The IUCr Newsletter is the web magazine of the International Union of Crystallography. Since 1993, the IUCr Newsletter has been published quarterly and distributed to over 13,000 crystallographers worldwide. In August 2018, it was transformed into a dynamic digital platform with a fresh new look. Its aim remains to bring together the crystallographic community.
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William L. Duax Patricia Potter Jane Griffin The IUCr Newsletter is distributed electronically to 13,000 crystallographers and other interested individuals in 102 countries. Articles from the Newsletter are also available on this web site by following the links on the left-hand side. Feature articles, meeting announcements and reports, information on research or other items of potential interest to crystallographers may be submitted to the editor at any time. Items will be selected for publication on the basis of suitability, content, style, timeliness and appeal. Please send contributions to: newsletter@iucr.org Matters pertaining to advertisements should also be sent to the above address. Email address changes or corrections and requests to be added to the mailing list should be accomplished through the Subscribe and Unsubscribe hyperlinks above. Reuse permissions • The original article in which the material appeared is cited. • Copyright permission is indicated by the wording "Reproduced with permission of the International Union of Crystallography Newsletter". In electronic form, this acknowledgement must be visible at the same time as the reused materials, and must be hyperlinked to the IUCr Newsletter (http://www.iucr.org/news/newsletter). Please be sure to include the following information: • The title, author(s) and page extent of the article you wish to republish, or, in the case where you do not wish to reproduce the whole article, details of the section(s) to be reproduced. • The volume/issue number and year of publication in which the article appeared, and the page numbers of the article. • Details of the publication in which you wish to reprint the Newsletter material. • If the material is being edited or amended in any way, a copy of the final material as it will appear in your publication. • Contact details for yourself, including a postal address. |
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Annual Reports to the IUCr Executive Committee
The IUCr Newsletter (ISSN 1067-0696; coden IUC-NEB) is published quarterly (4x) by the International Union of Crystallography (IUCr Executive Secretary e-mail execsec@iucr.org). Members receive the IUCr Newsletter by virtue of country membership in the IUCr. Periodical postage rates paid at Buffalo, NY and additional mailing offices. POSTMASTER: Please send changes of address to IUCr Newsletter Editorial Office, c/o Hauptmann-Woodward Medical Research Institute, 700 Ellicott St. Buffalo, NY 14203 USA.
Professor Louise Dawe of the Department of Chemistry and Biochemistry, Wilfrid Laurier University, Waterloo, Ontario, Canada, has recently been appointed as a Section Editor for Acta Crystallographica, Section B.
Louise holds a Master’s in Science (Chemistry) from the University of Utah (USA), as well as Bachelor’s degrees in Chemistry and Education, and a PhD in Chemistry from Memorial University of Newfoundland (Canada). She took up her current position in 2013 and is currently associate professor. With over 140 peer-reviewed publications to her credit, Louise is recognized for her expertise in small molecule X-ray crystallography. Her research group specializes in designing, synthesizing, and characterizing novel ligands that enable the simultaneous coordination of Lewis acids and anions.
In addition to her academic pursuits, Louise holds several leadership positions within the scientific community. She serves as the chair of the Canadian National Committee for Crystallography, co-chair of the International Program Committee for the 27th Congress and General Assembly of the International Union of Crystallography and is a member of the IUCr Meeting Support Committee. Furthermore, since 2019 Louise has taken on the role of organizer for the Canadian Chemical Crystallography Workshops, fostering knowledge exchange and collaboration.
Since 2020, Louise has been a co-editor for Acta Crystallographica, Section C. In 2022, she assumed the role of Teaching and Education co-editor for Journal of Applied Crystallography and will continue in this role in parallel with her new Section Editor one.
Her unwavering passion for the science and community of crystallography drives her commitment to supporting the publication of high-quality research. She aims to enable the publication of superior work related to the fundamental understanding of structure, crystal growth, and the development and application of new molecules and materials. Moreover, Louise is enthusiastic about welcoming new authors and providing emerging researchers with a strong publishing community.
The three existing Section Editors (Sandy Blake, Marc de Boissieu and Ashwini Nangia) are delighted to welcome Louise to the team and look forward to working with her on the further development of the journal.
In this blog (based on the webinar "Boosting Research Efficiency in Industry with FAIR Data") we discuss the FAIR data principles and their potential. Topics include how these principles are applied at the CCDC and how the chemical industry can benefit from them. Read more.
We have six online training courses to help you learn the basics of how to use the CSD software. The latest course added to the collection is "Surface Analysis with CSD-Particle", presented in a "watch, try, test" format, allowing you to receive a completion certificate for your efforts.
