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An Editorial in the November 2021 issue of Acta Cryst. F discusses plans for Topical Reviews and introduces the first of a series of concise articles in this category by Guest Editor John Helliwell, dedicated to the 50th anniversary of the Protein Data Bank.
It is with sorrow that we relay the news of the death of Uwe Grimm, Professor of Mathematics at The Open University, Milton Keynes, UK. Professor Grimm was a much-valued Co-editor of Acta Crystallographica Section A and Consultant to the IUCr Commission on Aperiodic Crystals, which he chaired from 2014 to 2017.
We regret to announce the death of John Westbrook, Data & Software Architect Lead at Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), Piscataway, NJ, USA, and member of several IUCr Committees/Commissions.
The best in crystallographic research
Uniquely among International Scientific Unions, the IUCr publishes its own primary research journals. Acta Crystallographica Sections A–F, IUCrJ, Journal of Applied Crystallography, Journal of Synchrotron Radiation and IUCrData communicate the highest quality peer-reviewed research findings across the many scientific areas to which crystallography is relevant.
The virus world is wide and vast. And we have just started venturing further in our explorations through metagenomics studies and the characterization of the multitude of variants in viruses relevant to human health.
Fortunately, help is coming to explore the virosphere – another term used to describe the virus world – in the form of a new server called virusMED (Metal binding sites, antigenic Epitopes and Drug binding sites, https://virusmed.biocloud.top) developed by Wladek Minor, Heping Zheng and their collaborators (see Zhang et al., 2021, in this issue of IUCrJ).
To understand the scale of the task at hand, viruses infecting bacteria, called phages, alone represent the most abundant biological entity on earth, outnumbering cellular organisms by a factor of 10 (Dion et al., 2020). They have been less studied than their medically relevant counterparts but a flood of data has begun, owing in part to the renewed interest in phage therapy to combat antimicrobial resistance (Gordillo Altamirano & Barr, 2019) and the proposed role of phages in regulating the population dynamics of bacteria playing an important role in carbon capture (Suttle, 2005). Sampling of our oceans, soil and even our own gut has already expanded our view of phage diversity and generated masses of viral and virus-like sequences (Paez-Espino et al., 2016; Camarillo-Guerrero et al., 2021; Dion et al., 2020).
The search for viruses that infect eukaryotes is equally raging. For some discoveries, like mimiviruses and related giant viruses (La Scola et al., 2003), the biological significance is complex but they represent a wealth of new proteins, novel biological processes and almost infinite research questions. For others, the impact is immediately evident such as the characterization of the RNA virome in animals that represent known reservoirs for zoonotic viruses such as flaviviruses, haemorrhagic fever viruses, influenza viruses and coronaviruses.
As a tool for exploration, sequencing is extremely powerful in organizing viruses into families and setting up a robust classification of these organisms in the ever-growing Taxonomy of Viruses (https://talk.ictvonline.org). A complementary approach has focused on the determination and cataloging of three-dimensional structures produced by viruses. Indeed, structure determination of intact viruses has been at the forefront of developments in structural biology since its birth (Harrison, 2015; Rossmann, 2013). These structures are made freely available to all through the Protein Data Bank (Johnson & Olson, 2021), which celebrates 50 years of existence this month, as well as the virus particle explorer database (VIPERdb; http://viperdb.scripps.edu) (Montiel-Garcia et al., 2021). These invaluable resources are highly curated and constant efforts have been made to improve the quality of their content and make it more accessible to all despite exponential growth (Smart et al., 2018; Montiel-Garcia et al., 2021).
While these resources are free, analysis of each viral structure is onerous and requires expertise in several inter-connected fields such as biochemistry, chemistry, molecular virology and immunology. This is where virusMED comes in to save the day. Think of it as your GPS navigation app that will guide you quickly and safely to your destination. Like a navigation app, it taps into tools that are readily available elsewhere: primary databases with sequence information, 3D structures, functional sites, metal and drug binding sites, and epitope repositories. The power of the server is to help researchers combine information from these different sources and make sense of it for the specific goal of understanding and combating viruses [Fig. 1(a)].
Figure 1. (a) virusMED is an atlas of hotspots present in viral proteins that correspond to metal binding sites, epitopes and drugs/small molecules. It is searchable by virus (not shown) and type of hotspot (top panel). Results are presented in a tabular form that can be filtered (middle panel) and mapped onto the 3D structure, providing context and a detailed view of the hotspot. (b) Schematic loosely based on a DIKW hierarchy. virusMED provides a navigation tool tailored to molecular virology that consolidates curated data available in various databases. This atlas is likely to facilitate research for viral families with a high volume of data, where expert analysis is time-consuming (coronaviruses, HIV, influenza viruses etc.). The dotted lines indicate possible future developments that will further integrate the individual atlases and facilitate comparative analysis (e.g. overlapping drug and epitope hotspots shown in green).
Taking SARS CoV-2 as an example, in the space of 21 months (February 2020–October 2021) over 117 000 publications were made available in PubMED and 1555 structures in the PDB. This represents an average of over 180 articles and 2 new structures every day. Organizing, curating and providing visualization tools for this large amount of data is essential to extract the most relevant information in a format that will help generate novel insights [Fig. 1(b)].
virusMED provides an integrated portal to navigate through 7041 structures across 75 viral families. One can browse the database using several pre-set entry points or design specific searches to rapidly gain an overview of where and how metals and small molecules bind to a specific target. Many of these ‘hotspots’ will be important functionally and may represent targets for drug development. With drug repurposing in mind, the results can be filtered to focus only on known drugs found in Drugbank or those that are already FDA approved.
The same portal allows mapping of antigenic sites in viral proteins, providing a database of more than 5000 B- and T-cell epitopes for 329 individual proteins. These can be combined to determine the antigenic landscape of viral proteins, identify variants likely to escape vaccination or reveal targets for potent and broadly neutralizing epitopes.
