My favorite crystal

To celebrate IYCr2014, all readers of the IUCr Newsletter are being invited to identify a crystal of his/her personal signifiance.

The applicant should explain the reason for their choice of crystal in 500 words or less that can be understood by non-scientists of all ages. The first 50 people to identify a crystal will receive a glass that has the molecule of their crystal etched on its surface and ten words or less etched on the bottom of the glass identifiying the molecule and its significance.

There are dozens of valid reasons to nominate a crystal structure: crystals that improved health and daily living, led to Nobel Prizes or just to your PhD, were used to test new technologies of crystallography, improved the economy and changed the world. Every member country of the IUCr and every state in the US could have a national or state crystal.

Serving drinks to your guest in glasses that have your favorite crystal etched on them is a great way to explain to people what you do and why there is an International Year of Crystallography. You can win one glass free or buy a half dozen with any structure you choose from the Abino Mills Glass Company of Buffalo (if interested, contact iucrnewsletter@gmail.com). The manufacturer has agreed to share a part of the profit from glass sales with the ACA to be used to support the attendance of students from outside the USA to attend future ACA Meetings.

Member profile and favorite crystal

Crystals that bend reversibly and can be calibrated.

Elena Boldyreva with her students.

My favorite crystal is that of [Co(NH₃)₅NO₂]Cl(NO₃). The compound has been known since the end of the 19th century and was mentioned in Gmelin's Handbuch. Iorgensen described photo-induced nitro–nitrito linkage isomerization in this compound and the reverse nitrito–nitro isomerization on storage or heating. Grenthe and Nordin followed the structural changes on thermal nitrito–nitro isomerization in the crystalline state by X-ray diffraction. Others studied the kinetics of the isomerization reaction and measured the quantum yield of photo-isomerization at different wavelengths.

This compound is related to the best memories of my scientific youth – my Diploma work at the Novosibirsk State U. in 1982, my PhD thesis at the Novosibirsk Inst. of Solid State Chemistry and Mechanochemistry in 1988, my first patent, my first invited talks at an international conference, my first Erice School in 1991, my research stays in foreign laboratories in the 1990s with fellowships from the Royal Society (Durham with Judith Howard), CNR (Milan with Angelo Gavezzotti and Angelo Sironi), DFG, and a Humboldt Fellowship (Marburg, with Friedrich Hensel, Hermann Uchtmann, and Hans Ahsbahs). The research ended with my Habilitation in Novosibirsk in 2000 and its results have been summarized in a number of reviews and book chapters.

Thirty years after my first experiments with Anatoly Sidel'nikov, I remember our excitement, when we observed the crystals 'disappearing from the microscope table' while we were trying to bring them into focus. Close examination revealed that the crystals had 'jumped' a very large distance away. Such observations of 'photosalient effects' became a subject of studies of many research groups, but at that time everyone took this as a curiosity, not more. We could grow long thin crystals of the same compound that would not split into smaller fragments or jump on irradiation, but bend elastically and reversibly. This was really great! We published these results in the Proceedings of the USSR Academy of Sciences [E. V. Boldyreva, A. A. Sidelnikov, A. P. Chupakhin et al., Doklady Physical Chemistry (1984), 277(4), 893–896], which at that time was as prestigious for USSR scientists as today's publications in Science or Nature. A practical outcome was to suggest a photometer, since the number of absorbed light quanta was proportional to the curvature of the crystals that could be easily and sensitively measured by deviation of light from a mirror glued to its end. Light-induced bending of crystals of other compounds was reported by the groups of Avakumov and Nevodchikov from Nizhnii Novgorod, and Ivanov and Urban of Novokuzneck, and we all got patents for different systems.

