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International Union of Crystallography

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.

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Brookhaven lab study explores nanoscale structure of thin films

The world’s newest and brightest synchrotron light source—the National Synchrotron Light Source IIbillinge (NSLS-II) at the U.S. Department of Energy’s Brookhaven National Laboratory—has produced one of the first publications resulting from work done during the facility's science commissioning phase.

The paper [Jensen et al. (2015). IUCrJ, 2, doi: 10.1107/S2052252515012221] discusses a new way to apply a widely used local-structure analysis tool—known as atomic pair distribution function (PDF) analysis—to x-ray scattering data from thin films, quickly yielding high-quality information on the films' atomic structure. The work creates new avenues for studies of nanocrystalline thin films.

PDF provides local atomic structural information or in other words, data for neighborhoods of atoms, by yielding the distances between all pairs of atoms in the sample. These distances appear as peaks in the data. In recent years, PDF has become a standard technique in structural studies of complex materials and can be used for samples that are bulk or nanoscale, amorphous or crystalline.

The approach that Billinge and his colleagues devised leverages the high fluxes of photons coming from NSLS-II, which, together with novel data reduction methods recently developed in his group, creates data suitable for PDF analysis from a thin film. Essentially, it turns the standard grazing incidence experiment on its head: the beam is simply sent through the film from the back to the front.

The first sample studied was an amorphous iron-antimony film on an amorphous borosilicate substrate mounted perpendicular to the x-ray beam. In order to isolate the contribution from the film, the substrate contribution was first determined by measuring the scattering pattern from a clean substrate. The signal from the film is barely visible in the raw data on top of the large substrate contribution, but could be clearly extracted during data processing. This allowed for a reliable, low-noise PDF that can be modeled successfully to yield the quantitative atomic structure of the film.

The data led to high-quality PDFs for both amorphous and crystalline films—confirmed by comparison to control samples in a standard PDF setup. Based on the success of these first measurements, the Billinge group and the XPD team are now planning future experiments to watch the films crystallize in real time, in the beam.

This work shows that NSLS-II—a DOE Office of Science User Facility with ultra-bright, ultra-concentrated x-ray beams—is already proving to be a game-changer in studies of thin films, which play a vital role in a large number of technologies, including computer chips and solar cells.

This article is reprinted from material taken from Brookhaven National Laboratory, with editorial changes made by IUCr.

Posted 04 Aug 2015 

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Charge density and optical properties of multicomponent crystals

APIs in the design of multicomponent functional solidsOptical materials serve a major role in modern sciences and technology. Many of the devices we use feature technology resulting from material discoveries in this fast moving area of research. Nowadays, the need for more efficient devices and minimisation in optoelectronics requires a novel approach towards crystal engineering of functional solids. A solution can be multicomponent materials built from either organic or mixed organic and inorganic components selected in a specific way, to combine molecular and structural properties to form a 3D architecture. Optical properties of a crystal strongly depend on two factors, i.e. the spatial distribution of molecules in the crystal structure and the electronic properties of molecular building blocks. The latter are easy to predict whereas the former are not. Crystal symmetry is often a key to obtaining a desired property. Noncentrosymmetric crystal structure (chiral/polar) is a necessary (limiting) condition for such properties as nonlinear properties of even order and linear properties like optical activity, piezoelectricity, pyroelectricity and ferroelectricity. However, fulfilling symmetry rules does not guarantee the existence of a physical effect. The choice of building blocks is crucial; in ideal cases, push–pull molecules should be linked with constituents enabling synthon formation flexibility.

Active pharmaceutical ingredients (APIs), through their favourable donor/acceptor spatial distribution and synthon formation flexibility, are attractive building blocks in modern materials crystallography. An API is a substance or a mixture of substances used in the manufacture of a drug product and which becomes an active ingredient in the drug product itself. Here, a Polish scientist (working in Professor Katarzyna Stadnicka’s group at the Jagiellonian University in Kraków) presents design strategies for optical materials based on selected pharmaceutical molecules [Gryl (2015). Acta Cryst. B71, 392-405; doi:10.1107/S2052520615013505]. Gryl successfully presents the factors that contribute to molecular recognition in the four selected polar/chiral crystal phases. Theoretically predicted optical properties of the molecular/ionic building blocks as well as bulk effects were all confirmed experimentally. This work shows that quantitative crystal engineering techniques combining structural analysis, charge density studies, prediction of properties and their measurements enable the full analysis of the obtained functional materials in terms of their usefulness in practical applications. The study is just a first step in the design of novel optical materials based on push–pull molecules and APIs.

