The team from University of California (UC) Berkeley, and the Lawrence Berkeley National Laboratory, led by Carolyn Bertozzi, adapted the methodology known as ‘click-chemistry‘ to the particular conditions required by ‘in vivo’ conditions. Indeed, the original ‘click’ procedures, developed by Barry Sharpless (2), involved the use of toxic copper catalysts. In their article, the authors use a copper-free click reaction to label glycans – sugars particularly abundant on the surface of cells, where they are active in cell activity signalling, as well as in response to infections – which are thought of as appealing target for molecular imaging inside living organisms.

The first step involved the injection of azide-containing sugar derivatives, which are known to metabolically label glycans with the azide function. Then, a purposedly designed molecule carrying a signalling unit as well as a function reactive towards azides, had to be injected. The click reaction proceeded and as a result, glycans could be labeled in vivo, which paves the way for future specific biomolecule labeling inside living organisms.

Click chemistry inside a mouse (reproduced from ref. 1)

References:
(1) Pamela V. Chang, Jennifer A. Prescher, Ellen M. Sletten, Jeremy M. Baskin, Isaac A. Miller, Nicholas J. Agard,
Anderson Lo, and Carolyn R. Bertozzi, “Copper-free click chemistry in living animals”, Proc. Natl. Acad. Sci. USA, published online before print January 14, 2010. doi:10.1073/pnas.0911116107

(2) H. C. Kolb, M. G. Finn and K. B. Sharpless “Click Chemistry: Diverse Chemical Function from a Few Good Reactions”, Angew. Chem., Int. Ed. 2001, 40 2004–2021. doi:10.1002/1521-3773(20010601)40:11<2004::AID-ANIE2004>3.0.CO;2-5

Antonio Stradivari. Source: What We Hear in Music, Anne S. Faulkner, Victor Talking Machine Co., 1913.

A team led by Jean-Philippe Echard from the Laboratoire de recherche et restauration in the Musée de la Musique in Paris (an institution rarely found to contribute to Angewandte papers) recently published a study where investigations performed on 5 instruments that span 30 years of Stradivari’s career, are reported. They used complimentary analytical techniques to investigate the different varnish layers. To make the long story short, they found … nothing unusual or unexpected, but only materials broadly used in this time. The varnish is essentially made of two layers, the first (lower) one being used primarily to seal the wood and made of classical siccative oil. The second (upper) layer was found to caontain the same oil mixed with organic resins, and pigment particles. The latter were identified, and again, were found to belong to broadly used materials: inorganic salts (iron oxides, mercury sulfide) or organic crimson pigments.

Spanish Stradivarius II of c. 1687, on exhibit at Palacio Real de Madrid. Author H. Svensson

In conclusion, no trace of long hypothesized gums, amber or protein was found in any of the five instruments that have been investigated. Only common materials were used, and one must admit that the extraordinary quality of his instruments was (and still is) due to Stradivari’s exceptional talent as an intrument builder, but not to supernatural trick he may have used!

Reference: J.-P.Echard, L. Bertrand, A. von Bohlen, A.-S. Le Hô, C. Paris, L. Bellot-Gurlet, B. Soulier, A. Lattuati-Derieux, S. Thao, L. Robinet, B. Lavédrine, S. Vaiedelich, Angew. Chem., Int. Ed. published online. DOI: 10.1002/anie.200905131

It is well known that the ‘usual’ green colour is due to the presence of chlorophyll in the leaves, which harvest red and blue light to fuel photosynthetic reactions. In turn, photosynthesis allows the plant to produce carbohydrates (sugars) to sustain growth and development, together with converting carbon dioxide into oxygen. When temperatures start to decrease, and days to shorten, the amount of chlorophyll in the leaves slowly decays. Indeed, warm temperatures are required for the plant to replace the chlorophyll which is gradually decomposed over time. As the concentration of chlorophyll decreases, other dye molecules present in the leaves become more and more visible. These are essentially carotene (which gives carrots their colour) and anthocyanins (present in red grapes and wine). Depending on the tree, and on the weather conditions, the leaves become yellow or more red-brown as the green colour fades, giving rise to awesome landscapes. I spent some holiday in Japan just one year ago, and the weather forecast during this period includes very detailed maps showing the ‘red leaves forecast’!

Autumn colors in Japan, here in Shirakawa-go....

... and in Nikko.

And here are some of the molecules responsible for these various and impressive color changes:

In this context, lots of effort is dedicated to find ways to detect and destroy such compounds before they can cause harm. An appealing solution was recently proposed by a research team led by Julius Rebek, Jr. at the Scripps Institute. In an article recently published in Angewandte, they show how their novel molecules can signal the presence of organophosphorus compounds, but also render them harmless by undergoing a rapid reaction.

