The IUCr Newsletter is the web magazine of the International Union of Crystallography. Since 1993, the IUCr Newsletter has been published quarterly and distributed to over 13,000 crystallographers worldwide. In August 2018, it was transformed into a dynamic digital platform with a fresh new look. Its aim remains to bring together the crystallographic community.
|
William L. Duax Patricia Potter Jane Griffin The IUCr Newsletter is distributed electronically to 13,000 crystallographers and other interested individuals in 102 countries. Articles from the Newsletter are also available on this web site by following the links on the left-hand side. Feature articles, meeting announcements and reports, information on research or other items of potential interest to crystallographers may be submitted to the editor at any time. Items will be selected for publication on the basis of suitability, content, style, timeliness and appeal. Please send contributions to: newsletter@iucr.org Matters pertaining to advertisements should also be sent to the above address. Email address changes or corrections and requests to be added to the mailing list should be accomplished through the Subscribe and Unsubscribe hyperlinks above. Reuse permissions • The original article in which the material appeared is cited. • Copyright permission is indicated by the wording "Reproduced with permission of the International Union of Crystallography Newsletter". In electronic form, this acknowledgement must be visible at the same time as the reused materials, and must be hyperlinked to the IUCr Newsletter (http://www.iucr.org/news/newsletter). Please be sure to include the following information: • The title, author(s) and page extent of the article you wish to republish, or, in the case where you do not wish to reproduce the whole article, details of the section(s) to be reproduced. • The volume/issue number and year of publication in which the article appeared, and the page numbers of the article. • Details of the publication in which you wish to reprint the Newsletter material. • If the material is being edited or amended in any way, a copy of the final material as it will appear in your publication. • Contact details for yourself, including a postal address. |
![[Cover v25n2]](https://www.iucr.org/__data/assets/image/0018/135180/cover25n2.jpg) Click here for PDF Use menu on left to access previous digital issues |
Annual Reports to the IUCr Executive Committee
The IUCr Newsletter (ISSN 1067-0696; coden IUC-NEB) is published quarterly (4x) by the International Union of Crystallography (IUCr Executive Secretary e-mail execsec@iucr.org). Members receive the IUCr Newsletter by virtue of country membership in the IUCr. Periodical postage rates paid at Buffalo, NY and additional mailing offices. POSTMASTER: Please send changes of address to IUCr Newsletter Editorial Office, c/o Hauptmann-Woodward Medical Research Institute, 700 Ellicott St. Buffalo, NY 14203 USA.
The person you knew would have the answers. The person who would help you analyse a challenging situation. The person who would recommend just the right outdoor activity to clear away that gloom. The person who gave you a home in science, encouraged you and convinced you that you belonged. That you mattered. Marilyn was all of those people, to me and many others.
It’s a warm October day in the San Francisco bay area, two weeks to the day after I was awoken at 1am to receive the most tragic of news. The words at the time seemed hydrophobic and immiscible to my sleep-sodden mind - slipping and sliding across the surface of my consciousness, but not ever soaking in. Seeking solidarity in shock, I messaged a number of my academic siblings. Joined over the various apps that have recently become our social lifelines, we muttered the same phrases of disbelief. Struggling for words, we eventually ended our calls with promises to talk again soon. I then turned to social media and swiped through photos of happy times with Marilyn, until I couldn’t see through the tears.
Over the past two weeks, the slow diffusion of acceptance has illuminated more facets of this devastating loss. Memories of past adventures together are now glazed with a somber patina. Future plans and projects glow with a diminished lustre, seemingly without hope of being blessed with Marilyn Magic. However, amongst all this grief, we humans continue to do the thing we do so well: weave our stories into a mourning tapestry, rich in memories and comfort. Marilyn’s youth as a natural scientist, examining lizards and becoming a ham radio operator at the age of 13. Marilyn’s persistence and brilliance in academia, despite its hostility towards women. Marilyn’s patience and kindness while mentoring. Pomegranate-jelly-making sessions perennially marking the arrival of autumn. Trips to Tahoe in the summer for hiking and swimming; trips to Tahoe in the winter for skiing and snowboarding. Marilyn’s dedication to international collaborations, and her love of immersive travel, where she truly stretched herself to experience a culture while expanding her collaborative family. The whirlwind experience of being at a crystallography conference with Marilyn, and feeling like you are partying with a rockstar. Nearly all of these testimonials included hypothetical questions in the vein of “How will we go on without Marilyn?” I know I felt similarly; none of us feel ready to step into such colossal shoes. Another common thread within all these stories was the incredible amount of energy that Marilyn imbued into all her interactions. A dynamic energy when the tricky structure as well as a student’s success were close at hand. A courageous energy that defied all limits and encouraged others to dream bigger. A compassionate energy when the challenges seemed insurmountable and emotion ran high.
