What is our planet made out of? 3) Wadsleyite

What does it look like?

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

What is it?

As you delve deeper into our planet not only does the heat start increasing but the burden of the weight of rocks above means that pressures start rising too. At approximately 410 km under our feet these pressures and temperatures are enough to change the structure of olivine to sometime new. What happens is that the silica tetrahedral pair up to S₂O₇ groups, and the magnesium atoms are spaced between these.  Though, on Earth, it is thought to exist only within the mantle it has been found in a meteorite on the surface. It’s thought that in this case wadsleyite could have been formed by shock pressures from impacts out in space.

Where did the structure come from?

The structure of wadsleyite, from a crystal studied while it was under 9 GPa of pressure is #9002372 in the open crystallographic database.

What is our planet made out of? 2) Olivine

What does it look like?

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

What is it?

Many olivine crystals have a lovely grass-green colour to them. Photo taken by Azuncha

Olivine, like feldspar, comes in two main types (known as forsterite and fayalite) but unlike the feldspar minerals the crystal structure of these are both the same.  The difference is that forsterite has magnesium atoms living in between the silicate tetrahedra, and fayalite had iron instead. Most natural olivine actually has a mixture of iron and magnesium atoms within them. Olivine is an important mineral in the crust under the sea, but also in the first part of the mantle – the increasingly hot beginning of our Earth’s interior. Olivine is also, apparently, the ideal rock to use as hot stones in saunas. This is because of its high density and resistance to weathering.

Where did the structure come from?

The structure of olivine as originally determined by WL Bragg is #1010497 in the open crystallographic database.

What is our planet made out of? 1) Feldspar.

To take us over the Easter holidays we’ve a little bit of a theme lined up. What are the materials that make up our planet? It’s important when considering this to realise that most of the volume of material on the Earth is actually under our feet.

The internal structure of the Earth, by Kelvinsong

But lets start on the outside, looking at a group of minerals in the Earth’s crust.

What does it look like?

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

What is it?

Feldspar mineral by Rob Lavinsky

We could write a whole week of posts about feldspar minerals, there is that many of them. When you consider them all together they make up a large proportion of the Earth’s crust.  They all have the same arrangement of silicate tetrahedral (the blue shapes with red oxygen atoms at the corners), but differ in the elements that are stuffed into the channels. You usually can find some aluminium in there, but other elements found in feldspars are potassium (as shown by the purple atoms), sodium and calcium. The bigger elements, like calcium, can actually distort the silica, so that the whole structure of the material changes.

This strain from different elements means that there are two main types of feldspars found on Earth, known as Orthoclase and Plagioclase. These can grow together in some cases will give a nice pearly lustre to the resultant material, which is known as moonstone.

Where did the structure come from?

As explained, the dimensions of the feldspar crystal structures are highly dependent on the elements that are stuffed in the channels of the tetrahedral. Here’s a great reference with lots of crystal structure examples of the more symmetric monoclinic feldspars.

Botox: Toxic medicine

What is it?

Botulinum toxin A –- more commonly known today as Botox – is a neurotoxin produced by the bacterium Clostridium botulinum. It acts on nerves at the point at which they meet the muscles that they control, where it disrupts transmission of chemical messenger molecules causing muscular paralysis. Botulinum toxin is one of the most potent human toxins and C. botulinum infection causes botulism, a serious paralytic illness. Thankfully botulism is rare. More common today is the deliberate localised injection of the toxin for cosmetic purposes, where its paralytic properties can be used to banish wrinkles, laughter lines, and the ability of professional actors to convincingly convey normal human facial expressions. Botox also has a number of important medical applications and is now routinely used to treat eye misalignment (strabismus), excessive sweating (hyperhidrosis), migraine and urinary incontinence, with no side effects upon acting ability yet reported.

What does it look like?

Botulinum toxin A is made up of three functional domains which each play a distinct role in delivery and action of the toxin. The receptor-binding domain (yellow and red) is important for entry into the nerve cells where the toxin is initially encapsulated within a small membrane bordered compartment called an endosome. Next the toxin’s translocation domain (green) induces a pore in the compartment to allow transport of the enzymatic domain (blue) out of the endosome and into the cytoplasm of the cell where it cuts target proteins in the nerve to block chemical messenger release and induce paralysis. This image was generated using PDB ID 3BTA¹ and the molecular graphics software PyMOL.

Where did the structure come from?

The crystal structure of botulinum toxin A was first published ¹ in the scientific journal Nature in 1998, using toxin isolated from liquid cultures of Clostridium botulinum.

1. Lacy et al., Nature (1998) 5: 898-902

 

X is for xenotime

What is it?

So far we’ve had a crystal structure starting with every letter of the alphabet, except one. Xenotime is not some kind of bizarre extra-terrestrial timekeeping system, but is in fact a mineral. Ironically, it was supposed to be spelled with a “k”, after the ancient greek kenós (κενός) which means “vain”, but an early misprint replaced the “k” with an “x”, which stuck. The main component of xenotime is yttrium orthophosphate. It also contains relatively high levels of uranium and thorium impurities, which make it very useful for U-Th-Pb isotopic dating of sedimentary rocks.

What does it look like?

A xenotime crystal. Source: http://www.mindat.org

 

 

Yttrium orthophosphate, the main component of xenotime. Yttrium atoms are shown in green, phosphorus in purple, and oxygen in red. Image generated using the VESTA (Visualisation for Electronic and STructual Analysis) software http://jp-minerals.org/vesta/en/

Where did the structure come from?

The structure was determined by M. Strada and G. Schwendimann in 1934, and can be found in the Open Crystallography database (#1011143).