Alongside these free courses, if you want to learn more about CSD-Particle, we have two new self-guided workshops: "Surface Analysis with CSD-Particle Tools in Mercury" and "Investigation of New Plastic and Elastic Properties Tools in Mercury." In these workshops, you can explore the chemical and topological properties of particle surfaces and slip planes in crystals using a step-by-step workshop guide.
Discover how Mercury makes it easy to explore symmetry in crystal structures and how Mogul can be used as a structure validation tool during crystal structure refinement. Watch the videos to learn more.
In 2023 we are attending and sponsoring many events worldwide and delivering free virtual workshops and webinars. Visit our events page here for the full list.
Join the CCDC talk on Algorithm Development and Data Analysis in Chemical Space (CINF), presented by Jeff Jeff Lengyel, Materials Scientist. Find out more.
The CCDC is exhibiting, holding workshops, presenting and chairing talks and running the CSD leaderboard. Don’t miss this opportunity to meet our team. Find out more.
If you would like to suggest topics for our workshops and webinars email us at hello@ccdc.cam.ac.uk.
Want to learn more about CCDC events, blogs, case studies and software updates? Follow us on LinkedIn, Facebook and Twitter.
We are happy to share that Kirara#4 recently returned from its mission to the International Space Station (ISS) and that we are already planning and preparing for the upcoming mission. Read more about the samples flown so far by the Kirara service.
Kirara#5 is already under preparation! And so we are calling for samples for the upcoming missions, and these are not strictly limited to proteins, as shown through the examples of previous missions.
In case you missed it, Space Commerce Matters, together with ICE Cubes and the Japan Manned Space Systems Corporation (JAMSS), organized a webinar focused on "Crystal Growing in Microgravity". The keynote speaker, Dr Anne Wilson from Butler University, Indianapolis, IN, USA, presented her project on a meta-analysis of Crystals Grown in Microgravity. The recorded webinar can be viewed here.
What is Kirara? A low-cost crystallization service in space, providing the opportunity to take advantage of the unique microgravity environment on board the International Space Station (ISS) for crystal growth in support of many applications, such as drug discovery. The service uses an original small incubator unit developed by JAMSS and accommodated inside the ICE Cubes Facility on the ISS.
![[Fig. 1]](https://www.iucr.org/__data/assets/image/0003/155784/Fig.-1.jpg)
Why space? The microgravity environment on-board the ISS has been proven beneficial to enable and study complex molecule crystallization processes. In space, gravity and convective forces do not get in the way of crystal formation, allowing crystals to grow larger, with a more rigid, ordered, near-perfect structure compared with those produced on Earth. The unique microgravity laboratory and environment of the ISS can therefore be used to support, for example, the investigations for the development of novel drugs that could treat viral outbreaks or antibiotic-resistant bacteria.
Why Kirara? Because it offers a unique end-to-end service where microgravity and crystallization experts determine the ideal crystallization conditions for the user. Several options are available to users to analyze their crystals once returned to Earth. These include support to crystal testing with the same experts also helping in the set up and performance of post-flight analysis (e.g. X-ray diffraction of the crystals), as requested. All the deliverables and intellectual property rights obtained belong to the customers.
The Kirara crystallization service has had four successful missions so far. During the first mission in December 2019, seven pharmaceutical companies and research centers participated and the first ever cellulose synthesis by enzyme in microgravity took place. On Kirara#2 in December 2020, the Kirara service was used to investigate Veklury, a redemsivir-based medicament for treating COVID-19, from InnoStudio Inc. and CycloLab Cyclodextrin C&D Laboratory Ltd. In December 2021, Kirara#3 exposed to microgravity the research of five different customers from Pharma/AgBio companies and research institutes from three different continents – Asia, US and Europe. Recently, Kirara#4 hosted samples for drug R&D (COVID-19 related research) and academic research (life sciences and agriculture), as well as educational and inspirational projects.
ICE Cubes/Space Applications Services contacts:
Leonardo Surdo: leonardo.surdo@spaceapplications.com
Dr Miguel Ferreira: miguel.ferreira@spaceapplications.com
The Laboratory of Crystallographic Studies (CSIC-UGR) has successfully organised the 8th International School on Biological Crystallization (ISBC2023) under the auspices of the IUCr through the Commissions on Crystal Growth and Characterization of Materials, Biological Macromolecules and Crystallographic Teaching, with the support of the International Doctoral Summer School Programme of the School of Science, Technology and Engineering (University of Granada), the Spanish Royal Society of Chemistry (RSEQ) and the Spanish Specialized Group of Crystallography and Crystal Growth (GE3C). The School was held at Hotel Abades Nevada Palace close to the centre of the beautiful city of Granada, an ideal place to promote close scientific and social interactions between attendees.
