Cambridge Crystallographic Data Centre

The ACA Video Library (AVL) is a collection of educational and insightful videos on various scientific topics. The AVL is continuously being developed and expanding, with generous support from the American Institute of Physics. Website maintenance is in place and we are accepting submissions. This presentation will inform the membership about goals and updates for this valuable resource. Further details can be found at: https://avl.memberclicks.net

Educating the public about crystallography and structural chemistry is part of the charitable mission of the Cambridge Crystallographic Data Centre (CCDC). At the CCDC, we are continuously developing resources for structural chemistry education aimed to reach different learners. This talk will highlight our activities, initiatives, and resources to introduce future scientists to the wonder of crystals. First, we will present our involvement in science festivals and the resources we have developed for younger scientists to learn about structural science concepts such as polymorphism and docking. These resources range from activities for in-person events to home-friendly materials, as well as games and videos. We have also launched a community engagement initiative, the CCDC Engagement Grants, which provides educators with financial support to develop outreach projects. The materials created from the grant are shared with the community to inspire the next generation of scientists and other educators who wish to do the same. We will briefly present some of the activities created so far with the CCDC Engagement Grants and other outreach activities in the community. Finally, we will look at resources that introduce advanced scientific concepts leveraging the data in the Cambridge Structural Database (CSD). You will leave the discussion with a new set of tools and educational materials you can use to inspire the next generation of structural scientists.

A crystal structure is often an integral component in the development of a new pharmaceutical product, and these structures are frequently used to understand, assess and often predict both the manufacturing and in vivo behaviour of these compounds. Combining a range of analytical methods with computational analysis of the crystal surfaces, Zmeškalová et al. [(2025). IUCrJ, 12, 141–154] link the properties of three solid forms of a biologically active molecule to its dissolution behaviour.

This comprehensive chapter covers various aspects of the biology and natural history of the Javan rhinoceros Rhinoceros sondaicus, including names, subspecies and distribution, descriptive notes, habitat, movements and home range, activity patterns, feeding ecology, reproduction and growth, behaviour, parasites and diseases, status in the wild and in captivity. The chapter includes a distribution map, several photos of the species, and a list of key literature.

In this first of a two-part series, we introduce the concept of a FAIRSpec-ready spectroscopic data collection – that is, a collection of instrument data, chemical structure representations, and related digital items that is ready to be automatically or semi-automatically extracted for metadata that will allow the production of an IUPAC FAIRSpec Finding Aid. Associating this finding aid with the collection produces an IUPAC FAIRSpec Data Collection. The challenge we set for researchers is relatively simple: to maintain their data in a form that allows critical metadata to be extracted in a discipline-specific way, increasing the probability that the data will be findable and reusable both during the research process and after publication. We focus on a few specific suggestions that researchers can use to maximize the “fairness” of their spectroscopic data collection. Most importantly, following these guidelines ensures that instrument datasets are unambiguously associated with chemical structure. The guidelines promote the inclusion of the instrument dataset itself in the collection and describe ways of organizing the collection such that automated metadata creation is possible. In these guidelines we emphasize the importance of systematically organizing data throughout the entire research process, not just at the time of publication.

Wellbore instability caused by hydration during the development of shale gas reservoirs poses significant challenges to drilling engineering. In this study, a novel and environmentally friendly shale inhibitor, TIL-NH2, was synthesized via free radical polymerization using 1-vinylimidazole and N-(2-bromoethyl)-1,3-propanediamine dihydrobromide as the main raw materials. The molecular structure of TIL-NH2 was characterized by infrared spectroscopy and nuclear magnetic resonance. Incorporating imidazole cations and amino bifunctional groups, TIL-NH2 exhibits excellent inhibitory performance and environmental friendliness. Its performance was systematically evaluated through linear swelling tests, shale cuttings rolling recovery tests, permeability recovery experiments, and dynamic adsorption analyses. The results indicate the following: (1) At a concentration of 1.2 wt%, TIL-NH2 reduced the linear swelling height of shale by 65.69%, significantly outperforming traditional inhibitors like KCl and NW-1. (2) Under conditions of 140 °C, the cuttings rolling recovery rate of TIL-NH2 reached 88.12%, demonstrating excellent high-temperature resistance. (3) Permeability recovery experiments showed that at a concentration of 2.0 wt%, TIL-NH2 achieved a permeability recovery rate of 90.58%, effectively mitigating formation damage. (4) Dynamic adsorption experiments indicated that at a concentration of 2.5 wt%, the adsorption capacity tended toward saturation, reaching 26.00 mg/g, demonstrating stable adsorption capability. Additionally, environmental friendliness evaluations revealed that TIL-NH2 has a degradation rate exceeding 90% within 28 days, and its acute toxicity is significantly lower than that of traditional inhibitors like KCl (the LC50 of TIL-NH2 is 1080.3 mg/L, whereas KCl is only 385.4 mg/L). This research provides a high-efficiency and environmentally friendly new inhibitor for green drilling fluid systems in horizontal shale gas wells, offering important references for technological advancements in unconventional energy development.