Through all these stories, we are reminded that Marilyn believed in us. She trusted us to take the tools she gave us and go forth. When our confidence flagged, she cheered us on. When we were unsure, she helped us determine the facts of the matter and weigh them appropriately. We are now faced with this grievous time, where we are without her counsel and cheer, and are feeling adrift in this loss. May we all follow Marilyn’s encouragement, and see ourselves more as she saw us; going forward together, with courage and compassion, would certainly make her proud.
The IUCr has learned that Dr Geoffrey Pitt, a crystallographer who trained in Dorothy Hodgkin's lab in Oxford, UK, after WW2, has four bound volumes of Acta Crystallographica dating from 1948 to 1951 (Volumes 1 to 4) available free of charge to a good home. Collection from the M3/North Hampshire area required. Please contact support@iucr.org if interested.
Subsequent note: these back issues have now found a home and are no longer available.
Since its inception in Brookhaven (USA) in 1968, the International Conference on the Chemistry of the Organic Solid State (ICCOSS) has become the premier forum for discussing groundbreaking research on the chemistry and physics of organic materials. We were proud to host the 24th conference, ICCOSS XXIV 2019, at New York University, NY, USA, from 16 to 21 July 2019. The program showcased frontier research from a slate of international experts, with curated sessions that represent the cutting edge of organic solid-state chemistry. The conference had many opportunities for informal conversations as well as some special sessions that addressed societal and career issues. The scientific program for ICCOSS XXIV included invited and contributed lectures, as well as poster sessions. In addition, an exhibition of scientific instruments, electronic resources and books took place. The conference schedule consisted of eight technical sessions: (1) Crystals that Move, (2) Crystals in Computers, (3) Crystals that Grow, (4) Crystals in Devices, (5) Crystals in Nature and Medicine, (6) Crystals and Light, (7) Crystals in 2D and (8) Crystals with Holes. These topics represent the forefront of research in organic solid-state chemistry, from dynamics in crystals to machine learning for crystal structure prediction to crystals in medicine.
There were 53 oral presentations in total, of which 17 were contributed from female speakers (32%) and 36 from male speakers (68%). One of them come from Africa, 12 from Asia, 1 from Australia, 13 from Europe, 25 from North America, and 1 from South America.
The conference hosted 162 registered attendees, of which 60 were female (37%) and 102 male (63%). Three of them come from Africa, 39 from Asia, 1 from Australia, 26 from Europe, 90 from North America, and 3 from South America.
![[Fig. 1]](https://www.iucr.org/__data/assets/image/0018/150345/Fig.-1.png)
Group photo of attendees.
Three young scientists were selected to receive financial support from the IUCr to attend ICCOSS XXIV:
María Cecilia Dávila, an undergraduate student at the Universidad de Los Andes, Venezuela, working in the research group of Graciela Díaz de Delgado. Her research focuses on crystallography of pharmaceutical polymorphs. She presented a poster titled “Metal Derivatives of an API with Incommensurate Modulated Structures”.
Qiang Zhu, an assistant professor at the University of Nevada, Las Vegas, NV, USA. His research focuses on the development of first-principle structure predictions based on evolutionary algorithms and their applications. He gave an oral presentation titled "Crystal Structure Prediction: From Code Development to Applications”.
Noa Marom, an assistant professor at Carnegie Mellon University, Pittsburgh, PA, USA. Her research focuses on quantum mechanical simulations combined with machine learning and optimization algorithms to computationally design materials with desired properties for various applications. She delivered an oral talk on “Property-Based Genetic Algorithm Optimization of Molecular Crystals for High Carrier Mobility”.
![[Fig. 2]](https://www.iucr.org/__data/assets/image/0019/150346/Fig.-2.png)
(Left photo) María with Bruce Foxman (left) and Ian Duncan Williams (right) in the poster session, and (right photo) Qiang Zhu presenting his research.
Yael Tsarfati (Weizmann Institute of Science, Israel) won the IUCr Journals Poster Prize. She received a voucher for the second edition of Joel Bernstein's book Polymorphism in Molecular Crystals. She is working on the understanding of crystallization of organic molecules in the group of Boris Rybtchinski. Her winning poster’s title was “The Mechanism of Non-Classical Organic Crystallization”.
![[Fig. 3]](https://www.iucr.org/__data/assets/image/0020/150347/Fig.-3.png)
Yael Tsarfati talking about her poster.
The success of ICCOSS XXIV relied on many factors, of which one of the most important was the financial support to the young scientists attending the conference. The conference organizers are very grateful to the many organizations generously providing support to these brilliant young scientists.
Up until a decade ago, photographic film provided the best performance for the recording of cryo-electron microscopy (cryo-EM) images. Digital cameras using a phosphor scintillator have also been available since the late 1990s, but despite being more convenient to use their signal-to-noise characteristics were significantly inferior to those of film. Irrespective of their differences, both recording methods were far from the theoretically achievable performance and limited the typical resolution of cryo-EM reconstructions to a ‘blobology’ (~10 Å) level. The inadequacy of these legacy image capture methods was resolved around 2012 with the first commercial introduction of direct electron detectors (DEDs). Together with substantial advances in image processing algorithms, these new cameras played a fundamental role in the great leap in cryoEM performance.
