​What is quantum crystallography? [1]

Is it a hyped-up fad?

Is it “theory” or “experiment”?

What can it do? Is it useful?

Why has it become a new (perhaps better: reborn) IUCr commision?

The past

At the 2002 IUCr meeting in Geneva (rescheduled from Jerusalem) I was asked to speak after Jerome Karle, Nobel Laureate and one of those who had coined the term quantum crystallography (QCr) [2]. The room was packed, and soon there was a (second order?) phase change in the audience: either asleep or fidgeting. When Karle finished there was an immediate and astounding rush of people to leave. It was a bit disheartening for me; I had to shout over the commotion. Then there was more chaos, as some even turned back. I like to think it was because of me, but more likely it was defeat. I will review some of this 2002 material and show that QCr was in fact born with quantum mechanics itself [3]. I want to also highlight the work of Tibor Koritsanszky, recently lost to us, who together with Ewald medallist Philip Coppens brought about the “golden age” of our field [4].

The present

In a recent Australian Research Council grant application of mine assessor B lamented: “QCr is slowly creeping into crystallographic refinement to provide a better treatment of light i.e. hydrogen atoms … but how useful will it be in the vast majority of structural refinements?”. Even assessor D found it “hard to get excited about hydrogen atoms (sorry)”. Perhaps D is a physicist: only a non-chemist could be so callously unmoved by the proton, which forms the skin of all molecules, and is the fat positive partner of the beauteous electron! Surely these two are the hands of chemistry itself?! But I am actually rather pleased by that creeping comment: to me, it evokes a kind of desease-like inevitability: it resonates with the lack of direct funding [5]. In any case, I will explain why QCr is hard work, and I will review the impressive current progress by several groups.

The future

I think, except for Arthur C. Clarke, there have been no futorologist of note. Nevertheless, I will attempt to describe my vision for the use of model “experimental” wavefunctions to encode much more than just structral information; how QCr, the synthesis of quantum chemistry and crystallography will produce high quality databases worth mining; and how QCr has much to offer cognate fields like single-molecule and electron “diffraction”.

​[1] (a) Jayatilaka, D., N. C. (2012). Modern Charge-Density Analysis, edited by C. Gatti & P. Macchi, pp. 213-257. Springer.
(b) Grabowsky, S., Genoni, A., Buergi, H.-B. (2017). Chem. Sci. 8, 4159;
(c) Genoni, A.., et. al. (2018). Chem. Eur. J. 24, 10881. ​[2] Massa, L., Huang, L., Karle, J. (1995). Int. J. Quantum Chem. 56, 371. ​[3] James, R.W., Waller, I., Hartree, D.R. (1928) Proc. Royal Soc. London Ser. A 118, 334

[4] Koritsanszky, T.S., Coppens, P. (2001). Chem. Rev. 101, 1583

​[5] Take heart east-coast scientists! Research can continue, even in Western Australia where, to paraphrase W. Pauli and P. Doherty, we are not even of the Pacific bogan variety, https://tinyurl.com/jmv6uyne .

Single particle cryo electron microscopy (cryo-EM) has developed into a powerful technique to determine 3D structures of large macromolecular complexes. Due to improvements in instrumentation and computational image analysis, the number of high-resolution structures is steadily increasing. The method cannot only be used to determine high-resolution structures but also to study the dynamic behavior of macromolecular complexes and thus represents a very complementary method to X-ray crystallography. Furthermore, the maximum attainable resolution by cryo-EM has constantly improved in recent years. Most of the high-resolution structures are still in the 3 Angstrom resolution regime but some have even crossed the 2 Angstrom barrier. We have recently installed a new prototype electron microscope which is equipped with a monochromator and a next-generation spherical aberration corrector. This microscope is optically superior to the currently commercially available instruments and can therefore be used to test the resolution limits in cryo-EM. We have used the test specimen apoferritin to determine its structure at 1.25 Angstrom resolution which is sufficient to visualize for the first time individual atoms clearly separated in the density map without the need for computational beam tilt corrections.

Recently, we managed to use this microscope not only to improve the resolution of the very stable and rigid protein apoferritin. We also obtained significant improvement in resolution for other more dynamic macromolecular complexes for which one could have expected that the microscope itself may not be a major resolution limiting factor.

In current high-resolution cryo-EM structures less water molecules become visible compared to X-ray crystallographic structures at nominally the same level of resolution. The number of water molecules that can be reliably build into the EM density is also not independent from the image processing software used for the three-dimensional reconstruction. We made a first attempt to use the number of water molecules that can be build into a 3D structure as a quality criterium for cryo-EM data since until now such high-resolution quality estimators are entirely missing in the cryo-EM field.

We are currently upgrading our microscope with an energy filter and a faster direct pixel detector. This will not only improve throughput but also the maximum attainable resolution even further. Therefore I will address the question of how much the resolution in cryo-EM can still be realistically improved and how this compares to X-ray crystallography.

The major part of condensed matter in the Universe - deep inside planets and stars - exists under ultra-high pressures of several hundred gigapascals (GPa) and beyond. At such extreme conditions theoretical modelling predicts very unusual structures and chemical and physical properties of materials. Their synthesis and characterization at above 150 GPa have been hitherto hindered by the technical complexity of experiments involving samples’ heating and by a lack of relevant methods of the composition and structure investigations. Here on examples of simple elements, hydrides, oxides, carbonates, nitrides and silicates we will discuss single crystal X-ray diffraction experiments at static pressures from about 150 GPa to over 900 GPa in a laser-heated conventional and double-stage diamond anvil cells (ds-DAC).

RNA-Puzzles is a collective endeavour dedicated to the advancement and improvement of RNA 3D structure prediction. With agreement from crystallographers, the RNA structures are predicted by various groups before the publication of the crystal structures. Systematic protocols for comparing models and crystal structures are described and analyzed. In RNA-Puzzles, we discuss a) the capabilities and limitations of current methods of 3D RNA structure based on sequences; b) the progress in RNA structure prediction; c) the possible bottlenecks that hold back the field; d) the comparison between the automated web server and human experts; e) the prediction rules, such as coaxial stacking; f) the prediction of structural details and ligand binding; g) the development of novel prediction methods; and h) the potential improvements to be made.

Till now, 28 RNAs with crystal structures have been predicted, while many of them have achieved high accuracy in comparison with the crystal structures. We have summarized part of our results in three papers and two community-wide meetings. With the results in RNA-Puzzles, we illustrate that the current bottlenecks in the field may lie in the prediction of non-Watson-Crick interactions and the reconstruction of the global topology. Correct coaxial stacking and tertiary contacts are key for the prediction of RNA architecture, while ligand binding modes can only be predicted with low resolution.

We now further extend the prediction to RNA sequences in the Rfam families. We have predicted structures for 20 RNA families, while some of the predictions have been confirmed by crystal or cryo-EM structures, indicating the possibility to use predicted models for functional inference. The predicted models also helped in 'Molecular Replacement' for crystal structures.

For the model evaluation, we present RNA-Puzzles toolkit, a computational resource including (i) decoy sets generated by different RNA 3D structure prediction methods (raw, for-evaluation and standardized datasets), (ii) 3D structure normalization, analysis, manipulation, visualization tools (RNA_format, RNA_normalizer, rna-tools) and (iii) 3D structure comparison metric tools (RNAQUA, MCQ4Structures).

With the increasing number of RNA structures being solved as well as the high-throughput biochemical experiments, RNA 3D structure prediction is becoming routine and accurate. Experimental data-aided structure modelling may effectively help in understanding the noncoding RNA function, especially the viral RNAs.

The experimental models archived in the Protein Data Bank provide a rich source of structural information on proteins and nucleic acids. Complex architectures of RNA molecules as well as non-canonical DNA structures prove that the sugar-phosphate backbone is not a scaffold-like structure more or less passively accommodating to and enabling base pairing and stacking motifs formed by the four nitrogenous bases. In the past, RNA structures attracted more attention [1-5] as their 3D folds are formed by visibly rich ensemble of the backbone geometries. The self-recognition of DNA duplexes posed seemingly fewer challenges to analysis of their structural details. However, a detailed look showed structurally well defined conformers [6, 7] that proved useful in discriminating different modes of binding of DNA to transcription factors and the nucleosome core particle in histones [8]. The analysis has shown that differences in the local DNA structure relate to specificity of the binding. In the year 2020, the conformational spaces of DNA and RNA, which were traditionally analyzed separately, were described by one unified set of dinucleotide conformers, which are called NtC, and by a related structural alphabet CANA, Conformational Alphabet of Nucleic Acids [9]. I will briefly describe the principle of fully automated and robust assignment of the NtC classes and CANA symbols and overview related tools that help to annotate, validate, refine experimental structures, and build computer models of NA molecules. All these tools are feely available at the web service dnatco.datmos.org [10].
[1] Duarte et al. NAR 31:4755 (2003). [2] Murray et al. PNAS USA 100:13904 (2003). [3] Hershkovitz et al. NAR 31:6249 (2003). [4] Schneider et al. NAR 32:1666 (2004). [5] Richardson et al. RNA 14:465 (2008). [6] Svozil et al. NAR 36:3690 (2008). [7] Schneider et al. Acta Cryst D74:52 (2018). [8] Schneider et al. Genes 8:278 (2017). [9] Černý et al. NAR 48:6367 (2020). [10] Černý et al. Acta Cryst D76:805 (2020).

Recent developments in the field of evolutionary covariance and machine learning have enabled the precise prediction of residue-residue contacts and increasingly accurate inter-residue distance predictions. Access to accurate covariance information has played a pivotal role in the recent advances observed in the field of protein bioinformatics, particularly the improvement of prediction of protein folds by ab initio protein modelling. As this work seeks to showcase, this data is of equal value in the field of X-ray crystallography, with several practical applications in MR, model validation and map interpretation.

The most prevalent technique for the solution of the phase problem in macromolecular crystallography is molecular replacement (MR). In most cases, the availability and detection of a suitable search model, typically a solved structure homologous to the target of interest, is the key limitation of conventional MR. In those cases where no such structure is available, unconventional MR approaches are used. Recent results suggest that even in those cases where no homologous structures are found for a given target, it may still be possible to find suitable search models among unrelated structures, in the form of regions that share high, albeit local, structural similarity with the target. The challenge then becomes the accurate identification of such search models among the vast number of available solved structures. Here we present SWAMP, a novel pipeline for the solution of structures of transmembrane proteins, which exploits the latest advances in residue contact predictions for the detection of fragments later to be used as search models. SWAMP includes a library of ensembles built by clustering commonly observed packings of transmembrane helical pairs in close contact, mined from the available databases. Residue contact predictions are used in the process of search model selection: the contact maximum overlap between the target’s predicted contacts and the observed contacts of each member of the library is used to estimate the likelihood of the helical pair being a successful search model. Preliminary results show that SWAMP is capable of detecting valid search models originating from unrelated solved structures solely exploiting this contact information. This enables the solution of new and challenging structures without the use of experimental phasing techniques, and opens a whole new avenue of research in which predicted contact information is used to extend the reach of unconventional MR.

The final outcome of X-ray crystallographic experiments is the determination of the structure of interest, which requires building a model that satisfies the experimental observations. However, experimental limitations can lead to the presence of unavoidable uncertainties during model building resulting in regions that require validation and potentially further refinement. Many metrics are available for model validation, but are mostly limited to the consideration of the physico-chemical aspects of the model or its match to the map. We present new metrics based on the availability of accurate inter-residue distance predictions, which are then compared with the distances observed in the emerging model. Early results suggest that these metrics are capable of detection of register and other errors, even in challenging cases where conventional metrics may struggle.

Residue contact and inter-residue distance predictions are usually represented respectively as two-dimensional binary matrices called contact maps and distograms. These typically omit contacts between sequential near neighbours resulting in a blank space on and near the diagonal axis of the matrix. A multitude of properties can be predicted by other sequence-based methods and researchers often need to consider diverse sources of information in order to form a complete and integrated picture for the inference of structural features that can facilitate the structure solution. Here we present ConPlot, a web-based application which uses the typically empty space near the contact map or distogram diagonal to display multiple coloured tracks representing other sequence-based predictions. These predictions can be uploaded in various popular file formats. This web application is currently available online at www.conplot.org, along with documentation and examples.

I will present some recent developments of our Pepsi package for integrative modeling of macromolecules guided by small-angle scattering profiles. These include very fast tools for the all-atom computations of X-ray and neutron small-angle scattering profiles, called Pepsi-SAXS and Pepsi-SANS, respectively [1,2]. These tools implement algorithms specifically designed to handle two notable properties of large macromolecules and their complexes, such as for instance viral capsids, namely their high flexibility and high degree of symmetry. Flexibility of macromolecules is not spontaneous but linked with their structure and function. Computationally, it can be often approximated with just a few collective coordinates, which can be computed e.g. using the Normal Mode Analysis (NMA). NMA determines low-frequency motions at a very low computational cost and these are particularly interesting to the structural biology community because they give insight into protein function and dynamics. On our side, we have proposed a computationally efficient nonlinear NMA method that can be applied to largest complexes from the Protein Data Bank (PDB), and which also very well preserves local stereochemistry [3-5].

Flexibility of macromolecules is often linked with their structure and function. Computationally, it can be approximated with just a few collective coordinates computed using the Normal Mode Analysis (NMA). NMA determines low-frequency motions at a very low computational cost. This technique is particularly interesting for the structural biology community as it allows extrapolating biologically relevant motions starting from high-resolution structures. Recently, we have shown that it can be extended to model local deformations and to better preserve the stereochemistry of the protein. We have developed a computationally efficient nonlinear NMA method that can be applied to the largest complexes from the Protein Data Bank (PDB) [3-5].

Large symmetrical protein structures have seemingly evolved in many organisms because they carry specific morphological and functional advantages compared to small individual protein molecules. Recently we have proposed a novel free-docking method for protein complexes with arbitrary point-group symmetry [6]. It assembles complexes with cyclic symmetry, dihedral symmetry, and also those of high order (tetrahedral, octahedral, and icosahedral). We also proposed an efficient analytical solution to the inverse problem, that is the identification of symmetry group with the corresponding axes and their continuous symmetry measures in a protein assembly [7-8].

With Pepsi-SAXS and Pepsi-SANS, one can leverage the above-mentioned developments, by optimizing structures along low-frequency « normal modes », performing automatic and adaptive coarse-graining of molecular models, rescoring free-docking predictions, including those of symmetric assemblies, and also optimizing structural transitions. Structural models produced by Pepsi-SAXS/SANS were ranked top in the recent data-assisted protein structure prediction sub-challenge in CASP13 [9].

[1] Grudinin, S. et al. (2017). Acta Cryst. D, D73, 449 – 464. For more information https://team.inria.fr/nano-d/software/pepsi-saxs/
[2] https://team.inria.fr/nano-d/software/pepsi-sans/
[3] Hoffmann, A. & Grudinin, S. (2017). J. Chem. Theory Comput. 13, 2123 – 2134. For more information https://team.inria.fr/nano-d/software/nolb-normal-modes/
[4] Grudinin, S., Laine, E., & Hoffmann, A. (2020). Predicting protein functional motions: an old recipe with a new twist. Biophysical journal, 118(10), 2513-2525.
[5] Laine, E., & Grudinin, S. (2021). HOPMA: Boosting protein functional dynamics with colored contact maps. The Journal of Physical Chemistry B, 125(10), 2577-2588.
[6] Ritchie, D. W. & Grudinin, S (2016). J. Appl. Cryst., 49, 1-10.
[7] Pages, G., Kinzina, E, & Grudinin, S (2018). J. Struct.Biology, 203 (2), 142-148.
[8] Pages, G. & Grudinin, S (2018). J. Struct.Biology, 203 (3), 185-194.
[9] Hura, G. L., ... & Tsutakawa, S. E. (2019). Small angle X‐ray scattering‐assisted protein structure prediction in CASP13 and emergence of solution structure differences. Proteins: Structure, Function, and Bioinformatics, 87(12), 1298-1314.

Displacement parameters (B-factors) play a crucial role in macromolecular structure determination, yet are rarely used for biological interpretation. This is somewhat egregious, since they account for the local flexibility of individual protein states/conformations. We have developed a new approach^[1] for dividing the disorder information in a macromolecular model into a hierarchical series of components on different length-scales, which reveals the components of the atomic disorder that result from molecular disorder, domain disorder, or local atomic disorder. This makes both molecular and atomic disorder intuitively understandable in terms of likely domain motions and internal atomic motions. We demonstrate this new approach by studying the flexibility of the catalytic site in crystal structures of the SARS-CoV-2 main protease. Additionally, we apply the method to structures determined by cryo-EM, where we can investigate and visualize the flexibility in both the extended and non-extended receptor-binding domains of the SARS-COV-2 spike glycoprotein, and in the iron-reductase STEAP4, which hint at a mechanism for electron transfer.

Ribonucleic acid (RNA) molecules are master regulators of cells. They are involved in many molecular processes: they transmit genetic information, sense cellular signals and communicate responses, and even catalyze chemical reactions. RNA function and in particular its ability to interact with other molecules such as proteins, is encoded in the sequence. Understanding how RNAs and RNA-protein complexes carry out their biological roles requires detailed knowledge of the RNA structure.

Due to limitations in experimental structure determination, complete high-resolution structures are available for a tiny fraction of all the known RNA molecules crucial for numerous fundamental cellular processes. <1% of RCSB entries represent RNA structures, and only around 3% of RNA families available in the Rfam database have at least one experimentally determined structure. This relative paucity of information compared to what is available for proteins also makes computational RNA 3D structure prediction much less successful. Currently, purely computational RNA 3D structure prediction is limited to sequences shorter than 100 nt.

I will present strategies for computational modeling of RNA and RNA-protein complex structures that utilize SimRNA, a suite of methods developed in my laboratory, which use coarse-grained representations of molecules, rely on the Monte Carlo method for sampling the conformational space, and employ statistical potentials to approximate the energy and identify conformations that correspond to biologically relevant structures. In particular, I will discuss the use of computational approaches for RNA structure determination based on low-resolution experimental data, including low-resolution crystallographic electron density maps and cryo-EM maps.

References

1 Ponce-Salvatierra, A. et al. Biosci. Rep. 39, BSR20180430 (2019)
2 Boniecki, M. J. et al. Nucleic Acids Res. 44, e63 (2016)

Atomic model refinement and completion at low resolution (cryo-EM or crystallographic) is often a challenging task. This is mostly because the experimental data aren’t sufficiently detailed to describe using atomic models. To make refinement practical and ensure a refined model is geometrically meaningful additional a priori information about model geometry needs to be used. This information includes restraints on Ramachandran plot distributions or side chain rotameric states. However, using Ramachandran plot or rotameric states as refinement targets diminish the validating power of these tools. Therefore finding additional model validation criteria that are not used or difficult to use as refinement goals is desirable. Hydrogen bonds are one of most important non-covalent interactions that shape and maintain protein structure. These interactions can be characterized by specific geometry of hydrogen donor and acceptor atoms. Systematic analysis of these geometries performed for all quality-filtered high-resolution models of proteins from PDB shows they have distinct and conserved distribution that can be characterized by only two parameters. Here we demonstrate how these two parameters can serve as unique validation metrics and how they can pinpoint severe modeling problems that no other validation tools can detect. This tool is now a part of Phenix model validation suite; guidelines to its use and interpretation will be given.

Hybrid and integrative modeling methods that combine computational molecular mechanics simulations with experimental data are powerful in describing the structure and dynamics of large biomolecules. In particular, flexible fitting is a powerful technique to build the 3D structures of biomolecules from cryo-electron microscopy (cryo-EM) density maps. While flexible fitting methods work nicely with very high-resolution maps, there are limitations for medium resolution maps (~5-10 angstrom) in the case of complex conformational transitions. To overcome such issues, we proposed a refinement based on conformational ensemble, i.e., performing multiple fittings trials using various parameters. An automatic adjustment of the biasing force constants during the fitting process was introduced via a replica-exchange scheme to improve the success rate. From such multiple fittings, clustering analysis of the models obtained can be an effective approach to avoid over‐fitting. In addition, we have looked into the pixel size parameter as it can impact the resolution and accuracy of a cryo-EM map, and we proposed a computational protocol to estimate the appropriate pixel size parameter. In our protocol, we fit and refine atomic structures against cryo-EM maps at multiple pixel sizes. The resulting fitted and refined structures are evaluated using the GOAP score. We have demonstrated the efficacy of this protocol in retrieving appropriate pixel sizes via several examples.

Structural biology, the study of the 3D structures of biological entities on scales from small molecules to cells, has had an enormous impact on our understanding of biology and biological processes in health and disease. The results of these structural studies (mainly by MX, NMR and 3DEM) have been captured in the single global archive of atomistic models of biomacromolecules and their complexes, the PDB, operated by the wwPDB consortium. In addition, since 2002 the cryo-EM community has been depositing their maps and tomograms in EMDB.

A few years before the resolution revolution, wwPDB and EMDB jointly convened an EM Validation Task Force (VTF) which met in 2010 to discuss initial recommendations (published in 2012) regarding validation of cryo-EM data and models. In the following decade, the resolution revolution happened, EMDB grew from 1,000 to 15,000 entries, an archive for raw cryo-EM data was established (EMPIAR), community challenges related to EM validation were organised, and many labs began to develop new approaches to validating EM structures. This made it clear that a second EM VTF meeting was urgently needed. This meeting took place (in person!) in January 2020. During two days several dozen experts from all over the globe discussed cryo-EM data
management, deposition and validation.

A white paper summarising the discussions and recommendations of the second EM VTF meeting is currently in preparation. I will provide an overview of the major consensus recommendations emanating from the meeting and also address how wwPDB and EMDB are implementing these.

Cryo-EM is becoming an increasingly popular method of structure determination in structural biology. As the number of cryo-EM structures increases, it is important to maintain standards that measure the quality of those structures. The correctness of atomic models is very important because they often serve as targets for novel drugs or the knowledge base of such developments. Also, such standards are important to prevent the accumulation of errors of the structures in the databases. Thus, careful curation and validation of cryo-EM maps and derived atomic models are of utmost importance.

We have developed the EMDA Python package [1] that includes tools for cryo-EM map and model manipulation. In this presentation, the emphasis is given to those for validation. The majority of the current validation tools used in single-particle cryo-EM analyses are global metrics. They provide summaries of the global quality of maps or map-model fits. In order to reveal the local variation of the signal in maps and map-model fits, a new set of tools based on the local correlation have been developed. To calculate the local correlation, a spherical kernel is convolved with the map in image space to yield a correlation value at each voxel resulting in a three-dimensional (3D) correlation map. The variation of calculated correlation depends on the size of the kernel. The local correlation calculated using half maps captures the local variations in the signal, whereas the local correlation calculated between a map and a model indicates the quality of their fit. Map-model local correlation can be used to identify model regions outside the density or poorly fitted. Also, it can highlight unmodeled regions on the map. While the half map local correlation is useful to identify the presence/absence of the signal, its comparison with the map-model local correlation can be used to validate the map-model fit. In this presentation, we will demonstrate the use of local correlation through several examples. Also, EMDA includes several tools based on the maximum likelihood method. EMDA’s map-overlay and map magnification refinement are based on the maximisation of the joint probability distribution between two maps by a quasi-Newton method. We will demonstrate the use of map overlay and magnification refinement implemented in EMDA through examples.

To obtain more accurate atomic models from cryoEM and increase their impact on biomedical research, metrics are needed that carefully evaluate these constructed models. In this poster we present further developments on FSC-Q, a map-to-model quality issue recently introduced [1], with the capability to detect those areas of the model that are better supported by the experimental data (Figure1). The algorithm performs a careful analysis of the Signal-to-Noise Ratio in the half maps and in map generated from the proposed model through local resolution. It is intuitive and, yet, very precise, introducing quality information that we have quantitatively shown is new, in the sense that some of it was not captured in previous quality assessment metrics.

Electron cryo-microscopy (cryo-EM) is rapidly becoming a mainstream area of structural biology and medicine, enabling visualization and modelling of a wide variety of biologically important complexes. This recent explosion of new cryo-EM structures raises several important questions. How accurate are these maps and their model interpretations? What criteria are currently being used and are they good enough? This paper describes the outcomes of the 2019 Model Metrics Challenge sponsored by EMDataResource (https://challenges.emdataresource.org). The goals of this challenge were two-fold: (1) to evaluate the quality of models that can be produced using current modelling software, and (2) to assess the performance of metrics currently in use to evaluate cryo-EM models. In both instances the focus was on map targets selected the near-atomic resolution regime (1.8-3.1 Å), with an innovative twist: three of four maps formed a resolution series from the same specimen/imaging experiment.The results permit several specific recommendations to be made about validating near-atomic cryo-EM structures, both in the context of an individual laboratory experiment and for in the context of a structure data archive. We will also touch on preliminary results from our ongoing 2021 Ligand Model Challenge.

Q-scores are calculated locally for individual atoms in a model fitted or built into a cryo-EM map. They can be averaged over groups of atoms to represent resolvability of larger features such as residues in proteins, nucleotides in nucleic acids, and ligands. Plotting of residue or nucleotide Q-scores helps to identify which parts of a model are resolved in the map, and which parts may be unresolved or may need further refinement. A useful property of Q-scores is that for well-fitted models, they correlate strongly to the resolution of the map estimated by FSC; this answers the question ‘what is a good score’ for a map at a certain resolution. Several examples and related structural insights are shown with models and maps ranging from 2 to 5Å resolution. The connection between Q-scores and atomic B-factors is also explored. Finally, Q-scores are used to help detect and assess water and ion molecules in maps at 3Å and higher resolutions.

Materials with negative thermal expansivity (NTE) attracts great attention of scientists because they can be combined with numerous materials with positive thermal expansion (PTE) in order to prepare a composite material with a tailored coefficient of thermal expansion, namely, zero expansion. This allows decreasing a performance deterioration caused by a large difference in expansion coefficients.[1] Among numerous metal-organic frameworks (MOFs), zeolitic imidazolate frameworks (ZIFs) are highly popular because of the possibility to combine electronic properties of the transition metal ions with structural features of zeolites. They possess large porosity, therefore alkali metals that form dense and hyper coordinated structures stayed out of the focus for its synthesis. On the other hand, magnesium imidazolate has a porous structure, as well as its borohydride(s). Although the preparation of manganese imidazolates is challenging, probably due to the difficulties of formation of non-distorted tetrahedral Mn²⁺-4N geometry preferable in ZIFs, the similarity of magnesium and manganese borohydrides was reason to try synthesis with both metals and compare the results.

Mechanochemical reactions of alkali metal imidazolates and magnesium or manganese borohydride gave novel bimetallic imidazolates AMIm₃ (A=Na, K; M=Mg, Mn) whose crystal structures have been solved from synchrotron radiation X-ray powder diffraction (PXRD) data using global optimization in program FOX[2].Pores of 30-35 ų (5-6 % of the unit cell volume) are incorporated in all structures. Detailed study of temperature-aided structural and microstructural changes, obtained from the synchrotron in situ HT-PXRD data, gave a deeper understanding of crystallization processes in the borohydride-imidazolate system and have elucidated mechanisms of the reactions which occurs during mechanochemical synthesis and thermal treatment of these systems.

Extensive study of thermal expansion properties of a series of isostructural compounds AMIm₃ (A=Na, K; M=Mg, Mn) revealed a common behavior characteristic for a structural type. However, very interesting drastic changes of thermal expansion were noticed when alkali metal imidazolate (NaIm) coexist with compound-of-interest (NaMgIm₃); volumetric thermal expansion coefficient changes from positive α_V = 35 × 10⁻⁶ K⁻¹ to colossal negative values α_V = −460 × 10⁻⁶ K⁻¹ and linear thermal expansion changes from α = 34 × 10⁻⁶ K⁻¹ to α = -210 × 10⁻⁶ K⁻¹ (Figure 1). This is caused by coherent intergrowth, lattice mismatch, a tensile strain, and microstructural properties [3] of mentioned phases and leaves a possibility of design of the material with zero thermal expansivity.

[1] Ren, Z.; Zhao, R.; Chen, X.; Li, M.; Li, X.; Tian, H.; Zhang, Z.; Han, G. (2018) Nat. Commun. 123, 1638.

[2] Favre-Nicolin, V.; Černý, R. (2002) J. Appl. Crystallogr. 35, 734−743.

[3] Matěj, Z.; Kužel, R.; Nichtová, L. (2010) Powder Diffr. 25, 125-131.

The research was supported by OP RDE project No. CZ.02.2.69/0.0/0.0/18_053/0016976 International mobility of research, technical and administrative staff at the Charles University .

The financial support of the SNSF project (SCOPES) “Metal-Hydride Organic Frameworks (HOF) - new solids for gas adsorption and separation” is acknowledged.

Molecules can crystallise either in the presence or absence of the solvent used to crystallise them with a range of intermolecular interactions between both the molecule and the solvent occurring to sustain and propagate the crystal structure. Molecules that crystallise as solvates or clathrates could be considered as host-guest materials, but it is often unclear whether a guest-free material can be obtained by heating the solvated material. If the solvent can be removed this can, in turn, lead to vacant void spaces or a partially closed material that can be used to store a secondary guest (either a gas or secondary solvent). Understanding how these materials behave upon removal of the solvent contained within them is crucial in assessing their potential applications. With the CSD recently reaching 1 million deposited crystal structures [1] there is a large resource of untested solvate structures, which may provide inspiration for new guest-uptake materials.[2]

This work presents an attempt to further understand a previously reported family of halogen-functionalised organic molecules which has been reported in 3 distinct phases (two inclusion phases and one solvent-excluded phase)[3]. The two inclusion phases adopt a 2D halogen-bonding network propagated through a halogen-halogen bonded trimer. The work presented here, initially focusing on the bromine-functionalised host molecule, used liquid-assisted grinding to screen a series of solvents to identify desirable inclusion phases. The grinding experiments also identified a previously unreported inclusion phase. Thermal stability studies demonstrated that these inclusion phases transformed to the solvent-excluded phase upon heating. Further work has involved altering the halogen functionality (using fluorine, chlorine or iodine) to see how this affects the propensity to form the desired inclusion phases and the thermal stability of these phases, as well as exploring whether phase transformation can be observed when samples are exposed to a vapour environment.

Figure 1. Overview of the solvent-dependent phases of a family of halogen-bonded networks.

MOFs, COFs, and HOFs as highly ordered porous architectures attract wide interest owing to their broad potential of application in heterogeneous catalysis, storage, sensing, drug delivery, separation, etc.

Research of organic frameworks assembled by supramolecular interactions without metal or covalent bonds taking part in the framework construction has come in the focus of interest the most lately. A well-orchestrated interplay of supramolecular interactions, molecular inflexibility, and spatial effects characterize the non-covalently bonded organic frameworks. All mentioned aspects affect the molecular and crystal symmetries. We reported recently the preparations and structures of ionic hydrogen-bonded organic frameworks, their polymorphic and solvatomorphic forms were described [1]. Further attempts were made to prepare hydrogen-bonded organic frameworks, either ionic or neutral. Our systematic study inspired by the Maruoka type chiral phase-transfer catalysts resulted in some new series of solvatomorphic hydrogen-bonded organic framework materials. We will present (Fig. 1), that the most important aspects in the HOF formation include (1) the intramolecular interactions which are responsible for the inflexibility of the molecule, (2) the intermolecular interactions which are responsible for framework construction, (3) the terminal spacer groups for void formation, (4) the molecular symmetries which prove to be important in the tightening of the molecule, and (5) all the aforementioned features affect the crystal symmetry which may coincide with the molecular symmetry.

The presented work contributes to the understanding of hydrogen-bonded organic framework formation. It supports the still challenging design and preparation of framework structures with high porosity.

Figure 1. The most important aspects in the HOF formation.

[1] Horváth D. V., Holczbauer T., Bereczki L., Palkó R., May N. V., Soós T., Bombicz P. (2018) CrystEngComm, 20, 1779-1782.

This work was supported by the National Research, Development and Innovation Office-NKFIH through OTKA K124544 and KH129588.

Chirality is a property that real images are non-superimposable on their mirror images. The importance of chirality has commonly been known through drug incidents of thalidomide all over the world ₁ ^1, ₂ ². Chirality exists not only molecules, crystals, membranes and other objects in nature. Crystal chirality is derived from not only molecular chirality but also helical arrangement of molecules in crystals. In the latter case, even if achiral molecules are put in a right-handed or a left-handed helical arrangement in crystals, the crystals occur chirality. It has already been known that the same amount of left-handed and right-handed crystals are obtained when chiral crystals composed of achiral molecules are grown ₃³. Among crystals composed of achiral molecules, about 8% of them are chiral crystals, so it is very important to grow chiral crystals that have particular chirality. However, it is extremely difficult to grow only right-handed or left-handed crystals from achiral molecules. In this study, we succeeded in growing right-handed or left-handed crystals from achiral molecules.

We have focused on Triglycine sulfate (TGS) crystals composed of glycine and sulfuric acid (Figure 1(a)). We found that TGS with particular chirality has grown by doping with L-, or D-alanine (Figure 1(b)). L-alanine-doped TGS (LATGS) crystals showed left-handedness, while D-alanine-doped TGS (DATGS) crystals showed right-handedness (Figure 2). This is an extremely interesting phenomenon. We discuss that this phenomenon is derived from polarity because TGS is ferroelectricity. The relationship between chirality and polarity helps the elucidation of the explicit mechanism of preferred chirality of TGS crystal by alanine.

While small molecule activation processes underpin transformations in catalysis, gathering structural information about the reactive metal-based species responsible can be challenging. Such species are often coordinatively unsaturated or possess labile ligands; they are therefore highly reactive and transient. Building on research trapping reactive species within the cavities of supramolecular assemblies or frameworks,[1] we have been using metal-organic frameworks (MOFs) to "matrix isolate" and structurally characterise catalytically important metal-based species.[2, 3] The building block synthetic approach of MOFs using chemically mutable links, coupled with long range order (crystallinity), and excellent chemical and thermal stability,[4] allows them to be used to stabilise and characterise reactive species.

To garner these insights we use a bespoke, flexible Mn-based MOF, [Mn₃L₂L’] (MnMOF-1, where L = bis-(4-carboxyphenyl-3,5-dimethylpyrazolyl)methane) with a site poised for allowing single crystal-to-single crystal (SCSC) post-synthetic metalation.[2, 3] This contribution will expand these ideas and examine ligand exchange chemistry occurring at trigonal planar Cu(I) sites chemically isolated in the MOF.[5] Insights into catalysis obtained by structurally characterising the initial catalysts and by targeting sequential “snapshots” of the catalytically active structure by single crystal X-ray crystallography will be reported.

1. R. J. Young, M. T. Huxley, E. Pardo, N. R. Champness, C. J. Sumby and C. J. Doonan, Chem. Sci., 2020, 11, 4031-4050
2. W. M. Bloch, A. Burgun, C. J. Coghlan, R. Lee, M. L. Coote, C. J. Doonan and C. J. Sumby, Nat. Chem., 2014, 6, 906-912; A. Burgun, C. J. Coghlan, D. M. Huang, W. Chen, S. Horike, S. Kitagawa, J. F. Alvino, G. F. Metha, C. J. Sumby and C. J. Doonan, Angew. Chem. Int. Ed., 2017, 56, 8412-8416; R. A. Peralta, M. T. Huxley, R. J. Young, O. M Linder-Patton, J. D. Evans, C. J. Doonan and C. J. Sumby, Faraday Discussions, 2020, 225, 84-99.
3. R. A. Peralta, M. T. Huxley, J. D. Evans, H. Cao, M. He, X. S. Zhao, S. Agnoli, C. J. Sumby and C. J. Doonan, J. Am. Chem. Soc., 2020, 142, 13533-13543; R. A. Peralta, M. T. Huxley, Z. Shi, Y.-B. Zhang, C. J. Sumby and C. J. Doonan, Chem. Commun., 2020, 56, 15313-15316.
4. H. Furukawa, K. E. Cordova, M. O’Keeffe and O. M. Yaghi, Science, 2013, 341, 1230444.
5. R. A. Peralta, M. T. Huxley, J. Albalad, C. J. Sumby and C. J. Doonan, unpublished results, 2021.

In recent years, convergent-beam electron diffraction (CBED) has been widely used for refining crystal structure parameters and low-order structure factors. It enables nanometer-scale structure analysis with high sensitivity to the distribution of valence electrons. The determination of low-order structure factors with higher precision is essential to precisely determine the chemical bonding state of materials which are closely related to their physical properties. Till date, it is considered that refinement of structure factors using CBED pattern taken at the Bragg-excited condition increases the sensitivity to the corresponding structure factor [1]. However, the origin of precision and correspondence between precision and sensitivities of CBED patterns in the refinement of structure factors, is still lacking.

In this analysis, a local structure analysis method developed by Tsuda and Tanaka [2] has been applied to potassium tantalate KTaO₃ (KTO). Isotropic atomic displacement parameters and five low-order structure factors were refined using energy-filtered CBED patterns taken at three zone-axis (ZA) and five Bragg-excited conditions. Compared to ZA patterns, the Bragg-excited CBED patterns showed higher precision in the refinement of structure factors. One to one correspondence between higher precision and sensitivity of Bragg-excited CBED pattern has been found only for structure factors of the outer zeroth-order Laue zone (ZOLZ) reflection having larger reciprocal lattice vectors. Smaller correlation coefficients among the refined structure factors in the refinement of Bragg-excited patterns lead to higher precision. From the point of view of higher precision, Bragg-excited patterns are advantageous over ZA patterns. To achieve higher precision and sensitivities in the refinements of structure factors it would be better to use both of the ZA and Bragg-excited CBED patterns. The use of large angle CBED (LACBED) or large angle rocking beam electron diffraction (LARBED) techniques should be effective for this purpose.

[1] Ogata, Y., Tsuda, K. & Tanaka, M. (2008). Acta Cryst. A64, 587.

[2] Tsuda, K. & Tanaka, M. (1999). Acta Cryst. A55, 939.