As the database grows, future developments can be anticipated such as more complex visualization options and an integrated search engine allowing the comparison of new structures with known hotspots. Data on binding sites for other viral proteins and cellular factors accumulate rapidly (Goodacre et al., 2020; Gordon et al., 2020) and, while a huge task, would deserve a similar atlas. For now, there is little doubt that many in the structural virology community will adopt this tool to accelerate their research and facilitate the development of antiviral strategies.
Camarillo-Guerrero, L. F., Almeida, A., Rangel-Pineros, G., Finn, R. D. & Lawley, T. D. (2021). Cell, 184, 1098–1109.e9.
Dion, M. B., Oechslin, F. & Moineau, S. (2020). Nat. Rev. Microbiol.18, 125–138.
Goodacre, N., Devkota, P., Bae, E., Wuchty, S. & Uetz, P. (2020). Semin. Cell Dev. Biol.99, 31–39.
Gordillo Altamirano, F. L. & Barr, J. J. (2019). Clin. Microbiol. Rev. 32(2).
Gordon, D. E., Jang, G. M., Bouhaddou, M., Xu, J., Obernier, K., White, K. M., O’Meara, M. J., Rezelj, V. V., Guo, J. Z., Swaney, D. L., Tummino, T. A., Hüttenhain, R., Kaake, R. M., Richards, A. L., Tutuncuoglu, B., Foussard, H., Batra, J., Haas, K., Modak, M., Kim, M., Haas, P., Polacco, B. J., Braberg, H., Fabius, J. M., Eckhardt, M., Soucheray, M., Bennett, M. J., Cakir, M., McGregor, M. J., Li, Q., Meyer, B., Roesch, F., Vallet, T., Mac Kain, A., Miorin, L., Moreno, E., Naing, Z. Z. C., Zhou, Y., Peng, S., Shi, Y., Zhang, Z., Shen, W., Kirby, I. T., Melnyk, J. E., Chorba, J. S., Lou, K., Dai, S. A., BarrioHernandez, I., Memon, D., Hernandez-Armenta, C., Lyu, J., Mathy, C. J. P., Perica, T., Pilla, K. B., Ganesan, S. J., Saltzberg, D. J., Rakesh, R., Liu, X., Rosenthal, S. B., Calviello, L., Venkataramanan, S., Liboy-Lugo, J., Lin, Y., Huang, X. P., Liu, Y., Wankowicz, S. A., Bohn, M., Safari, M., Ugur, F. S., Koh, C., Savar, N. S., Tran, Q. D., Shengjuler, D., Fletcher, S. J., O’Neal, M. C., Cai, Y., Chang, J. C. J., Broadhurst, D. J., Klippsten, S., Sharp, P. P., Wenzell, N. A., Kuzuoglu-Ozturk, D., Wang, H. Y., Trenker, R., Young, J. M., Cavero, D. A., Hiatt, J., Roth, T. L., Rathore, U., Subramanian, A., Noack, J., Hubert, M., Stroud, R. M., Frankel, A. D., Rosenberg, O. S., Verba, K. A., Agard, D. A., Ott, M., Emerman, M., Jura, N., von Zastrow, M., Verdin, E., Ashworth, A., Schwartz, O., d’Enfert, C., Mukherjee, S., Jacobson, M., Malik, H. S., Fujimori, D. G., Ideker, T., Craik, C. S., Floor, S. N., Fraser, J. S., Gross, J. D., Sali, A., Roth, B. L., Ruggero, D., Taunton, J., Kortemme, T., Beltrao, P., Vignuzzi, M., García-Sastre, A., Shokat, K. M., Shoichet, B. K. & Krogan, N. J. (2020). Nature, 583, 459–468.
Harrison, S. C. (2015). Annu. Rev. Biochem. 84, 37–60.
Johnson, J. E. & Olson, A. J. (2021). J. Biol. Chem. 296, 100554.
La Scola, B., Audic, S., Robert, C., Jungang, L., de Lamballerie, X., Drancourt, M., Birtles, R., Claverie, J. M. & Raoult, D. (2003). Science, 299, 2033.
Montiel-Garcia, D., Santoyo-Rivera, N., Ho, P., Carrillo-Tripp, M., Iii, C. L. B., Johnson, J. E. & Reddy, V. S. (2021). Nucleic Acids Res.49, D809–D816.
Paez-Espino, D., Eloe-Fadrosh, E. A., Pavlopoulos, G. A., Thomas, A. D., Huntemann, M., Mikhailova, N., Rubin, E., Ivanova, N. N. & Kyrpides, N. C. (2016). Nature, 536, 425–430.
Rossmann, M. G. (2013). Q. Rev. Biophys. 46, 133–180.
Figure 1. Illustration of accessible reciprocal space through a diamond anvil cell with a conical opening angle α. The colored toroidal volume VDAC is given by VDAC = 4π/λ3[sin α(α — sin α cos α)] (Merrill & Bassett, 1974; Miletich et al., 2000). Tchoń & Makal (2021) quantify systematically how a sample crystal of given symmetry needs to be oriented relative to the DAC in order to maximize the number of independent reflections in the toroidal volume. Figure modified after Miletich et al. (2000).
