its final shell to protect it, an immature virus will be much more defenseless to antiviral agents," he says.

Knowing how viruses build these vessels to protect the naked viral DNA inside is also useful in the field of medical nanotechnology, he adds. "The immature coat has lots of holes in it through which we could load drugs, and then seal it in the mature form to produce a potent delivery system," Johnson says.

Johnson and his research team have long studied HK97, and had "solved" the structure of the virus's mature outer coat. It is made up of 72 protein rings - 12 pentagons and 60 hexagons - locked together like the chain mail suits worn by knights. This coating forms the head of the virus, which is extremely small - thousands of times narrower than a human hair.

The thin viral armor offers protection and stability as well as freedom of movement, Johnson says. "This is a container that works very well."

But the researchers say they spent five "painful" years trying to produce a crystal structure of the intermediate particle they knew was assembled first. They had produced images using electron microscopy, but they weren't detailed enough to understand the molecular processes involved.

The scientists built the viral shells in a test tube. Genes that encode the 420 proteins that make up the coat were expressed in e coli bacteria, the normal host of the virus. These proteins spontaneously assemble and form the immature particles. In the presence of viral DNA and the enzymes that pump it into the particles, they instantly form a mature coat that engulfs the genes.
The study's first author, Ilya Gertsman, a researcher in Johnson's lab, kept trying to capture the crystal structure of the intermediate form of the virus, but it always quickly morphed into its final armored form, even without DNA present. Finally, working with collaborators from the University of Pittsburgh, Gertsman used a form of HK97 that was mutated in such a way that made it slow to mature.

What the researchers saw from the crystal structure "was so beautiful," Gertsman says. The proteins that made up the spherical, soccer ball-like form were flat in shape and pointed outward, like hands placed palm to palm in prayer. But the moment the structure "sensed" the presence of DNA it immediately changed shape. In essence, the fingers on the praying hands folded down together, fingers interspersed and grasping each other. "That's why the final protein coat is so stable. The proteins are all intertwined around each other," Johnson says. Previously it was thought that the proteins went through this motion as a nearly rigid unit. This study showed that the proteins significantly changed in structure during the transition. The researchers don't yet know if this structural change happens all at once, or if it moves like a wave around the sphere.

They hypothesize that domains that hang from each of the proteins that eventually form the viral coat drive the process of changing the structure. The tails interact with each other to distort the shape of the proteins, Johnson says. "As long as the tails are there, the process of change is reversible. When the tails are gone (removed by a viral enzyme), the structure becomes stable," he says. Researchers had thought these tails, which are scaffolding proteins, guided assembly of the particle "but we think they actually change the structure," Johnson says. "That offers us another target by which we may be able to interrupt assembly of the coat."

Paper: "An unexpected twist in viral capsid maturation," Nature online, February 8.

Source: Scripps Research Institute

Unnatural selection: How far will parents go?

2009-02-08T22:49:00.000-08:00

February 8th, 2009 by Marlowe Hood in General Science / Biology

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Blood serum samples in a clinic in Manila. Picture this: prospective parents excitedly clicking through an online catalogue, ticking off the optimal mix of traits for their yet-to-be-conceived child

Picture this: prospective parents excitedly clicking through an online catalogue, ticking off the optimal mix of traits for their yet-to-be-conceived child.

Will they opt for blue eyes or brown. Perhaps green, for a touch of originality? What colour skin? And do they want a boy or a girl?

Are they aiming for an Olympian athlete, or will they stack the deck in favour of intellectual prowess? Why not both?

For some people, this would be a dream come true. For others, a nightmare of widening inequality touching on eugenics.

For biologists, it raises acute questions about evolution.

The principle of species change through natural selection was set down by Charles Darwin, who was born 200 years ago on February 12.

But what "natural selection" means when it comes to Homo sapiens is hard to define. It has already been challenged by medicine, habitat, diet and other factors that affect lifespan, reproduction and survivability.

