From Crystallography to Light!

As the International Year of Crystallography gives way to the International Year of Light, we end the #Crystallography365 series with a retrospective of how research in optics has advanced crystallography, and a prospective on how it will do so in the future.

There was crystallography before x-rays, but since 1912 the field has been intimately connected to x-ray optics [1]. In 1895, just after Maxwell had shown that light was a transverse electromagnetic wave, Rontgen discovered x-rays while conducting experiments of the optical properties of cathode rays. Rontgen’s mysterious x-rays captured worldwide attention; but particularly that of Arnold Sommerfeld’s. Although a theoretician himself, he had assembled an impressive group of experimentalists in his research group. Sommerfeld had surmised that that x-rays were transverse EM waves with a wavelength on the order of 1 angstrom, and furthermore that diffraction through a suitably sized slit would prove this fact.

In 1912 Max Von Laue, then an experimentalist in Sommerfeld’s group, showed that crystalline materials diffract x-rays, thus in just one single experiment demonstrating the wave nature of x-rays and the lattice structure of crystals [2]. Then using mathematical arguments from wave optics W.L Bragg (the son) developed his groundbreaking formulas relating the intensity of spots and structure. Later, using optics and engineering, W.H. Bragg (the father) constructed the first x-ray spectrometer, and Weissenberg invented the x-ray camera named after him [3].

The invention of synchrotron light sources and advances in x-ray optics have boosted crystallography to new heights. Synchrotrons were first built for particle physics applications. X-ray radiation production in synchrotrons is an energy-sapping nuisance, and literally holes needed to be drilled in the particle pipe to let the x-rays out. Of course scientists soon realized that this ‘waste radiation’ might be useful after all [4]. Today with many exotic x-ray optical designs, large synchrotron machines give crystallographers more and more brilliant monochromatic x-rays, and with the ability to get higher and higher resolutions in both space and time. This has been particularly useful in powder and macromolecular applications.

In the coming years research in optics holds many exciting opportunities for crystallographers. Advances in plasma photonics are reducing the size of x-ray sources such that light with characteristics previously only available at large synchrotron user facilities becomes available from machines small enough for individual labs [5-7].

Free electron lasers (FELs) provide peak brilliance 8 orders of magnitudes larger than synchrotron light sources, and pulses on the order of 10s of femtoseconds [8]. FELs are enabling ultra-short, but still ultra-bright light pulses that allow reliable structure determination from much smaller crystals. This is extremely important for protein crystallographers, shaving possibly years off the current process and opening the door to bigger and more membrane bound complexes [9]. The ultra-short pulse length and high repetition rates mean that chemical dynamics will routinely be studied crystallographically [10].

At the end of this celebration of 100 years of x-ray crystallography, crystallographers are in a sense where they’ve been all along, at the forefront of optics research. So the International Year of Light is a perfect successor to the International Year of Crystallography.

[1] Nave, C. (1999), Matching X-ray source, optics and detectors to protein crystallography requirements, Acta Cryst. D55, 1663-1668, doi:10.1107/S0907444999008380

[2] Von Laue, M. (1915), Nobel Lecture: Concerning the Detection of X-ray Interferences”. Nobelprize.org. Nobel Media AB 2014. Web. 31 Dec 2014. http://www.nobelprize.org/nobel_prizes/physics/laureates/1914/laue-lecture.html

[3] Weissenberg K., Ein neues Röntgengoniometer. Z. Physik, 23 (1924),229-238, doi: 10.1007/BF01327586

[4] Phillips, J. C., Wlodawer, A., Yevitz, M. M., & Hodgson, K. O. (1976). Applications of synchrotron radiation to protein crystallography: preliminary results. Proceedings of the National Academy of Sciences of the United States of America, 73(1), 128–132, PMCID: PMC335853

[5] Corde, S., Phuoc, K. T., Lambert, G., Fitour, R., Malka, V., Rousse, A., … & Lefebvre, E. (2013). Femtosecond x rays from laser-plasma accelerators. Reviews of Modern Physics, 85(1), 1, doi: 10.1103/RevModPhys.85.1