Diamond anvil cells (DACs) are simple devices that allow experiments involving electromagnetic radiation as a probe to be performed in the visible, IR and hard X-ray range at pressures between ~108 and 1011 Pa. Like almost anything of significance in the realm of DACs, their use for single-crystal X-ray diffraction was pioneered by Bill Bassett in Cornell in the 1970s (Merrill & Bassett, 1974). These simple devices allowed a pressure dimension to be added to crystallography for the first time, thus providing an invaluable tool in the quest to experimentally explore the nature of the chemical bond in chemistry, physics and mineralogy. Not surprisingly, DACs found immediate acceptance and countless groups all over the world adopted this simple but powerful concept for high-quality structural studies at high pressures, which led to further refinements of DAC design and use (Allan et al., 1996; Finger & King, 1978; Kudoh et al., 1986; Miletich et al., 2000). For high-pressure single-crystal diffraction data to be of sufficient quality to enable accurate bond lengths, bond angles and displacement parameters to be extracted, a series of experimental artifacts and difficulties specific to DACs have to be overcome. These include precise crystal centering with reduced optical access (King & Finger, 1979), diamond absorption (Angel et al., 2000), gasket shadowing (Katrusiak, 2004) and intensity modulation through diamond anvil diffractions (Loveday et al., 1990).
An intrinsic limitation on data that comes with single-crystal diffraction in ancillary equipment is the restriction of accessible reciprocal space, thus making the collection of a complete set of unique diffraction intensities either difficult or impossible. In the case of DACs, this restriction was quantified for the first time, true to my comment above, by Bill Bassett (Merrill & Bassett, 1974) who found that the accessible reciprocal space forms a toroidal annulus (Fig. 1) whose volume is determined by the accessible q-range (i.e. wavelength and maximum diffraction angle) as well as the conical opening angle α of the DAC. Consequently, attempts to improve the completeness of high-pressure diffraction data were primarily directed towards improved DAC design (Allan et al., 1996; Kantor et al., 2012; Miletich et al., 2000) and improved diamond design (Boehler & De Hantsetters, 2004) to maximize the effective opening angle α and thus the toroidal subspace of the reciprocal lattice (Fig. 1).
One important aspect that crucially affects data completeness and is complementary to hardware development, and which was also already mentioned in Merrill & Bassett (1974), is the orientation of the sample crystal relative to the DAC geometry. This has never been fully quantified in a systematic way. Tchoń & Makal (2021) in this issue of IUCrJ, close this gap with a comprehensive and thorough study that systematically assesses the relative contributions of sample orientation, X-ray energy and DAC opening angle to the completeness of the diffraction data as a function of Laue class (symmetry). The level of completeness for a given experimental arrangement (i.e. combination of 2θmax, X-ray energy/wavelength, sample Laue class, DAC opening angle α and crystal orientation relative to DAC geometry) is quantified by a ‘Potency’ P that is the ratio between the ‘classical’ completeness as defined in International Tables Volume G and an ‘applicable’ completeness which depends on the experimental set-up (i.e. accessible reciprocal space and sample orientation). The results are visualized for a series of important Laue classes and in-house experimental conditions in the form of heat maps projected on a unit sphere. These heat maps are of real immediate practical value for any high-pressure crystallographer in that the maps allow them to get a quick sense of the sensitivity of their experiment to crystal orientation. They furthermore allow for a rough quantitative estimate of the best crystal orientation. An obvious and important relatively low hanging next step based on this work is to create an app to assess the Potency (i.e. achievable completeness) of a given experimental set-up and make the app available to the crystallography community as an on-line tool. And the equally logical but harder to achieve step after that is to develop a set of micromanipulation tools in conjunction with orientation photographs of the sample to achieve the perfect sample orientation of a ~100-µm crystal on a diamond culet of slightly larger dimensions. This for the time being is still reliant on the skills and calm hands of invaluable graduate students and postdocs.
Besides these practical aspects, the results of the numerical simulations also demonstrate – somewhat surprisingly – that the energy range chosen is only of secondary importance for the completeness of the dataset. This conclusion may well be biased by the limited energy range considered (20 keV versus 22 keV), as those two energies are relevant for in-house laboratory X-ray sources, and will probably have to be revisited once synchrotron-accessible energy ranges (up to 40 keV, ~0.3 Å) are taken into consideration.
Allan, D. R., Miletich, R. & Angel, R. (1996). Rev. Sci. Instrum.67, 840–842.
Angel, R. R., Downs, R. T. & Finger, L. (2000). Rev. Mineral. Geochem.41, 559–597.
Boehler, R. & De Hantsetters, K. (2004). High. Press. Res. 24, 391–396.
Finger, L. & King, H. (1978). Am. Mineral.63, 337–342.
Kantor, I. V., Prakapenka, A., Kantor, P., Dera, A., Kurnosov, S., Sinogeikin, N., Dubrovinskaia, N. & Dubrovinsky, L. (2012). Rev. Sci. Instrum.83, 125102.
Katrusiak, A. (2004). Z. Kristallogr.219, 461–467.
Submission of structural biology data for review purposes
Edward N. BakerCharles S. Bond, Elspeth F. Garman, Janet Newman, Randy J. ReadMark J. van Raaij
The IUCr stable of journals are proponents of the FAIR and FACT principles of publishing: data should be Findable, Accessible, Interoperable and Reusable (Wilkinson et al., 2016) and Fair, Accurate, Confidential and Transparent (van der Aalst et al., 2017; Helliwell, 2019). This has been manifested by a number of leading contributions to the field of structural biology including publication standards for a variety of data types (Kroon-Batenburg & Helliwell, 2014; Adams et al., 2019; Guss & McMahon, 2014) as well as mandatory deposition of coordinates, and subsequently structure factors, for publication of macromolecular crystal structures. This approach has largely satisfied the FAIR and FACT principles. However, a further step is required to ensure that the data deposited in a third-party database fully support the conclusions drawn from those data. This step requires the mandatory submission of data (e.g. coordinates and reduced diffraction data, discussed further below) to accompany the manuscript describing the work.
