Author: David Bradley

Illicit CD-ROMs

An Australian chemist friend of mine was giving a lecture recently on how Western chemists might best help their colleagues in the developing world gain access to the mountains of chemical information available without eating into their own budgets too much.

Various systems based around the Web were discussed but industrial delegates were surprisingly more than a little interested in one particular idea concerning CD-ROMs.

My chemist friend planned to set up a cheap subscription service for a monthly CD-ROM that would mirror chemistry sites on the web and so bring the internet to those scientists in poverty-struck institutes with no access. When the queue for samples of the CD-ROM had stretched to the back of the lecture hall my friend asked the next person in line why they were so keen to see the CD-ROM. The startling reply was that their employer was so scared of staff wasting time on the web that all net access was blocked – a CD-ROM could be viewed illicitly without needing a net connection.

Where there’s muck, there’s brass

Where’s there’s muck there truly is brass according to the late Benjamin Luberoff writing in Chemistry & Industry. Luberoff reported that in Sacramento, California, someone is stealing the trash. Not just any old rubbish, mind, the stuff that’s getting the attention of the local criminal fraternity, or sorority, is the tonnes of recyclables residents kindly sort and leave out for collection every week.

It’s easy to load a pickup truck with aluminium Coors cans, paper and glass, drive to the local recycling plant and pick up a few nickels and dimes in return for one’s efforts, he reckons. The local police department estimates that some $400,000 worth of recyclables are being scavenged from among the garbage of the citizenry each year.

A sizeable loss to the city coffers to add to the $250,000 they spend on disposal of old fridges and tyres. I’m waiting with interest to see the same happening in Cambridge where a kerb-side recycling scheme was implemented last year. If it’s good enough for California.

Stick with grubby bedsheets

My Dad is a retired civil engineer and unfortunately for him recently suffered a severe and itchy allergic rash on his legs caused by exposure to a biological washing powder.

After trying a topical antihistamine cream Dad went to his GP who prescribed antibiotics then, as a last resort, a steroid cream known as Betnovate-C.

According to the information leaflet accompanying the tube of cream it ‘may stain hair, skin, or fabric’. So, what’s it doing to your skin, my Dad wondered.

That aside, after a successful treatment, he was a bit puzzled as to how wash out a particularly stubborn mark on the bedsheets. His mind was put at rest by the instructions on the cream’s leaflet – ‘stains may be removed with a biological washing powder,’ it said.

Of course.

Elemental Discoveries

Elemental Discoveries was first published as a spread of chemistry news items written by David Bradley in the mid-1990s for the young chemists magazine New Elements (the name for which, incidentally, DB came up with). In 1996, he began hosting it on the web and by 1999 that proto-blog had morphed into the Sciencebase site, which ultimately became the Sciencebase Science Blog.

If you follow through the Sciencebase archives you may notice gaps, there are legacy pages that are not part of the main content management system (CMS), unfortunately, and so old, and perhaps out of date now, that it would be pointless to fold them into the CMS.

Issue 49

The visible way

The efficient conversion of sunlight to chemical energy has generally been the preserve of photosynthesising life. Until now.

Stellar system stifles landfill stench

Anyone living near a landfill will be familiar with the awful smell of decomposing waste. But, those nasty niffs could soon be history, thanks to British researchers who are tearing the odour molecules apart with a plasma.

A closed view of life

In the growing field of research into biospheres, scientists hope to improve their understanding of what sustains life and so improve our chances of colonising space and even saving the earth from environmental disaster.

Science news site Sciencebase

X-rays Make Smoother Chocolate

Chocolate

For manufacturers of drugs and chocolate bars, an understanding of how they crystallise can mean the difference between a best-selling product and a flop. X-ray diffraction could help them get a clearer picture at the atomic level.

