Electrochemical Synthesis of Metal and Semimetal Nanotubes

A rather intriguing paper has just been published by the Cambridge-based publishing wing of the Royal Society of Chemistry and highlighted by the scathing, satiricial crew at The Register (don’t visit that link if easily offended). It’s an outrage says The Register, but they’ve given the team a vulgar acronym award for their abbreviation of “copper nanotubes” and “bismuth nanotubes” nevertheless.

I’ll say no more except that apparently “Philip of Cambridge” tipped off The Register about this paper. Now, I’d like to know is “Philip” an aggrieved ex-member of the RSC’s Cambridge staff or is this another of that organisation’s rather adventurous (and some would say pointless) attempts to get its name mentioned in the media in the context of some spurious chemical happening (remember Carol Vorderman in mauveine dyed Victorian costume, or Superman on the side of buses in Hull?)

Magnolia Gum, Organic Uranium, Biotech Sweetener

Magnolia flower

I’ve got a weird and wonderful mix of chemistry news again on the Reactive Reports site and my Alchemist column on ChemWeb.com

Barking Up the Right Tree for Fresh Breath – A traditional Chinese extract from the bark of the magnolia tree could give you fresh breath and kill off the oral microbes that cause halitosis.

Cats Don’t Work Like That – The three-way catalytic converter in your car does not, it turns out, work the way chemists thought it did. One of the key functions of a “cat” is to convert toxic carbon monoxide into carbon dioxide.

Double Vision With Coordination Polymers – Calcite crystals can make you see double. You don’t ingest them to achieve some kind of mind warp effect; they are simply birefringent, having essentially two focal points.

Organic Uranium – The first ever uranium methylidyne molecule has been synthesized by US chemists despite the reactivity of the heavy, heavy metal.

And, in The Alchemist this week, we hear of an award to an entire nation for its efforts in energy research and development. In research news we hear of a record-breakingly short metal-metal bond that beats the textbook great, counterintuitive results of electron pairing comes to light in bismuth, and how to extract the organic impurities from water with an old filter for a fresher taste. Also in this week’s issue, a biotech solution to sweetness and a heads up for a Mickey Mouse protein involved in channeling potassium ions. The Alchemist Newsletter is available via ChemWeb.com, online since 1997.

Find Antioxidants Online

A new database of antioxidant values for a wide range of foods is now online. The main application will be in ongoing research on the purported health benefits of antioxidants. For example, many fruits and vegetables are known to be good sources of antioxidant vitamins, such as vitamin E, C, and beta-carotene, but these natural foods also contain other compounds, collectively known as phytonutrients, that may contribute to health effects. You can find the ORAC database here.

Sweet Proteins, Crystallised Proteins

Brazzein sweet protein

A new naturally derived artificial sweetener could soon hit the market, thanks to the development of a mass production technique devised by University of Wisconsin-Madison research Fariba Assadi-Porter. The sweetener, known as brazzein, is a 54 amino acid protein derived from an extract of the fruit of the tropical plant Pentadiplandra brazzeana Baillon. It has been eaten in West Africa across the millennia, but only recently caught the attention of the West because of its incredible sweetness. The protein extract tastes sweet only to humans and old-world monkeys and is is 2000 times sweeter than sucrose when compared to a 2% solution of sugar.

Assadi-Porter and her colleagues are using spectroscopy to help them understand the relationship between the structure of this protein and its sweetness. They have recently devised a new approach to fermenting it on a large scale and startup company Natur Research is now seeking FDA approval to commercialise the protein as a food stuff for the low-calorie drinks and food industries. A paper detailing the production process has now been accepted by Protein Expression and Purification Journal, and you can read more about the story in the NMR channel on SpectroscopyNOW.

