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)

Trademark this mineral!

Today Dr Sara tells us of about a mineral she was suspicious of to begin with:

What does it look like?

(structure made with Vesta) Colors – Blue: Cu, Brown: Fe, Yellow: S

(structure made with Vesta) Colors – Blue: Cu, Brown: Fe, Yellow: S

What is it?

Upon first encountering chalcopyrite, I was convinced it had to be a weird autocorrect rather than an actual mineral name. But after a bit of internet sleuthing, I learned that it’s a real, and very useful material. Also that it’s probably pronounced “calko-pyrite” rather than “cal-copyrite”, since it comes from the Greek words “chalkos” meaning “copper” and “pyrites” which means “striking fire”. This stems from the fact that chalcopyrite, or CuFeS2, is a bright yellow semiconducting material with a metallic lustre and is often confused with gold or pyrite. However, it is much softer than pyrite and more brittle than gold. It has long been a primary source for copper and has contributed to technology in both Bronze Age societies and in the modern era.

Where did this structure come from?

The chalcopyrite structure was first reported in 1931 by none other than Linus Pauling and graduate student Lawrence Brockway. While a previous study of the chalcopyrite structure was published in 1917, Pauling and Brockway demonstrated that it wasn’t quite right. You can find evidence of Pauling’s study in his lab notebook, although the data was put into Brockway’s notebook. A brief post on the history of this discovery can be found at The Pauling Blog.

Bonus: Crystal structure rebus!

Put your answers in the comments!

Chalcopyrite_Pun

Let’s Get Popping! – Ruddlesden-Popper Structures

What does it look like?

Left: Sr2RuO4 Right: Sr3Ru2O7, both images made with VESTA.

Left: Sr2RuO4 Right: Sr3Ru2O7, both images made with VESTA.

What is it?

If you’re familiar with the perovskite (which regular readers should be by now), then you are familiar with one of the building blocks of Ruddlesden-Popper structures. The slightly complicated looking formula for this type of material is An-1A’2BnX3n+1. What this means is that this material has two types of cations, A and B atoms, with X being the anions in the system. Shown above are the cases for n = 1 (left) and n = 2 (right).

All types of Ruddlesden-Popper structures share same basic layout: in the middle of the unit cell is a perovskite layer, where an ABX3 structure forms. Above and below that is a layer comprised of B cations surrounded by X octahedral. The A’ cations appear between at the boundary of the two types of layers.

But this series of structures extends beyond n = 2, although making those materials can be quite the challenge! However, research groups that specialize in thin film growth, such as those from Cornell University  or Argonne National Lab have recently been able to fabricate a variety of Ruddlesden-Popper samples.

Where did this structure come from?

As you may have guessed from the name of these structures, they were first synthesized and described by S.N. Ruddlesden and P. Popper, with the n = 1 structure (left) published in 1957 and the n = 2 (right) following a year later in 1958.

Bi George, it’s bismuth!

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/

 

Why is bismuth our next crystal structure? Because bismuth crystals are just plain cool looking!

If you don’t believe me, then check this one out:

(image courtesy of Wikipedia)

(image courtesy of Wikipedia)

Bismuth is a commonly used metal, in part because of its low toxicity, and can be found in lots of everyday products like makeup and medications, including the aptly named Pepto-Bismol. Naturally, however, bismuth isn’t bright pink, but light gray, like in the cube above. The rainbow sheen on the large crystal actually comes from a surface oxide layer that forms on the bismuth during crystal growth.

The crystal structure of bismuth is relatively simple, as is shown above. Bismuth has a rhombohedal unit cell, which means that here only two of the lattice parameters are the same and two of the angles in the unit cell are 90° while the third is 120°. But this crystal structure isn’t what causes such a distinct type of crystal to form. This type of “staircase” like growth is called a hopper crystal. These types of crystals form because the outside of the crystal grows faster than the inside, so the large crystals never get “filled in”. However, the growth of the inside portion of the crystal is still dictated by the crystal structure, which is how the “step” features form.

Since bismuth is a relatively safe and easy to obtain metal, you can actually make bismuth crystals at home in your kitchen (or garage if you happen to have a gas torch around). You can check out a video of stove-top bismuth crystals here.

Where did this structure come from?

The first determination of the structure of bismuth was reported in 1962 by P. Cucka and C.S. Barrnett. (http://onlinelibrary.wiley.com/doi/10.1107/S0365110X62002297/abstract) You can also find the structure at #5000215 in the Crystallography Open Database. (http://www.crystallography.net/5000215.html)

Putnisite: Brand New and Completely Unique

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/

Green: Strontium, Light blue: Calcium, Dark blue: Chromium, Yellow: Sulphur, Brown: Carbon, Red: Oxygen, Dark grey: Water, Pink: Hydrogen

What is it?

Putnisite is a brand new mineral that was recently discovered in Australia. As you can see in the structure above, there’s a lot going on within the structure, leading to the lengthy chemical name: SrCa4Cr3+8(CO3)8SO4(OH)16*25H2O. What makes Putnisite, which is named after mineralogists Andrew and Christine Putnis, is that it is truly a one-of-a-kind mineral. The authors of a recent paper introducing putnisite call it “unique among minerals and synthetic compounds”. The complex framework that makes up the crystal is not related to any other material that scientists currently know of. Even the elements that make up this material: strontium, calcium, chromium, sulphur, carbon, oxygen, and hydrogen, are an unusual combination.

Image from Elliot et al., Mineral. Mag. 78, 131-144

Image from Elliot et al., Mineral. Mag. 78, 131-144

Putnisite was found in the Polar Bear Peninsula in Western Australia. It appears as roughly ½ mm cubic crystals that are purple with pink streaks.

Where did this structure come from?

A detailed structure was recently reported in Mineralogical Magazine by lead author Peter Elliot from The University of Adelaide. Information can also be found in the American Mineralogical Crystal Structure Database.