The X-ray restrained/constrained wavefunction (XRW/XCW) fitting approach [1, 2] is one of the well-established methods of modern quantum crystallography [3-5], an approach that allows the determination of wavefunctions from experimental X-ray diffraction measurements by minimizing a functional (i.e., the so-called Jayatilaka functional) given by the sum of the electronic energy of the system under exam and of the statistical agreement between experimental and computed structure factor amplitudes.

Initially proposed in the framework of the restricted Hartree-Fock formalism [1, 2], over the years the method has been gradually extended to other techniques of quantum chemistry (e.g., unrestricted Hartree-Fock formalism, density functional theory, relativistic methods and extremely localized molecular orbital (ELMO) strategy), but practically remaining always limited to a single Slater determinant ansatz for the wavefunction to be determined.

In this presentation, two recent XRW fitting techniques that went beyond the previous limitation will be discussed: the X-ray restrained extremely localized molecular orbital – valence bond (XR-ELMO-VB) method [6, 7] and the X-ray restrained spin-coupled (XRSC) strategy [8, 9]. Both of them are multi-determinant XRW approaches and, above all, they are strongly rooted in Valence Bond theory, thus allowing the extraction of traditional chemical descriptors (e.g., weights of resonance structures) compatible with measured X-ray diffraction data

The XR-ELMO-VB technique, which can be considered as the first prototype multi-determinant XRW approach, exploits the use of pre-computed and frozen ELMOs to define the basis of pre-determined Slater determinants on which expanding the desired wavefunction [6]. The method is particularly useful to investigate systems characterized by a multi-reference character. The performed calculations have also clearly shown that the technique is able to reveal how the relative importance of resonance structures changes when structure factors measured at different conditions (e.g., at ambient or high pressure) are used as external restraints [7].

The XCSC method can be considered a step forward compared to the XR-ELMO-VB strategy. In fact, through the coupling of the XRW philosophy with the spin-coupled technique of Valence Bond theory, the approach enables not only the determination of resonance structure weights, but also the optimization of the so-called spin-coupled orbitals, which are quite localized and allow us to shed light on the spatial rearrangements of the electronic clouds and the hybridization of atoms [8, 9]. Preliminary tests have shown that XCSC computations can provide resonance structure weights, spin-coupled orbitals and global electron density distributions that are different from those obtained through corresponding gas-phase calculations [9]. These differences are probably due to the capability of the X-ray restrained spin-coupled approach in getting information contained in the experimental data employed in the computations (e.g., correlation and crystal filed effects).

References:

[1] Jayatilaka, D. (1998). Phys. Rev. Lett. 80, 798.

[2] Jayatilaka, D. & Grimwood, D. J. (2001). Acta Cryst. A57, 76.

[3] Genoni, A., Bučinský, L., Claiser, N., Contreras-García, J., Dittrich, B.; Dominiak, P. M., Espinosa, E., Gatti, C., Giannozzi, P., Gillet, J.-M., Jayatilaka, D., Macchi, P., Madsen, A. Ø., Massa, L. J., Matta, C. F., Merz, K. M. Jr., Nakashima, P. N. H., Ott, H., Ryde, U., Schwarz, K., Sierka, M. & Grabowsky, S. (2018). Chem. Eur. J. 24, 10881.

[4] Grabowsky, S., Genoni, A. & Bürgi, H.-B. (2017). Chem. Sci. 8, 4159.

[5] Genoni, A. & Macchi, P. (2020) Crystals 10, 473.

[6] Genoni, A. (2017). Acta Cryst. A73, 312.

[7] Casati, N., Genoni, A., Meyer, B., Krawczuk, A. & Macchi, P. (2017). Acta Cryst. B73, 584.

[8] Genoni, A., Franchini, D., Pieraccini, S. & Sironi, M. (2018). Chem. Eur. J. 24, 15507.

[9] Genoni, A., Macetti, G., Franchini, D., Pieraccini, S. & Sironi, M. (2019). Acta Cryst. A75, 778.

Acknowledgments:

The French Research Agency (ANR) is gratefully acknowledged for financial support of this work through the Young Investigator Project “QuMacroRef” (Grant No. ANR-17-CE29-0005-01).

We are developing in the CRM2 laboratory a new software: Mollynx. As MoPro or XD, Mollynx is derived from Molly (Hansen and Coppens, 1978) but allows to differentiate the electron spins. This new algorithm has been successively applied to paramagnetic coordination compounds (Deutsch et al., 2012, Deutsch et al., 2014) to organic radicals (Voufack et al., 2017) and to small unit cells inorganic crystals (Voufack et al., 2019).

A more general model based on atomic orbitals (Tanaka, 1988; Tanaka, 1993; Bytheway et al., 2001; Schweitzer, 2006), has also been coded in the Mollynx software. This model should allow calculation of properties derived from the atomic wave functions such as covalency, populations of atomic orbitals, energy, optical properties and can in principle describe bonded pair of atoms with orbitals centered on different atoms (two centres orbital products). This model, extended to spin resolved orbitals, has been applied to the YTiO₃ perovskite (figure 1, Kibalin et al., 2021) The radial extension, orientation and population of outer atomic orbitals for each atom have been modelled leading to a clear description of the bonding in this crystal .

Thus Mollynx can refine a spin resolved electron density model based on multipolar or on orbital approach. This presentation will describe some of these results and will focus on the experimental spin resolved atomic orbitals model obtained on the YTiO₃ including a comparison with a refinement based on theoretical structure factors calculated using density functional theory and the WIEN2k code (Blaha et al., 2020).

Blaha, P.; Schwarz, K; Tran, F.; Laskowski, R; Madsen G. K. H. and Marks, L. D., WIEN2k: An APW+lo program for calculating the properties of solids editors-pick, J. Chem. Phys. 152, 074101 (2020); https://doi.org/10.1063/1.5143061

Bytheway, I., Figgis, B. N. & Sobolev, A. N., 2001. Charge density in Cu(glygly)(OH2)2·H2O at 10 K and the reproducibility of atomic orbital populations. J. Chem. Soc., Dalton Trans., Volume 22, pp. 3285-3294.

Deutsch, M., Claiser, N., Pillet, S., Ciumacov, Y., Becker, P. J., Gillon, B., Gillet, J.-M., Lecomte, C. & Souhassou, M. (2012). Acta Cryst. A 68, 675-686.

Deutsch, M., Gillon, B., Claiser, N., Gillet, J.-M., Lecomte, C. & Souhassou, M. (2014). IUCR J, 194-199.

Hansen, N. K. & Coppens, P. (1978). Acta Cryst. A34, 909–921.

Kibalin I., Voufack A.B., Souhassou M., Gillon B., Gillet J.M., Claiser N., Gukasov A., Porcher F. and Lecomte C. (2021) Acta Cryst A77, 96-104

Schweizer, J. (2006). Chapter 4: Polarized Neutrons and Polarization analysis, in Neutron Scattering from magnetic materials. Ed. T. Chatterji, Elsevier

Voufack, A. B. et al., 2017. When combined X-ray and polarized neutron diffraction data challenge high-level calculations: spin-resolved electron density of an organic radical. Acta Cryst., Volume B73, pp. 544-549.

Voufack, A. B. et al., 2019. Spin resolved electron density study of YTiO3 in its ferromagnetic phase: signature of orbital ordering. IUCrJ, 6(5), pp. 884-894.

Tanaka K., (1993). Acta Cryst., B49, 1001-1010.

Tanaka, K., (1988) Acta Cryst., A44, 1002-1008.

This work retraces different methods that have been explored to account for the atomic thermal motion in the reconstruction of one-electron reduced density matrices from experimental X-ray structure factors (XSF) and directional Compton profiles (DCP).
Attention has been paid to propose the simplest possible model, which obeys the necessary N-representability conditions, while accurately reproducing all available experimental data.
The deconvolution of thermal effects makes it possible to obtain an experimental static density matrix, which can directly be compared with theoretical 1-RDM. It is found that above a 1% statistical noise, the role played by Compton scattering data becomes negligible and no accurate 1-RDM becomes reachable.
Since no thermal 1-RDM is available as a reference, the quality of an experimentally derived temperature-dependent matrix is difficult to assess. However, the accuracy of the obtained static 1-RDM is strong evidence that the Semi-Definite Programming method is robust and well-adapted to the reconstruction of an experimental dynamical 1-RDM.

Several physico-chemical properties of materials and biological molecules crucially depend on the hydrogen atom positions. Therefore, obtaining reliable three-dimensional structures of molecules and materials is a crucial step to have accurate results.

Unfortunately, the weak X-rays scattering power of hydrogen atoms makes them usually very hard to detect accurately. Besides, the choice of the refinement method has also a strong influence. The most widely used approach, the independent atom model (IAM), describes the total electron density as the sum of spherical atomic densities centred on the nuclei. This approximation evidently fails when applied to hydrogen atoms because their only electron is delocalized in forming a bond. As a result, bonds lengths involving hydrogen atoms are generally too short.

Over the years, different methods have been proposed to overcome this drawback. Within the field of quantum crystallography, the Hirshfeld atom refinement (HAR) approach is one of the most promising strategies [1]. HAR is a technique exploiting fully quantum mechanical calculations to obtain tailor-made ab initio electron densities, which are partitioned into aspherical atomic contributions to fit experimental structure factors without further approximations. HAR is able to provide X-H bond distances that are in very good agreement with those obtained from neutron diffraction experiments [1-3]. Moreover, the introduction of crystal environment effects is crucial to carry out better refinements, especially when strong intermolecular interactions are present. This is usually done by adding point charges at symmetry-related atomic positions around the selected reference crystal unit [1-3].

In this contribution, we introduce an improvement to the description of crystal field effects in HAR exploiting the recently developed quantum mechanics/extremely localized molecular orbitals (QM/ELMO) technique [4,5]. In our new modified version of HAR, the reference crystal unit is treated variationally at quantum mechanical level as in the traditional HAR, while the symmetry-related crystal units are described using pre-computed frozen extremely localized molecular orbitals [6]. The ELMOs contribution describing the crystal environment is included in the Hamiltonian of the reference crystal unit through an electrostatic embedding.

Other than discussing the theoretical framework at the basis of the new strategy, we will show test refinements performed on the xylitol crystal, a system characterized by an extended network of strong hydrogen bonds. The results show that the new ELMO-embedded HAR approach gives bond lengths involving hydrogen atoms in optimal agreement with neutron results, outperforming not only the traditional HAR but also the charge-embedded HAR technique in practically all the cases [6].

Given the promising results, we envisage the application of the new ELMO-embedded HAR technique to refine structures of crystals with strong intermolecular interactions. However, further test-bed refinements will be necessary to draw final conclusions, also considering other aspects such as basis-sets and theoretical methods dependence.

[1] Jayatilaka, D. & Dittrich, B. (2008). Acta Cryst. A64, 383.

[2] Woińska, M., Grabowsky, S., Dominiak, P. M., Woźniak, K. & Jayatilaka, D. (2016). Sci. Adv. 2, e1600192.

[3] Capelli, S., Bürgi, H.-B., Dittrich, B., Grabowsky, S. & Jayatilaka, D. (2014). IUCrJ 1, 361.

[4] Macetti, G. & Genoni, A. (2019). J. Phys. Chem. A 123, 9420.

[5] Macetti, G, Wieduwilt, E. K., Assfeld, X. & Genoni, A. (2020). J. Chem. Theory Comput. 16, 3578.

[6] Wieduwilt, E. K., Macetti, G. & Genoni, A. (2021). J. Phys. Chem. Lett. 12, 463.

Relativistic effects in chemistry manifest themselves in many ways and influence various physical and chemical properties of materials. The well-known of them is the yellow color of gold or the high voltage of the lead-acid car battery^1,2. Therefore, a description of these effects is of great importance for a better understanding of the chemistry of heavy atoms.

A perspective method is quantum crystallography that relies on the high-resolution and high-quality XRD data to describe crystal structure in unprecedented detail^3-4. Intensities of the diffracted beam are affected not only by relativistic effects but also by absorption⁵, anharmonic motion⁶, anomalous dispersion⁷, and many other effects which highly influence electron density distribution in the crystal and, in consequence, derived properties.

We collected the data sets for the chloro(triphenylphosphine)gold(I) and di(triphenylphosphine)mercury(II) nitrate using Mo X-ray source at 100K, where the data sets for (3-(4-chlorophenyl)-3-oxoprop-1-yn-1-yl)(triphenylphosphine)gold(I) and chloro(dimethylsulfide) gold(I) were collected using synchrotron radiation at 80K.

Here, we present the results of relativistic Hirshfeld atom refinements⁸ carried out as implemented in NoSpherA2⁹ for high-resolution X-ray diffraction data sets. The outcome of DFT-based refinements with the nonrelativistic and quasi-relativistic approaches will be compared, including analysis of the influence of disorder on relativistic effects, description of aurophilic interactions, and the nature of the Me–X bonds in Au and Hg crystals.

Acknowledgment:

Support of this work by the National Science Centre, Poland through grant PRELUDIUM no. UMO-2018/31/N/ST4/02141 is gratefully acknowledged.

The experiment was carried out at the Spring-8 with the approval of the Japan Synchrotron Radiation Research Institute (Proposal Number 2019A1069).

References:

1. Pyykko, P. (1988). Chemical Reviews, 88, 563–594.

2. Yatsimirskii, K. B. (1995) Theoretical and Experimental Chemistry, 31, 153–168.

3. L. J. Farrugia, C. Evans, D. Lentz and M. Roemer, Journal of the American Chemical Society, 2009, 131, 1251–1268.

4. T. S. Koritsanszky and P. Coppens, Chem. Rev., 2001, 101, 1583–1628.

5. J. Als‐Nielsen and D. McMorrow, in Elements of Modern X-ray Physics, John Wiley & Sons, Ltd, 2011, pp. 1–28.

6. R. Herbst-Irmer, J. Henn, J. J. Holstein, C. B. Hübschle, B. Dittrich, D. Stern, D. Kratzert and D. Stalke, The Journal of Physical Chemistry A, 2013, 117, 633–641.

7. S. Caticha-Ellis, Anomalous dispersion of x-rays in crystallography, University College Cardiff Press, Cardiff, Wales, 1981.

8. Bučinský, L., Jayatilaka, D., Grabowsky, S. (2016) The Journal of Physical Chemistry A, 120, 6650–6669.

9. Kleemiss, F.; Dolomanov, O. V.; Bodensteiner, M.; Peyerimhoff, N.; Midgley, L.; Bourhis, L. J.; Genoni, A.; Malaspina, L. A.; Jayatilaka, D.; Spencer, J. L.; White, F.; Grundkötter-Stock, B.; Steinhauer, S.; Lentz, D.; Puschmann, H.; Grabowsky, S. (2021) Chem. Sci., 12, 1675-1692.

Due to the ever-increasing demands on the materials with enhanced properties, the task of searching for them using atomistic modeling methods is becoming increasingly important. The problem of designing novel materials comes down to finding a global minimum in a very noisy landscape in a multi-dimensional space (potential energy surface). This problem can be solved using several methods, yet the USPEX [1,2,3] evolutionary algorithm proved its effectiveness. The USPEX limitations are calculation at zero temperatures and small number of atoms in the unit cell, since the calculation of the energy of the structures (and their selection) takes place within the framework of the density functional theory (DFT). Here we present a new method (T-USPEX) which is capable of finding stable structures at finite temperatures and pressures.

T-USPEX is based on the previously developed evolutionary algorithm USPEX. The main differences come from crystal structure relaxation at finite temperature and from the way of fitness function calculation (in this case – Gibbs free energy). Relaxation part is done using molecular dynamics in the NPT ensemble with pressure corrections taken into account. Gibbs free energy is calculated using thermodynamic integration with the corrections from thermodynamic perturbation theory. For these methods a big supercell is needed, so MTP [4] machine learning interatomic potentials is used. In this talk results for high-temperature phases of Al, Fe, Ti, U and MgSiO₃ will be presented.

Acknowledgments: This work was supported by RFBR foundation № 19-73-00237.

[1] C. W. Glass, A. R. Oganov, and N. Hansen, Comput. Phys. Commun. 175, 713 (2006).

[2] A. R. Oganov, A. O. Lyakhov, and M. Valle, Acc. Chem. Res. 44, 227 (2011)

[3] A. O. Lyakhov, A. R. Oganov, H. T. Stokes, and Q. Zhu, Comput. Phys. Commun. 184, 1172 (2013).

[4] A. V. Shapeev, Multiscale Model. Simul. 14, 1153 (2016)

The design of molecular crystals with targeted properties is the goal of crystal engineering. However, our predictive understanding of how a crystal’s properties relate to its structure, and how crystal structure in turn relates to molecular structure, are not yet sufficiently reliable to confidently design functional materials. Computational methods for crystal structure prediction (CSP) have been developed to help anticipate the crystal structure that a molecule will form. These methods are based on a global search of the lattice energy surface and a ranking of local energy minima according to their calculated relative stabilities. Thus, each molecule is associated with a list of potential crystal structures, each of which then leads to a set of predicted properties. The resulting ensemble of structures, their relative energies and associated properties can be interpreted to judge a molecule's promise for a target function. These methods have been demonstrated to be valuable in guiding experimental materials discovery programmes. A remaining challenge is the best choice of molecules that should be assessed, given the enormous chemical space of possible molecules. To address this, we have combined evolutionary searching of chemical space with large scale crystal structure and property prediction as a route to the discovery of novel molecules with high likelihood of yielding good properties [1]. The approach will be discussed with example studies in the area of organic semiconductor discovery.

[1] Cheng, C. Y., Campbell, J. E. and Day, G. M. (2020) Chem. Sci.,11, 4922-4933

Metal-organic frameworks (MOFs) are microporous materials with many exciting applications, such as gas storage and separation, catalysis, platforms for artificial photosynthesis and energetic materials. The wide range of applications is strictly related to the modular node-and-linker composition, where different combinations of building blocks yield materials with various properties. The presence of a vast number of combinations for different node and linker, however, poses a real challenge for the experimental MOF design.

An ab initio crystal structure prediction (CSP) method for MOFs has been reported by our group recently, and the method is based on the ab initio random structure searching (AIRSS) [1] and Wyckoff Alignment of Molecules (WAM) [2] algorithms. In this publication, a wide range of existing MOF structures have been investigated. Herein, we will demonstrate the first examples for the prediction of new MOF materials from metal azolate framework (MAF) and hexafluorosilicate families using our CSP method, combined with experimental mechanochemical synthesis and crystal structure determination. The solvent-free mechanochemical synthesis guided by theoretical structure prediction provides for an efficient and green approach to MOF design.

The concept of MOF design goes beyond just the prediction of crystal structures. The connections between the crystal structures and chemical reactivity of freshly designed MOFs will also be studied by utilizing periodic density functional theory (DFT). Furthermore, our theory-based MOF structure and property predictions will be validated experimentally via mechanochemical screening and thermal studies, and ultimately aiming to improve our understanding of MOFs.

[1] Pickard, C. J.; Needs, R. J. (2011). J. Phys. Condens. Matter 23, 53201.

[2] Darby, J. P.; Arhangelskis, M.; Katsenis, A. D.; Marrett, J. M.; Friščić, T.; Morris, (2020). Chem. Mater. 32, 5835–5844.

Autonomous materials discovery with desired properties is one of the ultimate goals for materials science [1]. In this work, we have developed constrained crystal deep convolutional generative adversarial networks (CCDCGAN, Figure 1(a)) based on a proper construction of the latent space [2], which can predict stable crystal structures. In particular, physical properties can be optimized in the latent space, where the formation energy is considered in the current model so that stable structures are predicted directly. We have successfully applied the approach on a randomly chosen binary Bi-Se system and observed that most known phases can be validated with quite a few distinct structures predicted [3]. Furthermore, trained using more than 50,000 compounds in the Materials Project database, we recently extended the algorithm to multicomponent systems coving most elements in the periodic table. As shown in Figure 1(b), two novel structures can be obtained for the Cd-Li system. Detailed analysis reveals that the approach can be used to predict novel crystal structures for various materials systems, and the generation efficiency can be further improved by considering a larger training set. It is expected that the other physical properties (such as band gaps) can be optimized in the latent space as well, giving us the chance to perform multi-objective optimization in the future.

Design of new types of metal-organic frameworks (MOFs), the microporous materials with a wide range of functional properties, is an active area of materials research. The vast variety of available linker and node combinations leads to an incredible variety of potential MOF structures, providing an opportunity for tailoring the functional properties and thermodynamic stability of the new materials. At the same time, navigating the vast structural space of putative MOFs is proving to be a challenge for experimental screening, that can benefit from the guidance provided by computational chemistry methods. In this presentation we will describe the application of periodic density-functional theory (DFT) calculations together with state-of-the-art ab initio crystal structure prediction (CSP) calculations in elucidating the structural aspects of MOF thermodynamic stability and performing computational property-driven design of new MOFs.

The presentation will commence with a theoretical study of the systematic effects of linker substituents on the thermodynamic stability of a series of isostructural zeolitic imidazolate frameworks (ZIFs) with sodalite topology.[1] We will show how periodic density functional theory (DFT) calculations offer highly accurate predictions for the thermodynamic stability of the ZIF structures as a function of linker substitution, also taking into account the effects of crystal packing of pure ligands. The accuracy of periodic DFT calculations will be backed up by the excellent correlation with the experimental solution calorimetry measurements. Moreover, it will be demonstrated how simple descriptors, such as Hammett σ-constants and electrostatic surface potentials (ESPs) offer convenient tools for rapid pre-screening of linker substituents, before performing a more in-depth computational analysis.

We will continue with a demonstration of our recently-developed method for ab initio CSP, which uses the Wyckoff Alignment of Molecules (WAM) procedure to predict the structures of new MOFs, with improved computational efficiency enabled through careful consideration of molecular and crystallographic symmetry.[2] We will demonstrate the use of our CSP approach for predicting polymorphism, thermodynamic stability, porosity and optical properties of new MOFs in a series of computational studies backed up by experiment. It will also be shown how MOF CSP can be used as a tool to elucidate the crystal structures of poorly-crystalline MOFs, which are difficult to determine with X-ray diffraction methods.

[1] Novendra, N., Marrett, J. M., Katsenis, A. D., Titi, H. M., Arhangelskis, M., Friščić, T. & Navrotsky, A. J. (2020). J. Am. Chem. Soc. 142, 21720.

[2] Darby, J. P., Arhangelskis, M., Katsenis, A. D., Marrett, J. M., Friščić, T. & Morris, A. J. (2020). Chem. Mater. 32, 5835.

Hydrogen-rich hydrides attract great attention due to recent theoretical [1] and then experimental discovery of record high-temperature superconductivity in H₃S (T_C = 203 K at 155 GPa [2]).

Here we perform a systematic evolutionary search for new phases in the Fe-H [3], Th-H [4], U-H [5] and other numerous systems under pressure [6] in order to predict new materials which are unique high-temperature superconductors.

We predict new hydride phases at various pressures using the variable-composition search as implemented in evolutionary algorithm USPEX [7-9]. Among the Fe-H system two potentially high-T_C FeH₅ and FeH₆ phases in the pressure range from 150 to 300 GPa were predicted and were found to be superconducting within Bardeen-Cooper-Schrieffer theory, with T_C values of up to 46 K. Several new thorium hydrides were predicted to be stable under pressure using evolutionary algorithm USPEX, including ThH₃, Th₃H₁₀, ThH₄, ThH₆, ThH₇ and ThH₁₀. ThH₁₀ was found to be the highest-temperature superconductor with T_C in the range 221-305 K at 100 GPa. Actinide hydrides show, i.e. AcH₁₆ was predicted to be stable at 110 GPa with T_C of 241 K.

To continue this theoretical study, we performed an experimental synthesis of Th-H phases at high-pressures including ThH₁₀. Obteined results can be found in Ref. [10].

Acknowledgments: This work was supported by RFBR foundation № 19-03-00100 and facie foundation, grant UMNIK №13408GU/2018.

[1] D. Duan et al., Sci. Rep. 2018, 4, 6968.

[2] A.P. Drozdov et al. Nature. 2015, 525, 73–76.

[3] A.G. Kvashnin at al. J. Phys. Chem. C 2018, 122 4731-4736.

[4] A.G. Kvashnin et al. ACS Applied Materials & Interfaces 2018, 10, 43809–43816.

[5] I.A. Kruglov et al. Sci. Adv. 2018, 4, eaat9776.

[6] D.V. Semenok et al. J. Phys. Chem. Lett. 2018, 8, 1920-1926.

[7] A.O. Lyakhov et al. Comp. Phys. Comm. 2013, 184, 1172-1182.

[8] A.R. Oganov et al. J. Chem. Phys. 2006, 124, 244704.

[9] A.R. Oganov et al. Acc. Chem. Res. 2011, 44 227-237.

[10] D.V. Semenok et al. 2019, Mat. Today.

The synthesis of inorganic compounds in form of nanoparticles of few nanometers has opened a new world for chemistry, with the discovery of unexpected properties and also of entirely new crystal structures. At the beginning, simple stoichiometries related with crystal structures of low complexity have been mainly explored. As far as nanochemistry grew searching for exotic properties, the exploration has extended towards more complex phase diagrams, where the complexity of the crystal structure is a real challenge. In these cases, the crystallographer is hampered by the limited crystal size that enlarges the powder x-ray diffraction peaks and quite often cannot rely on the knowledge of the bulk structure, which can be different from the nanocrystalline form or even not stable in the same conditions. Conversely, 3D electron diffraction (3D ED) has demonstrated its potential for solving crystallographic problems where the size of the crystal grains was the limiting factor [1]. A 3D ED single crystal diffraction experiment is performed with a beam that can be as small as few hundreds of nanometers, and the collected 3D intensity data sets are suitable for structure solution [2]. We report here the application of 3D ED to extreme cases, where the size of the crystalline grains was smaller or in the range of 100 nm and the powder x-ray diffraction was not able to give a definite answer. The challenge is to establish which is the minimum crystal size that we can investigate in this way. All the nanoparticles we analysed have unknown and not trivial crystal structures.

As first example we report the crystal structure of Cu_2-xTe, a not stoichiometric plasmonic nanocrystal that exhibits a complex 1x3x4 super-structure of a pseudo-cubic basic cell, due to the ordering of copper vacancies. The pseudosymmetry of the underlying basic structure induces a strong twinning and therefore data on single individuals could be taken only from grains smaller than 150nm. 3D ED allowed the determination of the super-structure with the identification of 27 Te and 32 Cu in the asymmetric unit and the location of copper vacancies [3].

A second example is the perovskite-related structure of Cs₃Cu₄In₂Cl₁₃ nanocrystals. This crystal structure was synthesized with the aim to obtain a double perovskite of composition Cs₂CuInCl₆, isostructural to Cs₂AgInCl₆. 3D ED on nanoparticles of 100 nm revealed that the obtained structure is instead a vacancy ordered perovskite, A₂BX₆, in which 25% of the A sites are occupied by [Cu₄Cl]³⁺ clusters and the remaining 75% by Cs⁺, while the B sites are occupied by In³⁺ ions. Interestingly, while a Rietveld refinement on powder x-ray data results in a crystal structure where Cs⁺ and [Cu₄Cl]³⁺ are disordered on 8 equivalent sites, 3D ED shows that they exists nanoparticles where [Cu₄Cl]³⁺ clusters and Cs⁺ are ordered on different sites, lowering the symmetry from cubic Fm-3m to cubic Pn-3m [4].

The last example is the crystal structure determination of Pb₄S₃Br₂, a compound never reported in bulk that we synthesised in form of nanoparticles. 3D ED revealed that this compound is isostructural with the high pressure phase of Pb₄S₃I₂ and attested that the colloidal synthesis is able to freeze a high pressure metastable phase in form of nanoparticles. 3D also revealed that once the size of the nanoparticles has increased above a certain size (> 50nm) and their shape has changed from spherical to elongated platelets, the structure relaxes with the longest cell parameter that increase from 14.6 to 15.5 Å [5]. In this last case we have reached our minimum crystal size, being able to reconstruct the 3D reciprocal space of a 50 nm nanoparticle. The examples reported demonstrate that 3D ED is a powerful tool for exploring the crystal structure of not trivial nanoparticles and we expect that, with the use of smaller parallel beam and a dedicated set up, this limit can be pushed further to investigate the crystal structure of nanoparticles in the 10 nm range.

[1] Gemmi, M., Mugnaioli, E., Gorelik, T.E., Kolb, U., Palatinus, L., Boullay, P., Hovmöller, S., Abrahams, J.P. (2019). ACS Cent. Sci. 5, 1315.

[2] Gemmi, M., Lanza, A. (2019). Acta Crystallogr. B75, 495.

[3] Muganioli, E., Gemmi, M., Tu, R., David, J., Bertoni, G., Gaspari, R., De Trizio, L., Manna, L. (2018). Inorg. Chem. 57,10241. [4] Kaiukov, R.,Almeida, G., Marras, S., Dang, D., Baranov, D., Petralanda, U., Infante, I., Mugnaioli, E., Griesi, A., De Trizio, L., Gemmi, M., Manna, L. (2020). Inorg. Chem. 59, 548.

[5] Toso, S., Akkerman, Q. A., Martín-García, B., Prato, M., Zito, J., Infante, I., Dang, Z., Moliterni, A., Giannini, C., Bladt, E., Lobato, I., Ramade, J., Bals, S., Buha, J., Spirito, D., Mugnaioli, E., Gemmi, M., Manna L. (2020). J. Am. Chem. Soc. 142, 10198.

2D nanosheets are intensely researched as new quantum materials and components of next-generation electronic and spintronic devices with unprecedented magnetic, transport and optical properties. In particular, the thickness-dependency of structural and physical properties is subject of close scrutiny. α-RuCl₃ is a spin ½ honeycomb material that exhibits exotic magnetic ground states both in bulk¹ and exfoliated² forms. Its flakes and intercalates feature high environmental stability and retain the in‐plane honeycomb structure during wet-chemistry functionalization². RuCl₃ nanosheets are a robust test-bed for fabrication of new nanocomposites in both acidic or basic aqueous solutions, and their performance as electrodes for electrochemical reduction/ion transfer reactions can be further optimized. Reliable structural and compositional characterization during downscaling and intercalation is one of the goals that will enable well-controlled nanosheet functionalization. We synthesized K-intercalated RuCl₃ by electrochemistry in an aqueous KCl solution. Conventional X-ray diffraction methods fail to characterize such intercalates due to the presence of multiple nm-sized domains, stacking faults and other defects associated with the layered morphology. Instead, we for the first time determine the local structure and capture the essential properties on the nm-length scale by collecting the multimodal 3DED–STEM–EELS–EDX data. The 3DED method is one of the very few that provides both in-plane and out-of-plane structural information, which is indispensable for layered materials. The K_0.5RuCl₃ layered intercalate (sp. gr. P-31m) is stacked differently than the α-RuCl₃ parent compound (sp.gr. C2/m): the K atoms in the interlayer space are coordinated by six equivalent Cl atoms to form the [KCl₆] octahedra that share corners with the six equivalent [RuCl₆] octahedra. As a hallmark of STEM, EELS, and EDX spectroscopy, spatial mapping techniques were used to trace local changes in the chemical composition. A multimodal data fusion³ helped to overcome the severe spectral overlap and high sparseness of EDX data. The retrieved abundance profiles revealed spatially resolved phases with differing in the K:Ru:Cl ratio, the Ru oxidation state and in the oxygen content. This microinhomogeneity is a rather local disorder, which might cause only minor local symmetry changes, and could be associated with concomitant water molecules co-intercalating into the α-RuCl₃ matrix together with the K⁺ cations.

Figure 1. a,b Reconstructed 3D reciprocal lattice of the K-doped α-RuCl₃, scale bar is 4 nm^-1, c In-plane and out-of-plane structure of K_0.5RuCl₃ found by 3DED, d TEM overview image, e,f Abundance maps from fused EDX and EELS data. Scale bar is 200 nm.

[1] Roslova, M., Hunger, J., Bastien, G., Pohl, D., Haghighi, H. M., Wolter, A. U. B., Isaeva, A., et al. (2019). Inorg. Chem. 10, 6659-6668; Bastien, G., Roslova, M., Haghighi, M. H., Mehlawat, K., Hunger, J., Isaeva, A., et al. (2019). Phys. Rev. B. 99, 214410.

[2] Weber, D., Schoop, L. M., Duppel, V., Lippmann, J. M., Nuss, J., Lotsch, B. V. (2016). Nano Lett. 16(6), 3578–3584.

[3] Thersleff, T., Budnyk, S., Drangai, L., Slabon, A. (2020). Ultramicroscopy. 219, 113116; Thersleff, T., Jenei, I. Z., Budnyk, S., Dörr, N., Slabon, A. (2021). ACS Appl. Nano Mater. 4 (1), 220–228.

Many functional materials seem to have surprisingly simple average structures with some disordered components. To understand the relationship between the structure of a material and its complex physical properties, a full description including local order is necessary. Hence, the diffuse scattering has to be analysed. The recently established three-dimensional delta pair distribution function (3D-ΔPDF) maps local deviations from the average structure and allows a straightforward interpretation of local ordering mechanisms [1].

Many functional materials can only be grown as powders. While powder X-ray and neutron diffraction experiments can give limited insight into disordered structural arrangements, electron diffraction techniques allow to capture large portions of reciprocal space even for nanocrystals. Here, we demonstrate how the 3D-ΔPDF can be used with electron diffraction to understand the complete local structure of the ion conductor calcium stabilized zirconia (Zr_0.82Y_0.18O_1.91).

Zr_0.82Y_0.18O_1.91 crystallizes in the fluorite structure and shows composition disorder on both the metal and oxygen site. Due to the vastly different bond lengths of Y-O and Zr-O, strongly structured diffuse scattering is observed alongside the Bragg reflections (see Figure (a)). By employing the 3D-ΔPDF to electron diffraction data, we can directly interpret the local correlations (see Figure (b)).

Large single crystals of Zr_0.82Y_0.18O_1.91 that are also suitable for X-ray and neutron measurements were investigated. By comparing the results from our electron ΔPDF to X-ray and neutron ΔPDFs we demonstrate the reliability of the 3D-ΔePDF.

To our knowledge, this is the first 3D-ΔePDF ever reported and this proof of principle is an important step towards the full description of a disorder model. This has important implications for the large variety of disordered materials of which single crystals for X-ray or neutron techniques are not available. In those cases, the 3D-ΔePDF will pave the way to understanding and tailoring physical properties.

Figure 1. (a) hk0 reciprocal space section with diffuse scattering and Bragg reflections. (b) 3D-ΔePDF in the ab0.25 layer showing the relaxation of metal oxygen bond distances around (0.25,0.25,0.25).

[1] Weber, T., & Simonov, A. (2012). Z. Kristallogr., 227(5), 238-247.

Metal-organic frameworks (MOFs) are a class of nanoporous materials that have developed into one of the most widely studied research fields in chemistry of the past two decades. Single crystal X-ray diffraction still remains as the preferred method for structure determination, but the technique requires sufficiently large crystals. Traditionally and still predominantly to this day, MOFs are prepared using synthesis conditions that are optimized for producing larger single crystals, which includes dissolving starting materials with polar organic solvents, such as DMF or methanol, followed by heating under solvothermal conditions.

With the emergence of fast electron diffraction (ED) techniques such as 3D ED or MicroED, solving crystal structures from small nano-sized crystals has never been easier for crystals with organic constituents that traditionally were considered too beam sensitive for transmission electron microscopy. This provides the opportunity to easily study MOFs that can only be synthesized as small nanocrystals. Many of the more stable MOFs have a tendency to form as smaller crystallites, which can now be conveniently studied by ED. In addition this also makes it easier to study MOFs made using less typical synthesis conditions which may be less hazardous, more environmentally friendly and require less energy input.

Access to fast ED has allowed us to easily focus on the development of new stable MOFs prepared under green and ambient synthesis conditions. SU-101 was prepared using nonhazardous and edible starting materials which were stirred in water at room temperature without any other energy input.[1] The reaction starts and ends as a suspension in water, nonetheless the starting materials are fully converted into the MOF. Scaling up the synthesis of SU-101 is easily achieved as the MOF forms at room temperature and ambient pressure in water. For the first time in a MOF, ellagic acid was used as the organic linker. Ellagic acid is common in many plants and is one of the building units of naturally occurring polyphenols known as tannins. It is well known as an antioxidant and is common in fruits, berries, nuts, and wine. Unlike most MOF linker molecules, ellagic acid does not contain carboxylic acids groups but instead has multiple phenol groups which can chelate to metal cations forming strong bonds and hence robust framework structures. SU-101 demonstrates excellent stability in organic solvents and water even at elevated temperatures, simulated physiological media, and also in a wide pH range (2-14). In addition to demonstrating good stability, SU-101 exhibits promising behavior in the capture of hazardous sulfur containing gases, and demonstrated one of the highest uptake capacities for hydrogen sulfide among MOFs. Due to the stable structure, the lack of heating during synthesis and the use of a poor solvent (water), SU-101 was synthesized as small nanocrystals. The crystal structure of SU-101 was solved by ED with relative ease.

The advent of fast ED techniques and the relative ease now in solving structures of nanocrystals containing organic components, has changed our habits in the chemistry laboratory regarding the synthesis of novel crystalline materials. Rather than by default using organic solvents, elevated temperatures and pressures, we now focus on using greener reagents and ambient synthesis conditions directly from the early stages in the development of novel biocompatible and stable MOFs.