This action does not imply that the various databases [PDB (Burley et al., 2019), EMDB (Lawson et al., 2016), SASBDB (Kachala et al., 2016), BMRB (Ulrich et al., 2008) etc.] are not doing a good job of validating data submitted to them. Indeed, the validation reports produced by databases are an important pillar in the FAIR approach to structural biology. Nevertheless, it is not the role of the databases to test the extent to which the interpretations and conclusions of a manuscript incorporating structural biology research (possibly by multiple methods) are supported by the deposited data. This role belongs in the manuscript review cycle.
Authors may ask why submission of data needs to be made mandatory. After all, the Notes for Authors for Acta Cryst. D, Acta Cryst. F and IUCrJ all indicate that editors may request such data from the author. However, the current system causes delays in the review system when editors have to request data. The added inconvenience increases the possibility of poorly supported interpretations avoiding scrutiny and being published. In order to clarify the situation, and maintain the IUCr’s position leading the field in data quality standards in structural biology, submission of deposited data for review is best practice.
Historically there has been reticence to provide data for review as this might provide a competitor with an advantage. This concern has reduced substantially over recent years as increasing numbers of macromolecular structures are released prior to publication, and complementary methods such as accurate and precise computational predictions are more widely used. Indeed, the increasing prevalence of preprint versions of papers has further expedited the release of non-peer-reviewed data. Data submitted to IUCr Journals will be mandated for review purposes only, and thus the ethical position of a reviewer receiving them is clearly defined.
The concept of data deposition can be extremely broad, so it is important that we clarify what is mandated and what is recommended. The non-negotiable starting point is that for any manuscript containing conventional structures determined by the most common techniques (crystallography, NMR, cryoEM, SAXS) the data that are deposited with the relevant database to obtain the accession code and validation reports must be uploaded prior to editorial review. This set of standard files (which may include coordinate files, reduced diffraction data, restraint lists, electron-density maps, buffer-subtracted scattering curves, along with any validation reports) should already be immediately at hand to the submitting author. Additionally, depending on the manuscript in question there are cases where additional data should be provided. For example, many crystal structures may have indications of space-group ambiguity, twinning, anisotropy, alternate unit cells or other pathologies for which the review process would benefit from the submission of scaled but unmerged intensity data. We do not mandate submission for review of primary data as this is not practicable, however we continue to recommend that such data be made publicly available (Guss & McMahon, 2014).
To accompany the requirement for data, which will apply from the start of 2022, the journals Acta Cryst. D, Acta Cryst. F and IUCrJ are unifying their requirements for information to be included in the standard tables for various experiment types (colloquially Table 1 for crystal structures). These new requirements will be described in detail in the revised Notes for Authors for the journals.
Burley, S. K., Berman, H. M., Bhikadiya, C., Bi, C., Chen, L., Costanzo, L. D., Christie, C., Duarte, J. M., Dutta, S., Feng, Z., Ghosh, S., Goodsell, D. S., Green, R. K., Guranovic, V., Guzenko, D., Hudson, B. P., Liang, Y., Lowe, R., Peisach, E., Periskova, I., Randle, C., Rose, A., Sekharan, M., Shao, C., Tao, Y.., Valasatava, Y., Voigt, M., Westbrook, J., Young, J., Zardecki, C., Zhuravleva, M., Kurisu, G., Nakamura, H., Kengaku, Y., Cho, H., Sato, J., Kim, J. Y., Ikegawa, Y., Nakagawa, A., Yamashita, R., Kudou, T., Bekker, G. J., Suzuki, H., Iwata, T., Yokochi, M., Kobayashi, N., Fujiwara, T., Velankar, S., Kleywegt, G. J., Anyango, S., Armstrong, D. R., Berrisford, J. M., Conroy, M. J., Dana, J. M., Deshpande, M., Gane, P., Gáborová, R., Gupta, D., Gutmanas, A., Koča, J., Mak, L., Mir, S., Mukhopadhyay, A., Nadzirin, N., Nair, S., Patwardhan, A., Paysan-Lafosse, T., Pravda, L., Salih, O., Sehnal, D., Varadi, M., Vařeková, R., Markley, J. L., Hoch, J. C., Romero, P. R., Baskaran, K., Maziuk, D., Ulrich, E. L., Wedell, J. R., Yao, H., Livny, M. & Ioannidis, Y. E. (2019). Nucleic Acids Res. 47, D520–D528.
Lawson, C. L., Patwardhan, A., Baker, M. L., Hryc, C., Garcia, E. S., Hudson, B. P., Lagerstedt, I., Ludtke, S. J., Pintilie, G., Sala, R., Westbrook, J. D., Berman, H. M., Kleywegt, G. J. & Chiu, W. (2016). Nucleic Acids Res. 44, D396–D403.
Ulrich, E. L., Akutsu, H., Doreleijers, J. F., Harano, Y., Ioannidis, Y. E., Lin, J., Livny, M., Mading, S., Maziuk, D., Miller, Z., Nakatani, E., Schulte, C. F., Tolmie, D. E., Kent Wenger, R., Yao, H. & Markley, J. L. (2008). Nucleic Acids Res. 36, D402–D408.
van der Aalst, W. M. P., Bichler, M. & Heinzl, A. (2017). Bus. Inf. Syst. Eng. 59, 311–313.
Wilkinson, M. D., Dumontier, M., Aalbersberg, I. J., Appleton, G., Axton, M., Baak, A., Blomberg, N., Boiten, J.., da Silva Santos, L. B., Bourne, P. E., Bouwman, J., Brookes, A. J., Clark, T., Crosas, M., Dillo, I., Dumon, O., Edmunds, S., Evelo, C. T., Finkers, R., Gonzalez-Beltran, A., Gray, A. J. G., Groth, P., Goble, C., Grethe, J. S., Heringa, J., ’t Hoen, P. A. C., Hooft, R., Kuhn, T., Kok, R., Kok, J., Lusher, S. J., Martone, M. E., Mons, A., Packer, A. L., Persson, B., Rocca-Serra, P., Roos, M., van Schaik, R., Sansone, S.., Schultes, E., Sengstag, T., Slater, T., Strawn, G., Swertz, M. A., Thompson, M., van der Lei, J., van Mulligen, E., Velterop, J., Waagmeester, A., Wittenburg, P., Wolstencroft, K., Zhao, J. & Mons, B. (2016). Sci. Data, 3, 160018.
