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We are sad to report the death of Jack Dunitz, Professor Emeritus at ETH-Zürich, Switzerland, at the age of 98. Professor Dunitz was widely valued as an insightful scientist, an inspirational teacher and a witty raconteur, who shaped the development of modern crystallography over more than 70 years.
Acta Cryst. B has launched a new section on the growth of crystals of non-biological “small” molecules and those of extended organic, inorganic or hybrid materials, and actively welcomes submissions that match the scope of the journal.
Professor Santiago García-Granda (University of Oviedo, Spain) has been elected as Vice-President of the IUCr, and Dr Thomas Proffen (Oak Ridge National Laboratory, Oak Ridge, TN, USA) the first of the three new ordinary members of the IUCr Executive Committee.
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.
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On the 75th birthday of Professor Mikhail Kovalchuk
Mikhail Kovalchuk presenting his talk "Crystallography in the Russian Federation" at the IYCr2014 Opening Ceremony at the UNESCO Headquarters in Paris, France, in January 2014. Photo credit: Radomír Kužel.
The IUCr wishes to congratulate Mikhail Kovalchuk on the occasion of his 75th birthday on 21 September 2021.
Professor Kovalchuk is Director of the Kurchatov Institute of Crystallography, Russian Academy of Sciences, Moscow, and chairs the Russian National Committee for Crystallography. He is involved in many international projects related to synchrotron radiation and neutron facilities in Europe and in Russia, including the XFEL project, and the synchrotron and neutrons programme in Russia.
Recognising his enormous influence on the development of crystallography in the Russian Federation, he was invited to speak at the IYCr2014 Opening Ceremony (see photo above).
Professor Kovalchuk chaired the First Russian Crystallographic Congress, which took place in Moscow in November 2016. More than 2000 participants were registered at the conference, more than 40% of whom were under 35 years of age.
Mikhail Kovalchuk (fourth from left) with fellow organisers and guests Hanna Dabkowska and Mike Glazer from the IUCr Executive Committee (third and sixth from left) and Alessia Bacchi and Andreas Roodt from the ECA Executive Committee (second and first from right) at the First Russian Crystallography Congress held in Moscow in 2016. Photo contributed to the IUCr gallery by Hanna Dabkowska.
For a list of papers by Professor Kovalchuk appearing in IUCr journals click here.
An open-access future for Journal of Synchrotron Radiation – Editorial from the Main Editors and IUCr Journals Editor-in-Chief
Kristina KvashninaYoshiyuki Amemiya, Dibyendu Bhattacharyya, Ingolf LindauAndrew J. Allen
The entire Journal of Synchrotron Radiation (JSR) editorial team would like to take this opportunity to inform all our readers, authors and supporters about the coming transition to open access. All papers submitted to JSR after 1 October 2021 will be for open-access publication. By taking this step, JSR is supporting a journey towards open science in general.
JSR was founded in 1994 (Hasnain, Helliwell & Kamitsubo, 1994) with the aim of providing comprehensive coverage of the entire field of synchrotron radiation. Almost immediately its coverage also started to include free-electron laser research (Doniach, 1996) including instrumentation, theory, computing and scientific applications in areas such as biology, nanoscience and materials science. Just in the last year, authors from 35 different countries published in the journal, the top five countries represented being the USA, Japan, Germany, China and France. Throughout the past 26 plus years JSR has been an up-to-date information resource for scientists and engineers in the field of synchrotron radiation.
Now, the JSR Main Editors, with the International Union of Crystallography (IUCr) Journals Editor-in-Chief and the IUCr Editorial Office, supported by the IUCr Executive Committee, believe that switching to open access will benefit research in this area by disseminating it more easily and rapidly to the global synchrotron and free-electron laser science communities. The clear goal of this initiative is to induce the smoothest and most research-oriented transformation possible of JSR from a behind-paywall subscription-based publishing model to an open-access-based publishing model. All of us increasingly work under conditions in which open access supports researchers in every aspect of their workflow. New detailed instructions on general policies for submission, possible open-access discounts, and other guidelines and templates are discussed at https://journals.iucr.org/s/services/openaccess.html. However, we wish to emphasize that all open-access articles will undergo initial editor assessment and the same rigorous peer review process as at present. The management of the peer review process will continue to focus on the high standards and rapid publication expected for IUCr journals.