As the name suggests, DEDs detect electrons through their direct interaction with the active silicon layer of the camera chip (McMullan et al., 2016). They are based on CMOS technology that gives them radiation resistance and fast readout speeds. Unlike previous methods that recorded a single integrated image, DEDs are read out continuously during the exposure with a frame rate of a few hundred frames per second. Each frame contains a small number of incident electron events that are sufficiently dispersed to allow on-the-fly numerical identification and localization of individual electrons. The process is known as ‘electron counting’ and virtually eliminates detection noise, resulting in a superior signal-to-noise ratio. Furthermore, the localization of electron events can be performed with sub-pixel accuracy to extract information beyond the physical Nyquist frequency of the detector. The current approach for recording of the counted electron data is to accumulate the counts from several frames on an image grid and store it as an ‘exposure fraction’ in a movie. The pixel dimensions of the fraction are either the same as the detector or two-times oversampled for the so-called ‘super-resolution’ mode. The number of detector frames that are accumulated into each fraction is a parameter that must be decided before the experiment and cannot be changed after the data have been collected. Smaller fractions and super-resolution sampling can produce higher quality results but also significantly increase the size of the recorded movies. Therefore, researchers must make a compromise by selecting recording parameters that will provide close to optimal results without requiring excessive data storage space. In some unfortunate cases, after processing the data the a priori parameter choice may turn out to have been suboptimal, but apart from performing another experiment there is no way to correct it.
In a recent IUCrJ paper, Guo and colleagues (Guo et al., 2020) present a new data recording and storage format for direct electron detectors called ‘electron-event representation’ (EER). Instead of recording movies, it captures each individual electron event and saves its coordinates in (x, y, time) space (Fig. 1). Consequently, the EER method preserves the spatial and temporal information for every electron and resolves completely the compromise between information retention and data size that is currently imposed by the movie recording format. Furthermore, EER uses fourfold spatial supersampling which allows it to capture high-resolution image components beyond the physical Nyquist periodicity of the detector, with sufficient signal-to-noise ratio to be usable in cryo-EM reconstructions. The authors provide an experimental demonstration with an apoferritin test sample that has reached a resolution 1.2 times the Nyquist frequency. Having good information preservation up to and even beyond Nyquist will allow researchers to comfortably collect data at lower microscope magnifications that give a larger sample area field of view, without high-resolution signal loss. This will increase the number of particles per image or the captured cellular area in cryo-tomography and boost the experimental throughput. The complete preservation of temporal information will also improve the performance by allowing finer sampling and interpolation on the single frame level during the beam-induced motion correction step of data processing. This will provide means for recovering a much larger portion of the high-resolution information that is present only in the very beginning of the exposure, before radiation damage of the sample has progressed, but also when the majority of beam-induced motion of the specimen is taking place. Because the EER format contains a complete representation of the electron events, experimentation and optimization of the motion correction fractionation parameters can be performed freely during data processing.
EER is another significant step in the development of cryoEM detector technology. It removes experimental restrictions and improves detector performance while also freeing researchers from mandatory data reduction decisions that had to be made with previous recording methods.
McMullan, G., Faruqi, A. R. & Henderson, R. (2016). Methods in Enzymology, Vol. 579, edited by R. A. Crowther, pp. 1–17. New York: Academic Press.
This article was originally published in IUCrJ (2020). 7, 780–781.
Computational modelling is now integrated into almost all areas of science; and as well as being widely used for gaining insight and guidance in analysing and explaining experimental data, modelling has acquired an increasingly predictive capacity. This editorial will provide a brief review of its current status and role in structural science and will consider the likely future developments of the field. We focus first on our ability to model and predict crystal structures, after which we consider the challenges posed by disordered solids.
The use of computational methods in modelling crystal structures goes back many decades and in the 1970s and 1980s rapid progress was made with the use of methods based on interatomic potentials or force fields, coupled with energy minimization, to model accurately the crystal structures of a wide range of solids, both inorganic materials, including oxides, halides and silicates, and organic, molecular solids. These methods could be used to refine approximately known structures, as was also widely done in structural molecular biology. They could be enhanced by the use of molecular dynamical (MD) simulation methods and later by the use of density functional theory (DFT) based quantum mechanical methods, which as well as further refining crystallographic structures, generated models for the electronic structures of the materials. The article of Takada et al. (2018) provides an illustration of how MD methods can be used to gain insight into complex structures, in this case, those associated with tridymite, while many examples of the applications of DFT techniques will be found in recent issues of IUCrJ.
