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”. Nobel Media AB 2014. Web. 31 Dec 2014.

[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,

[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 tree bark suspension and a Nobel Prize later…. We wonder less about the structural basis of the action of aspirin

Today we have another guest post from Lawrence Norris of @BlackPhysicists.  A super read that charts how the every day drug aspirin went from being ancient medicine to how modern crystallography could explain how it works.  Enjoy!

Today’s post spans the bridge between ancient pharmacognosy and modern biophysics. The history of aspirin and its medical use can be traced back to the second millennium BC.  Medicines from willow and other salicylate-rich plants appear in the Egyptian pharmacology papyri.  Hippocrates, the father or modern medicine, administered willow tree bark to women to help relieve pain associated with childbirth.  Later the tree bark was used to alleviate general pain and fevers.

In 1763 Oxford University chemist, Edward Stone, isolated the active compound from Hippocrates preparation, which turned out to be salicylic acid.  In 1853 French chemist Charles Frédéric Gerhardt synthesized acetylsalicylic acid, albeit in an unstable and impure form.  In 1897 German chemist Felix Hoffman, working for Bayer, first synthesize pure acetyl salicylic acid, which later became known as aspirin.  Bayer took aspirin to market almost immediately, and established a complete market association of Bayer AG with the drug.  “Bayer Aspirin” had been on the market for nearly 50 years when Wheatly determined the crystal structure of aspirin in 1964 [1].  There have been several reports of an elusive second crystal polymorphs of aspirin. (See 7 Feb 2014 post on this blog.)

Aspirin-3D-balls“. Licensed under Public domain via Wikimedia Commons.

Aspirin took on the moniker of “wonder drug” as it worked wonders against the miseries of aches, pains, fever and inflammation, and scientists wondered why.   Here is where the story of aspirin merges with the Nobel Prize winning work of Bergstrom, Samuelsson and Vane [2] .   This trio and their co-workers elucidated the structure [3] and function of prostaglandins, which are paracrine hormones that mediate many physiological functions having to do with platelet aggregation and smooth muscle tone.   They identified prostaglandin H synthase (PGHS),  as being the key control point enzyme in the “prostaglandin cascade”.   Vane in particular showed that it was possible to block the synthesis and thus the action of prostaglandins with aspirin [4].

Still it was not known exactly how aspirin works.  Enter the work of Picot, Loll and Garavito who solved the crystal structure of PGHS (aka COX)  in 1994 [5].  It bears mentioning here that the crystallization of PGHS, being a membrane protein,  was a tour de force in protein crystallography.  When its structure was published in 1994, there were less than a dozen other membrane proteins in the PDB database.

COX-2 inhibited by Aspirin.png
COX-2 inhibited by Aspirin” by Jeff Dahl – self-made, release to public domain. Licensed under Public domain via Wikimedia Commons.

Following their initial work, Loll, et. al., were able to solve the structure of the enzyme with aspirin bound [6], and also with other drugs that compete with aspirin in the marketplace, e.g., ibuprofen [7].   Others showed how Naproxen (Alleve) binds to the enzyme [8].   Aspirin, it turns out, is an irreversible inhibitor of PGHS.  It acetylates a key serine residue in the enzyme’s active site, and that prevents the natural substrate from situating itself for productive enzyme activity.

Alas though, this is not the whole story of how this wonder drug works physiologically.  Recent results indicate that aspirin is an antiporter partner to protons in mitochondria.  Also aspirin apparently induces formation of inflammation-reducing NO radicals, and signaling through NF-κB.