At this time, we wish to express our enormous appreciation of JSR’s supporting (facility) institutions. We also hope that more supporting institutions will join with JSR as we move forward from here. JSR supporting institutions are entitled to a certain number of open-access article processing charge (APC) vouchers per year for papers reporting work carried out at their facilities. Alternatively, if the contact author’s home institution is included in a transformative or read-and-publish arrangement with the IUCr’s publication partner, Wiley, those authors will be able to publish open-access research or review articles in JSR with no direct (APC) charge. Currently, such arrangements exist in Austria, Finland, Germany, Hungary, Ireland, Italy, Liechtenstein, the Netherlands, Norway, Spain, Sweden, Switzerland and the UK. Contact authors with connections to IUCr (Associates, members of national affiliates, World Directory of Crystallography, etc.) will receive modest APC discounts. Meanwhile, discounts (50%) for authors from lower middle income countries and waivers (100%) from low income countries will be issued. However, please note that a major difference from present arrangements is that all submitting authors will need to apply for such discounts and waivers at the time of submission and payments will be handled via Wiley authors services (for more details see https://journals.iucr.org/s/services/openaccess.html).
As the transition to open access proceeds, the JSR Editorial Board welcomes feedback from the JSR research community, especially from authors, on the new open-access procedures, and is keen to know what is working well and what needs some adjustment.
The change to open access is made with every faith in the future. The Editors fully believe that the publishing of scientific research with global open access providing worldwide visibility without barriers demonstrably leads to more downloads, citations and more impact for authors. The increased citation of open-access articles published in JSR since 2018 is shown graphically in the figure.
Figure 1. Graphic showing the increased citation of open-access articles published in JSR since 2018.
The JSR Editors embrace both the idea and concept of making research freely available to all researchers, and are committed to coordinate and establish best principles to facilitate a smooth transition from subscription to open access. The Editors wish all the best to all JSR authors for the future and look forward to seeing your forthcoming high-quality open-access research submissions to JSR.
Carroll Johnson’s professional career adhered to the postulate that one should change directions every five years to avoid stagnation. His career profile, in approximately five-year segments as he described himself, starting in 1955, was as follows: (1) graduate school (MIT-PhD): biophysics & fiber diffraction theory, (2) postdoctoral positions: X-ray crystallography (Institute for Cancer Research, Philadelphia) & neutron diffraction (Oak Ridge National Laboratory), (3) staff member at ORNL until retirement in 1996: thermal motion & computer graphics, (4) crystal physics, (5) artificial intelligence concepts, (6) artificial intelligence applications, (7) machine vision engineering & project management, and (8) crystallographic topology & neutron diffraction. Carroll remained very active in retirement. His post-retirement activities involved “crystallographic topology, personal computing and enjoying life.” He personally noted selected professional activities in his career: 1975–1976 sabbatical, studying artificial intelligence at the Computer Science Department, Stanford University, 1977 President of the American Crystallographic Association (ACA), 1981 studying more artificial intelligence at the Naval Research Laboratory, 1996 Chairing the ACA General Interest Group, and 1997 receiving the ACA Buerger Award.
He was a native of Colorado and started a pre-med program in 1947 at the University of Colorado, which was put on hold by four years in the United States Marine Corps, which included a year in the Korean war. Afterward, he completed a BS degree in Animal Nutrition and Physiology (1955) from Colorado State University. He went on to complete a PhD degree in Biophysics (1959) at MIT, doing his thesis on polypeptide packing studied by X-ray diffraction. After that, he did a postdoc (1959–1962) at the Institute for Cancer Research (now the Fox Chase Cancer Center), Philadelphia, with Lindo Patterson, whose group at that time included Jenny Glusker, Dick van der Helm, Max Taylor, Eric Gabe and Jean Minkin. During his postdoctoral work in Philadelphia, he began working on the computer program for plotting atomic thermal ellipsoids, which he later finished at ORNL.
Carroll started at ORNL in 1962, beginning as a postdoctoral assistant working on neutron diffraction in Henri Levy’s group. After converting to a staff scientist, he spent his entire professional career in the Chemistry Division at ORNL, retiring in 1996. Over the years at ORNL, his immediate colleagues and his group’s mission changed a lot. In the early days, he worked with Henri Levy, Bill Busing and George Brown. Later he worked with Michael Burnett on many programming applications. He was an independent thinker, mathematically inclined, and pursued projects always at the forefront and often beyond current thinking. Carroll Johnson’s scientific success grew markedly with the publication of his most celebrated computer program, ORTEP (Oak Ridge Thermal-Ellipsoid Plot Program). This rapidly became a favorite of crystallographers and protein crystallographers to make illustrations of crystal structures for conference presentations and publications. ORTEP was first released in an ORNL Technical Report in 1965; see historical note https://www.umass.edu/molvis/francoeur/ortep/ortepnews.html. A key strength of ORTEP was its capacity to generate stereoscopic images automatically. ORTEP 2 was released in 1976 and ORTEP 3 in 1996. The latter is still available from the official ORTEP website, https://ornl-ndav.github.io/ortep/ortep.html. ORTEP is one of the most cited and miscited publications in crystallography, with over 30,000 citations. ORTEP even is commonly used as a word for a crystal structure drawing with atomic displacement ellipsoids, whether it was made with ORTEP or not. A Google search on “ORTEP” returns 798,000 hits. Atomic displacement ellipsoid drawing options are now standard in all the major crystal and molecular structure drawing programs. Carroll was an expert on thermal motion analysis as studied by diffraction and sought better and new ways to use this aspect of crystal structure analysis.
