Science – Page 324 – David Bradley

Nanoparticles keep buses moving

The 7000-strong Stagecoach UK bus fleet is now using nanoparticles of the Envirox oxidation catalyst as a fuel additive.

Envirox is based on a well-established oxidation catalyst but has now been formulated for use in diesel fuel at just five parts per billion without any need to modify the engine. The result is a cleaner and more complete combustion, which the company claims produces an up to 12% fuel saving as well as reducing carbon deposits in the engine and lowering emissions.

The fuel-borne catalyst is composed of particles of cerium oxide 10 nm across, a material commonly used in conventional catalytic converters to clean up vehicle exhausts. Cerium oxide catalyses the conversion of carbon monoxide and hydrocarbon gases to carbon dioxide and water. It also reduces nitrogen oxides.

Researchers have attempted to formulate the compound as a fuel additive before but have generally failed to improve on fuel efficiency or cut emissions. Cerulean believe they have circumvented the problems with their nanoscale approach because at this size, the catalyst remains evenly suspended in the liquid fuel.

Stagecoach intends to try the product in up to 1000 of its buses across the UK. According to Chief Executive Brian Souter, “We believe this new product has huge potential and we are delighted to once again be leading the way in the UK bus industry in developing new ideas.”

Cerulean International Ltd is a subsidiary of Oxonica Ltd an Oxford University spin-out company. Oxonica’s Christopher Harris recently patented an improvement to the Envirox system that uses an organic solvent system to comminute, or coat the nanoparticles with an organic anhydride or acid, an ester, or a Lewis base. This coating is intended to help the particles disperse still more evenly in diesel fuel.

The permutations for nanoparticles additives are not to merely coating cerium oxide. In the initial nanoparticle patent, Gareth Wakefield describes how the particles might also be doped with a divalent or trivalent metal or metalloid. Doping might improve the properties further, although Stagecoach will be trialling only the undoped version.

The original version of this article by David Bradley originally appeared in The Alchemist in October 2003.

Mutant Venus Flytraps Catch TNT

Computation could allow new high-affinity and specific protein receptors and sensors to be designed for any number of small molecules of interest, thanks to researchers in the US. Such artificial receptors could ultimately find a role to play in medical diagnostics, drug design, and sensors.
According to biochemist Homme Hellinga and colleagues at the Duke University Medical Center, Durham, North Carolina, the formation of complexes between proteins and ligands is a fundamental interaction in molecular biology that lies at the heart of countless biological process.

Hellinga points out that manipulating the molecular recognition between ligands and their associated proteins is crucial to basic biological studies. From a technological standpoint though, improved understanding could also allow us to create bespoke enzymes, tailor-made biosensors, genetic circuits, and to carry out chiral separations very effectively. With such rewards in the offing it is not surprising that the systematic manipulation of binding sites is still “a major challenge”, Hellinga emphasises.

The team has taken a novel approach to improving our understanding of protein-ligand interactions. They have devised a structure-based computational method that can be used to redesign protein ligand-binding specificities, which can then be engineered into a microbial genome for fermentation-like protein manufacture. In a commentary on Hellinga’s research, William DeGrado of the University of Pennsylvania School of Medicine, Philadelphia, explains how organisms use many different small molecules that bind to proteins. Receptors, enzymes, and antibodies for instance all interact with small molecules to control cell communication, signalling, and protection against pathogens. Exploitation of these interactions has so far been limited, but diagnostics and new disease therapies could emerge from greater understanding of them.

The researchers have demonstrated how the approach works by constructing new soluble receptors for the explosive TNT (trinitrotoluene), the sugar L-lactate and the medically important hormone serotonin (5-HT). The new receptors have high selectivity and affinity for their ligands and could be used as the sensing component of a detector. Intriguingly, the team has also incorporated their new proteins into a synthetic bacterial signal transduction pathway, which means they can be used to regulate the switching on and off of various genes in response to the presence of TNT or L-lactate in a bacterial culture. “The aim is to create synthetic signal transduction pathways that may allow bacteria to function as biological sentinels to chemical threats and pollutants in the environment by switching on a reporter gene,” Hellinga told us.