There followed a period of special attention to the role of strain and stress in the reactivity of solids, and research groups in many countries pursued these studies – McBride and Hollingsworth in the USA, Luty in Poland, Buchachenko in Russia, to name just a few. Our 'bending crystals' provided us with a superb tool to study the interrelation between strain and reactivity, not only at a qualitative but also at a quantitative level. We have measured the quantum yield in the crystals elastically bent by external load, and followed the anisotropic strain induced in the crystals by the reaction itself, both at macroscopic and microscopic levels. At that time, we could not even dream of the instruments that enabled the success of modern photocrystallography thirty years later. Still, even with our modest experimental tools of the 1990s we succeeded to monitor the structural changes on irradiation, to solve and refine the structures of photo-products from powder diffraction data. We used this reaction as a model to develop the concepts of feedback and of flexible and active reaction cavities. I then decided to study this reaction under hydrostatic compression in a diamond anvil cell, and it is from these studies that my long-term interest in high-pressure research evolved. We started with high-pressure IR spectroscopy, proceeded with X-ray powder diffraction and eventually ended up with X-ray single-crystal diffraction. This was a really great time, when we had to start developing experimental methods and computational techniques (ranging from data processing to calculations of free space distribution, the shape and size of the reaction cavity, or Voronoi–Dirichlet polyhedra for molecular packing) 'from scratch', and could achieve the experimental precision that made it possible to follow reliably not only the changes in molecular packing but also the distortion of intermolecular hydrogen bonds and even of intramolecular bond lengths and the rotation of the nitro ligand.

All of this could justify my 'nostalgic' personal selection. But the story had a continuation – many years afterwards, as new instruments became available, linkage isomerization in general, and nitro–nitrito isomerization in particular, were revisited by other groups, and new exciting experiments were and are being performed ever since by Coppens et al., Raithby et al. and other research groups worldwide. Photo- and thermo-mechanical effects of crystals became a 'hot topic' in view of their potential applications in supramolecular and biomimetic devices, and more examples of 'bending crystals' were reported. I myself have revisited it in a new collaboration with representatives from the younger generation [P. Naumov, S. C. Sahoo, B. A. Zakharov & E. V. Boldyreva, Angew. Chem. Int. Ed. Engl. (2013). 52; doi: 10.1002/anie.201303757]. As 'my favorite crystal' and 'my favorite solid-state reaction' experience 'a second youth', I also feel younger again. It is so nice to see how much has developed from our days and nights of 'playing' in the lab, when doing research was our only concern, and we did not even know of such terms as 'grant application', 'rating' and 'impact factor'.

Huge high-pressure crystal structure

Barium at 19 GPa: representative unit (left) of 768 atoms, forming a 'host' framework (grey) and 'guest' chains with two different relative positions – 'up' (yellow) and 'down' (blue) – along channels in the host structure, in a sequence of two zigzag, two square-wave, two zigzag, etc. 'up'/'down' arrangements. There is a random single step to the left or right between the square-wave pairs on either side of each zigzag pair. [I. Loa, R. J. Nelmes, L. F. Lundegaard & M. I. McMahon. Nature Materials (2012), 11, 627–632; doi: 10.1038/nmat3342.]

At the Seattle Congress in 1996, the IUCr Executive Committee decided to create a Commission for High Pressure. At that time, new powder diffraction techniques developed from 1990 had already borne a lot of fruit, and we were starting to look for ways to extend high-pressure single-crystal diffraction as well. In 1998, we obtained single-crystal data from barium at 12 GPa that revealed a very surprising incommensurate host–guest structure – a well known structural form in binary systems, but a very weird thing to find in an element. There was clearly an even weirder version at a higher pressure, but the structure was far too complex to solve without much more refined single-crystal methods. Now 15 years later, after developments made by my Edinburgh colleagues Malcolm McMahon and Lars Lundegaard, we have been able to determine a host–guest structure with a 768-atom representative unit – huge for a metallic element – with an intriguing S-shaped patterning of the guest-chain positioning and a disordered sequencing from one row of S-shaped arrays to the next. This very remarkable structure solution was achieved by my colleague, Ingo Loa. It will surely stand as the most puzzlingly intricate of elemental structures – unless there are more surprises yet to come! And, for me, nearly 25 years after starting out with the hope of extending the range of high-resolution crystallography at high pressure, it is astonishing that it has proved possible to get this far!

