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

 

Negative Compression! Silver(I) tricyanomethanide

What does it look like?

Silver(I) tricyanomethanide, Ag(tcm) has a layer-like network topology. In this network each Ag+ cation is coordinated to three tcm- anions in an approxomately trigonal arrangement: likewise each tcm- anion is coordinated to three Ag+ centres. The resulting hexagonal (6,3) topology is sufficiently open that two honeycomb networks interpenetrate within each layer of the crystal structure. Adjacent layers interact via long Ag...N contacts that are sufficiently weak that the material behaves essentially as a two-dimensional framework.

Silver(I) tricyanomethanide, Ag(tcm) has a layer-like network topology. In this network each Ag+ cation is coordinated to three tcm- anions in an approxomately trigonal arrangement: likewise each tcm- anion is coordinated to three Ag+ centres. The resulting hexagonal (6,3) topology is sufficiently open that two honeycomb networks interpenetrate within each layer of the crystal structure. Adjacent layers interact via long Ag…N contacts that are sufficiently weak that the material behaves essentially as a two-dimensional framework.

What is it?

In the absence of a structural phase transition, it is a thermodynamic requirement that a system reduce its volume under hydrostatic pressure. The phenomenon of negative compressibility is the counterintuitive effect whereby this volume reduction couples to an expansion of the material in at least one linear dimension. In principle, the most extreme such response allowed thermodynamically is that of negative area compressibility (NAC), whereby a material expands along two orthogonal directions on increasing hydrostatic pressure. The remarkably few negative compressibility materials that have been characterised unambiguously expand only along one principal axis when compressed hydrostatically. The material Ag(tcm) exhibits both area negative thermal expansion and NAC due to a layer rippling mechanism illustrated in the figure above. The materials therefore expands within the layers under hydrostatic pressure and contracts with increasing temperature. It is also noteworthy that the magnitude of NAC is almost as high as positive compressibility for conventional engineering materials.

Where does it come from?

Negative area compressibility in silver(I) tricyanomethanide. S A Hodgson, J Adamson, S J Hunt, M J Cliffe, A B Cairns, A L Thompson, M G Tucker, N P Funnell and A L Goodwin, Chem Comm 50, 5264-5266 (2014).

CCDC deposition numbers: 961474 – 961482

Chasing complex molecules in the stars – looking for L-Serine.

Amino acids are the building blocks of life.  They are small molecules, 500 different one – but there’s a subset of 21 that build up to make all of the proteins and peptides that make us, and the machinery of life around us.   For many years astronomers have been searching for the signal of amino acids in the stars, as it would be a sign that complex life could be built elsewhere in the universe.

On Friday, a group of astronomers announced that they has seen the signal for the most complex molecule yet found in the stars.  In a star-forming cloud 27,000 light years from us, they spotted a signal from the molecule iso-propyl cyanide.  Similar work back in 2009 identified Ethyl Formate, leading the researchers to conclude that the centre of the galaxy would taste of raspberries…  

Image of the  iso-propyl cyanide molecule recently detected 27,000 light years away.

Image of the iso-propyl cyanide molecule recently detected 27,000 light years away.

Though iso-propyl cyanide itself is not an amino acid, it’s the closest to this type of molecule yet found – mainly because it has a ‘backbone’ of carbon atoms.

But what does the crystal structure of an amino acid look like?

Here the red atoms are oxygen, the pink hydrogen, light blue nitrogen and the brown atoms are the carbon atoms.  Image generated by the VESTA (Visualisation for Electronic and STructual analysis) software http://jp-minerals.org/vesta/en/

Here the red atoms are oxygen, the pink hydrogen, light blue nitrogen and the brown atoms are the carbon atoms. Image generated by the VESTA (Visualisation for Electronic and STructual analysis) software http://jp-minerals.org/vesta/en/

What is it and did the structure come from?

This is L-Serine, one of the 21 amino acids that builds the cells which make up most life on Earth.  Like iso-propyl cyanide it has a backbone of three carbon atoms.  The structure of Serine was first determined in the 1950’s, but the structure we’ve feature here is from a high-pressure study by Moggach et al.  It is #2100237 in the Crystallography Open Database.

 

Sodium hydride, simple yet historic.

What is it?

Though it looks pretty simple, this structure has a special place in history as it was one of the first structures to be discovered with neutron diffraction.  Though the positions of the sodium atoms in sodium hydride were known for some time (from x-ray diffraction), there was still debate if the hydrogen atoms were at the ½, ½, ½ point in the unit cell (a zinc blende structure) or at the ½, 0, 0 point in the unit cell (a rock salt structure).

In the 1940’s a number of researchers realised that instead of using x-rays to diffract off a material, they could use some different radiation – a beam of neutrons.  This was only possible with the development of nuclear reactors, which could provide a steady source of neutrons.

Neutrons interact with matter in a very different way to x-rays.  With  x-rays, the amount they scatter from an atom is proportional to the number of electrons they have in their outer shell – for instance sodium atoms (with 11 electrons each) scatters much better than hydrogen atoms (with only one electron for each atom).  Instead of interacting with the ‘cloud’ of electrons, neutrons diffract by interacting with the nucleus of the atom itself, and are not affected by it’s size, and so have a much more complex trend as you move through the elements of the periodic table.    For instance heavy hydrogen (deuterium) has a scattering cross length from neutrons that is twice that of sodium.