X‐ray Diffraction Computed Tomography (XRD‐CT) represents a cutting‐edge method for non‐destructive material analysis, offering the unique capability of providing molecular‐level information with spatial resolution. In this study, we have applied XRD‐CT to investigate pharmaceutically relevant tablets that have been subjected to a range of compression pressures typical in tablet manufacturing. By employing XRD‐CT to pharmaceutical tablets, we reveal material changes without tablet destruction, thereby avoiding potential phase transformations during sample preparation that could lead to errors in the interpretation of the processes that have occurred. Utilizing a pressure‐sensitive marker, glycolide, we have tracked changes within tablet structures induced by compression, pinpointing locations where glycolide undergoes pressure‐induced transformation. Additionally, we conducted a follow‐up study with analysis one month later, observing an in situ hydrolysis reaction of glycolide within the tablets. Through the complementary use of electron diffraction, we have elucidated the structure of the hydrolysis product, further enhancing our understanding of temporal changes in the tablets.

BindingDB (bindingdb.org) is a public, web-accessible database of experimentally measured binding affinities between small molecules and proteins, which supports diverse applications including medicinal chemistry, biochemical pathway annotation, training of artificial intelligence models and computational chemistry methods development. This update reports significant growth and enhancements since our last review in 2016. Of note, the database now contains 2.9 million binding measurements spanning 1.3 million compounds and thousands of protein targets. This growth is largely attributable to our unique focus on curating data from US patents, which has yielded a substantial influx of novel binding data. Recent improvements include a remake of the website following responsive web design principles, enhanced search and filtering capabilities, new data download options and webservices and establishment of a long-term data archive replicated across dispersed sites. We also discuss BindingDB’s positioning relative to related resources, its open data sharing policies, insights gleaned from the dataset and plans for future growth and development.

X‐ray Diffraction Computed Tomography (XRD‐CT) represents a cutting‐edge method for non‐destructive material analysis, offering the unique capability of providing molecular‐level information with spatial resolution. In this study, we have applied XRD‐CT to investigate pharmaceutically relevant tablets that have been subjected to a range of compression pressures typical in tablet manufacturing. By employing XRD‐CT to pharmaceutical tablets, we reveal material changes without tablet destruction, thereby avoiding potential phase transformations during sample preparation that could lead to errors in the interpretation of the processes that have occurred. Utilizing a pressure‐sensitive marker, glycolide, we have tracked changes within tablet structures induced by compression, pinpointing locations where glycolide undergoes pressure‐induced transformation. Additionally, we conducted a follow‐up study with analysis one month later, observing an in‐situ hydrolysis reaction of glycolide within the tablets. Through the complementary use of electron diffraction, we have elucidated the structure of the hydrolysis product, further enhancing our understanding of temporal changes in the tablets.

A seventh blind test of crystal structure prediction was organized by the Cambridge Crystallographic Data Centre featuring seven target systems of varying complexity: a silicon and iodine-containing molecule, a copper coordination complex, a near-rigid molecule, a cocrystal, a polymorphic small agrochemical, a highly flexible polymorphic drug candidate, and a polymorphic morpholine salt. In this first of two parts focusing on structure generation methods, many crystal structure prediction (CSP) methods performed well for the small but flexible agrochemical compound, successfully reproducing the experimentally observed crystal structures, while few groups were successful for the systems of higher complexity. A powder X-ray diffraction (PXRD) assisted exercise demonstrated the use of CSP in successfully determining a crystal structure from a low-quality PXRD pattern. The use of CSP in the prediction of likely cocrystal stoichiometry was also explored, demonstrating multiple possible approaches. Crystallographic disorder emerged as an important theme throughout the test as both a challenge for analysis and a major achievement where two groups blindly predicted the existence of disorder for the first time. Additionally, large-scale comparisons of the sets of predicted crystal structures also showed that some methods yield sets that largely contain the same crystal structures.