Structure of high temperature “Al₃Mn” (T) phase was investigated numerously. Studies of binary and ternary extensions of T-phase resulted in many published atomic models [1-8]. Until today, exact space group and atomic positions of transition metals in this structure is a matter of dispute. In current research, atomic model of the Al₇₈Mn_17.5Pt_4.5 phase (quenched from 800 °C) was successfully derived using a combination of electron crystallography methods. This structure was regarded as ternary extension of the “Al₃Mn” T–phase. The lattice parameters of the Al₇₈Mn_17.5Pt_4.5 T-phase were found to be a = 14.720(4) Å, b = 12.628(2) Å, c = 12.545(3) Å (as refined against X-ray diffraction data). Using convergent beam electron diffraction (CBED), the space group of this ternary composition was proved to be non-centrosymmetric Pna2₁, instead of Pnam - which describes the symmetry of the binary T-phase. Atomic model was determined applying direct methods, utilized in SIR2011 [9], on electron diffraction tomography data and refined using ShelXL [10]. At the Al₇₈Mn_17.5Pt_4.5 composition, the Pt atoms were not distributed randomly in the Mn/Al sublattices, but adopted two specific Wyckoff sites, therefore, thiscomposition should be regarded as an ordered variant of the T-structure. On the other hand, CBED study of the T-phase samples with a bit different stoichiometry (Al_71.3Mn_25.1Pt_3.6) allowed attribution of their structure to the original T-phase structure type, i.e. centrosymmetric. Using Barnighausen tree [11], these two structures (centrosymmetric and non-centrosymmetric) were found to be related.

References:

1. M. A. Taylor, The space group of MnAl₃, Acta Cryst. 14(1) (1961) 84. https://doi.org/10.1107/S0365110X61000346
2. M. Audier, M. Durand-Charre, M. de Boissieu, AlPdMn phase diagram in the region of quasicrystalline phases, Phil. Mag. B 68(5) (1993) 607-618.‏ https://doi.org/10.1080/13642819308220146
3. K. Hiraga, M. Kaneko, Y. Matsuo, S. Hashimoto, The structure of Al₃Mn: Close relationship to decagonal quasicrystals, Phil. Mag. B 67(2) (1993) 193-205.‏ https://doi.org/10.1080/13642819308207867
4. N. C. Shi, X. Z. Li, Z. S. Ma, K. H. Kuo, Crystalline phases related to a decagonal quasicrystal. I. A single-crystal X-ray diffraction study of the orthorhombic Al₃Mn phase, Acta Cryst. B 50(1) (1994) 22-30.‏ https://doi.org/10.1107/S0108768193008729
5. V. V. Pavlyuk, T. I. Yanson, O. I. Bodak, R. Černý, R. E. Gladyshevskii, K. Yvon, J. Stepien-Damm, Structure refinement of orthorhombic MnAl₃. Acta Cryst. C 51(5) (1995) 792-794.‏ https://doi.org/10.1107/S0108270194012965
6. Y. Matsuo, K. Yamamoto, Y. Iko, Structure of a new orthorhombic crystalline phase in the Al-Cr-Pd alloy system, Phil. Mag. Let. 75(3) (1997) 137-142.‏ https://doi.org/10.1080/095008397179688
7. Y. Matsuo, M. Kaneko, T. Yamanoi, N. Kaji, K. Sugiyama, K. Hiraga, The structure of an Al₃Mn-type Al₃(Mn, Pd) crystal studied by single-crystal X-ray diffraction analysis, Phil. Mag. Let. 76(5) (1997) 357-362.‏ https://doi.org/10.1080/095008397178968
8. H. Klein, M. Boudard, M. Audier, M. de Boissieu, H. Vincent, L. Beraha, M. Duneau, The T-Al₃(Mn, Pd) quasicrystalline approximant: chemical order and phason defects, Phil. Mag. Let. 75(4) (1997) 197-208.‏ https://doi.org/10.1080/095008397179624
9. M. C. Burla, R. Caliandro, M. Camalli, B. Carrozzini, G.L. Cascarano, L. De Caro, R. Spagna, IL MILIONE: a suite of computer programs for crystal structure solution of proteins, J. Appl. Cryst. 40(3) (2007) 609-613.‏ https://doi.org/10.1107/S0021889807010941
10. G.M. Sheldrick, SHELXL-97, Program for Crystal Structure Refinement, University of Goettingen, Germany, 1997, release 97-2.
11. H. Bärnighausen, Group-subgroup relations between space groups; a useful tool in crystal chemistry. MATCH-Commun. Math. Chem. 1980, 9, 139.

Structural biologists are undertaking increasingly challenging projects including the study of membrane proteins and complex multi-component machines. Structural investigations are also transitioning beyond solving a single static structure, to the application of a series of sequential structural snapshots to provide details of the atomic positions and motions that define the relationships involved in molecular recognition, transition state stabilization, and other aspects of the biocatalytic process. The success of these experiments requires careful optimization of samples and experimental setups, often involving multiple experiments at the laboratory bench and the beamline, where automation serves as an enabling technology to efficiently deliver multiple crystals and meet stringent timing requirements.

Developments at SSRL and LCLS-MFX will be presented that tackle challenges involved in the use of very small and radiation-sensitive crystals. To facilitate the handling and optimization of delicate crystals, new in situ crystallization and remote data collection schemes have been released that avoid direct manipulation of crystals, support robotic sample exchange, and allow full rotational access of the sample in a controlled humidity environment. By simplifying crystal handling and transport at near-physiological temperatures, these technologies remove barriers to enable more widespread use of serial crystallography methods for studies of metalloenzyme structure and protein dynamics. Data analysis tools that provide rapid feedback for experimental optimization during fast-paced experiments will also be described.

Right from its initial conception, the micro-focus beamline I24 at Diamond Light Source has looked beyond the assumption that an experimenter’s structural question would be answerable with a single, well diffracting, cryo-cooled sample. A multi-crystal approach to data collection has become a modus operandi. Initially attention was focused on small volume and weakly diffracting samples that would typically receive a destructive X-ray dose before complete and redundant data could be recorded. To help tackle this requirement, pipelines for rapid collection and intelligent merging of thin wedges of data from multiple crystals have been developed. Additionally, Serial Synchrotron crystallography (SSX) has become a core activity, with the intention of probing structural dynamics obtainable within protein crystals at room temperature. This brings the requirement for many thousands of crystals, each contributing only a tiny proportion of the final dataset and providing a challenge in terms of collection and processing. I present latest results from SSX and multi-crystal experiments, describe the tools available for users of the beamline and consider optimum methods for successful many-crystal experiments.

Infrared (IR) absorption spectromicroscopy is a powerful, non-invasive probe that provides access to spatio-chemical information at the micron scale. The physical basis of IR spectroscopy lies in the oscillations of dynamic dipole moments in chemical bonds, with resonant frequencies in the IR spectral region of 4,000-400 cm-1 wave numbers. The bending or stretching of chemical bonds between atoms with different electronegativities, such as O-H or C=O, will lead to intense absorption and thus provide a unique fingerprint of specific chemical groups within the sample. The presence - or absence - of specific spectral fingerprints provide the opportunity to locate and identify chemical processes throughout the sample, and track these processes in time or as a function of external perturbation.

We can perform these types of measurements using a Synchrotron Fourier Transform Infrared (SFTIR) spectromicroscopy setup, as it provides orders of magnitude more photons than traditional bench-top machines1. Even with an ultra-bright IR source as provided at the Advanced Light Source, acquisition times typically take multiple hours. These long acquisition times are in part caused by the size of the field of view, as compared to the probe size: users typically analyze a 70 um by 100 um sample using a regular grid with a spacing of 1 um. With an acquisition time of 4 seconds per pixel, we would need about 8 hours to measure the full sample. Given that access to instruments is scarce, compounded by the desire to characterize different samples, being able to speed up data acquisition is of paramount importance.

Here we present a strategy that drastically increases the efficiency of SFTIR spectromicroscopy by coupling the data collection with Gaussian Process based surrogate model 2,3. This approach models the full hyperspectral datasets across the entire field of view, including regions we haven’t measured yet, by multivariate Normal distribution. By analyzing this distribution, we gain insight into which future measurement locations provide the greatest reduction in total uncertainty, and can also predict various quality metrics of the surrogate model we can use to end an experiment. Preliminary experiments show we can increase the throughput of SFTIR experiments by a factor of ~20.

References

1. Holman, H. ‐Y N. & Martin, M. C. Synchrotron Radiation Infrared Spectromicroscopy: A Noninvasive Chemical Probe for Monitoring Biogeochemical Processes. Advances in Agronomy 79–127 (2006) doi:10.1016/s0065-2113(06)90003-0.

2. Chang, H. et al. Building Mathematics, Algorithms, and Software for Experimental Facilities. in Handbook on Big Data and Machine Learning in the Physical Sciences 189–240 (World Scientific, 2020).

3. Noack, M. & Zwart, P. Computational Strategies to Increase Efficiency of Gaussian-Process-Driven Autonomous Experiments. in 2019 IEEE/ACM 1st Annual Workshop on Large-scale Experiment-in-the-Loop Computing (XLOOP) 1–7 (2019).

The rotation method is the most common approach of collecting macromolecular diffraction data. In the days of image plates and charge-coupled device detectors (CCDs), substantial readout time and noise made sophisticated data collection strategies necessary. The correct starting angle of data collection would help minimize the number of images. A rotation increment of up to 1°/image served to raise weak reflections above the detector noise. Datasets took hours to collect.

This is not a sensible way of collecting data anymore. Hybrid Photon Counting detectors, which are installed on essentially all MX beamlines around the world and on many laboratory diffractometers, are free of dark current and readout noise and limited only by Poisson counting statistics. Using rotation increments of around 0.1°/image (fine slicing) decreases the measured background and increases the signal to noise of the experiment. With fast detectors, full 360° datasets can be collected in seconds to a few minutes.

Does the new standard of 360° of data collected at 0.1°/image excuse crystallographers from thinking and optimizing their experiments? Not at all. We show how the full-rotation approach to data collection can accommodate such scenarios as extremely radiation-sensitive samples and experimental phasing. Solving structures by single-wavelength anomalous dispersion from atoms native to the sample becomes possible even with data collected at room temperature. A successful experimental strategy comprises adjustments to beam energy, photon flux, detector distance, starting angle, number of full rotations, orientation of the crystal, and many more.

The recording of data at the highest possible quality makes all subsequent steps of data processing, phasing and model building easier. It will result in a more precise atomic model to answer the biological questions that prompted the structural work. Despite the apparent simplicity of the full-rotation method, data collection, the last experimental step of MX, is as critical as ever. There is no excuse for walking away with less than best data.

A recent surge in reports of crystals exhibiting elastic flexibility has changed the way we view these materials. With potential applications in flexible electronics, in depth research is required to understand why some crystals can be tied into knots, while others shatter under an applied force. Different rationales for elastic flexibility have been proposed: many crystals have been engineered to impart flexibility through isotropic interactions, although other elastic crystals have anisotropic interactions [1]. Clearly, the different interactions present result in diverse bending mechanisms. The mechanism of flexibility in elastic crystals can be resolved on an atomic-scale by use of micro-focused synchrotron radiation [2]. By examining the localised crystal structure at multiple positions across a bent crystal, the deformations of the cell parameters can be quantified (Fig. 1). Isotropic and anisotropic crystals have been analysed using this technique to determine their respective mechanisms.

Unfortunately, structural mapping quickly produces large volumes of data, and manual processing would be inefficient when there are only small changes to the data. Instead, software was developed to automatically process these datasets. It is capable of taking raw frames and providing finalised CIF files with results graphically analysed. This allows for greater insight into these elastic crystals, as more data can be analysed in a reasonable time frame. This software, CX-ASAP, consists of a series of independent modules which can be placed together into an auto-processing pipeline. The advantage of this modular approach, is the fact that it is applicable to a wider range of large crystallographic dataset analysis, such as variable temperature experiments. The main consideration of this software is the limit of computer knowledge, as there are key steps during the automation where user input is mandatory for reliable results.

[1] Ahmed, E., Karothu, D. P. & Naumov, P. (2018). Angew. Chem. Int. Ed. Engl. 57, 8837-8846.

[2] Worthy, A., Grosjean, A., Pfrunder, M. C., Xu, Y., Yan, G., Edwards, G. & Clegg, J. C. (2018). Nat Chem. 10, 65-69.

Keywords: flexible crystal; elastic crystal; automation; mechanisms; synchrotron

The author wishes to acknowledge the work of Dr Arnaud Grosjean for preliminary automation work.

The decision on the high-resolution cutoff has an apparent impact on the quality of a structure model. To determine the optimal cutoff automatically, we developed a software tool PAIREF [1]. The program performs the paired refinement protocol that allows linking the data and structure model quality. This analysis goes beyond the conventional criteria based on the indicators of data quality only (e.g. I/σ(I), R_meas).

PAIREF is freely available for multiple platforms and can be run from the command-line or graphical user interface. Two refinement engines are currently supported: REFMAC5 from the CCP4 software suite [2] and PHENIX.REFINE [3]. The program creates a compact comprehensive report. The final decision on the cutoff is based on several statistics that are calculated and monitored: R-values, correlation coefficients, optical resolution, merging statistics, etc. The consequent comparison between CC_work and CC* allows the assessment of overfitting. Moreover, a unique feature of the program is the complete cross-validation scenario: the protocol is run in parallel for each free-reflection set selection individually which leads to averaged, more general and meaningful results.

During the work on PAIREF, we confirmed previous findings and proved that useful signal can be often still present in the high-resolution data not fulfilling the obsolete conventional criteria. To give an example: In the particular case of interferon gamma from Paralichthys olivaceus (PDB entry 6f1e), the cutoff was originally applied at 2.3 Å, according to the criterion for I/σ(I) higher than 2 in the highest resolution shell. Nevertheless, we ran paired refinement up to 1.9 Å and observed a systematic decrease in R_free while including data up to 2.0 Å [1]. Hence, the structure was improved, despite very poor statistics relating to the last resolution shell 2.1-2.0 Å (I/σ(I) = 0.1, CC_1/2 = 0.03).

Furthermore, we similarly examined the high-resolution data from endothiapepsin (PDB entry 4y4g). This structure was originally solved at 1.44 Å resolution. However, we could observe a significant improvement in the quality of electron density of the partially occupied fragment after refinement up to 1.20 Å (Fig. 1). This observation was in harmony with corresponding drops in R_free [1].

Generally, the quality of a structure model can benefit from the involvement of even weak high-resolution data. Thus, the application of paired refinement could be recommended for any structural project in X-ray macromolecular crystallography. PAIREF provides automation of the routine and gives all the relevant statistics for users to make a precise decision on the cutoff.

Figure 1. Improvement in omit maps of the partially occupied fragment B53. Electron density after refinement up to 1.44 (purple) and 1.20 Å (orange) is shown at a level of 0.56 eÅ⁻³. Atomic coordinates were adapted from PDB entry 4y4g.

[1] Malý, M., Diederichs, K., Dohnálek, J. & Kolenko, P. (2020). IUCrJ 7, pp. 681–692.

[2] Winn, M. D., Ballard, C. C., Cowtan, K. D., Dodson, E. J., Emsley, P., Evans, P. R., Keegan, R. M., Krissinel, E. B., Leslie, A. G., McCoy, A., McNicholas, S. J., Murshudov, G. N., Pannu, N. S., Potterton, E. A., Powell, H. R., Read, R. J., Vagin, A., & Wilson, K. S. (2011). Acta Cryst. D 67, pp. 235–242.

[3] Adams, P. D., Afonine, P. V., Bunkóczi, G., Chen, V. B., Davis, I. W., Echols, N., Headd, J. J., Hung, L. W., Kapral, G. J., Grosse-Kunstleve, R. W., McCoy, A. J., Moriarty, N. W., Oeffner, R., Read, R. J., Richardson, D. C., Richardson, J. S., Terwilliger, T. C., & Zwart, P. H. (2010). Acta Cryst. D 66, pp. 213–221.

This work was supported by the MEYS CR (projects CAAS – CZ.02.1.01/0.0/0.0/16_019/0000778 and BIOCEV – CZ.1.05/1.1.00/02.0109) from the ERDF fund, by the Czech science foundation (project 18-10687S), and by the GA CTU in Prague (SGS19/189/OHK4/3T/14).

Your research is finally out? Congratulations! But, let’s not forget that the research publication is not the end of the process, but the beginning of another one, also important: communication. Mastering communication, and all communications tools, especially social media, is now crucial to promote your research. Scientists themselves are sometimes embracing roles that were conventionally taken on by trained science communicators.

But how to exist regarding the huge flow of communication generated on social media? How to engage with new audience? How do people, outside of the scientific life, learn about science or crystallography?

The ESRF’s communication group has developed a digital strategy based on humanising science to reach new audience but also to engage people with science. This strategy aims to explain the stories behind the science carried out at the ESRF, to highlight the people behind the research projects, through digital campaigns such as “Humans of ESRF”, EBS stories or video portraits.

Social media, as the name suggests, is a useful tool for staying connected socially with one another, however more recently it has also been used to spread ideas and communicate science to a broad audience. Social media platforms such as Instagram, Twitter, Facebook and Youtube are increasingly being used to explain difficult scientific concepts in easy to understand language to a broad audience of both other scientists and other members of the public. This presentation will discuss how scientists can use social media to communicate their science, and how I have used platforms such as Instagram and Twitter to talk about crystallography and biochemistry in an accessible manner. This presentation will also dive into how scientists and science communicators have used social media in an attempted to break down the barriers between scientists and the rest of the public, and improve public perception of who scientists are and what we do.

Social media has the power to change people’s lives, from what we wear and eat, to where we go and who we socialise with. How can we leverage this influence to help inspire a new generation of scientists and crystallographers?

At the Cambridge Crystallographic Data Centre (CCDC) we are involved in several projects to demonstrate the power of structural data in fun and engaging ways on social media. Over the last year we have created games and content targeted at inspiring a new generation of scientists. This has included a wide variety of activities and social media campaigns and is often done in conjunction with people in our community.

This talk will highlight some of these efforts and explore what we have learnt along the way. We will demonstrate how we have used social media to enable people to play fun educational card games, to share instructional videos and playlists, to share educational tips (#CSDTopTipTuesday) and to encourage good data sharing practices.

We will conclude by summarising what we have learnt along the way and explore how we can better help others to spread the science of crystallography and its application as far as possible inside and outside the crystallographic community.

There is no doubt that the internet and social media has changed the way in which information is communicated and spread throughout the world today. Perhaps one of the fastest moving forms of media are memes, a small statement, image or video that is spread across platforms similarly to the game of ‘telephone’. Wikipedia defines a meme (/mi:m/MEEM) as “an idea, behaviour, or style that spreads by means of imitation from person to person within a culture – often with the aim of conveying a particular phenomenon, theme, or meaning represented by the meme.” [1] With the rise of meme groups such as “Inorganic Memes for C2v Teens” and “X-ray Crystallography May-Mays” on platforms such as Facebook, we see the spread of scientific memes and crystallographic ideas across the younger generation [2,3]. In this presentation, we will provide an overview on the use of memes to spread scientific information and their use as a tool for education and outreach for the next generation of crystallographers.

Since the turn of the century, secondary batteries have become big business. The portable electronics industry in the 1990’s was driven by the design of the Li-ion battery, and in more recent times, these batteries are underpinning the drive for electrification of vehicles to mitigate the increasingly apparent effects of climate change; thus Li-ion batteries can be described as being everywhere in everyday life.

With our reliance on portable electronics, and the growth of the electric vehicle market, it is important to not only inspire the younger generation to think of their future career in the sciences, but also allow for important concepts which relate to policy to be accessible and understandable to the wider public.

Common current outreach demonstrations for battery work make use of potato-/lemon-electrolyte batteries with a copper coin and zinc nail. Although a great demo to introduce the concept of electrochemical potentials between the metals and circuits, students often struggle to differentiate between the two types of batteries – primary (non-rechargeable) and secondary (rechargeable) and often mistakenly assume the voltage generated to originate from the potato/lemon itself.

With this in mind, we have set out to create demonstrations, which can complement primary battery demos, while showcasing operation of rechargeable batteries using the LiCoO₂ – graphite as a basis of the set-up. The talk will highlight our work from the past year through a variety of demonstrations, including our battery jenga¹ set-up and the Royal Society of Chemistry IYPT2019 funded Lithium Shuffle Project battery operation videos². The talk will also touch on outreach funding – the highs and lows, and how the group has continued their engagement work during the difficult period of COVID19.

The Italian Young Crystallographers (trad. Giovani Cristallografi Italiani aka GCI) group was formally established in 2019 driven by the need of having a common place for students and young researchers to share their experiences and develop a common sense of affiliation to the main national association.

However, the possibility to meet each other at conferences and congresses are rather modest even without the well-known pandemic constraints, so, we decided to use social media to share information among the community on a regular basis. The social media platforms soon became a virtual place where the young generation of crystallographers are informed of job vacancies around the world, promote their latest research and enrich their crystallographic knowledge.

As a consequence, the number of younger scientists associated increased significantly in the last two years and the GCI, fully supported by the national crystallographic association, plays a central role in all the scientific activities organized locally and at the national level.

I here report the strategies used to develop the social media platforms and the initiative promoted by GCI to engage young researchers in crystallography.

An-Pang Tsai, professor at Tohoku University, Sendai, Japan, passed away on May 25 2019 at the age of 60. He was a pioneer and a leader in the field of quasicrystals and complex intermetallic phases. With him the community has lost one of the brightest scientist in this field. This symposium is dedicated to his memory and illustrates the many different fields he has been contributing in crystallography, metallurgy, material science and solid-state physics and chemistry.
In this presentation we will highlight the many important contributions of the research conducted by An-Pang Tsai going from fundamental and basic research to their applications and the important impact it had on the scientific community. We can quote: the discovery of most of the thermodynamically stable quasicrystals including the stable binary quasicrystals named ‘Tsai-type’ quasicrystals, the physics allowing to understand which systems is favorable for quasicrystal growth, their atomic structure and physical properties, lattice dynamics, magnetism, mechanical properties. In view of applications he has been one of the first to promote the use of quasicrystals for light alloy reinforcement and more recently he developed a completely new field with new ideas for the development of new catalytic materials.
An-Pang Tsai also had a decisive impact in training the younger generation in the different labs he has ben leading. He always was enthusiast to explore new fields, proposing ambitious targets, but with the long-term perspective, without pressure and with the entire necessary scientific environment. He has coordinated researches in the field of quasicrystals and material sciences in Japan and abroad. In particular he started to organize annual meetings on quasicrystals in Japan in 1996, which continued for more than 20 years andhas organized or initiated number of international conferences.
From very early on in his career, An-Pang Tsai built up an impressive large number of collaborations all across the world, in Japan, Europe, USA, Canada, China and Taiwan. His generosity in sharing his discoveries, his constant curiosity and inspiring ideas have irrigated the quasicrystal community, promoting collaboration rather than competition, leading to major results in almost all aspects of quasicrystal researches and from experiments to theory. He always was available and ready to share his knowledge with senior scientists as well as with young students.
We have lost a great colleague and a good friend, and we will honour his memory by continuing his interdisciplinary research work, keeping his enthusiast and collaborative approach.
[1] de Boissieu M and Ishimasa T (2019) Acta Cryst. B 75 763.

The Al-Mn icosahedral quasicrystal discovered by Shechtman was a metastable phase [1]. Attempts at its structure solution immediately began after the discovery was declared. After the subsequent discovery of stable icosahedral quasicrystals, the study of their physical properties became more active in addition to the elucidation of their structures, but these quasicrystals were all formed in ternary systems [2]. Because chemical disorder of inherent in ternary icosahedral quasicrystals, it was difficult to achieve any structure solution which is comparable to what is obtained for ordinaryl crystal. Discovery of a stable binary icosahedral quasicrystal in a Cd-Yb alloy opened a route to the structure solution to at least for this particular type of quasicrystal [3]. This quasicrystal, now known as Tsai-type icosahedral quasicrystal, forms the largest group among known quasicrsytals and their approximant crystals forming systems. Although I was not directly involved in the discovery of this quasicrystal, I was present at the scene as a member of Tsai's group and took the first X-ray transmission Laue photographs (Fig. 1), which were appeared in the paper announcing the discovery [3]. In the beginning, the quality of Cd-Yb quasicrystal was not very good, but soon good quality was obtained, and higher-dimensional crystal structure analysis by means of single crystal X-ray diffraction became possible [4]. Here is the story of how we arrived at the structural solution of this particular icosahedral quasicrystal.

We had collaborated exciting themes in materials science together with Professor An Pang Tsai for 17 years (since 2002). Prof. Tsai began the investigation of catalytic materials in term of metallurgy at NIMS [1].

There are three important topics in the collaborative research with Professor Tsai. Firstly, we succeeded that novel catalytic materials were prepared by the leaching method of Al-Cu-Fe quasicrystalline (QC) [2]. The Al₆₃Cu₂₅Fe₁₂ QC is a promising precursor for Cu catalysts, whose constituent elements, compositions and quasi-periodic structure are in favor of processing high performance catalysts. Brittleness resulting from quasi-periodic structure enables one to obtain powder form for processing catalysts. Relatively low dissolution rate of Al due to quasi-periodic structure upon leaching with NaOH solution, generated homogeneous nanocomposite consisting of Fe₃O₄ and Cu and hence gave rise to high activity and thermal stability for steam reforming of methanol. Secondary, Prof. Tsai proposed a concept for a psudo-element material such as “PdZn = Cu” [3]. A clear correlation between electronic structure and CO₂ selectivity for steam reforming of methanol (SRM) was obtained with PdZn, PtZn, NiZn, and PdCd intermetallics on the basis of experiments and calculations. PdZn and PdCd also exhibited valence electronic densities of states and catalytic properties similar to that of Cu. Thirdly, a new concept of active sites for bulk-type metallic materials was proposed by Prof. Tsai, i.e., nano twin boundary [4]. According to the DFT calculation, surface density of the active six-coordinated atoms in nano porous gold (NPG) was comparable with that of supported gold nanoparticle catalysts. In addition, the energy profiles of reaction pathways for CO oxidation indicated that the six-coordinated sites created by twinning significantly contributed to the catalytic activity of NPG. I will overview of these topics in my presentation.

Two years have passed since Professor A.P. Tsai passed away. Taking over Prof. A.P. Tsai’s spirits, now we are conducting research on novel metallic catalysis materials under the new system. We hope that those concepts of Prof. Tsai’s will lead to a principal for the development of metallic functional materials as well as metallic catalysts in the future.

[1] A.P. Tsai, M. Yoshimura, “Highly active quasicrystalline Al-Cu-Fe catalyst for steam reforming of methanol”, Applied Catalysis, A, 214 (2001) 237-241.; M. Yoshimura, A.P. Tsai, “Quasicrystal application on catalyst”, J. Alloys Compounds, 342 (2002) 451-454.

[2] For example T. Tanabe, S. Kameoka, M. Terauchi and A.P. Tsai, “Microstructure of leached Al-Cu-Fe quasicrystal with high catalytic performance for steam reforming of methanol”, Applied Catalysis, A, 384 (2010) 241-251.

[3] A.P. Tsai, S. Kameoka and Y. Ishii, “PdZn=Cu: Can an intermetallic compound replace an element ?”, J. Physical Soc. Jpn., 73 (2004) 3270-3273.

[4] M. Krajci, S. Kameoka and A.P. Tsai, “Twinning in fcc lattice creates low-coordinated catalytically active sites in porous gold”, J. Chem. Phys., 145 (2016) 084703.; ibid., 147 (2017) 044713.

The name of An-Pang Tsai is in first line connected with his pioneer work on quiasicrystalline and related crystalline materials, e.g. on the atomic structure of quasicrystals [1]. Less known are the studies of his group on chemical properties, in particular on catalytic materials. A mutual origin of the interest to this research field may be found in the search for possible application fields for quasicrystals and investigations on surface properties of quasicrystalline and approximant phases, i.e. oxidation behaviour [2] or etching reactions [3]. Logical continuation of these studies is the work of An Pang Tsai and his group on hydrogen absorption on intermetallic compounds [4,5] and high catalytic activity of amorphous intermetallic hydrides in hydrogenation of ethylene and CO₂ [6,7]. The subsequent studies were devoted to the influence of real structure of materials (Renee catalyst) or electronic factors on the catalytic activity [8,9]. Coming back to the possible applications of quasicrystals, the group of A. P. Tsai was working on activation of quasicrystalline surface and fabrication of a fine nanocomposite layer with high catalytic performance [10]. In the following years several new results were produced by A. P. Tsai and his co-workers on composite catalyst with mixed lamellar structures and dual catalytic functions, dominant factors of porous gold for CO oxidation, effects of Cu oxidation states on the catalysis of NO+CO and N₂O+CO reactions, preparation of dispersive Au nanoparticles on TiO₂ nanofibers from Al-Ti-Au intermetallic compound. The last product of the work of An Pang Tsai in the field of catalysis – although not finished by himself – was the special issue of Science and Technology of Advanced Materials giving an comprehensive overview of current research activities around the world [11].

[1] Takakura, H., Goméz, C. P., Yamamoto, A., de Boissieu, M., Tsai A. P. (2007). Nature Materials 6(1), 58. [2] Yamasaki, M., Tsai A. P. (2002). J. Alloys Compd. 342(1), 473. [3] Saito, K., Saito, Y., Sugawara, S., Shindo, R, Guo, J.-Q., Tsai, A. P. (2004) Phil. Mag. A, 84(10), 1011. [4] Endo, N., Kameoka, S., Tsai, A. P., Zou, L., Hirata, T., Nishimura, Ch. (2009). J. Alloys Compd. 485, 588. [5] Endo, N., Kameoka, S., Tsai, A. P., Zou, L., Hirata, T., Nishimura, Ch. (2010). J. Alloys Compd. 490, L24.

[6] Endo, N., Kameoka, S., Tsai, A. P., Hirata, T., Nishimura, Ch. (2011). Mat. Trans. 52, 1794.

[7] Endo, N., Ito, Sh., Tomishige, K., Kameoka, S., Tsai, A. P., Hirata, T., Nishimura, Ch. (2011). Catalysis Today, 164, 293.

[8] Nozawa, K., Endo, N., Kameoka, S., Tsai, A. P., Ishii, Y. (2011). J. Phys. Soc. Jpn. 80, 064801.

[9] Murao, R., Sugiyama, K., Kameoka, S., Tsai, A. P. (2012). Key Eng. Mat. 508, 304.

[10] Kameoka, S., Tanabe, T., Satoh, F., Terauchi, M., Tsai A. P. (2014). Sci. Techn. Adv. Mat. 15, 1878.

[11] Special issue IMc (2019). Sci. Techn. Adv. Mat. 20

We will present several interesting structures of thin films grown on Tsai-type quasicrystal, icosahedral (i)-Ag-In-Yb, studied by various experimental techniques including scanning tunnelling microscopy (STM). The results include three dimensional quasicrystalline films of single elements [1] and molecular films [2] (Figure 1).

The i-Ag-In-Yb quasicrystal is built by rhombic triacontahedral (RTH) clusters and its surface is formed at the bulk atomic planes that bisect the RTH clusters [3]. When Pb is deposited on the fivefold i-Ag-In-Yb surface, the Pb atoms adsorb at the sites that were originally occupied by the cluster atoms and thus produce quasicrystalline film in three-dimension [1]. This observation is evidenced in other systems as well, namely Pb on the threefold and twofold i-Ag-In-Yb surfaces [4, 5] and In, Sb and Bi on the fivefold i-Ag-In-Yb surface [6].

We also found that Pentacene molecules deposited on the fivefold i-Ag-In-Yb surface adsorb at tenfold-symmetric sites of Yb atoms around surface-bisected RTH clusters, yielding quasicrystalline order [2]. The selective adsorption of Pentacene on Yb sites is also observed on the threefold and twofold surfaces of the same sample.

The phenomena of adsorption on selective sites is also found on Al-based quasicrystals. C₆₀ molecules preferably adsorb on Fe or Mn when deposited on surfaces of i-Al-Pd-Mn and i-Al-Cu-Fe [2, 7], yielding quasicrystalline order of C₆₀. The compatibility between the characteristic lengths of the substrate and the size of adsorbates has led to the growth of unprecedented epitaxial structures

His ideas about AuSi

Phyre2 is a web server to predict protein structure from sequence (www.imperial.ac.uk/phyre2) that processes ~1,000 individual sequences submitted by users every day. Since its introduction in 2011, Phyre2 has processed well over 4M jobs with ~55,000 unique users per year, each submitting ~20 sequences on average. The Phyre2 (Fig 1) web portal [1]provides both a rapid and user-friendly interface to predict protein structure using homology based template modelling and also resources for analysing the results. The papers describing Phyre2 and its predecessors (3D-PSSM and Phyre) have had over 12,000 citations in the literature.

The performance of different protein structure prediction implementations is compared in a biennial exercise, the Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction; the 14th edition, CASP14, took place in 2020 [2]. The outstanding performance of one program, AlphaFold2 [3] in CASP14 drew the attention of the world's media to this field. The results might lead the casual observer to conclude that the protein structure problem is solved, but at the moment AlphaFold2 itself is not readily accessible to the vast majority of users and the underlying methods employed have not yet been revealed in any detail.

We will show how the carefully designed interface to Phyre2 allows users to generate 3D protein structures from their sequence data in a flexible and straightforward way that makes good models readily available to the community at large.

In addition to a simple mode that allows modelling from single sequences, the Phyre2 web portal proves a range of extra functionality: i) a facility for batch submission of processing of proteomes, ii) searching model genomes for a protein structure, iii) PhyreAlarm, which automatically updates a user if a superior model can be predicted as a result of a newly-deposited structure in the protein data bank, and iv) facilities to analyse a predicted model in terms of accuracy and sequence conservation.

Phyre2 is a resource with the UK node of ELIXIR, the European–wide network of bioinformatics facilities.

Fig 1 – Main results page of the Phyre2 web server showing hits with confidence scores and origin of templates

[1] Kelley et al. (2015) Nature Protocols, 10, 845.

[2] CASP14, https://www.predictioncenter.org/casp14/index.cgi

[3] see, e.g. https://en.wikipedia.org/wiki/AlphaFold

Today the study of two-dimensional (2D) materials has become one of the key objectives of materials science. Unlike their three-dimensional counterparts, 2D materials can simultaneously demonstrate unique transport and mechanical properties due to their dimensionality and quantum size effect. Weak van der Waals interaction between layers in heterostructures of 2D materials, electron confinement inside the layers, and high surface-to-volume ratio lead to remarkable changes in electronic and optical properties of the materials, as well as in their chemical and mechanical response. Besides, a wide range of ways to tune properties using lateral and vertical heterostructures fabrication, chemical functionalization, strain, defect and substrate engineering, makes 2D materials ideal candidates for developing a new class of electronic devices. In their fabrication and application, 2D materials are usually located on top of the substrate or combined into heterostructures, which makes their structures and properties strongly depend on the nature and quality of the environment. Here, we present a novel method for studying the atomic structures of two-dimensional materials and epitaxial thin films on arbitrary substrates. The method can predict successful stages of epitaxial growth and the regions of stability of each atomic configuration with experimental parameters of interest (Figure 1). We demonstrate the performance of our methodology in the prediction of the atomic structure of MoS₂ on Al₂O₃ (0001) substrate. The method is also applied to study the CVD growth of graphene and hexagonal boron nitride on Cu (111) substrates. In both cases, stable monolayer and multilayer structures were found. The stability of all the structures in terms of partial pressures of precursors and temperature of growth is predicted within the ab initio thermodynamics approach.

Prediction of crystal structures has reached a high level of reliability, but much less is known about the mechanisms of structural transitions and pertinent barriers. The barriers related to nucleation of crystal structure inside another one are critically important for kinetics and eventually decide what structure will be created in experiment.

We show here an NPT metadynamics simulation scheme [1] employing coordination number and volume as collective variables and illustrate its application on a well-known example of reconstructive structural transformation B1/B2 in NaCl. Studying systems with size up to 64000 atoms we reach beyond the collective mechanism (Fig.1 (a)) and observe the nucleation regime (Fig.1 (b)). We reveal the structure of the critical nucleus and calculate the free-energy barrier of nucleation and also uncover details of the atomistic transition mechanism and show that it is size-dependent.

Our approach is likely to be applicable to a broader class of structural phase transitions induced by compression/decompression and could find phases unreachable by standard crystal structure prediction methods as well as reveal complex nucleation and growth effects of martensitic transitions.

Figure 1. (a) Collective mechanism - A typical frame of supercell during the course of the B1/B2 transition in NaCl at 40 GPa and 300 K in the system of size of 512 atoms. (b) Nucleation - A typical nucleus of the B2 phase in the B1 phase (with shape of ellipsoid), during the transition at 40 GPa and 300 K in the system of 64 000 atoms. Plane of view cuts the ellipsoid through its centre. Figure was produced using OVITO [2].

[1] M. Badin and R. Martoňák, arXiv:2105.02036

[2] A. Stukowski, Modelling Simul. Mater. Sci. Eng. 18, 015012 (2010).

Keywords: pressure-induced phase transitions; nucleation; martensitic transition; metadynamics

This work was supported by the Slovak Research and Development Agency under Contracts APVV-15-0496 and APVV-19-0371, by VEGA project 1/0640/20 and by Comenius University under grant for young researchers - UK/436/2021.

RNA viruses such as coronaviruses, flaviviruses, and henipaviruses represent major international health threats. Whilst these viruses replicate in the cytoplasm, they encode accessory proteins that target the host nuclear transport machinery to suppress innate immune pathways. Specifically, these virus proteins target the nuclear import receptor importin-a (IMPa) and inhibit host immune responses from entering the nucleus and triggering interferon (IFN) release. This immune evasion strategy is a critical component of virus pathogenicity, yet details of these interactions (including mechanism(s) of binding specificity with IMPa isoforms) remain unresolved. Here we describe the interfaces between these viral immune regulatory proteins and specific IMPA host receptors as targets for development of novel antivirals.