Bill Busing, Henri Levy, Hal Smith and Pete Peterson had built and were operating a three-circle neutron diffractometer at the Oak Ridge Research Reactor for several years working on chemical crystallography prior to Carroll Johnson’s arrival at ORNL. Data collection by that diffractometer was controlled by a computer program run on the ORACLE (an early main-frame computer at ORNL), which prepared a paper punch control tape conveying the angle settings to the motors. The intensities were also recorded on paper punch tape. When minicomputers became available in 1965, Busing and Levy programmed a PDP-5 computer to control a four-circle Picker diffractometer, first as an X-ray instrument and then as a neutron instrument at ORNL’s High Flux Isotope Reactor (HFIR), which had just started operating. Seminal crystal structural studies of hydrogen-containing compounds were done with the HFIR diffractometer. Still, the science it could do was limited because no low-temperature sample cooling device was available on the instrument. The HFIR four-circle diffractometer was operated only intermittently through the 1980s. After a 3+ year safety review shutdown of HFIR ending in 1990, Carroll Johnson and Michael Burnett upgraded the neutron diffractometer at HFIR, with a new Huber goniometer, a low-temperature sample stage (5–300K), and a new 7-pixel array detector. I was responsible for the powder diffractometer at HFIR at that time but was interested in doing structural studies with single crystals as well, so I worked with Carroll to learn as much as I could about the operation of his single-crystal diffractometer. The interest in single-crystal neutron diffraction studies by the Chemistry Division kept dwindling with each retirement and passing of Levy’s old group members. Carroll had been the youngster in that group when he started, but now he was ready for a change: retirement was next, and it was at that time that he transferred the HFIR four-circle diffractometer to me in the neutron scattering group. Since then, we have upgraded that instrument multiple times, and it has grown with the help of a new younger generation of scientists hired in the ORNL Neutron Scattering Division to be extremely productive doing research in materials physics and chemistry. I thank Carroll for setting us on that course.
The American Crystallographic Association was his professional society home. He began attending ACA meetings in 1964 and, with few exceptions, attended all their meetings until he retired, and some after that. The ACA was an extended family for him, and he often planned family vacations around the annual meetings, bringing along Carol, his wife, and his children, which numbered five in the end. He gave back to the ACA by presenting many talks and posters, serving on the Crystallographic Computing Committee in 1965–1967, then as President-elect in 1976, President in 1977, Past-President in 1978, and Chairing the General Interest Special Interest Group 1994–1996.
Carroll Johnson was married to Carol for 69 years and had five children, ten grandchildren and seven great-grandchildren. His family especially enjoyed how his curiosity and inquisitiveness were not limited to his work and touched all aspects of his life.
Lipid transport across the mycobacterial cell envelope
Figure 1. Schematic representation of the results reported by Asthana et al. (2021) within the context of cholesterol import through the M. tuberculosis cell envelope. Mce4A is shown to be monomeric in solution, likely forming a hetero-hexameric arrangement with other Mce4 proteins to form a tunnel for lipid transport. A schematic model of the M. tuberculosis cell envelope is also shown for comparison, adapted from Chiaradia et al. (2017). The schematics are not drawn to scale.
Tuberculosis is a devastating disease that has afflicted humans since antiquity. Known as Phthisis (Greek), the ‘white plague’ or consumption, tuberculosis appears as a common theme in art, music and literature, and has shaped many elements of human social history (Daniel, 2006). Even today, one-quarter of the world’s population is estimated to carry latent infections by Mycobacterium tuberculosis, the bacterium that causes tuberculosis (Getahun et al., 2015). So why is this disease so recalcitrant to treatment? This is, in part, due to the distinctive cell envelope of M. tuberculosis, which provides a physical barrier against antibiotics (Batt et al., 2020). Furthermore, this envelope also helps M. tuberculosis survive attacks by the host immune system (Batt et al., 2020), allowing the bacterium to persist in a non-replicating (‘dormant’) state in the host cells (Gengenbacher & Kaufmann, 2012). A key feature of M. tuberculosis is its ability to acquire and metabolize lipids, notably cholesterol and fatty acids, from its human host (Wilburn et al., 2018). These lipids provide the bacterium with the essential carbon and energy sources to maintain viability over many years (Warner, 2014). Understanding how these lipids are transported into M. tuberculosis may expose vulnerabilities that could then be exploited to develop new therapeutic agents against tuberculosis.