Henry Chapman of the Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, and Xiaodong Zou of the Department of Materials and Environmental Chemistry, Stockholm University, have recently been appointed as Main Editors of IUCrJ. Henry Chapman, who was already a Co-editor of IUCrJ, will succeed the late John Spence in leading the journal section on Physics and Free Electron Laser Science and Technology. Xiaodong Zou will lead a new section on Electron Crystallography, which will act as a home within the IUCr journals for high-quality, high-impact papers in this field. We are assembling a team of Co-editors to work with Xiaodong Zou and details of this section will be provided in the next issue of IUCrJ.
Henry Chapman is a physicist who is a world leader in exploiting modern high-brightness X-ray sources for high-resolution structure determination and imaging of soft matter or biological systems. His work in developing experimental methods and analysis for coherent diffractive imaging of non-periodic objects includes the first experimental demonstration of X-ray ptychography, as well as his pioneering work in serial femtosecond crystallography. His international status in these FELS fields also includes his association with multiple world-class high-brightness coherent X-ray source developments around the world. Henry completed his PhD in 1992 at The University of Melbourne, Australia, for which he was awarded the Bragg Gold Medal from the Australian Institute of Physics. He explored lensless X-ray imaging at Stony Brook University (NY, USA), and first demonstrated X-ray flash imaging while at Lawrence Livermore National Laboratory in California where he also contributed to the development of extreme ultraviolet lithography. He joined DESY and the University in Hamburg in 2007 as a founding director of the Center for Free-Electron Laser Science. He was awarded the Leibniz Prize of the German Research Foundation (DFG), the Roentgen Medal, and an honorary doctorate of Uppsala University, and is a Fellow of the Royal Society (FRS).
Xiaodong Zou is a leading expert in electron crystallography and porous materials. Her research interests have been developments of electron crystallographic methods and design of novel porous materials. She is one of the pioneers in establishing electron crystallography as an important technique for accurate atomic structure determination of unknown 3D crystals. Her group has demonstrated the power of electron crystallography in studying complex structures including zeolites, metal-organic frameworks, pharmaceuticals and proteins. Professor Zou has also made key contributions in design, synthesis and applications of novel zeolites and metal–organic frameworks. Xiaodong is a full professor in structural chemistry and deputy head of the Department of Materials and Environmental Chemistry, Stockholm University. She received her BSc in Physics at Peking University in 1984, and PhD in structural chemistry at Stockholm University in 1995. One of her main research interests is method development for accurate atomic structure determination of nano-sized crystals by electron crystallography. Her group has solved a number of complex structures of zeolites and mesoporous crystals by transmission electron microscopy. She is also working on synthesis, structure determination, topology analysis and applications of inorganic open-framework materials and metal–organic frameworks. She has received several prestigious awards given by the Royal Swedish Academy of Sciences. She is an elected member of the Royal Swedish Academy of Sciences (KVA), member of the Royal Swedish Academy of Engineering Sciences (IVA), Fellow of the Royal Chemical Society (FRCS) and council member of the International Zeolite Association.
Uwe Grimm, in his capacity as retiring Chair of the IUCr Commission on Aperiodic Crystals, meeting with the IUCr Executive Committee during the 24th IUCr Congress in Hyderabad, India, in 2017. Photo contributed to the IUCr gallery by R. Kužel.
Uwe Grimm, Professor of Mathematics at the Open University, Milton Keynes, died suddenly and unexpectedly on 28 October 2021. Uwe was a leading mathematical physicist, well known for his work on quasicrystals. These non-periodic solids (discovered in 1982 by Dan Shechtman and earning him the 2011 Nobel Prize in Chemistry) share many properties with better understood periodic crystals but also exhibit properties more often associated with non-periodic and randomly structured materials. Uwe’s 2013 book Aperiodic Order, written and edited with his friend and long-time collaborator Michael Baake of Bielefeld University, is one of the most up-to-date and authoritative guides to this still relatively young research field. The book contains a preface by Roger Penrose, whose famous tiling continues to play a big role in the field. Uwe authored around 150 scientific articles, starting originally with studying the solutions and (conformal) symmetries of one-dimensional integrable systems while a PhD student in Bonn, Germany, under the supervision of Vladimir Rittenberg. He then spent eight years as a postdoctoral researcher in Melbourne, Amsterdam and Chemnitz before coming to Milton Keynes in late 2000.
Uwe’s interest in quasi-periodic systems emerged around 1990, when he realized how interesting conformal symmetries in integrable systems with quasi-periodic couplings can be, and how non-trivial concepts from algebra and geometry show up in the spectral theory of aperiodic Schrödinger operators. He quickly became fascinated with emerging aperiodic structures not only in one-dimensional systems, but also with the beauty that is inherent in two- and three-dimensional aperiodic tilings. Visualizing the intriguing patterns that seemingly extend indefinitely without ever truly repeating was one of his ‘professional hobbies’ and many of his publications are a treasure trove of visual as well as mathematical beauty.
Early on in his career, Uwe became interested in communicating this beauty to a wider audience. Among other activities, he co-organized and participated in Royal Society Summer Exhibitions, in 2004 with his friend and colleague Ronan McGrath from the University of Liverpool, and in 2009 with colleagues from the Open University and others. He wrote general overview articles for the wider science community and even ‘Beat the Brain’ as a member of the Weapons of Math Instruction Open University Maths team in a 2015 BBC show. He used his Twitter account @RealLateStarter as a further and quite successful means of engaging as a scientist with the wider public.