Great Australian crystals

Halite (salt) crystals.

Segmented representation of the neuraminidase inhibitor compound sitting inside a cave-like contour of the neuraminidase enzyme surface.

Two extremely important single crystals connected with Australia are those of sodium chloride and neuraminidase. Sodium chloride, the first crystal for which the atomic structure was determined, was the Nobel Prize winning work of the Braggs (Australians working in the UK). The neuraminidase structure determined by Peter Colman and Jose Varghese in Australia led to the first major drug designed in Australia, Relenza, and was very influential in persuading the government to support structural biology and the construction of the Australian Synchrotron facility.

Sulfur nitride or nitrogen sulfide?

Ball-and-stick model of the tetrasulfur tetranitride molecule, S₄N₄, from the crystal structure.

My favorite crystal is sulfur nitride (S₄N₄). It took me 4 years to prepare a single crystal which revealed that in the structure four nitrogens are in a plane with two sulfurs above and two below that plane, as opposed to the proposal by Nobel Laureate Hassel who claimed from electron diffraction that it was nitrogen sulfide with four sulfurs in a plane and two nitrogens above and two nitrogens below. After a decade of acrimony involving the likes of F. Albert Cotton, it was agreed that my crystallographic work proved S₄N₄ to be sulfur nitride not nitrogen sulfide as claimed by Hassel.

The S₄N₄ structure is important as it led MacDiarmid et al. of the U of Pennsylvania to create new plastic electrical conductors and the award of the 2000 Nobel Prize in Chemistry.

Crambin

Crystal structure of crambin from PDB 3nir.

I nominate as my favorite crystal for IYCr2014 the 46-residue protein crambin. The anomalous scattering method of solving protein structures was first developed with crambin (SAD phasing) in early 1980 (Hendrickson and Teeter). Crambin diffracts to the highest resolution of any protein crystal to date (0.38 Å; Chen, Ginell et al., unpublished). In crambin, one-third of the protein residues adopt alternative conformations and waters link these alternates. This cooperative water side-chain interaction has been linked to protein function. Finally, rings of water in pentagons, hexagons and heptagons are seen at low temperature, with pentagon water rings present at room temperature.

The Verwey phase of magnetite, an all-time important crystal structure

Magnetite (Fe₃O₄) is the original substance from which our concept of a magnet and the words 'magnetic' and 'magnetism' derive. It occurs as a mineral and as nanoparticles in magnetotactic bacteria. Our ancestors extracted iron from magnetite and discovered magnetism leading to the development of the compass. Magnetite has many modern applications, from ferrite magnets and memories to nanoparticles for water remediation and MRI imaging.

The importance of electron transfer between different valence states (Fe²⁺ and Fe³⁺) to the properties of magnetite was identified in the mid-twentieth century, and other important mixed-valent materials such as the high-temperature superconducting copper oxides were subsequently discovered. Fe²⁺/Fe⁺³ electron transfer is central to redox reactions of iron complexes in solution, and to the role of iron in biology. In 1939, the Dutch scientist E. J. W. Verwey reported that electron transfer in magnetite diminishes sharply on cooling below −150°C, accompanied by a complex distortion of the crystal structure. He attributed this to the freezing of Fe²⁺ and Fe³⁺ states into a regular array, a phenomenon now known as 'charge ordering' that is important to many electronic materials. However, the low-temperature structure proved difficult to determine and became a contentious issue, leading to research over many decades to uncover the nature of the Verwey phase. The full single-crystal X-ray structure was published in 2012 and shows that Verwey's charge-ordering idea is correct to a good first approximation. However, some residual electron transfer still occurs within linear groups of three iron atoms known as 'trimerons'. The complex electronic order is shown as a network of trimerons superimposed on the Fe²⁺/Fe³⁺ charge-ordered array in the image.