A crystal sandwich – Vermiculite

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?

Vermiculite is a layered silicate (also known as a phyllosilicates) mineral.  It is very similar to Kaolinite in that respect by differs in the fact that it has an extra silicate layer (the blue tetrahedrons) that sandwiches the layer of magnesium (in this case) and oxygen (which are you can see as orange tetrahedrons).  These layers themselves then sandwich other elements (often water molecules with some small metals) that can sit in-between.  This layered structure means that the structure of a vermiculite and swell up to take up elements from its surroundings, but can shrink at high temperatures when the water is expelled from the sandwich.

Where did the structure come from?

There’s a lot of variation in the elements found in the vermiculite structure.  This particular example is magnesium vermiculite, and is #9000146 in the open crystallography database.

Saturating your food – Palmitic acid

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?

As we move into the holiday season, here’s a molecule that we’ll probably be disgesting quite a bit of over the next month or so – palmitic acid.  Palmitic acid is one of the fatty acids, and along with stearic acid is one of the simple linear molecules of this kind.  It is, in fact, the most common of these essential molecule found in the animals, plants and microorganisms around us.  Fatty acids are an important source of fuel for our bodies, especially effecting –  it is thought – to our heart and skeletal muscles.

Though you can get ‘free’ palmitic acid in nature, just the long chain of the molecule existing by itself, most palmitic acid is found in the form of triglycerides.  We’ve met these molecular on the blog before, in the form of cocoa butter.  Today we’ve featured the structure of pure tripalmitin, a triglyceride where each of the branches are made from a palmitic acid molecule.

Where did the structure come from?

The structure of tripalmitin was solved by van Langevelde et al. in 1999, and is #2003033 in the Crystallography Open Database.

Surreal Microscopic Environments – Negative Crystals

A few months ago a story did the rounds about a “negative crystal floating in space” [1] which was accompanied by a rather spectacular image (Image 1).

Image 1: Negative crystal in spinel. Image by Danny Sanchez

Image 1: Negative crystal in spinel. Image by Danny Sanchez

This picture was described as a negative spinel and was one of the most perfectly formed crystal inclusions found and photographed by Danny Sanchez using photomicrography techniques [2]. This unique photography technique allows small regions within crystals to be photographed with exceptional clarity, creating extraordinarily surreal images of crystal inclusions. Negative crystals aren’t the only type of crystal inclusion however, and they certainly aren’t the only ones to produce stunning images.

Crystal Inclusions

Generally speaking, negative crystals are a specific kind of crystal inclusion. Inclusions are when a foreign material is trapped within a host crystal. The foreign substance can be solid, liquid or gaseous and can become trapped within the crystal either during its growth or once the host crystal has formed. The exact method of inclusion formation depends on the type of inclusion and the conditions under which the crystal was grown [3].

Solid inclusions

The most well known solid inclusions are ancient insects or plant life suspended in amber. However, solid inclusions can also include different types of gemstones embedded inside another crystal, typically quartz (Image 2).

Image 2: Rutile on hematite in quartz. Image by Danny Sanchez

Image 2: Rutile on hematite in quartz. Image by Danny Sanchez

These mineral inclusions either form simultaneously with the host crystal or were pre-existing and the host crystal has grown around it, encasing the foreign material. In the case of quartz which usually forms in hydrothermal conditions (basically a hot water soup of dissolved minerals) the included gem existed in the solution prior to the growth of the quartz and over time the quartz grows around it (Image 3).

Image 3: Purple and blue fluorite in quartz. Image by Danny Sanchez

Image 3: Purple and blue fluorite in quartz. Image by Danny Sanchez

Alternatively, as many crystal growth conditions are under high temperature and pressure conditions and in aqueous media, liquid inclusions highly saturated with dissolved minerals can form. As the crystal cools these minerals begin to precipitate forming a second crystal inside the host.

Liquid inclusions

As mentioned, many famous crystals (such as the Naica crystal caverns) were formed in hot, mineral-rich water solutions. As a result, sometimes this solution can become trapped inside the crystal during growth. A rather unique liquid inclusion which occurs under pressurised conditions is liquid CO2, which remains trapped in liquid form due to the pressure maintained inside the inclusion.