At the Open University, Uwe was a valued member of staff, leading the formation of the aperiodic order research group. He successfully funded his research by obtaining several major grants as Principal Investigator from UK funding agencies. He served as Head of the School of Mathematics and Statistics, and as Associate Dean (Research) he helped the university shape its wider profile. He discharged these duties with a light touch, supreme modesty and a great sense of respect for colleagues and students.
Uwe was also a much-valued Co-editor for Acta Crystallographica Section A and a Consultant for and Chair (2014–2017) of the International Union of Crystallography’s Commission on Aperiodic Crystals. He was elected Fellow of the Institute of Physics (IOP), was a former Honorary Secretary and Chair of the IOP’s Mathematical and Theoretical Physics Group Committee, and a member of the London Mathematical Society. He also organized many influential meetings and conferences, including APERIODIC’09 in Liverpool, again jointly with McGrath. Recently he had instigated and organized regular online meetings of the UK aperiodic academic community to help maintain research connections during the COVID-19 pandemic. Uwe loved Australia since having been a postdoc there in the mid-1990s. He was an Honorary Associate of the University of Tasmania, Hobart, and he and his family spent a fondly remembered sabbatical on the island.
Uwe was trained as a physicist and mathematician. He developed our knowledge of aperiodic order but also worked on problems including the mathematical structure of groups and point sets, the theory of long-range order, the physics of electronic transport and evolution in parasites. He was also a talented pianist, juggler, and a jovial board-game enthusiast. He is survived by his wife Kathrin and two sons, Jasper and Moritz.
We, his friends, co-authors and colleagues, will miss him greatly. Our thoughts and condolences go to his family.
Uwe Grimm delivering his Keynote Lecture "Diffraction from aperiodic crystals: the state of the art" at the 25th IUCr Congress in August 2021.
International Years are proclaimed by the United Nations (UN) to mark particular events or topics in order to promote, through awareness and action, the objectives of the UN itself and, in turn, of society at large. The IUCr and the crystallographic community know this very well as they have certainly benefitted greatly from the International Year of Crystallography in 2014 (IYCr2014). Awareness about the importance of crystallography has increased enormously within the scientific community and the general public thanks to IYCr2014.
It is difficult to enumerate the many outcomes of IYCr2014:
we have seen the birth of two new regional crystallographic associations, namely the Latin American Crystallographic Association and the African Crystallographic Association, and several national crystallographic associations;
new crystallography laboratories and training centres have been inaugurated in several countries, particularly in the most disadvantaged regions of the world (see, for example, the many IUCr-UNESCO OpenLabs or the X-TechLab in Benin);
the IUCr is now actively involved in joint programmes with other scientific unions of the ISC network (e.g.the LAAAMP project) and in a number of initiatives in collaboration with other institutions.
It is then with great expectations that we look forward to the forthcoming International Year of Basic Sciences for Sustainable Development (IYBSSD) that will be celebrated from mid-2022 to mid-2023 – see the official announcement below. This International Year, coordinated by the International Union of Pure and Applied Physics, will focus on the links between basic sciences and the UN Sustainable Development Goals. Its main objectives are to enhance inclusive participation in science, strengthen education and scientific training, encourage increased funding of basic sciences and promote the concept of open science.
This is in fact perfectly in line with the aims of the IUCr, and the IUCr is proud to be one of the Founding Members of IYBSSD2022, as reported in an earlier issue of the IUCr Newsletter.
It is particularly interesting that celebrations for the Year of Mineralogy 2022, as proclaimed by the International Mineralogical Association (IMA) under the auspices of UNESCO, will be formally part of IYBSSD. The IUCr will partner with IMA in this initiative as well.
In conclusion, IYBSSD offers a new opportunity to enhance the stature of crystallography, build capacity in developing regions of the world and extend further the public understanding of science, which are the three main objectives of the “Crystallography for the Next Generation” manifesto, and to establish new collaborations within the scientific community. There are many exciting events ahead that the crystallographic community is not going to miss!
The International Year of Basic Sciences for Sustainable Development proclaimed by the United Nations General Assembly for 2022
We need more basic sciences to achieve Agenda 2030 and its 17 Sustainable Development Goals (SDGs). This is the message sent to the world by the United Nations General Assembly on 2 December 2021: Member States approved by consensus the resolution 76/A/L.12 promulgating the year 2022 as the International Year of Basic Sciences for Sustainable Development (IYBSSD2022).
With this resolution, the United Nations General Assembly ‘invites all [its] Member States, organizations of the United Nations system and other global, regional and subregional organizations, as well as other relevant stakeholders, including academia, civil society, inter alia, international and national non-governmental organizations, individuals and the private sector, to observe and raise awareness of the importance of basic sciences for sustainable development, in accordance with national priorities’.
The United Nations General Assembly motivated its decision with ‘the high value for humankind of basic sciences’, and with the fact that ‘enhanced global awareness of, and increased education in, the basic sciences is vital to attain sustainable development and to improve the quality of life for people all over the world’. It also stressed that ‘basic sciences and emerging technologies respond to the needs of humankind by providing access to information and increasing the health and well-being of individuals, communities, and societies’. The successes and difficulties of the global fight against the COVID-19 pandemic have been for two years a stark reminder of this importance of basic sciences, such as (but not limited to) biology, chemistry, physics, mathematics and anthropology.