This work presents an alternative application for pharmaceutical solids that are of major interest in the pharmaceutical industry. Dr Gryl’s journey with optical materials based on API started with three polymorphs of urea and barbituric acid adduct [Gryl, Krawczuk & Stadnicka (2008). Acta Cryst. B64, 623-632; doi:10.1107/S0108768108026645]. The co-crystals display synthon polymorphism (a possibility to use the same donor and acceptor sites in many ways) and hence enable the manipulation of the outcome of the engineering process. Why not use the same “flexible” molecules and incorporate them in a lattice containing components with high molecular (hyper)polarizability? This is a next step in Dr Gryl’s research. First, of course, as much as possible needs to be known about the selected building blocks and there is no better way than to study crystal structures containing those building blocks.

Posted 29 Jul 2015 

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Introduction to selected articles from the 15th ICCBM

The July 2015 issue of Acta Crystallographica Section F, Structural Biologyme0585 Communications features a special selection of papers that elaborate on presentations made at the 15th International Conference on the Crystallization of Biological Macromolecules (ICCBM15), which was held in Hamburg, Germany, 17-20 September 2014.

The first international meeting of this kind was held in 1985 at Stanford, California. ICCBM15, organized under the umbrella of the International Organization for Biological Crystallization (IOBCr), represents an unbroken span of 30 years of these biennial meetings. With 300 conference participants, the continuing and growing interest of crystallographers, chemists, physicists and engineers in crystal growth is confirmed, and this special section is a fine example of the range of research that these meetings continue to attract and support.

The articles are a useful addition to Acta Cryst. F and cover important structural biology topics related to crystallization. These include progress in nucleation studies, new techniques for detection of crystalline precipitates, production and scoring of nano- and micro-sized crystal suspensions in support of emerging applications of X-ray free-electron laser data collection procedures. These and more are examples of responses to the continued challenges to produce crystals for structural biology, featured at the Hamburg meeting.

We draw your attention to this special section of the issue, confident you will find much of interest you might not encounter elsewhere in your reading, and we hope that it whets your appetite for ICCBM16 which will be held on 2-7 July 2016 in Prague, Czech Republic.

Posted 23 Jul 2015 

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Journey into the crystal

[Touring exhibition]In our quest for the riches of the centre of the Earth, we have been discovering stones of varying shapes and substances since prehistoric times. Some stones have very unusual angular shapes with flat, fairly smooth sides, as if they had been manufactured. These natural angular shapes have long been a source of inspiration to learn more about the structure and composition of these fascinating objects.

Crystallography is little known to the public, even though it underpins much of the research into matter in physics, chemistry, new materials and life sciences. You could say crystallography originated with humanity’s exploration and interaction of these natural wonders. The study of matter continues apace today where we see crystallography is present in almost every field of science and technology.

The importance of crystallography provides a compelling argument to show as wide a community as possible, including children and junior students, the value of this scientific discipline [Hodeau and Guinebretière (2015). J. Appl. Cryst. 48, doi:10.1107/S160057671501064X].

With this goal in mind a travelling exhibition, Journey into the crystal, was launched to share with the general public the importance of the science and beauty of matter in the crystalline state. The exhibition takes visitors on a journey of discovery about matter, but also on a journey through time to the beginning of crystallography.

Through the journey into the crystal, the public discover why the crystal is intriguing, how it is so useful to science and how it plays such an important role in our daily lives. Visitors learn about the birth of crystallography and the multiple facets of crystals as objects of beauty, objects of science and contemporary objects with numerous applications.

The discoveries in crystallography of the 20th century have dispelled the mysteries about atomic structure and the physical properties of crystals, giving them a new place at the heart of modern civilisation. Crystals are now research tools used in investigations that cover an immense range, from the composition of our planet Earth to the microscopic structures of materials and the molecules of life.