Genetic selection means our species' evolutionary path would be even more radically changed.

We are not there yet -- but this vision clearly does not belong to the hazy future of science fiction.

Dozens of clinics in the United States, one of the least regulated markets for fertility services, already provide would-be parents in-depth profiles of potential sperm and egg donors.

Atlanta-based Xytex Corporation, for example, offers a long list of genetically-coded physical attributes, right down to the length of eyelashes, the presence of freckles and whether ear lobes are detached.

There is also a summary of the donor's medical history and -- for an additional fee -- personality and educational profiles, a personal essay and photos, as an adult and a baby.

Much of this information has no relation to genetic pedigree and even when it does, the result -- a human child -- may not come out as advertised. But that has not dampened enthusiasm for the tests.

Most heterosexual couples shop in this market to compensate for either male or female infertility.

But there is nothing -- in science or, in some countries, law -- to prevent matching a donor egg with donor sperm to create an embryo that can be purchased and implanted in the buyer's womb.

This option was offered by at least one "embryo bank" in Texas before it reluctantly withdrew the procedure under an ethical firestorm.

Even parents who don't need outside help to procreate may soon be clamouring for "preimplantation genetic diagnosis" of embryos to check not only for genetic defects and disease -- the original intent -- but also for sex and desirable traits as well, experts say.

"We need to look carefully at these selection technologies," said Marcy Darnovsky of the Center for Genetics and Society in Oakland, California.

"It is not bad to have a desire for a girl or a boy," she said by phone. "But in chatrooms and on bulletin board you can find moms, for example, that don't just want a girl, but a particular kind of girl -- 'I want to go shopping with her, play Barbie Dolls, paint her toenails pink'."

"What are they going to do if they don't get that kind of kid -- take her back?" she said.

An even more problematic scenario for some is the leap from genetic selection to genetic engineering.

That can happen in two ways. Gene therapy alters genes, for example, in a diseased organ in order to effect a cure.

But changes wrought by so-called germ-line therapy alter the blueprint itself, the human genome, and would thus be passed on to offspring.

"The pressure to change genes will probably come from parents wanting to guarantee their child is a boy or a girl, or to endow them with beauty, intelligence, musical talent or a sweet nature," notes Peter Ward, a scientist at the University of Washington and author of "Future Evolution".

For now, germ-line therapy is out of reach. But were science to master the genome, the temptation to tweak it to increase smarts, looks and longevity would be overwhelming, Ward argued last month in Science.

"One day, we will have it in our power to bring a new human species into this world," he said.

Not all researchers agree. "I think that all of these worries are misplaced -- genetics is far too complex to allow for easy manipulation of human traits," said Steven Pinker, an evolutionary biologist at Harvard University.

Nearly all diseases and traits are determined not by one or two genes but the interaction of many, he pointed out.

There is no such thing, in other words, as a master gene for intelligence or musicality.

"I doubt that parents would take a risk greater than five percent that something would go wrong," he told AFP. "Testing is easy and safe. Manipulation is hard and risky."

Can cannibalism fight infections?

2009-02-08T22:46:00.000-08:00

February 2nd, 2009 in General Science / Chemistry

Enlarge

Competition between two sibling colonies of the Paenibacillus dendritiformis bacteria grown side by side. The cells in the marked regions near the gap between the two colonies are dead. Credit: AFTAU

Whenever humans create a new antibiotic, deadly bacteria can counter it by turning into new, indestructible super-bugs. That's why bacterial infection is the number one killer in hospitals today. But new research from Tel Aviv University may give drug developers the upper hand in outsmarting bacteria once and for all.

The secret weapon against a colony of bacteria may be to stress it with its own protection system, which forces it to reduce its population through cannibalism.

"Our studies suggest this is a new way to fight off bacteria," says Prof. Eshel Ben-Jacob, an award-winning scientist from Tel Aviv University's School of Physics and Astronomy. "If we expose the entire colony to the very same chemical signals that the bacteria produce to fend off competition, they'll do the work for us and kill each other. This strategy seems very promising -- it's highly unlikely that the bacteria will develop resistance to a compound that they themselves produce."

