Seasons greetings. The crystal structure of Cocoa Butter.

What does it look like?

Image generated by the Mercury Crystal structure visualisation software from the Cambridge Crystallographic Database Centre 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?

Who’d have thought that a bundle of hydrogen, carbon and oxygen could be so tasty!  Here is the structure of cocoa butter fat, one of the main tasty ingredients in chocolate.  Chocolate is a very sophisticated material, and requires the right blend of sugar, milk and cocoa butter fats for it to taste right.  An added complication is that you can get different crystal structures of cocoa butter depending on how you solidify it.  These have different melting temperatures, so can affect the whole experience of the chocolate tasting.  The type you want to have is called ‘Type V’ or ‘Beta 2’, and is why chocolate has to be tempered – to make sure you get the right type.

Where did the structure come from?

The image was generated using the structure determined by van Mechelen et al. in 2006. They used synchrotron x-rays to determine this structure and were trying to understand how fat bloom (which is, in fact, a different structure of cocoa butter ‘type VI’) forms in chocolate.

It’s making a list – Santite

What does it look like?

Purple atoms (potassium) interwoven with borate (green boron and red oxygen) chains.  The empty hydrate, ice VXI. Image generated by the VESTA (Visualisation for Electronic and STructual analysis) software http://jp-minerals.org/vesta/en/

Purple atoms (potassium) interwoven with borate (green boron and red oxygen) chains. The empty hydrate, ice VXI. Image generated by the VESTA (Visualisation for Electronic and STructual analysis) software http://jp-minerals.org/vesta/en/

*sings*

‘and checking it twice, gonna find out who’s nautghy or nice….’

SANTITE is on Crystallography 365!

What is it?

It’s a little bit of a stretch, we know (go on, you go and look for more Christmas-inspired minerals!) but here is Santite! This mineral was first identified from synthetic means, it’s crystal structure found in 1937. Then in 1970 a group of Italian scientists identified this material in the hills of Tuscany (hard field work, eh?). They named it after a former director of the Museum of Natural History of Italy, George Santi.

It’s a very rare borate mineral, where the boron hooks up to oxygen and (rather pleasingly) forms paper chain like features running thought the structure – interwoven with potassium ions.

Where did the structure come from?

Santite, or its synthetic name potassium acid dihydronium pentaborate #9011411 in the Crystallographic Open Database, and was found by Zachariasen in 1937.

Methane under pressure – the strange co-incidence of methane B

Hello, Helen here – coordinator of the blog.  As we look to the ‘sprint finish’ to the end of the year I thought I would write about a structure that I’m personally connected too – in fact it got me a PhD!

What does it look like?

The structure of methane B, the red spheres are the carbon atoms found at the centre of the molecules. This was found with high-pressure x-ray synchrotron diffraction and unfortunately did not reveal the positions of the hydrogen atoms.

The structure of methane B, the red spheres are the carbon atoms found at the centre of the molecules. This was found with high-pressure x-ray synchrotron diffraction and unfortunately did not reveal the positions of the hydrogen atoms.

What is it?

Normally you only think of methane as a gas, but if you cool it to -145 °C it will liquefy, and then pretty soon after solidify to a solid that is quite like jelly (known a plastic solid – argon gas does the same thing).

But another way to freeze methane, like water too, is to compress it to very high-pressure. 5 GPa in fact (which is equivalent to five fully-grown African elephants standing on one stiletto heel. At this point methane freezes to a structure know as methane A, which we wrote about earlier this year. But if you keep squeezing methane, up to 8 GPa, then it undergoes a change to a new structure that, until yesterday, was a bit of a mystery.

This form of methane is known as methane B, and is a rather complex cubic structure with 58 molecules needed in each repeating unit to describe it. It’s pretty important as the pressure range that it is stable over spans to pressures that you would find inside the giant planets Uranus and Neptune. These wonders of our solar system are both thought to have an interior of mainly methane, water and ammonia, so knowing the structure of methane at these pressures really helps our understanding of them.

The rather strange thing about this structure is that we’ve seen it before – in manganese. Alpha-manganese also take up the same complex structure with 58 atoms all arranged the same. Not a pairing that you immediately put together, methane and manganese, but this is perhaps giving us a very vital clue as to how methane interacts at high-pressures.

Where did the structure come from?

This structure was published YESTERDAY in the Journal of Chemical Physics and was found, well, by me!  The structure probably looks a little strange as I was only able to find the carbon atom positions (i.e. the centres of the methane molecules).

It’s so shiny new that I’ve not got round to putting it into a database yet, but you can read the paper for free for the next 30 days! Though I promise I will put it into the Crystallography Open Database, first thing in the new year.