Despite the significance of lipid metabolism in the survival and pathogenesis of M. tuberculosis, it is not clear how lipids are transported into the cell, with no structural or mechanistic details on mycobacterial lipid transporters being available. The genome sequence of M. tuberculosis, and subsequent studies, have identified four homologous mammalian-cell-entry (Mce) multiprotein complexes that are proposed to play crucial roles in translocating various lipid molecules across the cell envelope (Cole et al., 1998; Casali & Riley, 2007). These membrane-bound assemblies, however, have so far defied structural analysis. In the September 2021 issue of IUCrJ, Asthana et al. (2021) now provide the first insights into the structure and potential assembly of the Mce1 and Mce4 proteins in M. tuberculosis.
Mce proteins play crucial roles in M. tuberculosis pathogenesis through reimporting fatty acid and mycolic acid (Mce1), and importing cholesterol from the host cells (Mce4) (Pandey & Sassetti, 2008; Nazarova et al., 2017). Each mce operon encodes proteins with various roles in the formation of their respective Mce complexes, including six Mce proteins (MceA, MceB, MceC, MceD, MceE and MceF) that act as substrate-binding proteins (SBPs) (Casali & Riley, 2007). The homologous SBPs from E. coli (Ekiert et al., 2017; Isom et al., 2020; Liu et al., 2020; Coudray et al., 2020) and Acinetobacter baumannii (Kamischke et al., 2019; Mann et al., 2020) have been shown to form hexameric structures, leading to their central role in lipid transport through either a tunnel- or ferry-based mechanism.
The results presented by Asthana et al. (2021) reveal several advances in our understanding of the Mce proteins in M. tuberculosis. They used sequence analysis and secondary-structure prediction to show that all SBPs of Mce1–4 display a conserved four-domain architecture. This arrangement comprises an N-terminal transmembrane (TM) domain, the MCE domain, a helical domain and a tail domain of variable size. They also showed that all these individual domains, except for the MCE domain, require detergents for solubility and stability. Interestingly, the full-length and individual domains of M. tuberculosis Mce1A and Mce4A are predominantly present as monomers in solution. This was further confirmed by the crystal structure of the single MCE domain present in Mce4A (Mce4A39–140), indicating that this domain could not form homo-hexamers due to steric clashes between monomers. This is a notable difference from the previously reported hexameric SBPs observed in E. coli (Ekiert et al., 2017; Isom et al., 2020; Liu et al., 2020; Coudray et al., 2020) and A. baumannii (Kamischke et al., 2019; Mann et al., 2020). Finally, using small-angle X-ray scattering (SAXS) experiments and structure-based modelling, they showed that the helical domains of Mce1A and Mce4A interact with the detergent micelles, implying that they either interact with the membrane or the lipid substrates.
These results have consequently led to a proposed model on the likely assembly of the Mce proteins in M. tuberculosis (Asthana et al., 2021). Based on this model (Fig. 1), the six MCE domains of MceA–F SBPs may interact with each other to form hetero-hexamers, with the helical domains of each polypeptide coming together to form a long and hydrophobic channel for lipid transport. This structure would be held in between the plasma membrane and the cell surface via interactions with the TM domains and the tail domains, respectively. This model resembles the tunnel-based mechanism described in Ec-Pqi (Ekiert et al., 2017), providing the first experimental model towards the Mce-mediated lipid transport in M. tuberculosis.
The proposed model by Asthana et al. (2021) establishes a unique foundation for future studies of the Mce multiprotein complexes, elucidating structural and mechanistic details of lipid transport in M. tuberculosis. Such endeavours may also facilitate the development of specific compounds to target cholesterol import as a therapeutic intervention, particularly restricting M. tuberculosis growth and survival during persistence.
Cole, S. T., Brosch, R., Parkhill, J., Garnier, T., Churcher, C., Harris, D., Gordon, S. V., Eiglmeier, K., Gas, S., Barry, C. E., Tekaia, F., Badcock, K., Basham, D., Brown, D., Chillingworth, T., Connor, R., Davies, R., Devlin, K., Feltwell, T., Gentles, S., Hamlin, N., Holroyd, S., Hornsby, T., Jagels, K., Krogh, A., McLean, J., Moule, S., Murphy, L., Oliver, K., Osborne, J., Quail, M. A., Rajandream, M., Rogers, J., Rutter, S., Seeger, K., Skelton, J., Squares, R., Squares, S., Sulston, J. E., Taylor, K., Whitehead, S. & Barrell, B. G. (1998). Nature, 393, 537–544.
Coudray, N., Isom, G. L., MacRae, M. R., Saiduddin, M. N., Bhabha, G. & Ekiert, D. C. (2020). eLife, 9, e62518.
Daniel, T. M. (2006). Respir. Med. 100, 1862–1870.
Ekiert, D. C., Bhabha, G., Isom, G. L., Greenan, G., Ovchinnikov, S., Henderson, I. R., Cox, J. S. & Vale, R. D. (2017). Cell, 169, 273– 285.e17.
Gengenbacher, M. & Kaufmann, S. H. E. (2012). FEMS Microbiol. Rev.36, 514–532.