A Sophisticated Secret Weapon to Foil Attack

Cannibalism among bacteria, explains Prof. Ben-Jacob, is a strange cooperative behavior elicited under stress. In response to stressors such as starvation, heat shock and harmful chemicals, the bacteria reduce their population with a chemical that kills sister cells in the colony.

"It works in much the same way that organisms reduce production of some of their cells when under starvation," says Prof. Ben-Jacob. "But what's most interesting among bacteria is that they appear to develop a rudimentary form of social intelligence, reflected in a sophisticated and delicate chemical dialogue conducted to guarantee that only a fraction of the cells are killed."

The researchers' findings, published this month in the Proceedings of the National Academy of Sciences, were carried out in collaboration with a group from Texas University led by Prof. Harry Swinney and his post-doctoral fellow Dr. Avraham Be'er, formerly of Tel Aviv University. Prof. Ben-Jacob believes that the discoveries offer new hope for fighting both bacterial infections of today and the super-super-bugs of the future.

In the current study, the researchers investigated what happens when two sibling colonies of bacteria --Paenibacillus dendritiformis (a special strain of social bacteria discovered by Prof. Ben-Jacob) -- are grown side by side on a hard surface with limited nutrients. Surprisingly, the two colonies not only inhibited each other from growing into the territory between them but induced the death of those cells close to the border, researchers found.

Even more interesting to the scientists was the discovery that cell death stopped when they blocked the exchange of chemical messages between the two colonies. "It looks as if a message from one colony initiates population reduction in the cells across the gap. Each colony simultaneously turns away from the course that will bring both into confrontation," says Prof. Ben-Jacob.

Getting to Know the Enemy

In only a year, bacteria can develop resistance to a new drug that may have taken years and a small fortune to develop, but drug developers haven't utilized bacteria's cooperative behavior and social intelligence yet.

Bacteria, Prof. Ben-Jacob says, know how to glean information from the environment, talk with each other, distribute tasks and generate collective memory. He believes that bacterial social intelligence, conveyed through advanced chemical language, allows bacteria to turn their colonies into massive "brains" that process information, learning from past experience to solve unfamiliar problems and better cope with new challenges.

"If we want to survive the challenges posed by bacteria, we must first recognize that bacteria are not the simple, solitary creatures of limited capabilities they were long believed to be," concludes Prof. Ben-Jacob, who is now investigating practical applications for his current research findings.

Source: American Friends of Tel Aviv University

Scientists deconstruct cell division

2009-02-08T22:41:00.000-08:00

February 8th, 2009 in General Science / Biology

Enlarge

This image shows an in vitro assay for the assembly of lamin B containing spindle matrix along microtubules during spindle assembly. Yellow arrows point to the lamin B network assembled along the microtubules. Credit: Image courtesy Yixian Zheng

The last step of the cell cycle is the brief but spectacularly dynamic and complicated mitosis phase, which leads to the duplication of one mother cell into two daughter cells. In mitosis, the chromosomes condense and the nucleus breaks down.

Fibrous structures called spindles form, which then move the chromosomal material toward opposite ends of a cell and help partition other cell contents. If something goes wrong, diseases such as cancer can arise. Scientists have tried for years to unravel the process of spindle assembly. Now, researchers at Carnegie's Department of Embryology have found that two proteins— dynein and Nudel—involved in other cell-division functions, are essential to regulate assembly of the spindle matrix.

"The mechanisms that cells use during division to partition both chromosomes and regulatory factors into their daughters are widely recognized as among the most fundamental processes in all of biology. During the last several years no one has done more than Yixian Zheng to broaden our understanding of how dividing cells control these critical events," said Allan Spradling, Department of Embryology director.