The taste and feel of chocolate in the mouth depends a lot on the crystal form of the cocoa solids, while some medicines work more effectively in one polymorphic form than another. Until now a crystal clear understanding at the atomic level of how different polymorphs form in everything from chocolate to medicine has been little more than trial and error except in the laboratory setting of the vacuum. Now, Elias Vlieg of the Department of Solid State Chemistry, at the University of Nijmegen, describes how X-ray diffraction (XRD) techniques can be used to study crystals as they form and so provide clues as to how their growth can be better controlled. The chance of tastier chocolate and more efficacious drugs is on the horizon.

If the growth of crystals were clear-cut, there would be no need to study crystal growth, but many compounds can crystallise in different – polymorphic – forms. Even a material as seemingly simple as carbon has several polymorphs – graphite, diamond and fullerite. The differences between polymorphs of the same compound can be tiny, an atom shifted slightly to the left, or a tighter angle between two bonds. But, they can also be quite large differences that impact on the overall properties of the solid. For a drug in solid form this can have a real impact on how well it is absorbed by the body. One polymorph may take longer to be dissolved and absorbed while another might be faster acting. The result can also alter the drug’s side-effects. A slowly absorbed drug might sit in the stomach too long and cause irritation of the lining of the stomach for instance.

On the lighter side, the minute crystals of cocoa solids in a chocolate bar affect how the bar melts in the mouth. One crystal form may have a more pleasing texture on the tongue than another. According to Vlieg, XRD has been wholly successful in observing crystal growth in a vacuum. But for crystal growth from the more industrially realistic setting of a solution, melt or solid, it has until recently been little more than a dream tool.

Now, XRD is beginning to offer information on the structure of both sides of a growing interface. This, explains Vlieg, means that structural details like relaxation and reconstruction on the crystal surface and ordering in the solution can be included in the theoretical description of crystal growth.

Understanding crystal growth in vacuum and beyond, Surface Science, in press.

September 11

I am actually writing this article in the future…it’s the 11th of September 2023.

In 1988, I spent a summer working in the US. It was the time of my life at the time. I’d just graduated university and flew into JFK not a week later, spent just one night in NYC but took photos of the “twin towers” etc from the top of the Empire State Building. I fell in love with New York. Several months later I’d be staying in the same YMCA again and then flying home via JFK to a miserable London and then back to Newcastle. On that final night in NYC, window open, there were sirens and gunshots, outside it was American…my flight home was just days away from the Lockerbie disaster…

When the 9/11 attacks were underway, I was working on a deadline for one of the very early online science news sites I helped establish back in the late 90s. I had disabled my internet (modem) and had been focused on nothing but the research I was writing about. I hadn’t had a moment to leave my office to switch on the TV to catch the news. In fact, it got to 3:15 in the afternoon before I knew anything was happening in NYC and elsewhere. Mrs Sciencebase too had been working on something else and was also unaware until we reconvened in the living room to switch on BBC News 24, as it was called then. It was a shock to say the least. Unreality bit.

There has been, as the cliche goes, much water under the bridge since then.

Water, water

This article originally appeared in my Catalyst column in the original incarnation of ChemWeb.com back in the year 2000, it seems like ancient history now. However, the PI got in touch recently and was asking if there were an archived version of the article online. Sadly, there wasn’t other than his own site’s copy, so here’s my original for the record.

I always fancied the idea of polywater and what it might be able to do. But, then I also quite like the idea of using chemistry to convert lead into gold, a money tree and the magic porridge pot. While, polywater may have turned out to be a lost cause, chemists have for many years unearthed some quite bizarre properties from the liquid of life, writes David Bradley.

The discoveries about this elemental material continue to this day with a collaborative team from Japan and the US publishing results in Nature recently (30 November 2000) that show that water becomes a two-dimensional glass and shrinks under extreme pressure when cooled and confined.

To the ancients, water must have seemed such a simple yet marvellous material – primordial, straightforward, life-giving, ubiquitous and, to them, elemental. Indeed, until we began looking more closely at its physical properties and the underlying physical chemistry, the hydrogen bonds, polarity and such it remained that way.