Getahun, H., Matteelli, A., Chaisson, R. E. & Raviglione, M. (2015). N. Engl. J. Med.372, 2127–2135.
Isom, G. L., Coudray, N., MacRae, M. R., McManus, C. T., Ekiert, D. C. & Bhabha, G. (2020). Cell, 181, 653–664.e19.
Kamischke, C., Fan, J., Bergeron, J., Kulasekara, H. D., Dalebroux, Z. D., Burrell, A., Kollman, J. M. & Miller, S. I. (2019). eLife, 8, e40171.
Liu, C., Ma, J., Wang, J., Wang, H. & Zhang, L. (2020). J. Mol. Biol.432, 1008–1019.
Mann, D., Fan, J., Farrell, D. P., Somboon, K., Muenks, A., Tzokov, S. B., Khalid, S., Dimaio, F., Miller, S. I. & Bergeron, J. R. C. (2020). bioRxiv. https://doi.org/10.1101/2020.05.30.125013.
Nazarova, E. V., Montague, C. R., La, T., Wilburn, K. M., Sukumar, N., Lee, W., Caldwell, S., Russell, D. G. & VanderVen, B. C. (2017). eLife, 6, e26969.
Pandey, A. K. & Sassetti, C. M. (2008). Proc. Natl Acad. Sci. USA, 105, 4376–4380.
Warner, D. F. (2014). Cold Spring Harb. Perspect. Med. 5, a021121.
Wilburn, K. M., Fieweger, R. A. & VanderVen, B. C. (2018). Pathog. Dis.76, fty021.
Eighth Polish Crystal Growing Competition for Schools 2021
A selection of winning and distinguished entries to the Eighth Polish Crystal Growing Competition for Schools 2021. Photo credit: Dr Marcin Łaciak, Faculty of Science and Technology, University of Silesia.
The competition was organized at the Institute of Physics, University of Silesia, Poland, at the invitation of the IUCr in 2014 and IUCr Commission on Crystal Growth member Dr Hanna Dabkowska. For the 2021 competition, 620 people were registered, and 289 sent 456 crystals from 72 towns. The jury selected 3 winners and more than 20 works were distinguished. The awards ceremony took place on 17 June 2021 during the seminar "Crystals: order, beauty and usefulness" at the Institute of Physics, University of Silesia, Chorzów.
The poster advertising the scientific seminar and award ceremony.
The Director of the Institute of Physics, University of Silesia, Professor Sebastian Pawlus, and the Dean of the Faculty of Mathematics, Physics and Chemistry, Professor Danuta Stróż, opened the Seminar connected with the award ceremony. The patronage of the competition included the Polish Society for Crystal Growth and the Committee of Crystallography, Academy of Sciences (detailed in the poster above). The organizing committee included Professor Ewa Talik, Dr Magdalena Szubka, Dr Monika Oboz, Dr Adam Guzik, Dr Aneta Szczygielska-Łaciak and Dr Marcin Łaciak.
The three winners of the competition. Photo credit: Dr Marcin Łaciak, Faculty of Science and Technology, University of Silesia.
Three lectures devoted to the subject of crystals were delivered during the seminar:
“Crystallography” – Professor Maria Gdaniec (Department of Chemistry, Adam Mickiewicz University, Poznań, Poland)
“Luminescent crystals” – Dr hab. Dobrosława Kasprowicz (Poznan Faculty of Technical Physics Institute of Materials Research and Quantum Engineering Division of Optical Spectroscopy, University of Technology, Poznań, Poland)
“Looking inside the materials” – Dr Maciej Zubko (Faculty of Exact and Technical Sciences Institute of Materials Science, University of Silesia, Chorzów, Poland).
The organizing committee expresses its thanks to Professor Juan Manuel García-Ruiz from the University of Granada, Spain, for sharing the video “The Mystery of the Giant Crystals” presented at the seminar.
Before the COVID-19 pandemic, winners participated in a scientific visit to CERN, Geneva, Switzerland, and the Solaris Synchrotron Radiation Centre, Kraków, Poland. For a full list of winners since 2014, please see here.
Operando structural science of functional materials
C. Richard A. Catlow
Classical structural science examined samples using diffraction and/or spectroscopic techniques under ambient conditions. Studies as a function of temperature have, of course, become routine and high-pressure experiments also have made a major contribution to structural science. In recent years, however, the availability of more sophisticated sample environments has enabled a rapid growth in the use of ‘in situ and operando’ techniques, in which a functional material, such as a catalyst, is probed under conditions which resemble as closely as possible those used under the real operating environment, with measurements often being made with time resolution. The field is growing rapidly in sophistication and poses exciting challenges to, and opportunities for, the structural science of materials.