The effect that is to x-rays the structure of sodium hydride looks like this:

The structure of sodium hydride showing the relative scattering of the sodium (yellow) and hydrogen (pink) atoms.

The structure of sodium hydride showing the relative scattering of the sodium (yellow) and hydrogen (pink) atoms.

and to neutrons it looks like this!

And this shows the relative scattering of the heavy hydrogen (pink) and sodium atoms (yellow) to neutron diffraction.

And this shows the relative scattering of the heavy hydrogen (pink) and sodium atoms (yellow) to neutron diffraction.

This meant that the first researchers using neutron diffraction could work out that the structure of sodium hydride was, in fact, the rock salt structure.  This paved the way for many other structures to be solved with neutron diffraction, locating atoms that would be difficult to see with x-rays.
Shull, one of the authors of this work on sodium hydride, was later to share the Nobel Prize in Physics for his development of neutron diffraction.

Neo-mag: The strongest permanent magnet of them all!

What does it look like?

Left: High-resolution transmission electron microscopy image of Nd2Fe14B; right: crystal structure with unit cell marked.  Nd in blue, Fe in red and B in yellow (source: http://en.wikipedia.org/wiki/Neodymium_magnet)

Left: High-resolution transmission electron microscopy image of Nd2Fe14B; right: crystal structure with unit cell marked. Nd in blue, Fe in red and B in yellow (source: http://en.wikipedia.org/wiki/Neodymium_magnet)

What is it?

Many of today’s technological devices that we often take for granted (cars, mobile phones, laptops, memory devices) rely heavily on the magnetic properties of materials. One such property of a magnet that scientists are trying to enhance is its “hardness” – or strength as a permanent magnet. This can be seen in the rare-earth magnetic material Nd2Fe2B, which is considered to be the strongest permanent magnet around and is ferromagnetic (with all magnetic moments aligned in the same direction) for all temperatures up to 400°C. It has an exceptionally high anisotropy, indicating that the magnetic moments have a strong preference to align along one crystallographic direction. When we apply a magnetic field in the opposite direction to the moments, Nd2Fe2B also shows a strong resistance to flip the spins indicating a high coercivity (750–2000 kA/m). It is these properties that make Nd2Fe2B such a useful magnetic material. Another hard magnet with similar properties to Nd2Fe2B is SmCo5.

Where did the structure come from?

Since the development of this material by General Motors and Sumitomo Special Metals in 1982 Nd2Fe2B has found its way into a myriad of modern devices such as computer hard disks, magnetic resonance imaging (MRI) scanners, door locks, electric motors (in particular for cordless devices), hybrid and electric cars, and electric generators. There are, however, caveats to consider when using this material – it is highly corrosive necessitating Ni plating of all parts, and the rare-earth component makes them relatively expensive to produce.

Iron trans-4,4’-azopyridine thiocyanate – Letting things down…

What does it look like? droop1

 

droop2

What is it?

A feature of coordination polymers (or metal-organic frameworks – MOFs) is that many are porous, allowing the passage of gases and solvent molecules in and out of holes within their structures. An interesting feature of the coordination polymer shown here (Fe2(azopyridine)(NCS)2) is that those molecules coming in and out of the structure illicit a change in the magnetic properties and colour of the material.

It happens through a process known as spin-crossover. Magnetism is caused by unpaired electrons in atoms. Electrons have a ‘spin’, which can be either ‘up’ or ‘down’, and usually like to pair up with another electron in various orbitals around an atom. The two electrons in each orbital have opposite spin and thus cancel each other out. In some atoms, however, there are more orbitals available than pairs of electrons, and thus the electrons have a choice of spreading out amongst the orbitals as much as they can, or forming as many pairs as they can. The former case leads to a maximum number of unpaired electrons (and is known as the high spin state), and the later case has the fewest number of unpaired electrons possible, and is known as the low spin state. In spin crossover the atoms can swap between the high spin and low spin states when the temperature is changed, pressure is applied, or the environment around that atom is changed.

In the example shown above, there are iron atoms that are bridged by long linear ligands. Importantly, the iron atoms also have two short thiocyanate ligands on opposite sides. When the coordination polymer is made, it crystallises with ethanol molecules in the lattice that cause the thiocyanate ligands to lay over somewhat. In this state the material swaps from high spin to low spin as it is cooled, and the colour changes. When the ethanol is removed from the lattice, however, the thiocyanates become ‘erect’, standing up and bonding straight-on. This and other resulting movements in the lattice changes the environment around the iron atoms enough to force them to stay high spin at all temperatures. Exposure of the material to ethanol vapour causes it to reabsorb the ethanol molecules, the thiocyanates flop over again, and it returns to the low spin state.

The fact that the presence or absence of ethanol in the structure has such a large effect on the thiocyanate geometry and hence the overall magnetic properties, particularly since they are not directly bonded to the iron atoms, is fascinating and has very interesting implications for tuning the guest responsiveness and signalling in this and other materials. It might also be the first example of “Brewer’s Droop” on a molecular scale…

Where did the structure come from?