A seventh blind test of crystal structure prediction has been organized by the Cambridge Crystallographic Data Centre. The results are presented in two parts, with this second part focusing on methods for ranking crystal structures in order of stability. The exercise involved standardized sets of structures seeded from a range of structure generation methods. Participants from 22 groups applied several periodic DFT-D methods, machine learned potentials, force fields derived from empirical data or quantum chemical calculations, and various combinations of the above. In addition, one non-energy-based scoring function was used. Results showed that periodic DFT-D methods overall agreed with experimental data within expected error margins, while one machine learned model, applying system-specific AIMnet potentials, agreed with experiment in many cases demonstrating promise as an efficient alternative to DFT-based methods. For target XXXII, a consensus was reached across periodic DFT methods, with consistently high predicted energies of experimental forms relative to the global minimum (above 4 kJ mol ⁻¹ at both low and ambient temperatures) suggesting a more stable polymorph is likely not yet observed. The calculation of free energies at ambient temperatures offered improvement of predictions only in some cases (for targets XXVII and XXXI). Several avenues for future research have been suggested, highlighting the need for greater efficiency considering the vast amounts of resources utilized in many cases.

The InChI (International Chemical Identifier) standard stands as a cornerstone in chemical informatics, facilitating the structure-based identification and exchange of chemical compounds across various platforms and databases. The InChI as...

Online courses and innovative teaching methods have triggered a trend in education, where the integration of multimedia, online resources and interactive tools is reshaping the view of both virtual and traditional classrooms. The use of interactive tools extends beyond the boundaries of the physical classroom, offering students the flexibility to access materials at their own speed and convenience and enhancing their learning experience. In the field of crystallography, there are a wide variety of free online resources such as web pages, interactive applets, databases and programs that can be implemented in fundamental crystallography courses for different academic levels and curricula. This paper discusses a variety of resources that can be helpful for crystallographic symmetry handling and visualization, discussing four specific resources in detail: the Bilbao Crystallographic Server, the Cambridge Structural Database, VESTA and Jmol. The utility of these resources is explained and shown by several illustrative examples.

BindingDB (bindingdb.org) is a public, web-accessible database of experimentally measured binding affinities between small molecules and proteins, which supports diverse applications including medicinal chemistry, biochemical pathway annotation, training of artificial intelligence models, and computational chemistry methods development. This update reports significant growth and enhancements since our last review in 2016. Of note, the database now contains 2.9 million binding measurements spanning 1.3 million compounds and thousands of protein targets. This growth is largely attributable to our unique focus on curating data from US patents, which has yielded a substantial influx of novel binding data. Recent improvements include a remake of the website following responsive web design principles, enhanced search and filtering capabilities, new data download options and webservices, and establishment of a long-term data archive replicated across dispersed sites. We also discuss BindingDB's positioning relative to related resources, its open data sharing policies, insights gleaned from the dataset, and plans for future growth and development.

The Mycobacterium cell wall is a capsule‐like structure comprising of various layers of biomolecules such as mycolic acid, peptidoglycans, and arabinogalactans, which provide the Mycobacteria a sort of cellular shield. Drugs like isoniazid, ethambutol, cycloserine, delamanid, and pretomanid inhibit cell wall synthesis by inhibiting one or the other enzymes involved in cell wall synthesis. Many enzymes present across these layers serve as potential targets for the design and development of newer anti‐TB drugs. Some of these targets are currently being exploited as the most druggable targets like DprE1, InhA, and MmpL3. Many of the anti‐TB agents present in clinical trials inhibit cell wall synthesis. The present article covers a systematic perspective of developing cell wall inhibitors targeting various enzymes involved in cell wall biosynthesis as potential drug candidates for treating Mtb infection.