Celebrating one of the founders of the field – the crystal structure of Braggite

‘The gift of expression is important to them as scientists; the best research is wasted when it is extremely difficult to discover what it is all about …’  WL Bragg

The motivation behind this blog was to show the world as many crystal structures as we could. We’re hope that so far, as we’re now three months in, we’ve shown off the diverse world of crystallography and given a bit of an insight into the sciences that it is shaping.   We’re exploiting the fact, that no matter what the field, crystallographers describe their crystal structures in a standard format and often store them in publicly assessable databases for the world to see. We’re hoping that us picking out a few (365 out of nearly a million structures available across various databases) is expressing to the world what our science is about.

WL Bragg after winning the Nobel Prize for Physics in 1915

WL Bragg after winning the Nobel Prize for Physics in 1915

Today is the birthday of one of the founders of our field, WL Bragg. Together with his father, WH Bragg, and Max von Laue they put together the methods and equations that describes how the phenomena of diffraction can lead to an understanding of where atoms are in a structure.   WL Bragg still is the youngest recipient of the Nobel Prize for Physics, he was 25 when he was recognised for his efforts in determining the first crystal structures from diffraction. He didn’t stop there, and the efforts that he put into expanding this field and teaching others massively increased the reach of the technique, especially in the determining of the structure of DNA.

So it’s a good day to write about a mineral that was name after WL Bragg and his father.

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?

Braggite is the mineral name for a mixed metal sulfide, composed of palladium, platinum and nickel, found within palladium and platinum ore deposits in South Africa. It was named after the Braggs because it the first mineral to be discovered with by X-rays.  This is because it looks very similar to other metal sulfides it forms near, Cooperite and Laurite, and it was only when sample were investigated with x-ray diffraction that it was realised some of the samples had a very different crystal structure.

Where did the structure come from?

Though Braggite was discovered in 1932, it wasn’t until 1973 that the atomic arrangement in its structure was described with single crystal x-ray diffraction. It is structure #9007574 in the open crystallography database.

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The crystal structure rainbow – Glowing in UV, Andersonite

Just to extend on our theme for this week a little – how about a crystal structure that glows in UV light?  It’s also one of the minerals in this post we mentioned yesterday, so it ties up things very nicely!

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?

Andersonite is a rare Uranium carbonate mineral that was first found in Arizona in the US. It’s fluorescent and will glow a yellowy-green under UV light. As you can see hinted in the picture, it’s crystal structure is quite complex – with units of carbonate (CO3, brown carbon atoms surrounded by red oxygen atoms), sodium (yellow atoms) and calcium (blue) atoms which all surround the uranium (green) atoms. Because of the way uranium are made up, they can bond with up to 6 other atoms at a time. This makes for quite a variety of minerals that it can form.

Where did the structure come from?

The crystal structure of Andersonite was determined in 1981, and it #907645 in the open crystallography database.

A very rare gem – Uvarovite

In our travels on the internet we stumbled upon this page on ’10 beautiful minerals you won’t believe come from Earth’.   Fabulous pictures by Ryoji Tanaka, but what (we hear you cry) are the atomic arrangements behind these? We’ve covered one of them already (Gold) but we’ve picked out a couple of the others for this weekend.

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?

Uvarovite green crystals from Saranovskii Mine, Urals Region, Russia.  Photo by Rob Lavinsky, iRocks.com

Uvarovite green crystals from Saranovskii Mine, Urals Region, Russia. Photo by Rob Lavinsky, iRocks.com

This is the atomic arrangement of Uvarovite, which one of the rarest garnet minerals and found in the Urals of Russia. If it looks familiar… then it’s because you recall our post back in January on Garnets in general. Uvarovite is particular because in between the silicate tetrahedrons (show by blue silicon atoms sitting in the middle of four red oxygen atoms) sits calcium (grey atoms) and chromium (dark blue) atoms. It’s these metal atoms, which give this mineral its beautiful dark green colour.

Where did the structure come from?

Like many natural minerals, the structure of Uvarovite is complicated by the number of other elements that can substitute into the structure. The structure we’ve shown here was determined from a synthetic Uvarovite crystal in 2002; it is number #9007149 in the open crystallography database.

