|The IUCr is an International Scientific Union. Its objectives are to promote international cooperation in crystallography and to contribute to all aspects of crystallography, to promote international publication of crystallographic research, to facilitate standardization of methods, units, nomenclatures and symbols, and to form a focus for the relations of crystallography to other sciences.|
John Spence main editor of IUCrJ is one of the latest Foreign Members of the Royal Society announced 1 May 2015. Professor John Spence is distinguished for his innovative world-leading contributions to both biology and materials science. He led the team which conceived the first application of X-ray free-electron lasers (XFELs) to structural biology using protein nanocrystals and he pioneered femtosecond serial crystallography. He is also a world leader in the development and application of atomic-resolution electron microscopy, he co-invented a widely used technique for locating impurity atoms in nanocrystals and published the first observation of dislocation kinks, at atomic resolution. He has developed new microscopies and spectroscopies which have given scientists new eyes to understand atomic processes in solids.
You can see a full list of John’s papers published in IUCr journals here.
This article is reprinted from material taken from The Royal Society, with editorial changes made by IUCr.
The May issue of Acta Crystallographica Section F Structural Biology Communications (http://journals.iucr.org/f) is a dedicated special issue on the structural investigation of proteins associated with molecular parasitology, specifically research linked to protozoan pathogens. Parasitic protozoa threaten the lives of millions of human beings by causing a range of diseases including malaria, leishmaniasis, Chagas disease, toxoplasmosis and African sleeping sickness.
Researchers have sought to understand the processes that allow pathogens to exist, to invade a host, to evade the immune response and to cause these debilitating and often fatal diseases. Structural biology, and in particular crystallography, complements such investigations. It can play a key role in drug discovery by providing accurate
chemical information to guide the assessment of drug targets and computational design projects, in the search for pharmaceutical compounds.
The publication of this special issue represents an exciting new departure for Acta Crystallographica Section F. The journal hopes to provide a natural home for new research in molecular parasitology, as well as welcoming contributions from the structural biology community as a whole.This special issue includes fundamental studies in molecular parasitology and also research directed toward protozoan drug target characterization, including both NMR and crystal structures. The articles include an overview and perspective from Professor Wim Hol, an inspirational champion for the role of crystallography in drug discovery. There is also a short review from Professor Inari Kursula on cytoskeletal proteins related to the infection process, a topic that may provide opportunities in future drug discovery work.
X-ray free-electron lasers (FELs) are coming of age Schlichting, I. et al. (2015). J. Synchrotron Rad. 22, 471; doi:10.1107/S1600577515008176. Fifteen years ago, first lasing was achieved with a SASE (self-amplified spontaneous emission) FEL at the Tesla Test Facility at DESY, the forerunner of the VUV FEL FLASH in Hamburg. Hard X-rays became available a little over five years ago when the Linac Coherent Light Source (LCLS) at SLAC National Accelerator Laboratory opened its doors to users, followed by the SPring-8 Angstrom Compact Free Electron Laser (SACLA) three years ago. With their femtosecond short pulses and ultra-high peak brilliance, FELs have enabled the advance of many different areas of science. To name just a few applications, FELs have provided novel insight into light-matter interactions, enabled ultrafast time-resolved measurements at high spatial resolution, provided a tool long-awaited for the study of matter under extreme conditions and of nanoscale objects, including biological materials.
It thus seems timely for a special FEL-related issue in the Journal of Synchrotron Radiation (JSR). Feature articles describe the sources and facilities: LCLS, SACLA and the VUV FEL FERMI, giving insight in the development of and possibilities at these facilities. Beamline papers describe the instruments, providing detailed information on the experimental capabilities along with recent scientific results highlighting the possibilities. Various laser systems for time-resolved measurements are described, giving background information on planning experiments, along with contributions on X-ray detectors, non-linear signal response issues and data acquisition systems. Diagnostics are critical to single-pulse machines like FELs. Thus, some contributions describe diagnostic tools and techniques, including new approaches for focus characterization driven by developments in nanofocusing to study smaller and smaller objects at increasingly higher flux densities. New capabilities are constantly being developed at FEL sources and a few such capabilities are described, including spectroscopy techniques and the use of the seeded beam in crystallography. The increasing interest in using these machines is not only accommodated by developments in multiplexing the single FEL beam to different instruments or to use the spent beam but also by the construction of a number of new FELs such as FLASH2 and the European XFEL in Germany, the SwissFEL in Switzerland, and the PAL-XFEL in Korea. A future special issue on FELs in JSR will focus on these upcoming facilities.Ilme Schlichting, William E. White and Makina Yabashi
In the latest issue of IUCrJ, three essays have been published that consider the concept of interatomic bonds in crystals from different perspectives.
