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Things We Don’t Know about Chemistry

All too often when I read a personal statement, I notice that it’s about is research. The new frontiers of science are crucial to its identity – but these writers are not applicants for a PhD – they're applicants for an undergraduate degree.

What's the difference?

In simple terms, undergraduates read about science that has been discovered, and explore the breadth, width and height of the subject (slanted by their institution's interests, such as industrial application or blue sky research), whilst postgraduates select a niche unsolved problem and make an incremental step towards solving it.

So they’re not really writing about the programme they’re applying for at all! 

On the other hand, I don't want to turn off that creative interest in the science that hasn't yet been solved. And I guess, when I think about it, what I said isn't entirely true... there is some science on the undergraduate syllabus that touches on the unknown.

In chemistry – the subject I studied for my undergraduate at Oxford – this starts at the most basic level: with the hydrogen atom. The simplest atom of them all, hydrogen is just one proton and one electron, and that’s what makes it special. Other ions, such as Li+ or Be2+ that have only one electron are known as hydrogenic, and these have a special and unique quality: we know where their electrons are. For all other atoms, we don’t.

Electrons sit in discrete and quantised energy levels – but what are the energies of these levels? We have experimental data known as emission or absorption spectra from electrons jumping between energy levels, but knowing the difference between energy levels isn’t the same as knowing what their energies are (just like knowing you’ve grown an inch this year doesn’t tell you how tall you are). We can solve the problem exactly and mathematically for hydrogenic atoms, but as soon as there are two electrons it becomes so mathematically complicated chemists have literally never solved the problem – only made good approximations. 

Simple model of an atom
Simple chemistry glassware selection

Astrochemists are currently using hydrogen spectra to work out the mass of black holes. How much they are red or blue shifted from the expected energy tells us how fast hydrogen is swirling round, and so how heavy the black hole is. In fact, absorption and emission spectra, which you measure and study throughout a chemistry undergraduate, are hugely useful in cutting edge research into space.

But the unknowns go even deeper into the core of chemistry. On 28th January 2016, Chemistry World published an article pointing out that we chemists don’t even know what a molecule is – or, rather, that we’ve never agreed. Molecules are made from atoms, or could be one atom, and they have a size limit, or a particular type of bonding – or do they? As we’ve expanded our discoveries in chemistry, we’ve expanded, twisted, deformed and rewritten our definitions, and obviously that has led to a few problems.
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But the molecule is something we could clear up. One thing we can never know is how big atoms are. Yes. Although we have approximations, atoms don’t have defined edges (they are made of a “cloud” of electron probability density that fades away to nothing at infinite distance from the nucleus), and can change their size and shape when they bond. This leads us to approximate their radii (where 95% of the electron density is), and different approximations for different purposes lead to different definitions – the Pauling, Shannon-Prewitt, Landé...

At a slightly more complex level, undergraduate chemists will learn about the Sonogashira reaction, which uses a palladium catalyst to join organic fragments together. What’s never mentioned is that the full mechanism remains a mystery. Some chemists think small amounts of copper contaminating the reaction are essential for making it work, but it’s difficult to prove them right or wrong, as copper impurities in palladium are extremely hard to get rid of. The selectivity of the reaction is also hard to justify: the two different fragments always pair together, never with an identical fragment – why? 


Another fascinating topic is the realm of thermodynamics and residual entropy – a quantity the average undergraduate will calculate to death for structures such as spin ice. Residual entropy is the idea that at absolute zero (-273oC) not everything is perfectly ordered (and it should be, because disorder is linked to energy, and there is no energy at absolute zero).

At Oxford, one researcher is looking into geometric frustration: when geometry restricts a structure from perfect order. For example, imagine a tetrahedron (triangular-based pyramid) with an atom with an up or down spin at each corner. Each spin would like to be adjacent to opposite spins to minimise its energy (“coupling”), but this is literally impossible! Geometric frustration is key to the structural science of amorphous materials like glasses, to dilute magnets, and to very cold science. Understanding geometric frustration could lead to scientists the discovery of new fundamental constraints. 

A university quad at Oxford University

Dr Rowena Fletcher-Wood, Science Communicator, Get in touch at: rowena@thingwedontknow.com