Prevalence of drug-resistant strains of causative agents of age old diseases pneumonia and tuberculosis (TB), has urged focus on exploring novel targets and development of new therapeutics with a fresh perspective in the battle against antibiotic resistance. Now-a-days bioactive compounds from natural origin are superseding the use of synthetic compounds due to structural and chemical diversity [1]. Our research illustrates the power of integrative structural biology in the discovery of inhibitors against two potential drug targets - (1) Serine acetyltransferase (also known as CysE), an enzyme of de novo cysteine biosynthetic pathway, and (2) Isocitrate lyases with role in both glyoxylate cycle and methylcitrate cycle

(1) CysE catalyzes the production of O-acetyl-L-serine (OAS) from acetyl-CoA and L-serine. The enzyme, essential for survival in a mouse model of TB infection [2], is absent in Homo sapiens. Therefore, this target is worth exploring for developing new antimicrobial compounds. The crystal structure of K. pneumoniae (Kpn) CysE was solved and used as a receptor for blind docking of natural compounds with documented antioxidant, antibacterial, respiratory stimulant, anti-inflammatory, and bronco-dilatory activities. L-Cys, a feedback inhibitor of CysE which binds at the active site was also docked as a positive control (Fig.1a). The best binders were tested for the inhibitory potential of CysE and quercetin was identified as the most potent inhibitor (Fig. 1b). MD simulations verified it as an allosteric inhibitor that binds at the trimer-trimer interface distal to the active and cofactor binding site.

(2) Isocitrate lyases (ICL1/ICL2) are essential for persistence of M. tuberculosis (Mtb) in its host [3] as they play an important role in metabolism of even and odd chain fatty acids via β-oxidation. Though high resolution crystal structures of Mtb ICL1 are available in PDB since 2000, and GlaxoSmithKline-TB Alliance launched high throughput screening of 900,000 compounds to identify ICL1 inhibitor, their efforts culminated in modest succes, in view of poor characterization of ICL2 structure-function relationship. We purified both Rv1915 and Rv1916 and characterized them possessing dual isocitrate and methylisocitrate lyase activities akin to ICL1[4]. In silico screening of natural compounds has yielded an inhibitor which is able to abolish both the activities in all Mtb ICLs.

[1]. Pereira D. M., Andrade C., Valentão P., & Andrade P. B. (2017). “Natural Products Targeting Clinically Relevant Enzymes, pp. 1–18. Wiley-VCH Verlag GmbH & Co. KGaA,

[2]. Sassetti C. M. & Rubin E. J. (2003).Proc. Natl. Acad. Sci. USA 100:12989-94

[3]. McKinney J. D., zu Bentrup K. H., Muñoz-Elías E. J., et al (2000). Nature 406:735–738.

[4]. Gould T. A., van de Langemheen H., Munoz-Elias E. J., et al (2006). Mol Microbiol 61:940–947.

Metal ions are essential for all forms of life. In prokaryotes, ATP-binding cassette (ABC) permeases serve as the primary import pathway for many micronutrients including the first-row transition metal manganese. However, the structural features of ionic metal transporting ABC permeases have remained undefined. This presentation will describe the crystal structure of the manganese transporter PsaBC from Streptococcus pneumoniae in an open-inward conformation. The Type II transporter has a tightly closed transmembrane channel due to ‘extracellular gating’ residues that prevent water permeation or ion reflux. Below these residues, the channel contains a hitherto unreported metal coordination site, which is essential for manganese translocation. These structural features are highly conserved in metal-specific ABC transporters and are represented throughout the kingdoms of life. Collectively, our results define the structure of PsaBC and reveal the features required for divalent cation transport.

We know so little about how bacteria utilise surface virulence factors to colonise, infect, persist and cause disease in their hosts. The largest group of these virulence factors are the autotransporters, where although they employ a simple process for translocation to the bacterial surface, their functional passenger domains show a diverse range of pathogenic functions such as promoting adhesion, biofilm formation, invasion and tissue destruction. Despite extensive international efforts at the genotype-phenotype level that have confirmed the association of autotransporters with bacterial pathogenesis, less than 0.6 % of their structures have been determined with very little information on their molecular mechanisms of action.

With 10 new structures of autotransporter passenger domains over the past few years our group has been leading this area of research. Taking advantage of many autotransporter passenger domains being based upon large >500 residue β-solenoid structures, we have successfully employed Xenon derivatisation at the Australian Synchrotron to acquire anomalous signal for structure determination by single isomorphous replacement. More importantly, we have used our crystal structures to inform a comprehensive array of biophysical, biochemical and microbiological approaches to uncover the mode of action of the autotransporters and their roles in bacterial pathogenesis. Using this approach we were the first to determine the molecular mechanism of an autotransporter adhesin¹. We found that this Ag43 adhesin from Uropathogenic E. coli (UPEC) promoted bacterial biofilms through a self-association mechanism between neighbouring E. coli cell surfaces. This knowledge on biofilms is critical given their contribution to bacterial chronic infections and the development of antibiotic resistance.

Here we present the first crystal structure and mechanism of action of an autotransporter adhesin that binds to host tissue to facilitate bacterial colonisation². The crystal structure of UpaB from UPEC was found to display significant modifications to its β-helix that creates two different binding sites, allowing it to interact simultaneously with both host surface proteins and polysaccharides. As shown in live animal models, both sites co-operate to achieve bacterial colonisation. In contrast to Ag43 that forms self-associations that lead to biofilms, UpaB through directly binding host factors to facilitate colonisation creates a second mechanistic group of the autotransporter adhesins.

Returning to Ag43, we also investigate the conservation of its self-association mechanism with 3 new crystal structures of Ag43 homologues from widespread E. coli pathogens³. We show that adaptations to this mechanism of action alter the kinetics of bacterial aggregation and biofilm formation, presumably to suit the different E. coli pathogens to their specific infection sites. Even more importantly, we are using our molecular knowledge on autotransporters such as Ag43 to develop new classes of anti-bacterial inhibitors. To date we have developed and patented a successful inhibitor that targets Ag43 to prevent pathogenic E. coli biofilms⁴. Again using X-ray crystallography we have determined the structure of the first autotransporter adhesin-inhibitor complex to fully understand how this novel inhibitor interacts with Ag43 and blocks its funtion.

Figure 1A: Ag43 self-associates between E. coli surfaces to promote aggregation and biofilm formation. B. UpaB directly binds both host proteins and carbohydrates to promote UPEC colonisation.

[1] Heras B, Totsika M, Peters KM, Paxman JJ, Gee CL, Jarrott RJ, Perugini MA, Whitten AE and Schembri MA (2014). Proc Natl Acad Sci USA 111, 457-462.

[2] Paxman JJ, Lo A, Sullivan MJ, Panjikar S, Kuiper M, Whitten AE, Wang G, Luan CH, Moriel DG, Tan L, Peters KM, Gee C, Ulett GC, Schembri MA and Heras B. (2019). Nat. Commun. Apr 29;10(1);1967.

[3] Vo J, Martínez Ortiz GC, Totsika M, Lo A, Whitten AE, Hor L, Peters KM, Ageorges V, Caccia N, Desvaux M, Schembri M, Paxman JJ and Heras B (2021). ELife (under revision).
[4] Heras B, Paxman JJ, Schembri M and Lo A (2019) International Patent (PCT/AU2019/050893).

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The evolutionarily conserved Retromer complex (Vps35-Vps26-Vps29) is a master regulator responsible for endosomal membrane trafficking and signalling. It is known that mutations in Retromer can cause late-onset Parkinson’s disease, and can also be hijacked by viral and bacterial pathogens during cellular infection. Seeking tools to modulate Retromer function would provide new avenues in understanding its function and the associated diseases. Here we employed the random nonstandard peptides integrated discovery (RaPID) approach to identify a group of macrocyclic peptides capable of binding to Retromer with high affinity. Our crystal structures show that five of the macrocyclic peptides bind to human Vps29 via a di-peptide Pro-Leu sequence. Interestingly, these peptides structurally mimic known interacting proteins including TBC1D5, VARP, and the bacterial effector RidL, and potently inhibit their interaction with Retromer in vitro and in cells. In addition, we found that these Vps29-binding macrocyclic peptides also mimic the binding between thermophilic yeast Vps29 and the unstructured N-terminal domain of Vps5. Disruption of this previously uncharacterized interaction by macrocyclic peptides negatively affect yeast Retromer, Vps5 and Vps17 to form stable heteropentameric complex. By contrast, mutagenesis and cryoEM show that macrocyclic peptide RT-L4 binds Retromer at the Vps35 and Vps26 interface, and it can act as a molecular chaperone to stabilise the complex with minimal disruptive effects on Retromer’s ability to interact with its accessory proteins. Finally, using reversible cell permeabilization approach, we demonstrate that both the Retromer inhibiting and stabilizing macrocyclic peptides can specifically co-label Vps35-positive endosomal structures, and can be used as baits for purifying Retromer from cells and subsequent proteomic analyses. We believe these macrocyclic peptides can be used as a novel toolbox for the study of Retromer-mediated endosomal trafficking, and sheds light on developing novel therapeutic modifiers of Retromer function.

The class D serine β-lactamases comprise a superfamily of almost 900 enzymes capable of conferring high-level resistance to β-lactam antibiotics, predominantly the penicillins including oxacillin (Fig. 1) and cloxacillin, and some early generation cephalosporins. In recent years it has been discovered that some members of the class D β-lactamase superfamily have evolved the ability to deactivate carbapenems (Fig. 1), last resort β-lactam antibiotics generally held in reserve for highly drug resistant bacterial infections. These enzymes are collectively known as Carbapenem-Hydrolyzing Class D serine β-Lactamases or CHDLs [1,2]. Most alarmingly, a large number (>500) of these CHDLs have appeared in several Acinetobacter baumannii strains, leading the CDC to elevate this once nosocomial infection of little clinical importance into a major opportunistic pathogen, now deemed to be an urgent global threat [3] with mortality rates from infections by resistant strains often exceeding 50% [4].

The mechanism of β-lactam deactivation by the class D serine β-lactamases involves the covalent binding of the antibiotic to an active site serine to form an acyl-enzyme intermediate (acylation). This is followed by hydrolysis of the acyl bond (deacylation), catalysed by a water molecule activated by a carboxylated lysine residue [5]. It was initially thought that the carbapenems acted as potent inhibitors of the class D enzymes since formation of the covalent acyl-enzyme intermediate expelled all water molecules from the active site, and stereochemistry of the side group at carbon 6 of the β-lactam ring effectively blocked access into the pocket housing the catalytic lysine, thus preventing the deacylation step. Our recent structural studies on three CHDLs (OXA-23, OXA-48 and OXA-143) [4,6,7] have indicated that their carbapenem hydrolysing ability may be due to small-scale dynamics of two surface hydrophobic residues which form a hydrophobic lid over the internal pocket housing the catalytic lysine. Movement of one or both of these residues allow for the transient opening and closing of a channel (Fig. 2) through which water molecules from the milieu can enter the lysine pocket to facilitate the deacylation reaction. Although the hydrophobic residues responsible for the channel formation are present in all class D β-lactamases, sequence and structural differences nearby may be responsible for the evolution of carbapenemase activity in the CHDLs. Current and future work aimed at non-covalent inhibitor development in OXA-23, and improved covalent inhibitor design focused on blocking access to the catalytic lysine pocket in OXA-23 and OXA-48 will be presented.

[1] Queenan A.M. & Bush K. (2007). Clin. Microbiol. Rev. 20:440.

[2] Walther-Rasmussen J. & Hoiby N. (2006). J. Antimicrob. Chemother. 57:373.

[3] https://www.cdc.gov/drugresistance/biggest-threats.html

[4] Smith C.A., Antunes N.T., Stewart N.K., Toth M., Kumarasiri M., Chang M., Mobashery S. & Vakulenko S.B. (2013). Chem. Biol. 20:1107.

[5] Golemi D., Maveyraud L., Vakulenko S., Samama J.P. & Mobashery S. (2001). Proc. Natl. Acad. Sci. 98:14280.

[6] Toth M., Smith C.A., Antunes N.T., Stewart N.K., Maltz L. & Vakulenko S.B. (2017). Acta. Crystallogr. D73:692.

[7] Smith C.A., Stewart N.K., Toth M. & Vakulenko S.B. (2019). Antimicrob. Agents Chemother. 63:e01202-19.

The inflammasome signaling pathways are activated by infections and sterile stimulation, which lead to the maturation of inflammatory caspases that promote the secretion of inflammatory cytokines such as IL-1b and IL-18. The recognition and cleavage of the gasdermin family members by caspases trigger the activation of their pore-forming activities that lead to pyroptotic cell death. A prominent example is the targeting of gasdermin D (GSDMD) by inflammatory caspases-1/4/5/11 as an essential step in initiating pyroptosis following inflammasome activation. Previous work has identified cleavage site signatures in caspase substrates such as GSDMD and inflammatory cytokines, but it is unclear if these are the sole determinants for caspase engagement. Here we describe structural studies of a complex between caspase-1 (CASP1) and the full-length GSDMD, which reveals that the cleavage site-containing linker in GSDMD adopts a long loop structure that engages the CASP1 active site. In addition, an exosite is observed between the caspase-1 L2 and L2’ loops and a hydrophobic pocket within the GSDMD C-terminal domain distal to its N-terminal domain. The exosites endows a novel function for the GSDMD C-terminal domain as a caspase-recruitment module, in addition to its role in autoinhibition. The dual site recognition may allow stringent substrate selectivity while facilitating efficient cleavage and pyroptosis upon inflammasome activation. Such mode of tertiary structure recognition may be applicable to other physiological substrates of caspases.

Plants and animals detect pathogen infection via intracellular nucleotide-binding leucine-rich repeat receptors (NLRs) that directly or indirectly recognize pathogen effectors and activate an immune response. How effector sensing triggers NLR activation remains poorly understood. Structure-function studies of these complexes are hampered by low levels in native tissue, our inability to express them recombinantly, and their instability in solution. We overcame sample limitation problems and solved a 3.8 Å resolution cryo-EM structure of the activated ROQ1, an NLR native to N. benthamiana with a Toll-like interleukin-1 receptor (TIR) domain, bound to the Xanthomonas effector XopQ. ROQ1 directly binds to both the predicted active site and surface residues of XopQ while forming a tetrameric resistosome that brings together the TIR domains for downstream immune signaling. Our results suggest a mechanism for the direct recognition of effectors by NLRs leading to the oligomerization-dependent activation of a plant resistosome and signaling by the TIR domain.

Plant nucleotide-binding leucine-rich repeat (NLR) immune receptors recognize pathogen effectors to trigger cell death and confer disease resistance. The Toll/interleukin-1 receptor (TIR) domains of plant NLRs can hydrolyze nicotinamide adenine dinucleotide in its oxidized form (NAD+), which is required for NLR-mediated immune signaling. The Cryo-EM structures of the RPP1 and Roq1 resistosomes show that formation of two asymmetric dimers of TIR domains is critical for the NADase activity. However, the structural mechanism underlying TIR-catalyzed NAD+ cleavage remains unknown. Here, we report a crystal structure of RPP1-TIR in complex with NAD+. The TIR domain forms a tetramer in an asymmetric unit, which is nearly identical with that seen in the RPP1 resistosome. The NAD+ is bound to the catalytic center between the asymmetric head-to-tail TIR homodimers, with the adenosine group contacting one TIR monomer (TIRb) and the phosphate groups and the nicotinamide ribose contacting the other TIR (TIRa). The nicotinamide-ribose bond of NAD+ has been cleaved, and the free nicotinamide stacks against the adenosine group. The carboxylate oxygen of the catalytic Glu158 interacts with the C-2 and C-3 hydroxyl groups of the nicotinamide ribose, and the interactions are highly conserved in the cADPR-bound ADP-ribosyl cyclase CD38. Our study reveals NAD+ recognition mechanism of a plant TIR domain and provides insight into NAD+ hydrolysis catalyzed by the TIR protein.

Most T cells found in jawed vertebrates express functional heterodimeric receptors (TCRs) on their surface formed by either α and β or γ and δ chains. Each chain possesses two domains, an amino-terminal variable domain (V) and a constant domain (C) on the carboxy-terminus (V-C pattern). In most cases, the ability of T cells to recognize diverse antigens relies on the surface (or paratope) located within Vα – Vβ or Vγ – Vδ segments. Recent genomic studies of non-eutherian mammals identified clusters of genes that resemble the classical TCR loci but surprisingly contain an additional variable segment. The functional product common for marsupials and monotremes called ‘μ chain’ was predicted to contain two variable (Vμ and Vμj) and one constant (Cμ) domains. Single cells analysis of blood and spleen from Monodelphis domestica showed that some of the splenic T cells co-express the μ and γ chains suggesting that both polypeptides could form a novel type of T cell receptor, the γμTCR. Using obtained sequences, we generated and structurally characterized two different γμTCRs. Here, we present the novel and unusual architecture of a third lineage of T cell receptor found in marsupials and monotremes [1].

[1] Morrissey K.A., Wegrecki M., Praveena T., Hansen V.L., Bu L., Sivaraman K.K., Darko S., Douek D.C., Rossjohn J., Miller R.D., Le Nours J. The molecular assembly of the marsupial T cell receptor defines a third T cell lineage. SCIENCE, 371, 1383-1388, 2021.

Human surfactant protein D is a collectin and member of the C-type lectin superfamily of proteins that forms an essential part of the mammalian innate immune system. The collectins have been recognised to not only bind to invading pathogens, allowing for recognition by immune cells, but also play an important role in activating and regulating the response of both the innate and acquired immune systems. Crystal structures of a biologically and therapeutically active recombinant homotrimeric fragment of human SP-D (hSP-D) complexed with the inner core oligosaccharides from gram negative bacterial human pathogens Haemophilus influenzae, Salmonella enterica sv Minnesota rough strains [1-2] and Escherichia coli provide unique multiple insights into the recognition and binding of bacterial lipopolysaccharide (LPS) by hSP-D. LPS binding is achieved through calcium dependent recognition of the proximal inner core heptose dihydroxyethyl side chain coupled with specific interactions with the binding site flanking residues Arg343 and Asp325 and evidence for an extended binding site for LPS inner cores. Where this preferred mode of binding is precluded by the crystal lattice, oligosaccharide is bound through a terminal core glucose.

The structures thus reveal that hSP-D specifically and preferentially targets the LPS inner core via the innermost conserved heptose (Hep) with the flexibility and versatility to adopt alternative strategies for bacterial recognition, utilising alternative LPS epitopes including terminal or non-terminal sugars, when the preferred inner core Hep is not available for binding. Alongside binding studies of both whole bacteria and LPS the structures also demonstrate that carbohydrate extensions to the core LPS oligosaccharide, previously thought to be targets for collectins, are important in shielding the more vulnerable target sites in the LPS core. Recent structures of hSP-D bound with small synthetic LPS core component ligands which include phosphorylation of specific carbohydrate residues further demonstrate not only the ability to adopt alternative modes of recognition but also that LPS phosphorylation can provide an additional mechanism by which pathogens can efficiently evade a first-line mucosal innate immune defence.

[1] Clark, H. W., Mackay, R. M., Deadman, M. E., Hood, D. W., Madsen, J., Moxon, E. R., Townsend, J. P., Reid, K. B. M., Ahmed, A., Shaw, A. J., Greenhough, T. J. & Shrive, A. K. (2016). Infection & Immunity 84, 1585.

[2] Littlejohn, J. R., da Silva, R. F., Neale, W. A., Smallcombe, C. C., Clark, H. W., Mackay, R. M. A., Watson, A. S., Madsen, J., Hood, D. W., Burns, I., Greenhough, T. J. & Shrive, A. K. (2018). PLOS One 13, e0199175.

Metabolite based T cell immunity is emerging as a major player in antimicrobial immunity, autoimmunity and cancer. Here, small molecule metabolites were identified to be captured and presented by the major histocompatibility complex (MHC) class-I related molecule MR1 to T cells, namely Mucosal Associated Invariant T cells (MAIT) and diverse MR1-restricted T cells. Both MR1 and MAIT T cell receptors (TCR) are evolutionarily conserved in many mammals, suggesting important roles in host immunity. Namely, during infection with riboflavin-producing microorganisms, MR1 trapped riboflavin-based metabolites and presented on the surface of the antigen-presenting cells encountering the MAIT TCR leading to the activation of the MAIT cells. How modifications to these small molecule-metabolites affect presentation by MR1 and MAIT cell activation remains unclear.
To dissect the molecular basis underpinning MR1 antigen capture and MAIT recognition, we chemically synthesized and characterized a large panel of these naturally occurring metabolites, termed “altered metabolite ligands” (AMLs), and investigated functionally and structurally their impact on the MR1-MAIT axis. Through the generation and detailed analysis of 13 high-resolution MAIT TCR-MR1-AML crystal structures, along with biochemical and functional assays, we show that the propensity of MR1-upregulation on the cell surface was related to the nature of MR1-AML interactions. MR1-AML adaptability and a dynamic compensatory interplay at the TCR-AML-MR1 interface impacted the affinity of the TCR-MR1-AML interaction, which ultimately underscored the ability of the AMLs to activate MAIT cells. Here, I will provide a generalized framework for metabolite recognition and modulation of MAIT cells. Further, I will discuss the design, use and implications of “AMLs” for selective and specific tailoring of T cell immune responses.

1. Awad, W. ^#, Ler, G.M.^# et al. (2020). The molecular basis underpinning the potency and specificity of MAIT cell antigens. Nature Immunology 21, 400-411.
2. Salio, M.^#, Awad, W.^# et al. (2020). Ligand-dependent downregulation of MR1 cell surface expression. PNAS, 117(19), 10465–10475.
3. Awad W, et al. (2020). Atypical TRAV1-2- T cell receptor recognition of the antigen-presenting molecule MR1. J. Biol. Chem. 295(42), 14445–14457.

As part of a continuing project, the challenging room-temperature crystal structures of eight commercial pharmaceutical APIs have been solved by Monte Carlo simulated annealing techniques using synchrotron X-ray powder diffraction data (11-BM at APS), and optimized using density functional techniques. Tofacitinib dihydrogen citrate (Xeljanz®), (C15H21N6O)(H2C6H5O7), crystallizes in P212121 with a = 5.91113(1), b = 12.93131(3), c = 30.43499(7) Å, V = 2326.411(6) Å3, and Z = 4. All of the “interesting” hydrogn atoms could be located by analysis of potential hydrogen bonding patterns. Eltrombopag olamine Form I (Promacta®), (C2H8NO)2(C25H20N4O4) crystallizes in P21/n with a = 17.65884(13), b = 7.55980(2), c = 22.02908(16) Å, β = 105.8749(4)̊, V = 2828.665(11) Å3, and Z = 4. The initial structure solution reversed the orientation of one of the cations. Levocetirizine hydrochloride Form I (Zyzal), C21H27ClN2O3Cl, apparently crystallizes in P21/n (even though it is a chiral molecule and exhibits weak second-harmonic generation) with a = 24.1318(21), b = 7.07606(9), c = 13.5205(7), β = 97.9803(4)̊, V = 2286.38(12) Å3, and Z = 4. Edoxaban tosylate monohydrate Form I (Lixiana®), (C24H31ClN7O4S)(C7H7O3S)(H2O), crystallizes in P21 with a = 7.55097(2), b = 7.09010(2), c = 32.08420(21) Å, β = 96.6720(3)̊, V = 1744.348(6) Å3, and Z = 2. Tezacaftor Form A (Symdeko), C26H27F3N2O6, crystallizes in C2 with a = 21.05142(2), b = 6.60851(2), c = 17.76032(5) Å, β = 95.8255(2)̊, V = 2458.027(7) Å3, and Z = 4. Pomalidomide Form I (Pomalyst), C13H11N3O4, crystallizes in P-1 with a = 7.04742(9), b = 7.89103(27), c = 11.3106(6) Å, α = 73.2499(13), β = 80.9198(9), γ = 88.5969(6)̊, V = 594.618(8) Å3, and Z = 2. Palbociclib isethionate Form B (Ibrance®), (C24H30N7O2)(C2H5O4S), crystallizes in P-1 with a = 8.71337(4), b = 9.32120(6), c = 17.73722(20) Å, α = 80.0258(5), β = 82.3581(3), γ = 76.1560(2)̊, V = 1371.284(5) Å3, and Z = 2. Osimertinib mesylate Form B (Tagrisso), (C28H34N7O2)(CH3O3S) crystallizes in P-1 with a = 11.4291(3), b = 11.7223(4), c = 13.3221(4), α = 69.0246(8), β = 74.5906(7), γ = 66.4001(7)̊, V = 1511.466(13) Å3, and Z = 2. Other new structures may be discussed as they become available.

Structure determination of organic materials directly from powder X-ray diffraction (XRD) data [1,2] is now carried out extensively by researchers in both academia and industry. Most research in this field uses the direct-space strategy for structure solution [3,4] followed by Rietveld refinement. Although the structure determination process is generally carried out solely using powder XRD data, significant advantages may be gained by augmenting the process of structure determination from powder XRD data by utilizing information obtained from other experimental and computational techniques. Such multi-technique approaches are particularly advantageous in tackling complex and challenging structure determination problems, both by providing independent information that may be used directly to facilitate the structure determination process and by allowing robust validation of the final structure obtained in the Rietveld refinement. The lecture will focus on the use of solid-state NMR spectroscopy and periodic DFT-D calculations to augment the process of structure determination of organic materials from powder XRD data [5-11]. The lecture will present several case studies from recent research, including several examples of polymorphic systems and pharmaceutical materials. Recent examples exploiting the complementary advantages of 3D electron diffraction data and powder XRD data within the structure determination process will also be presented.

[1] Harris, K. D. M., Tremayne, M. & Kariuki, B. M. (2001) Angew. Chemie Int. Ed. 40, 1626.

[2] Harris, K. D. M. (2012) Top. Curr. Chem. 315, 133.

[3] Harris, K. D. M., Tremayne, M., Lightfoot, P. & Bruce, P. G. (1994) J. Am. Chem. Soc. 116, 3543.

[4] Kariuki, B. M., Serrano-González, H., Johnston, R. L. & Harris, K. D. M. (1997) Chem. Phys. Lett. 280, 189.

[5] Dudenko, D. V., Williams, P. A., Hughes, C. E., Antzutkin, O. N., Velaga, S. P., Brown, S. P. & Harris, K. D. M. (2013) J. Phys. Chem. C 117, 12258.

[6] Williams, P. A., Hughes, C. E. & Harris, K. D. M. (2015) Angew. Chemie Int. Ed. 54, 3973.

[7] Watts, A. E., Maruyoshi, K., Hughes, C. E., Brown, S. P. & Harris, K. D. M. (2016) Cryst. Growth Des. 16, 1798.

[8] Hughes, C. E., Reddy, G. N. M., Masiero, S., Brown, S. P., Williams, P. A. & Harris, K. D. M. (2017) Chem. Sci. 8, 3971.

[9] Hughes, C. E., Boughdiri, I., Bouakkaz, C., Williams, P. A. & Harris, K. D. M. (2018) Cryst. Growth Des. 18, 42.

[10] Al Rahal, O., Hughes, C. E., Williams, P. A., Logsdail, A. J., Diskin-Posner, Y. & Harris, K. D. M. (2019) Angew. Chemie Int. Ed. 58, 18788.

[11] Al Rahal, O., Williams, P. A., Hughes, C. E., Kariuki, B. M. & Harris, K. D. M. (2021) Cryst. Growth Des. 21, 2498.

Crystal engineering has emerged as an important field of solid-state chemistry, developing tools to deliberately design functional organic solids. A particularly exciting aspect of crystal engineering is the tuneability of physicochemical properties of organic solids such as solubility, thermal stability, bioavailability etc. without altering the underlying molecular structure(s) – a concept of high relevance for pharmaceutical industry.^[1] Altering physisochemical properties can be achieved by relying on different solid forms, such as polymorphs, cocrystals, and salts.^[2] The latter two are multicomponent systems that, in organic solids, are essentially distinguished by the position of a proton within the crystal structure. While different chemical systems can appear in different forms, proton transfer has rarely been observed for multicomponent systems with identical stoichiometric composition.^[3]

In this contribution, we present an extremely rare case of polymorphism between a metastable molecular (cocrystal) and ionic (salt) form of a two-component system based on nicotinamide and a dicarboxylic acid, induced by supramolecular tautomerism. In specific, we show the polymorphic transition from a metastable cocrystal to a salt, monitored using time-resolved powder X-ray diffraction (PXRD) and solid-state nuclear magnetic resonance spectroscopy. Both formerly unknown structures of were solved ab initio from PXRD data and further analyzed using spectroscopic methods, as well as density functional theory calculations.

Figure 1: Monitoring the polymorphic transition from metastable cocrystal to salt using (a) PXRD and (b) ¹⁵N ssNMR spectroscopy.

[1] Almarsson, O. & Zaworotko, M, J. (2004). Chem. Commun., 17, 1889-1896. [2] Aitipamula, S. et al. (2014), Cryst. Growth Des., 12, 2147−2152 [3] Bernasconi, D., Bordignon, S., Rossi, F., Priola, E., Nervi, C., Gobetto, R., Voinovich, D., Hasa, D., Tuan Duong, N., Nishiyama, Y., Chierotti, M. R., (2020). Cryst. Growth Des., 20, 906-915.

In the pharmaceutical crystal, hydration/dehydration phase transitions are often observed phenomena during manufacturing or storage. They lead the substantial crystal structure change, so they are critical for the important physicochemical properties that depend on the crystal structure, such as stability, solubility, and bioavailability. However, after dehydration, single-crystal integrity tends to degrade, resulting in powdery crystals. We have successfully revealed solid-state structural rearrangements using ab initio Structure Determination from Powder X-ray Diffraction data (SDPD) technique [1-4]. Interestingly, some crystals show "isomorphic desolvation," in which the XRD pattern does not change significantly after dehydration, meaning the initial molecular arrangement is well preserved. We can reveal an isomorphic desolvation mechanism by comparing the crystal structures from powdery crystals in the hydration/dehydration phase transitions, which can be achieved using the SDPS technique.

Carbazochrome sodium sulfonate trihydrate, a hemostatic agent, undergoes stepwise dehydration by humidity control or heating. The hydration number decreased from 3 to 2.5, 2, 1, and anhydrous form I under dry condition, and it showed isomorphic desolvation (Fig. 1). Their crystal structures were analysed by SDPD technique to show the API molecules are linked through Na cations to form polymeric structure, and the molecular arrangements were very similar. It is noteworthy that the first dehydration did not occur at non-coordinated crystalline water C, but water molecules A and B which coordinated to Na cation were dehydrated in sequence. This removal order was explained by the crystal structures' stability after each dehydration, calculated using CASTEP quantum mechanics calculations. Even after dehydration, the molecular arrangements were almost kept by adjusting the molecular positions slightly. After removing crystalline water C, the crystallinity degraded significantly, indicating the molecule C is essential for stabilizing the whole crystal structure. Thus, the mechanism of the stepwise dehydration behaviour, and isomorphic desolvation were revealed by SDPD technique.

Figure 1. Chemical diagram and molecular arrangement of trihydrate, dihydrate, and monohydrate phases of Carbazochrome sodium sulfonate.

[1] Fujii, K., et al. (2010) J. Phys. Chem. C 114, 580.

[2] Fujii, K., Uekusa H., Itoda N., Yonemochi E. & Terada K. (2012) Cryst. Growth Des. 12, 6165.

[3] Fujii, K., Aoki, M. & Uekusa, H. (2013) Cryst. Growth Des. 13, 2060.

[4] Putra, O. D., Yonemochi, E., Pettersen A. & Uekusa H. (2020) CrystEngComm 22, 7272.

Keywords: Structure Determination from Powder X-ray Diffraction data; dehydration; crystal structure, pharmaceutics; quantum mechanics

Part of this work was supported by JSPS KAKENHI Grant Number JP18H04504 and 20H04661 (HU).

Trichlormethiazide is a thiazide derivative, an important group of diuretic drugs, which is used in the treatment of hypertension. The Cambridge Structural Database (CSD) contains only one report (KIKCUD) associated with this pharmaceutical [1], corresponding to the orthorhombic form of anhydrous S-Trichlormethiazide. The PDF-4/Organics database contains two entries. One is the calculated pattern of the CSD entry (PDF 02-094-5865) and the other is an experimental unindexed pattern (PDF 00-039-1828). In this contribution the structure of racemic Trichlormethiazide was determined from laboratory X-ray powder diffraction data. This material was also characterized by FT-IR, TGA and DSC. The structure was determined with DASH [2] and refined by the Rietveld method with TOPAS-Academic [3]. The final unit-cell parameters are a = 8.4389(6), b = 8.8929(7), c = 9.7293(8) Å, α = 91.315(3)°, β = 106.113(2)°, γ = 97.1580(17)°, V = 694.73(9) ų, Z = 2. The refinement converged to R_p = 0.0512, R_wp = 0.0694, and GoF = 2.704. In the crystal structure, the molecules form chains along the a-axis connected by cyclic N-H···N and N-H···Cl hydrogen bonds. The chains are connected by additional cyclic N-H···Cl hydrogen bonds to form layers almost parallel to the ab plane. The fingerprint plots and energy frameworks diagrams of S and racemic forms clearly show the different intermolecular interactions and their topologies. A detailed discussion will be present in this work.

Ab initio structure determination from Powder X-ray Diffraction (PXRD) data is continuously demonstrating its merit thanks to advances in modern phasing algorithms, computing power and X-ray instrumentation. As the technique has long passed the question “can it be done”, there is another question to answer: “how far can it be pushed”. In this respect, this presentation has two aims: (i) to show methodologies that allow for solving of difficult structures of organic molecules and (ii) to highlight the level of accuracy that can be obtained from PXRD data.

This presentation is focused on structure determination of crystals that feature large molecules, disorder, or radiation-induced changes. The first part of the presentation outlines a phasing methodology that can result in an interpretable structural model. The methodology relies on the phasing process in the charge-flipping program [2] Superflip [3] by introducing a partial or incorrect structure obtained by a direct-space algorithm FOX [4]. The second part of the presentation will address structure completion and refinement, and highlight examples of how high quality data can be used for restraint-free Rietveld refinement, modeling disorder from difference Fourier map, and for obtaining insights in bond order disambiguation.

While the majority of shown examples rely on PXRD data collected at synchrotron sources, the potential of data collected in a laboratory diffractometer will also be discussed.

[1] Šišak Jung, D. et al. (2014). J. Appl. Cryst. 47, 1569-74
[2] Oszlanyi, G., Sütő, A. (2004). Acta Cryst. A60, 134-141
[3] Palatinus, L., Chapuis, G. (2007). J. Appl. Cryst. 40, 786-790
[4] Favre-Nicolin, V., Černý, R. (2004). Z. Kristallogr. 219(12), 847-856.

It is of interest to build realistic charge distribution models of biological macromolecules. For this purpose, there are computationally efficient approaches based on transferable building blocks. Transferable quantities can be electron density parameters of atoms or of functional groups, or localized orbitals giving access to molecular charge distributions [1]. The first case is at the basis of libraries of transferable multipolar pseudoatoms built either from X-ray diffraction experiment [2], or from single point quantum calculations [3,4]. Electron density parameters transferred to molecular structures from these libraries are however either averaged, or issued from gas-phase quantum calculations. They are therefore practically devoid of any intermolecular effects due to the non-covalently bonded environment. These effects should be accounted for, especially in protein-ligand complexes.

To compensate this drawback, we implemented in the MoProViewer software methods designed to account for intermolecular dipolar induction in a transferred multipolar electron distribution [5]. For this purpose, atomic anisotropic polarizabilities have been added to the definition of transferable multipolar pseudoatoms, as defined in the ELMAM2 library.

The construction of this database of polarizabilities associated to ELMAM2 transferable pseudoatoms will be described, and comparisons of the resulting polarization energies against a theoretical reference will be presented. Finally, application examples on protein ligand complexes will be discussed.

[1] Meyer B, Guillot B, Ruiz-Lopez M & Genoni A (2016). J. Chem. Theory Comput, 12, 1052.

[2] Domagala S, Fournier B, Liebschner D, Guillot B & Jelsch C (2012). Acta Cryst. A68, 337.

[3] Kumar P, Gruza B, Bojarowski S.A, Dominiak P.M. (2019). Acta Cryst. A75, 398.

[4] Dittrich B, Hübschle CB, Pröpper K, Dietrich F, Stolper T & Holstein JJ (2013). Acta Cryst. B69, 91.

[5] Leduc T, Aubert E, Espinosa E, Jelsch C & Guillot B (2019) J. Phys. Chem. A, 123, 7156.

Single-molecule magnet (SMM) is the generic name given to a broad class of molecules, which exhibit an energy barrier to magnetization reversal. In simpler terms, SMMs have that special trait that once they have become magnetized by an external magnetic field, the induced magnetic moment (which we, for simplicity, could call spin up or spin down) resists reorientation. For that reason, such fascinating molecules are envisaged to act as molecular bits, or quantum bits, qubits. The origin of this effect is magnetic anisotropy, i.e. the different magnetic response to an external field (quantified by the magnetic susceptibility) depending on the relative orientation of field and molecule. Magnetic anisotropy splits the magnetic substates, and the reason for this is the presence of unquenched orbital angular momentum. Thus, at the very core, to be able to develop novel SMMs we need to understand how to control the electronic ground state of a complex. This has followed two paths, depending on whether the electron-carrier is a 3d or 4f element.

For 4f-based SMMs, a widespread approach has aimed at developing complementary ligand fields relative to the valence electron density shape of the most magnetic Mj-state of the 4f-ion in question. However simple and unvalidated by experiment, this approach has been fantastically useful. Recently, we showed how the experimental electron density from X-ray diffraction could reveal hitherto unseen details in the electronic structure of a Dy-based SMM, thus elucidating the mechanism[1]. For 3d-systems, the ligand field is much stronger and the approach is thus different. The magnetic anisotropy is enhanced in distorted tetrahedral complexes of Co^II, as has recently been shown[2-4].

Herein, I will show how a combination of high-resolution synchrotron X-ray diffraction (XRD) and polarized neutron diffraction (PND) can be used to quantify the magnetic anisotropy in [CoX₂tmtu₂] (X=Cl, Br, tmtu = tetramethylthiourea). The XRD data provides a multipole model of the electron density, while the PND provides the full magnetic susceptibility tensor. The experimental results are supported by ab initio calculations.

Figure 1. ORTEP drawing of the Cl-complex studied here based on 20 K synchrotron data, showing 90% ellipsoids.

[1] Gao, C., Genoni, A., Gao, S., Jiang, S., Soncini, A. & Overgaard, J. (2020). Nat. Chem. 12, 213.