The sensing systems is based on an aromatic ring equipped with an oxime group (C=N-OH), which is known to react with organophosphorus compounds. The intermediate product instantaneously reacts further (which is important since at this point, the toxicity survives) to form a harmless decomposition compound and a fluorescent unit, which is used to signal the fact that the reaction has occured, and therefore the presence of toxic chemicals! Really smart approach!

References:
T. J. Dale, J. Rebek, Jr. Angew. Chem., Int. Ed. 2009, 48, 7850 –7852. DOI: 10.1002/anie.200902820

Press release: Ring Closure as Warning

Of course, I am not critisizing the recipients‘ work (anyway, I couldn’t since I am a chemist and don’t know lots of things about ribosomes, apart from their double-potato shape they always have in basic biology textbooks) nor the fact that it deserves recognition, but the point is that the Nobel prize in chemistry went to people who actually do chemistry, say, five times in the last 10 years (2000: conductive polymers, 2001: catalysis, 2002: mass spec and NMR, 2003: cell membranes, 2004: ubiquitin and protein degradation, 2005: metathesis, 2006: eukaryotic transcription, 2007: chemistry on surfaces, 2008: GFP and 2009: ribosomes). So, what about creating a Nobel Prize in biology? They did it for Economics in the 60s…

Well now we just have to wait for next year – and hope that people working with molecules lighter than 50 kDa will be recognized as chemists. I’m quite sure there are hosts of guys working in organic synthesis, catalysis, nanotechnology or physical chemistry – to mention a few – who deserve to get the next Nobels. And regarding Grätzel… I keep my celebrating post for next year!

Now, to be complete, I must mention that WolframAlpha comes with some limitations – or should I say, it is still being developed – but may well become an interesting alternative to other search engines. Among the limitations, if for example you enter ‘taxol’ in the query bar, you obtain a very approximate structure of the molecule, with no mention of stereochemistry, although it is of prime importance for this type of molecules. It also seems that the notion of ‘buffer’ does not (yet) exist, even though a ‘buffer calculator’ would be quite useful…

So have a look at WolframAlpha if you need simple information (on chemistry or whatever else btw) and also have a look at their blog, reporting their latest innovations and ideas.

If you drive on the highway between Bern and Zurich, you will see at some point (in Kölliken) a huge metallic, white structure somewhat looking like one of these artificial ski resorts which have been flourishing here and there around the world. However what this gigantic cage contains is not snow, but roughly 550 000 tons (!) of waste, mostly toxic chemicals, stored here completely unlabeled, unclassified and without any kind of precaution. Among others, drums with production residues from the chemical industry, electroplating sludges, phosphoric waste, oil contaminated soil, or bag containing unsorted loose waste were delivered to the landfill. In 1985, foul smells and strangely-colored dusts lead to the dump to be closed – at that time, this meant the waste was covered by around 10 meters earth… It was then observed that underground water was becoming polluted, threatening the drinking water. The authorities finally decided the site had to be decontaminated and the waste properly treated.

An impressive draining system was build to prevent water flowing under the contaminated area from polluting further ground water. Then the huge building (of a total surface equivalent to that of ten football pitches) covering the whole area was built, and kept under slightly reduced pressure such as to prevent any escape of dust, gas or odors. The access to the main building is severely restricted, and one can enter only fully equipped with airtight suit and oxygen supply. There, samples are prelevated from rust covered tanks to try and identify what had been buried 25 years ago. The waste are then separated and sent for proper treatment. This goes not without any risk, since in summer 2008 a violent fire suddenly broke out, due to fortuitous contact between magnesium and air moisture…

A view of the inside of the main building.

This is shown in this impressive video recorded by safety cameras (in Swiss-German, but the images really show how ruined the place is, and what are the working conditions. Another video (in French) can be found here telling about the landfill.

If everything goes as planned, the waste evacuation should last until 2012, and the area should ‘look like before’ in 2015. The cost of the whole operation will likely reach 1 billion swiss francs (ca. 965 millions US$) – a good sum just to repare mistakes from the past. The good news is that is was acknowledged at some point that these mistakes were putting populations and environment at risk, and appropriate arrangements were made in order to fix the situation, whatever the costs were to be. There are some lessons to take home there!