Quite often liquid inclusions come paired with a bubble of gas, such as in Image 4 in which liquid petroleum and a bubble of methane are trapped in quartz.

Image 4: Petroleum and methane bubble in quartz. Image by Danny Sanchez

Image 4: Petroleum and methane bubble in quartz. Image by Danny Sanchez

Gaseous inclusions

Finally, “negative crystals” form when a pocket of air is trapped within a crystal. These gaseous inclusions can be a specific gas, depending on the conditions the crystal grew in, or just plain old air. These inclusions can form either due to crystal growth which occurs in multiple directions that then intersect or because crystal growth in a particular direction is inhibited temporarily. Since gaseous inclusions are enclosed by crystal faces the shape will reflect the crystal habit (or defined external shape of the crystal) of the host and they are always oriented parallel to the host crystal (Image 5). While they may look like a typical gemstone, it is actually an inversion with air “inside” the crystal boundaries and crystal material on the “outside”. Hence these inclusions are named “negative crystals”.

Image 5: Negative crystals in amethyst. Image by Danny Sanchez

Image 5: Negative crystals in amethyst. Image by Danny Sanchez

A special aspect of any type of inclusion is that the foreign material is suspended in time. In this way, the inclusion contains a “piece of the past” which provides insight into what the earth and the environment were like when the crystal grew, often millions of years ago. For example, the discovery from air inclusions in amber that the oxygen content in air reached 35% during the Cretaceous period, before suddenly dropping to near the current level of ~21% [4].

There are many other forms of inclusions in addition to those shown. Quite often they can produce stunning visual effects and increase the value of the gemstone. For example, star sapphires which produce a unique six-rayed star effect under certain light sources contain tiny inclusions of aligned needle shaped rutile (Image 6).

Image 6: Star sapphire under a direct light source. Image from http://www.gemselect.com/.

Image 6: Star sapphire under a direct light source. Image from http://www.gemselect.com/.

Ordinarily, most inclusions are microscopic in size and can only be properly visualised under a microscope. For the majority of images featured here highly specialised and expensive equipment is required.

More images of crystal inclusions can be found in Gübelin and Koivula’s Photoatlas of inclusions in gemstones [5] or at http://www.dannyjsanchez.com/.

[1] Hooper, R.; New Scientist 2014, 2975, 24.
[2] The Art of Photomicrography: Gemstone Inclusions by Danny Sanchez <http://www.dannyjsanchez.com/&gt; (Accessed 11/14)
[3] Benz, K. W.; Neumann, W. Introduction to Crystal Growth and Characterization; Wiley, 2014
[4] Kump, L.R.; Kasting, J.F.; Robinson, J.M. Global and Planetary Change 1991, 5, 1.
[5] Gübelin, E.J.; Koivula, J.I. Photoatlas of Inclusions in Gemstones; Vol 1-3, Opinio Publishers

Your crystallographic Thanksgiving – Tryptophan!

Our contributor from the good US of A, Sara Callori, celebrates Thanksgiving on Crystallography 365!

What does it look like?

Crystal structure made with VESTA Red: Oxygen, Blue: Nitrogen, Brown: Carbon, White: Hydrogen

Crystal structure made with VESTA
Red: Oxygen, Blue: Nitrogen, Brown: Carbon, White: Hydrogen

What is it?

As an American living in Australia, this is the time of year when I get a bit homesick for a real autumn, and this week I’m especially missing Thanksgiving. I could make up for it by hosting one myself, but since it’s basically summer Down Under, it’s way too hot to do all that cooking. However, I can celebrate in a crystallographic way – by posting the structure of tryptophan!

Tryptophan is an essential amino acid that helps cells form new proteins. It’s found in most-protein based foods. The pseudo-scientific urban legend surrounding tryptophan is that it’s the tryptophan in turkey that makes you sleepy after a big Thanksgiving dinner. However, this isn’t actually the case, as turkey has the same amount of tryptophan in it as chicken or pork and many other types of foods, so it isn’t what causes that post-pumpkin pie slump. (Personally I blame it on a very large meal accompanied by several glasses of wine.)