[6] Schlenvoigt, H-P., K. Haupt, A. Debus, F. Budde, O. Jäckel, S. Pfotenhauer, H. Schwoerer et al. (2007). A compact synchrotron radiation source driven by a laser-plasma wakefield accelerator. Nature Physics, 4(2), 130-133, doi:10.1038/nphys811

[7] Lyncean Technologies, http://www.lynceantech.com/

[8] Margaritondo, G., & Rebernik Ribic, P. (2011). A simplified description of X-ray free-electron lasers. Journal of synchrotron radiation, 18(2), 101-108, doi: 10.1107/S090904951004896X

[9] Spence, J. C., & Chapman, H. N. (2014). The birth of a new field. Philosophical Transactions of the Royal Society B: Biological Sciences, 369(1647), 20130309, doi: 10.1098/rstb.2013.0309

[10] Minitti, Michael P., James M. Budarz, Adam Kirrander, Joseph Robinson, Thomas J. Lane, Daniel Ratner, Kenichiro Saita et al. Toward structural femtosecond chemical dynamics: imaging chemistry in space and time. Faraday discussions 171 (2014): 81-91, doi: 10.1039/C4FD00030G

 

A material for another world – Sulfuric Acid Hexahydrate

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?

This material forms when a water-rich mixture of sulfuric acid and water are cooled below 200 K (about -80 °C).   It is a mix of six water molecules to one sulfate molecule.  Most of the water molecules (which are represented by the red atoms) form in layers with the ones left over filling the gap with the sulfate molecules (blue and yellow atoms).  The box that can be used to describe the structure is 7.4 x 7.5 x 17.0 Å.  Though it probably doesn’t form all that much on Earth, it could occur on the surfaces of the icy moons of Jupiter – Europa, Ganymede and Callisto.   The sulfur that could make this material is thought to be transported from the volcanoes of their sister moon Io, via the magnetic field of Jupiter, before being bombarded onto the icy surfaces.

Where did the structure come from?

This structure was determined from synchrotron x-ray diffraction, and was only discovered last year.  It’s reported in Maynard-Casely et al 2013.

HLA Molecules – How the body detects infected cells

What does it look like?

The structure of the class I human leukocyte antigen (HLA-A2) (pdb code: 3HLA http://www.rcsb.org/pdb/explore.do?structureId=3hla). Image generated by Pymol (http://www.pymol.org/ )

The structure of the class I human leukocyte antigen (HLA-A2) (pdb code: 3HLA http://www.rcsb.org/pdb/explore.do?structureId=3hla). Image generated by Pymol (http://www.pymol.org/ )

What is it?

During her PhD studies in Harvard, Pamela J. Björkman solved the structure of a protein (HLA) that tells the immune system whether a cell is healthy or infected. The studies by Björkman confirmed that both the protein AND the bound peptide are important for the recognition event, and supported the Nobel Prize winning work of Rolf Zinkernagel and Peter Doherty (see http://www.nobelprize.org/nobel_prizes/medicine/laureates/1996/)

The most beautiful part of this structure is the deep groove on its upper surface, encased by two alpha helical jaws (pink), which holds small peptides. The role of these HLA molecules is to present these peptides as sort of a barcode to be scanned by cells of the immune system. These peptides tell the immune system whether a cell is healthy and can be ignored, or infected and should be destroyed.

Where did the structure come from?     

The structure was published in a 1987 Nature paper. It took Pamela eight trips to the German Synchrotron to solve the structure.

 

The structure that started it all – Rock salt

What does it look like?

rock_salt

What is it?

One of the crystal structures that started everything any you’ll always have it in your kitchen.  The structure of sodium chloride rock salt (or NaCl), was one of a handful of structures that WL Bragg presented to the Cambridge philosophical society on the 11th November 1912.  This was the first time scientists had used diffraction (the patterns of scatter from crystalline solids discovered by Max von Laue)  In the image above (taken from the book WL Bragg wrote with his father WH Bragg, X-ray’s and Crystal structure) the black circles represent sodium atoms and the while chloride atoms.    It is a very simple structure, in a cubic unit cell where each of the repeating lengths are 5.6 Å, and can be described with just two atoms.

Where did the structure come from?

We took this image of the structure of rock salt straight from WL and WH Bragg’s book, which is avaible at the open library here.