For more informations

The society responsible for the decontamination of the landfill: SMDK (in German)

A detailed study conducted at Appalachian State University in Boone, North Carolina, by Dr. Tonya S. Coffey, showed that, in addition to the candy roughness and porosity (they even made AFM study on Mentos candies !!), a second factor deeply influences the success or failure of a coke fountain: the surface tension of the liquid directly influences the bubbles formation rate, and a liquid containing an artificial sweetener (such as aspartam in diet coke) has a lower surface tension than a liquid containing a natural sugar. Furthermore, the gum arabic contained in mentos candies also brings a contribution to lowering the surface tension of the mixture.

It was also observed than, contrary to what is frequently postulated, no acid-base reaction is involved (actually, there is no base in a mentos candy, and the pH of the beverage does not change during the course of the ‘reaction’), the caffeine present in coke has hardly any influence on the result, contrary to the speed at which mentos candies sink into the liquid, which turns out to be of great importance!

In summary, the chemical geyser is due to the presence of a rough, porous ‘material’, in addition to chemicals that decrease the surface tension of the liquid, which contains dissolved carbon dioxide: these are the three basic ingredients of this funny recipe.

For more details:
T. S. Coffey, Am. J. Phys 2008, 76, 6, 551-557. DOI: 10.1119/1.2888546

Thanks Sophie for having suggested the topic of this post – btw, ideas always welcome!

Now researchers from University of Cambridge in UK and from University of Jyväskylä in Finland report in Science a tetrahedral cage-like molecule which can encapsulate tetrahedral molecules of white phosphorus. In addition of being ‘inactivated’, phosphorus was also rendered water soluble by encapsulation, and both forms, either solid or dissolved in water, were found to be literally indefinitely stable. Interestingly, the release of phosphorus from the cage can be controlled by addition of a competing guest (benzene) which expels phosphorus. Dr. Jonathan Nitschke, who led the research, underlines the potential applications of such container molecules (source: sciencedaily.com): “It is foreseeable that our technique might be used to clean up a white phosphorous spill, either as part of an industrial accident or in a war zone. In addition to its ability to inflict grievous harm while burning, white phosphorous is very toxic and poses a major environmental hazard.” In the future, this method can probably be adapted to target other harmful molecules.

For more information:
P. Mal, B. Breiner, K. Rissanen, J. R. Nitschke, Science 2009, 324, 1697. DOI: 10.1126/science.1175313

ScienceDaily, retrieved July 14, 2009.

Among the few ladies who presented talks during this symposium, the most amazing was the performance of Prof. H. Sleiman about incredible DNA assemblies. It is not exagerate to say the audience was stunned by the impressive pictures and videos displayed during this (super high-speed) presentation! In the same morning we had Nobel Prize Jean-Marie Lehn giving a philosophico-chemical lecture on adapative, almost darwinian, chemistry.

In the afternoon we attended a special session dedicated to six professors celebrating their 65th birthday in 2009. This session was chaired by the very funny Prof. H. Ringsdorf, who had great cartoons and quotes, but who also reminded the audience of the time when people were giving presentations with the help of transparencies and overhead projectors ! We then had presentations given by Profs Javier de Mendoza, Seiji Shinkai (who, as retired now, occupies simulataneously four different positions), Roeland Nolte (who found time to prepare a talk in spite of being main organiser of the whole conference), Julius Rebek (who fears to be killed by Barry Trost as his chemistry is highly non-atom-economical), Peter Tasker (who introduced us to the subject of extractive hydrometallurgy) and finally Jean-Pierre Sauvage (who is still considered as an inorganic chemist despite ligands syntheses involving more than 30 steps).

Prof JKM Sanders opened the next morning with a neat presentation, concluded by a very interesting advice: “expect, welcome and search carefully for the unexpected”! Prof S. Otto then explained why sometimes, chemistry requires to be “shaken, not stirred” and Prof. L. Cronin was the first people I ever saw who cited Kylie Minogue in a talk (he went too fast on it, unfortunately, I had no time to write the quote on my notebook). But his talk was quite impressive as well, dealing with huge systems obtained through self-assembly.

I finally must pay tribute to the great conference dinner we had… Dutch really know how to welcome guests (host-guest chemistry at its best…) and the result was a sparse audience in the next morning, as well as a lesser motivation in making notes… Remarkable was the talk given by K. Suzuki, a PhD student from Prof M. Fujita – and remarkable as well the possibility offered to a PhD student to present his work at this conference! And finally, after the presentation of Prof I. Goldberg, a discussion about the general question ‘what is it good for?’ a remarkable answer was given by Prof. Izatt, as another question: ‘What a new-born baby is good for?’ – I should remember this one for next time some friends of mine ask me why people do research…