They started with a series of bacterial periplasmic binding proteins (PBPs) from Escherichia coli, which DeGrado describes as “Venus-flytrap-like receptors”. These PBPs are composed of two protein domains that snap shut on their ligand, just as the fly-catching plant’s specialist leaves grab their prey. When the ligand binds, a signal is transmitted. “In vivo the signal is binding of the closed form of the protein to a transmembrane receptor that triggers a cytoplasmic phosphorylation cascade that ultimately results in transcriptional activation of a reporter gene,” explains Hellinga. The natural function is the control of chemotaxis or outer membrane protein expression, depending on the system, and the natural ligands include sugars and amino acids. The researchers wanted to redesign the PBP’s trap so that it would bind a range of other small molecules in order to engineer “biological sentinels”. They chose L-lactate, serotonin (5-HT), and TNT as their targets as these compounds demonstrate great molecular diversity structurally and chemically diverse, both from one another and the natural PBP ligands.

A computer model of the PBPs was then investigated by placing a “virtual” version of TNT, 5-HT or lactate in the trap. Their powerful algorithms then mutated the binding site amino acids one at a time and scanned for new protein sequences that had a surface into which the ligand would fit. The results are astounding, with just 12 to 18 amino acids being changed, 10^23 possible sequences are generated, many more than achievable with conventional methods. Moreover, if ligand approach is also considered the combinatorial possibilities rocket to between 10^53 and 10^76.
To screen such a vast array of virtual proteins, Hellinga’s team then used another algorithm – an enhanced version of “dead-end elimination”. The original algorithm was developed by Frank DeSmet of the Catholic University of Leuven, Belgium, but was then enhanced substantially by Hellinga’s team. Further work then allowed them to handle the design of ligand-binding sites needed for their research. The algorithm queries an entry in the library on the basis of hydrogen bonds, van der Waals interactions, electrostatic interactions and atomic solvation. However, rather than scanning each individual entry those library members lower down the diversity tree are pruned off if they don’t fit. The rationale for this being that if a lower member does not fit, then any twiglets further along its branch won’t either. In this way, only the mutant Venus fly traps with a global energy minimum are retained for further investigation. The result – from billions and billions of possibilities, the researchers have pruned down to a top seventeen.

The researchers synthesised these seventeen potential receptors and tested them in vitro against their target small molecules. Fluorescence measurements shed great light on each, revealing them to be highly specific and selective for their respective ligands.

Until now, explains De Grado, the proteins in question have been “developed” either through the generation of large libraries of proteins for testing and improved through evolutionary type methods. However, this is time wasteful and energy consuming. As De Grado points out the Hellinga team has now accomplished the task of creating such a library and screening it by a very rapid computational means.

References

Nature 2003, 423, 185; Loren L. Looger, Mary A. Dwyer, James J. Smith & Homme W. Hellinga
Nature 2003, 423, 132; William F DeGrado.

The old ones are the best

An apocryphal story was doing the rounds of the chemistry discussion groups on the internet a while ago. You can substitute your own alma mater and personal weekend hobby for greater comic effect when relating the tale.

Two undergraduate chemists at Newcastle University did very well in their mid-term exams, their practical results were squeaky clean – both were headed for a first. In fact, the two friends were so certain of their chances they spent the weekend before the crucial final fell walking and partying at a hill-top youth hostel.

Either suffering from all the fresh air or one or two more beers than they should have had on the Sunday night they didn’t make it back to Newcastle until early Monday morning. Rather than taking the crucial final they spoke to Professor Bunsen after the exam and explained that their car got a flat tyre on the way back to University and the spare was dud.

flat-tyre

Bunsen was a lenient chap and agreed they could take the exam the following day. The friends were so relieved and studied hard that night. For the exam they were put in separate rooms and given the question booklet. Question One was a simple test of chemical reactions (5 points) and each thought the exam was going to be easy. They were unprepared, however, for what they saw on the next page. It said: “Which tyre? (95 points)”.