[1]  Wheatley, P. J. “The crystal and molecular structure of aspirin.” J. Chem. Soc., 1163 (1964), 6036-6048, 10.1039/JR9640006036

[2] “The Nobel Prize in Physiology or Medicine 1982”. Nobel Media AB 2014. Web. 25 Nov 2014. <>

[3]   Abrahamsson, S. “A direct determination of the molecular structure of prostaglandin F2-1.” Acta Crystallographica 16.5 (1963), 409-418, 10.1107/S0365110X63001079

[4]  Vane, J. R. “Inhibition of prostaglandin synthesis as a mechanism of action for aspirin-like drugs.” Nature 231.25 (1971): 232-235, 10.1038/newbio231232a0

[5]  Picot, D, P. J. Loll, and R. M. Garavito. “The X-ray crystal structure of the membrane protein prostaglandin H2 synthase-1.” Nature 367.6460 (1994), 243-249, 10.1038/367243a0

[6]  Loll, P. J., D. Picot, and R. M. Garavito. “The structural basis of aspirin activity inferred from the crystal structure of inactivated prostaglandin H2 synthase.” Nature Structural & Molecular Biology 2.8 (1995), 637-643, 10.1038/nsb0895-637

[7]  Selinsky, Barry S., et al. “Structural analysis of NSAID binding by prostaglandin H2 synthase: time-dependent and time-independent inhibitors elicit identical enzyme conformations.” Biochemistry 40.17,  5172-5180, (2001), 10.1021/bi010045s

[8]  Duggan, Kelsey C., et al. “Molecular basis for cyclooxygenase inhibition by the non-steroidal anti-inflammatory drug naproxen.”  Journal of Biological Chemistry 285.45 (2010), 34950-34959, 10.1074/jbc.M110.162982


Solid carbon dioxide.

What does it look like?


What is it?

Solid carbon dioxide, aka, dry ice is a well-known cooling agent amongst meat packers and ice cream makers. Where at normal atmospheric pressure, water freezes at 0 degrees C, CO2 solidifies at -78.5 degrees C. Besides its lower temperature, dry ice’s main advantage over water ice is that it is a refrigerant with no liquid residue. That is, it goes from solid to gas without an intervening liquid phase (at least at normal atmospheric pressure); a process called sublimation. Dry ice is also popularly used in smog machines.

High pressure and temperature phases of solid CO2 are especially important for understanding planetary interiors [2-3] and star formation [4]. Like solid water, solid CO2 has several polymorphs [1]. So far there have been 7 different polymorphs of solid CO2 identified. Below is the phase diagram of solid CO2 at high temperature and pressure. Phases I, III, and VII are typical molecular solids, while phases V and VI are extended phases similar to those of silicate (SiO2). Phase II is a poorly understood intermediary phase. The nature of phase IV is starting to come into view.

Where all the structures of CO2 sit in pressure and temperature space, from reference [4]

Where all the structures of CO2 sit in pressure and temperature space, from reference [4]

Normally CO2 is a linear molecule with double bonds between the carbon and oxygen atoms. In 2002 Park, et. al. reported results suggesting that phase IV has a bond length 30% larger than in phase I and were no longer linear, exhibiting an OCO angle of 160° [5]. However, such a distortion was in conflict with other experimental and theoretical results, and a strong debate emerged about the actual structure of this phase. In 2009 Datchi, et al, reported an X-ray structure of a single crystal of CO2 in phase IV that did not exhibit this bent structure [4]. Instead they found the structure to be rhombohedral, space group R-3c, with 8 molecules in the primitive unit cell. The C=O intramolecular bond length was found to be slightly smaller (1.155 Å) than the one of the isolated molecule.

Iota, et. al., reported results indicating that that phase V is an extended covalent solid with carbon-oxygen single bonds, [7] a result subsequently confirmed by Santoro, et al., [8] and Datchi et. al. [10]. Seto, et. al., likewise solved the crystal structure of solid CO2-V which is consistently interpreted in terms of a tetragonal unit cell [11]. Sun, et. al., reported that phase VI is also amorphous, layered and tetrahedral [9]. These results also suggest that CO2 may be present in the Earth’s mantle with structures that are similar or identical to structures of SiO2 having either 4- or 6-coordinated carbon atoms.