Structure modelling, based on known structures, which may be approximate, remains a useful tool. Far more challenging, however, is structure prediction based simply on the composition of the solid. Indeed, a celebrated challenge was issued over thirty years ago in a ‘News and Views’ article in Nature by John Maddox, who provocatively wrote: ‘One of the continuing scandals in the physical sciences is that it remains impossible to predict the structure of even the simplest crystalline solids from a knowledge of their composition.’ The field has responded well to the Maddox challenge over recent years and successful structure prediction has now been achieved for many classes of material, as discussed in the reviews of Woodley & Catlow (2008), Price (2018), Oganov (2018) and Woodley et al. (2020). The general approach is to navigate the configurational space defined by the structural parameters, using a rapidly computable ‘cost function’ which may be a simple energy evaluation; regions of low cost function are identified and the resulting structures may then be refined using energy minimization coupled with a more accurate energy evaluation employing a force field or quantum mechanical technique. The navigation of configurational space can use a variety of techniques and algorithms, including simulated annealing, genetic algorithms, and topological and molecular packing approaches.
An elegant recent example of the success of structure prediction in inorganic materials is provided by the work of Collins et al. (2017), who used a Monte-Carlo-based simulated annealing algorithm to predict a new structure in the complex phase field of an Y–Sr–Ca–Ga-oxide; the material was subsequently synthesized and the predicted structure confirmed experimentally. Prediction methods have also been successfully applied to organic materials, especially porous organic solids as illustrated by the recent work of Pulido et al. (2017).
Structure prediction is also extensively used in nano-science as reviewed by Catlow et al. (2010) for nano-clusters of inorganic systems. Recent work of Lazauskas et al. (2018) provides a good illustration of the application to metallic nano-clusters with the structures for titanium clusters with 2 to 32 atoms predicted by combining an MC search procedure using a force field with DFT refinement. The resulting structures are shown in Fig. 1.
An important recent development is the growing use of machine learning techniques, as discussed by Woodley et al. (2020). More generally, the field continues to take advantage of both developments in technique and algorithms and the continuing expansion of computer power. Crystal structure prediction is still far from routine, but it is an increasingly important tool in structural science. As structure prediction becomes more widespread, it will be essential that the metadata accompanying the structure make it clear whether the structure is experimentally determined, predicted or some combination of the two.
Turning now to disordered solids there are many challenges to both experiment and computation as shown by several articles in IUCrJ over recent years. The first concerns the structures and energies of defects in crystalline solids. Modelling of point defects in solids was indeed one of the earlier successes of computational condensed matter science, where work in the 1970s and 1980s using force-field-based methods was able to achieve good agreement between calculated and experimental defect properties, especially in inorganic materials. The field was extended to include more complex defect structures, including point defect clusters and line and planar defects, and it has continued to develop rapidly. Contemporary work still makes some use of forcefield methods, but is increasingly based on quantum mechanical methods using quantum mechanical/molecular mechanical (QM/MM) methods and periodic DFT techniques. Modelling is now an integral tool in the physics and chemistry of defective solids.
Heavily disordered solids including solid solutions and systems with high defect concentrations are attracting growing attention as again shown by articles over recent years in IUCrJ, and pose substantial challenges to theory and modelling. A common approach is to set up a supercell, aiming to model a disordered distribution within that cell. Realistic models may require very large cells and sampling of large numbers of configurations, although these requirements can be reduced by the use of symmetry as in the widely applied site occupancy disorder (SOD) approach developed by Grau-Crespo et al. (2007). Monte-Carlo techniques including those available in the knowledge led master code (KLMC) approach developed by Woodley and co-workers (see e.g. Lazauskas et al., 2017) also assist in modelling complex disordered solids, but the field is one of the most difficult and demanding in structural science.
Computational methods have for many years been used to construct models of amorphous solids. The general approach is to mimic the way by which glasses have traditionally been made, that is to quench from the liquid state. The process is simulated by a molecular dynamics ‘melt quench’ cycle in which MD is used to simulate the melting of the crystalline form of the material, followed by rapid cooling in which the system freezes into the amorphous state. Due to limitations in the time sampled by even the most ambitious MD simulations, the method has the problem that the timescale of the MD quench is far shorter that of an experimental quench. A number of approaches have been developed to mitigate this problem and the MD modelling of disordered materials has enjoyed considerable success, although challenges remain. A detailed discussion of the field is given in the monograph of Massobrio et al. (2015); and there is no doubt that the structural science of amorphous solids will continue to gain valuable input and insight from modelling techniques.
The capabilities of modelling tools are advancing rapidly and the range and ambitions of applications will grow. IUCrJ will continue to welcome articles which develop and apply modelling techniques as a tool in structural science.
Catlow, C. R. A., Bromley, S. T., Hamad, S., Mora-Fonz, M., Sokol, A. A. & Woodley, S. M. (2010). Phys. Chem. Chem. Phys. 12, 786–811.