In the poo of Eden

We recently visited the Eden Project near St Austell in Cornwall and were impressed not only by the vast “biomes” and their horticultural contents but by the detail into which the designers of some of the exhibits have gone. Particularly intriguing was the Spindigo exhibit that is being undertaken with researchers at the University of Reading. Spindigo as the name might hint at, aims to find a sustainable way to supply the textile industry with the unique blue jeans dye indigo from natural renewable resources rather than synthetic chemicals. Certainly a worthwhile cause.

The Spindigo exhibit went into some detail about how all kinds of natural materials have been used to release the blue colouring from its natural plant sources. The seemingly endless list included dates, grapes, yeast, molasses, figs, papaya, green bananas. Our colleague began to wish he hadn’t visited the Eden Project’s restaurant for a “Cornish pastie” when he got further down the list. Rotten meat as well as urine (they don’t mention whose) have also been used to extract the blue. But, the last entry was the most off-putting – dog poo! On reflection though, perhaps this secret ingredient is part of what makes those shrink-to-fit jeans so trendy. Just don’t tell the marketing department.

Riding the mineral wave

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The Real Butterfly Effect

The tropical butterfly Morpho sulkowskyi flashes bright blue as its iridescent wings flutter by. Not only is it astonishingly beautiful, but Japanese chemists believe the secret of what gives these wings their brilliance could lead to a new approach to stay-clean coatings for cars and other surfaces.

Osamu Sato of the Kanagawa Academy of Science and Technology and colleagues have discovered the secret of why the butterfly’s shiny wings never seem to get dirty and intend to put their discovery to good use.

They already knew that butterfly wings have a special surface structure. This consists of an array of highly ordered microscopic scales, which produce colour by scattering and refracting light from the scales. This “structural colouring” is unlike the colourful pigments used elsewhere in the natural world which rely on reflecting light at different wavelengths. Structural colour, however, unlike a baboon’s rear, relies on keeping pristine, otherwise the butterfly would revert to a dull grey.

Sato and his team discovered that there are countless air-filled cavities within the scaly surface of the wing. These, he explains, carry out cleansing duties across the wing’s surface. Any minute droplets of water on the surface ride on a cushion of air and as they roll off they drag with them any clinging dirt particles. This helps maintains the scales’ smooth lustre.

Now, the team have copied the butterfly effect. First, they produced a liquid suspension containing finely divided polystyrene beads just a few micrometres across. They then added powdered silicate whose particles are a few tenths the diameter of the beads. A blast of ultrasound makes the particles disperse evenly throughout the liquid. The researchers then dipped a glass slide into this mixture and slowly withdrew it.

As the plastic beads stick to the slide, they pack together like so many apples on a tray into an arrangement known as hexagonal close packing. The beads act as a template for the silicate particles, which fill the gaps between the beads. “During the lifting process, the polystyrene beads self-assemble into a highly ordered structure,” explains Sato. It is the patterned silicate layer in which the researchers are interested though so they next burn off the polystyrene beads at 450 Celsius. This leaves behind a honeycomb of tiny hollow cells formed from the compacted silicate particles.

Size is important when it comes to hollow air pockets. To mimic the colourful effects of the butterfly wing, the holes have to have a diameter close to the wavelength of visible light so they can scatter incoming light waves, explains Sato. By changing the size of the templating beads, the researchers, can fine tune the diameter. In this way, they have made brilliant blue, green and red layers and could produce all the colours in between.

Their preliminary tests show that these silicate layers, are water repellent because of their air holes. Thus, like the butterfly’s wing any droplets of water are dispersed readily and dirt particles carried away with them. “The sample is not yet very tough, it will peel off if it is scratched,” confesses Sato, “but we are collaborating with Japanese companies to solve this problem.”

The researchers say their new materials might first find use in quantum dot devices, as optical materials for telecommunications, and as scaffolds for tissue engineering. More immediately commercial applications may be possible such as the self-cleaning car. Whatever colour it is to be, such a vehicle with its butterfly-wing coating is sure to cause a flap.