More on proteins in this week’s issue: Roderick MacKinnon and his colleagues at Rockerfeller U have come up with a novel technique, lipid-detergent-mediated crystallization, that allows them to crystallise membrane proteins, such as the voltage-dependent potassium ion channel, in as near as natural state as possible. The approach could open the door to countless studies of membrane proteins using crystallography that have not previously been possible. More on that in the SpectroscopyNOW X-ray ezine, here

Also in this week’s round up, news not related directly to proteins and molecular biology. Researchers in Canada and the US have used MRI to demonstrate that there is something like a three-year delay in the development of certain regions of the brain in children with ADHD. The most obvious delay is seen in the front cortex, a region important in thinking, concentration, and planning. Rather than worrying parents, the discovery should be reassuring to parents and sufferers, says Philip Shaw of the NIMH Child Psychiatry Branch who led the research because although there is a delay, brain development is otherwise normal. “Finding a normal pattern of cortex maturation, albeit delayed, in children with ADHD should be reassuring to families and could help to explain why many youth eventually seem to grow out of the disorder,” he says.

The research also revealed that the regions affected by the developmental delay are coincident with the regions that develop precociously in children with autism. More on the scan results, again in SpectroscopyNOW.

Open Access Scientific Publishing

Imperial College’s Bob MacCallum runs an interesting site called Compare Stuff, which I’ve reviewed on various occasions elsewhere. Recently, he started blogging about some of the interesting results that emerge when you compare search engine hit rates for different terms against each other. One of the most interesting comparisons was run using the terms “open access” versus “journal”.

The results produce an intriguing chart in which there appear to be far more mentions of bioinformatics in the context of the term journal and open access compared with, say, maths, astronomy, or psychology. As MacCallum is bioinformaticist he says that this makes sense as many of the leading figures in the open access movement come from this field. However, physicists and computer scientists have been enormously active, if less vocal, about OA, so it is odd that those two fields do not show up quite so sharpy. What about open access chemistry, you say? Hmmmm.

Give MacCallum’s Compare Stuff site a try, it’s quite amazing what charts you can make. I just tried Organic versus Inorganic in the context of “emotions”. It looks like organic and inorganic are equally stressful but leave few people anxious, scared, lonely, happy, jealous, angry or sad.

Taking the P out of Urine Testing

Blood pressure hormone

A new approach to testing urine samples without having to purify them first has led to the discovery of a new hormone that controls sodium excretion and so could be involved in controlling high blood pressure. Too much sodium equates to raised bp. The discovery solves a riddle that confronted medical scientists for more than four decades and could lead to new approaches to treating high blood pressure.

I asked team leader Frank Schroeder about the work and discuss it in detail in this week’s SpectroscopyNOW. One issue that must be addressed before such a discovery can be applied realistically to the develop of new therapies for high blood pressure, or even low blood pressure, is to find out whether the hormone is involved in other control systems in the body. This is somewhat likely given that most other known hormones multitask. I asked Schroeder about this aspect of the research:

“At this point, it is difficult to speculate about what other biological processes might be influenced by the newly identified compounds, and the next step will be to find the receptor(s) that the [hormonal] xanthurenic acid derivatives bind to,” he told me. “From our analyses, it appears that the two xanthurenic acid derivatives represent the actual signalling molecules – the activity is very well-defined and the compounds are of high specific potency. Furthermore, a closely related metabolite, xanthurenic acid itself, is not active.”

Also, in this week’s issue, in the field of atomic spectroscopy, Jordanian scientists have found that garlic extract can reduce the levels of the toxic heavy metals, cadmium and lead, in vital organs, such as the liver, heart, and kidneys. You can read more about that here.

In pure chemistry, it has been a record-breaking year for coordination chemists Klaus Theopold and Kevin Kreisel of the University of Delaware and their colleagues who have synthesised an organometallic chromium compound with the shortest Cr-Cr bond ever. Not since the 1978 work of F. Albert Cotton and his team at Texas A&M University has such a short one been seen. Theopold told me that he does not think it will be too long before this new record is broken. “I don’t think it will be another 30 years, although I’d like to hold on to the record for a while,” he said, “As to who, there are three possibilities: somebody who is not trying for it, and discovers it accidentally (like us), Phil Power, or myself, because I am now interested and have some ideas.”