The totality of the all the investigations of solid CO2 reveal a very complex picture of changing structure as a function of temperature and pressure. There are still several open questions and a need for perhaps new techniques in x-ray diffraction to resolve some of the issues. What is also interesting about this line of research is the role of electronic structure calculations [12,13] and complimentary experimental methods, e.g., x-ray Raman spectroscopy [15].

1. Yoo, C., et al., Crystal structure of carbon dioxide at high pressure:“Superhard” polymeric carbon dioxide. Physical Review Letters, 1999. 83(26): p. 5527.

2. Matson, J., Deep Freeze: Mars Orbiter Finds Massive Stores of Buried Dry Ice, Scientific American, April 21 2011, Nature Publishing Group

3. Malin, Michael C., Michael A. Caplinger, and Scott D. Davis. “Observational evidence for an active surface reservoir of solid carbon dioxide on Mars.” Science 294, no. 5549 (2001): 2146-2148.

4. Nummelin, A., D. C. B. Whittet, E. L. Gibb, P. A. Gerakines, and J. E. Chiar. “Solid carbon dioxide in regions of low-mass star formation.” The Astrophysical Journal 558, no. 1 (2001): 185.

5. Datchi, Frédéric, Valentina M. Giordano, Pascal Munsch, and A. Marco Saitta. “Structure of carbon dioxide phase IV: Breakdown of the intermediate bonding state scenario.” Physical review letters 103, no. 18 (2009): 185701.

6. Park, J-H., C. S. Yoo, V. Iota, H. Cynn, M. F. Nicol, and T. Le Bihan. “Crystal structure of bent carbon dioxide phase IV.” Physical Review B 68, no. 1 (2003): 014107.

7. Iota, V., C. S. Yoo, and H. Cynn. “Quartzlike carbon dioxide: An optically nonlinear extended solid at high pressures and temperatures.” Science 283, no. 5407 (1999): 1510-1513.

8. Santoro, Mario, Federico A. Gorelli, Roberto Bini, Giancarlo Ruocco, Sandro Scandolo, and Wilson A. Crichton. “Amorphous silica-like carbon dioxide.” Nature 441, no. 7095 (2006): 857-860.

9. Sun, Jian, Dennis D. Klug, Roman Martoňák, Javier Antonio Montoya, Mal-Soon Lee, Sandro Scandolo, and Erio Tosatti. “High-pressure polymeric phases of carbon dioxide.” Proceedings of the National Academy of Sciences 106, no. 15 (2009): 6077-6081.

10 Datchi, Frédéric, Bidyut Mallick, Ashkan Salamat, and Sandra Ninet. “Structure of Polymeric Carbon Dioxide CO2-V.” Physical Review Letters 108, no. 12 (2012): 125701.

11. Seto, Y., D. Nishio-Hamane, T. Nagai, N. Sata, and K. Fujino. “Synchrotron X-ray diffraction study for crystal structure of solid carbon dioxide CO2-V.” In Journal of Physics: Conference Series, vol. 215, no. 1, p. 012015. IOP Publishing, 2010.

12. Plašienka, D., Martoňák, R., “New amorphous forms of solid CO2 from ab initio molecular dynamics”, arxiv/1307.3854

13. Li, Jinjin, Olaseni Sode, Gregory A. Voth, and So Hirata. “A solid–solid phase transition in carbon dioxide at high pressures and intermediate temperatures.” Nature Communications 4 (2013).

14. Bonev, S. A., Francois Gygi, T. Ogitsu, and G. Galli. “High-pressure molecular phases of solid carbon dioxide.” Physical review letters 91, no. 6 (2003): 065501.

15. Shieh, Sean R., Ignace Jarrige, Min Wu, Nozomu Hiraoka, S. Tse John, Zhongying Mi, Linada Kaci, Jian-Zhong Jiang, and Yong Q. Cai. “Electronic structure of carbon dioxide under pressure and insights into the molecular-to-nonmolecular transition.” Proceedings of the National Academy of Sciences 110, no. 46 (2013): 18402-18406.