Source: “Guest-Dependent Spin Crossover in a Nanoporous Molecular Framework Material”, G.J. Halder, C.J. Kepert, B. Moubaraki, K.S. Murray, J.D. Cashion, Science, 2002, 298, 1762. DOI: 10.1126/science.1075948

CCDC Deposition codes: 189340-189342

The world’s most underappreciated gemstone – Red Spinel

Ruby may be the most iconic gemstone, but often this status has been at the expense of the gemstone spinel. Thanks to the similarity of red spinel to ruby and its extremely high quality, spinels have historically been overlooked and incorrectly labelled as rubies. Some of the most historically iconic rubies aren’t even rubies! Spinels are so often confused for other gemstones that they were never even established as a birthstone (poor spinel).

What is Red Spinel?

The spinel structure has been described in an earlier post and MgAl2O4 is no different. Spinels consist of a nearly ideal cubic close-packed array of oxygen atoms with one eighth of tetrahedral sites occupied by magnesium and one half of octahedral sites filled aluminium. The AlO6 octahedra share edges with each other and are corner sharing with the MgO4 tetrahedra.[1]

Figure 1: Crystal structure of MgAl2O4. The Mg atoms sit within the yellow tetrahedral and the Al atoms sit within the blue octahedra. Image generated by the VESTA (Visualisation for Electronic and STructual analysis) software.

Figure 1: Crystal structure of MgAl2O4. The Mg atoms sit within the yellow tetrahedral and the Al atoms sit within the blue octahedra. Image generated by the VESTA (Visualisation for Electronic and STructual analysis) software.

Pure red spinel is colourless, so to obtain red spinel small quantities of chromium are substituted for aluminium, which is also the reason why rubies are coloured red. Only around 1 % of chromium substituted for aluminium is required within the crystal structure to generate the brilliant red colour. However, the higher the concentration of chromium, the darker the shade of red obtained. There are actually a range of colours that spinel can adopt depending on the foreign element substituted into the basic structure, from orange and pink to purple and deep blue. In fact, blue spinels, which are so coloured due to the presence of iron or cobalt (rarer), are often used as a substitute, and mistaken, for sapphire.[2]

Figure 2: Spinel gemstones come in a diverse range of colours. (Image obtained from http://www.gia.edu/spinel)

Figure 2: Spinel gemstones come in a diverse range of colours. (Image obtained from http://www.gia.edu/spinel)

While rubies and sapphires are the more famous and well known gemstones, spinels are equally comparable in appearance and arguably better due to the deeper, richer colours which are more readily obtainable (especially compared to ruby). The heightened brilliance of spinels is a result of being singularly refractive. This means that the gemstone only has a single refractive index, which measures the amount by which light is slowed (and thus bent) when entering the gemstone. In comparison, the overwhelming majority of gemstones exhibit birefringence which results in the splitting of light when it enters the crystal (see below). The most well known singularly refractive gemstones are garnet, diamond and spinel.

Figure 3: An example of a crystal exhibiting birefringence. A singularly refractive crystal would only produce a single image. (Image obtain from http://www-g.eng.cam.ac.uk/CMMPE/lcintro4.html)

Figure 3: An example of a crystal exhibiting birefringence. A singularly refractive crystal would only produce a single image. (Image obtain from http://www-g.eng.cam.ac.uk/CMMPE/lcintro4.html)

A Checkered Past

The high quality of spinels and fact that they are compositionally similar to rubies has meant that historically they were treated as the same crystal. As a result, there are many infamous rubies which are actually just red spinels. The most well known of these is the Black Prince’s ruby which is set in England’s Imperial State Crown and displayed in the Tower of London. This particular gem has been passed from several Moorish and Spanish Kings before reaching Edward, Prince of Wales (the Black Prince) in 1367. The gem has survived fires, attempted theft and World War II bombing raids to become one of the centerpieces of England’s Crown Jewels.[3]

Spinel Applications

Spinels are not just aesthetically pleasing; they also have some interesting applications. The singularly refractive nature of spinel in combination with the relative ease of producing synthetic spinel has led to its use as high strength window material in military applications. In addition, the relative ease and low cost associated with its manufacture, spinel has come to replace the previous state-of-the-art material, sapphire.[4]

Finally, since spinels are so underappreciated, it is much cheaper than ruby! So it is possible to buy polished and cut spinel gemstones which look almost identical to rubies at a fraction of the cost. So there is some benefit to being the underdog of the gemstone world.

MgAl2O4 spinel is number 1010129 in the Crystallographic Open Database.

[1] Passerini, L. Gazzetta Chimica Italiana 1930, 60, 389

[2] Shigley, J. E.; Sloclzton, C. M. Gems and Gemology 1984, 20, 34.

[3] Spinel <http://www.gia.edu/spinel&gt; (Accessed 09/14)

[4] Mroz, T. J.; Hartnett, T. M.; Wahl, J. M.; Goldman, L. M.; Kirsch, J.; Lindberg, W. R. SPIE Proceedings 2005, 5786, 64.