Finally, the rather delicate subject of turning raw sewage into compost for farms. Remy Albrecht of the Paul Cézanne University in Aix-Marseille and colleagues have developed an infra-red technique that could be used to monitor how well the composting process is going for biological wastes, such as sewage sludge. Obviously, compost quality for land application must be monitored and controlled closely, but there are so many benefits, such as quickly raising nutrient levels and improving soil quality that it is worth the effort. An analytical approach to near infrared reflectance spectroscopy can provide an inexpensive way to monitor the composting process, Albrecht told me.

“NIRS is a highly reproducible technique able to draw a precise chemical fingerprint of an organic material Moreover, NIRS is rapid and makes it possible to analyse a large number of samples in a practical and timely manner. Control of maturation can be easily simplified with good calibrations and a data bank in reference,” he said.

I do worry about the accumulation of heavy metals from such biological sources as with each iteration from crop/livestock, to dinner table, to sewage plant, back to farm, they could increase in concentration. There is also the issue of pathogens. I’d be interested to learn what safeguards are in place to prevent their circulation.

Virtualizing the Lab Book

I am a lab-note-freak who loves to write extremely detailed, organized lab notes, so organized that I really want to see the design of a really effective computer-based lab book software system.

With such a system, I’d want to be able to divide my lab work into several categories: Synthesis, Measurement, and other Manipulations. I’d also want to be able to create new categories by selecting and combining from a set of basic operations provided by the software.

Each type of lab work requires a unique form to fill in.Some fields are universal among all types of lab work such as Date, Title, Purpose, Results, Discussion, etc. But some fields depend on the type of lab work you are noting. For example Observations in the progress of a Synthesis lab work are important, but you don’t have any if you are doing NMR (a Measurement lab work) because you cannot see the sample.

With the help of database techniques your software labnotes could be searched, tagged, and, if online, shared! You could search people’s lab notes with “broadening” in Discussion field and “NMR” in Title field, for instance to learn from others’ experiences in the peak-broadening effects of an NMR study. And, of course, the digital chemical noting techniques (Smiles, InChI KEY etc.) connected to search engines could be incorporated into the software, too. I believe this is not very difficult technically speaking.

When I first heard of the online Open Notebook idea I thought it would be like the above-mentioned ideas, but now it seems that the current open notebook instances are essentially mere wikis and blogs. Wikis may be nice if you manually organize them into a labnote database but that’s much more tedious than directly using a database with a user-friendly shell. Blogs can be of some help with their datestamp format. Combined with tags you could make a blog-based lab notebook searchable, but it would still not be as good as specialized software designed for the purpose.

Perhaps I am missing the point of Open Notebook. Maybe it does encompass all my desires. I hope to learn more in the follow-up comments to this post.

— Guest blog post by PhD chemist Andrew Sun who is based in Guangzhou, southern China. You can find Andrew Sun via his Nature Networks blog where he discusses his life in chemistry.

Open Notebook Science

I just listened to Cameron Neylon’s fascinating talk given at Drexel a short time ago, it’s available as a podcast/mp3 via the UsefulChem Blogspot. Neylon has turned to modified blog software to help his team capture their ongoing science and is now opening his laboratory notebooks to the world.

Several things struck me from his talk. First, he points out that grad students are generally reluctant to get involved if it means more work, especially if they are not so hot on keeping a neat paper labbook, but also because their work is suddenly on show to the world. In Neylon’s field there is also the problem of tagging the materials with which his group works – short DNA sequences and proteins. Chemists, of course, have Smiles strings and InChI keys, but there is no single, simple way of tagging a protein like this, that would make it readily searchable across the blogosphere, web or database. This is especially problematic given that many research groups will be working with their own unique sequences.