A terminological confusion can arise from the use of both ‘in situ’ and ‘operando’, with the latter denoting an experiment where the structural measurements are made together with measurements relating to its functional performance, which, for example, for a catalytic material would be the reaction product yield and distribution. A good illustration of an operando structural study was reported recently in IUCrJ by Rabøl Jørgensen et al. (2020), who investigated the thermoelectric material Zn4Sb3 using a setup which permitted simultaneous measurements of X-ray diffraction data and electrical resistance on samples subject to an electric current. From the analysis of the data, they were able to infer that zinc ions are mobile and also to demonstrate sample degradation at higher current densities. Their work paves the way for further in operando studies of thermoelectrics – materials of growing importance in energy technologies – and, as the authors comment, of solid-state battery and piezo- and ferroelectric materials.
The most extensive applications of in situ/operando techniques are probably those in catalytic science, using synchrotron-based X-ray diffraction and X-ray absorption spectroscopy. Here they have had a huge impact in recent years and good reviews of earlier work in this area are available from Beale et al. (2010), Newton & van Beek (2010) and Bentrup (2010). Several recent examples can be found in the Faraday Discussions held this year on Reaction Mechanisms in Catalysis, including the study of Bugaev et al. (2021) which examined the industrially relevant reaction of ethylene hydrogenation using palladium catalysts, monitored by both XRD and XAS, illustrating the well established and increasing trend to apply multiple measurement techniques during in situ experiments. The data obtained allow the structural evolution of the working catalyst to be monitored as well as the transitions between metallic, hydride and carbide phases of palladium as the catalytic reaction progresses. Another excellent illustration of the current state of the art is provided by the recent study of van Ravenhorst et al. (2021) on the topical Fisher–Tropsch Co/TiO2 catalyst (which catalyses the synthesis of hydrocarbons from syngas, i.e. CO/H2 feed). They again combine synchrotron-based XAS with both synchrotron- and laboratory-based XRD to study the evolution of the catalyst on stream for 48 h. They are able to follow the formation of cobalt carbide as the reaction progresses, although the product distribution is largely unaffected. Interestingly, the formation of carbide is detected in XAS before XRD, as the former is more sensitive to short-range order. The paper nicely illustrates how detailed structural information on the evolution of complex catalytic systems can be obtained by this type of multi-technique operando study. A further recent example showing technical innovation is provided by the work of Matras et al. (2021), who used advanced tomographic imaging techniques in an operando study of a Ni–Pd/CeO2–ZrO2/Al2O3 catalyst during the partial oxidation of methane. The study gives detailed information both on the evolution of the metal and oxide species during the catalytic reaction and on the role of the heterogeneity in the catalyst particles.
A significant recent development is the ability to undertake experiments within a catalytic reactor, which is nicely illustrated by the work of Nieuwelink et al. (2021), again from the recent Faraday Discussions. The study followed hydrogenation reactions in a microreactor and was able to probe single particles during the reaction. ‘In reactor’ experiments can also give spatially resolved information as in the recent work of Decarolis et al. (2021) who investigated the widely studied selective catalytic oxidation of ammonia using a catalyst comprising palladium supported on alumina. The study shows that the nature of the catalytic species changes along the reactor and that these changes can be correlated with product distribution. This type of spatial analysis will grow in importance as the ability to undertake spatially resolved experiments develops.
In operando methodologies are not confined to X-ray techniques; they have been exploited, albeit less widely, using neutron scattering. Good examples in catalytic science include the work using neutron spectroscopy which was reported by Parker (2011), who clarified the role of surface hydroxyls in CO oxidation over a model palladium catalyst; the study also illustrates the power of neutron spectroscopic techniques to probe catalytic systems, which would be difficult to study by photon-based spectroscopies. A further illustration is provided by Youngs et al. (2013) who employed neutron total scattering methods to probe time-resolved catalytic chemistry in a Pt/SiO2 catalyzed benzene hydrogenation reaction.
Finally, we should note that although the extensive range of applications in catalysis have had notable impact, operando techniques can be applied to many other classes of functional material, such as energy materials, highlighted earlier. Structural studies of functional materials will increasingly be made under ‘operando’ conditions. IUCrJ would welcome submissions in this exciting and growing field.
Beale, A. M., Jacques, S. D. M. & Weckhuysen, B. M. (2010). Chem. Soc. Rev. 39, 4656.
Bentrup, U. (2010). Chem. Soc. Rev.39, 4718.
Bugaev, A., Usoltsev, O. A., Guda, A. A., Lomachenko, K. A., Brunelli, M., Groppo, E., Pellegrini, R., Soldatov, A. V. & van Bokhoven, J. A. (2021). Faraday Discuss.229, 197–207.
Decarolis, D., Clark, A. H., Pellegrinelli, T., Nachtegaal, M., Lynch, E. W., Catlow, C. R. A., Gibson, E. K., Goguet, A. & Wells, P. P. (2021). ACS Catal. 11, 2141–2149.