[2] Vaidya, S., Shukla, P., Tripathi, S., Rivière, E., Mallah, T., Rajaraman, G. & Shanmugam, M. (2018). Inorg. Chem. 57, 3371.

[3] Rechkemmer, Y., Breitgoff, F. D., van der Meer, M., Atanasov, M., Hakl, M., Orlita, M., Neugebauer, P., Neese, F., Sarkar, B. & van Slageren, J. (2016). Nat. Commun. 7, 10467.

[4] Damgaard‐Møller, E., Krause, L., Tolborg, K., Macetti, G., Genoni, A. & Overgaard, J. (2020). Angew. Chem. Int. Ed. 59, 21203.

X-ray charge density is the most powerful experimental method to study interatomic and intermolecular interactions, such as two-electron multicentric (2e/mc) covalent bonding [1-3]. However, it is limited to high-quality crystals and good enough data can be collected only at low temperature and ambient pressure. In order to gain more information on behaviour of novel 2e/mc interactions, a broader range of conditions (temperatures and pressures) are required. These are normally limited to resolutions of 0.8 Å or lower and are thus unsuitable for multipolar refinement and study of charge density.

If good high-resolution diffraction data are not available, charge density can be obtained using transferrable multipoles from optimal data set [4]. Thus, multipoles obtained by multipolar refinement of high-resolution data can be transferred to lower-resolution variable-temperature (VT) and high pressure (HP) diffraction data, allowing us to study charge density at a broad range of conditions. We have tested this method in study of 2e/mc bonding in 4-cyano-N-methylpyridinium salt of 5,6-dichloro-2,3-dicyanosemiquinone radical anion ([4-CN-N-MePy]⁺[DDQ]^-), which we have recently studied by VT and HP X-ray diffraction [5] and by X-ray charge density [6]. Multipolar parameters obtained by a multipolar refinement of high-resolution data measured at 100 K [6] were thus transferred to lower-resolution VT and HP data; the results and their validity are discussed. Since 2e/mc is an intermolecular interaction, which involves a non-localised electron pair, its electron density is low; so its study is less reliable than that of stronger intramolecular covalent bonding. Therefore, our transferred-multipole models must satisfy the following three criteria to be considered valid:

(i) overall reduction of disagreement R-factors and residual density compared to regular spherical refinement;

(ii) electron densities should follow a clearly defined trend;

(iii) experimentally obtained electron densities should be in a good agreement with theoretical ones.

[1] Kertesz, M. (2018). Chem. Eur. J., 25, 400-416.

[2] Molčanov, K. & Kojić-Prodić, B. (2019). IUCrJ, 6, 156-166.

[3] Molčanov, K.; Milašinović, V. & Kojić-Prodić, B. (2019). Cryst. Growth Des., 19, 5967-5980.

[4] Domagała, S.; B. Fournier, D. Liebschner, B. Guillot, Jelsch, C. (2012). Acta Cryst. A., A68, 337-351.

[5] Bogdanov, N. E.; Milašinović, V.; Zahkarov, B.; Boldyreva, E. V.; Molčanov, K. (2020). Acta Cryst. B., B76, manuscript XK5067, in print.

[6] Milašinović, V.; Krawczuk, A.; Kojić-Prodić, B.; Molčanov, K. (2020). Manuscript in preparation.

Keywords: charge density; high pressure; variable temperature; transferrable multipoles; two-electron multicentric bonding

This work was funded by the Croatian Science Foundation, grant no. IP-2019-04-4674.

Non-covalent interactions uniquely define the structure of macromolecules. Therefore, a thorough analysis of the non-covalent interaction network is crucial to gain insights into functions and dynamics of macromolecules.

A strategy that is able to detect non-covalent interactions for a large variety of molecules is the Non-Covalent Interactions (NCI) method [1,2], a technique simultaneously based on the electron densities and the reduced density gradients of the molecules under exam. Unfortunately, accurate molecular electron densities can be obtained through traditional quantum chemistry computations at a feasible computational cost only for small to medium-sized systems, whereas these calculations become impractical for larger molecules. Therefore, until now, for NCI analyses on large systems one had to resort to the promolecular density approximation, where the electron density of the investigated molecule is described as a sum of independent and spherically averaged atomic densities. These promolecular densities lack accuracy, and although they might lead to visually similar results when compared to those obtained from fully quantum mechanical calculations, the underlying electron density is known to be incorrect. Hence, the analysis of the non-covalent interactions is also biased.

To overcome the previous shortcoming, one should exploit techniques that allow to rapidly obtain accurate and reliable electron densities for macromolecules. In this context, one possibility is represented by the recently constructed database of extremely localized molecular orbitals (ELMOs) [3-5]. In fact, ELMOs are orbitals strictly localized on small molecular fragments, i.e. atoms, bonds or functional groups [3]. Due to this strict localization, they are easily transferable from one molecule to another, provided that the subunits on which they are localized have the same chemical environment in the starting and final systems [3,4]. By exploiting this intrinsic transferability, a databank of ELMOs has been constructed [5]. It currently contains orbitals associated with all the fragments for the twenty natural amino acids and allows rapid and reliable reconstructions of wavefunctions and electron densities of very large biomolecules.

The coupling of the NCI technique with the ELMO database gave rise to the new NCI-ELMO method [6] that was successfully applied to analyse a variety of non-covalent interactions in polypeptides and proteins. Test calculations showed that qualitative results obtained with the NCI-ELMO technique are very similar to the ones based on fully quantum chemical calculations, but definitely better than those resulting from the promolecular-NCI approach. In this presentation, the previously mentioned qualitative results [6] will be discussed. Additionally, we will illustrate how the new NCI-ELMO technique has been recently extended to quantify non-covalent interactions. Other than applications to protein-ligand interactions, we will show the results of benchmark calculations on smaller systems (e.g., simple molecular dimers) to highlight the differences between the NCI-ELMO and promolecular-NCI approaches also at a quantitative level.

[1] Johnson, E. R.; Keinan, S., Mori-Sanchez, P., Contreras-García, J., Cohen, A. J. & Yang, W. (2010). J. Am. Chem. Soc. 132, 6498.

[2] Contreras-García, J., Johnson, E., Keinan, S., Chaudret, R., Piquemal, J.-P., Beratan, D. & Yang, W. (2011). J. Chem. Theory Comput. 7, 625.

[3] Meyer, B., Guillot, B., Ruiz-Lopez, M. F. & Genoni, A. (2016). J. Chem. Theory Comput. 12, 1052.

[4] Meyer, B., Guillot, B., Ruiz-Lopez, M. F., Jelsch, C. & Genoni, A. (2016). J. Chem. Theory Comput. 12, 1068.

[5] Meyer, B. & Genoni, A. (2018). J. Phys. Chem. A 122, 8965. [6] Arias Olivares, D., Wieduwilt, E. K., Contreras-García, J. & Genoni, A. (2019). J. Chem. Theory Comput. 15, 6456.

Eutectics are well-known multi-component systems used in various day-to-day applications. However, they are enigmatic in terms of structural organization (interactions and packing, the two prime features of a crystalline entity), despite having a long history. At the microstructural level, they are phase-separated (multi-phasic) solid solutions i.e. they are heterogeneous crystalline materials composed of homogeneous (single-phase) but multiple solid solutions [1]. This phase heterogeneity in structural integrity is what makes them complex-to-understand materials. Although research has been done in understanding the eutectic structural organization particularly in inorganic systems using advanced techniques such as atomic pair distribution function (PDF) analysis, X-ray microtomography, and atomic force microscopy (AFM), no comprehension of eutectic microstructural integrity was achieved [2]. Furthermore, the structural and microstructural arrangement of organic eutectic systems has not been addressed so far in the literature [3,4]. This complexity in organic eutectic systems is augmented by several aspects such as 1) the constituents are primarily C, H, N and O which makes them soft materials, 2) atomic number contrast essential to image the microstructure is lacking, 3) frequent existence of polymorphism, 4) occurrence in lower structural symmetry. In this regard, one can transfer the knowledge of inorganic eutectics to organic eutectics or can verify the organic eutectics with competent experimental techniques in search of an improvised understanding from the molecular perspective. Here, we manage to solve the microstructural features of organic eutectics through in-situ variable temperature (VT) PXRD experiments, DSC experiments with multiple heating and cooling cycles, in-situ VT Raman spectroscopic studies, gas-phase energy calculations using Gaussian09 and electron microscopy imaging technique on a series of systems. We observe for the first time, the evolution of eutectic systems through the formation of multi-domain eutectic particles at higher temperatures. The eutectic particles melt altogether near the melting point of the eutectic system as showed in DSC experiments, via thermal energy induced heteromolecular interaction through the domain boundaries as confirmed from VT-Raman studies.

A key feature of metal-organic frameworks (MOFs) is their ability to capture, transport, and release guest molecules. The nature, quality, and quantity of the associated absorption depend on pore size and volume, surface area, solvent, and in particular the host-guest intermolecular interactions.

Various methods for the analysis of intermolecular interactions have been described in the literature and were applied to study e.g. chemical reactivity, catalysis, biomolecular interactions, or organic electronics. However, the application of such methods to host-guest interactions in MOFs is still scarce. For this reason, we computed periodic and finite wavefunctions for well-chosen MOF-guest systems and tested these tools [1]. This includes the interaction energy, its decomposition with different energy decomposition schemes, investigation of the electron density with Bader’s quantum theory of atoms in molecules, the non-covalent interaction index [2], or the density overlap regions indicator [3]. This analysis contributes to the understanding of host-guest interactions, with the ultimate goal of rationally designing MOFs for targeted applications.

[1] Ernst, Michelle; Gryn'ova, Ganna (2021): Strength and Nature of Host-Guest Interactions in Metal-Organic Frameworks from a Quantum-Chemical Perspective. ChemRxiv. Preprint. https://doi.org/10.26434/chemrxiv.14363024.v1

[2] Johnson, E. R., Keinan, S., Mori-Sánchez, P., Contreras-García, J., Cohen, A. J., & Yang, W. (2010). J. Am. Chem. Soc. 132, 6498.

[3] De Silva, P., & Corminboeuf, C. (2014). J. Chem. Theory Comput. 10, 3745

That composition and structure profoundly impact the properties of crystalline solids has provided impetus for exponential growth in the field of crystal engineeringover the past 25 years. Crystal engineering has evolved from structure design (form) to control over bulk properties (function). Today, when coupled with molecular modeling, crystal engineering can offer a paradigm shift from the more random, high-throughput methods that have traditionally been utilized in materials discovery and development. Custom-design of the right crystalline material for the right application could therefore be at hand.

Porous crystalline materials exemplify this situation. Whereas purely inorganic materials (e.g. zeolites) and those based upon coordination chemistry (e.g. Metal-Organic Frameworks, MOFs, and Porous Coordination Polymers, PCPs) are well studied and offer great promise for separations and catalysis, they are often handicapped by cost or performance (e.g. poor chemical stability, interference from water vapour, low selectivity) limitations. Ultramicroporous Materials, UMs, are built from metal or metal cluster “nodes” and combinations of organic and inorganic “linkers” and their pore chemistry and size (< 0.7 nm) can overcome some of the weaknesses of existing classes of porous material (Figure 1). Three families (platforms) of UMs will be detailed and their performance with respect to important gas separation (e.g. CO₂ capture [1], C₂H₂ capture [2]) and water purification applications will be discussed. Most recently, we have shown that UMs can function synergistically to address complex gas mixtures [3] or perform effectively for CO₂ capture even in the presence of humidity [4].

[1] Nugent, P. Nugent, P.; Belmabkhout, Y.; Burd, S.D.; Cairns, A.J.; Luebke, R.; Forrest, K.; Pham, T.; Ma, S.; Space, B.; Wojtas, L.; Eddaoudi, M.; Zaworotko, M.J. (2013) Nature 495, 80-84.

[2] Cui, X.; Chen, K.J.; Xing, H.; Yang, Q.; Krishna, R.; Bao, Z.; Wu, H.; Zhou, W.; Dong, X.; Li, B.; Ren, Q.; Zaworotko, M.J.; Chen, B. (2016). Science 353, 141-144.

[3] Chen, K.J.; Madden, D.G.; Mukherjee, S.; Pham, T.; Forrest, K.A.; Kumar, A.; Space, B.; Kong, J.; Zhang, Q.Y. Zaworotko, M.J. (2019). Science, 366, 241-246.

[4] Mukherjee, S.; Sikdar, N.; O’Nolan, D.; Franz, D.M.; Gascon, V.; Kumar, A.; Kumar, N.; Scott, H.S.; Madden, D.G.; Kruger, P.E.; Space, B.; Zaworotko, M.J. (2019). Science Adv. 5, eaax9171.

Noncovalent interactions play a fundamentally important role in the properties of solid materials. For instance, guests are taken up into the host framework of porous materials as a result of the interactions between these species, while the manner in which they interact has an influence on the sorption ability of the porous material. In this work calculations on a range of porous frameworks allow us to explain the role that noncovalent interactions play in the sorption properties of these compounds. For instance, the origin of anomalous sorption isotherms are shown to be the result of interactions between acetylene^[1] or carbon dioxide^[1,2] and the host frameworks, as well as interactions between guests. Similarly, noncovalent interactions are responsible for the change in colour along an hourglass pattern of a crystalline porous compound during sorption of particular solvents. Calculations show that the origin of this effect is that the channels in the porous framework are anisotropic, allowing sorption only from particular faces.^[3]

References

[1] Jacobs, T.; Lloyd, G. O.; Gertenbach, J. A.; Esterhuysen, C.; Müller-Nedebock, K. K.; Barbour, L. J., Angew. Chem. Int. Ed., 2012, 51, 4913-4916.

[2] Bezuidenhout, C. X.; Smith, V. J.; Bhatt, P. M.; Esterhuysen, C.; Barbour, L. J., Angew. Chem. Int. Ed. 2015, 54, 2079–2083.

[3] Bezuidenhout, C. X.; Esterhuysen, C.; Barbour, L. J., Chem. Commun., 2017, 53, 5618–5621.

Mesoporous materials are excellent materials to be used in energy and environmental related applications. Methods to characterize the pore structures and the filling and emptying processes are physisorption and small-angle scattering. Gas physisorption in mesoporous materials and the associated capillary hysteresis intrigue the scientific community since decades. These phenomena are largely exploited for the characterization of porous solids, which justify the strong need for their complete understanding. To date, the major hurdle lies in a reliable description of the state of the confined fluid, which is usually given by measuring macroscopic observable, i.e. the amount of adsorbed gas.

Despite computational methods, in situ techniques combining gas physisorption with X-ray scattering methods showed in the last years to be valuable tools to get deeper insights into gas adsorption phenomena [1, 2]. Combining the different contrasts of SAXS and SANS and applying contrast matching [1], a more detailed, locally resolved description of the process could be given by the analysis of the scattering signals of the material pore structure. However, clear and comprehensive assessment of the adsorption process is still missing since the adsorbate evolution in the mesoporous host could be only indirectly investigated.

This presentation deals with the development of a novel in situ method based on the combination of anomalous small-angle X-ray scattering (ASAXS) and X-ray absorption near edge structure (XANES) spectroscopy to directly probe the evolution of the xenon adsorbate phase in mesoporous silicon during gas adsorption at its boiling point of 165 K [3]. The interface area and size evolution of the confined xenon phase alone were determined from ASAXS demonstrating that filling and emptying the pores follows two distinct mechanisms. The mass density of the confined xenon was found to decrease prior pore emptying. XANES analyses showed that Xe exists in two different species when confined in mesopores. This combination of methods provides a smart new tool for the study of nanoconfined matter for catalysis, battery electrodes, and for gas and energy storage applications.

The instrumental setup used allowed us to reach the Xenon L₃ X-ray absorption edge at 4.781 keV. The combination of that three experiments, ASAXS, XANES and physisorption were done in situ on different points of the adsorption and desorption branch of the isotherm. Thus, from the resonant scattering curves of xenon the mesoscopic evolution of the adsorbate (multilayer formation, capillary condensation and desorption) could be directly investigated.

[1] Mascotto, S., Wallacher, D., Brandt, A., Hauss, T., Thommes, M., Zickler, G. A., Funari, S. S., Timmann, A. & Smarsly, B. M. (2009). Langmuir 25, 12670−12681.

[2] Jähnert, S., Müter, D., Prass, J., Zickler, G. A., Paris, O. & Findenegg, G. H. (2009). J. Phys. Chem. C 113, 15201−15210.

[3] Gericke, E., Wallacher, D., Wendt, R., Greco, G., Krumrey, M., Raoux, S., Hoell, A. & Mascotto, S. (2021). J. Phys. Chem. Lett. 12, 4018−4023.

Mankind is now in the “age of gas”[1] and there are urgent needs in gas purification that will likely only be solved by a new generation of physisorbent porous materials that offer reduced cost and superior performance. Engaging the principles of crystal engineering, hybrid ultramicroporous materials, HUMs (pore size < 0.7 nm) [2], by means of combining small pores (< 0.7 nm) with strong electrostatics offer an ideal sorbent platform suited for tight-fit of the target sorbate, resulting in performance benchmarks over the recent years [3, 4]. However, due to narrow pore networks imposing steric restrictions, crystal engineering of modular HUMs on account of organic ligand functionalisation has remained largely elusive.

Moving one step ahead of the synergistic sorbent separation technology[5], herein we address single-step purification of ethylene (C₂H₄), the highest volume product of the chemical industry, by crystal engineering of two HUMs of formula [Ni(pyz-NH₂)₂(MF₆)]_n (pyz-NH₂ = aminopyrazine, 17; M = Si, Ti), MFSIX-17-Ni [6]. Isostructural pyrazine analogues (SIFSIX-3-Zn [7], SIFSIX-3-Ni [8]) are the benchmark physisorbents for trace carbon capture but are unsuited for acetylene capture. No single physisorbent has the requisite selectivity to purify C₂H₄ from ternary C₂-CO₂ mixtures (C₂H₄/C₂H₂/CO₂) under ambient conditions until now. Indeed, both MFSIX-17-Ni sorbents produce polymer grade ethylene (> 99.95% purity) from a 1:1:1 ternary mixture (Figure 1). Regarding insights for the future, we attribute the observed properties to the unusual binding sites in MFSIX-17-Ni that offer comparable affinity to both CO₂ and C₂H₂, thereby enabling coadsorption of C₂H₂ and CO₂. In situ synchrotron x-ray diffraction, in situ IR spectroscopy and molecular modelling provide insight into these binding sites and why they differ from those of the pyrazine-linked materials.

Metal-Organic frameworks (MOFs) and porous molecular materials represent a new platform for achieving and exploring high-performance sorptive properties and gas transport. The key lies in the modular nature of these materials, which allows for tuning and functionalization towards improved gas capture.

Self-assembly of polyfunctional molecules containing multiple charges, namely, tetrahedral tetra-sulfonate anions and bi-functional linear cations, resulted in a permanently porous crystalline material in which the channels are decorated by double helices of electrostatic charges that governed the association and transport of CO₂ molecules (Fig. 1). These channels electrostatically compliment the CO₂ molecules and forms strong interactions of 35 kJ mol⁻¹, ideal for CO₂ capture/release cycles.[1]

The CO₂ adsorption properties were modulated for an isoreticular series of Fe-MOFs by varying the decoration of fluorine atoms within their channel (Fig. 2). A host of complementary experimental and computational techniques gives a holistic view of the host-CO₂ properties towards the potential selective removal of CO₂ from other gases. GCMC and DFT were employed for a detailed description of the CO₂ diffusion and interactions in the porous materials. CO₂–matrix adsorption enthalpies of 33 kJ mol−1 was accurately measured in-situ by simultaneous acquisition of micro-calorimetric and volumetric-isotherm data. Direct measurements of adsorption heats are not common and such data helps to validate mathematical models and protocols for sorption-derived adsorption enthalpies. [2]

[1] Xing, G.; Bassanetti, I.; Bracco, S.; Negroni, M.; Bezuidenhout, C.; Ben, T.; Sozzani, P.; Comotti, A., Chemical Science 2019, 10 (3), 730-736.

[2] Perego, J.; Bezuidenhout, C. X.; Pedrini, A.; Bracco, S.; Negroni, M.; Comotti, A.; Sozzani, P., Journal of Materials Chemistry A 2020, 8 (22), 11406-11413.

Metal-Organic Frameworks (MOFs) are a class of synthetic porous crystalline materials based on metal ions connected through spacing ligands. They possess interesting properties such as high porosity [1], high concentration of metal centres and flexibility [2]. Additionally, MOFs can maintain their crystal structure upon removal, inclusion, exchange or reaction of a wide selection of guests, making them useful for multiple applications, e.g. in selective gas adsorption/separation. The synthesis of chemically and thermally stable MOFs, the comprehension of their properties and knowledge of their crystallographic features, are indispensable for the design and development of well performing materials. As MOFs’ properties are intrinsically related to their crystal structure, a deep understanding of the host-guest interactions during adsorption processes is a fundamental aspect [3].

Here, a high-resolution powder X-ray diffraction (HR-PXRD) crystallographic study of the host-guest interactions in Fe₂(BDP)₃ [H₂BDP = 1,4-bis(pyrazol-4-yl)benzene] upon CO₂ adsorption is presented. This MOF is characterised by a 3D network with 1D triangular channels. The peculiar shape of its channels and its good Brunauer-Emmett-Teller specific surface area (1230 m²/g) [4] prompted its investigation as CO₂ storage material, revealing an uptake capacity of 298.0 cm³/g at P_CO2 = 0.99 bar and T = 195 K.

At the ESRF ID22 beamline, HR-PXRD data were collected in situ and operando at T = 273 and 298 K while varying the CO₂ loading in the pressure range 0-8 bar. The obtained results will be presented after an in-depth data analysis, ranging from assessment of unit cell parameters variation to location of the primary adsorption sites and quantification of the adsorbed guest (Fig. 1). These results provide key information to better understand the CO₂-host interactions during the whole adsorption process, thus disclosing the chemical and structural features a MOF should possess to favour CO₂ uptake at mild conditions.

[1] I. M. Hönicke, I. Senkovska, V. Bon, I. A. Baburin, B. S. Raschke, J. D. Evans, S. Kaskel, Angew. Chem. 2018, 57, 42, 13780-13783 [2] A. Schneemann, V. Bon, I. Schwedler, I. Senkovska, S. Kaskel, R. A. Fischer, Chem. Soc. Rev. 2014, 43, 6062-6096; J. H. Lee, S. Jeoung, Y. G. Chung, H. R. Moon, Coord. Chem. Rev. 2019, 389, 15, 161-188 [3] C. Giacobbe, E. Lavigna, A. Maspero, S. Galli, J. Mater. Chem. A 2017, 5, 16964 [4] Z. R. Herm, B. M. Wiers, J. A. Mason, J. M. van Baten, M. R. Hudson, P. Zajdel, C. M. Brown, N. Masciocchi, R. Krishna, J. R. Long, Science 2013, 340, 960-964

Oxygen deficient perovskites are investigated as oxygen carriers for many different energy applications, based on the possibility to change their oxygen content while maintaining the cation framework. The most well-known oxygen deficient perovskite type structure is brownmillerite, with alternating layers of octahedra and tetrahedra. However, even for this common structure there are complexities such as ordered rotations of tetrahedra that are often missed during structure determination using, for example, powder diffraction, resulting in the persistent use in literature of inaccurate structure models for DFT calculations and properties explanations. When the extra reflections corresponding to the anion related order are picked up in single crystal neutron or X-ray diffraction, the refinement is often still hindered by high amounts of twinning or correlated disorder. In such cases, TEM can shed a light on the structure, in the past through mostly qualitative techniques like high resolution imaging of the structure and visualization of the reflections using electron diffraction, nowadays also through refinement of the structure from single crystal 3DED data. Electron diffraction is more sensitive to low Z atoms such as oxygen next to heavier atoms than X-rays and can be used on submicron sized crystals; the problems there once were with dynamical scattering are overcome using 3DED [1] combined with dynamical refinement [2]. Using TEM, compounds that were commonly accepted to be brownmillerites were proven to have a completely different anion deficient perovskite type structure, for example Pb₂Fe₂O₅ [3] and related compounds, "disordered" brownmillerites like Sr₂Fe₂O₅ [4] and Sr₂Co₂O₅ [5] were shown be ordered, and clear oxygen-vacancy order that escaped characterization with other techniques was found in many oxygen deficient perovskites, such as in LaSrCuO_3.5 [6] and SrMnO_3.5 [7]. So far, such crystal structures were derived in TEM experiments after reduction outside the microscope, however, the results of the first in situ 3DED redox experiments will also be shown, which allow to follow the structure evolution between oxygen deficient and oxidized perovskite by acquiring in situ 3DED data on submicron sized single crystals in different oxidizing and reducing gasses. In short, I will show that there might be more complexity underlying still many published structures, which we are now better equipped to uncover using electron crystallography, no longer only by observing the superstructures but now also by quantifying them, reliably refining the structures and taking control of the oxygen content during the TEM experiments themselves.

[1] Kolb, U., Gorelik, T., Kübel, C., Otten, M.T., Hubert, D. (2007) Ultramicroscopy 107, 507. [2] Palatinus, L., Petříček, V., Antunes Corrêa, C. (2015) Acta Crystallogr., Sect. A: Found. Adv. 71, 235-244 [3] Abakumov, A.M., Hadermann, J., Bals, S., Nikolaev, I.V., Antipov, E.V., Van Tendeloo, G.(2006) Angew. Chemie Int. Ed. English. 45, 6697–6700

[4] D’Hondt, H., Abakumov, A.M., Hadermann, J., Kalyuzhnaya, A.S., Rozova, M.G., Antipov, E.V., Van Tendeloo, G., (2008) Chem. Mater. 20, 7188–7194

[5] Sullivan, E., Hadermann, J., Greaves, C. (2011) J. Solid State Chem. 184, 649–654

[6] Hadermann, J., Pérez, O., Créon, N., Michel, C., Hervieu, M. (2007) J. Mater. Chem. 17, 2344

[7] Gillie, L.J., Wright, A.J., Hadermann, J., Van Tendeloo, G., Greaves, C. (2002) J. Solid State Chem. 167, 145–151

Ferroelectric perovskite oxides have recently been used in solar applications because their polarity allows for the separation of photocarriers when under illumination to generate a photocurrent. Oxides, however, often have band gaps that are beyond the solar-optimal regime (>3.3 eV); for this reason, perovskite-structured chalcogenides have been proposed as suitable candidate materials owing to their lower band gaps (≈ 2 eV). An understanding of the thermal expansion behavior of photovoltaic materials is important so as to prevent large stresses and strains during fabrication and operation of the photovoltaic device. Here, we evaluate the structural, lattice dynamical, and thermodynamic properties of Ruddlesden-Popper chalcogenide Ba_n+1Zr_nS_3n+1 (n=1,2,3, ∞) using the self-consistent quasi-harmonic approximation within density functional theory. These responses are compared to the thermal expansion of Ruddlesden-Popper oxides and recent experimental data, which allows us to suggest guidelines for engineering thermal expansion in the Ruddlesden-Popper structure type with diverse chemistries.

This work was supported by the National Science Foundation’s MRSEC program (DMR-1720139.) at the Materials Research Center of Northwestern University.

Octahedral tilting is integral to the structure and functionality of perovskites: tilt distortions influence the electronic and magnetic properties [1] and reduce the macroscopic symmetry, as rationalised by group theory [2]. Since tilts are driven by the relative sizes of the metal ions, compositional modification can allow for the control of tilt patterns to achieve desired functionality, such as multiferroicity [3]. A class of materials closely related to perovskites are the Prussian blue analogues (PBAs), where cyanide anions replace the oxides to give the formula A_xM[Mʹ(CN)₆]_1−y□_y⋅nH₂O (A is an alkali metal, M and Mʹ are transition metals and □ denotes a vacancy). Like double perovskites, the parent structure (aristotype) adopts the space group Fmm, although ordered A-site cations (x > 1) or vacancies (y > 1) may reduce the symmetry to F3m or Pmm.

Due to the similarity to perovskites, octahedral tilting also features in PBAs and can have a strong impact on the functional response. To illustrate, the tilts in Na₂MnMn(CN)₆ nearly triples the magnetic ordering temperature compared to the cubic Cs₂MnMn(CN)₆ [4]. However, the tilting in PBAs is poorly understood, which is evidenced by considerable confusion in the literature. A systematic understanding of the factors underlying octahedral tilting in PBAs would be highly beneficial and facilitate tilt engineering approaches.

Here, density functional theory (DFT) calculations and literature surveys are used to identify and rationalise the trends in octahedral tilting for PBAs. A high concentration of A-site cations is a prerequisite for tilting and PBAs with x < 1 are almost invariably cubic, even upon cooling. Moreover, the A-site cation radius dictates the particular tilt pattern [Fig. 1], in line with the behaviour of perovskites. Mʹ(CN)₆ vacancies—which have no analogue in oxide perovskites—do not appear to play a major role, but the presence of interstitial water dictates which tilt pattern that appears in response to external or chemical pressure. Functional implications of the tilts include the tilt-driven improper ferroelectricity in the high-pressure Pn phase of RbMnCo(CN)₆ [5], or the undesirable tilt transition upon Na intercalation in cathode materials based on PBAs [6]. More generally, our results help develop a unified picture of the structural behaviour of PBAs and also improve the understanding of tilting distortions in general.

[1] Bull, C. L., & McMillan, P. F. (2004). J. Solid State Chem., 177, 2323.[2] Howard, C. J., Kennedy, B. J., & Woodward, P. M. (1999). Acta Cryst. B, 59, 463. [3] Pitcher, M. J., Mandal, P., Dyer, M. S., Alaria, J., Borisov, P., Niu, H., Claridge, J. B. & Rosseinsky, M. J. (2015). Science, 347, 420.

[4] Kareis, C. M., Lapidus, S. H., Her, J.-H., Stephens, P. W., & Miller, J. S. (2012). J. Am. Chem. Soc., 134, 2246.

[5] Boström, H. L. B., Collings, I. E., Daisenberger, D., Ridley, C. J., Funnell, N. P., & Cairns, A. B. (2021). J. Am. Chem. Soc., 143, 3544.

[6] Asakura, D., Okubo, M., Mizuno, Y., Kudo, T., Zhou, H., Ikedo, K., Mizokawa, T., Okazawa, A., & Kojima, N. (2012). J. Phys. Chem. C, 116, 8364.

Study of pressure induced structural phase transitions in perovskites has received considerable attention as it can tune many physical properties like band gap, resistivity, piezoelectric coefficients and ferroelectric polarization, etc. PbTiO₃ (PT) is one such model compound whose high pressure behaviour has been a topic of extensive research in recent years because of its technological importance as the end member of the commercial piezoelectric solid solution compositions in the electronics industry [1]. However, the structural phase transition sequence of PT at high pressures has remained very controversial with two entirely different propositions. As per the first principles calculations of Wu & Cohen [2] and subsequent experimental studies [3], pressure can induce polarization rotation due to a tetragonal to monoclinic phase transition much in the same way as the composition does in the morphotropic phase boundary (MPB) based commercial piezoelectric solid solution systems. First principles calculations and experimental studies by Kornev and his co-workers [4], on the other hand, present a completely different picture whereby PT undergoes a pressure induced antiferrodistortive (AFD) structural phase transition, albeit with decreasing tetragonality, until a ‘pseudo-cubic’ like non-ferroelectric phase appears which is followed by the emergence of a reentrant ferroelectric phase at still higher pressures. However, the evidence for AFD superlattice reflections were not observed at moderate pressures predicted theoretically [4]. Recently, we have addressed these controversies by carrying out a careful study of high pressure structural phase transitions in a tetragonal composition of PbTiO₃ solid solution containing 50% BiFeO₃ (PT-0.5BF) using synchrotron x-ray diffraction measurements at P02.2 Extreme Conditions Beamline of PETRA III at DESY. A tetragonal composition in the solid solution of PbTiO₃ with BiFeO₃ was chosen to enhance the AFD instability and hence the intensity of the superlattice peaks [5]. Our results [5] show that even at moderate pressures (~2.15 GPa), the tetragonal P4mm phase of PT-0.5BF system transforms to a monoclinic phase in the Cc space group, which permits MPB type rotation of ferroelectric polarization vector as well as oxygen octahedral tilting induced by a concomitant AFD transition (see Fig. 1). The transition pressure is very close to the theoretically predicted moderate pressure values for pure PT [4]. Our results also show that with increasing pressure, the ferroelectric distortion decreases and the structure acquires a pseudo-cubic character at intermediate pressures, as expected on the basis of Samara’s criterion [6] (see Fig. 2). But interestingly, our studies reveal that the ferroelectric distortion starts increasing above a critical pressure (~7 GPa) due to the emergence of a reentrant ferroelectric phase through an isostructural phase transition in which the oxygen octahedral tilting provides an efficient mechanism for volume reduction. Our results show that the DFT based theoretical predictions of both the groups [2,4] are correct in parts but none of the two provides the complete picture. Our results not only resolve the existing controversies but also provide an insight towards designing of new environmentally friendly Pb-free piezoelectric compositions.

Metal halide perovskites (MHPs) has shown impressive results in solar cells, light emitting devices, and scintillator applications, but its complex crystal structure is only partially understood and many open questions are still to be answered [1]. In particular, a method to image the dynamics of the nanoscale ferroelastic domains in MHPs requires a challenging combination of high spatial resolution and long penetration depth. With the recent development in X-ray optics it is now possible to focus X-rays down to the nanoscale. Combining the traditional high sensitivity to lattice spacing and tilt, as well as its characteristic to probe deep into the sample, nanofocused scanning X-ray diffraction is a unique powerful technique on the study of MHPs domain dynamics [2].

In this work, we demonstrate in situ temperature-dependent imaging of ferroelastic domains in a single nanowire of metal halide perovskite, CsPbBr₃, using scanning X-ray diffraction with a 60 nm beam [3] to retrieve local structural properties for temperatures up to 140 °C [4]. We observed a single Bragg peak at room temperature, but at 80 °C, four new Bragg peaks appeared, originating in different real-space domains, as depicted in Fig. 1 (left panels). The originally random domains were arranged in periodic stripes in the center and with a hatched pattern close to the edges, as one can see in Fig. 1 (right panels). Reciprocal space mapping at 80 °C was used to quantify the local strain and lattice tilts, revealing the ferroelastic nature of the domains. The domains display a partial stability to further temperature changes. Our results show the dynamics of nanoscale ferroelastic domain formation within a single-crystal perovskite nanostructure, which is important both for the fundamental understanding of these materials and for the development of perovskite-based devices.

[1] Zhang, W.; Eperon, G. E.; Snaith, H. J. (2016). Nature Energy 1 (6), 16048. DOI: 10.1038/NENERGY.2016.48 [2] Chayanun, L.; Hammarberg, S.; Dierks, H.; Otnes, G.; Bjorling, A.; Borgstrom, M. T.; Wallentin, J. (2019). Crystals 9 (8), 432. DOI: 10.3390/cryst9080432 [3] Bjorling, A.; Kalbfleisch, S.; Kahnt, M.; Sala, S.; Parfeniukas, K.; Vogt, U.; Carbone, G.; Johansson, U. (2020). Opt. Express 28 (4), 5069. DOI: 10.1364/OE.386068 [4] Marçal, L. A. B.; Oksenberg, E.; Dzhigaev, D.; Hammarberg, S.; Rothman, A.; Björling, A.; Unger, E.; Mikkelsen, A; Joselevich, E; Wallentin, J. (2020). ACS Nano 14, 15973. DOI: 10.1021/acsnano.0c07426

Antiferroelectric perovskites form an important family of functional electric materials, which have high potential in energy storage and conversion applications. However, a full understanding of their crystal structural formation is still lacking. PbZrO₃-based materials can serve as a model system for investigation, not only because PbZrO₃ was the first discovered antiferroelectric, but also because it undergoes a typical phase transition sequence from a high-temperature paraelectric to the low-temperature antiferroelectric phase, passing through a possible intermediate (IM) phase that is poorly understood. The IM phases usually exist only in a narrow temperature interval in pure PbZrO₃, and therefore it is hard to capture them. On the other hand, with a small amount of Ti substitution, the Zr-rich PbZr_1-xTi_xO₃ (PZT, x ≤ 0.06) also displays a room-temperature antiferroelectric structure and goes through the same phase transition process as PbZrO₃. In this case, the temperature range of the IM phase becomes wider, which makes a detailed study of the IM structures possible.

Here we employ a combination of optical and scattering experiments and theoretical calculations to reveal the nature of the intermediate state. Experimental results show that the IM phase is not a pure phase but a state containing a mixture of several short- and long-range correlated structural components that compete energetically in a complicated way. To emphasize this, we shall henceforth refer to it as the IM state rather than the IM phase. There are several types of superstructure reflections that appear in the IM state temperature range in the single-crystal diffuse scattering pattern (Fig. 1). With the aid of synchrotron powder total scattering and high-resolution neutron diffraction data analysis, we constructed the complex structural models in this temperature range [1]. Evidence is found that this peculiar state consists of multiple short-range and long-range structural components, as well as complex mesoscopic domain structure [2]. External stimuli such as temperature change or chemical substitution can easily alter each component’s energy landscape and thereby change the materials' electrical properties. These findings provide new insights in understanding antiferroelectric-ferroelectric competition and hence in designing new antiferroelectric materials.

[1] An, Z., Yokota, H., Zhang, N., Pasciak, M., Fábry, J., Kopecký, M., Kub, J., Zhang, G., Glazer, A. M., Welberry, T. R., Ren, W., & Ye, Z.-G. (2021) Phys. Rev. B 103, 054113.

[2] An, Z., Xie, S., Zhang, N., Zhuang, J., Glazer, A. M., Ren, W., & Ye, Z.-G. (2021) APL Mater. 9, 030702.

The Protein Data Bank (PDB) was established in 1971 as the first open-access digital data resource in biology with just seven X-ray structures of proteins. During its first 50 years of continuous operations, PDB holdings have grown to more than 175,000 structures becoming the single global archive of 3D-structures of proteins, nucleic acid, and their complexes with one another and small-molecule ligands. Open access to expertly biocurated PDB structures enables the efforts of many millions of basic and applied researchers, educators, and students around the world. Their work impacts fundamental biology, biomedicine, bioengineering, biotechnology, and energy sciences.