Water is indeed a simple-seeming substance – a couple of hydrogen atoms stuck on an oxygen making a boomerang shape. Couldn’t really have been any more uncomplicated, really, straight perhaps? But, water is not, as any high school science student would hopefully be able to tell you. Up to a point it expands when it is cooled below 4 Celsius. It expands just enough to make the perfect Scotch on the rocks and to have left the Titanic in the same predicament.

Water is also rather unusual in that unlike most other materials it exists in all three standard states of matter – solid, liquid and gas – at temperatures that are not at all outside our everyday experience. The likes of carbon dioxide, common salt and egg white, just don’t have that ability to flip between states within a 100 degree range. Add to that the fact that it is far more viscous than other similarly sized molecules, it can readily be converted into that increasingly familiar supercritical fluid state for which chemists are finding green applications at every turn. The list goes on – unexpectedly high heat capacity, solubilising capacity, hydrating ability?

Microstructure of water

Much of water’s anomalous behaviour boils down to the formation of hydrogen bonds between those dangling hydrogens on the boomerang tips and the oxygens on neighbouring molecules and the tiny clusters of water molecules that exist fleetingly in the liquid state but lost in the gas and frozen in the solid.

In 1992, I reported on work from Sydney Benson and Eleanor Siebert of the University of Southern California at Los Angeles for New Scientist (see New Scientist archives). They used experimental data for ice and for pairs of water molecules in the gas phase to construct a theoretical model of liquid water. They claimed that the microstructure of water could help explain many of water’s unusual properties. Their model help them envisage transient cubes of water molecules held together briefly in groups of three or more – with their hydrogen bonds breaking and reforming some 500 billion times a second.

Where are the clues?

Later work provided further solid theoretical clues about water’s hidden properties. David Clary and John Gregory of the chemistry department at University College London used quantum Monte Carlo methods to simulate millions of possible random configurations of water molecules and came up with a hexamer that would be plausible under Schroedinger’s equation. While such theorising may ultimately lead to a way to predict the properties of water from first principles, since it is this molecular behaviour that gives rise to the bulk effects, water still holds plenty of surprises for those scientists who keenly take to it.

Xiao Cheng Zeng, Associate Professor of Chemistry at the University of Nebraska, Lincoln, working with Kenichiro Koga of Fukuoka University of Education and Hideki Tanaka of Okayama University in Japan have found that they can make water form a glass rather than ice crystals at -10 Celsius by confining it in a tiny slit just 1 nm across.

Three years ago, Zeng and Koga who was at the time a postdoctoral fellow at UNL, and `ice expert Tanaka’ were using computer modelling to look at the way water changes when it is put under extremes of pressure. The model showed that rather than expanding on freezing water it can contract if it is squeezed at 493 atmospheres at -40 Celsius between two hydrophobic plates held a nanometre apart. The model showed that water was freezing into ice crystals with a hexagonal structure where every water molecule is hydrogen bonded to its four nearest neighbours but rather than being in a three-dimensional lattice the crystals were planar. Zeng confesses that he figured Koga’s model was simply incorrect, they were looking for water glass, or ice glass, and had stumbled across a new two-dimensional crystalline form instead. “We ran many, many trials for about six months,” Zeng says, “but we found the water froze into crystals and shrank every time.”

Koga, Zeng and Tanaka were actually hoping to find a mixture of pentagons, hexagons and heptagons in the molecular structures of the water and thought it would be fairly easy to reproduce in the laboratory. But, it has taken three more years to come up with the real thing.

Frustration was the answer

The trick that finally did it was to introduce `frustration’ into the process. This simply involved holding the two hydrophobic plates immobile while the water was compressed and frozen. The effect was to totally inhibit the formation of a true crystal and force the water to form a glass instead. It worked.

Zeng says he has nicknamed the new form of ice `Nebraska’ ice from the Otoe word for `flat water’. But, aside from an interesting addition to the list of water’s bizarre behaviour is there likely to be any immediate applications? Zeng does not think so, his reward, he says, is the simple joy of discovery. “Water is such a fundamental substance that it deserves a lot of attention and we want to understand it from every aspect, from its nanoscale behaviour, from its molecular properties, and all the way up,” he explains.