ISBC2023 attracted the interest of postgraduate/postdoctoral students as well as research scientists from industry and academia who deal routinely with crystallization processes but seek fundamental knowledge on the crystallization phenomena and the behaviour of crystallizing solutions. The participants came to Granada to learn from top-quality international speakers, to hear case study presentations, to watch practical hands-on demonstrations and to present their research results in the purposely dedicated poster sessions.
ISBC2023 delivered five days of lectures and practical demonstrations related to the crystallization of biological macromolecules, including large crystals for neutron diffraction and tiny crystals for XFEL or EM. One day was fully devoted to case studies on the crystallization of membrane proteins, viruses and large macromolecular complexes, and sample preparation for cryoEM.
As in previous editions, the Demonstration Fair was very successful with much positive feedback from the participants. A round-table discussion on “Teaching Crystallography” was also highly appreciated among tutors, academics, students and industrial representatives.
The turnout of the School was excellent having a total of 113 participants from 19 different countries, most of whom were students (41%), speakers (24%) and academics (17%), the rest being composed of industrial representatives (1) and exhibitors (7). The participants were supported by a team of four people from the organization. We achieved our goal of gender balance, having 53% female participants and 47% male.
Considerable effort was also made to provide financial support to as many students as possible. All of the 39 applicants were awarded a bursary to attend the School, including all 24 students coming from outside Spain.
The first day, Monday, started with an introduction to the School and was fully dedicated to explaining the whole process of crystallization “From solution to protein crystals”, from the purification and preparation of protein solutions to the basic concepts of crystallization, nucleation, phase diagrams, crystal growth kinetics and the different crystallization techniques (Fig. 1).
![[Fig. 1]](https://www.iucr.org/__data/assets/image/0008/156959/Fig.-1.jpg)
Tuesday was devoted to special hot topics, including femtosecond crystallography, microseeding, microfluidics, how to grow crystals for neutron diffraction, the crystallization of membrane proteins and large macromolecular complexes (Fig. 2).
![[Fig. 2]](https://www.iucr.org/__data/assets/image/0009/156960/Fig.-2.jpg)
On Wednesday there were sessions on especially relevant topics such as optimization of crystal growth for neutron diffraction, SAXS and EM (Fig. 3).
![[Fig. 3]](https://www.iucr.org/__data/assets/image/0010/156961/Fig.-3.jpg)
Thursday was dedicated to the very popular ‘Demonstration Fair’, at which specialists offered 23 short (20–40 minutes) practical sessions periodically at scheduled times. Participants were free to choose what sessions they wanted to attend and in the order they wished, so that they selected their own learning programme “a la carte”. The Demonstration Fair proved to be an excellent teaching tool as it provided students with plenty of opportunities to interact on a personal basis with the teachers and to watch closely how to perform crystallization experiments (Fig. 4).
![[Fig. 4]](https://www.iucr.org/__data/assets/image/0011/156962/Fig.-4.png)
The last day of the School started with a very appealing lecture given by Professor Bernhard Rupp titled “The Chemistry of Mushroom Magic (Why you should not lick toads)” followed by the round-table discussions on “Teaching Crystallography” driven by Professor JuanMa Garcia-Ruiz on how to present the successful story of the “Crystallization Competition” with the help and presentations of Dr Ivana Kuta Smatanova and Dr Janet Newman (Fig. 5). There were also 5-min talks given by the poster winners.
![[Fig. 5]](https://www.iucr.org/__data/assets/image/0003/156963/Fig.-5.jpg)
The students made a great contribution to the success of the School with 41 posters. There were poster sessions on Monday, Tuesday and Wednesday coffee breaks, proving to be a very valuable time in order to discuss the scientific work. The six poster winners (Fig. 6), who were selected by an international panel of lecturers composed of Bernhard Rupp, Crissy Tarver, Christian Biertümpfel, Lata Govada, May Marsh and Joe Ng, gave a 5-min presentation on Friday morning.
![[Fig. 6]](https://www.iucr.org/__data/assets/image/0014/157001/Fig.-6.png)
In addition to the scientific course, there was a parallel social programme, which consisted of a welcome cocktail on Sunday, a night guided walk of Albaicín and Sacromonte on Wednesday (Fig. 7) and a Flamenco Dinner Party on Thursday in the traditional district of Albayzin (Fig. 8), which is known worldwide for its flamenco music.