"To ensure proper cell division, the mother cell needs to separate its genetic materials, the chromosomes, equally, but also partition its cellular content properly into daughter cells," explained co-author Yixan Zheng. "Cell division allows a fertilized egg to develop into multicellular organisms with different types of cells. It also replenishes adult tissues, such as skin and bones. Forming a spindle requires the assembly of a 'skeleton' from tube-like microtubules and the construction of a poorly defined scaffold called a spindle matrix."

In 2006, Zheng and colleagues discovered that a protein found in the nucleus during the interphase of the cell division cycle, called lamin-B, is a structural component of the spindle matrix (Science 31 March 2006, 311: 1887-1893). Based on this finding, she and colleagues have now isolated the spindle matrix. Interestingly, both dynein and Nudel are components of the spindle matrix. Nudel binds to lamin-B and brings it to microtubules where both Nudel and dynein then help the lamin-B assemble into the spindle matrix. The lamin-B-containing spindle matrix, in turn, works with microtubules to orchestrate spindle assembly and cell division.

"Isolating the spindle matrix and identifying its components has also allowed us to show that the matrix contains not only factors important for spindle assembly, but also proteins essential for cell fate choices," remarked Zheng. "We believe that by understanding how the spindle matrix is assembled in mitosis, it will be possible to understand how, after mitosis, two daughters can chose to become the same or different cell types—a decision that cells need to make both during the development of an organism and during the maintenance of adult tissues."

The research is published on line in the February 8 Nature Cell Biology (http://www.nature.com/ncb/).

Source: Carnegie Institution

A new gene silencing platform -- silence is golden

2009-02-08T22:38:00.000-08:00

February 8th, 2009 in General Science / Biology

A team of researchers led by Rutgers' Samuel Gunderson has developed a novel gene silencing platform with very significant improvements over existing RNAi approaches. This may enable the development and discovery of a new class of drugs to treat a wide array of diseases. Critical to the technology is the approach this team took to specifically target RNA biosynthesis.

The research findings are reported in the journal Nature Biotechnology, published online in the February 8th issue.

Gunderson, an associate professor in the Department of Molecular Biology and Biochemistry at Rutgers, The State University of New Jersey, has created highly efficient gene silencing agents that function via a novel mechanism of action. The agents are single-stranded oligonucleotides, called U1 Adaptors, that have dual, and independent, functions. First is a target-gene binding domain that can be tailored to any gene. The second domain inhibits mRNA maturation by binding U1 snRNP, a component of the cellular splicing apparatus.

By combining both capabilities in the same molecule, the U1 Adaptor can inhibit the pre-mRNA maturation step of polyA tail addition in a gene specific manner. Further, the domains of the oligonucleotide are independent so transcript binding and U1 snRNP binding can be independently optimized and adapted to a wide array of genes associated with disease.

"The U1 Adaptor platform expands on early technologies that used 5'-end-mutated U1 snRNA," Gunderson explained. "The U1 Adaptor is an oligonucleotide version of this older method and instead targets the 3' end processing step. U1 Adaptors have high activity when used alone and are synergistic when used in combination with RNAi." Gunderson went on to say that the range of possible targets is very broad due to the mechanism of action in which inhibition occurs during the biosynthesis of mRNA at the near universal 3' end processing step. Perhaps the most interesting aspect of this technology is that U1 Adaptors can possibly inhibit genes that do not respond to current RNAi methods.

The applications of U1 Adaptors expand on those currently available using standard RNAi approaches. They can be used as a research tool to determine gene function and to validate gene targets. Gene silencing molecules also have potential prophylactic and therapeutic applications based upon ongoing clinical trials using RNAi and traditional antisense approaches. For some genes that cause disease, these other approaches may not be effective enough and U1 Adaptors may provide a novel solution.'

Source: Rutgers University

Chemistry Lab Demonstrations: LIQUID CO2 Extraction!