Good anger, bad anger

Anger management is not all about controlling and stifling anger especially if you want to be good to your heart.

It’s not five minutes since researchers revealed that anger, particularly among men could cause heart problems. Now, it seems a different group has observed the opposite effect – expressing anger may protect against heart attack and stroke. So, should we chill out or indulge that road rage? Vote now.

Frustrated magnets

Scientists sometimes take magnetism for granted. But some materials behave badly and scientists funded by the UK’s Engineering and Physical Sciences Research Council (EPSRC) are trying to find out why. They are looking at the conventional wisdom of modern theories and finding it does not always stick to exotic magnets.

Scientists from archaeologists to zoologists are attracted to magnetic measurements. Archaeologists use magnetic artefacts to date sites, while a zoologist might be investigating the effects of magnetism on bird brains. Magnetism is fundamental to science, but despite their ubiquity scientists still cannot fully explain magnetic materials.

Professor of Solid State Chemistry at Edinburgh University, Andrew Harrison hopes with the help of EPSRC funding to get inside some exotic magnets, which could provide insight into more common magnetic materials and ultimately help in the design of computer memory and electrical devices. “The study of the fundamental properties of magnets gives us valuable insights into the principles that govern the structure of solids,” he explains, “This has implications that stretch beyond magnetism and into superconductivity.”

The conventional picture of a magnet says each atom in a material acts like a tiny magnet. The magnetic moment, or direction of the North-South divide on the atoms line up parallel (in permanent ferromagnets like iron) or anti-parallel in an up-down arrangement in antiferromagnetic materials, such as manganese oxide. “The reason why such materials behave this way,” says Professor Harrison, “is that below a certain critical temperature the magnetic moments ‘freeze’, or become locked in position.” For an iron magnet this critical temperature is well above room temperature but for other materials they have to be cooled near to absolute zero before they become magnetic. The picture was fairly simple until high-temperature cuprate superconductors were discovered and started throwing up strange results. For instance, some of these materials, at first sight seemed not to have frozen magnetic moments. Such findings inspired researchers to seek new understanding of magnetic materials.

Because the magnetic moments in some superconducting magnets were very small, quantum fluctuations in their orientation overpower the usual forces that normally lock the magnetic moments in place. In the case of lanthanum cuprate, this is not quite enough to upset the conventional picture but a new ingredient – frustration – changes completely the conventional picture. Frustration is found in materials where the magnetic moments are on a triangular rather than a square lattice. “You cannot physically align all the moments antiparallel with their neighbours!” says Harrison. In such a ‘frustrated’ lattice, the conventional forces between magnetic moments are much reduced and the quantum fluctuations are more influential. This kind of magnet may never freeze and the material fluctuates between different states with the moments twitching between the sides of the triangles. The result is that the material exists as a “spin fluid” and such materials could help explain magnetism and possibly superconductivity.
According to Harrison, however, materials that have a small magnetic moment in a frustrated lattice are very rare and have proved difficult to synthesize. “Such a material is one of the Holy Grails in this area of science” he muses There are many materials with triangular lattices, such as vanadium(II) chloride, but they have conventional magnetism. “The challenge is to swap the elements such as vanadium, which have relatively large atomic moments, for magnetic copper ions, which have small atomic moments, while retaining a triangular lattice. So far the wrong lattice forms,” adds Harrison, “It’s as if nature doesn’t want to produce such a material with this kind of unstable ground state, what happens is that the magnet distorts to some other form as it cools down.”
Harrison and collaborators have tried an alternative material type over the last few years. A material of chemical formula ABO2 (A and B are two different metals, O2 is oxygen) can crystallize with the rock salt, sodium chloride NaCl, structure but instead of Na-Cl-Na-Cl? it would contain A-O-B-O-A-O? making a triangular lattice. If A is magnetic and B non-magnetic, as in NaTiO2, one might be able to make a frustrated magnet. Making this material was a huge challenge but eventually Harrison’s collaborators Matt Rosseinsky (Liverpool University) and Simon Clarke (Oxford University) succeeded. Unfortunately, on cooling below its critical temperature, the atoms in the initially triangular lattice layers, jostled each other and the structure distorted. “The strategy of simply knowing which materials might produce the right lattice structure does not always produce a positive result,” says Harrison.
“With our EPSRC grant we are setting our own agenda as chemists, so instead of saying, ‘right nature gives us these materials to work with’, we could try and direct the lattice’s architecture by choosing chemical groups, or ligands, to join the metal ions.” One approach was to build a template that would bind to three metal ions, but not only that it would have to allow the magnetic moments of the metal atoms to couple with each to produce a magnetic material despite their being locked in a triangular lattice.