![[Fig. 7]](https://www.iucr.org/__data/assets/image/0015/157002/Fig.-7.jpg)
![[Fig. 8]](https://www.iucr.org/__data/assets/image/0016/157003/Fig.-8.jpg)
Overall, the School was deemed to be very successful as judged by the majority of positive comments written by the participants. The attendees were asked about three major items: the quality of the scientific programme, the Demonstration Fair and the organisation. These are some of the comments:
“I really enjoyed my time, learned a lot, met some really enthusiastic students and thankfully didn't have much of a hangover from the sangria on Thursday night.” (Martin Caffrey, speaker).
“It was my great pleasure to be a part of your School... you did super job and I am looking forward to the 9th run:)... (Ivana Smatanova, speaker).
“Was a pleasure and honour to be a part of ISBC2023. The meeting, the talks, the posters were all of such high standard. This year we got to experience 'the Rain in Spain on the plains' for the first time 😀. Thank you once again for everything”. (Lata Govada, academic).
“It was wonderful to see everyone again in 3D after such a long time! Thank you Gavi, JuanMa and team for organizing such a wonderful workshop again. I know it is a lot of work, but everyone one of us including students and instructors, appreciate everyone's effort, energy and enthusiasm.” (Joseph Ng, speaker).
“Yes, indeed – thanks to all of the organisers for putting together a wonderful course for the students and participants.” (Tom Peat, speaker).
“It really was a pleasure to be a part of ISBC2023! I enjoyed the science, time in Spain, and time with friends. Thank you and your team for everything.” (Crissy L. Tarver, academic).
“MUCHAS GRACIAS to you and to all the school organisers. It was a great pleasure to take part in ISBC2023 and to have the opportunity to meet the biological crystal grower community again after such a long time for such a high quality event in Granada.” (Monica Spano, speaker).
“Thank you very much for hosting us for such a great meeting! I enjoy the energy of teachers and students, active discussions, and exchanges of ideas. I am glad that everybody is well after 4 years. Take care and see you again!” (Naoko Mizuno, speaker).
“Thank you so much for organizing such a great event! I am really grateful for the opportunity to contribute and meet you all in person! Muito obrigada :) (Filipa Castro, speaker).
“Thanks very much for organizing this wonderful meeting/workshop. As always, everything was superb. The talks very exciting; the students, very talented and had great posters. Thanks also to everyone for this effort.” (Guillermo Calero, speaker).
“Thank you to you and your team for organizing the workshop again, and making it run so smoothly. It brings together many old friends and helps creates new ones. It also showcases the amazing beauty of Spain. I love Granada and I love the country. I will say it once more – Thank you.” (Edward H. Snell, speaker).
There was a general feeling among the participants that the School had been very valuable partly because of the quality of the programme and partly due to the contribution of some of the best lecturers for the wide range of topics covered.
All in all, the ISBC2023 was an enriching experience for all of those involved triggering several fruitful scientific discussions. The positive approach, the openness and active participation of each of the participants made it a wonderful experience worthwhile to be repeated in the future.
Finally, we would like to express our gratitude to all of the participants; to the teachers for their full commitment and to the students and colleagues from academic and industrial background for believing in these Crystallization Schools. We also wish to express our heartfelt thanks to the Members of the Organizing Committee for their substantial contributions to the Schools. We are very grateful to all the people who have worked very hard in preparing the Schools to make it successful. Last but not least, we would also like to express our special gratitude to the Sponsors and Exhibitors for their great support.
The Course, the 58th edition of the International School of Crystallography, was held at the Ettore Majorana Foundation and Centre for Scientific Culture from 2 to 10 June 2023. The Centre is situated in the old pre-mediaeval city of Erice, Italy, where four restored monasteries provide an ideal setting for scientific and professional exchanges. The event was initially scheduled for 2020 but postponed because of the COVID-19 pandemic.
The number of participants was limited to 83; in addition there were 28 lecturers and workshop presenters, and the organizers of the conference. The participants, from 23 countries, were largely from university (PhD students, postdoctoral and young researchers), with some industry participants. IUCr funds were used to support the attendance of three female and four male young scientists, from Belgium, the Czech Republic, Greece, Mexico, Norway, Poland and South Africa.
The schedule for a typical day included a morning session with four 45-minute lectures, followed by a lunch break. The afternoon session included different workshops/tutorials.