The debate is framed by Professor Jack D. Dunitz [Dunitz, J. D. (2015). IUCrJ, 2, 157-158; doi: 10.1107/S2052252515002006], who questions whether the transfer of the concept of interatomic bonds to the world of intermolecular arrangements in crystals is tenable. His essay poses some specific questions: (1) Should the observation of short distances between pairs of atoms on the peripheries of different molecules in crystals be regarded as evidence of specific intermolecular bonding between the atoms concerned? (2) If the answer is not "yes" but "no" or "perhaps" or "sometimes", how are we to distinguish the bonding atom–atom interaction from the energetically neutral or anti-bonding type?
Thakur, T.S. et al. (2015), IUCrJ, 2, 159-160; doi: 10.1107/S205225251500189X consider Dunitz’s questions from a chemical and crystal engineering perspective. They believe that in most cases the answer to the first question is “yes”, in a few cases "perhaps" and in the rarest of cases "no". This is evident from experimental observations that individual atom-atom contacts are, more often than not, adequate to exert a controllable structure-directing influence over molecular crystal structures. Merely because some short contacts in crystal structures might be repulsive, or even destabilizing, this should not dismiss all short contacts as not being of any significance in determining crystal packing.
Lecomte, C. et al. (2015), IUCrJ, 2,161-163; doi: 10.1107/S2052252515002067 approach the discussion from a more fundamental position, articulating the validity and usefulness of the bond path concept. Within the framework of Bader’s Quantum Theory of Atoms In Molecules (QTAIM) theory, observing bond paths and their associated bond critical points provide sufficient conditions to establish bonding interactions, whether intra- or inter-molecular. Thus, they suggest that the answer to Dunitz’s second question can be found in the analysis of high-quality diffraction data. In a crystal engineering context, QTAIM theory provides the theoretical basis for the supramolecular synthon approach.
The debate provides an illustration of how chemical and crystallographic concepts come together to frame the vibrant research field of crystal engineering. To read these and other articles in the current issue of IUCrJ, go to http://journals.iucr.org/m/issues/2015/02/00/.Dr Andrew Bond, University of Copenhagen, Denmark
Combining powder diffraction data with electron crystallography can give us a clearer view of modulated structures [Batuk et al. (2015). Acta Cryst. B71, 127-143; doi: 10.1107/S2052520615005466].
Electron crystallography has begun to be used routinely for solving otherwise intractable structures. When performed in an aberration-corrected microscope and combined with spectroscopic techniques, it can offer unprecedented detail down to sub-angstrom resolution. "The result of all this progress is that electron crystallography gives answers to more and more questions that used to be the domain of X-ray or neutron diffraction, and is especially useful when the X-ray or neutron experiment needs to be performed on a powder material, which limits the diffraction information available," explains Lukas Palatinus of the Czech Academy of Sciences in Prague in a commentary piece in Acta Crystallographica Section B [Palatinus (2015). Acta Cryst. B71, 125-126; doi: 10.1107/S2052520615005910].
Palatinus points out that when confronted with modulated structures, in which every atomic position is perturbed from one unit cell to the next by a modulation function, the construction of the structure model is much more complicated than for non-modulated materials. While effective techniques have been developed techniques to solve this problem from single-crystal diffraction data, for powder diffraction data another approach to get around the problem is needed, which is where the work of Batuk and colleagues comes to the fore.
Batuk and colleagues have now shown how electron crystallography tools can be used to sidestep the limitations of powder diffraction and complement the structure analysis of modulated structures by powder diffraction. "The authors combine the results of their previous research with new results to provide an impressive overview of the available methods and information they can provide," explains Palatinus. The team investigated a series of anion-deficient perovskites to demonstrate proof of principle. In these materials, modulation arises as a consequence of the presence of crystallographic shear planes that have an average periodicity that is not in synchrony with the materials' basic periodicity.