Where’s this structure from?

Apparently tryptophan is difficult to successfully crystalize, so successful reports on its structure have only surfaces in the last decade. The structure above is L-typtophan that was recently published by C. H. Görbitz, K. W. Törnroos and G. M. Day in Acta Crysltallographica B. (http://scripts.iucr.org/cgi-bin/paper?S0108768112033484)

November’s birthstone – Orange Topaz

Helen Brand gives us the low-down on the penultimate of the year’s birthstones.

What does it look like?

 The topaz structure. Image created using diamond crystal structure visualisation package. Al is grey, Si is green, O white and F pink.


The topaz structure. Image created using diamond crystal structure visualisation package. Al is grey, Si is green, O white and F pink.

What is it?

Topaz is another silicate mineral, this time containing aluminium and fluorine. The formula is Al2SiO4(F,OH)2. It is usually colourless and can become tinted by impurities. It is the orange topaz which is traditionally known as the birthstone of November. It has an orthorhombic structure made up of corner-sharing aluminium octahedra and silicate tetrahedra.

Figure 2. A gem quality Orange Topaz. Image from http://www.minerals.net/

Figure 2. A gem quality Orange Topaz. Image from http://www.minerals.net/

Talking about topaz gives me an opportunity to talk a little bit about one of my favourite rocks: Pegmatites. Pegmatites are intrusive igneous rocks which are composed of crystals which are typically > 2.5 cm in size and this is usually where topaz is found. To be classed as a pegmatite, a rock must be all crystalline with almost all crystals >1 cm in size. There is no typical composition for a pegmatite. The large crystal size is the most striking feature of a pegmatite, with individual crystals reaching > 10 cm in size. Some of the largest single crystals in the world (not counting those mega-cryst caves), are found in pegmatites. Most pegmatites are composed of quartz, feldspar and mica, plus a few other minerals and have a similar composition to granite.

An excellent place to find pegmatitic rocks is in Cornwall in South West England. Cornwall has a strikingly different geology to the rest of the UK. Cornwall is underlain by a large batholith – an intrusive body of granite. In various places, this granite is exposed at the surface. Figure 3 was taken at Rinsey Cove in Cornwall. It shows a pegmatitic dyke surrounded by granite.
While I was unable to find any literature to say that there have been topaz crystals found at Rinsey cove, topaz was found about a mile along the cliffs at Megiliggar rocks, where a slightly different part of the complex is exposed.

 Figure 3. A pegmatitic vein from Rinsey cove, Cornwall.


Figure 3. A pegmatitic vein from Rinsey cove, Cornwall.

These granites were intruded approximately 300 – 275 million years ago as the northern boundary of a mountain building event called the Variscan-Hercynian orogeny (orogeny just means mountain building event) which occurred when the ancient continents of Euramerica and Gondwana collided to form a super-continent – Pangaea.

The granites were molten when they were emplaced and then subsequently crystallised. The hot magma rose upwards and moved through weaknesses in the country rock. As it did this it changed (– metamorphosed), and consumed, the country rock surrounding it.
The granites in Cornwall have shaped the economy of the area. They have provided resources which have been exploited by the inhabitants for years. Hydrothermal fluids concentrate precious metals such as tin and copper, they carry the ions in solution and deposit them when new minerals crystallise. Cornwall is littered with mines which extracted these precious metals and also famous for wide occurrence of tourmaline minerals, the birthstones for December which I’ll tell you about next month!

Where did the structure come from?

Diego Gatta G, Nestola F, Bromiley G D, Loose A (2006) New insight into crystal chemistry of topaz: a multi-methodological study. American Mineralogist 91 1839-1846.

It is available on the American Mineralogist Crystal Structure Database.

Alpha plutonium – a rebel element

What does it look like?

The crystal structure of alpha plutonium, image generated by the VESTA (Visualisation for Electronic and STructual analysis) software http://jp-minerals.org/vesta/en/.