Collins, C., Dyer, M. S., Pitcher, M. J., Whitehead, G. F. S., Zanella, M., Mandal, P., Claridge, J. B., Darling, G. R. & Rosseinsky, M. J. (2017). Nature, 546, 280–284.
Grau-Crespo, R., Hamad, S., Catlow, C. R. A. & Leeuw, N. H. (2007). J. Phys. Condens. Matter, 19, 256201.
Lazauskas, T., Sokol, A. A., Buckeridge, J., Catlow, C. R. A., Escher, S. G. E. T., Farrow, M. R., Mora-Fonz, D., Blum, V. W., Phaahla, T. M., Chauke, H. R., Ngoepe, P. E. & Woodley, S. M. (2018). Phys. Chem. Chem. Phys. 20, 13962–13973.
Lazauskas, T., Sokol, A. A. & Woodley, S. M. (2017). Nanoscale, 9, 3850–3864.
Massobrio, C., Du, J., Bernasconi, M. & Salmon, P. S. (2015). Molecular dynamics simulations of disordered materials. Heidelberg: Springer.
Oganov, A. R. (2018). Faraday Discuss. 211, 643–660.
Price, S. L. (2018). Faraday Discuss. 211, 9–30.
Pulido, A., Chen, L., Kaczorowski, T., Holden, D., Little, M. A., Chong, S. Y., Slater, B. J., McMahon, D. P., Bonillo, B., Stackhouse, C. J., Stephenson, A., Kane, C. M., Clowes, R., Hasell, T., Cooper, A. I. & Day, G. M. (2017). Nature, 543, 657–664.
Takada, A., Glaser, K. J., Bell, R. G. & Catlow, C. R. A. (2018). IUCrJ, 5, 325–334.
Woodley, S. M. & Catlow, R. (2008). Nat. Mater. 7, 937–946.
Woodley, S. M., Day, G. M. & Catlow, C. R. A. (2020). Philos. Trans. Roy. Soc. A. In the press.
This article was originally published in IUCrJ (2020). 7, 778–779.
In his article, Krivovichev (2020) examines the emerging class of polyoxometalate-bearing minerals and the origins of their unusual complexity in terms of information content. The 42 minerals in this class constitute less than 1% of recognized mineral species, but their descriptions mostly require the current generation of X-ray diffractometers, and it is likely that many more will be discovered by new mineral hunters in the future. Indeed, this is a rapidly growing class with 34 (81%) of its species described within the past two decades.
The average complexity of mineral crystal structures is about 220 bits per unit cell, and all 42 polyoxometalate-bearing minerals exhibit much higher than average complexity owing to the presence of nanoscale metal oxide clusters in their structures. The information content of the most complex of these, the uranyl carbonate ewingite, is more than 100 times higher than average. The structure of ewingite is also the most complex known mineral structure.
In 1783, Carl Wilhelm Scheele provided the first surviving written report of blue waters in the Idaho Springs (USA) region, but undoubtedly these had been observed previously. The blue waters are thought to be colored by soluble molybdenum oxide clusters (Mo3O8.nH2O) that crystallize as ilsemannite (and related species), which was first described in 1871. The mineral is inadequately characterized even today, in part because of its poor crystallinity and likely corresponds to several different species containing a variety of molybdenum oxide clusters that are examples of natural polyoxometalates. Dissolution of so-called ilsemannite in water produces a greenish-blue solution that later deepens to a typical molybdenum blue.
Under the right conditions, metal oxide clusters spontaneously self-assemble in aqueous solution. These anionic clusters can contain several hundred atoms and have dimensions ranging up to several nanometres. These have been extensively studied by inorganic chemists, who have revealed the impressive range in cluster structures and compositions. Owing to their lower charge densities and well defined structures, metal oxide clusters behave very differently in solution than simpler metal-bearing species, and high solubility is a hallmark of such clusters. There are many potential and realized applications of metal oxide clusters, and they are excellent model systems for studying structure–composition–size–property relations.
Differences in chemical bonding distinguish self-assembling metal oxide clusters in aqueous solutions that persist at the nanoscale, as compared to nucleation of nanoscale clusters that continue to grow and become crystals. Polyoxometalates are generally defined as the class of metal oxide clusters that contain multiple bonds between metal cations and oxygen. Such bonds are common in the case of d0 transition metals of groups V (V5+, Nb5+, Ta5+) and VI (Mo6+, W6+), as well as the actinides U, Np and Pu in their pentavalent and hexavalent oxidation states. The doubly or triply bonded oxygen atoms tend not to bridge to other metal centers and instead serve to stabilize the surface of the polyoxometalate. As such, polyoxometalates are inherently nanoscale materials and they have no macroscale analogs. Other types of nanoscale metal oxide clusters have surfaces that are stabilized by different chemical features, including protonation of oxygen atoms and capping by organic ligands.
