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Funding of $2 million from NIH could boost research into tuberculosis drugs at Florida State University, The Alchemist learns this week, and in chemistry news there is a novel twist on the standard substitution reaction mechanism. Chemists in Taiwan are this week threading molecules to make a daisy chain while new understanding of the biochemistry of ancient microbes that live in oceanic sediments to this day could help us understand the global methane balance. The structure and properties of doped up silver clusters are also being investigated this week for their potential in molecular electronics. Finally, publish or be damned, is the word on the street for US scientists with NIH money who have been ordered to deposit their papers in PubMed Central irrespective of the copyright claims of the conventional journal publishers.

A $2 million grant from NIH could help researchers at the National High Magnetic Field Laboratory at Florida State University develop new, effective drugs against tuberculosis. Team leader Timothy Cross and his colleagues are working towards mapping the proteins on the bacterial surface using NMR spectroscopy. Their efforts could help identify targets for novel drugs against the disease. "We ought to be able to solve the molecular structure of these drug targets," Cross says, "If you know the shape of the protein, then you can design a drug that can bind to it specifically."

An unexpected twist in one of the mechanistic stalwarts of organic chemistry, the bimolecular nucleophilic substation, or SN2, reaction has been observed in the gas phase. Researchers in Germany and the US have obtained direct evidence for this substitution mechanism in the reaction of chloride ion with methyl iodide. Surprisingly, however, their study also revealed a roundabout mechanism in which the collision of the chloride ion with the methyl group of the iodo-compound spins the molecule through a full rotation before the chloride switches places with the iodide. To some extent, the findings challenge one of the most cherished models of elementary organic reactions.

Interlocking pseudorotaxanes and rotaxanes to form a molecular daisy chain is the result of working by Sheng-Hsien Chiu of the National Taiwan University, Taipei and his colleagues. These supramolecular systems represent another iteration towards building molecular electronics devices from the bottom up. Chiu's supra synthesis involves is not quite as simple as threading daisies. In it he passes the "flower head" through a hole in the "stalk" and then expanding the "flower head" to stopper it on to the chain and so far the researchers have created only a two-daisy structure. "The challenge remains to overcome entropy and assemble larger cyclic and acyclic molecular daisy chains," says Chiu. This might involve using stiffer daisies that would disfavor dimerization and lead to longer chains.

Two microbes, known as Archaea, consume 90% of the greenhouse gas methane that would otherwise be released into the atmosphere from melting methane hydrates. However, these anaerobic microbes, which live in the ocean sediments, do so using a sulfur compound, methyl sulfide, rather than simply reversing the biochemistry of methane-making microbes. According to Christopher House and colleagues at Pennsylvania State University: "The Archaea take in the methane and produce a methyl sulfide, and then the sulfur-reducing bacteria eat the methyl sulfide and reduced it to sulfide," explains House. Understanding how these symbiotic organisms remove methane from the oceans is important because without them the average global atmospheric temperature would likely be warmer by about 10 degrees Celsius.

Sub-microscopic nuggets of silver composed of just a few hundred atoms doped with semiconductor atoms have been synthesized by Dieter Fenske and his colleagues at the University of Karlsruhe. The nanoclusters contain chalcogen dopants (sulfur, selenium, and tellurium) and may one day be built into arrays for molecular electronics applications. The team has now used X-ray crystallography to characterize in detail the complex structures of these materials. The most silver-rich compound they produced consists of about 490 silver atoms and 188 sulfur atoms, as well as 114 organosulfur ligands.

The Public Access Policy of the National Institutes of Health is set to become mandatory under US law following President Bush's approval on Dec 26th 2007. This change will mean that NIH-funded researchers will be obliged to submit an electronic version of any of their final, peer-reviewed manuscripts to PubMed Central, as soon as the paper has been accepted for publication. Many researchers are pleased with the move but traditional publishing is concerned with the implications for its intellectual property rights. If NIH had adopted an open access mandate in 2004 when Congress originally asked it to do so, it would have been the first organization to do so, at this point it will be 21st in a growing list.