Matras, D., Vamvakeros, A., Jacques, S. D. M., di Michiel, M., Middelkoop, V., Ismagilov, I. Z., Matus, E. V., Kuznetsov, V. V., Cernik, R. J. & Beale, A. M. (2021). J. Mater. Chem. A, 9, 11331–11346.
Newton, M. A. & van Beek, W. (2010). Chem. Soc. Rev. 39, 4845.
Nieuwelink, A., Vollenbroek, J. C., Ferreira de Abreu, A. C., Tiggelaar, R., van den Berg, A., Odijk, M. & Weckhuysen, B. M. (2021). Faraday Discuss.229, 267–280.
Approximate symmetry in the third reported structure of a metal complex of L-DOPA
Carolyn Pratt Brock
Figure 1. Projection along a* of part of a layer of molecules having centroids in the range 0 < x < 1. The projection of the a axis is visible because β = 104.7°. The crystallographic 21 axes are shown in black and the approximate 42 axes are shown in blue.
The 2021 article ‘cis-Bis(L-DOPA-2N,O)copper(II) monohydrate: synthesis, crystal structure, and approaches to the analysis of pseudosymmetry’ by O’Brien et al. (2021) is notable for two reasons. First, it reports only the third crystal structure of a metal complex containing the medicinally important ligand L-DOPA (3,4-dihydroxy-L-phenylalanine). Second, the article includes a tutorial on finding approximate symmetry relationships between molecules that are chemically equivalent but crystallographically independent. Identification of approximate symmetry in molecular crystals is not yet a solved problem; rather, it is an area of considerable recent activity. Rekis (2020) proposed a method for finding approximate inversion centers; Brock & Taylor (2020) described software for finding approximate translations; Brock (2020) identified layers that have higher approximate symmetry than does the whole crystal; Baggio (2019, 2020) outlined a general method that can be used to find approximate symmetry of all types and applied it to a large number of Z' = 4 structures.
L-DOPA is a major drug that has been used for more than 50 years to treat the motor symptoms of Parkinson’s disease; global sales of its various forms are measured in the billions of USD. It is then very surprising to find that the Cambridge Structural Database (CSD; Groom et al., 2016) contains only two structures (FETTON and FETVEF; Suzuki et al., 1998) in which L-DOPA is coordinated to a metal, and two more (XOYXUH and XOYXUH01; Shemchuk et al., 2019) in which it is part of an ionic cocrystal (with LiCl).
There are numerous structures in the CSD of metal complexes containing the naturally occurring amino acids tyrosine (Tyr; 4-hydroxy-l-phenylalanine) and phenylalanine (Phe) that are the biological precursors of L-DOPA. In almost all of those structures the amino acid coordinates through both its amino and carboxylate groups. The CSD version of May 2021 includes 61 different R ≤ 0.075 structures of metal complexes of Tyr and 83 of Phe; there are, however, only two structures of any precision of L-DOPA complexes. Given its medical significance and market value it seems certain that many attempts have
been made to grow diffraction-quality crystals of metal complexes of L-DOPA, but if so, then most of those attempts failed. It would seem that the addition of the second hydroxy substituent on the phenyl ring must be determining, but why?
O’Brien et al. note that they had difficulty finding a crystal that diffracted well. Shemchuk et al. (2019) mention the low quality of the data for XOYXUH; their structure of the polymorph XOYXUH01 was determined from powder data. The R factors for FETTON and FETVEF (0.073 and 0.079, respectively; Suzuki et al., 1998) are surprisingly high. The small number of L-DOPA structures with metals and the problems with data quality suggest that some feature of L-DOPA interferes with crystal packing. Looking at the hydrogen-bonding tendencies of vicinal hydroxy groups located on phenyl rings might be a way to approach the problem.
The reported structure is particularly unusual in having two amino acid ligands. Of the 61 Tyr complexes in the CSD, only 18 have two Tyr ligands; of the 83 Phe complexes, only 9 have two Phe ligands. In many of those structures, especially those containing Cu2+, the free O atom of a carboxylate group from a neighboring molecule completes the fivefold coordination sphere consistent with a d9 ion capable of exhibiting a Jahn–Teller distortion. Sometimes, two such O atoms complete a sixfold coordination sphere. In the structure reported by O’Brien et al., it is the 3-hydroxy O atom on the phenyl ring that fills this role, although one of the independent Cu—O distances is considerably shorter than the other (2.74 versus 2.97 Å). In none of the 18 Mn+(Tyr)2L complexes is the phenyl-ring OH group coordinated in that way.
The other notable feature of this structure is its approximate symmetry. There are hydrogen-bonded columns of molecules along c that have easily recognizable, although quite distorted, 42 axes. O’Brien et al. explain how to find and quantify this relationship using the MATCH routine in Crystals for Windows (Betteridge et al., 2003) along with software they developed locally. The FIT routine in PLATON (Spek, 2020) gives essentially the same results for the rotation angle, the rotation axis, and the r.m.s. deviation (rmsd) for the best fit of the two molecules. When using PLATON (and perhaps when using MATCH) it was necessary to remove the 3-OH substituents on the phenyl rings so that the program recognized the two complexes as independent rather than bonded, with each of them having approximate twofold symmetry.