The vote is the result of the mobilization of the international scientific community, led since 2017 by the International Union of Pure and Applied Physics (IUPAP), CERN (the European Laboratory for Particle Physics), and 26 other international scientific unions and research organizations from different parts of the world, under the auspices of UNESCO. Over 90 national and international science academies, learned societies, scientific networks, research and education centres are also supporting this initiative. They will organize events and activities all over the planet during this special year, to showcase and improve the links between basic sciences and the 17 SDGs.
The resolution was proposed to the United Nations General Assembly by Honduras, and co-sponsored by 36 other countries. Its vote confirms resolution 40/C 76 adopted unanimously by the UNESCO General Conference on 25 November 2019.
The International Year of Basic Sciences for Sustainable Development (IYBSSD2022) will be officially inaugurated with an opening conference 30 June–1 July 2022 at the UNESCO headquarters in Paris, France. Events and activities will be organized around the world until 30 June 2023.
In the past few issues of Acta Crystallographica Section B, including the current one, several articles have reported research work on quantum crystallography. Collectively they comprise a virtual special issue on the subject, the first on such an extended concept in the IUCr journals. Previously, a special issue, dedicated to Philip Coppens (1930–2017), was published in Acta Crystallographica Section B (August 2017). It contained many contributions in the field of charge density (as well as photo-crystallography). Originally intended to celebrate his retirement with contributions on two of the main topics developed during his career, the issue appeared just a few weeks after Professor Coppens passed away and became a kind of memorial issue.
The occasion of the present special issue is the principal authors’ participation in the first online quantum crystallography meeting (QCrOM2020) held in August 2020. It was organized (and mostly improvised) to replace the sessions on this subject initially programmed for the IUCr Congress in Prague, which, as we know, was postponed to 2021. Its virtual modality (and its subsequent free of charge registration) made it possible to attract attendees from a wider range of expertise. It was the opportunity to present the latest results and reviews on the field and share opinions during fruitful discussion sessions that normally do not take place at large scale and tightly scheduled meetings like those of the IUCr Congress.
Despite all the difficulties caused by the pandemic the field is currently blooming, and the community is undergoing a generational turnover with many new young researchers involved and new groups established. The field’s momentum is testified by the rather broad spectrum of studies published in this special issue, with a variety of research themes and many topics analyzed or reviewed in detail.
Quantum crystallography is a modern name for a field that started when quantum mechanics itself was put forward, coinciding with the early days of X-ray crystallography. In keeping with Peter Debye’s early intuition (Debye, 1915), the discovery of X-ray diffraction offered a whole new possibility ‘to establish by experiment the particular arrangement of the electrons in the atoms’. Many studies became possible thanks to the interplay between crystallographic techniques and quantum physics. For example, experimental crystallography was used to unveil the nature of electrons (waves and corpuscles; see De Broglie, 1929), to investigate the electronic structures of metals (Weiss & Demarco, 1958), to map the charge density around atoms to form bonds and molecules or solids (Coppens, 1967), and the electron polarization upon application of external stimuli (such as the electric field, see Hansen et al., 2004) or upon temperature changes.
Quite remarkably, these kinds of studies are those that originally attracted the interest of quantum physicists for the emerging field of X-ray crystallography in the 1920s. At the same time, chemists also envisaged the exceptional outcome from crystallographic studies and the vast array of details useful in developing theories of chemical bonding (Pauling, 1939).
This sentiment has always accompanied studies on accurate charge density, which has become the favourite observable for revealing the nature of chemical bonding and the supramolecular interactions, especially – but not only – within the paradigm of the quantum theory of atoms in molecules (Bader, 1990) that becomes, in the crystallographic framework, the quantum theory of atoms in molecules and crystals (Gatti, 2005).
In the past two decades, and especially in recent years, we have witnessed a renewal of the interest in a direct determination of the crystal wavefunction, which has indeed been a goal since the beginning of the X-ray diffraction era (Pauling, 1926). For example, there is growing attention being given to calculations of wavefunctions restrained to reproduce the X-ray diffracted intensities (Jayatilaka, 1998), as well as to the refinement of orbital coefficients (Tanaka et al., 2008) or of reduced-density matrices (Gillet, 2007).
A search in the database of papers published in Acta Crystallographica Section B since 1998 (online versions), returns more than 500 papers directly or indirectly related to quantum crystallography (and overall, ∼4000 in all IUCr journals). Most of them report accurate charge density studies and their applications, encompassing the technological progress which has occurred over the years, such as the availability of area detectors, the development of synchrotron sources and low-temperature devices (see for example, Iversen et al., 1999). Moreover, a discussion on the future of topological analysis of experimental charge density took place (Dittrich, 2017; Macchi, 2017).
The virtual special issue that we have edited seamlessly combines the recent developments and an outlook on future research in this field, highlighting fundamental questions, scientific cases and broad applications in other disciplines.
Despite the growing appeal of molecular/crystal orbital calculations, orbital-free quantum crystallography is emerging, in keeping with the emergence of orbital-free density functional theory (see Finzel, 2021; Tsirelson & Stash, 2021; Bartashevich et al., 2021).
While quantum crystallography often deals with molecular aspects of electron distribution, the role of environment and of intermolecular interactions is being ever more scrutinized (see Zheng et al., 2021; Macetti et al., 2021; Bergmann et al., 2021; Forni et al., 2021; Kleemiss et al., 2021).
Although scientists often think of electron density as the mere distribution of charge in a molecule/crystal, one should not forget that electrons do have a spin as well and that molecular or extended systems may feature an overall spin magnetic moment. Thus spin-density models are essential (see Souhassou et al., 2021), especially in view of the increasing development of spintronics. The paper by Souhassou et al. (2021) also deals with the refinement of orbital coefficients in inorganic solids, another frontier topic. The role of ligand coordination for setting the oxidation state of a metal is also discussed by Adamko Koziskova et al. (2021).