The Worldwide Protein Data Bank (wwPDB, wwpdb.org) manages the PDB archive according to the FACT principles of Fairness-Accuracy-Confidentiality-Transparency and the FAIR principles of Findable-Accessible-Interoperable-Reusable. Current wwPDB members include the US RCSB Protein Data Bank (RCSB PDB), Protein Data Bank in Europe (PDBe), Protein Data Bank Japan (PDBj), Electron Microscopy Data Bank (EMDB), and Biological Magnetic Resonance Bank (BMRB).

All data in the PDB archive conform to the wwPDB PDBx/mmCIF data dictionary, which is fully extensible both human- and machine-readable. PDB structures are composed of amino acids or nucleotide building blocks that comprise biopolymers, and associated small molecules such as water molecules, solute molecules, ions, co-factors, metabolites, enzyme inhibitors, drugs, etc. Every new structure coming into the PDB is processed using the wwPDB OneDep global system for deposition, validation, and biocuration. All PDB structures are accompanied by an official wwPDB Validation Report, exemplifying standards developed collaboratively with wwPDB Task Forces composed of community experts.

Small-molecule constituents of PDB structures are defined in the wwPDB Chemical Component Dictionary (CCD). This dictionary contains detailed chemical descriptions for standard and modified amino acids/nucleotides, small molecule ligands, solvent molecules, and others. Precise knowledge of interactions between macromolecules and small-molecule ligands is central to our understanding of biological and biochemical function, drug action, mechanisms of drug resistance, and drug-drug interactions.

Recent enhancements to the CCD and the wwPDB Validation Report will be described, together with value-added information concerning ligand quality now available on the US Research Collaboratory for Structural Bioinformatics Protein Data Bank PDB website (RCSB PDB, RCSB.org).

wwPDB members are US RCSB PDB (supported by NSF, NIH, DOE, and Rutgers Cancer Institute of New Jersey), PDBe (EMBL-EBI, Wellcome Trust, BBSRC, MRC, and EU), and PDBj (NBDC-JST), and BMRB (NIGMS).

Peer review of supporting data for submitted research articles is currently assuming great significance in scientific publishing, but is not new for the journals of the IUCr. Co-editors of Acta Crystallographica C under the editorship of Sidney Abrahams (1924-2021) were expected to validate the consistency of crystal structure data for reported structures, for which cell parameters and symmery, coordinates, geometry and anisotropic displacement parameters were mandatory. The journal developed software to reduce the calculational burden, and this evolved into the checkCIF service that allowed authors to participate in the validation effort, and to account for apparent anomalies or outliers in their derived structures. An early consequence was the almost complete elimination of corrigenda that resulted from post-publication surveys by individual scientists or by database aggregators. Over the years checkCIF increased in sophistication and power (authors were required to supply structure factors in machine-readable form), and has been adopted by other journal publishers and by structural databases. The IUCr Diffraction Data Deposition Working Group (2011-2017) emphasised the value of access to raw experimental data in evaluating structure interpretation, and IUCr Journals have responded by encouraging authors to make available their diffraction data sets. The journals continue to explore ways to improve the refereeing process with regard to data, in their effort to make the initial publication of the version of record of an article as error-free as possible.

The Cambridge Structural Database (CSD) was founded on a vision that collective use of data would lead to the discovery of new knowledge which transcends the results of individual experiments. Excellent data sharing practices in the crystallographic community as well as deposition and curation processes at the CCDC have enabled that vision to come to true.

This talk will demonstrate a number of ways in which a structural database such as the CSD can work with the community to help set standards from validation to publication and explore what part we play in the pre and post publication peer review of crystallographic data. We will share our experiences evolving our interactive deposition service, from the integration of checkCIF, to the establishment of links to raw diffraction data. We will also look at how repositories can support the peer review of data and what impact an increase of data published solely through the CSD might have. The presentation will conclude by looking at how reviewing crystallographic results might change in the future, how the CSD could evolve and how we can better help the community increase the integrity of data that is shared.

High-resolution macromolecular structures determined using crystallography, NMR, and cryo-EM provide a gold standard for evaluation of important properties of biomolecules, but the quality of some structures, as well of their presentation, is not always fully acceptable. Whereas quality checking tools provided by the PDB during deposition process may flag some common problems, the resulting red flags are not always addressed by deposition authors. Some journals require that manuscripts be accompanied by validation reports in order to assist reviewers in evaluation of the validity of presented structures, whereas other journals do not have such requirements. Additionally, validation reports are more helpful in identifying global problems, while some local problems may not be apparent. Utilization of additional tools and interactive software might assist readers in making the best use of published structural data. Using examples extracted from the Protein Data Bank, as well as from journal publications, some common problems will be identified and suggestions will be made on how to avoid their reoccurrence.

Over the last decades, the PDB has been developing tools and standards for the assessment of the quality of the structural models deposited in its archives. Similarly, more and more journals are now requiring validation reports generated by the PDB as a prerequisite for manuscript submission. Such quality metrics have been used previously to gauge the relationship between structural model quality and publication venues [1,2]. More recently, these indicators have been applied to assess the evolution of the quality of the PDB deposits with time [3] using the concept of a percentile (P_Q1) metric, which combines such measures as R_free, RSRZ (normalized Real Space R-factor) outliers, Ramachandran outliers, Rotamer outliers, and Clashscore.

In this paper we will show how the quality of macromolecular models deposited in the PDB has changed over the years (Fig. 1) and how the P_Q1 parameter can be converted to a new measure, P_Q1(t,d), that takes into account time (t) and data resolution (d). The proposed new measure can be used to reveal how structure quality in a given moment of time was related to such issues as:

• differences between proteins and nucleic acids;
• comparison with structural genomics projects;
• assessment of deposits without journal publications (To be published);
• journal impact factor (Fig. 2).

The paper will also discuss how the quality of crystallographic macromolecular structures in the PDB has improved over the last years and highlight some crucial periods in this history.

[1] Brown, E. N. & Ramaswamy, S. (2007). Acta Cryst. D63, 941–950.

[2] Read, R. J. & Kleywegt, G. J. (2009). Acta Cryst. D65, 140–147.

[3] Shao, C., Yang H., Westbrook, J. D., Young, J. Y., Zardecki, C. & Burley, S. K. (2017). Structure 25, 458–468.

https://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/emda/emda.html

http://www.xray.cz/mstruct

http://crm2.univ-lorraine.fr/lab/en/software/mopro/

https://team.inria.fr/nano-d/software/

Metal nanocatalysts typically consist of noble metal nanoparticles (NPs) anchored on a metal oxide support, where the NP surface exposes active sites to catalyse target chemical reactions. The catalyst’s economic viability demands high activity, high selectivity, and high stability. It is well established that the performance of catalytic NPs is closely related to their size, shape and interparticle distance. Synthesis methods that can tailor the structural properties of noble metal NPs are therefore attractive to elucidate performance-structure relationships. In this regard, there is an increasing interest in Atomic Layer Deposition (ALD), a vapour-phase deposition method which proved its efficiency in dispersing noble metal NPs on complex high surface area supports with atomic-scale control over the metal loading (atoms per cm²) and nanoparticle size [1]. However, an improved understanding of how the deposition parameters influence the formation and growth of the noble metal NPs is required to fully exploit the tuning potential of ALD.

We designed a high-vacuum setup for thermal and plasma-enhanced ALD that is compatible with synchrotron-based in situ X-ray fluorescence (XRF) and grazing incidence small-angle X-ray scattering (GISAXS) monitoring [2]. Using this setup, we resolved the dynamics of Pt and Pd NP formation and growth on planar SiO₂ and Al₂O₃ surfaces [3-5]. In situ XRF was used to quantify the evolution of metal loading with the number of ALD cycles, while analysis of the key scattering features allowed us to correlate the amount of deposited material with the evolution of structural parameters such as cluster shape, average size and areal density.

In a first study we focused on the growth of Pt deposits on SiO₂ with the thermal ALD process comprising sequential MeCpPtMe₃ and O₂ exposures at 300°C [3]. The results indicated a nucleation stage, followed by a diffusion-mediated particle growth regime during which the size and spacing of the Pt NPs is largely determined by adsorption of migrating Pt species on the surface and diffusion-driven particle coalescence. Interestingly, diffusion phenomena and ripening of the Pt NPs during ALD could be suppressed by using N₂ plasma as a reactant instead of O₂ in the ALD cycle. By combining O₂-based and N₂ plasma-based ALD processes, we developed a tuning strategy that offers independent control over the Pt NP size and areal density [4].

Secondly, we studied the initial nucleation of Pd NPs deposited at 150°C on oxide substrates (SiO₂ or Al₂O₃) by combining Pd(hfac)₂ and H₂ plasma in an ALD sequence [5]. The results confirmed a long nucleation process and revealed a relatively low NP areal density, in line with the occurrence of surface poisoning during the initial ALD cycles [6]. The reaction of the Pd precursor with the oxide surface leaves site blocking surface species behind, thereby inhibiting the nucleation. To enhance the nucleation, we explored two potential methods to ‘clean’ the surface: (1) introducing trimethylaluminum (TMA) exposures during the initial ALD cycles, and (2) introducing an O₂ plasma exposure, either before or after the H₂ plasma step, throughout the ALD process. Both these approaches had a significant impact on the evolution of NP size and spacing, and the insights obtained were used to develop a strategy that enables precise control of the Pd NP dimensions and coverage [5].

[1] Lu, J., Elam, J. W. & Stair, P. C. (2016). Surf. Sci. Rep. 71, 410.

[2] Dendooven, J., Solano, E., Minjauw, M. M., Van de Kerckhove, K., Coati, A., Fonda, E., Portale, G., Garreau, Y. & Detavernier, C. (2016). Rev. Sci. Instrum. 87, 113905.

[3] Dendooven, J., Van Daele, M., Solano, E., Ramachandran, R. K., Minjauw, M. M., Resta, A., Vlad, A., Garreau, Y. Coati, A., Portale, G. & Detavernier, C. (2020). Phys. Chem. Chem. Phys. 22, 24917.

[4] Dendooven, J., Ramachandran, R. K., Solano, E., Kurttepeli, M., Geerts, L., Heremans, G., Rongé, J., Minjauw, M. M., Dobbelaere, T., Devloo-Casier, K., Martens, J. A., Vantomme, A., Bals, S., Portale, G., Coati, A. & Detavernier, C. (2017). Nat. Commun. 8, 1074.

[5] Feng, J.-Y., Ramachandran, R. K., Solano, E., Minjauw, M. M., Van Daele, M., Vantomme, A., Hermida-Merino, D., Coatia, A., Poelman, H., Detavernier, C. & Dendooven, J. (2021). Appl. Surf. Sci. 539, 148238.

[6] Goldstein, D. N. & George, S. M. (2011). Thin Solid Films 519, 5339.

Soft-matter bicontinuous networks find a double gyroid structure from block copolymer (BCP) self-assembly. A gyroid structure composed of dissimilar blocks has proven its potential as a soft crystal, of which the lattice dimension is variable with molecular weight of the polymer. Using an asymmetric polystyrene-b-poly(methyl methacrylate) (PS-b-PMMA), recently we showed that the self-assembled gyroid films formed via a solvent vapor annealing (SVA) process undergo unique structural distortion due to directional deformation immediately upon deswelling [1]. During the SVA process with PS-b-PMMA films, initially transient cylinders developed from the as-cast morphology transform into a cubic gyroid structure in a swollen state. We then observed that upon solvent evaporation the gyroid lattice contracts along the film normal direction while retaining the swollen lateral dimension. The degree of contraction is turned out to be related to the evaporation speed. Rapid and spontaneous deswelling processes lead to triclinic gyroid structures with z-directional contraction ratios (C_z) of 2.5 and 2.0, respectively.

Our X-ray analysis reveals that symmetries of the resulting gyroid structures are partially broken due to the non-affine transformation, eliciting several forbidden reflections such as {110} and {200} reflections. For further characterization of the symmetry-breaking, we delineate the structural features of noncubic gyroid films by computing electron-density difference maps from grazing incidence small angle X-ray scattering (GISAXS) data. We employed iterative phase retrieval method to solve the phase problem. Level-set approach is accordingly developed to quantitate the structural characteristics of the maps in terms of inversion symmetry-breaking, suggesting its possible application to optical Weyl photonic crystals. This presentation will focus on X-ray data collection and analysis.

[1] Jo, S., Park, H., Jun, T., Kim, K., Jung, H., Park, S., Lee, B., Lee, S., Ryu, D. Y. (2021), Applied Materials Today 23, 101006.

GISAXS measurements were performed at Pohang Accelerator Laboratory (Korea) and Advanced Photon Source (APS) at Argonne National Laboratory (US). The APS is supported by the US department of Energy, Office of Basic Energy Sciences, under contract no. DE-AC0206CH11357. This research was supported by Samsung Research Funding & Incubation Center of Samsung Electronics under Project Number SRFC-MA1801-04.

Thin films of thickness 100 nm or less are typically deposited on a much thicker substrate, making it difficult to obtain the required high-quality total scattering data for analysis in real-space with pair distribution functions (PDF) [1]. In recent years, total scattering in reflection geometry at grazing incidence (GI), that is, below the critical angle of total external reflection, has been used with success to increase the surface sensitivity and scattering intensity [2, 3]. GI-PDF gives high-quality PDFs from films as thin as 3 nm with a 20 x 2.5 µm² focused X-ray beam with 100 keV photon energies at PETRA III [2]. Using this same setup we have developed a novel ultra-high vacuum compatible deposition chamber, that allows for the demanding sample alignment of the thin film sample under vacuum conditions as well as a 180 degree in-plane rotation [4]. Via a rotary feedthrough and bellows combination the surrounding vacuum chamber is not affected by translation of the sample, allowing for film deposition equipment such as a magnetron sputter source. This has been employed at the P07-EH2 beamline with a radio-frequency magnetron sputter source, as pictured in the figure below. We will show how this has been applied to observe the formation of thin films during the initial stages of deposition in real time with sub-second time resolution.

[Fig 1 with figure + picture]

Figure 1. PDFs of a Pt thin film at 10, 20, 30, 40, 50 and 60 seconds of sputter deposition with approximately 1 Å/s and a picture of the equipment installed on the surface diffractometer at beamline P07-EH2, PETRA III, Hamburg, Germany, as seen from the detector side.

[1] K. M. Ø. Jensen et al., IUCrJ 2 (2015), 481

[2] A.-C. Dippel et al., IUCrJ 6 (2019), 291

[3] K. Stone et al., APL Materials 4 (2016), 076103

[4] M. Roelsgaard et al., IUCrJ 6 (2019), 299

Molecular replacement (MR) is the primary method used to solve the phase problem in macromolecular crystallography. When there are no suitable homologues available for conventional MR, one alternative option is to predict the structure via bioinformatic means. This is referred to as ab initio or de novo modelling and has dramatically increased in accuracy in recent years with the availability of better residue-contact predictions derived through covariance analysis and deep learning. Covariance-assisted ab initio models are now available on a large scale in new generation databases, and therefore provide an easily obtainable source of potential search models as a supplement to the PDB. We have previously shown that using such structure predictions obtained from the GREMLIN and PconsFam databases could be processed with AMPLE to successfully solve structures through MR [1]. Here we explore the use of alternative model sources such as DMPfold and Alphafold2, considering which model preparation protocols are optimal.

We also present MrParse, a tool to access structures deposited to the PDB and predicted structures deposited in databases in a single, unified interface. This resource, which will also enable facile access to the latest automated homology models, will also present model quality assessment scores to help assess the quality of database-derived models. Presenting PDB structures and database-derived models in a common dashboard will help the crystallographer maximise the chance of success through MR.

[1] Simpkin et al. (2019) Acta Cryst D75(12) 1051-1062

The molecular recognition of carbohydrates by proteins plays a key role in many biological processes including immune response, pathogen entry into a cell and cell-cell adhesion (e.g., in cancer metastasis). Carbohydrates interact with proteins mainly through hydrogen bonding, metal-ion-mediated interaction and non-polar dispersion interactions. The role of dispersion-driven CH-π interactions (stacking) in protein-carbohydrate recognition has been underestimated for a long time considering the polar interactions to be the main forces for saccharide interactions. However, over the last few years it turns out that non-polar interactions are equally important. Using the Protein Data Bank (PDB) structural data, we analyzed the CH-π interactions employing bioinformatics (data mining, structural analysis), several experimental (ITC, X-ray crystallography) and computational techniques. Within 12 000 protein complexes with carbohydrates from PDB, the stacking interactions were found in about 39% of them. The calculations and the ITC measurement results suggest that the CH-π stacking contribution to the overall binding energy ranges from 4 kcal/mol up to 8 kcal/mol. All the results show that the stacking CH-π interactions in protein-carbohydrate complexes can be considered to be a driving force of the binding in such complexes.

Protein folding relies on the formation of secondary structures as helices, beta-strands, turns, with specific values of the backbone torsion angles ϕ and ψ for each secondary structure.

β-turns represent the most prevalent type of nonrepetitive secondary structure in proteins. A β-turn is a region of four consecutive residues, where the polypeptide chain reverses its direction and the distance between the α-carbon atoms of the residues i and i+3 is less than 7 Å.

In 1968 Venkatachalam recognized the existence of β-turns as a result of a conformational study of four consecutive amino acid residues [1].He evidenced three distinct conformations characterized by specific values of the phi, psi torsion angles and by the presence of a hydrogen bond between the peptide backbone carbonyl group of the first residue C=O(i) and the backbone amino group of the fourth residue N-H(i+3).

In the next 50 years of research, several classifications of beta-turns were proposed, based exclusively on the evaluation of the dihedral angles phi and psi [2].

Recently, Newberry and Raines evidenced the importance of weak chemical interactions in the formation of protein secondary structures [3].

Thus, in this work we aimed to identify repeated patterns of n → π* interactions between carbonyl groups of successive residues in proteins and cyclic peptides. The survey considered 1424 X-ray protein structures in the Protein Data Bank with a resolution of 1.2 Å or better, R-factor of 0.2 or better and sequence identity of 50% or lower. We also performed a statistical analysis on the geometrical feature of CO…CO interactions in turn mimetic compounds as cyclic peptides, cyclic depsipeptides and cyclic peptoids, considering a total of 232 compounds.

The obtained results show that the n → π * interactions could allow to discriminate among different turn types and explain the peculiar differences from a chemical point of view.

References

[1] Venkatachalam, C. M. Stereochemical criteria for polypeptides and proteins. V. Conformation of a system of three linked peptide units. Biopolymers 1968, 6, 1425-1436.

[2] Shapovalov, M.; Vucetic, S.; Dunbrack, R.L. A new clustering and nomenclature for beta turns derived from high-resolution protein structures. PLoS Comput. Biol. 2019, 15, e1006844.

[3] Newberry, R. W.; Raines, R. T. Secondary Forces in Protein Folding. ACS Chem. Biol. 2019, 14, 8, 1677–1686. (https://pubs.acs.org/doi/10.1021/acschembio.9b00339

Breast cancer type 2 susceptibility (BRCA2) protein plays an essential role in the repair of DNA double-strand breaks and interstrand cross-links by Homologous recombination [1]. Germ-line mutations in BRCA2 confer an increased risk of hereditary breast and ovarian cancer [2]. A large number of missense mutations have been identified in the DNA binding carboxy-terminal domain of BRCA2 which is also known to interact with FANCD2 [3]. However, majority of these missense mutations are classified as variants of ‘Uncertain Significance’ due to lack of structural, functional, and clinical studies. Accurate and reliable methods to predict the pathogenicity of variants are utmost required for better clinical management of the disease. Here we present a multi-disciplinary approach to characterize a missense mutation identified in the C-terminal domain of BRCA2. Different functional domains of the wild-type and mutant BRCA2 protein were cloned and the proteins were expressed and purified in bacterial system. Circular -dichroism and Fluorescence spectroscopic techniques were employed to evaluate the differences between secondary and tertiary structures of wild-type and mutant protein. Molecular Dynamics Simulation was further utilized to measure the effect of mutations on the structural conformation of the protein.

References:[1] Xia, B. et al. (2006). Molecular Cell, Vol. 22, 719-729[2] Venkitaraman, A.R. (2002). Cell, Vol. 108, 171–182[3] Hussain S, et al. (2003). Human Molecular Genetics, Vol. 12, No. 19, 2503-2510

Keywords: BRCA2; Molecular Dynamics Simulation

As the number of macromolecular structures solved by the electron microscopy method (EM) rapidly increases, the need for improved methods for processing and improving all aspects of the EM structure determination methods also grows. One possible approach to improving the processing of experimental data is by using the symmetry information. To this end, all major cryo-EM software suites provide an option to use the symmetry information to improve the final resolution of the solved structure. This technique is based on averaging density over all asymmetric units, thus reducing noise and increasing signal to noise ratio in the data.

Nonetheless, all currently available EM suites do require the user to supply the symmetry of the structure and sometimes rotating the structure so that the symmetry axes are in a particular orientation relative to the system axes in order to work. In this contribution, we present a novel method for determining density map symmetries de novo as well as a new software tool called ProSHADE implementing this method.

The presented method relies on computing the optimised self-rotation function [1] using the spherical harmonics decomposition coefficients and converting these onto SO(3) space coefficients as described by [2]. By subsequently computing the inverse Fourier transform in SO(3) space, the self-rotation function is obtained. Next, the self-rotation function values are mapped onto a set of concentric spheres with radius equal to the angle of rotation in the axis-angle rotation representation, while the position on the sphere represents the rotation axis of the axis-angle rotation representation. This representation allows for fast detection of any axis which has high self-rotation function values along any particular set of angles. This in turn allows for detection of cyclic (C) symmetry groups as they are by definition a set of rotations, along the same axis, which do not change the shape (i.e. have high self-rotation function value). Once all C symmetries are detected, the dihedral (D), tetrahedral (T), octahedral (O) and icosahedral (I) symmetries can be detected by finding for the required C symmetries combinations forming the larger symmetry groups.

Since the self-rotation function values are proportional to real-space correlation between the original and rotated density map values, they are affected by the shape of the density map; this relationship is such that the more spherical the density map is, the higher the overall real-space correlation will be irrespective of the actual symmetry in the density. Therefore, to reduce the number of false positive results, the method also uses the Fourier Shell Correlation (FSC) to confirm any detected symmetry, increasing the reliability of the method.

The current implementation of this method in ProSHADE is capable of correctly detecting the symmetry type and fold for over 85% of symmetrised structures deposited in the EMDB database [3] with approximately half of the incorrectly determined symmetries being a subgroup of the originally reported symmetry. The symmetry detection does not require any user input and is therefore readily available for inclusion into cryo-EM structure solving pipelines. ProSHADE is an open source project available under the GPL version 3 license on all major operating systems either as stand-alone executable or as a python language module.

References:

[1] Navaza J. (1994). Acta Cryst, A50, 157-163.[2] Kostelec P.J., Rockmore D.N. (2008). Journal of Fourier Analysis and Applications, 14, 145–179.[3] Lawson C.L., Baker M.L., Best C., Bi C., Dougherty M., Feng P., van Ginkel G., Devkota B., Lagerstedt I., Ludtke S.J., Newman R.H., Oldfield T.J., Rees I., Sahni G., Sala R., Velankar S., Warren J., Westbrook J.D., Henrick K., Kleywegt G.J., Berman H.M., and Chiu W.C. (2011). Nucleic Acids Research, 39, 456-464.

Reliable determination of the quaternary structure of a protein is often crucial to a full understanding of its function. However, for decades, crystallographers have sometimes struggled to distinguish between biologically meaningful interfaces observed in a crystal structure, and the unnatural lattice contacts that allow for crystal formation. In order to solve this problem, Eugene Krissinel developed PISA, and later jsPISA, a CCP4 tool that sorts different candidate quaternary structures according to a likelihood obtained from results on dissociation free energy [1, 2]. Additionally, jsPISA incorporates an "interaction radar" that allows for a rapid visualisation of how likely an interface is according to a number of physico-chemical parameters.

In order to provide jsPISA with an additional -- independent -- source of information to determine the probability of a given interface to biologically exist, we propose the use of evolutionary covariance data. This proposal is based upon the observation that pairs of residues whose interaction contributes to a biologically important interface are constrained in their evolution [3, 4]. Consequently, the detection of a pair covariation signal points at the existence of a contact between the two residues contributing to the formation of a biologically important interface. The new extension, named PISACov, aims to enhance the results currently displayed by jsPISA with an additional score and new data based on evolutionary covariance analysis, thereby helping determine the relevant quaternary structure in difficult cases.

[1] Krissinel, E.; Henrick, K. J. (2007) Mol Biol., 372 , 774-797.
[2] Krissinel, E. (2015) Nucleic Acids Research, 43, W314–W319.
[3] Ovchinnikov, S.; Kamisetty, H.; Baker, D. (2014) eLife, 3:e02030.
[4] Hopf, T.A. et al. (2014) eLife, 3:e03430.

The Protein Data Bank in Europe - Knowledge Base (PDBe-KB, https://pdbe-kb.org) is a community-driven, collaborative data resource that provides literature-derived, curated and predicted structural and functional annotations of molecular structure data. Consortium members provide annotations including catalytic sites, ligand binding sites, protein flexibility, post-translational modification sites, and the effect of genetic variability or mutations. PDBe-KB aims to increase the visibility and reduce the fragmentation of these annotations and place macromolecular structure data in their biological context, thus facilitating their use by the broader scientific community in fundamental and applied research.

PDBe-KB currently collaborates with 31 resources from 11 countries, and we integrate their annotations with core PDB structural data in a novel and distributable PDBe graph database. Researchers can access all the annotations either by using the graph database or programmatically via API endpoints. We have also created web pages called “Aggregated Views” that provide an overview of all the structure data related to a full-length protein (i.e. UniProtKB accession). These views are better at displaying the biological context of proteins instead of the conventional PDBe entry-page focus on a single PDB entry.

We have been continuously improving and expanding PDBe-KB since its inception in 2018. Last year we rolled out a significant update to support the global effort to tackle the COVID-19 pandemic by creating dedicated pages gathering all the structural information for the new coronavirus SARS-CoV-2 (e.g. https://www.ebi.ac.uk/pdbe/pdbe-kb/protein/P0DTC2 ). We have also added new functionalities, such as viewing the superposition of every PDB chain that corresponds with a protein of interest. These views are instrumental in identifying ligand-binding hotspots and conformationally flexible regions.

Evolution has led to proteins being able to specifically bind molecules. They have evolved to bind a great variety of chemical substances, from carbohydrates to small organic molecules as well as ions or other macro molecules. This power of evolution can also be harnessed in silico, using applications like Rosetta, to engineer proteins so that they bind ligands with higher specificity.

However, these bioinformatical algorithms are limited as they often cannot take all aspects of molecular modeling, like protein flexibility, solvent simulation, or energy calculation, reliably into account. In addition, most complex applications are usually difficult to use for novices.

Here, we present EvoDock, a modular and easy-to-use pipeline which is capable of integrating multiple molecular modeling programs into an evolutionary algorithm, to predict optimized variants of ligand-binding proteins.

Furthermore, we demonstrate how its predictions could be confirmed by crystallographic structures and will discuss the potential usage of binding energy and the energy of the overall structure to determine a protein’s fitness.

N-methyl-D-aspartate receptors (NMDARs) are central to the pathophysiology of neurodegenerative diseases such as schizophrenia [1], however despite significant structural insights of the receptor [2,3,4,5] the importance of mutations in the NMDAR have been poorly described in the literature. Here we present molecular dynamics simulation data combined with modelling and binding free energy calculations to outline the effects of mutations [6] in the GluN1 subunit of the NMDAR on agonist binding affinity and ligand-receptor interactions. Our data demonstrates the changes caused by the positioning of an introduced tyrosine residue at the binding pocket and its associated changes in the conformation upon ligand binding. Furthermore, molecular dynamics simulations demonstrate the changes in ligand environment in the ligand-receptor complex leading to a loss of key interactions and an associated instability of the bound complex. Lastly, binding free energy calculations show that it is no longer energetically favourable for ionic interactions to form and an associated overall increase in Gibbs free energy for ligand binding. These data are important in explaining the changes in behaviour for mutations in the GluN1 ligand binding region and are consistent with previously reported experiments [7]. We are also pursuing experimental approaches to further understand the action of ligand binding.

[1] Coyle JT (2012). NMDA receptor and schizophrenia: a brief history. Schizophr Bull 38: 920-926.

[2] Amin JB, Gochman A, He M, Certain N, & Wollmuth LP (2021). NMDA Receptors Require Multiple Pre-opening Gating Steps for Efficient Synaptic Activity. Neuron 109: 488-501.e484.

[3] Yu A, & Lau AY (2018). Glutamate and Glycine Binding to the NMDA Receptor. Structure (London, England : 1993) 26: 1035-1043.e1032.

[4] Tajima N, Karakas E, Grant T, Simorowski N, Diaz-Avalos R, Grigorieff N, et al. (2016). Activation of NMDA receptors and the mechanism of inhibition by ifenprodil. Nature 534: 63-68.

[5] Furukawa H, & Gouaux E (2003). Mechanisms of activation, inhibition and specificity: crystal structures of the NMDA receptor NR1 ligand-binding core. The EMBO journal 22: 2873-2885.

[6] Zehavi Y, Mandel H, Zehavi A, Rashid MA, Straussberg R, Jabur B, et al. (2017). De novo GRIN1 mutations: An emerging cause of severe early infantile encephalopathy. Eur J Med Genet 60: 317-320.

[7] Skrenkova K, Song J-m, Kortus S, Kolcheva M, Netolicky J, Hemelikova K, et al. (2020). The pathogenic S688Y mutation in the ligand-binding domain of the GluN1 subunit regulates the properties of NMDA receptors. Sci Rep 10: 18576.

Nucleobases form base pairs, and the question of what are the main driving forces behind the base pair formation is a prevalent one. In our approach to tackle this question we used data from Cambridge Structural Database – we searched for base pair types found in small molecule crystal structures. Obtained base pair types, their frequencies of occurrence and protonation patterns lets us analyze the tendencies of nucleobases to form base pairs.

The reason of why such tendencies occurred varied by the nucleobase, but some general trend were present. The protonation patterns followed the pK_a values of particular nucleobases and the hydrogen bond lengths did not depend on the charge of nucleobases. We compared our findings with analogous data stored in the RNA Basepair Catalog – we found base pairs exclusive for small molecule crystal structures, exclusive for RNA crystal structures and these which were present in both environments. Basing on the frequencies of base pairs, we proven that the pairs often occurring in crystals of small molecules also often occur in RNA crystals [1].

Many base pairs can form higher order structures (Fig. 1) – either some larger aggregates, ribbons, tetramers or whole layers. We wanted to see if there are any rules that govern over the tendency to form particular higher order structure. Is it more of a question of strength of hydrogen bonds (when hydrogen bonds incorporating O or N atoms are favored over these with C), overall interaction energy, or is it rather determined by a simple geometry.

[1] Cabaj, M. K., Dominiak, P. M. (2020). NAR, 48, 8302.

Identifying the probable positions of the protein side-chains is one of the protein modelling steps that can greatly improve the prediction of protein-ligand, protein-protein interactions. With some exceptions, most of the strategies predicting the side-chain conformations use predetermined angles, also called rotamer libraries, that are usually generated from the subset of high-quality protein structures. Although, these libraries are very useful when selecting possible side-chain atom positions, the overall validity and usability with regard to specific protein structure should be studied further.

In order to get well-rounded rotamer library, there should be the balance between the coverage and the quantity of possible side-chain positions. The lack of possible side-chain rotamers will hinder the correct selection of atom positions and the over abundance – the fast selection for protein structure predictions.

We are suggesting the approach that would cover both the coverage and the accuracy of the rotamer library. The rotag software was developed in order to accommodate both these problems. It scans side-chain conformations using dead-end elimination strategy and evaluating potential energies on each calculation step.

The additional challenge that we faced was to have proper method to compare rotamer libraries. The best-case RMSD, best-case dihedral angles and average rotamer choice parameters were selected as good candidates for the comparisons. Multiple rotamer libraries were compared: Dunbrack, Dynameomics, Penultimate and those generated with rotag.

The comparisons revealed that the rotamer libraries that were created from the subset of existing protein structures sometimes lack rotamer positions for certain side-chains of the target proteins. Using more flexible methods, such as rotag, increases the probability of the inclusion of correct conformations. However, not in all cases these flexible methods produce the correct subset of potential candidates.

Many macromolecular data sets suffer from being more or less incomplete mainly as a result of experimental difficulties. Often axes are missing which should be inspected for systematic absences. Even data sets considered complete usually miss very low resolution reflections due to beam stop issues. Low resolution reflections are important as they to a large extent define the protein/solvent boundary. Seriously incomplete data sets can hamper many crystallographic calculations.

A direct space constraint on intensities is the positivity of the Patterson map. All intensities should also make statistical sense and conform to distributions based on observed intensities. Statistics include histograms of normalized and full intensities and scaling as a function of resolution or intensity. Here it is demonstrated how Patterson positivity combined with statistical matching can estimate unobserved intensities. Among applications are space group determination from observation of systematic absences on missing axes and classical rotation functions for molecular replacement. Also any ab initio phasing procedure based on intensities alone is expected to benefit from a complete data set.

The calculations towards a complete data set consist of flipping negative values in the Patterson map followed by histogram match and scaling of the back transformed intensities on order to conform with observed intensities. The generated intensities for observed reflections are in turn flipped relative to the true observations while the unobserved reflections are kept as is. The procedure is initiated by fitting the observed intensities as a function of resolution and determine F000 using knowledge of the solvent content. Initially fitted intensities are substituted in for unobserved data. The calculations are iterative gradually reducing the flipping factor in direct as well as reciprocal space. For cross validation a free data set with 5 % of the observed intensities are kept aside and treated as unobserved.

Figure 1. Structure factor amplitudes of Aspergillus aculeatus rhamnogalacturonan acetylesterase in space group P2₁2₁2₁
Left: 95.45 % complete data set, 0kl-section. Right: Data set completed by Patterson positivity and statistical matching. Systematic absences on missing l-axis are clearly visible.

As a further test of the procedure a virtually complete data set is subjected to various omissions. Omissions include: Low resolution cut off (beam stop issues), high resolution cut off (detector misplaced too far), thin shells of resolution (ice rings), the 10 % strongest intensities (overloads) and increasing omissions around axes and planes in reciprocal space.

In the order of minutes a completed data set can be produced with estimates of unobserved intensities along with estimated standard deviations based on how well the free intensities are reproduced by following the ideas of Read (1986) [1].

[1] Read, R. (1986). Acta Cryst. A42, 140-149

The NPC1 (Niemann-Pick type C1) is one of the main players of cholesterol control in the lysosome and almost its action is closed combined with NPC2 (Niemann-Pick type C2) protein. The dysfunction of one of the proteins can cause problems in overal chloesterol homestasis and leads to a disease, called the Niemann-Pick type C (NPC) disease. It has been reported that many mutations are responsible to the disease. The point mutation R518W or R518Q on the NPC1 is one of such examples. Even though many details on the cholesterol transport mechanism of NPC1 is elucidated especially with the full-length NPC1 structure obtained from cryo-EM study, it is not obvious how the simple mutation can leads such a big difference in proper function of NPC1. In this respect, the single mutation mentioned above could be a good candidate to relate the dynamical function of NPC1 to its structure in cholesterol transport.

In this presentation, we report how the corresponding mutation can induces the structural change in NPC1 by molecular dynamics simulations. Detailed analysis of the resulting simulation trajectory reveals important structural features that is essential for proper function of the NPC1 for cholesterol transport. It has been found that the mutation leads to structural change that is required for proper interaction with NPC2.

The current study can provides some insights into how the structure is closed related to the function of NPC1 in cholesterol transport in terms of its interaction with NPC2 protein.

References

[1] Saha, P., et al. (2020) Inter-domain dynamics drive cholesterol transport by NPC1 and NPC1L1 proteins. Elife 9, e57089.

[2] Dubey, V., et al. (2020) Cholesterol binding to the sterol-sensing region of Niemann Pick C1 protein confines dynamics of its N-terminal domain. PLoS Comput Biol 16, e1007554.

The increasing number of protein structures and the increasing size of protein structures calls for automated methods. The Protein Topology Graph Library (PTGL) [1, 2] models the topology of protein structures as graphs. PTGL supports three levels of abstraction: amino acids, secondary structure elements (SSEs) and chains. For each level of abstraction, the vertices correspond to the level, i.e., vertices correspond to amino acids on amino acid-level and so on. On all abstraction levels, edges denote spatial neighborhoods (contacts). Contacts are based on the computation of Euclidean atom-atom distances. On SSE-level, vertices are labeled as helix or strand. Edges are labeled by the orientation of their SSEs as parallel, antiparallel or mixed. On chain-level, edges are weighted with the number of residue-residue contacts (see Fig 1.).

We used chain-level Complex Graphs (CGs) as a highly abstracted and meaningful view on respiratory complex I. We compared the CGs of the core subunits of complex I between T. thermophilus and H. sapiens. The Complex Graphs shared 29 edges. Each CG had one edge that the other has not. Therefore, the CGs were able to capture the topology of structurally conserved regions.

We applied hierarchical clustering to the edges of a CG. We compared the resulting dendrogram with an assembly process proposed in the literature [4]. Solely based on the CG, we found similarities between the dendrogram and the proposed assembly process. We also applied graph clustering to investigate whether complex I’s modules could be extracted solely from the CG. We showed that CGs could identify modules and guide the finding of the assembly process for complexes.

Concluding, PTGL provides graphs modeling the topology of protein structures on different levels of abstraction for 151.837 PDB structures, including 921 large structures. The webserver provides a search for predefined motifs and user-defined arbitrary patterns. The computation is automated and the implementation publicly available. The representation of graphs enables the application of graph-theoretic methods, such as graph partitioning. This allows feasible analyses on the rapidly growing PDB.