Approximate symmetry relating independent molecules is often associated with approximate symmetry that is periodic in at least two dimensions (Brock, 2020), but O’Brien et al. point out that the approximate 42 axis does not lead to any supergroup description. In a three-dimensional supergroup including a 42 axis the crystallographic 21 axis along b would have to be accompanied by an at least approximate 21 axis along a, but along a there is no symmetry of any kind other than translation (Fig. 1). Layers having approximate symmetry that is periodic in two dimensions are also impossible because layer groups cannot include n-fold rotation or screw axes, n > 2, that lie within the layer or any screw axis perpendicular to the layer. Any such axis within the layer could relate molecules through which it passes, but the axis would have to be local because if periodic it would move adjacent unit cells out of the layer.
The article concludes with a tribute to the first author, Professor Paul O’Brien of the University of Manchester, who passed away in 2018 while the manuscript was being formulated but before it could be completed. Since the delay was probably the result of the difficulty in finding a crystal that gave an acceptable diffraction pattern, the authors are to be applauded for their persistence. The finished article is a fitting tribute to Paul O’Brien.
So, the IUCr Congress in Prague has passed successfully. I have to
take my hat off to Radek Kužel and his team, working under the most difficult
of circumstances, caused by … you know what. I don’t know how they managed it,
but I think it is likely that hybrid meetings like this will probably become the
standard in the future. It went off so smoothly and professionally. I was able
to tune into several talks from France, where I was staying at the time.
Marvellous! One result is that we have a new President, Hanna Dabkowska, and
Vice-President, Santiago García-Granda. Congratulations to them both.
I am sorry to say that it has been a lousy year for
crystallographers this year, as so many have gone. In this issue, we have
obituaries for Carroll Johnson, John Reid, Hans Boysen, John Squire, John Spence and Tibor
then, very recently, we have heard of the death of Jack Dunitz, a well-known figure to all crystallographers. I hope
we shall have an obituary for him in the next issue.
Here, we have several articles on the great J. D. Bernal, who
died 50 years ago. These articles were recently printed in the British
Crystallographic Association’s Crystallography News, and I am pleased that John Finney, the
Editor, has allowed us to reprint them here. Bernal was one of those towering
figures in crystallography, a man of incredible intellect and influence. Every
crystallographer should know about him. There is an excellent book on his life
by Andrew Brown entitled J. D. Bernal: The Sage of Science. It is well worth a read,
especially if you are interested in the history of our subject. Bernal was not
only a key figure in crystallography, he was someone with many other interests.
He was controversial for his views on Marxism, with the result that he was
better known in the Soviet Union than here in the West.
This reminds me of a story. Many years ago, I was having a
coffee at Birmingham (UK) airport when I noticed at the next table a man
reading Andrew Brown’s book. So, I leant over to him and said to him that I had
known Bernal myself. It appeared that he was writing a review for one of our
newspapers, The Daily Telegraph (https://www.telegraph.co.uk/culture/books/3649528/The-unknown-polymathic-crystallographer.html).
He said to me, “You know, Bernal was such an evil man!” Of course, I swiftly
tried to put him right, but I don’t think to much avail.
I recall meeting Bernal a few times at Birkbeck College,
London. The first time was when the late Howard Flack and I were students in
1966 in the laboratory of Kathleen Lonsdale and used to attend evening classes
on crystallography at Birkbeck. At one point, Bernal came in to address us. He
was by this time very ill, having had a stroke. I remember that he was in a
wheelchair and had a massive loudspeaker through which he could try to talk. It
was sad to see him in this state, and the poor man must have felt very
frustrated. He was at that time President of the IUCr, but, because of
illness, he was unable to attend the Moscow IUCr Congress that year; instead,
Kathleen Lonsdale stood in for him as acting President.
So do get a copy of Brown’s book if you can. It is well
written and fully explores all the intriguing aspects of the life of Bernal.
One minor correction I would make. Brown mentions that Bernal invented the
phrase “weapons of mass destruction.” However, this first appeared in a book
called We (Мы) by Yevgeny Zamyatin in
1921, which described a dystopian world. I am reasonably sure that, given
Bernal’s interest in Russia, he must have been aware of this.
Another major article in this issue is on the 100 years
history of ferroelectricity, written by Nicola Spaldin and Ram Seshadri.
Ferroelectricity is a phenomenon exhibited by certain crystalline materials in
which an electric polarization can be switched by an external electric field,
much like the way magnetisation can be switched by an applied magnetic field in
ferromagnets. Nicola tells me that she had a lot of fun researching this topic.