The aim of the organizers was to provide the students with an overview of the current structural and biophysical techniques and informatic tools used in the field and their applications in different areas. The program was subdivided by topic, each day covering a particular theme: introduction to the general techniques (crystallography, cryo-EM, machine learning), biophysics and binding (computing and measuring binding affinity, conformational and allosteric landscapes), informatics (machine learning, docking, FEP, molecular dynamics), small-molecule chemistry (compound design, compound optimization, crystal structure prediction), biologics (rational design, and developability) and case studies describing the many steps in the process of drug discovery, from initial library screening to back-up studies. After each lecture, some time was set aside for discussion.
Nine workshops were offered to the participants in the afternoons, providing hands-on experience in a diverse set of techniques necessary in drug discovery from ligand fitting into electron density maps, to cryo-EM data processing, to in silico drug discovery and optimization using different software to biologics design. Each workshop was repeated at least twice, to give the participants more opportunity to attend.
Two poster sessions were held in the evening, giving the young participants a chance to showcase their work and discuss with the lecturers and more senior participants. Sixty-six posters were presented in total, half in each session. Each poster session was preceded by a poster preview session (at lunchtime), to increase the time for poster viewing and informal discussions.
During the last afternoon, two talks, one describing the trials and tribulations of starting a new company and one offering a vision of where structural biology and drug discovery could be in 10 years, provided ground for a final discussion.
The lecturers and workshop organizers were a mix of individuals from pharmaceutical companies and academia, all with a very high level of expertise and that represented the different branches of science required to meet the diverse challenges of drug design.
Sixty-six abstracts were submitted for poster presentation, among these, ten were selected for a short oral presentation (12 minutes + 3 minutes question time).
During the closing ceremony, several awards were presented. For the posters, the first place was assigned to Zuzanna Kozicka (University of Basel, Switzerland), the second place to Francesca Vallese (Columbia University, New York, NY, USA) and the third to Dennis Peter Stegmann (Swiss Light Source, Villigen PSI, Switzerland).
![[Fig. 2]](https://www.iucr.org/__data/assets/image/0006/156957/Fig.-2.png)
The Lodovico Prize (acknowledging the most active student inside and outside the lecture hall) was given to Kristýna Adámková (Institute of Biotechnology of the Czech Academy of Sciences, Prague, Czech Republic).
![[Fig. 1]](https://www.iucr.org/__data/assets/image/0005/156956/Fig.-1.png)
At the end of the Course, participants were asked to participate in a survey to judge and comment on the quality of the Course. Their responses indicate that a similar meeting should be held at least in 3–4 years’ time and that the course had been successful in most of its objectives (score 85/100).
During the course a special Icebreaker event was organized to further promote socialization and interaction outside the lecture and workshop halls. Eight groups were formed (each including a lecturer) and given the objective of identifying one aspect of the Course they most enjoyed, and then presenting the outcome in a 5-minute presentation at the end of the last day. The presentations were very creative and extremely entertaining and provided a nice introduction to the Course final remarks.
On the northern summer solstice of 2016, Max IV opened in Lund, Sweden, the first of a new generation of synchrotron radiation facilities based on the multibend achromat (MBA). This new innovation provides a way to control the trajectories of giga-electron-volt electrons to micrometre precision. The X-ray beam generated from such an improved ‘fourth generation’ storage ring, measured at the experiment 50 m away, is largely spatially coherent because the angular width of the source, as seen from this distance, is exceedingly small – the same reason why starlight is spatially coherent. Basically, the difference between the distances of paths that rays take to reach the observer from one side of the source or the other is less than a wavelength, such that an optical instrument (including diffraction from the eponymous Young’s double slit or its generalization to a macromolecular crystal) does not yield a result any different to that obtained with a single point emitter. Such can easily be the case when the Young’s ‘slits’ or scatterers are placed very close together. Indeed, the coherence of beams from a laboratory source was adequate for von Laue, Friedrich and Knipping to observe the first diffraction from zinc sulfide and for Rosalind Franklin to create Photograph 51 of the B-form of DNA. (Periodic structures allowed many coherence ‘patches’ to contribute to produce a measurable signal.) The new MBA sources fulfil this condition for scatterers placed at any spacing within the entire microradian extent of the beam (thereby dropping the need for periodicity in the sample). In some new source designs and for photon energies softer than about 10 keV, the entire beam is coherent – referred to as diffraction limited. This implies that the source itself is exceedingly bright. And it is brightness (or brilliance as some call it) that truly defines these sources and provides opportunities in all fields of research that synchrotrons cater to today.
