Celebrating Laue – complex structures very quickly!

In a slight oversight at crystallography 365 HQ, we missed that it was Max von Laue’s birthday on Thursday.

von_laueVon Laue received the Nobel prize for physics in 1914 for his discovery of the diffraction of x-rays by crystals, the first crucial step to the science of crystallography as it is today.  Though von Laue went on to concentrate on theoretical physics, one particular technique of diffraction is named after him – Laue diffraction.   With this technique of diffraction the sample is kept still and the x-rays it is exposed to are polychromatic – they occur in a range of wavelengths.  This means that lots of planes of atoms satisfy the Bragg condition at once, and makes for some very pretty pictures.

An image of Laue diffraction from http://staff.chess.cornell.edu/~hao/research.html

An image of Laue diffraction from http://staff.chess.cornell.edu/~hao/research.html

Laue diffraction is particularly useful for a number branches of crystallography – and over the next few days we’ll be featuring a few of them.  Today we’ll introduce one use – taking rapid data!

What does it look like?

Image generated by the VESTA (Visualisation for Electronic and STructual analysis) software http://jp-minerals.org/vesta/en/

Image generated by the VESTA (Visualisation for Electronic and STructual analysis) software http://jp-minerals.org/vesta/en/

What is it?

As you can see this is a pretty complex arrangement of atoms, it’s a complex of the metal rhodium in a state that only exists for a few seconds at a time.  The advantage of Laue diffraction, is that if you can push the material into its excited state as well as hitting it with a pulse of x-rays – you can find even the most fleeting of crystal structures.

Where did the structure come from?
This is structure came from work by Makal et al. and is #2019360 in the open crystallographic database.

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Interdigitation, Interpenetration, Intercalation

There is an old adage that “Nature abhors a vacuum”. This applies particularly to crystals. When crystals form the molecules try to use up as much of the volume in the crystal as possible. Even when the crystal is forced to form “porous” crystals, when they’re first made those pores are usually full of, at the very least, solvent molecules which must be forced out to access and use those pores.

In structures where the molecules form networks, the spaces within the crystal formed by those networks can be minimised through the (un?)holy trinity of crystal packing – interdigitation, interpenetration and intercalation. This is perhaps best illustrated by three structures which, chemically, are very closely related but display very different crystal packing in each case.

inter            All these three structures consist of copper atoms bridged by the small tricyanomethanide anion and another organic ligand, and all three form simple square grid two-dimensional networks. When the organic ligand is hexamethylenetetraamine, the 2D networks are quite corrugated and the anions project above and below the layers like bristles on a brush. So much so, in fact, that they poke into the holes of the adjoining network, and thus the nets interdigitate (literally meaning they have interlocked digits, much like your own digits do when you clasp your hands together).

When the ball-shaped hexamethylenetetraamine is replace by the rod-like 4,4’-bipyridine, the layers interpenetrate rather than interdigitate. This means that (in this case) there are two networks that pass through each other to form discrete layers. The pairs of sheets are not directly connected to each other but are nonetheless interlocked such that they couldn’t be separated without the breaking of bonds. Fortunately this is not the case with interdigitation, or otherwise we’d need surgery every time we clasped our hands together.

If the length of the ligand is extended slightly (by replacing 4,4’-bipyridine with 1,2-trans(4-pyridyl)ethene) the same square grid is formed, however this time the sheets stack to form channels, and the structure fills the extra space by trapping (intercalating) solvent and 1,2-trans(4-pyridyl)ethene molecules in those channels.

So, on the whole, crystals are quite clever things, with a range of tools in their arsenal when it comes to packing molecules together efficiently. So if we want to make crystals with lots of spaces inside, we need to be even clever…

Source: “Interdigitation, Interpenetration and Intercalation in Layered Cuprous Tricyanomethanide Derivatives”, S.R. Batten, B.F. Hoskins, R. Robson, Chem. Eur. J., 2000, 6, 156.

CCDC Deposition codes: 118844-118846

 

Ordering matters: Not all brownmillerites are created equal

What is it?

Early in the blog we were introduced to perovskite, one of the simplest and most common mineral structures. A vast number of crystals are derived from the perovskite structure, which typically contains two different metals (A and B) and a counteranion, such as oxygen (O), in the ratio ABO­3.

The brownmillerite structure (blogged on March 5) is one such derivative of perovskite, created by removing one-sixth of its oxygen atoms in rows. The B-metal atoms nearest the “missing” oxygens now have only four oxygen neighbours, which form a tetrahedral shape around them; the other B-metals have a full set of six oxygen neighbours, which form an octahedral shape. (Why octahedral? Six corners = eight faces!) Each tetrahedral shape is linked at the corners to two others, making long parallel chains of tetrahedra which extend throughout the crystal in one direction.

Removal of the black-boxed O atoms from perovskite (left) produces the brownmillerite structure (right).

Removal of the black-boxed O atoms from perovskite (left) produces the brownmillerite structure (right).

Now it gets complicated…

The tetrahedra, with their two missing oxygen corners, turn out to be a bit too big for the space they’re in, so they twist slightly to make a better fit. Because each tetrahedron is linked in a chain, the whole chain has to twist the same way, either left (L) or right (R). The question is: if the first chain twists to the left, which way will the next chain try to go? The same way (L)? The opposite (R)? Or will it choose an orientation at random, without any reference to its neighbour?