Landeros-Rivera, Contreras-García & Dominiak (2021) discuss refinement strategies in electron wavefunctions obtained from X-ray diffraction data while Launay & Gillet (2021) deal with the N-representability of reduced density matrices reconstructed from several X-ray scattering techniques. Shteingolts et al. (2021) instead discuss transferable aspherical atom models for improving the quality of refinements.
One of the appeals of quantum crystallographic techniques, especially in the past few years, is the possibility of using very accurate modelling (such as atomic multipolar coefficients and molecular wavefunctions) to improve the standard (bio)chemical crystallographic studies. Such a link is fundamental because quantum crystallography should be intimately connected with the rest of crystallography and all related sciences. The quest for highly accurate observations and ever more precise calculations, inherent to the most fundamental aspects of quantum crystallography, has many implications for applied science and technology. In this respect, the present state bears little difference to quantum mechanics, originally developed as a very sophisticated theory for elite scientists, which has proved to be vital for several technological applications, up to quantum computing.
We are confident that this special issue will contribute to attracting ever-growing interest not only in the fundamental bases of quantum crystallography, but also in its applicative aspects. We also thank all the authors of contributions to this special issue for their dedication and excellent work, and the Main Editors of Acta Crystallographica Section B for this opportunity.
We would like to acknowledge the excellent work accomplished by Sara Delahaie, Hugo Julien, Antoine Marras and Nizar Melk, who were – at the time – first year engineering students at CentraleSupelec. Their enthusiasm and hard work were decisive in the organization (in such a short timeframe) of the first online quantum crystallography meeting (QCrOM2020). We also thank CentraleSupelec for their permission to use their logo for the conference (and the cover page of this issue) as well as for their essential financial and technical support.
Fractal Circle Limit III, by permission of the artist Vladimir Bulatov.
We do live in strange times. Just when COVID-19 seemed to be getting under control, along comes Omicron to foul up any arrangements we had planned for the next few weeks. Let’s hope that this variant turns out not to be as harmful as the others.
We have some recent changes to the Editorial Board of the IUCr Newsletter. Regional Editors Ted Baker and Serena Chiara Tarantino have both retired from the Board, and I thank them very much for their support. At the same time, we welcome some new members of the Board:
Chris Sumby (Asia including Australia, New Zealand, and Pacific Island Territories)
Anders Madsen (Europe including Russia and the Middle East)
Panče Naumov (Europe including Russia and the Middle East)
We also bid a fond farewell to Patti Potter, who is standing down from the Newsletter after having worked on the publication since its launch in 1993. Originally based in Buffalo, Patti was employed as the Production Manager alongside Editors Bill Duax and Judy Flippen-Anderson, and then, when production moved to Chester in 2018, continued in advertising sales. We thank Patti for her role in disseminating news to the crystallographic community for 28 years, and send our best wishes for the future.
The IUCr, initially proposed by P. P. Ewald in 1944 (see https://www.iucr.org/iucr/history/early-history), has represented the crystallographic community throughout the world since its founding in 1947. In its first international meeting in 1948, participants came from Belgium, Canada, France, Germany, India, Italy, Netherlands, Spain, Sweden, UK and USA. In the intervening years, we have seen the IUCr promote the growth of crystallography further around the world. In most countries, national crystallographic associations were founded, followed by supranational bodies such as the American Crystallographic Association (representing the USA and Canada), the European Crystallographic Association, the Asian Crystallographic Association and then later, the Latin American Crystallographic Association. This left a noticeable gap (are there any crystallographers in Antarctica?), which has been filled, finally, with the foundation of the African Crystallographic Association (AfCA) – read all about the launch from the AfCA Executive Committee here. The African crystallographers are to be applauded for reaching this momentous step and are welcome members of our community. To reach this point has taken much hard work by stalwarts such as Claude Lecomte and Michele Zema, with support from the IUCr through its various schemes, such as OpenLabs, together with a number of commercial companies who have donated equipment to some African countries.
Also of note is the recent rise of crystallographic research in the Arab world. Panče Naumov, Sharmarke Mohamed, Liang Li and Wael Rabeh tell us about this research here. The Emirates Crystallographic Society was set up and is now an adhering body of the IUCr. Another example of the widespread crystallography community can be seen here, where we have an article about crystallography in Guatemala, which also became a member of the IUCr in 2021.
I am looking forward to the next IUCr Congress, which will be held in Melbourne, Australia, in 2023. I hope that we shall all be able to attend in person by then. Australia is such an exciting country, with strange animals and plants, and I have always enjoyed visiting. Now, how about an Australian walk-about? Chris Sumby suggests a road trip with stops at places that should be of interest to crystallographers. Looks great!
To mark the inauguration of the new Sir William Henry Bragg Building at the University of Leeds, a major exhibition devoted to the work of W. H. Bragg, the father of Sir William Lawrence Bragg, is currently under way. As every crystallographer surely knows, both father and son shared the 1915 Nobel Prize in Physics for their work on crystal structure determination by X-ray diffraction. You can read about the exhibition here.
Another of our Nobel Laureates, Herbert Hauptman, is featured in an article by Istvan Hargittai, focussing on his creation of stained glass polyhedral models with close packing of spheres. Istvan includes a brief biographical sketch.
All crystallographers who publish crystal structures, and that is no doubt the majority, are well used to creating the infamous CIF, which I always called the Crystallographic Information File. I now see from the fascinating article by James Hester and Brian McMahon that CIF stands for “Crystallographic Information Framework”! James and Brian relate the history of this all-important development that has become so standard in the lives of most crystallographers. I remember when the CIF all started but had forgotten how many people had involvement in its creation.
Finally, The Royal Society has just published a biographical memoir on Nobel Laureate Tom Steitz here written by Venki Ramakrishnan and Richard Henderson.