[1] Wolf, J.N., Keßler, M., Ackermann, J. & Koch, I. (2020). Bioinformatics. 37(7), 1032-1034.

[2] May, P., Kreuschwig, A., Steinke, T. & Koch, I. (2009). Nucleic Acids Res. 38, D326-D330.

[3] Baradaran, R., Berrisford, J.M., Minhas, G.S. & Sazanov, L.A. (2013). Nature. 494, 443-448.

[4] Guerrero-Castillo, S., Baertling, F., Kownatzki, D., Wessels, H.J., Arnold, S., Brandt, U. & Nijtmans, L. (2017). Cell Metabolism. 25(1), 128-139.

SARS-CoV-2 (Severe Acute Respiratory Syndrome-Corona Virus 2) spike protein which is the viral protein that causes human cell infections by binding to host cell receptor ACE2 and initiates the membrane fusion. After the entry process, the S-protein needs to be called up and activated by the furin and TMPRSS2 which are the cellular proteases, which stimulates the virus entry into the human cells. By inhibiting the furin protease leads to suppress the spike protein activation in the host cell. The present study aims to understand the intermolecular interactions and binding affinity of furin with its inhibitors decanoyl-RVKR-chloromethylketone (CMK) and Naphthofluorescein which are reported experimentally. The molecular docking studies show the binding affinity of two inhibitors with furin; docking scores for CMK and Naphthofluorescein are -9.727 and -6.036 kcal/mol respectively. The docked complexes of both inhibitors form key interactions with furin and exhibits high docking scores. Further, the molecular dynamics (MD) simulation for both complexes have been performed to understand their stability, shows both inhibitors are stable in the active site region of furin. The RMSD and RMSF plots retrieved from the MD results confirm that CMK molecule having high stability on compare with the Naphthofluorescein. The investigation on furin inhibitors help to evaluate these drugs to be used as a repurposed drug for the SARS-CoV-2. The detailed study will be presented.

Proteins and nucleic acids evolved in the aqueous environment, and water is therefore deeply interrelated with both biomolecular structure and function. The first layer of water molecules around the biomolecular surface - the hydration shell - has properties different from the bulk water [1]. The dynamics of these water molecules is significantly reduced, and the shell mostly consists of ordered (localized) water molecules. However, the first shell water molecules do not have an ice-like structural properties. These ordered water molecules play significant role in recognition and binding of ligands.

In our work, we utilize crystallographic data to compile the average hydration patterns around biomolecules. Firstly, we investigated hydration of DNA building blocks [2, 3], and later hydration of amino acids in proteins as a function of their rotameric state and the secondary structure [4, 5]. Recently, we analyzed hydration of DNA dinucleotides as a function of their conformation and sequence [6]. Here, we present the overview of these results as well as the methodology we used to obtain the data and the potential application of the results.

REFERENCES
[1] Biedermannová L. & Schneider B.: Hydration of proteins and nucleic acids: Advances in experiment and theory. A review. BBA - Gen. 1860: 1821-1835 (2016).
[2] Schneider B. & Berman H.M.: Hydration of the DNA Bases Is Local. Biophys. J. 69: 2661-2669 (1995).
[3] Schneider B., Patel K. & Berman H.M.: Hydration of the Phosphate Group in Double-Helical DNA. Biophys. J. 75: 2422-2434 (1998).
[4] Biedermannová L. & Schneider B.: Structure of the ordered hydration of amino acids in proteins: analysis of crystal structures. Acta Cryst. D71: 2192-2202 (2015).
[5] Černý J., Schneider B. & Biedermannová L.: WatAA: Atlas of Protein Hydration. Exploring synergies between data mining and ab initio calculations. PCCP 19, 17094 (2017).
[6] Biedermannová L. et al., to be published (2021).

Lore of chemical biology guides us that drug discovery of protein binding relies on either optimize the active site complexity of lock and key or induced-fit with conformation selection dynamics; yet, the latter that often-coupled protein interior transport dynamics was much harder to study due to its lack of strong interactions in transient states. This study starts to make progress in using in-situ operando X-ray and neutron contrast variation techniques to depict the landscape of protein binding substrate dynamics in solution. We herein demonstrate, for the first time, the 3-D dynamical structures of hydrated CYP450 protein exterior surfaces to interior buried heme site by a distributed connection of channels that direct the reactant in and out. Using CYP450s of prostacyclin synthase (PGIS) and thromboxane synthase (TXAS) as prototypes we have unveiled the unique dynamics of P450 functional channels in/out the haem site, which drive a variety of water molecules motion, water density change and pre-organization toward the heme active site and hence harness the substrate-binding selectivity. The result is able to clarify how these two proteins catalyze the same substrate of prostaglandin H₂ by entirely different regio-chemical-selective pathways.

SARS-CoV-2, known as severe acute respiratory syndrome coronavirus 2, is a new type of coronavirus responsible for 2019 pandemic of COVID-19. SARS-CoV-2 main protease (M^pro), also a 3C-like cysteine protease (3CL^pro), is one of the key enzymes of coronaviruses and plays a crucial role in mediating viral replication and transcription. Five non-covalent ligands were designed and grown for Southampton 3C-like protease (SV3CP) based on a hit from crystal-based fragment screening. These five ligands were crystalised with SARS-CoV-2 M^pro because of the similar active sites shared by SV3CP and SARS-CoV-2 M^pro, and we determined crystal structures of SARS-CoV-2 M^pro in complex with two ligands (S04 & S05). SARS-CoV-2 M^pro in complex with S05 is shown in Figure 1. We also developed a kinetic assay specific to SARS-CoV-2 M^pro showing Ki values of these five ligands range from 9.3 μM to 0.87 mM. These ligands show their potential as broad spectrum drug leads due to their inhibition activity in different 3CL proteases.

FmtA is a penicillin-recognizing protein (PRP) with novel hydrolytic activity toward the ester bond between d-Ala and the backbone of teichoic acids (TA), the polyol-phosphate polymers found in the S. aureus cell envelope. Two of the PRPs conserved motifs, namely SXXK and Y(S)XN, are involved in this hydrolysis, but its catalytic mechanism remains elusive. Here we determined the crystal structure of FmtA. FmtA shares the core structure of PRPs: an all α-helical domain and α/β domain sandwiched together. However, it does not have the typical PRPs active-site cleft. Its active site is shallow, solvent-exposed and wide. Furthermore, the SXXK and Y(S)XN motifs of FmtA offer all that is necessary for catalysis: the active-site nucleophile (serine) and the general base (lysine) required for acylation and deacylation steps and an anchor (tyrosine) to hold the active-site serine, and possibly the substrate, in an optimum conformation for catalysis [1]. Our study establishes that the FmtA esterase activity represents an expansion of the catalytic activity repertoire of the PRPs core structure, which typically displays peptidase activity. The structure of FmtA provides insights to the design of inhibitor molecules with the potential to serve as leads in the development of novel antibacterial chemotherapeutic agents.

[1] Dalal, V., Kumar, P., Rakhaminov, G., Qamar, A., Fan, X., Hunter, H., Tomar, S., Golemi-Kotra, D. and Kumar, P., (2019). Journal of molecular biology, 431(17), pp.3107-3123.

The antibiotic resistance incidence is alarmingly increasing in both human and veterinary medicine and is one of the major concerns of contemporary healthcare. Because most of the currently used antibiotics have natural analogs with similar native structures, AMR-associated genes are widely present in bacteria in the environment, and they can be easily distributed to clinically important strains through horizontal gene transfer. Such bacteria pose a threat primarily in hospitals, where infections of immunocompromised patients often end fatally. A small group of bacteria causing nosocomial infections are present in both the developed and developing world; it is called ESKAPE in abbreviation and is comprised of Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and other Enterobacteriaceae species. These pathogens represent the most significant threat among the so-called superbugs, which can rapidly acquire resistance to several classes of antibiotics and can cause a variety of nosocomial infections, mostly in the respiratory or urinary tract, but bloodstream, wound, and skin infections are also frequent. Overall, nosocomial infections result in increased mortality and morbidity rate in the affected patients.

For endolysins targeting Gram-negative bacteria the specific activity against a broad host range is a known phenomenon, however, the molecular mechanisms specifying their broad spectrum of action are obscure. There is still no global understanding, whether bacterial cell lysis with endolysins is determined by the action of the enzymatic activity of the proteins or by additional functional domains containing in their structure, or the action of endolysins against Gram-negative microorganisms is determined by the joint interaction of several distinct domains.

Here we propose to investigate in details the structural aspects of LysSi3 endolysin mechanism of action. The LysSi3 is a peptidoglycan hydrolyzing, lysozyme-like enzyme with predicted muramidase activity (GH24 family) and broad bactericidal activity against ESKAPE pathogens.

Thalidomide (Thal) exerts adverse effects such as teratogenicity, but it is used for the therapy of multiple myeloma and other haematologic malignancies as immunomodulatory imide drugs (IMiDs). The molecular mechanism of thalidomide's pharmacological action has been gradually elucidated through the search for multiple target proteins that thalidomide acts on. Celebron (CRBN) is the intracellular receptor for Thal and induces Thal-dependent degradation of target protein (neosubstrate) as a component of an E3-ubiquitin ligase. Although C2H2 zinc finger (ZF) transcription factors, IKZF1 and SALL4, are concerned in immunomodulatory effects and teratogenicity of Thal, respectively, a primary Thal metabolite, 5-hydroxythalidomide (5HT), induces degradation of SALL4 but not IKZF1. Due to the action of the enzyme cytochrome P450 in the body, the administered thalidomide produces 5HT. Here, we focused on the molecular mechanism in which the selectivity of Thal toward C2H2 ZF-type neosubstrates is altered with its metabolism. First, we characterized the enantioselectivity of the formation in the SALL4-CRBN complex. The (S)-enantiomer of Thal and 5-HT showed more effect than the (R)-enantiomer, which is consistent to “Left-hand (S-form) theory of teratogenicity” of Thal. Based on the enantioselectivity, we determined the crystal structures of the ternary complexes of the Thal-binding domain (TBD) of human CRBN and the second ZF domain (ZF2) of human SALL4 induced by (S)-Thal and (S)-5HT. As a result, Thal and 5HT positioned between the interface of SALL4 ZF2 and CRBN TBD to mediate the protein-protein interaction as molecular glues. Although both compounds occupy at the same position in the SALL4-CRBN complex, the 5-hydroxy group of 5HT forms an additional hydrogen bond with CRBN TBD through a water molecule, which enhances the formation of the SALL4-CRBN complex. The 5-hydroxy group is also located near the 2nd and 9th residues of the β-hairpin structure in SALL4 ZF2, and these residues are different from IKZF1. The complex formation and proteasomal degradation experiments using the residue-swap mutants of SALL4 and IKZF1 elucidated the variation in the 2nd residue of β-hairpin structure defines the neosubstrate selectivity of 5HT. Thalidomide’s action on its target is altered through its metabolism in the body and if the hydroxylation of thalidomide found in this study is avoided, a new designed drug can be expected to reduce teratogenicity. Furthermore, our findings indicate that the structural differences found in C2H2 ZF-type transcription factors may be exploited to increase the efficiency of action of IMiDs, including thalidomide, on target proteins required for drug efficacy.

Antimitotic agents that target mitotic kinesins such as centromere associated protein E (CENP-E), are expected to be more likely to work on dividing cells but not non-dividing cells. Thus, antimitotic agents that inhibit the functions of the kinesin motor domains will minimize toxicities to non-dividing cells, causing lower side effects [1].

The motor domain, located at the N-terminus of CENP-E, is the active site of ATPase activity. Up to now, the only one crystal structure of CENP-E motor domain in complex with MgADP has been reported [2]. It is difficult to perform rational drug designing by fragment-based drug discovery (FBDD) or structure-based drug design (SBDD) due to the lack of structural information about CENP-E. Therefore, it is necessary to determine the crystal structure of CENP-E motor domain in complex with its inhibitors.

Here, in order to elucidate the mechanism how CENP-E motor domain binds to its inhibitor, we tried to cocrystallize CENP-E motor domain in complex with its ligand, 3-chloro-4-isopropoxyl benzoic acid (CIBA), one of the ATP-competitive inhibitors, or GSK923295, one of the ATP-uncompetitive inhibitors. First, we crystallized CENP-E motor domain in complex with CIBA, and determined the structure at 1.9 Å resolution (Figure 1). Endogenous ADP instead of CIBA was observed at the nucleotide-binding site, although ATP or ADP was not added. The determined structure of the CENP-E motor domain was compared with other kinesin motors. Based on the characteristic structure of CENP-E, the mechanism by which ADP is retained in CENP-E is discussed [3].

Next, in order to elucidate the structure in complex with an ATP analog, we tried to determine the structure of CENP-E motor domain in the presence of AMPPNP and Mg²⁺ at 1.8 Å resolution. Crystals belong to space group P2₁2₁2 with two molecules in the asymmetric unit. Structure refinement is now in progress.

[1] Sakowicz, R., Finer, J. T., Beraud, C., Crompton, A., Lewis, E., Fritsch, A., Lee, Y., Mak, J., Moody, R., Turincio, R., Chabala, J. C., Gonzales, P., Roth, S., Weitman, S. & Wood, K. W. (2004). Cancer Res. 64, 3276–3280.

[2] Garcia-Saez, I., Yen, T., Wade, R. H. & Kozielski, F. (2004). J. Mol. Biol. 340, 1107–1116.

[3] Shibuya, A., Ogo, N., Sawada, J., Asai, A., & Yokoyama, H. (2021). Acta Crystallographica Section D, D77, 280-287.

We would highly appreciate the cooperation and support rendered to us by all the staff members of High Energy Accelerator Research Organization in Tsukuba. We thank all involved in holding this congress.

Despite progress in vaccine development, antivirals targeting SARS-Co-2 are needed for those who are immunocompromised, and for future outbreaks. Proteases cleave peptide bonds of a very specific sequence making them strong drug targets. Antivirals that target proteases are already used clinically to treat HIV and Hepatitis C virus. We have developed inhibitors of the SARS-CoV-2 protease to prevent the main protease (M^pro or 3CL^pro) from cleaving the viral polypeptide and subsequent viral replication in cells. We developed novel α-acyloxymethylketone warhead peptidomimetic compounds with a 6-membered lactam glutamine mimic in P1. Compounds with potent SARS-CoV-2 3CL protease and in vitro viral replication inhibition were identified with low cytotoxicity and good plasma and glutathione stability. α-Acyloxymethylketone compounds also exhibited antiviral activity against an alpha- and non-SARS beta-coronavirus strains with similar potency and better selectivity index than remdesivir. X-ray crystallography revealed the mechanism of inhibition, and has helped the optimisation of new derivatives. Moving forward, these inhibitors will be tested with variant proteases, followed up by studies in animals to determine efficacy and pharmacokinetics in preparation for clinical trials.

The idea to use data mining techniques to derive force field basing on crystallographic structural information we reported first on the ECM18 (1998) in Prague. We will give an outline of the machine learning, present the results of the validation, and give an insight to some applications.

The approach is based on the idea that experimental the lattice energy of crystals must fulfill three conditions regarding the Gibbs energy. The lattice energy must be below zero, the crystal structure must be a local minimum, and, if available, the experimental and the calculated lattice energy must coincide. These equations can be used for the parametrization of a given model (Force Field or DFT-functional) by machine learning. The properly parametrized data mining force field¹ allows to calculate the Gibbs lattice energy of all known crystal structures within a few hours. Since the Gibbs energy defines the reaction energy, the obtained energies can be used to predict chemical-physical properties of crystals, for instance, the formation of co-crystals, polymorph stability, and solubility.

The parametrized “data mining force field” was validated regarding the three conditions mentioned above: firstly, the experimental lattice energies of the reference structures have been compared with the calculated energies. The observed errors are in the order of experimental errors. Secondly, the Gibbs lattice energies were calculated for all crystal structures available in CSD. Their energies were found below zero in 99.4 %. Finally, for 500 random structures the change in density and energy was checked. The mean errors for density was found below 5%, for the energy below 2%.

The very high speed, around 5 s per minimization, makes the model attractive for more complex tasks: for crystal structure prediction. Crystal structure prediction requires several hundred minimizations and a proper similarity index between crystal structures². Even more complex is an in silico co-crystal screening³. It requires hundreds of crystal structure predictions in a reasonable time. On the high performance computing cluster of CRS4 this can be done with a few days.

1. Hofmann, Detlef WM. "Data mining in organic crystallography." Data Mining in Crystallography. Springer, Berlin, Heidelberg, 2009. 89-134.

2. Hofmann, Detlef Walter Maria, and Ludmila Kuleshova. "New similarity index for crystal structure determination from X-ray powder diagrams." Journal of applied crystallography 38.6 (2005): 861-866.

3. Stepanovs, Dmitrijs, et al. "Cocrystals of pentoxifylline: In silico and experimental screening." Crystal Growth & Design 15.8 (2015): 3652-3660.

Figure 1: The crystal structure of the cobalt complex JUDLEZ is found positive during validation. The reason is a misplaced hydrogen. As consequence to one carbon is assigned the atom type “hypercovalent carbon” C and during the energy calculation a strong repulsive interaction between C4 and C is found. The force field and the data base are constantly improved by analyzing such kind of outliers.

Porous organic cages are a subset of porous materials which are made up of covalently bonded organic molecules forming cages with intrinsic porosity. Unlike extended framework materials, such as metal organic frameworks which are connected through covalent or coordination bonds, the assembly of porous organic cages is defined by weak dispersion forces. Therefore, the connectivity between the cages can be easily manipulated by varying the chemical functionality or solvent [1]. This leads to a variety of porous organic cage solids which, depending on the packing behaviour, may contain only intrinsic cavities or have extrinsic pores between the cages resulting in one, two, or, three dimensional pore networks [2]. Consequently, the packing behaviour of the porous organic cages can have a vast effect on the properties of the material [3]. It has been suggested that in principle, different cages can be combined to produce structures with specific properties [4]. However, the challenge in reliably predicting the packing behaviour of molecular crystals, due to the lack of strong bonding networks, results in difficulty in targeted design [4].

Although crystal structure prediction can accurately determine crystal energy landscapes, it is computationally expensive to apply to multiple molecular combinations [5]. Here we aim to determine the packing behaviour of porous organic cages through coarse graining. We start by creating a coarse grained Hamiltonian containing the dominant intermolecular interactions between the cages, informed by force field models. We then aim to employ Monte Carlo simulations using our model in conjunction with hard particle Monte Carlo simulations [6] to determine the thermodynamic phase behaviour of the packing of the cages. This work focuses on the well-studied porous organic cage CC3 [1] as a proof-of-concept example to determine the extent to which we can use coarse graining to analyse the packing behaviour of other, less well-studied porous organic cages.

References: 1. T. Tozawa, J. Jones, S. Swamy, et al. Nature Mater 8, 973–978 (2009)

2. Y. Liu, G. Zhu, W. You, et al. J. Phys. Chem. C 123, 3, 1720–1729 (2019)

3. M. E. Briggs and A. I. Cooper Chem. Mater. 29, 1, 149–157 (2017)

4. J. Jones, T. Hasell, X. Wu, et al. Nature 474, 367–371 (2011)

5. T. Hasell, S. Y. Chong, K. E. Jelfs, et al. J. Am. Chem. Soc. 134, 1, 588–598 (2012)

6. J. A. Anderson, M. E. Irrgang, and S. C. Glotzer. Computer Physics Communications 204, 21-30 (2016)

The ability to predict physicochemical properties starting from 2-dimensional molecular information is of paramount importance within the crystal engineering discipline, finding applications in industries as diverse as pharmaceuticals, agrochemicals, and pigments.

Within the CCDC, we have been developing a suite of predictive methods to help scientists assess the likely properties of a given small molecule.

The large amount of data available and the fast-growing Artificial Intelligence (AI) field can now facilitate the development of software tools allowing such predictions. Due to the rise of new and easy to implement Machine Learning (ML) algorithms in recent years^1–3 multiple scientific questions have been answered by applying AI approaches. It is now possible to quickly predict NMR spectra using ML models based on quantum calculations¹ which help with the interpretation of experimental NMR spectra. Space groups can be predicted solely based on Pair Distribution Functions,² and for the first time a new antibiotic was identified using ML, thus significantly reducing the number of experiments required.³

We have developed a method that provides an early-stage assessment of the likelihood of solvate formation, so that this can be factored into target compound selection and experimental solid form screening can be planned more effectively. Using a sophisticated machine-learning approach we can predict solvate formation quickly using only 2D molecular information. The addition of effective assessment of the likelihood of solvate formation to our solid form design toolbox takes us a big step closer towards more a complete understanding of the behaviour of compounds in the solid state as well as the ability to factor in prediction of solid-state properties in the design stage of a project.

1 W. Gerrard, L. A. Bratholm, M. J. Packer, A. J. Mulholland, D. R. Glowacki and C. P. Butts, Chem. Sci., 2020, 11, 508–515.

2 C. H. Liu, Y. Tao, D. Hsu, Q. Du and S. J. L. Billinge, Acta Crystallogr. Sect. A Found. Adv., 2019, 75, 633–643.

3 J. M. Stokes, K. Yang, K. Swanson, W. Jin, A. Cubillos-Ruiz, N. M. Donghia, C. R. MacNair, S. French, L. A. Carfrae, Z. Bloom-Ackerman, V. M. Tran, A. Chiappino-Pepe, A. H. Badran, I. W. Andrews, E. J. Chory, G. M. Church, E. D. Brown, T. S. Jaakkola, R. Barzilay and J. J. Collins, Cell, 2020, 180, 688-702.e13.

Structural information on ternary metal-aromatic amine-nucleotide complexes is required to explicate the role of metal ions in protein-nucleotide interactions. In the present work, we report two ternary copper complexes i.e., Cu-tpy-GMP (A) and Cu-tpy-CMP (B) [ tpy - 2, 2’:6’, 2” terpyridine, GMP – Guanosine 5’-monophosphate, CMP – Cytidine 5’-monophosphate], where both are 1D(linear) coordination polymers. They are crystallized in space groups P2₁(A), and P2₁2₁2₁(B) with habit block and rhombus, respectively. In polymer A, the monomer is hexanuclear and the metal ions are bridged by two ‘O’s of phosphate group, O6 and N7 of the heterocyclic base, giving distorted square pyramidal geometry to all the Cu centres. In tetranuclear monomeric unit of polymer B, the metal ions are bridged by one ‘O’ of the phosphate group, O2 and N3 of the heterocyclic base, giving two different geometries i.e., distorted octahedral to 2 Cu and distorted square pyramidal to 2 other Cu centres. Polymer A has 2 units of 5’-GMP and B has the same number of 5’-CMP units in the monomeric asymmetric unit. The spectator molecules are 6 perchlorates, 1 H₂O and 3MeOH in Polymer A, whereas Polymer B has 4 perchlorates and 16 H₂O. The point of polymeric chain extension is at O6 of one nucleotide and Cu ion in Polymer A, but in Polymer B it is at sugar ring OH of one nucleotide and Cu ion. Both the structures are stabilized by H-bonding and pi-pi stacking interactions.

The greatest usage of paracetamol is in the pharmaceutical industry. Paracetamol shows a considerable tendency to polymorphism and the aim of this work was to predict the crystal structure of its most stable polymorph. We achieved the goal by generating a large number of structures by Grid Search and subsequent reducing of the number of structures using the global optimization algorithm Particle Swarm Optimization.

Photocrystallography is a technique used to determine light-induced structural changes accompanying formation of excited-state species, or other photoreaction products, in crystals via X-ray diffraction methods. Among others, it can be employed to investigate photo-linkage isomerism in the solid state. Photoswitchable compounds of this kind contain ambidentate ligands, e.g., NO₂, SCN or NO groups, which can bind to a metal centre in several different ways. Such linkage isomers can exhibit different physical properties such as: colour, density, or conductivity, which makes them interesting materials for various applications. Photoswitchable systems can be used in data storage devices, solar panels, as biological markers, etc.

The current project is dedicated to comprehensive investigations of a series of trinitrocobalt(III) coordination compounds[1] which are potential photoswitchable systems. According to literature cobalt nitrocomplexes may exhibit thermoswitchable properties[2], but there is in general very limited information about light-induced linkage isomerism of this group of compounds. In turn, three nitro groups attached to a metal centre interact in a crystal structure in different ways, which enables analyses of the crystal packing effect on photoswitchable properties. In the course of our research conditions assuring the most effective isomerisation reaction in the examined crystal systems were determined on the basis of multi-temperature X-ray diffraction, photocrystallographic and spectroscopic measurements results. Additionally, the influence of packing and intermolecular interactions on the isomerisation reaction was examined. The experimental findings were supported by theoretical computations.

It appeared that some of the studied compounds undergo the nitro group isomerisation reaction along with temperature changes, while the metastable-state form, nitrito isomer, may exist up to a relatively high temperature (about 240 K). Nevertheless the thermo-induced conversion usually does not exceed 30%. UV-Vis-light irradiation (230-660 nm) of the crystal samples elevates the observed conversion by only several percent. It was observed that the nitro groups engaged in relatively strong hydrogen bonds with the amine fragments of adjacent molecules do not undergo any transformation. Also, the stabilisation of the potential metastable-state form in the crystal structure is of great importance.

The authors thank A. Krówczyński and W. Buchowicz (Warsaw, Poland) for assistance during the syntheses of the examined compounds. The PRELUDIUM grant (2017/25/N/ST4/02440) of the NCN (Poland) is gratefully acknowledged for financial support. The X-ray diffraction experiments were carried out at the Department of Physics, UW, on a Rigaku Oxford Diffraction SuperNova diffractometer, which was co-financed by the EU within the European Regional Development Fund (POIG.02.01.00-14-122/09).

This research work reports the crystal structure, chemical bonding, cation distribution of three series of Cr³⁺ substituted cobalt ferrite with general formula Co_1-xCr_xFe₂O₄, Co_1+xCr_xFe_2-xO₄ and Co_1-xCr_xFe_2+xO₄ for x=0.0, 0.125, 0.25, 0.375 and 0.5, where first of the three series were calculated with stoichiometric and others were calculated with non-stoichiometric ratio. All three series of samples have been synthesized by solid-state reaction technique via ball milling for 12 hours and performing the sintering temperature of 1250o C. From the analysis of crystal structure studied by powder X-ray diffraction (XRD) technique, it is confirmed that the first two series of samples formed into a single phased cubic structure with a space group of Fd3m. But for the third series despite showing the cubic structure with a space group of Fd3m some impurity peaks of α-Fe2O3 have been observed which may due to the excess Fe. The cation distribution for the three series of samples has been estimated by the Reitveld analysis. The refinement result shows the occupancy of Cr has been found in both the tetrahedral site (A-site) and octahedral site (B-site) with exact ratio. The theoretical lattice constant has been calculated from the Reitveld refined data. For the first stoichiometric series after increasing of Cr concentration the increasing trend of experimental lattice constant related to theoretical lattice have been found but for the other two non-stoichiometric series, both types of lattice constant are decrease. Chemical bonding analyses made using Raman spectroscopic studies further confirm the cubic inverse spinel phase. Specific vibrational modes from the Raman data suggest a gradual change of inversion of the ferrite lattice with the increase of Cr concentration that is also confirm from Reitveld refined data.

Since the strain/structural defects strongly influence the physical properties [1], considerable work has been devoted for revealing their effects in both planar epitaxial layers and nanostructured materials [2]. Thus, the study of the strain field in nanomaterials represents a very important topic among different fields of applications. The quantitative analysis of the structural defects, as well as a deeper understanding of their source and nature became a highly desirable task associate to the further device development [3].

For this purpose, one of the common techniques used to detect the structural defects and quantify their density is X-ray diffraction (XRD). Recently, it was shown that the standard mosaic block or diffuse scattering models fail in the quantification of the structural defects in nanowires, and thus development of a new method became necessary [4]. In this paper, varying the incidence angle of the source, we get different penetration depths of the X-rays for different Si nanowire array morphologies – Figure 1.

Figure 1. The incidence angle of the source was varied to get different penetrationdepths of the X-rays. Recording X-ray profiles along ω and φ, we obtained bendingand torsion energy profiles.

Furthermore, implementing a new formalism based on these data, we obtained the bending and torsion profiles along z-direction, as well as the bending and torsion energy profiles. Attributing the entire energy lost to the dislocations’ formation at the coalescence regions we were able to estimate the dislocation density in nanowire arrays. The obtained results clearly suggest the close relationship between array morphology and the density of the edge and screw threading dislocations. Moreover, the impact of graphene quantum dots (GQDs) in the strain relaxation processes will be discussed.

[1] Lewis, R. B., Corfdir, P., Küpers, H., Flissikowski, T., Brandt, O. & Geelhaar, L. (2018). Nano Lett. 18, 2343–2350.

[2] Kaganer, V. M., Jenichen, B. & Brandt, O. (2016) Phys. Rev. Appl. 6, 064023.

[3] Mihalache, I., Radoi, A., Pascu, R., Romanitan, C., Vasile, E., Kusko, M. (2017) Engineering graphene quantum dots for enhanced ultraviolet and visible light p-Si nanowire-based photodetector, ACS Appl. Mater. Interf. 9, 29234-29247.

[4] Romanitan, C., Kusko, M., Popescu, M., Varasteanu, P., Radoi, A., Pachiu, C. (2019) J. Appl. Crystallogr., 52, 1077-1086.

The financial support was offered by the PN-III-P4-ID-PCE-2020-1712 project within PNCDI III, and Core Program PN 1916/2019 MICRO-NANO-SIS PLUS/08.02.2019.

Resolution of ferrocene and deuterated ferrocene conformations using dynamic vibrational IR spectroscopy

N. T. T. Tran¹, R. M. Trevorah¹, C. T. Chantler¹, D. R. T. Appadoo², F. Wang³

¹ School of Physics, The University of Melbourne, Parkville, Victoria 3010, Australia, ²Australian Synchrotron, 800 Blackburn Rd, Clayton Victoria 3168, Australia, ³Department of Chemistry and Biotechnology, Swinburne University of Technology, Hawthorn, Victoria 3122, Australia

nicholast2@student.unimelb.edu.au

The signature of molecular vibrations and distortions in dynamic molecules gives a complex fingerprint which is insightful and can substantiate chemical hypotheses regarding molecular and conformer stability. Using high-accuracy experimental data of ferrocene (Fc) and deuterated ferrocene (dFc, Fc−d¹⁰) at temperatures from 7 K through to 388 K, we obtain complex spectral profiles which require an advanced reaction coordinate model to explain [1]. We obtain compelling evidence that the single conformer model (staggered D_5d or eclipsed D_5h) used to interpret and explain many experimental results on ferrocene is invalid. We also present compelling evidence that mixed conformer models are invalid, where ferrocene is represented by an effective dihedral angle between the cyclopentadienyl (Cp) rings; or by a mixture of Boltzmann populations of the two conformers. We find no evidence for single or mixed conformer models despite covering almost all conclusions from past literature for gas, solution or solid phase Fc [1].

A new principle based on the reaction coordinate is introduced using advanced spectroscopy and modelling for hypothesis testing, to articulate the nature of the potential surface, the reaction coordinate, and subtle conformational changes in dilute systems [1]. Theoretical calculations of the infrared spectra of D_5h and D_5d with the B3LYP/m6-31G(d) functional highlights a significant difference between Fc conformations around 450 – 500 cm^-1 [2] and early investigations provided key insight into the quantum dynamics of ferrocene [3]. A new methodology for obtaining defined uncertainties with high quality Fourier Transform Infrared (FTIR) measurements allow for quantitative hypothesis testing [4] for complex structural determination. Our experimental analysis shows that the lowest energy conformer is D_5h for both Fc and dFc at low temperatures, but as temperature increases, the population of occupied vibrational modes increases towards the D_5d conformation [1]. We obtain agreement of the model with the complex spectral evolution of profiles. These new techniques are sensitive discriminants of alternate models and chemical systems, which argues for wider application to other complex or impenetrable problems across fields arising for numerous other solutions, frozen or at room temperature.

[1] Trevorah, R.M., Tran, N.T.T., Appadoo, D.R.T., Wang, F., Chantler, C.T. (2020). Inorganica Chimica Acta, 506, 119491

[2] Mohammadi, N., Ganesan, A., Chantler C.T., Wang, F. (2012). Journal of Organometallic Chemistry. 713, 51-59

[3] Best, S.P., Wang, F., Islam, M.T., Islam, S., Appadoo, D., Trevorah, R.M., Chantler, C.T. (2016). Chemistry – A European Journal. 22 (50), 18019-18026

[4] Islam, M.T., Trevorah, R.M., Appadoo, D.R.T., Best, S.P., Chantler, C.T. (2017). Spectrochimica Acta -Part A: Molecular and Biomolecular Spectroscopy, 177, 86-92

Keywords: Infrared spectroscopy; Stereochemical analysis; Ferrocene; High-resolution FTIR

This research is supported by the AINSE Honours Scholarship Program.

For the first time the growth of a single GaAs nanowire (NW) was monitored by in-situ time resolved X-ray nano-diffraction (nXRD) using focused synchrotron radiation at beamline P09 of PETRA III storage ring (Hamburg) and a portable MBE chamber [1]. A particular position for nucleation and growth was selected within an array of holes with 5 micron pitch prepared on a lithography-free pre-patterned Si(111) substrate covered by 16nm thick oxide [2]. Exploiting a photon flux of 4·10⁹ Photons·s^-1 focused in a micro-beam of 2 x 6 micon² and probing the GaAs 111 Bragg reflection the first NW signal of above the background did appear about 24 minutes after opening the Ga and As shutters, corresponding to a NW length and diameter of about 45 nm and 28 nm, respectively. The time evolution of the NW signal could be monitored for 55 minutes up to the final length and diameter of about 2000nm and 45nm, respectively. Both parameters and the NW orientation with respect to the substrate normal were evaluated from the peak intensity and peak shape and position after background correction and separation of the NW signal from that of a parasitic island growing within the same probing volume. The final NW dimensions extracted from XRD analysis are in good agreement with ex-situ SEM data taken from the same NW after growth. In the experiment reported the observed time evolution of NW growth follows two subsequent stages: 1) dominant axial growth accompanied by unstable axial orientation of the NW followed by 2) increase of radial growth at stable axial orientation. Although successful proof of principle, quantitatively the experiment suffered from tiny fluctuations of the spatial position of the micro-beam during the entire growth cycle and/or limitations in the accuracy of angle settings.

Active research in the field of condensed matter and nanotechnology not only led to significant progress in understanding the mechanisms of formation of electrical polarization and magnetoelectric phenomena, but also showed the possibilities of creating new classes of devices based on a combination of magnetoelectric and piezoelectric properties. Meanwhile, macroscopic properties, such as multiferroism and piezoelectricity, are associated with local structural changes that occur under the influence of external perturbations. In a first step chosen crystal structures are analyzed by means of density functional theory (DFT) to validate the connection of external stress and internal change of lattice symmetry as well as atomic displacements. Among them are TeO₂, Li₂B4O₇, ZnO and SrTiO₃. Also in focus is the influence of oxygen vacancies on our structures. The research is currently accompanied by experiments in which standing acoustic waves are encoupled in crystal samples to change the structure parameters and particularly the structures' symmetry locally. Because the displacements are expected to be on the picometer scale, X-ray diffraction on forbidden reflections is applied to observe the induced effects. The obtained switching results can significantly widen the range of functional materials and can be directly used in modern technological applications.

Structures and luminescent properties of KGd_1−xEu_x(MoO₄)₂ (0≤x≤1) S. Posokhova, D. Deyneko, B. Lazoryak, V. Morozov ¹Lomonosov Moscow State University, GSP-1, Leninskie Gory, Moscow, 119991, Russian Federation posohovasm@gmail.com

Mo-based compounds with rare-earth elements are investigated as luminescent materials for photonic applications, such as phosphor converted LEDs (light-emitting diodes).¹ The influence of annealing temperature and Eu³⁺ concentration on the structure and luminescent properties of the KGd_1−xEu_x(MoO₄)₂ (0≤x≤1) was studied. Three polymorphs of KGd_1−xEu_x(MoO₄)₂ were present in the 923-1223 K range of annealing temperatures under ambient pressure: a triclinic α-phase, an incommensurately modulated monoclinic b–phase and an orthorhombic γ-phase with a KY(MoO₄)₂-type structure. The number and the character of phase transitions for KGd_1−xEu_x(MoO₄)₂ depend on the elemental composition. The formation of a continuous range of solid solutions with the triclinic α-KEu(MoO₄)₂–type structure and ordering of K⁺ and Eu³⁺/Gd³⁺ cations were observed only for the α-KGd_1−xEu_x(MoO₄)₂ prepared at 923 K.

The luminescent properties of KGd_1−xEu_x(MoO₄)₂ prepared at different annealing temperature were studied and related to their different structures. All samples’ emission spectra exhibit an intense red emission originating from the Eu³⁺⁵D₀→⁷F₂ transition. The maxima of the ⁵D₀ → ⁷F₂ integral emission intensities were found under excitation at, respectively, λ_ex = 300 nm and λ_ex = 395 nm for triclinic scheelite-type α-KGd_0.6Eu_0.4(MoO₄)₂ and for monoclinic scheelite-type β-KGd_0.4Eu_0.6(MoO₄)₂ prepared at 1173 K. The latter shows the brightest red light emission among the KGd_1−xEu_x(MoO₄)₂ phosphors. The maximum and integral emission intensity of β-KGd_0.4Eu_0.6(MoO₄)₂ in the ⁵D₀→⁷F₂ transition region is by ~20% higher than that of the commercially used red phosphor of Gd₂O₂S:Eu³⁺. β-KGd_0.4Eu_0.6(MoO₄)₂ with the incommensurately modulated structure is very attractive to be applied as a near-UV convertible red-emitting phosphor for LEDs.