2009-02-08T08:19:00.000-08:00

It’s the extraction lab this week in the OChem lab I’m TA’ing. It’s a straightforward aqueous base extraction of an acidic unknown from a neutral impurity. Acidify, filter the precipitate, and you’re done. I was trying to come up with a demonstration for the lab. I thought about extracting caffeine from coffee or tea leaves, but that would take a while, and isn’t all that visually appealing. I’ve only got a few minutes in my pre-lab lecture time.

So I looked around for a while, and finally found this paper by James Hutchison from the University of Oregon (doi: 10.1039/b405810k). They suggest a new lab for undergraduates involving the extraction of D-limonene from orange peels using liquid carbon dioxide. That’s right, I said liquid carbon dioxide.

The premise: create a removable filter using copper wire and filter paper to jam into the bottom of a disposable centrifuge tube. Add grated orange peel. Add crushed dry ice. Cap the centrifuge tube tightly (but not TOO tightly! The tube needs to be able to vent so as not to EXPLODE!) and immerse in warm water (T = 40-60 degC). The pressure rises (naturally) and the temperature increases and you jump into the liquid portion of carbon dioxide’s phase diagram (click for larger)

phasediagramco2

The liquid carbon dioxide percolates through the orange peels and extracts the limonene. the oil-in-solvent mixture drains through the filter paper to the bottom of the centrifuge tube. If you leave the tube in the water long enough, eventually the liquid all evaporates and the pressure decreases.

The goal is that the evaporation of the carbon dioxide leaves the pure oil at the bottom of the tube. The authors mention that for approximately 2.5 g of freshly-grated orange peel, 0.1 mL of oil should remain after 3 carbon dioxide extractions. They note this is a yield comparable to typical organic solvent extraction or cold pressing. I did one extraction on day-old chopped orange peel and did not isolate any oil whatsoever. Not a drop. I’m a little disappointed by that, but not really. It’s still an ok teaching point for the students. Not all experiments work all the time. I could examine my starting materials and get better quality reagents and it might work.

Now, inside the tube I don’t think we were past the critical point. I don’t think the temperature inside the centrifuge tube actually makes it up to the temperature of the surrounding water. I say this because after the examining the tube after the experiment, the orange was cold and there were ice crystals in the tube. There are two possible explanations for this. One, the temperature inside didn’t make it past the critical temperature. Two, when I opened the tube after the experiment, some non-trivial amount of pressure was released. PV=nRT tells us that a sudden drop in the pressure simultaneously lowers the temperature, and I could have frozen the water out that way. In fact, the authors note that while exact temperature and pressure readings are impossible with this simple setup, they speculate that the conditions approach the triple point.

In any case, it was a very cool experiment to watch, even if it didn’t do what it was supposed to. Pictures below. These pictures are from Monday night when I was practicing the demonstration. It looked much cooler in person. The first shows the system when first submerged in the water. The second is about 15-30 seconds later. It’s hard to see, but if you look closely, all three phases are apparent in the system. The third is after the dry ice has completely liquified. Click for larger.

before3phasesliquidco2
by azmanam

Polyethylene bags

2009-02-08T08:16:00.000-08:00

Politicians in Switzerland have suggested to ban the polyethylene plastic bags used in supermarkets for environmental reasons. I am no expert, but I guess a thin plastic bag cannot be so bad as long as it’s properly disposed of. What really grabbed my attention was the statement of one politician, who said that the combustion of these bags releases dioxin.

Of course he was talking about polychlorinated dibenzodioxins (PCDDs) such as 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), which was involved in the Seveso disaster and was a contaminant of Agent Orange that caused many of its severe health effects. Any chemist can see immediately that there is no way polyethylene will release PCDDs because it contains no chlorine. Such a statement immediately indicates how little research the politician has done.

