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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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Combined effort for structural determination

me0573Combining 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.

Posted 15 Apr 2015 

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Making carboxyl(ate) friends

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.

Posted 14 Apr 2015 

announcement


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Building Science Capacity in Africa

We are proud to announce that the IUCr has been awarded a grant for the project "Building Science Capacity in Africa via Crystallography" under the ICSU Grants Programme 2015. The proposal was prepared as a follow-up to the IYCr Pan African Summit meeting (Bloemfontein, October 2014) and submitted by the IUCr (as an ICSU member) on behalf of Andreas Roodt, President of ECA and chair of the Summit meeting, and Michele Zema, IYCr Project Manager and IUCr representative for the proposal.

The IUCr project is supported by:

  • ECA
  • UNESCO
  • ICSU Regional Office for Africa
  • INDABA Series of meetings
  • SAASTA (South African Agency for Science and Technology Advancement) Public Engagement with Nanotechnology

The project aims at further cementing the African Crystallographic Association (AfCA), whose Steering Committee has been established at the Summit meeting in Bloemfontein in October 2014. The programme will be conducted as part of the IUCr Crystallography in Africa initiative.

The main actions will be:

  • (i) to set up a follow-up meeting to the Summit, preferentially in Northern Africa, to further work towards the formal formation of AfCA;
  • (ii) to arrange a workshop in Central Africa, preferably in the Democratic Republic of Congo, to offer local scientists the opportunity to interact, liaise and strengthen basic knowledge of crystallography;
  • (iii) to bring African scientists to the INDABA series of conferences in South Africa (in the latter part of 2015) to expose them to high-level international interdisciplinary science.
  • Moreover, the project includes many additional actions, which will be undertaken pending the availability of funds, infrastructure and human resources.

For more information, please go here.

Posted 02 Apr 2015 

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Fluctuation X-ray scattering

In biology, materials science and the energy sciences, structural information provides important insightsdc5005 into the understanding of matter. The link between a structure and its properties can suggest new avenues for designed improvements of synthetic materials or provide new fundamental insights in biology and medicine at the molecular level.

During standard X-ray solution scattering experiments, molecules tumble around during X-ray exposures, resulting in an angularly isotropic diffraction pattern because of the full orientational averaging of the molecules that scatter X-rays. When X-ray snapshots are collected at timescales shorter than a few nanoseconds, such that molecules are virtually frozen in space and time during the scattering experiment, X-ray diffraction patterns are obtained that are no longer angularly isotropic. These measurements, called fluctuation X-ray scattering, are typically performed on an X-ray free electron laser or on an ultra-bright synchrotron and can provide fundamental insights into the structure of biological molecules, engineered nanoparticles or energy-related mesoscopic materials not attainable via standard scattering methods. 

A group of scientists from the Lawrence Berkeley National Laboratory [Malmerberg et al. (2015). IUCrJ, 2, doi:10.1107/S2052252515002535] recently presented an intuitive view of the nature of fluctuation X-ray scattering data and their properties. The scientists have shown that fluctuation scattering is a natural extension of traditional small-angle X-ray scattering and that a number of fundamental operational properties translate from small- and wide-angle X-ray scattering into fluctuation scattering. The authors also show that even with a fairly limited fluctuation scattering dataset, the amount of recoverable structural detail is greatly increased compared with what can be obtained from standard SAXS/WAXS experiments. Given that the high-quality structural models can be obtained from fluctuation scattering data and the ever-increasing availability of X-ray sources at which these experiments can be performed, the researchers expect that fluctuation scattering experiments will become routine in the future.

”Although fluctuation scattering experiments are not standard or routine at the moment, this work enables us to assess the quality of experimental data and allows us to validate our experimental protocols and data reduction routines”, Peter Zwart says.

Posted 25 Mar 2015 

press release


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Biochemistry researchers at the University of Oxford share their work with the public in crystallography's centenary year

garman5_200px.jpgX-ray crystallography has never had so prominent a place in the world. The illustrious history of the field and its discoveries were celebrated by numerous events across the UK and elsewhere during 2014, the International Year of Crystallography, www.iycr2014.org. Researchers from the Department of Biochemistry at the University of Oxford participated in several of these events.

Jointly organised by the IUCr and UNESCO, the year commemorated the centennial of the birth of X-ray crystallography, thanks to the work of Max von Laue and the Braggs father and son.

The award of the Nobel Prize to Max von Laue in 1914 recognised his work on copper sulphate crystals. He was the first person to discover that X-rays can be diffracted by crystals and observed the characteristic spots from these crystals.

Taking the work a step further, William and Lawrence Bragg discovered that X-rays could be used to determine the positions of atoms within crystals accurately. By formulating "Bragg’s Law", they gave researchers the tool to interpret the diffraction pattern of spots and generate a detailed picture of the three-dimensional structure of compounds. They received a Nobel Prize for this achievement in 1915.

The International Year of Crystallography aimed to mark these and many other milestones in the field, from the discovery of the DNA double helix to groundbreaking work on graphene and the ribosome complex (around 280,000 non-hydrogen atoms). Through an incredible variety of activities including science fairs, exhibitions and professional-level training sessions, crystallography has been brought to life for many different audiences.

Several crystallography researchers from the Biochemistry department contributed to events marking ajonnybb century of crystallography; these included Professor Elspeth Garman; Jonny Brooks-Bartlett, a DPhil student in Elspeth's group; Associate Professor Matt Higgins; Professor Judy Armitage and Professor Mark Sansom.

Talking to a reporter Professor Garman comments, "The year has really raised the profile of the topic internationally and has resulted in lots of outreach and public engagement activities. There is a new energy and it has really benefited countries where there are limited activities in the field. Some of the initiatives will undoubtedly be continued".

This press release is reprinted from material taken from the Department of Biochemistry website at the University of Oxford. The link to the original press release can be found here.

Posted 19 Mar 2015 

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The ecstasy and the agony: compression studies of MDMA

ps5039MDMA (3,4-methyenedioxymethamphetamine), a Class A substance that is usually found in a tableted form, is a psychoactive drug which is structurally similar to methylamphetamine and acts as a central nervous system stimulant, producing mood enhancement, increased energy and other empathetic effects. MDMA was first synthesized by Merck as far back as 1912 as a potential appetite suppressant; however, the company never marketed it as such.

In the 1970s and 1980s the substance surfaced on the recreational drug scene and its widespread abuse led many countries to prohibit the possession, supply and manufacture of MDMA. Currently, in the UK, MDMA is controlled as a Class A, Schedule 1 substance owing to its illicit use as a recreational drug, and its implication in a number of highly publicized fatalities. It is usually found in tableted form; the tableting procedure subjects the material to elevated pressures in which conversion to other polymorphs may occur.

A group of scientists from Glasgow, Dundee and Manchester decided to investigate how MDMA behaves under such extreme pressure [Connor et al. (2015). Acta Cryst. B71, 3-9; doi:10.1107/S2052520614026389]

Under ambient conditions MDMA is only observed in one orthorhombic polymorph. The scientists found there was no change in polymorph even to extremely high pressures, i.e. it is very unlikely that, if starting with this form of MDMA, a polymorphic transition would occur during tableting.

The scientists mention that, owing to this being a single crystal study and the fact that pressure needed to be applied hydrostatically to the sample to obtain the 3-D information on the structure, one may find under non-hydrostatic conditions that a polymorphic change may indeed occur.

The scientists intend to keep investigating illicit materials under various conditions of pressure and temperature to gain a better understanding of their solid-state chemistry.

Posted 17 Mar 2015