The exhibition has already visited places such as Algeria, Ghana, India, Belgium, Argentina, and many other countries. The mission is to continue the road trip. If you would like to inquire about the exhibition visiting an institution near you please get in touch, med@iucr.org

You can find more details on our site Crystallography matters... more! http://www.iycr2014.org/resource-materials/voyage

Posted 20 Jul 2015 

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Advances in membrane protein crystallography

in situ data collectionMembrane protein structural biology has made tremendous advances over the last decade [Weyand & Tate (2015). Acta Cryst. D71, 1226-1227; doi:10.1107/S1399004715008317], as indicated by the exponential growth in the number of structures that have been published. These advances are a result of many factors including improvements in membrane protein overexpression, stabilization of proteins using antibodies or thermostabilizing mutations, and the enhancement of crystallization technologies such as crystallization in lipidic cubic phase (LCP).

However, there are still many challenges associated with membrane protein crystallization, data collection and structure determination. Major problems often arise because membrane proteins frequently form tiny crystals, which either cannot be improved in size or can be improved in size but, as a consequence, lose diffraction quality. In addition, crystal handling, such as mounting the crystals and soaking in cryoprotectants, is often the reason for the loss of diffraction quality through mechanical shear-induced microlesions. This is particularly true for membrane protein crystals, which are often very fragile because of their high solvent content and being very thin in one dimension. Two independent groups, Axford et al. and Huang et al., have published methods that make a major contribution to addressing these problems, which will facilitate high-resolution data collection from fragile crystals.

In the methodology demonstrated by Axford et al. [Acta Cryst. (2015). D71, 1228-1237; doi:10.1107/S139900471500423X], a standard in situ 96-well sitting-drop crystallization plate was used. The plate with the sample was left for several days until crystals grew to their maximum size. Instead of harvesting and mounting the crystals, the team mounted the entire plate on the beamline and standard procedures were then used for data collection from the membrane protein crystals. Results demonstrated that membrane protein structures can be determined at a synchrotron source using in situ room-temperature data-collection strategies.

Huang et al. [Acta Cryst. (2015). D71, 1238-1256; doi:10.1107/S1399004715005210] took the in situ approach one stage further and showed the applicability of room-temperature data collection for in meso/in situ crystallization and its use for high-throughput crystallography of membrane proteins crystallized in meso using LCP technology.

The two in situ high-throughput methodologies open up new perspectives in X-ray crystallography of membrane proteins and will provide a more rapid route to structure determination where the crystals are too small or fragile to mount, or where radiation sensitivity requires data collection from hundreds of crystals. In situ data collection therefore provides an excellent alternative to data collection at the X-ray free-electron laser, which cannot currently provide sufficient time for users.

Posted 09 Jul 2015 

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The silent partner in macromolecular crystals

jm5003The mother liquor from which a biomolecular crystal is grown will contain water, buffer molecules, native ligands and cofactors, crystallization precipitants and additives, various metal ions, and often small-molecule ligands or inhibitors. On average, about half the volume of a biomolecular crystal consists of this mother liquor, whose components form the disordered bulk solvent.

The solvent is therefore integral and also often an intrinsic part of almost any macromolecular crystal structure. Its disordered bulk components as well as its ordered constituents of varying nature need to be accounted for in modelling and refinement. The improvement of bulk-solvent description from a fundamental perspective is largely driven by methods development. In bulk-solvent refinement, users have limited choice beyond solvent-model selection and therefore not much opportunity for the introduction of bias or specific model errors, with the caveat that suboptimal masking sometimes can introduce density artefacts. In contrast, modelling of distinct solvent electron density almost always requires thoughtful interpretation, and using appropriate tools for (automated) building and validation can greatly improve the quality of structure models.

In a paper by [Weichenberger et al. (2015). Acta Cryst. D71, 1023-1038; doi:10.1107/S1399004715006045] a group of authors examine how to estimate the overall solvent content of a macromolecular crystal, how to account for and model disordered bulk solvent and how to properly identify and model distinct electron (or nuclear, in the case of neutron diffraction) density of ordered solvent molecules. The authors also emphasize that modelling of the biologically important interface region between the protein molecule and solvent is still incomplete, and advanced solvent models of these dynamic regions need to be developed.

Posted 25 Jun 2015