Palatinus also points out that the choice of these materials was good for the given purpose. "These structures exhibit a wide variety of features that complicate the structure analysis of modulated structures from powder patterns," explains Palatinus. "It allowed the authors to illustrate many techniques and applications like the simultaneous imaging of heavy and light elements, atomic resolution chemical mapping or the mapping of the coordination number." Additionally, given the advent of perovskites in recent years as the focus of research into solar panel materials and other semiconductor applications new detailed information about their structures and properties are increasingly important.
"The local crystallographic information acquired using the scanning transmission electron microscopy (STEM)-based methods in combination with the refinement from powder diffraction data can significantly improve the reliability of the crystal structure investigation," Batuk and colleagues report.
Of course, electron crystallography is very unlikely to make X-ray or neutron diffraction redundant any time soon, points out Palatinus, not least because a lot of materials are too short lived under the degrading eye of the electron beam. Moreover, electron techniques generally cannot be applied in situ in chemical reaction environments or under pressure, instead requiring near vacuum conditions. Nevertheless, he adds that the team "shows convincingly how the electron crystallography methods have grown to a rich source of detailed information on the crystal structures, and it should convince any reader that resorting to these methods may very quickly solve problems that seem intractable by the more traditional approaches." It seems that as with many areas of study, a combined effort, the teamwork between different techniques that can complement each others, is needed to obtain the best results. "The key to success indeed lies in exploiting the complementarity and synergy between various methods," Palatinus says.
When it comes to supramolecular chemistry, the carboxylic acid group (and its conjugate carboxylate base) is one of the chemist's most flexible friends. In pairs, they act as supramolecular synthons from which more complicated structures might be built but also offer up complex hydrogen bond connectivity. Luigi D'Ascenzo and Pascal Auffinger of the University of Strasbourg, France [D'Ascenzo, L. & Auffinger, P. (2015), Acta Cryst. B71, 164-175; doi: 10.1107/S205252061500270X], point out that until now there has been no exhaustive classification of these carboxyl(ate) motifs present in crystal structures, despite their prevalence and the fact that carboxyl(ate)s are among the most well-studied hydrogen bonding groups.
D'Ascenzo and Auffinger have now used what they describe as "simple stereochemical considerations" to identify just seventeen association types: thirteen carboxyl-carboxyl and four carboxyl-carboxylate motifs. This small number emerges from their analysis despite the seemingly overwhelming diversity of carboxyl–carboxyl(ate) dimers reported. To do so they took into account the free rotation that can take place around the hydrogen bond formed between the syn (C-O-H angle between 0 and 120 degrees) and anti (C-O-H angle between 120 and 180 degrees) carboxyl conformers and the syn and anti lone pairs of the oxygen atoms. They gleaned from this a simple rule that it is only possible for eight distinct catemer motifs (polymeric-like chains of carboxyl groups in the crystal) to form. They have identified examples of all dimers and catemers in compounds for which crystal data are recorded in the Cambridge Structural Database (CSD).
The researchers emphasize how the analysis of high-resolution structures of small molecules containing hydrogen atoms could offer new insights into the properties and behavior of much larger and far more complex biomolecular systems, the structures for which have been determined only at low resolution. They added that precise characterization and classification of these supramolecular motifs has implications for crystal engineering, pharmaceutical research (in particular drug co-crystallization) and the biomolecular sciences where related moieties are found, for instance, in the tertiary structures of proteins, in which hydrogen bonded pairs of amino acids or ligands containing carboxyl(ate) groups are present.
The team has not only classified the full gamut of dimers and catemers, but provided a systematic naming system, or nomenclature, for these and defined the recurrent hydrogen bonding themes among them. Despite their efforts to simplify the concept of carboxyl-carboxyl(ate) dimers and catemers that exist, they remain "astonished" that cyclic dimers do emerge rather than the single, simple hydrogen bonded dimers. Indeed, the cyclic dimer is actually the most prevalent motif.
Of course, classification, categorization and simplification do not necessarily provide a workaround for the creation of designer crystals. As crystal engineering pioneer Gautam Desiraju noted in 2007 on witnessing the constant discovery of unforeseen structures and assembly motifs, "it would seem that the brute force method will eventually win". Some rules do not always apply, some rules are there to be broken and in some circumstances these rules are just too complex to be comprehended and to guide the construction of supramolecular structures and novel crystals by chemists.