The brightness of a source describes how much light it emits per second and unit area into each solid angle and over a particular bandwidth. Given the above definition of spatial coherence, brightness is seen to be proportional to the number of photons per second passing through a ‘coherence volume’ of phase space (of position and momentum). One can strip away unwanted coherence modes by limiting the solid angle and area of the source that contributes to an experiment, such as by collimating the beam as Friedrich and Knipping first did, but it is a fundamental theorem of optics that one can never increase the number of rays per phase space volume. There are many ways to make things worse, but the source brightness dictates the upper limit on how quickly one can undertake a diffraction experiment, measure a spectrum, collect an image or tomogram, or expose a wafer. Brightness thus forms the basis of the comparison of sources, and the user meeting of every synchrotron radiation facility features one or more graphs of this quantity to boast the preeminence of their source or to justify the need for the next upgrade. What is astounding is the plot of the progression of the average brightness of sources since the discovery of X-rays by Röntgen in 1895. Not much happened until 1947 when synchrotron radiation was observed at the General Electric Research Laboratory in Schenectady, New York (Robinson, 2001). Since the late 1970s there has been a steady exponential growth that has brought 11 orders of magnitude increase in that time. This represents a doubling every 1.4 years, which can be compared with Moore’s law of a doubling of the number of transistors on a chip about every 2 years. Sirius, at the Brazilian Synchrotron Light Laboratory, is currently under commissioning and the ESRF in France has completed its upgrade to its Extremely Brilliant Source (EBS), giving a 30 times increase in brightness (Raimondi et al., 2023). Other facilities such as the Advanced Photon Source and the Advanced Light Source in the USA, SPring-8 in Japan, Diamond Light Source in the UK, and PETRA in Germany, are soon to follow, with even larger gains in brightness. As in the fields of microlithography (driving Moore’s law) and high-power optical lasers, the exponential growth of the performance of accelerator-based X-ray sources has relied on considerable effort and ingenuity to fuel progress punctuated by breakthroughs such as the MBA. Another key invention, the undulator, combined with optimized storage ring designs in the ‘third-generation’ synchrotron facilities that have served us for the last 30 years. The periodic magnetic structure delivers constructive interference of emission as the electron traverses each period [scaled from centimetres down to ångstroms by virtue of a double whammy of special relativity (Hwu & Margaritondo, 2021)]. X-ray free-electron lasers built upon this remarkable device by using enough periods that the radiation field influences the trajectories of the electrons (travelling at near light speed) and imprints itself onto their distribution, so that they all radiate in phase. This sets up a positive feedback that amplifies the FEL pulse and gains us yet another huge jump in peak brightness (and coherence) – both due to the increased number of photons, but also now because the X-rays are generated in femtosecond-duration pulses. Once also labelled as fourth-generation sources, current XFELs are more of a bifurcation that coexists with storage rings to expand X-ray science.
What new capabilities will fourth-generation synchrotron radiation sources bring? There is a clear benefit for imaging and tomography, where the speed at which an image is acquired is directly proportional to brightness. Thus, larger volumes (brains, computer chips) can be imaged in reasonable times, and if the sample can handle it, movies of processes in batteries, materials formation and processing, or energy harvesting can be made. Faster detectors and high-resolution X-ray optics are needed. The full coherence of the beam brings to fruition an idea first expressed by David Sayre, of utilizing the ability of crystallography to phase the wavefield scattering from a sample in order to synthesize an image of any object placed in the beam (Sayre, 1980). The method of ptychography, first developed in the electron microscope, provides an optimal way to recover the wavefield (Pfeiffer, 2018). These ideas could be driven all the way to atomic resolution – again, if the sample can handle it, or if information can be combined from many objects. The imaging of biological structures such as cells and macromolecules remains limited by radiation damage, and higher brightness just achieves the inevitable degradation sooner, for the same recorded diffraction information. Nevertheless, highly automated sample delivery methods enable rapid surveys of sensitive structures to be conducted over large parameter spaces, including time-resolved measurements, or to capture rare events, as needed to investigate relationships between structure and function.
Unlike previous transitions, many of the challenges faced by fourth-generation synchrotron facilities have solutions developed at the XFELs. Thirty years ago, the performance of beamlines was often limited by the speed of detectors. XFELs were such a startling jump of a billion times in peak brightness that large investments were necessary in high-speed integrating detectors. These are now a great match for the upgraded synchrotrons (Chapman, 2018) and can consume photons faster than a storage-ring-based source can provide them (Allahgholi et al., 2015). These detectors produce vast amounts of data, which is recognized as too large to fully archive and in need of new expertise to turn it into knowledge. Techniques such as serial crystallography, born out of the necessity to work with destructive X-ray pulses, are already being adopted at synchrotron facilities to make full use of the source output and provide a paradigm for high-throughput automated experiments (Standfuss & Spence, 2017). A strong connection between these different ‘fourth generation’ facilities is needed to tackle what are becoming joint challenges. Looking even further ahead, a higher diversity of sources including energy-recovery linacs (Shen, 2001), and compact accelerators utilizing high-power laser technologies (Graves et al., 2017), may benefit from such synergies and serve the needs of structural science with both specialized instrumentation for particular types of measurements or test beds for further development. IUCrJ will continue to chart the exciting outcomes emerging from this and future generations of sources.