Working with chemist Neil Robertson the team is trying to design a ligand for the job. They are exploring hexathiabenzene – six-carbon rings with sulfur atoms attached to each carbon. Pairs of sulfur atoms can grab metal ions like pincers, so each hexathiabenzene links three metals together giving a triangular building block for the lattice. Smearing of the electrons – delocalization – through the benzene ring then provides the machinery for magnetic coupling between building blocks. “Although there is an element of design in this, there is also an element of luck,” says Harrison. The team is now investigating what happens when hexathiabenzene templates a copper or cobalt structure, but he admits, “We are still just finding our way around what works, designing a material is a black art.”

The team has a couple of likely products – magnetic materials with what they hope is a triangular, frustrated lattice, which will make them behave as spin fluids. The problem remains that these materials form only fine powders, which means no conclusive crystal structure. The other problem they are yet to overcome is that for their materials that critical temperature is a rather chilly five degrees above absolute zero. “The long-term challenge of building molecular magnets that might have technological applications remains a distant target,” explains Harrison. But, while that remains so, they are developing interesting structures that are helping them probe the inner mysteries of magnetism. “Our and other studies might conceivably lead to new generations of functional magnetic materials, for computing and other applications, but I’d be wary of saying it’s just around the corner because it isn’t!”

Nature is not entirely mean. The magnetic jarosite minerals used as rich orange-red pigments and cosmetics for millennia contain iron. Harrison spotted the parent compound, potassium hydroxy iron sulfate, as containing a frustrated crystal lattice while still a post-doctoral researcher in Canada.
He and Andrew Wills of the Laue-Langevin Institute and colleagues, have since studied natural and synthetic jarosites from hundreds of rock samples. “We’ve also adapted the ‘natural preparation’ to include ions not commonly found in nature,” says Harrison. The resulting “spin glasses” are providing insights into magnetic phenomena.

By the way, if you want an answer to the question, “is there a material that blocks magnetic forces?”, check out the SciObs blog, the succinct answer is no.

Alternative Germans

A federal health report by the Robert-Koch-Institute in Berlin, Germany, has revealed that three quarters of Germans use, or have used, complementary medicine and so-called alternative remedies and 90% would recommend such treatments to others. Since 1995, health insurance companies in Germany have had discretion in including or excluding complementary medicine from the treatments they cover. A lack of definitive medical research could be said to assist the companies in reaching their decisions over certain treatments. Stats source: BMJ.

Telesales taken to task

A paper in a recent issue of the journal Archives Of Otolaryngology – Head & Neck Surgery (2002, Vol 128, Issue 5, pp 571-577) discusses the problems facing telesales people, particularly with regard to voice problems. Telesales staff, the study, led by Katherine Jones of the University of Nebraska found, were twice as likely to report one or more symptoms of vocal “attrition” compared with controls, after adjusting for age, sex, and whether they were smokers or not. Apparently, voice problems and “occupational vocal load” can adversely affect productivity and “are associated with modifiable risk factors.”

We hung-up before finding out what these factors are but was left wondering whether the researchers cold-called the people and whether those interviewed were in the middle of dinner or had had to get out of the bath to answer the phone. In a more malicious moment we’d like to think so.