However, it is the potential power of open notebook science that came across most strongly in Neylon’s talk and it is exemplified by a little anecdote he told in response to a question from the audience at the end of the lecture.

Apparently, one of his students had been struggling with a DNA experiment, finding the heatshock process difficult and not getting the results she expected. Nothing was awry in her procedures until she ran out of sample tubes and Neylon pointed out that the shelves needed restocking. It was at this point that the he and the student realised she had been using a different brand in her experiments to that used in the previously successful runs carried out by other team members.

Of course, the tube brand was not mentioned in anyone’s lab book, it was assumed they were generic components and so brand was irrelevant. Not so. At the scale they are working at, and with highly temperature sensitive materials, a minute difference in tube thickness and precise composition makes all the difference in heat distribution. The students experiments with the other brand failed because this was not taken into account. Industrial chemical engineers would have recognised the problem immediately, I’d assume. Anyway, switching back to the original brand have her almost instantaneous success and results are now being written up.

The point being, that in an open electronic notebook, such problems could be flagged so that group members and supervisor would be alerted. A meta tag in the experiment’s blog post SUCCESS=0,1,NULL could easily be included. Moreover, fields could be added in the equipment section to specify brands so that a failed experiment in which the wrong brand was used might be spotted and a different brand of tube, for instance, used next time. Such information would be archived and available to future generations so that similar mistakes would be circumvented.

Meanwhile, you can listen to the complete talk from Neylon here.

Passionate Publisher

My old friend Peter Gölitz this year celebrates a quarter century as Editor-in-Chief of the chemistry journal Angewandte Chemie. When he took over the editorship of the German Chemical Society’s premier chemistry journal in 1982, there were just four other chemists on the editorial staff and the journal published a mere 1000 pages a year. More than 9 out of 10 papers were from Germany. How things have changed.

Angewandte is now a weekly publication, is available online, and has an annual pagecount of 9000 pages. German authors are still the largest group of contributors, but four out of every five articles
published has an international team member. Oh, and Peter has a little more help these days than he did 25 years ago with 18 PhD chemists and 9 other colleagues helping run the show.

Peter is rather proud of the journal’s ISI impact factor, which ha srisen from a little over a “4” in 1982 to better than a 10 this year. It’s even surpassed several of its established competitors in this respect. During my New Scientist years, papers from Angewandte featured prominently in my reporting, partly this was because the journal seemed so much more accessible than the heavier grey tomes from other publishers. More than that though, much of the chemistry published seemed to have at least the potential of immediate applications and often flaunted this with an enticing graphic…perfect for pop science.

Congratulations, Peter, and here’s to the next quarter century ;-)

Grass Comes With Weedkiller

meta-tyrosine

No, it’s not another scare story about the dangers of illicit drugs, even if you don’t inhale. Researchers at Cornell U have discovered that at least one strain of common or garden grass, fescue grass to be precise, produces its own herbicide to prevent weeds growing in your lawn.

Frank Schroeder of the Boyce Thompson Institute for Plant Research at Cornell has identified an amino acid, meta-tyrosine, or m-tyrosine, produced by these lawn grasses and exuded from their roots in large quantities, which act as natural herbicides. It was colleague Cecile Bertin now research director for PharmAfrican, a Montreal-based biopharmaceuticals company, who made the initial discovery that fescue grasses inhibit plants from growing around them. The identification of m-tyrosine could lead to novel natural product garden herbicides. While m-tyrosine itself is too water soluble to be applied directly as a herbicide a less hydrophilic analog might be developed that could keep your lawn weed free, naturally.

In our household, lawn weeds are the least of our worries and I wish they would engineer a new strain of grass that prevents labrador puppies from urinating on the grass and leaving brown patches of dead turf.

InChI=1/C9H11NO3/c10-8(9(12)13)5-6-2-1-3-7(11)4-6/h1-4,8,11H,5,10H2,(H,12,13)/f/h12H