Allahgholi, A., Becker, J., Bianco, L., Delfs, A., Dinapoli, R., Goettlicher, P., Graafsma, H., Greiffenberg, D., Hirsemann, H., Jack, S., Klanner, R., Klyuev, A., Krueger, H., Lange, S., Marras, A., Mezza, D., Mozzanica, A., Rah, S., Xia, Q., Schmitt, B., Schwandt, J., Sheviakov, I., Shi, X., Smoljanin, S., Trunk, U., Zhang, J. & Zimmer, M. (2015). J. Instrum. 10, C01023.
Chapman, H. N. (2018). Nat. Methods, 15, 774–775.
Graves, W. S., Chen, J. P. J., Fromme, P., Holl, M. R., Kirian, R., Malin, L. E., Schmidt, K. E., Spence, J., Underhill, M., Weierstall, U., Zatsepin, N. A., Zhang, C., Hong, K.-H., Moncton, D. E., Limborg-Deprey, C. & Nanni, E. A. (2017). Proceedings of the 38th International Free Electron Laser Conference (FEL2017), 20–25 August 2017, Santa Fe, NM, USA, pp. 225–228. https://doi.org/ 10.18429/JACoW-FEL2017-TUB03.
Hwu, Y. & Margaritondo, G. (2021). J. Synchrotron Rad. 28, 1014–1029.
Pfeiffer, F. (2018). Nat. Photon. 12, 9–17.
Raimondi, P., Benabderrahmane, C., Berkvens, P., Biasci, J. C., Borowiec, P., Bouteille, J.-F., Brochard, T., Brookes, N. B., Carmignani, N., Carver, L. R., Chaize, J.-M., Chavanne, J., Checchia, S., Chushkin, Y., Cianciosi, F., Di Michiel, M., Dimper, R., D'Elia, A., Einfeld, D., Ewald, F., Farvacque, L., Goirand, L., Hardy, L., Jacob, J., Jolly, L., Krisch, M., Le Bec, G., Leconte, I., Liuzzo, S. M., Maccarrone, C., Marchial, T., Martin, D., Mezouar, M., Nevo, C., Perron, T., Plouviez, E., Reichert, H., Renaud, P., Revol, J.-L., Roche, B., Scheidt, K.-B., Serriere, V., Sette, F., Susini, J., Torino, L., Versteegen, R., White, S. & Zontone, F. (2023). Commun. Phys. 6, 82.
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This article was originally published in IUCrJ (2023). 10, 246–247.
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The role of computational modelling in structural science was discussed in an Editorial in 2020 (Catlow, 2020). The field is, however, evolving rapidly and it is timely to return to the theme of structure prediction, starting with the celebrated quotation from the News and Views article of John Maddox, Editor of Nature, published in 1988:
One of the continuing scandals in the physical sciences is that it remains impossible to predict the structure of even the simplest crystalline solids from a knowledge of their composition.
The statement was of questionable accuracy but provided a powerful stimulus to the growing field of crystal structure modelling and prediction, with a response by the present author and Price, published in Nature two years later (Catlow & Price, 1990). The field was then reviewed twenty years after Maddox's article (Woodley & Catlow, 2008), and more recently by Oganov (2018) and Woodley et al. (2020). But how far has the community responded to the 'Maddox Challenge' over thirty years after it was first issued?
It is first necessary to recall the distinction between 'modelling' and 'prediction'. The ability to model crystal structures has a long history including the early work of Pauling. Then in the 1980s, it became clear that relatively simple interatomic potential models coupled with energy minimization procedures could model accurately the structures of a wide range of solids including silicates (Catlow et al., 1982) and zeolites (Henson et al., 1994); similar success was enjoyed in modelling molecular crystals. However, this was not prediction: it showed that transferable potentials would generate an energy minimum structure that was close to that experimentally observed; and this capability could help in refining structures. But prediction requires a search of the configurational space spanned by the structural variables to identify regions, which may correspond to stable structures, and which can then be refined by minimization of the energy calculated either using an interatomic potential model or using quantum mechanical techniques.