Synthetic transition metal and actinide-based polyoxometalates have been extensively studied both in solution and the solid state. These clusters have been definitively demonstrated to self-assemble in solution, where they can persist indefinitely, or crystallization can be induced by evaporation from solution or various other methods. It is particularly important to recognize that such clusters can form and persist in natural aqueous solutions, where they can be highly soluble and mobile in geochemical systems. Minerals sometimes form that reveal and record their presence, but it is probably much more common for such clusters to enhance metal transport in a geochemical environmental system and then vanish without a trace. Indeed, the occurrence of polyoxometalates in natural systems presents a substantial challenge for geochemical models that traditionally do not account for nanoscale metal oxide clusters in aqueous systems, especially as it pertains to the mobility of these metals. Their solubilities are often much higher than those of simpler metal oxide complexes owing to their lower charge densities.
Crystallization of polyoxometalates and other types of metal oxide clusters in nature produces minerals with higher than normal complexities (information content). These minerals also are dominantly of lower-temperature origin, which in general tends to result in more complex structures. All but two of the polyoxometalate-bearing minerals form in aqueous systems, with notable exceptions that crystallize directly from volcanic gas.
Krivovichev, S. V. (2020). Acta Cryst. B76, 618–629.
This article was originally published in Acta Cryst. (2020). B76, 512–513.
In most crystal structure determinations with a given chemical composition, we expect that the number of formula units contained in the unit cell (Z) is at most equal to the multiplicity m of the general position, a fundamental characteristic of the corresponding space group. If this is the case, Z' which is equal to the quotient Z/m is one. Under such premises and if we are dealing with a molecular compound, finding the atomic structure and relative position of a single molecule is sufficient to characterize the entire crystal structure owing to the properties of the space group symmetry. However, cases may occur when Z' becomes an integer larger than one which often leads to interesting discoveries, for example, the existence of structural modulations.
The article by Brock & Taylor (2020) specifically deals with the identification of such cases by systematically scanning the organic structures stored in the Cambridge Structural Database. More specifically, the study focuses on translationally modulated molecular crystals which do occur, sometimes frequently, depending on the value of Z'. Each one of the Z' molecular structures presents numerous ways to deviate from an average form. Four types can be distinguished namely conformational, orientational, longitudinal and transverse.
In order to systematically scan the full set of molecular structures contained in the Cambridge Structural Database, the authors designed an algorithm to scan a large number of possible directions in the crystal structure in order to identify additional translational periodicities allowing the acceptance of minor deviations to be specified. The method is not always successful, and, in some cases, it has to be completed by visual observation.
The method proposed by the authors is certainly well adapted for a systematic search in a database of molecular structures and I consider it as complementary to another method which is also frequently used and based on the Fourier transform of the crystal structure, i.e. on the diffraction pattern of the structure. The intensity distribution of diffraction patterns is well adapted to identify any translational characteristic including approximate translations. Such a method has been used successfully, for example, by considering a family of inorganic compounds, scheelites, with many different periodicities where each member can be related to a single model based on a commensurately modulated structure (Arakcheeva & Chapuis, 2008).
The main interest in the search of any type of translationally modulated structures is that it reveals very subtle interatomic interactions which might not be obvious to detect. What are the main factors of structural modifications causing Z' to increase? Can molecular dynamical simulations reproduce such interactions? It appears that this is possible as shown, for example, by Pan & Chapuis (2005) provided that an adapted force field is selected.
There is another very interesting issue concerning very large Z' numbers which are not directly related to molecular structures but rather to inorganic or metallic structures under specific temperature or pressure conditions. Cases of structure with Z' reaching up to nearly 100 have been studied. Knowing that for metallic structures it is not uncommon to observe values of Z' = ![[1\over 48]](https://journals.iucr.org/b/issues/2020/04/00/me6090/teximages/me6090fi1.gif)
, one may wonder why a structure requires such a large number of independent atoms? After deeper studies it appears that the publishing authors have missed identifying the appropriate symmetries of the particular compound [see examples given by Perez-Mato et al. (2006) or Arakcheeva et al. (2017)].
The study of molecular structures presented by Brock and Taylor with Z' larger than a specific limit reveals the complexities of intermolecular interactions in crystals. The analysis of the results indicates various possible mechanisms of molecular distortions which will be very helpful for a deeper analysis of the molecular dynamical mechanisms that come into play. The task is certainly not simple but a combination of various methods, i.e. crystallographic analysis both in direct and reciprocal space combined with molecular dynamical simulations, would probably be the best bet for a deeper understanding of the interactions.
Arakcheeva, A. & Chapuis, G. (2008). Acta Cryst. B64, 12–25.
Brock, C. P. & Taylor, R. (2020). Acta Cryst. B76, 630–642.
Pan, Y. & Chapuis, G. (2005). Acta Cryst. A61, 19–27.
