Diamond Light Source has recently played a key role in helping to reveal the exact structure of the most complex non-DNA molecular knot prepared to date.
Whether we tie them into rope, string, ribbons or shoelaces, knots are useful for lots of reasons – to make something secure, to fasten things together, even as a reminder for something you mustn’t forget. But knots can play an even bigger role in our day to day lives without us even realising it.
Knots are found in DNA and proteins and even in the molecules that make up natural and man-made polymers where they can play an important role in the substance’s properties (for example, up to 85% of the elasticity of natural rubber is thought to be due to knot-like entanglements in the rubber molecules chains). Chemists are interested in studying these molecular knots to further understand how they affect a material’s properties. However, deliberately tying molecules into knots to study these effects is extremely difficult. Up to now only the simplest types of knot, the trefoil knot (three crossing points) and the topologically-trivial unknot (zero crossing points), have succumbed to chemical synthesis using non-DNA building blocks.
Diamond Light Source has recently played a key role in helping to reveal the exact structure of the most complex non-DNA molecular knot prepared to date. The Diamond synchrotron’s Small Molecule Single Crystal Diffraction beamline, I19, was used to collect data from a molecular pentafoil knot (also known as a cinquefoil knot or a Solomon’s seal knot) which looks like a five-pointed star.
A team from the University of Edinburgh led by Professor David Leigh prepared the molecular knot, the Engineering and Physical Sciences Research Council (EPSRC) National Crystallography Service collected the diffraction data on I19 at Diamond, and Academy Professor Kari Rissanen at the University of Jyväskylä, Finland, solved the structure.
Professor Leigh describes how they succeeded in creating the complicated tangle, “The scale we were working on is 80,000 times smaller than a hair's breadth. The thread that is tied into the star-shaped knot is just 160 atoms in length – about 16 nanometres long. We used a technique known as self-assembly to prepare the knot through a chemical reaction. The building blocks were chemically programmed to spontaneously wrap themselves up into the desired knot.”
Making knotted structures from simple chemical building blocks in this way should make it easier to understand why entanglements and knots have such important effects on material properties. Being able to produce materials with a specific number of entanglements, rather than the "random" mixture that occurs in present plastics and polymers, could allow them to exercise greater control when designing materials.
Professor Leigh concludes, “It's very early to say for sure, but the type of mechanical cross-linking we have just carried out could lead to very light but strong materials, something akin to a molecular chain mail. It could also produce materials with exceptional elastic or shock-absorbing properties because molecular knots and entanglements are intimately associated with those characteristics. By understanding better how those structures work and being able to create them to order we should be able to design materials that exploit those architectures with greater effect."
The image above shows the X-ray crystal structure of a 160-atom-loop molecular pentafoil knot featuring iron ions (shown in purple), oxygen atoms (red), nitrogen atoms (dark blue), carbon atoms (shown in metallic grey, with one of the building blocks shown in light blue) and a single chloride ion (green) at the centre of the structure. Image credit: Robert W. McGregor
Diamond Light Source is the UK's national synchrotron science facility, located at the Harwell Science and Innovation Campus in Oxfordshire.
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