I think this is indicative of a way of thinking predominant among a large part of the population here. Let me put it in a formula: Chemistry = Evil. It really annoys me when I see how little knowledge there is to support this general damnation of all things related to a scientific branch. In addition, because chemistry is bad, some people not only refuse to learn about it, but they are even proud of their lack of knowledge! I’m sure you have heard sentences like “You know, I never understood chemistry at school”, meaning “chemistry is for nerds and you don’t really need it in daily life”. Consider the same statement about art or literature, and you can see how little chemistry is appreciated. After all, modern life as we know it would be unthinkable without the advances of the chemical industry in the last century. But still, because polyethylene is made in a chemical plant, politicians will jump to the conclusion that it must be environmentally disastrous and should be banned.
by Phil

Objectives and skills checklists

2009-02-08T02:32:00.000-08:00

Objectives and skills checklists
The scientific method

* State the central objectives of chemistry (and this course).
* Outline the scientific method.
o Classify statements and explanations as observations, experimental data, laws*, hypotheses*, or theories*. Quiz Quiz
o Understand the importance of making controlled comparisons and obtaining reproducible data.

Measurement

* Use the SI* system.
o Know the SI base units*.
o State rough equivalents for the SI base units in the English system.
o Read and write the symbols for SI units.
o Recognize unit prefixes and their abbreviations.
o Build derived units* from the basic units for mass, length, temperature, and time.
o Convert measurements from SI units to English, and from one prefixed unit to another.
o Use derived units like density* and speed as conversion factors.
o Use percentages, parts per thousand, and parts per million as conversion factors.
* Use and report measurements carefully.
o Consider the reliability of a measurement in decisions based on measurements.
o Clearly distinguish between
+ precision* and accuracy*
+ exact numbers and measurements*
+ systematic error* and random error*
o Count the number of significant figures* in a recorded measurement. Record measurements to the correct number of digits.
o Estimate the number of significant digits in a calculated result.
o Estimate the precision of a measurement by computing a standard deviation*.

Matter

* Classify material properties as extensive properties*, intensive properties*, chemical properties*, and physical properties*. Give examples of each. Quiz Quiz
* Distinguish between gases*, liquids*, and solids*. Explain how these states differ at the molecular level.
* Classify samples of matter as pure substances*, homogeneous mixtures*, heterogeneous mixtures*, compounds*, and elements*. Quiz Quiz
* Use sketches to show how elements, compounds, and mixtures differ at the molecular level.
* Describe six different techniques for separating mixtures.
* Relate the names of elements to their international element symbols*.
* Describe the periodic table*. Name the major groups* and regions on the periodic table, and identify elements belonging to these groups.
* Distinguish between metals, nonmetals, and metalloids using the periodic table.

Atoms and ions

* Describe early milestones in the development of modern atomic theory.
* State and apply the law of conservation of mass* and the law of definite proportions* .
* State the premises of Dalton's atomic theory.
* Describe J. J. Thomson's experimental evidence for the existence of electrons*.
* Describe Rutherford's scattering experiments and show how the results of the experiments imply the existence of atomic nuclei*.
* List the three most important particles that all atoms are composed of, and describe their charges and relative masses.
* Understand the concept of atomic weight*.
* Describe how isotopic masses* and isotopic abundances* are measured experimentally using mass spectrometry*. Use a mass spectrum* to compute an average atomic mass. Given a table of isotopic masses and abundances, sketch a mass spectrum.
* Predict the most common ion formed by a main group element by consulting a periodic table.
* Name and write the formulas for common transition metal ions.

Molecules and compounds

* Describe two fundamental types of chemical bonding*.
* Compare properties of ionic compounds* and covalent compounds*.

Quiz Quiz
classifying compounds

* Classify compounds as ionic or covalent.
* Define and distinguish between empirical formulas*, molecular formulas*, and structural formulas* for compounds.
* Define, calculate, and relate formula weights* and molecular weights*.
* Name and write the formulas for

Quiz Quiz
names and formulas of polyatomic ions

o polyatomic ions*
o binary compounds*(covalent or ionic)
o simple ionic compounds*
o inorganic acids
o addition compounds*
* Explain the mole concept, and convert between grams, moles, and atoms and molecules.
* Determine mass percent composition of a sample from experimental data.
* Determine mass percent composition of a compound from its formula.
* Determine empirical formula of a compound from its mass percent composition.