Maybe what we have learned so far about water is just the tip of the iceberg. Now, pass me that Scotch, with a touch of water, of course.

Carpet Consumers

Trust a scientist to take consumer rights to the extreme. Analytical chemist Gerry Clark bought a new carpet for his son’s bedroom. The carpet had that common ‘new carpet’ smell but after several weeks it still hadn’t dissipated and Clark began to worry about the fumes to which his child was being exposed.

He took a chunk of the carpet into his lab and recorded a gas chromatograph (GC) for the volatile emissions. Sure enough, there were spikes due to several organic compounds. Clark took the test sample back to the shop together with his GC results, complained, and insisted the sample be sent to the manufacturer.

A week later, the company was in touch offering a replacement because the original carpet had obviously not been left to dry long enough before dispatch to the outlet. Needless to say everything smells rosy now.

Such tales are all very well for lab chemists, but what about the rest of us fobbed off with fusty floor coverings, smelly sofas, and pungent pouffes? Maybe consumers should set up an action group with its own labs to help people make a scientific case for complaints. It could be called the Prevention of Odourous New Gear Society. Or STENCH, STINK, REEK…or whatever.

Elemental Discoveries – April 2000: Exploding cubes

US chemists have synthesized a new type of explosive that could be more powerful than the most potent non-nuclear compound known.
The compound was synthesized by Philip Eaton and Mao-Xi Zhang at the University of Chicago by building on the building block hydrocarbon cubane. Cubane, first synthesized by Eaton and Thomas Cole, in 1964, is one of the most dense hydrocarbons ever made and has always been known as a highly strained compound that stores a great deal of energy,’ explains Eaton.
  Eaton and Zhang have developed a methodology involving non-standard procedures at each step to swap cubane’s corner hydrogen atoms with nitro groups – ultimately producing octanitrocubane. Nitro groups are common constituents of explosives for example in trinitrotoluene (TNT). The nitro groups provide oxygen for combustion of the carbon to carbon dioxide and release of nitrogen gas – explosively.

Eaton says the compound is shock insensitive so he can safely hit it and its hepta precursor with a hammer. However, deliberately detonating it is highly explosive. Calculations show that the detonation velocities and pressures will be far greater than those of TNT and more explosive than HMX (high-melting explosive. Eaton says octanitrocubane may prove to be the most powerful non-nuclear explosive around.
Octanitrocubane might have applications in mining and demolition and in propellant applications. Angew Chem Int Ed Engl, 2000, 39, 401

 

Throwing out the silicon

‘Silicon chips with everything’ was one of the great puns of the 1970s and for more than thirty years the tiny etched elemental slivers have spread like a rash over every facet of our lives – find their place in running phones, TVs, washing machines, medical equipment, cars, and of course computers.
Getting more power out a silicon chip means cramming in smaller and smaller logic units into the same space. But there is a limit dictated both by the shortest wavelength X-rays we could use to ‘print’ the features and the quantum uncertainty that may arise as these features are packed closer and closer together. Nature, of course, may have provided scientists with a model answer.
Nucleic acids RNA and DNA – the carriers of one of the neatest digital information systems we know – might in the coming decades begin to displace the computers of doped silicon and its inorganic cousins for certain computational problems and replace it with chips based on the stuff of life. Leonard Adleman at the University of Southern California was the first scientist to begin using nucleic acids to solve mathematical puzzles. In 1994, he solved a version of the ‘traveling salesman’ problem. He used the DNA bases to represent combinations of stretches of the salesman’s journey and an enzyme that could recognize and cleave those that did not correspond to an optimum journey to compute the most efficient route. Molecular biology tools – enzymes, nucleic acids and such, were thus used to demonstrate the feasibility of carrying out computations at the molecular level.
Two papers published in Nature and the Proceedings of the National Academy of Sciences demonstrate the proof of principle that shows just how plausible a nucleic acid computer might ultimately be.