Spins and Arrows: the Magnetic Story of MnO

What does it look like?

MnO_1

What is it?

It’s manganese oxide or MnO, mineral name manganosite. Chemically, it’s just a face-centred cubic structure structure like NaCl. The chemical structure was published in 1926.

 But MnO doesn’t just have a chemical structure, it also has a magnetic structure.

 Many elements in the periodic table have a magnetic moment, which means that each atom acts like a tiny magnet with its own north and south pole.  The arrows coming out of the manganese atoms in the image represent the direction of the moments- which way the north pole is pointing if you like. The magnetic behavior of everyday objects- such as a magnet picking up iron filings- is due to the collective behavior of all these atoms.

Iron is an example of a ferromagnet. A typical lump of iron consists of a myriad of randomly oriented micron sized crystal grains (or domains). Within each grain the moments are lined up in the same direction. If you persuade enough of the domains to line up, you create a magnet.

By the end of the 1920’s, physicists already had a reasonable understanding of ferromagnetism: it was one of Heisenberg’s first applications of quantum mechnics.  But some materials displayed magnetic behavior far from the ferromagnetic idea, and the French physicist Louis Neel suggested that the behavior could be explained in the magnetic moments alternate in direction – an antiferromagnet.

So given a hypothesis that explained the data, two more things were needed: a mechanism to explain why how the manganese atoms could interact given there was an oxygen atom in the way, and some sort of independent direct evidence of  the ordering. The mechanism of superexchange was suggested by H. A. Kramers, and later elucidated by P.W. Anderson: the electrons in the oxygen participate in the interaction.

The direct evidence was observed by Shull and Wollan in the early 1950’s using the then new technique of neutron diffraction. The neutron has a spin, so it too is like a little magnet which interacts magnetically with the atom’s magnetic moment. Because the manganese moments are arranged up-down-up, the magnetic unit cell is twice as big as the chemical unit cell.  Shull and Wollan observed an extra diffraction peak at low temperatures not seen in the magnetically disordered room temperature structure.

Here’s a picture of the structure again. This time, only the magnetic moments of the manganese are shown as blue and red arrows highlighting their alternate directions. The smaller cube shows the chemical unit cell. The larger cube shows the magnetic unit cell.

MnO_2

Magnetic crystallography is now a huge field in its own right. Louis Néel won the Nobel Prize for Physics in 1970 for his contributions to magnetism. Shull won the 1993 Physics Nobel for developing neutron diffraction.  Anderson won the 1977 Physics Nobel for his contributions to solid state physics.  Kramers died in 1952.

Where does it come from?

The chemical structure of MnO is #1010393 in the Crystallography Open Database.  The figures were produced with VESTA.

A celebration of x-rays – Roentgenium

Roentgen's X-ray image of his wife, Anna's, hand. On seeing this she exclaimed 'I have seen my death'

Roentgen’s X-ray image of his wife, Anna’s, hand. On seeing this she exclaimed ‘I have seen my death’

On this day, 169 years ago the man who was to receive the very first Nobel prize in physics was born. Wilhelm Conrad Röntgen, was working with a cathode ray tube when he made his discovery. He had shielded most of the tube, and found that when it was on it still caused a fluorescent effect on a plate covered with barium platinocyanide even two meters away. He named these invisible waves, X-rays, indicating the unknown nature of them at the time. Roentgen, who is largely recognised as the father of diagnostic radiology, refused to take out any patents on is discoveries, and donated the money his receive from his Nobel prize to his university.

In 2004, it was decided to name element 111 after Röntgen. This element had first been discovered in Germany in 1994 and its most stable isotope (Röntgenium 272) has a half-life of only 26 seconds. Writing about the crystal structure of Röntgenium is a little different to the others we’ve posted about, as there’s never been enough of the material made to actually determine its crystal structure! It’s predicted to have a body centred cubic structure, which is (as it sounds) a cubic structure of atoms with one atoms sitting in the middle of these. There are a number of other elements that take up this structure, such as the alkali metals Lithium, Sodium and Potassium. Here we’ve pictured Potassium, which is #9008539 in the open crystallography database.

