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Molecular Models at the Movies

Molecular Models at the Movies

Molecular Models at the Movies

A model situation
David Bradley
You may have noticed a recent spate of shiny ads in the Sunday supplements and glossy “style” magazines for sleek roller ball writing implements and exclusive walnut fountain pens and the like. It seems, intriguingly, that despite the billions upon billions of text messages, emails, and (these days) the occasional fax transmission there remains a deep-seated desire to “write”. What people write, I will not speculate but a love letter in Indian ink is presumably not so indelible nor open to litigation as a spurious email sent spinning across a wireless network from a Bolivian cybercafe to a Barcelona coffee shop.
This odd thought coupled with a missive from Michael Engel of Dainippon Ink & Chemicals, Japan, regarding molecular models got me thinking about an analogous situation that exists in chemistry. There are now countless chemical web sites that carry many disparate chemical structures displayable in glorious and rotating 3D. A lot of extra information can be held within a virtual molecule allowing clickable atoms and bonds to spawn spectra and other wonders.
But, where the pen may no longer be mightier than the sword, is the same true of those molecular modelling kits that fascinated us as student chemists? Is there a place in modern chemistry for a box of coloured balls and plastic sticks? A straw poll revealed that there is indeed. Perhaps it is the almost “back to basics” feel of real molecular models that allow users to gain something that is lost in the flat world of computer monitor.
Phil Ray working towards his Master’s in physical chemistry in the US explained that he uses the likes of RasMol but “will always use my plastic ball and stick kit because, although RasMol can make 3D structures, you can learn more by making the structure yourself.” Perhaps that suggests that getting a feel for the chemistry is easier with something tangible. “When I’m doing either stereochemistry or reaction site problems the plastic kit is indispensable,” Ray adds.
These model kits are very much still available and Robert Mouk who worked for years in industry and now teaches college chemistry agrees with Ray, “There is nothing like actually holding something in your hand to get a feel for it, he says. Crystallographer Armel Le Bail of Le Mans University France meanwhile believes that for eLearning, or distance learning, virtual models become the only choice, “But, for face to face learning,” he says, “nothing can replace real models.” The direct effect on learning can be powerful too, the “hands on” approach means students, and others, can gain a better understanding holding and manipulating a model rather than simply nodding in agreement at a monitor. “Visualization in 3D space can depend on the student; some see what they are supposed to see, and other students don’t have the aptitude for this,” adds Le Bail.
Engel explains the need for solid models as people being tired of the speed of technological development, “People want something they can rely on – a model is nothing abstract, a (non-virtual 3D) reality, using plastic models does not force one to think at high-speed, and there is no new software to learn,” he explains. The real models can, however, improve appreciation of the software alternatives, “The perception we have of a virtual model rotating on a PC screen possibly depends on our past understanding of real 3D models,” suggests Le Bail. Indeed, model kits can greatly help with understanding simple reactions, making bond breaking and making processes more intuitive.
Manchester University chemist Andrew Lund makes several important points about ball and stick models, “You can take B+S models into an exam, they don’t “crash”, and you can really feel the molecular strain in a plastic model,” he says, “Moreover, I still use them pretty regularly, more often than my Silicon Graphics Indy anyway.” He adds that the ease with which bonds can be rotated so that one can get a different view of a conformer is “quick and simple” with a ball and stick model. Stephan Logan of Indigo Instruments echoes the sentiment, “Although you can show stereo pairs on a computer screen, it may not be as easy to rotate them independently or move them forward and back,” he says, “Being able to look at one and then the other while doing this can make it easier to appreciate subtle differences.”
Logan highlights an interesting spin on molecular models, “There is no doubt that computers are a great asset and offer certain advantages that physical models cannot but the same argument can be made in reverse,” he says. Logan believes many students graduate from courses without understanding the nature of a molecule like DNA, for instance. “It was only by building it piece by piece that the elegance and beauty of the structure became apparent.” Building the model was, of course, half the story in the discovery of its structure in the 1950s, today, software will link atoms with the correct bond lengths and angles with virtually no user intervention. “In building the double helix you get to see the formation of the major and minor grooves…no computer program shows this,” adds Logan.
Having something more tangible than a virtual molecule allows us to recruit different senses. Build a model of diamond with Indigo Instrument’s Wobbly bonds and it gives way very little when you try to squash it. The graphite model on the other hand can be twisted. Both effects teach a valuable lesson about the nature of both these forms of carbon. Perhaps the biggest advantage for science educators of molecular model kits is that they are affordable. Try justifying in a school budget a Pentium desktop machine complete with the latest chemical modelling software for every student, much simpler to buy them the model kits to make their own and let them hand them round. That’s something that’s not easily possible with a model displayed on desktop PC, after all.
This article was prepared with award-winning science writer David Bradley. David is a freelance writer with almost fifteen years writing and editing experience. You can contact him through his sciencebase website with comments on this article of if you’d like to commission news, views, or interviews from him in almost any field of science. You might also like to check out the latest issue of his Reactive Reports chemical news webzine

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