Molecule of deceit – raspberry ketone

What does it look like?

The crystal structure of the raspberry ketone molecule, drawn with VESTA.

The crystal structure of the raspberry ketone molecule, drawn with VESTA.

What is it?

This small molecule packs a lot of flavour.  Raspberry ketone is one of the most expensive food additives currently about, used to add that raspberry fruity-ness to all sorts of things.  Part of the reason that it’s so expensive is because there’s actually very little of it in nature (it doesn’t take much raspberry ketone to make your raspberry taste good!).  But it can be manufactured synthetically much cheaper – and probably the reason that there’s so many raspberry flavoured things about.  This means that knowing the crystal structure is very important, as it can be used to check that you have synthesised the right molecule to add to your ice-cream!

The reason it’s a deceitful molecule is that recently it’s been marketed as a weight-loss supplement, but there is no clinical evidence that it does help humans loose weight.  The claims come from a study that showed some effects in rats. In the small doses used for flavour this molecule has little effect on our bodies, but the concerning thing is the companies suggesting people take large does for weight loss – we just don’t understand the effect these would have on our bodies. 

Where did the structure come from?

The crystal structure of the raspberry ketone molecule was reported by Wang in 2011, in Acta Crystallographia E. The structure is #2230481 in the Crystallography Open Database.

An correction to an earlier claim – Ice XVI is the newest form of ice!

What does it look like?

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

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

What is it?

Last month, after a year of monthly ice structures, we profiled the latest discovered ice structure – ice VX.  In a great example of the fact that science never stands still, last week a paper was published describing a new phase of ice – ice XVI.

This new form is a little different, in that we’ve kind of known about it for a while.  We mention clathrate hydrates before on the blog.  These are crystal structures that are made up of water cages with other small molecules, for instance methane, sitting inside them.  But can these water cages exist on their own – without anything sitting inside?

That what the investigators in this new study did, they form the sII type of clathrate with neon, and then cooled it down to 4 K and put a vicious vacuum on it to suck out all the neon atoms!  They were left behind with just the water cages, allowing them to declare that they had made a new form of ice!

Where did the structure come from?

The discovery of ice XVI was announced in the paper by Falenty et al. in the journal Nature last week.  What’s nice is that this news coincides with Nature making all of their papers free to view – so you can all read up on this if you like.  The structure parameters we’ve plotted have come from a CIF they they supplied in their supplementary information.

The researchers used neutron diffraction, collected at the Institute Laue Lavange, and theoretical work to show that they had sucked out all the neon atoms, and that this was a new phase of ice.

A rock with a cleavage – Augite

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?

Augite is a very dark green to black colourer mineral.  It is made up of silicate chains with principally magnesium, iron, calcium and aluminium atoms sitting between them.  There’s quite a variation in which of these elements are found in the structure, but the chains mark the structures as belonging to the pyroxene family of minerals – like Jadeite.    One of the striking features of this mineral is its, ahem, cleavage.  Many minerals will split open along particular directions, this is usually from a weakness in their crystal structures.  Augite has two prominent cleavages, which meet at about 90 degrees.

Where did the structure come from?

The crystal structure of wurtzite is #1200006 in the open crystallography database.

Now you’ve seen everything – superconductive concrete

What does it look like?

AMS_DATA-6What is it?

In 2006 a senior scientist remarked in the journal Nature ‘If that superconductors is made by doping concrete, I’ll know it’s time for me to retire’.  We wonder if, the very next year, he was clearing his desk and getting his gold watch with the discovery of what happen when you dope today’s crystal structure.

Dodecacalcium hepta-aluminate (12CaO.7Al2O3) – often just known as C12A7, is another of those useful crystal phases that crop up in cement, along with tricalcium aluminate.  It even occurs in nature, as the mineral Mayenite.  In the structure the calcium and aliuminium oxides form cages, which hold small amounts of oxygen ions.  A group in Japan, discovered that if you can replace the oxygen ions with electrons you can make the material behave like a metal, which is rather odd for concrete.

Crystal structure of C12A7. The cube is a unit cell. Two of the 12 baskets in the crystal contain oxygen ions. From http://techon.nikkeibp.co.jp/english/NEWS_EN/20070618/134409/

Crystal structure of C12A7. The cube is a unit cell. Two of the 12 baskets in the crystal contain oxygen ions. From http://techon.nikkeibp.co.jp/english/NEWS_EN/20070618/134409/

Then in 2007, the cooled the doped  to 0.4 K and found that C12A7 becomes a superconductor! The key to this was how the electrons can move between the cages in the structure.

Where did the structure come from?

The crystal structure of Mayenite was first discovered by Buessem and Eitel in 1936, and is #1011034 in the crystallography open database.