Perez-Mato, J. M., Elcoro, L., Aroyo, M. I., Katzke, H., Tolédano, P. & Izaola, Z. (2006). Phys. Rev. Lett. 97, 115501.
This article was originally published in Acta Cryst. (2020). B76, 510–511.
Here, I do not claim to appear or already be considered as an expert crystallographer. Far from it! In fact, this article simply aims to share a series of unforgettable training experiences on my road that will gradually lead me to become, one day, an expert crystallographer following my elders in science, who still make me want to learn more and more every day on the uses of X-ray techniques.
Thanks to the invaluable help and invitation from Sophie Cazalbou and Audrey Tourette of the “Phosphates, Pharmcotechnie et Biomatériaux” research team at the Interuniversity Center for Research and Materials Engineering (CIRIMAT) in Toulouse, France, I spent two months at their facilities in 2016. It was the first time I had come into contact with a powder X-ray diffractometer, and I was trained by Cedric Charvillat, Head of the X-ray Diffraction platform. This short, self-funded internship allowed me to complete my PhD thesis as quickly as possible under the supervision of my professor, Etienne Sagbo. This success opened up many other opportunities for training in crystallography and X-ray techniques by experts at IUCr-UNESCO OpenLabs, schools and workshops. As a compliment on my thesis defense, Professor Cazalbou gave me a copy of Cristallographie Geométrique by Nadine Millot. This book was dedicated “to encourage me to become soon an expert crystallographer”. It was a blessing!
![[Fig. 1]](https://www.iucr.org/__data/assets/image/0010/150301/Fig.-1.jpg)
Sidoine Bonou as a PhD student with a powder X-ray diffractometer at CIRIMAT (Toulouse, France) in 2016.
A year later, with my work on the “Conversion of Achatina snail shell acclimatized in Benin calcium phosphate for medical and engineering use”, partly carried out with Professor Cazalbou at CIRIMAT, I had the great pleasure of receiving the Best Poster Award at the Second Pan African Conference on Crystallography (PCCr2) in Accra, Ghana, in 2019. It was the first time I had received a prize at an international meeting with eminent crystallographers coming from all over the world. And to add to the occasion, I received the award from the hands of the IUCr Executive Outreach Officer, Michele Zema, who would go on to play a crucial role in the continuation of my adventure in crystallography. The prize consisted of the IUCr book A Little Dictionary of Crystallography, edited by A. Authier and G. Chapuis. Upon my request, Professor Zema dedicated this book to me, writing “To my friend Sidoine, wishing you a great career in crystallography”.
![[Fig. 2]](https://www.iucr.org/__data/assets/image/0011/150302/Fig.-2.jpg)
Sidoine Bonou with his prize for the Best Poster at PCCr2 (Accra, Ghana) in 2019.
At this stage, in my country, the Republic of Benin, great reflections had started and moved in the direction that the scientific future of Benin and all of Africa would be "crystalline" very soon! This is when LAAAMP (Lightsources for Africa, the Americas, Asia, Middle East and the Pacific), founded and coordinated at that time by Sekazi Mtingwa, Michele Zema and Sandro Scandolo (note Marielle Agbahoungbata and Özgül Öztürk were appointed as members of the LAAAMP Executive Committee at a later stage), comes into the picture. In fact, following the invitation of LAAAMP, Thierry d’Almeida from CEA (France) visited Benin - his home country - and managed to convince the President and his Cabinet to fund the implementation of a crystallography and tomography facility as part of the Sèmè City innovation center, which became known as X-TechLab. Professor d’Almeida saw in me the character of a young and engaged scientist who was very willing to learn and go further, and wanted me in his working group. I joined the X-TechLab team on the occasion of the organization of the first training sessions in X-ray crystallography, tomography and mathematical engineering, held in Cotonou in May and November 2019, within the framework of the Seme-City–IUCr-UNESCO–LAAAMP OpenLab. The sessions proved very successful and included contributions from eminent professors of international renown.
However, there was a crucial need for me to complete my training in crystallography before taking on the role of Research Coordinator at the X-TechLab, and from 29 August to 11 October 2019, I had the unique opportunity to travel across Italy for various training activities.
I was first in Naples, from 29 August to 4 September, where I attended the AIC International Crystallography School “Crystallographic Information Fiesta”, organized by Serena Tarantino, Brian McMahon and Michele Zema. This was such a fantastic experience, from both a scientific and a personal point of view. I had the opportunity to meet renowned lecturers and young researchers from around the globe, fundamental to building my network of contacts in the field. On the occasion of this workshop, the participants produced two articles, one on solving twinned structures and the other a macromolecular structure, which were subsequently published in IUCr Journals. My participation was supported by an IUCr Young Scientist Award, which was highly appreciated as it fully covered my accommodation and subsistence costs.