Chemical change

* Write balanced chemical equations from descriptions of chemical changes.
* Classify chemical reactions as synthesis, formation, decomposition, thermolysis, electrolysis, displacement, single displacement, metathesis, precipitation, neutralization, redox, and combustion reactions.
* Write formation and combustion reactions for given compounds.
* Understand the concept of equilibrium solubility* and use it to recognize saturated* and supersaturated* solutions.
* Explain why water can dissolve polar* and ionic substances.
* Visualize the link between a solution's ability to conduct electricity and the degree of ionic dissociation*.
* Classify solutes as strong acids*, weak acids*, strong bases*, and salts*.
* Classify solutes as strong electrolytes*, weak electrolytes*, and nonelectrolytes*.

skills to master for exam II

Molarity

* Distinguish between saturated and supersaturated solutions.
* Predict amounts of reactants or products involved in a reaction involving solutions by using solution molarities as conversion factors.
* Use molarity as a conversion factor in dilution problems.
* Use molarity as a conversion factor in titration problems.

Gases

* Understand the definition of pressure. Use the definition to predict and measure pressures experimentally.
* Describe experiments that show relationships between pressure, temperature, volume, and moles for a gas sample.
* Use empirical gas laws to predict how a change in one of the properties of a gas will affect the remaining properties.
* Use empirical gas laws to estimate gas densities and molecular weights.
* Use volume-to-mole relationships obtained using the empirical gas laws to solve stoichiometry problems involving gases.
* Understand the concept of partial pressure in mixtures of gases.
* Use the ideal kinetic-molecular model to explain the empirical gas laws.
* List deficiencies in the ideal gas model that will cause real gases to deviate from behaviors predicted by the empirical gas laws. Explain how the model can be modified to account for these deficiencies.

Energy and chemical change

* Describe, distinguish, and relate the following properties. Predict whether these properties increase, decrease, or stay the same over the course of a given chemical or physical change.
o temperature
o thermal energy
* Understand heat on both theoretical and experimental levels.
o Relate heat transferred to changes in thermal energy when no work is done.
o Relate heat to an object's mass and initial and final temperatures. Clearly distinguish heat and temperature.
o Explain how heat can be measured experimentally (calorimetry).
o Estimate the final temperature when hot and cold objects are brought into contact.
o Define heat capacity and specific heat. Describe how these quantities can be measured experimentally.
* Define enthalpy. Distinguish enthalpy from thermal energy.
* Describe how changes in enthalpy and thermal energy accompanying a chemical reaction can be measured calorimetrically.
* Define bond energy. Use tables of bond energies to estimate the enthalpy of a reaction.
* Write and manipulate thermochemical equations.
o Combine a set of step thermochemical equations to obtain a net thermochemical equation (Hess's Law)
o Write thermochemical equations for combustion and formation reactions.

The quantum theory

* Relate wavelength*, frequency*, and velocity of waves.
* Explain how electromagnetic radiation* is produced by an oscillating charge.
* Explain how electromagnetic radiation carries energy from a transmitter to a receiver.
* Describe the collapsing atom paradox.
* List wave behaviors, and distinguish them from particle behaviors.
* Cite experimental evidence that implies that electromagnetic radiation can display both wave and particle behaviors.
* Cite experimental evidence that implies that electrons display both wave and particle behaviors.
* Connect particle and wave properties of matter using de Broglie's hypothesis.
* Explain what a standing wave is.
* Compare a wave on a wire, a particle on a wire, and an electron on a wire.
* Show how de Broglie's hypothesis implies the existence of quantized energy states for standing electron waves.
* Show how quantum numbers arise for standing electron waves.
* State Heisenberg's uncertainty principle, and explain why it resolves the collapsing atom paradox.