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/

But mainly we wanted to say thanks to Röntgen for discovering X-rays and making the science of diffraction and crystallography possible.

The crystal structure rainbow – Imperial violet

What does it look like?

—Image generated by the Mercury crystal structure visualisation software http://www.ccdc.cam.ac.uk/Solutions/CSDSystem/Pages/Mercury.aspx

—Image generated by the Mercury crystal structure visualisation software http://www.ccdc.cam.ac.uk/Solutions/CSDSystem/Pages/Mercury.aspx

What is it?

What are our statuses of wealth? A sporty car? A swimming pool? Or maybe a beach house? In the time of Pliny the Elder a sure sign of a wealthy status was to wear purple.  To colour material purple 2000 years ago required a dye known as Tyrian purple, which at the time cost as much as silver did.  Made from thousands of crushed shells, much of the early production of this material was in the ancient city of Tyre (hence the name).

Pliny the elder wrote about the production of Tyrian purple dye in his ‘Natural History’

The most favourable season for taking these fish [i.e., shellfish] is after the rising of the Dog-star, or else before spring; for when they have once discharged their waxy secretion, their juices have no consistency: this, however, is a fact unknown in the dyers’ workshops, although it is a point of primary importance. After it is taken, the vein is extracted, which we have previously spoken of, to which it is requisite to add salt, a sextarius [just over 560 grams] about to every hundred pounds of juice. It is sufficient to leave them to steep for a period of three days, and no more, for the fresher they are, the greater virtue there is in the liquor. It is then set to boil in vessels of tin [or lead], and every hundred amphoræ ought to be boiled down to five hundred pounds of dye, by the application of a moderate heat; for which purpose the vessel is placed at the end of a long funnel, which communicates with the furnace; while thus boiling, the liquor is skimmed from time to time, and with it the flesh, which necessarily adheres to the veins. About the tenth day, generally, the whole contents of the cauldron are in a liquified state, upon which a fleece, from which the grease has been cleansed, is plunged into it by way of making trial; but until such time as the colour is found to satisfy the wishes of those preparing it, the liquor is still kept on the boil. The tint that inclines to red is looked upon as inferior to that which is of a blackish hue. The wool is left to lie in soak for five hours, and then, after carding it, it is thrown in again, until it has fully imbibed the colour.

Where did the structure come from?

Though it was synthesised in 1903, the crystal structure of Tyrian purple was not determined until 1980 with x-ray crystallography by Larsen and Watjen in 1980. The crystallographic information file for this structure can be found in the Cambridge Structure Database, refcode DBRING01

The crystal structure rainbow – Indigo in your batteries?

What does it look like?

The indigo carmine structure found by Yao et al.  Image take from thier paper.

The indigo carmine structure found by Yao et al. Image take from thier paper.

What is it?

This molecule is colourful, and perhaps an answer to humankind’s energy storage issues? Indigo carmine (or 5,5′-indigodisulfonic acid sodium salt) already has a number of uses because of its colour. This molecule can be used as an indicator of acidity. It also has medical uses, often being used to investigate how a urinary tract is working. It turns your pee indigo blue and can easily be broken down by your kidneys.

But some investigators have looked into the possibility of it being used as a battery material. This is because of the sodium ion in the structure (in the picture above these are purple). Much of the focus on increasing the effectiveness of batteries is investigating lithium ion batteries, but there’s an issue in that there’s only so much lithium the world has to offer. There’s a lot more sodium available, but it’s difficult to use as a battery material because the sodium atoms are quite a bit bigger than lithium ones (and you need them to be able to flow past the rest of the material in the electrode). Electrode materials (those that store up the charge in batteries) are often made out of inorganic materials, which are themselves quite big atoms. The difficulties is finding an electrode that can reproducible give away it’s sodium to generate charge, but then take it back to store up energy again. Could an electrode be made out of a smaller, organic material?       

Where did the structure come from?

These Japanese researchers investigated the potential that indigo carmine has as a battery material, and monitored how the structure changed as it was charged up and as the energy was used. As they were preparing the same they saw that the structure had changed, and this new structure had lots of ‘potential’ as an electrode material.