![[Fig. 3]](https://www.iucr.org/__data/assets/image/0012/150303/Fig.-3.jpg)
Michele Zema presenting Sidoine Bonou with the IUCr Young Scientist Award at the CIFiesta School (Naples, Italy).
With my great enjoyment and increased self-confidence, I learned that my application for an IUCr Young Scientist Award to attend the EXPO&more Workshop in Bari from 30 September to 3 October had also proved successful. Therefore, I had a three-week gap to fill between the end of the CIFiesta School in Naples and the start of the EXPO&more Workshop in Bari. Professor Zema suggested that I should spend this period in a crystallography lab in Bari, and introduced me to his friends and colleagues Gennaro Ventruti and Emanuela Schingaro, who quickly arranged to have me in their lab for an immersion internship. I learned a lot under their supervision and with the support and availability of their whole team. The training covered several topics, including selection, mounting and centering of single crystals, and data-collection strategies at ambient and high temperatures with a single-crystal diffractometer. Additionally, I received training in the maintenance of detector cooling devices and the programming of data collection on a powder diffractometer. In summary this internship allowed me to learn a bit of everything about powder and single-crystal diffractometers. These skills acquired during such a short period of three weeks deserved to be supplemented by other training.
The EXPO&more Workshop was also very enjoyable and useful as it offered a deep exposure to specific techniques and methods for X-ray powder diffraction.
![[Fig. 4]](https://www.iucr.org/__data/assets/image/0014/150305/Fig.-4.png)
Left: Angela Altomare presenting Sidoine Bonou with his IUCr Young Scientist Award at the EXPO&more Workshop (Bari, Italy). Right: Sidoine Bonou selecting and mounting single crystals for data collection at the University of Bari, Italy.
Like in a scientific adventure where you do not always know where the thirst for knowledge leads, I got the tremendous opportunity forwarded by Professor Mtingwa (LAAAMP) to apply for training on the XRD, XRF and XAS beamlines at the Elettra synchrotron in Trieste. So, very soon, it was already time to travel again and move from Bari to the north of Italy. Next stop was Trieste to attend the workshop “Instrumentation for Synchrotron Radiation Experiments” from 7 to 11 October, organized and funded by the International Atomic Energy Agency (IAEA).
I was very elated to interact with eminent scientists at this workshop, which was focused on the preparation, drafting and submission of a proposal for feasible experiments at a synchrotron and a visit to the facilities. Here too, I had very good trainers who impressed me with their teaching methods on X-ray techniques.
In addition to the background acquired in using powder and single-crystal diffractometers in the laboratories of the University of Bari, and to all the theory and practical sessions offered by the workshops in Naples and Bari, this training in advanced light sources at Elettra covered another important aspect, as it focused on the drafting of competitive proposals for an implementation on a synchrotron. Significantly, it was the first time a member of the young team of X-TechLab, i.e. I myself, had visited a synchrotron!
My travel experience in Italy for training in crystallography was wonderful because of the succession of opportunities. My commitment is now irreversible!
![[Fig. 5]](https://www.iucr.org/__data/assets/image/0015/150306/Fig.-5.jpg)
Sidoine Bonou at the XRF beamline at Elettra (Trieste, Italy), very excited to be on his first visit to a synchrotron.
My special thanks go to Audrey Tourette, Sophie Cazalbou, Cedric Charvillat and Etienne Sagbo for my thesis works; to Claude Borna, Head of Agence de Developpement de Sèmè City, to Thierry d'Almeida and Marielle Agbahoungbata, the X-TechLab Project Leader and Coordinator, respectively, and to Michele Zema (IUCr Executive Outreach Officer, Chair of the LAAAMP Executive Committee and Chair of the X-TechLab Scientific Committee) for his unwavering support and dynamism. My warm thanks also go to Sekazi Mtingwa (LAAAMP), who strongly supports and shares all opportunities to train young scientists at advanced light sources; Peter Ian Swainson (IAEA) and Hervé Djokpe (Benin Delegate at IAEA); Gennaro Ventruti, Emanuela Schingaro, Ernesto Mesto and Maria Lacalamita (University of Bari) and Anna Moliterni (CNR, Italy) for their fantastic hospitality during my stay in Bari; Serena Tarantino (University of Pavia and CIFiesta School, Naples); Angela Altomare (EXPO&more Workshop) and her team; Alessandro Migliori (XRF beamline), Guiliana Aquilanti (XAS beamline) and Jasper Plaiser (XRD beamline) at Elettra Sincrotrone Trieste; and all supervisors who contributed to my training during this special travel period.
The IUCr Newsletter (ISSN 1067-0696; coden IUC-NEB) is published electronically by the International Union of Crystallography. Feature articles, meeting announcements and reports, information on research or other items of potential interest to crystallographers may be submitted to the Editors at any time. Items will be selected for publication on the basis of suitability, content, style, timeliness and appeal.
Copyright © - All Rights Reserved - International Union of Crystallography