skills to master for exam III
Electrons in atoms

* Explain the difference between a continuous spectrum and a line spectrum.
* Explain the difference between an emission and an absorption spectrum.
* Use the concept of quantized energy states to explain atomic line spectra.
* Given an energy level diagram, predict wavelengths in the line spectrum, and vice versa.
* Define and distinguish between shells, subshells, and orbitals.
* Explain the relationships between the quantum numbers.
* Use quantum numbers to label electrons in atoms.
* Describe and compare atomic orbitals given the n and ell quantum numbers.
* List a set of subshells in order of increasing energy.
* Write electron configurations* for atoms in either the subshell or orbital box notations.
* Write electron configurations of ions.
* Use electron configurations to predict the magnetic properties of atoms.

The periodic table

* Understand the rationale behind the DEFINE[periodic table]; view the table as an ordered database of element properties.
* Explain how the periodic table reflects the quantum mechanical structure of the atom.
* Explain and use DEFINE[periodic trends] in:
o DEFINE[atomic radius]
o DEFINE[ionic radius]
o DEFINE[ionization energy]
* Explain the connection between ionization energy and metallic character.

Chemical Bonding

Intermolecular Forces

Liquids

Solids

Solutions

* Relate the following solution concentrations.
o molarity
o percentage (w/w, w/v, and v/v)
o molality
o mole fraction
o ppt, ppm, and ppb
o pX
* Explain how a dilute solution with specified volume and concentration can be prepared from a stock solution.
* Define the following colligative properties, and give a molecular explanation of each. Show how the properties can be measured experimentally.
o vapor pressure lowering (Raoult's Law)
o freezing point depression
o boiling point elevation
o osmotic pressure
* Use basic relationships involving colligative properties to estimate the molecular weight of nonelectrolyte solutes.
o Relate the vapor pressure of a solution with concentration and solvent vapor pressure.
o Use the relationship between freezing point depression and solution molality to predict the molecular weight of a solute.
o Use the relationship between osmotic pressure and solution molarity to predict the molecular weight of a solute.

About the practice exams

The tests available online and the tests on reserve at the library are actual tests given in other semesters.

The tests should be viewed as a study aid. They are not a list of questions that might reappear on future tests. Use the tests to diagnose trouble spots and topics that require further study.

The content of our general chemistry is continually being improved and modified, and the textbook is changed from time to time. Some of the tests may contain questions that are inappropriate for your course, and some areas covered in current lectures and labs are not represented in older tests.

To take a practice exam, follow any of the links below. The page will ask you for your local alias and email, but these are only kept to maintain the 'high score' file; your performance on practice exams does not affect your grade in the course at all! When you finish taking the test hit the Submit button on the bottom of the page to see how well you did.

Take Exam IA
Take Exam IIIA

..What is Chemistry ?

2009-02-08T02:21:00.000-08:00

Chemistry (from Egyptian kēme (chem), meaning "earth"^[1]) is the science concerned with the composition, structure, and properties of matter, as well as the changes it undergoes during chemical reactions.^[2] It is a physical science for studies of various atoms, molecules, crystals and other aggregates of matter whether in isolation or combination, which incorporates the concepts of energy and entropy in relation to the spontaneity of chemical processes. Modern chemistry evolved out of alchemy following the chemical revolution (1773).

Disciplines within chemistry are traditionally grouped by the type of matter being studied or the kind of study. These include inorganic chemistry, the study of inorganic matter; organic chemistry, the study of organic matter; biochemistry, the study of substances found in biological organisms; physical chemistry, the energy related studies of chemical systems at macro, molecular and submolecular scales; analytical chemistry, the analysis of material samples to gain an understanding of their chemical composition and structure. Many more specialized disciplines have emerged in recent years, e.g. neurochemistry the chemical study of the nervous system.

Wikipedia..

Download Sofware Chemistry

2009-02-08T00:37:00.000-08:00


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Chemistry Lab Demonstrations: LIQUID CO2 Extraction!

Polyethylene bags