In fact, there are many different ways that the chain-twists can be ordered in brownmillerite materials. Researchers in the 20th Century grouped brownmillerites into three categories based on their interchain relationships:

1) all chains the same type

2) layers of L alternating with layers of R

3) all chains completely random

In the early 2000s, however, A. Abakumov and coworkers began to notice features in their electron diffraction images that were inconsistent with these three simple models. Subsequent re-investigations using modern high-quality diffraction data revealed a range of more complicated patterns in many known brownmillerites, most of which had previously been contentious or identified as “random”-type structures.

Just three of the possible L-R chain ordering arrangements in brownmillerites

Just three of the possible L-R chain ordering arrangements in brownmillerites

Besides creating some interesting problems for crystallographers to solve, the brownmillerite superstructure can actually provide us with information about the physical properties of these useful materials. For example, it was recently shown that oxide-ion conductivity in Sr2Fe2O5 is triggered by the “loosening” of some of its oxygen atoms at temperatures above 600 °C, where thermal energy allows the chains to move and randomise. At lower temperatures, however, a complex ordering pattern is observed among the chains, demonstrating that there isn’t enough energy to allow the oxygen atoms to move around. (Auckett et al. Chemistry of Materials 25 (2013) p.3080-3087) In this way, crystallography might be used to predict which brownmillerites could potentially conduct oxide ions at lower (industrially useful) temperatures.

Where does it come from?

The common brownmillerite superstructures are described by Abakumov et al. in the Journal of Solid State Chemistry 174 (2003) p.319-328, and in other publications.

Another strange element – β Uranium

What does it look like?

Image generated by the VESTA (Visualisation for Electronic and STructual analysis) software http://jp-minerals.org/vesta/en/

Image generated by the VESTA (Visualisation for Electronic and STructual analysis) software http://jp-minerals.org/vesta/en/

What is it?

Uranium is a complicated element as it is, but like carbon is can also form in a number of crystals structures – three have been identified to date; known as α, β and γ forms. The α and γ structures were found to be relatively simple, that is with only a few atoms in each repeating unit of the structure. However, that wasn’t the case for β Uranium, it’s a very complicated structure with 30 atoms in the basic unit cell needed to build the whole structure. At the time it was discovered, in 1951, it was thought that this structure was the same as that being discovered in some metal alloys, known as ‘σ-phases’.  Though this was found not to be the case, this structure has still left many puzzling why elements (where the atoms should all be identical) would form such elaborate structures.

Where did the structure come from?

The image of the crystal structure was built from information in the paper by Tucker and Senio in 1953, which was an improvement on their original structure determination.

The machine of life – the sturcture of Ribosome

What is does it look like?

The image was generated using the molecular graphics software ccp4mg. http://www.ccp4.ac.uk/MG/

The image was generated using the molecular graphics software ccp4mg. http://www.ccp4.ac.uk/MG/

The atomic resolution structure of the large ribosomal subunit at 2.4 Å Resolution (PDB ID 1FFK, Ban et al., Science, 2000). Shown in grey are the RNA molecules of the ribosomal subunit, and ribosomal proteins are shown in different colours.

What is it?

The ribosome is the complex molecular machine that is found in all living cells.  Peptide-bond formation and protein synthesis by the ribosome, is essential to all life on earth. Ribsomes of every species are composed of two unequally sized subunits named, imaginatively, the large and small subunits.

In 2000 the structure of ribosomal subunits were finally revealed at atomic resolution through crystal structures determined in the labs of Ada Yonath, Tom Steitz and Venki Ramakrishnan. This work and work from others in the intervening years have pushed the envelope of crystal structure determination of enormous biological macromolecular complexes.

It remains one of the largest structures of an asymmetric macromolecule determined to date. The structure shown here is the original 2.4 Å resolution structure of the large ribosomal subunit from Haloarcula marismortui, which catalyzes peptide bond formation and binds initiation, termination, and elongation factors. It includes 2833 of the subunit’s 3045 nucleotides and 27 of its 31 proteins.

The domains of its RNAs all have irregular shapes and fit together in the ribosome like the pieces of a three-dimensional jigsaw puzzle to form a large, monolithic structure. Most of the proteins stabilize the structure by interacting with several RNA domains, often using idiosyncratically folded extensions that reach into the subunit’s interior.

Where did the structure come from? This structure was determined by the lab of Tom Steitz. You can view it at http://www.rcsb.org/pdb/explore.do?structureId=1ffk and read more about it in http://www.sciencemag.org/content/289/5481/905.long.

Tales from a PhD – Synthesising a catenane

What does it look like?

Movie made with CDC's Mercury which then generated Povray file and was edited to give some further detail.  http://www.ccdc.cam.ac.uk/Solutions/CSDSystem/Pages/Mercury.aspx http://www.povray.org/

Movie made with CDC’s Mercury which then generated Povray file and was edited to give some further detail.
http://www.ccdc.cam.ac.uk/Solutions/CSDSystem/Pages/Mercury.aspx
http://www.povray.org/

What is it?

Jason Price talks us though a crystallography tale from his student days, working on making interlocked chain-like molecules:

‘During my PhD I was interested in generating complicated molecular species from multiple small components. One target was to synthesize a catenane, interlocked molecules in a chain like structure (http://en.wikipedia.org/wiki/Catenane). Using a copper(I) metal ion I was able to generate a pre-organized complex that was suitable for catenane synthesis. The experiment appeared to work with with good supporting evidence (MS, NMR) but it was not irrefutable. When I saw those crystals as bright yellow/orange flat plates sparkling in the bottom of my crystallization flask, I was very excited indeed. Would they give that crystal structure that could be the proof I was after?  After a long wait and some very good crystallographic analysis (not by me, as there was twinning involved) the crystals were shown to be in the target catenane.’

Where did it come from?

Jason published his structure here.