The exploration of energy landscapes is a major field of theoretical and computational science with crystal structure prediction being one key area. Notable progress was made in structure prediction for inorganic materials by Jansen and Schön who explored energy landscapes using simulated annealing techniques, reviewed by Schön & Jansen (2009). In a series of studies, Woodley and co-workers have shown the power of Genetic Algorithm methods in structure prediction (Lazauskas et al., 2017). Successful predictions have been made in several cases by the simple expedient of generating a large number of random configurations which are then subjected to energy minimization with the resulting lowest energy structure being the predicted structure [see, for example, Pickard & Needs (2011)]. The approach is compared with search methods by Woodley & Sokol (2012).
Different types of crystal structure may need different methods. For network and framework structures, topological principles may be used – an approach that has a long history going back to the early work of Wells (1954). It has enjoyed considerable success in the field of structure prediction in microporous materials as illustrated by Bell, Klinowski, Treacy and co-workers [see, for example, Foster et al. (2004) and Treacy et al. (2004)]. While the very active area of molecular crystal structure prediction explores structural possibilities using packing algorithms. Recent developments in the field are reviewed by Price (2018), with the prediction of the structures of polymorphs of pharmaceutical compounds being of particular interest and importance.
This editorial cannot do justice to a large and increasingly diverse field and the interested reader should consult the articles cited and references therein. But what is the current status of the field and where are the opportunities and challenges?
Structure prediction methods can, of course, be extended to other areas of structural science, notably nano-particle structures, where recent illustrations include the work of Escatllar et al. (2019) using GA methods coupled with DFT refinement, which predicted the structures of magnesium silicate nano-particles of relevance to the study of the chemistry of cosmic dust grains.
The field continues to benefit from methodological developments. A major limitation of most methods used for CSP is the lack of information that they provide about the global structure of the lattice energy landscape: the pathways and energy barriers between predicted structures, and how structures group into superbasins. A recent article by Yang & Day (2022) analysing energy landscapes of molecular crystals applied a Monte Carlo approach to approximate energy barriers between crystal structures of known polymorphic molecules, showing how the results help us to understand the kinetic stability of high-energy structures.
Another interesting technical development is reported by Dickson et al. (2022), who examined systems with variable composition and were able to implement variable compositions within the runs while searching a space of compositions.
A further fascinating recent development is the work of Price & Price (2022), which offers insight into the sensitivity of organic crystal packing to the substituents, based on an analysis of 232 crystal structures of 'chalcones' with only one small substituent on each phenyl ring. Although most of each molecule was the (chalcone) molecular scaffold, remarkably there were over 170 different packings. The only large isostructural group was of 15 molecules with all substituents, mainly halogens, in the para position. How can such structural diversity be compatible with the molecules all having the same chalcone scaffold? This diversity is closely mirrored by the structures generated by a crystal structure prediction study of the unsubstituted chalcone. Hence the packing is dominated by the core, but since this has a wide variety of packings of similar stability, the packing changes required by the substituents produce a wide range of observed structures. There is little evidence for any crystal engineering principle of preferred chalcone scaffold packing beyond close packing of the specific molecule.
Some of the most important recent developments in the field relate to the application of machine learning (ML) techniques. ML can be used to reduce the computational cost associated with energy evaluations by using energies calculated from e.g. DFT as training sets to enable ML calculations of energies as a function of geometry: essentially ML potentials. More ambitiously, ML can be used in direct structure prediction by using known structural databases as a training set as in the work of Ryan et al. (2018). The use of these methods will continue to grow, and they will be increasingly used together with the simulation methods discussed above. Another possible development will be the increased use of potential-based methods in energy evaluations, including, of course, ML potentials, but also high-quality 'classical' potentials based on analytical functions. There remain, of course, many challenges including modelling of disorder where there is a recent intriguing contribution from Dittrich (2021) who discusses the inclusion of restraints from theory in disorder refinement.
Over thirty years after the Maddox challenge, structure prediction is an exciting and rapidly developing field. IUCrJ welcomes articles in this and related areas.
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Dittrich, B. (2021). IUCrJ, 8, 305–318.
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Lazauskas, T., Sokol, A. A. & Woodley, S. M. (2017). Nanoscale, 9, 3850–3864.
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This article was originally published in IUCrJ (2023). 10, 143–144.
The IUCr Newsletter (ISSN 1067-0696; coden IUC-NEB) is published electronically by the International Union of Crystallography. Feature articles, meeting announcements and reports, information on research or other items of potential interest to crystallographers may be submitted to the Editors at any time. Items will be selected for publication on the basis of suitability, content, style, timeliness and appeal.
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