Evolutionary biologist Laura Landweber collaborated with computer scientist Richard Lipton, Dirk Faulhammer and Anthony Cukras to see whether they could solve a basic chess problem. The so-called ‘knight problem’ asks how many and where can one place knights on a chessboard so they cannot attack each other. Such a problem is known mathematically as an example of an ‘NP-complete’, which means the possible answers increase exponentially with increasing variables – in this case squares on the chessboard.  The knight problem represents a class of mathematical problems that can best be solved by simple brute-force computation rather than a complex logical approach. So, to number crunch the problem, the team built a computational system from 1024 different strands of ribonucleic acid (RNA) combinations to look into this problem. Each strand of RNA represents a configuration of pairs of knights and to simplify the demonstration the system is equivalent to a nine-square chess board (3 x 3) so that there are a ‘mere’ 512 possible combinations of knights rather than the millions possible with a standard 64-square board.
The team used a targeted ribonuclease enzyme which seeks out specific combinations of bases along the strands of RNA and cleaves those that are marked by base-pairing to short DNA probes. By choosing to mark exactly the right bases the enzyme will cleave only those strands of RNA representing an incorrect combination – the wrong solutions to the knight problem, explains Landweber. All the team then needed to do was to analyze the remaining ‘whole’ RNA strands to find the answers to the problem.

Landweber and her colleagues correctly identified 43 solutions to the knight problem with their RNA computer. It’s a start but is it a total solution? Landweber explains: ‘Each molecule represents a solution. We do not need to recover all of the actual solutions, since that would just be tedious, and that is not the challenge. By sampling, if we collected a large enough set we would probably get them all, keeping in mind that some would come up more than once just by the probability distribution.’ The team also points out that their system also kicked up one incorrect solution, which re-emphasizes the need for error checking within any computer system.

The main advantage, of course, adds Landweber, is that nucleic acids can have a much higher information density than any silicon chip – a gram of dried DNA could hold as much information as a trillion CD-ROMs, it is thought.
Meanwhile, a team at the University of Wisconsin-Madison has demonstrated that it might be possible to incorporate DNA itself into more solid devices that might ultimately be interconnected to electronic components. The free-floating world of solutions has always been a barrier to the acceptance of molecular computing. The main question is always how would a chemical solution be connected to real-world input and output devices such as keyboards and monitors?

Chemist Lloyd Smith and his colleagues have now shown they can attach a potentially computing set of DNA strands by one end to a gold-coated glass surface. They use their DNA-device to eliminate incorrect solutions from another NP-complete problem known as the satisfiability problem, which is essentially the knight problem phrased differently. By exposing the tethered strands to free-floating strands carrying sequences complementary to those satisfying each criterion met by the correct solution they could produce double helices. The incorrect solutions at each step are then exposed to a cleaving enzyme. Gentle heating regenerates single strands and the next DNA complement is added as the next criterion and so on. Decoding the single remaining double strands provides the problems solution.

Smith concedes that nucleic acid computing is still a long way from approaching silicon technology. This is simply a test-bed for working out an improved and simpler chemistry for DNA computing, he says. Test-bed or not with the possibility of an information density a million million times higher than a CD-ROM there is an enormous incentive to get to grips with the shrinking world of computers.

L. M. Adleman et al., Science, 1994, 266, 5187.
L. Landweber et al., Proc. Natl. Acad. Sci. (USA), 2000, 97, 1385.
L.M. Smith et al., Nature, 2000, 403, 175.

Sperm tap

Richard Evans, Catrin Pritchard and their colleagues at GlaxoWellcome discovered a way of blocking the path of sperm from the testes, which could produce semen that is virtually sperm free without the need for an irreversible vasectomy.

On the other hand, as it were, the control they have discovered could also be used to enhance the movement of sperm from the testes and so may have potential in male fertility treatment too.

I often wonder with these fertility researcher people whether they do their research manually…maybe not. For more on male fertility research check out the sperm tap article over on Reactive Reports.