The crystal structure of alpha plutonium, image generated by the VESTA (Visualisation for Electronic and STructual analysis) software http://jp-minerals.org/vesta/en/.

What is it?

Over the year we’ve introduced the crystal structure of a number of elements. Most of them take up very simple crystal structures, those that you can also form by pouring ping pong balls into a box. Atoms of materials like gold, krypton and even curium pack like this.

We’ve also introduced elements that don’t conform to the ‘simple crystal structure’ rules at room temperature – the elemental rebels so to speak. These are the elements where the atoms are awkward – they need to be *that* bit further away from each other.

The latest of these ‘rebel’ element is plutonium. This element, actually has seven allotropes, with a face centred cubic phase (known as the delta-phase) stable at just above room temperature, 310 K. Below this it forms a crystal structure known as it’s alpha-phase, which is monoclinic, a low symmetry structure that has low thermal conductivity and is quite brittle. Not great for use in reactors.

We’ve actually learnt how to tame the plutonium crystal structure somewhat. Alloy plutonium with a little bit of gallium, aluminium, americium, scandium or cerium and it forms into a gold-like face-centred cubic structure that isn’t brittle and conducts heat much better.

Where did the structure come from?

The structure of alpha plutonium was discovered by Zachariasen, and Ellinger 1963. It’s #9008587 in the Crystallography Open Database.

DNA Polymerase in Celebration of Evolution Day

Today’s Anton tells us about a structure behind one aspect of evolution.

What does it look like?

The Klenow fragment of DNA polymerase I from E. coli (in blue) with template and new DNA strands (green and magenta respectively).

The Klenow fragment of DNA polymerase I from E. coli (in blue) with template and new DNA strands (green and magenta respectively).

What is it?

Today is evolution day, the day where the publication of Charles Darwin’s seminal work On the Origin of Species in 1859 is celebrated. DNA and its specific sequence of bases: A, T, C, and G, have a lot to do with evolution but since we’ve already blogged about the structure of DNA for Rosalind Franklin’s birthday, I thought I’d write about the protein that replicates the DNA when a cell divides: DNA polymerase.

DNA replication is semi-conservative: that is, each strand of DNA acts as the template for the new copy and one of copy each goes to the two new daughter cells. There are billions of A, T, C, and G’s that make up a genome thus it is of the utmost importance that DNA polymerase is extremely accurate in its job. Typically DNA polymerase will make one mistake for every billon bases copied. There are a number of reasons why DNA polymerase is so accurate. 1. DNA polymerase can select the correct bases for the correct pairing (i.e. A pairs with T and G pairs with C); 2. There is a proof reading mechanism and 3. Repair systems if a mistake is spotted.

Many those one in a billion mistakes will never show as a unique characteristic but some could result in a random mutation that is seen as observable characteristics (the phenotype) in an organism. If that mutation is in the reproductive cells then the mutation could be passed onto the next generation and with the favour of natural selection propagate for many generations.

As a mistake in copying DNA can prove to be disastrous as well a beneficial there is a lot of redundancy in DNA replication with many organisms having more than one DNA polymerase. E. coli for instance has five DNA polymerases. The structure shown today is the Klenow fragment of E. coli DNA polymerase I. The Klenow fragment is the part of the polymerase where replication and proof reading occur but other domains have been removed. The structure resembles the shape of a hand with the DNA being held between a finger and thumb.

Where did it come from?

DNA polymerase I from E. coli was discovered by Arthur Kornberg in 1956 (and later won the Nobel Prize for Physiology and Medicine in 1959 for the discovery). The structure shown here was solved in 1993 [1] by Lorena Beese, Victoria Derbyshire, and Thomas Steitz (who won the Noble prize for Chemistry in 2009 with Venkatraman Ramakrishnan and Ada Yonath for their work on the ribosome). The structure was taken from the Protein Data Bank (PDB number: 1KLN).

[1] L.S. Beese, V. Derbyshire, T.A. Steitz (1993) Structure of DNA polymerase I Klenow fragment bound to duplex DNA. Science 260: 352-355.