Collagen: Triple strength

What is it?

The best designs – in architecture, engineering, software development – are those that effectively solve a functional problem. The same is true in biology, and scientists have long since appreciated that a protein’s design is intrinsically related to the particular function that it carries out. This idea is exemplified by collagen, a highly abundant protein in the body found in the connective tissue of tendons, skin and ligaments. Collagen has a triple helical structure in which three individual chains are wound together to form a tightly organized protein rope. This organization lends collagen a high tensile strength enabling it to function as a robust structural protein that provides a scaffold within tissue and connects it to bone.

What does it look like?

Collagen is made up of three polypeptide chains (red, green, blue) wound tightly in a triple helical structure. The individual polypeptide chains have a very distinctive and unusual sequence in which every third amino acid is a glycine (the smallest amino acid) that faces into the interior of the protein rope. This pattern allows the three chains to pack snugly against each one another without clashing. Collagen also has an unusually high proline content. Proline is a rather geometrically constrained amino acid and its abundance helps the individual chains to spontaneously adopt a stable left handed helical conformation.

Where did the structure come from?

This structure is of a model peptide of Type III collagen that assembles as a homotrimer. It is a small part of the much larger protein that naturally exists in the body but it reveals the triple helical rod like structure of the protein. It was reported in Nature Structural Biology in 1999 and is PDB ID 1BVK¹.

1. Kramer et al., Nature Struc. Biol 1999. 6:454-457

An Explosive Result – Mercury (II) Fulminate

What does it look like?

Structure taken from original paper (see below)

What is it?

Mercury fulminate is what’s known as a “primary explosive”, being highly sensitive to shock and friction, it was commonly used as a detonator for dynamite and in percussion caps on muzzle loading firearms throughout the 19^th and 20^th centuries. Initially discovered in the 17^th and 18^th centuries, one early chemist, Johannes Kunckel noted:

“I once dissolved silver and mercury together in aqua fortis, and, having added spiritus vini, set the vessel aside in the stable. When by the next day, its temperature had risen, there occurred such a thunder clap, that the groom thought someone had shot at him through the window, or that the very devil had appeared in the stable. But I realized that it was my experiment that had exploded.”

Although some initial investigations were carried out by F. D. Miles as early as 1931, it wasn’t until 2007 that the full crystal structure of this molecule was first published.

Where did the structure come from?

Structure originally published by W. Beck, J. Evers, M. Gobel, G. Oehlinger, T. M. Klapotke, Z. Anorg. Allg. Chem. 2007, 1417-1422.  An excellent history on the discovery of fulminates and their role in history is given by F. Kurzer J. Chem. Ed. 2000 77, 7, 851-857

 

Hearing radio waves with galena

What does it look like?

What is it?

A collection of galena crystals, photo by Rob Lavinsky

Galena, which is a form of lead (II) sulfide, is the most important lead ore mineral. The structure image probably looks quite familiar, as Galena takes up the ‘classical’ rock salt structure. The separation of the metal lead atoms in the structures makes galena a natural semiconductor, one of the first materials to be indentified with these properties. This feature was exploited in ‘crystal radio’ sets. Like the telluride mineral that we featured last week, galena must always be handled with great care as lead is very toxic to humans.

Where did the structure come from?

Galena is #9000001 in the open crystallography database.

Cubic ice – does it exist or not?

What does it look like?

The diamond-like arrangement of water in ice Ic. Image taken from https://www.uwgb.edu/dutchs/Petrology/Ice%20Structure.HTM

What is it?

We’ve already introduced you to some strange ice structures, but both ice VI and ice IX only exist under pretty special conditions. So this month’s ice structure is the other form of solid water that has been proposed to form in our own world, cubic ice or ice Ic. This form of ice it thought to form in our atmosphere, from water droplets that are cooled very fast. Indeed it is often seen in protein crystallography experiments, where the protein is cooled fast to preserve it, and the water around it freezes.

Instead of forming the hexagonal arrangement of ice Ih, at this fast cooling speeds ice was though to form in a diamond-like arrangement, as pictured above.   It was thought that the existence of this different form of ice explained the atmospheric phenomena known as ‘Scheiner’s halo’. The idea is that this cubic form of ice could cause sunlight to refract by 28˚

But ever since it was identified ice Ic has been in the centre of a scientific debate, does it really exist? Or is it a stacking fault in ice Ih? Latest results supports the latter conclusion, but it goes to show how little we still know about the simplest of substances, water.

Where did the structure come from?

The structure of ice Ic was first proposed by Mayer and Hallbrucker in 1987, but was first proposed as an explanation for ‘Scheiner’s halo’ by Whalley in 1981.

Murder most foul – Potassium Cyanide

What does it look like?

Image produced by Vesta crystal imaging software using data from the Crystallography Open Database #5910129

What is it?

Perhaps more popularly associated with the crime underworlds of Agatha Christie or clandestine operations in a war torn Europe, potassium cyanide is probably one of the most well-known and potent poisons. Very similar in appearance to regular white sugar, only 200mg would be enough for a lethal dose, so you wouldn’t want to get the two mixed up!

The crystal structure of potassium cyanide is very similar to that of sodium chloride (rock-salt), forming a cubic lattice. The diatomic cyanide ions (CN^–) spin so rapidly that their time averaged shape appears spherical, with differentiation between the two atoms only possible at low temperatures and high pressures. 

Where did the structure come from?

Potassium cyanide has been the subject of numerous structural studies, but the first has been attributed to Richard. M. Bozarth J. Am. Chem. Soc. 1922 44, 2, 317-323 and so is one of the earliest crystal studies!