Figure 1. Comparative integral intensity of the ⁵D₀ → ⁷F₂ emission of different Eu³⁺ concentration for KGd_1−xEu_x(MoO₄)₂ phases prepared at different annealing temperatures and after different excitations. All intensities are normalized on the integral intensity value of α-KEu(MoO₄)₂ (I_int). [1] Li, J.; Yan, J.; Wen, D.; Khan, W.U.; Shi, J.; Wu, M.; Sua, Q.; Tanner, P.A. Advanced red phosphors for white light-emitting diodes. J. Mater. Chem. C. 2016, 4, 8611-8623

Keywords: structure; phase transitions; molybdate; luminescence; Eu³⁺; LEDs.

This research was supported by the Russian Foundation for Basic Research through grants 18-03-00611.

Schiff bases have a remarkable coordinative capability with a wide range of transition metals, making their application in various fields of chemistry of great importance as well as a key research area.¹ The ability of Schiff bases to coordinate with many different transition metals and to stabilize different oxidation states of the metals cause Schiff bases and their metal complexes to be effective catalysts.² The ease of Schiff base preparation also allows for innumerable different modifications and functionalizations to be done to promote their catalytic activity. Many Schiff base complexes are thermally and moisture-stable and are therefore useful catalysts in high-temperature reactions.³ It has also been found that these Schiff base ligands, upon complexation with transition metals, can play an important biological role in that they have anti-bacterial, anti-fungal, anti-cancer, antioxidant, anti-inflammatory and antiviral activity.⁴

Research and development in the field of fluorescence and particularly the design and synthesis of fluorescent chemosensors have grown tremendously in the last 50 years.⁵ The application of fluorescent chemosensors is important in biochemical, physiological, pharmacological and environmental studies with the scope of analytes including cations, anions, small neutral molecules and biomacromolecules. Schiff bases have found application in the field of fluorescence with numerous studies showing its efficiency, especially in the development of fluorescent chemosensors. The photoluminescence feature of Schiff base ligands also finds application in the development of radiopharmaceuticals.⁶ In this field, cellular imaging is used to identify possible compartmentalization of drugs within cells as well as the incorporation and distribution thereof within cells and the information obtained is used to elucidate the biochemical mechanism of these drugs.⁷ A recent study showed the possibility of incorporating a Schiff base into targeting radiopharmaceuticals where it acts as a linker/chelating agent to connect the biomolecule to the radionuclide. The ease of its synthesis and structure-manipulation to contain a variety of functional groups, as well as its possible cellular imaging abilities (due to its photoluminescence), made Schiff bases excellent candidates for this application.

Protein crystallography has proven vital in the field of drug design.⁸ The molecular structure of the protein can be obtained which is necessary for the design of a suitable drug. Protein crystallography further provides structural information regarding protein-ligand interactions and subsequent insight into required ligand-modifications for optimal pharmacological action on molecular targets.

For this study, the main objective is to synthesize and fully characterise various sterically and electronically modified Schiff base ligands (IR, NMR, UV/Vis and single-crystal X-ray crystallography) followed by coordination to transition metals of Rh, Re, Pt, Pd, Co and Ni. Thereafter to perform luminescent analysis and protein crystallization on these ligands and complexes to observe protein-ligand interactions. These organometallic complexes can also potentially be utilized as catalysts in homogeneous catalysis, namely carbonylation, hydroformylation and homologation.

Seven unique N,O-bidentate Schiff base ligands were synthesized and fully characterized using IR, NMR and UV/Vis. Multiple crystallization experiments were conducted. The crystal structures of four of the Schiff base ligands were obtained. Experiments to coordinate the ligands with Co(II), Ni(II), Cu(II) and Zn(II) were performed. Crystal structures of three of these organometallic complexes (two Ni-complexes and one Co-complex) were obtained using single-crystal X-ray crystallography. Luminescence studies on all ligands were conducted, four of which showed strong luminescence at 365 nm while the remaining three appeared dark at 365 nm. The results will be described in this presentation.

Since the development of the ^99mTc generator in the 1950’s and subsequent introduction of the ¹⁸⁸Re generator the development of technetium and rhenium radiopharmaceuticals has been of great interest to the scientific community.¹ Our research is focused on the development of a target specific radiopharmaceutical. [2] In particular we are interested in using chemical functionalities of biological significance as targeting vectors for model radiopharmaceuticals wherein potential theranostic applications are considered using both ^99mTc and ¹⁸⁸Re nuclides in a cluster complex. [3]

This study is focused on the fac-[Re(CO)₃]⁺ moiety [4–6] and utilizes the {2+1} mixed ligand concept, [7] which gives the freedom to coordinate a bioactive site-containing molecule as either a monodentate or bidentate ligand to the fac-[Re(CO)₃]⁺ core. Model complexes were synthesised, aimed at improving the linking between a biomolecule and the metal centre. Additionally investigations into altering the nuclearity of metal complexes for the development of theranostic radiopharmaceuticals will be discussed. In order to understand the possible pathways that a particular drug may partake in during administration, kinetic investigations were considered important. [8] For this reason we have conducted substitution kinetics to further our understanding on how these metal complexes could behave in vivo. Furthermore we will focus on exploring the weak interactions such as hydrogen bonding as observed in small molecule crystal structures and coordinate to a protein residue in an attempt to understand and predict how and where these compounds will interact in a biological setting.

[1] Jürgens, S.; Herrmann, W. A.; Kühn, F. E. (2014) J. Organomet. Chem. 751, 83–89.

[2] Top, S.; Hafa, H. El; Vessières, A.; Jaouen, G.; Quivy, J.; Vaissermann, J.; Hughes, D. W.; McGlinchey, M. J.; Mornon, J. P.; Thoreau, E. (1995) J. Am. Chem. Soc. 117, 8372–8380.

[3] Mokolokolo, P. P.; Frei, A.; Tsosane, M. S.; Kama, D. V; Schutte-smith, M.; Brink, A.; Visser, H. G.; Meola, G.; Alberto, R.; Roodt, A. (2018) Inorganica Chim. Acta 471, 249–256.

[4] Alberto, R.; Schibli, R.; Schubiger, P. A. (1996) Polyhedron 15, 1079–1089.

[5] Jacobs, F. J. F.; Brink, A. (2020) Zeitschrift für Krist. - New Cryst. Struct. 236, 253–255.

[6] Jacobs, F. J. F. FUNCTIONALISED NITROGEN BASED LIGANDS IN DINUCLEAR RHENIUM MODEL RADIOPHARMACEUTICALS, Univeristy of the Free State, 2020. (Supervisors Brink, A. & Venter, G.J.S.)

[7] Mundwiler, S.; Kundig, M.; Ortner, K.; Alberto, R. (2004) Dalton Trans. 99, 1320–1328.

[8] Tonge, P. J. (2018) ACS Chem. Neurosci. 9, 29–39.

Oxide nanophosphors are widely explored for their utility in lasing and solid-state lighting, owing to the presence of lattice defects [1-4]. SrZnO₂ nanophosphors, synthesized by combustion synthesis using monoethanolamine fuel, are found to be exhibiting energy dependent tunable luminescence. HR-TEM images indicated about presence of defects in the lattice, the effect of which was observed on local electronic structure of the material also. Experimental X-ray absorption near edge structure at Zn and Sr K-edges were studied using simulated absorption spectra for defect free structure based on full multiple scattering theory. The presence of extra feature in Zn K-edge and broadened near edge structure at Sr K-edge in experimental spectra were supposed as signature of lattice distortion due to presence of lattice defects in system. Extended X-ray absorption fine structure analysis of first coordination shell around Zn and Sr absorbers indicated oxygen vacancies in the system, accompanied by decreased Zn-O bond lengths and increased Sr-O bond lengths. The observed structure disorder was believed to be responsible for formation of band tail states with Urbach energy 247.1 meV near the edges of optical band gap of 3.95 eV. Thermoluminescence glow curve analysis obtained at varying gamma irradiation revealed presence of shallow and deep defect states in the band gap. A collective consequence of all the results were summed up in band model, shown in Fig. 1, depicting blue emission due to radiative recombination from shallow defect state to tail states above valence band and white emission due to radiative transition between shallow to deep defect states in the forbidden gap. The energy dependent dual visible emission in SrZnO₂ is expected to be utilized for various technological applications.

The importance of transition-metal switchable compounds of real-life applications is rapidly increasing, thus investigations of nickel (II) organic complexes in which metal centre is coordinated by molecular fragments that can exist in multiple isomeric forms (e.g. NO₂, SO₂ , N₂) cannot be overestimated. Hence, the current study was devoted to obtain novel promising photoswitchable materials (Fig.1a) characterized by desired reversibility, high conversion percentage and stability.

The designed model compound is shown in Figure 1. As can be seen, the nickel(II) centre is coordinated by the ambidentate nitro ligand and the (N,N,O)-donor moiety. For the purpose of thorough analysis of its photoswitchable properties and the isomerisation reaction features, IR spectroscopy, multi-temperature and photocrystallographic XRD experiments were conducted and supported by computational investigations. Optimal photoisomerisation conditions were determined on the basis of multi-temperature XRD and spectroscopic experiments.

The studied complex crystallises in the P-1 space group with one molecule in the asymmetric unit. Upon visible light irradiation the nitro isomer transforms to the endo-nitrito form reaching about 25% conversion in the form of a single crystal sample and 100% as a powder according to the IR spectroscopy results. The generated metastable state species exist up to 200 K. Intermolecular contacts, linkage isomers’ relative stability, reaction cavity volumes and crystal packing were thoroughly investigated to understand the nitro-nitrito linkage isomerisation mechanism.

The importance of transition-metal switchable compounds of real-life applications is rapidly increasing, thus investigations of nickel (II) organic complexes in which metal centre is coordinated by molecular fragments that can exist in multiple isomeric forms (e.g. NO₂, SO₂ , N₂) cannot be overestimated. Hence, the current study was devoted to obtain novel promising photoswitchable materials (Fig.1a) characterized by desired reversibility, high conversion percentage and stability.

The designed model compound is shown in Figure 1. As can be seen, the nickel(II) centre is coordinated by the ambidentate nitro ligand and the (N,N,O)-donor moiety. For the purpose of thorough analysis of its photoswitchable properties and the isomerisation reaction features, IR spectroscopy, multi-temperature and photocrystallographic XRD experiments were conducted and supported by computational investigations. Optimal photoisomerisation conditions were determined on the basis of multi-temperature XRD and spectroscopic experiments.

The studied complex crystallises in the P-1 space group with one molecule in the asymmetric unit. Upon visible light irradiation the nitro isomer transforms to the endo-nitrito form reaching about 25% conversion in the form of a single crystal sample and 100% as a powder according to the IR spectroscopy results. The generated metastable state species exist up to 200 K. Intermolecular contacts, linkage isomers’ relative stability, reaction cavity volumes and crystal packing were thoroughly investigated to understand the nitro-nitrito linkage isomerisation mechanism.

The authors thank the PRELUDIUM grant (2017/25/N/ST4/02440) of the National Science Centre in Poland and the Inter-Faculty of Individual Studies in Mathematics and Natural Sciences, University of Warsaw, for financial support. The Wrocław Centre for Networking and Supercomputing (grant No. 285) is gratefully acknowledged for providing computational facilities. The in-house X-ray diffraction experiments were carried out at the Department of Physics, University of Warsaw, on Rigaku Oxford Diffraction SuperNova diffractometer, which was co-financed by the European Union within the European Regional Development Fund (POIG.02.01.00-14.122/09)

The chemistry of hybrid halometallates attracting increasing interest of researchers. The interest is associated with a number of physical properties inherent in this class of compounds, such as semiconductivity, photochromism, luminescence, etc. One of the prominent representatives of this class are hybrid halosmuthates - promising candidates for solar energy.

The crystal engineering of halobismuthates to prepare the substances with given anion seems to be the highest priority. In this work we report the synthesis and crystal structure of organic-inorganic hybrid halobismuthates of 1,4’-bipyridine cations. The structure and optical properties of the isolated compounds were studied. The novel anion [Bi₆I₂₆]^6- was discovered in the structure [PyPy]₂[PyPyH]₂Bi₆I₂₆. The DFT calculation of this structure showed the total energy of six Bi-I interactions in BiI₆ polyhedra remains almost constant for all crystallographically independent bismuth atoms. In this case the correlation between Bi-I bond length values and interaction energy values (R² = 0.9993) was performed. Using this correlation, the statistical analysis of Bi-I bond energies in 262 iodine-bismuthate anions found in the CCDC database (ver 5.40 September 2019) was performed. The total energy of six Bi-I bonds in BiI₆ polyhedra forming various iodine-bismuthate anions does not depend on the structure of the anions was shown. The data suggest the main factor affecting the formation of the final structure of hybrid iodobismuthates is not the energy benefit of the formation of one form or another of a bismuth-containing anion, but a combination of weak intermolecular interactions. In this fact the synthesis of such compounds with a given anion is impossible.

The interaction between metals in homo- and heterometallic complexes are known as metallophilic interactions. The photoluminescent study of metal complexes with metallophilic interactions produces promising results. [1] [2] Bis(diphenylphosphine)amine (PNP) ligand systems were identified as the ligands of choice because they consist of a parameter for the measurement of its steric bulk on the nitrogen atom. The parameter is known as the Tolman based cone angle as introduced by Cloete et al. [3] The influence of the steric bulk on the catalytic activity of the ligand was investigated by Cloete et al. [3] A wide range of steric substituents are identified and a collection of dimeric metal complexes synthesised. The photoluminescent properties of these complexes were compared as a parameter for the metallophilic interactions present in the complexes. The influence of solvents is investigated and solid state luminescence is used for the luminescence study. Firstly the formation of exciplexes are possible with a semi-coordination between the solvent and the complex. [4] The solvent interaction and quenching effects correlate to photoluminescent data from other studies. [5] [6] The structural aspects are compared using single crystal X-ray diffraction analysis and DFT calculations. This makes the comparison between theoretical and experimental data possible. The manipulation of the metal to metal distance is observed and a correlation drawn between the metal to metal distance and the steric bulk of the ligand system. Figure 1 illustrates two metal complexes with metallophilic interactions.

[1] N. Kathewad, N. Kumar, R. Dasgupta, M. Ghosh, S. Pal & S. Khan. (2019), Dalton Transactions, 48, 7274.

[2] S. Pal, N. Kathewad, R. Pant & S. Khan. (2015), Inorg. Chem., 54, 10172.

[3] N. Cloete, H.G. Visser, I. Engelbrecht, M. Overett, W. Gabrielli, A. Roodt. (2013), Inorg. Chem., 52, 2268.

[4] A. Penney, V. Sizov, E. Grachova, D. Krupenya, V. Gurzhiv, G. Starova & S. Tunik. (2016), Inorg. Chem. 4720.

[5] I. Strelnik, V. Gurzhiy, V. Sizov, E. Musina, A. Tunik, E. Grachova, (2016), Cryst. Eng. Comm., 18, 7629.

[6] Z. Lei, J-Y. Zhang, Z-J. Guan, Q-M. Wang, (2017), Chem. Commun., 53, 10902.

Kinetic control is an upcoming method for producing a wide variety of desired functional structures [1, 2]. Thermodynamic assembly allows the reaction system to achieve equilibrium, thus forming thermodynamically stable compounds, whereas kinetic assembly traps metastable states via fast crystallization at low temperatures and at high concentrations. However, rapid crystallization causes difficulties with ab initio structure determination by X-ray diffraction, since the main products are crystalline powders rather than single crystals [1, 3].

We found that in the row of rare-earth cyamelurates three structural types exist. Room temperature synthesis (22 – 25 °C) leads to the formation of compounds [M(H₂O)₇C₆N₇O₃] (M = Y, Pr, Nd, Sm, Eu, Gd, Tb, Dy, Ho, Er), which we consider as a result of kinetic control. Synthesis with heating up to 100 °C yields thermodynamically more stable [M(H₂O)₄C₆N₇O₃]_n·nH₂O (M = Y, Ho, Er, Tm, Yb, Lu) and [M(H₂O)₅C₆N₇O₃]_n (M = Pr, Nd). Structures of erbium cyamelurates (Fig. 1) and neodymium cyamelurate were solved using data of the powder XRD.

Figure 1. Reaction pathway in formation of kinetic and thermodynamic product and structures of erbium cyamelurate, obtained at room temperature (left) and at 100 °C (right). Hydrogens are not shown.

Thermodynamic products have denser structures compared to kinetic products. In synthesized at increased temperature erbium and neodymium cyamelurates polymeric chains exist due to the fact that the cyamelurate anion acts as a bridging ligand (Fig.1, right). Kinetically trapped erbium cyamelurate, in contrast, consists of individual complex molecules [Er(H₂O)₇C₆N₇O₃] (Fig.1, left). Probably, steric difficulties caused a decrease in the coordination number of erbium from 9 to 8 in the thermodynamic product. The coordination number of neodymium remains equal to 9 in both types of compounds.

The statement that the most stable product also can form the fastest, indicating that the kinetic and the thermodynamic product is one and the same [4], is confirmed by synthesized at elevated temperatures Sm, Eu, Gd, Tb, Dy cyamelurates with a similar structure as in the case of products obtained at room temperature.

[1] Ohtsu, H., & Kawano, M. (2017). Chem. Commun. 53, 8818.

[2] Yan, Y., Huang, J. & Tang, B. Z. (2016). Chem. Commun. 52, 11870.

[3] Marti-Rujas, J. & Kawano, M. (2013). Acc. Chem. Res. 46, 493.

[4] Ji, Q., Lirag, R. C. & Miljanic, O. S. (2014). Chem. Soc. Rev . 43, 1873.

Keywords: IUCr2020; cyamelurates; crystal structure; kinetic control; thermodynamic control

This work is supported by grant 20-08-00097 from the Russian Foundation for Basic Research.

Carbon framework of graphite structure can host alkali metals between layers forming graphite intercalation compounds (GIC). In the case of GICs with multiple layers separated by metallic layer, one can imagine graphite-to diamond transformation in carbon framework, leading to “diamond intercalation compounds” (DIC). The design of such material(s) was the purpose of our work.

GIC with metals such as Li, Na and K form different compositions (and crystal structures) are produced by stacking along c-axis of metal (Me) and n carbon (A, B or C) layers. The n number indicate the stage of intercalation. Typically ordered compounds are obtained for n = 1 to 6 with various stacking sequences depending on metals: n = 1 for MeAMeB, n = 2 for MeABMeBAMeCA, n = 3 for MeABCMeBCAMeCAB, etc. Experiments show that both high pressure and high temperature leads to increasing n. We will discuss the structural features of GIC, the XRD, Raman and other structurally related data, as well as corresponding DIC structurally related to GIC. The pressure and temperature range of formation of DICs from GICs coincide with industrially accessible conditions, that allows considering them as new promising materials. We have also shown that powder XRD is a method o fchoice for study of such transformations.

Compounding of polystyrene (PS) with tetramethylsilyl cellulose (TMSi-Cell) and an organically modified montmorillonite (OMMMT) was carried out in two different ways. In the first way the PS of MW = 49000 and Mn = 32000 was solved in toluene, than mixed with the nanocomposite dispersion of TMSi-Cell/OM-MMT (10.5 %) in toluene and dried in an oven at 380 mbar/40°C for 20 hours. In the second way the bulk polymerization of PS was tried as a way to obtain PS/TMSi-Cell/OM-MMT nanocomposite. The polymerization followed in a mixture of styrene with TMSi-Cell/OM-MMT (10.5 %) in an oil bath at 80 °C for 4 hours and at 120 °C for 16 hours. Nanocomposites of TMSi-Cell/OM-MMT were firstly prepared by precipitation from toluene experimenting concentrations from 10.5 % to 29.35 % of OM-MMT to TMSi-Cell. The thermal properties of the nanocomposites, were investigated by thermogravimetry and the morphologies of these nanocomposites were evaluated through X-ray diffraction. The 10.50 % OMMMT/TMSi-Cell nanocomposite showed a completely exfoliated morphology. PS/TMSi-Cell/OM-MMT mixtures were characterized by X-Ray Diffraction, Thermogravimetry and Differential Scanning Calorimetry. Differences in the degradation temperature compared to pure PS show compounding.

Hybrid organic-inorganic compounds are receiving considerable attention in recent years due to the possibility of combining the different characteristics of the components to get unusual and enormous variety of interesting structural topologies and wide potential applications in the fields of catalysis, non-linear optics, sensors, magnetism and molecular recognition ^[1]. During our investigation, we synthesized three new hybrid organic-inorganic compounds of dapsone with antibacterial and second-order nonlinear optical properties ^[2]. The structural study and Hirshfeld surface analysis allowed us to establish the importance of hydrogen bond and intermolecular interaction in the crystal packing.and their role in the NLO properties.

In the porous material Science, Metal Organic framework (MOF) are intensely studied, among other qualities, for has the tailorable pores suitable for applications like gas separation and storage, catalysis and so on. . For definition the MOF’s are porous coordination networks, with void pores, formed by metallic sites organized in secondary building units (SBU) connected by organic linkers. The geometrical variety of the SBU’s result in different topologies and a variety of pores with different sizes (from micro- to mesopores). In particular, the MeMOF-74 (Me=Co, Zn, Mn, Mg e Ni) has a hexagonal structure with unidimensional porosity, where the metal cations are connected to 6 oxygens exhibiting a SBU with straight helical form. In this work, high quality powder X ray diffraction pattern of MeMOF74 (Me= Co, Ni, Zn, Mg e Mn) were investigated using the Rietveld refinement method. This analysis was used to compare the influence of metal on the local geometry of secondary building units (SBU) and to study the influence of bimetallic sites on the structure.

The propionic acid is the first simple carboxylic acid in the series of simple carboxylic acids starting from the formate where the hydrophobic character prevails. The propanoates make a text-book example of structures in which hydrophilic/cation-oxygen interactions and hydrophobic interactions (between the ethyl groups) are combined resulting in a rich variety of structures.

The structural motifs thus result in layer-like strutures, columnar structures or isolated clusters in which the inner part consists of a structural part where the hydrophilic interactions prevail in contrast to an outer part where the hydrophobic interaction dominate.

The structures are affected by the positional disorder of the ethyl chains.

Water inclusion into the structures is quite frequent which stabilizes the hydrophilic interactions in the structures.

Acknowledgments: This work was supported by the Czech Science Foundation (Project No. 19-28594X). Dr. Ivana Císařová from the Faculty of Science of the Charles University in Prague is thanked for the measurement of some samples

Porous coordination polymers (PCPs) with flexible framework have attracted much attention, because some of them have a high selective adsorption ability for specific gas molecules and a wide range of applications, e.g. gas separation, gas purification is expected. However, the mechanism of selective adsorption in PCPs is not unveiled. Crystal structure information of flexible framework and gas molecules is indispensable for clear understanding of the gas adsorption phenomena in PCPs.

In past decades, crystal structures of desorption and adsorption phases of PCPs were revealed by in-situ synchrotron powder diffraction measurements. Not only the framework but also the position and orientation of adsorbed gas molecules led to a deep understanding of the static gas adsorption state [1]. On the other hand, it is very interesting to know how the framework and/or pore surface of PCPs recognize gas molecules during the gas adsorption process. It will contribute to not only the development of PCPs with superior gas separation ability, but also the understanding of the whole gas adsorption process. However, there are few studies on the state at the beginning of gas adsorption process into PCPs. The dynamic structural information, which is the structural change of the gas molecules and framework in the overall gas adsorption process, will make it possible for us to gain the knowledge how gas molecules begin to interact with the pore surface and subsequently diffuse into the pores. In general, it is not so easy to elucidate the information on the early stage of the gas adsorption process by conventional measurement methods such as the adsorption isotherm. In order to obtain the dynamic structural information, we performed time-resolved synchrotron X-ray powder diffraction (XRPD) experiment in the gas adsorption process on PCPs.

In this study, XRPD measurements under gas pressure control were performed using the remote gas and vaper pressure control (RGVPC) system at beamline BL02B2 of SPring-8. The RGVPC system can control the gas and vaper pressure in online, and synchronize it with the powder diffraction data acquisition to obtain time-resolved data [2]. Using this system, a fixed amount of gas can immediately be introduced to a powder sample in a glass capillary (gas-shot mode). In the time-resolved XRPD measurement, the exposure time was set to be 1 s for each measurement. Previous to the measurement, powder samples are heated evacuating to remove guest molecules in the pore. After that, the temperature is lowered to 195 K and gas-shot measurement for CO₂ gas started. Such measurements were performed by changing gas pressure and temperature. Figure 1 shows one of the changes of XRPD pattern of gas-shot measurement for CO₂ gas adsorption in CPL-1 [3]. It was found that the CO₂ adsorption completed within a few tens of seconds after the introduction of gas. In order to investigate the change of crystal lattice during this adsorption process, Le Bail fitting was performed for each time-resolved XRPD data. The speed changes of the lattice parameters were slightly different for each axis. Furthermore, the transformed fraction from desorption to adsorption phase was derived from the change of integrated intensity of specific diffraction peak. The results show that the transformed fraction strongly depends on the gas pressure and temperature. Its fraction might be related with the dimensionality of gas diffusion into the pores. These data were analyzed using kinetic method such as the Kolmogorov-Johnson-Mehl-Avrami (KJMS) theory [4,5]. In the presentation, we will discuss the kinetics and the structural change in gas adsorption process in comparison with PCPs with different pore size and shape.

[1] Kitaura, R., Kitagawa, S., Kubota, Y., Kobayashi T.C., Kindo, K., Mita, Y., Matsuo, A., Kobayashi, M., Chang, H., Ozawa, T., Suzuki, M., Sakata, M. & Takata, M. (2002). Science 298, 2358-2361.

[2] Kawaguchi, S., Takemoto, M, Tanaka, H., Hiraide, S., Sugimoto, K., & Kubota, Y. (2020). J. Synchrotron Rad. 27, 616-624.

[3] Kondo, M., Okubo, T., Asami, A., Noro, S., Yoshitomi, T., Kitagawa, S., Ishii, T., Matsuzaka, H., & Seki, K. (1999). Angew. Chem. Int. Ed. 38, 140-143.

[4] Avrami, M. (1939). J. Chem. Phys. 7, 1103–1112.

[5] Kruger, P. (1993). J. Phys. Chem. Solids 54, 1549-1555.

We reported multi-interactive ligand, 2,5,8-tri(4’-pyridyl)-1,3,4,6,7,9-hexaazaphenalenate (4-TPHAP^-) with topologically isolated p-orbitals on an interactive HAP skeleton, can trap metastable states via intermolecular interactions during network formation. Kinetic assembly of porous coordination networks create interactive sites in the pore, which can trap guest molecules and visualize their structure, for example small reactive sulphur allotropes, and conversion.

In this study, a lower symmetry derivative of the HAP ligand containing 3-pyridyl groups (3-TPHAP^-) was developed. The purpose of this ligand was to obtain network structures with minimized dynamic motion compared to 4-TPHAP^- based networks. In 3-TPHAP^-, the pyridine ring rotation becomes suppressed after coordination to a metal centre. The lack of rotational motion may significantly influence the guest encapsulation behaviour in the resultant structures. This ligand was prepared by a one-pot condensation reaction. It was successfully reacted with a Co²⁺ salt and 1,4-benzenedicarboxylic acid co-ligand to give a porous coordination network. In the structure, HAP skeleton interacts with water to form an internal hydrogen bonding network, allowing to reveal the entire pore space by single crystal X-ray diffraction (SXRD). The network structure consists of dimeric Co clusters featuring labile sites occupied by solvent molecules. Several guest molecules, namely anthracene, triphenylene and iodine, were incorporated inside the network. The resultant encapsulated structures were elucidated by SXRD revealing unusual host-guest interactions with a subtle structure modulation.

The development of innovative environmentally friendly catalysts is of crucial importance for the establishment of a new sustainable chemical industry. The immobilization of the catalysts on a support can solve problems of selectivity and activity. We propose a scaffold based on Metal Organic Frameworks (MOFs). Under appropriate conditions they can be assembled into a porous material on which we can immobilize catalyst, making possible its recovery/reuse at the end of the process. The advantages of these scaffolds are clear: uniform, reproducible and controllable manufacture and the possibility to engineer the linkers. As a consequence, we can control and personalize the whole network structure. By using these networks as scaffolds for the immobilization of the catalysts, MOFs turn into actual nanoreactors. Our proposed nanoreactors will be designed and synthesized according to modular principles (based on isoreticular synthesis ^[1]). The desired MOFs will have to have some specific characteristics to be used as scaffold for catalyst: pore size in the range of mesopores (≥ 6nm), 1-D hexagonal structure (channel-like) to help the diffusion of reactants/products^[2] and easy/fast/cheap to synthesize in its organic components. In order to achieve the aim of the project, an easy and fast strategy has been optimized for the synthesis of novel tritopic and tetratopic organic linkers (Figure 1). Conventionally, the synthesis of organic linkers is based on the use of the well-known Suzuki coupling. This approach would require extra synthetic steps. Direct arylation ^[3], is the coupling of aryl halides with catalytically activated aryl C-H bonds. Therefore, the number of synthetic steps is reduced. The library of long star-shaped linkers is currently used for the synthesis of Zr-, La-, In- and Ga-based MOFs, and the first results will be presented here^[4].

[1] Deng, H.; et al. Science 2012, 336 (6084), 1018-1023

[2] Čejka, Morris, Nachtigall; RSC Catalysis Series No. 28 (2017)

[3] Yabo Li et al. J. Org. Chem. 2014, 79, 2890−2897

[4] Fucci, Vande Velde; Faraday Discussions, 2021, accepted.

Metal-organic frameworks (MOFs) have been used for many different applications over the last decades. Taking advantage of their resourcefulness, we have been exploring the possibility of designing MOFs using nalidixic acid as linker towards enhanced antibacterial activity. Nalidixic acid is a synthetic quinolone antibiotic used for the treatment of urinary tract infections caused by gram-negative microorganisms. We have already demonstrated that the direct coordination of this antibiotic to biocompatible metals, yielding what we call antibiotic coordination frameworks (ACFs), is a viable pathway to induce changes in important properties such as solubility. One further advantage is that synergistic effects of the metal often lead to an increase in the efficiency against different bacteria, including E. Coli.[1]

Herein we disclose a nalidixic acid-Ca(II) complex and a three new MOFs resulting from the coordination of nalidixic acid and other generally regarded as safe organic ligands (such as salicylic, nicotinic and isonicotinic acids) to Ca(II) centers. The novel compounds were synthesized by mechanochemistry,[2] ensuring the sustainability of the synthetic process. These new structures offer multiple possibilities for future applications arising from the combination of the antimicrobial activity of the ligand and the calcium important role in the human body.

Acknowledgements: Authors acknowledge Fundação para a Ciência e a Tecnologia (FCT, Portugal) (projects UID/QUI/00100/2019 and PTDC/QUI-OUT/30988/2017 and contracts under DL No. 57/2016 regulation and CEECIND/00283/2018) and FEDER, Portugal 2020 and Lisboa2020 for funding (project LISBOA-01-0145-FEDER-030988).

References:

1. a) V. André, F. Galego, M. Martins, Cryst. Growth Des. 2018, 18(4), 2067. b) V. André, A. Silva, A. Fernandes, R. Frade, P. Rijo, C. Garcia, A. M. M. Antunes, J. Rocha, M. T. Duarte, ACS Applied Bio Materials 2019, 2(6), 2347. c) C. Bravo, F. Galego, V. André, CrystEngComm 2019, 21, 7199-7203.

2. J. G. Hernández, I. Halasz, D. Crawford, M. Krupicka, M. Baláž, V. André, L. Vella-Zarb, A. Niidu, F. García, L. Maini, E. Colacino, European Journal of Organic Chemistry, 2020, 8-9.

Porous materials such as zeolites have made an indispensable impact in day-to-day life to commercial applications. The structural rigidity created by primary [SiO₄]^4- and [AlO₄]^3- units and associated with the framework stability are one of the prime criteria for its vast applications. At times the rigidity of the structure, difficulties in functional properties and nuances of the synthetic procedure.¹ Alternatively, materials made of coordination polymers (CPs) or metal-organic frameworks (MOFs) have gained enormous attention due to their simplicity in preparation, structural diversity, and the applications in gas-adsorption, separation of small molecules, catalysis, sensing of small molecules to hazardous materials, drug delivery, nonlinear optics, proton conductivity, and other biomedical related processes. These prominences of MOFs/CPs in the last three decades have stimulated a colossal amount of research interests in the study of frameworks having multifunctional properties. The diversity in applications is mainly attributed to the robustness of the MOFs against hydro- and thermal stability under different pH solutions besides maintaining the crystallinity and their porosity. In addition, in the presence of Lewis acidic/basic sites, these MOFs were potentially used as catalysts for various organic transformations.^1-3 In this talk, the preparations of some mixed metal oxides and CPs/MOFs derived imidazole-based carboxylic acid systems and metal substrates will be presented. In addition, the properties of these systems in the areas of gas adsorption, luminescence-based sensing/remediation of hazardous materials, and catalysis will be presented.⁴

Figure: SBU (left) and 3D cuboctahedral structure of Indium MOF

References:

1. (a) Kreno, L. E., Leong, K., Farha, O. K., Allendorf, M., Van Duyne, R. P., & Hupp, J. T. (2012) Chem. Rev. 112, 1105. (b) Kitagawa, S., & Kitaura, R.; Noro, S. (2004) Angew. Chem., Int. Ed. 43, 2334.

2. (a) Huang, Y.-B., Liang, J., Wang, X.-S., & Cao, R. (2017) Chem. Soc. Rev. 46, 126. (b) Zhou, H.-C., Long, J. R., & Yaghi, O. M. (2012) Chem. Rev. 112, 673.

3. (a) Wang, J., Liu, X., & Feng, X. (2011) Chem. Rev. 111, 6947. (b) Reinares-Fisac, D., Aguirre-Díaz, L. M., Iglesias, M., Snejko, N., Gutiérrez-Puebla, E., Monge, M. Á., & Gándara, F. A. (2016) J. Am. Chem. Soc. 138, 9089.

4. (a) Penke. Y. K., Anantharaman, G., Ramkumar, J., & Kar, K. K. (2019) J. Hazard. Mater. 354, 519. (b) Penke. Y. K., Anantharaman, G., Ramkumar, J., & Kar, K. K. (2017) ACS appl. Mater. Interfaces. 9, 11587. (c) Penke, Y. K., Anantharaman, G., Ramkumar, J., & Kar, K. K. (2015) RSC Adv., 6, 55608.

5. (a) Tripathi, S., & Anantharaman, G. (2015) CrystEngComm, 17, 2754. (b) Mohapatra, C., Tripathi, S., Chandrasekhar, V., & Anantharaman, G. (2014) Cryst. Growth. Des., 14, 3182. (c) Sachan, S. K., & Anantharaman, G. (2021) Inorg. Chem., 60, 9238.

Authors thank Science and Engineering Research Board (SERB, India, No. SB/S1/IC-49/2012), for funding. Authors also thank CSIR (SKS & ST), & IIT Kanpur (NS & RS) for the doctoral fellowship, and the infrastructural facilities (IITK).

The oxygen reduction reaction (ORR) is a common process in a variety of electrochemical devices, like fuel cells and metal air batteries. The sluggish kinetics of the ORR require an electrocatalyst to pass this bottleneck.^[1] Currently, the most used catalytical systems are platinum-based, with several drawbacks, such as the high cost, low availability, and deactivation by CO poisoning.^[2] Efforts are made to develop efficient, durable and low cost catalysts to promote the commercialization of fuel cells.

Non-precious metal catalysts are promising candidates for efficient ORR catalysis. It has been shown that pyrolyzing metal organic frameworks (MOFs) under inert conditions yields carbon-rich materials, with evenly distributed metal sites, which possess promising electrocatalytic activity.^[3] One widely used type of MOF as ORR catalyst precursors is the zeolitic imidazole framework (ZIF) where metal cations are linked through imidazole-based ligands. Their porous nature is partially retained after carbonization, making MOFs very suitable precursor materials.

Herein we report the mechanochemical synthesis and structural analysis of Co-doped ZIF-8 (Zn), as well as two polymorphs (dense and prorous) of fluorinated Co-doped CF₃-ZIF-8 (Zn). The samples showed electrochemical performance comparable to platinum after carbonization for 1 h at temperatures ranging between 850 – 1000°C.

Metal-organic frameworks (MOFs) have been recently known as novel precursors in nanomaterial synthesis. To understand the mechanism behind the phase transformation in atomic scale, we apply in-situ X-ray pair-distribution analysis to monitor the whole process, from distortion, destabilization, partial reduction, to the eventual nanoparticle formation and defect evolution of a series of bimetallic MOFs PCN-250. These MOFs with different trimeric node composition (Fe₃, Fe₂Co, and Fe₂Ni) allow us to control the structure, chemistry, and defect of resulting nanoparticles. Notably, we found selective reduction of Ni from the node with defect-rich frameworks retained. This can be a new route for future MOFs crystal engineering.

Ferroelectric / ferroelastic / ferroic domains are the volumes of a material where polarization / strain / any other order parameter are uniform. Domain patterns usually appear as a result of a structural phase transition between para and ferro-electric phases, which changes the symmetry (including crystal system and the space group type). Domain patterns play the central role for the materials properties, e.g. domain-wall motion may majorly contribute to the enhancement of piezoelectric effect and dielectric permittivity [1]. The knowledge of key parameters of domain patterns (such as orientation / mobility of domain walls, volume fraction of specific domains) can help to characterize, predict and even tailor the properties of ferroelectric materials.

Domain patterns may be extremely complicated, especially for a low symmetry material. Unfortunately, only a handful of experimental techniques are suitable for characterization of domain patterns directly. None of them are powerful enough to image domains in three-dimensional bulk volumes of a material and fast enough to probe their response to alternating external perturbation (e.g. temperature or electric field). Although, high-resolution X-ray diffraction is clearly capable to fill this gap, it still has to be significantly advanced and improved to be efficient and reliable. The geometry of single crystal X-ray diffraction pattern from a multi-domain crystal is as complex as domain patterns themselves. It might be very hard to recognize and observe individual domains types / domain walls in the bulk, especially in the case of monoclinic symmetry where the number of domains and domain walls between them is very large.

The morphology of domain patterns are governed by the lost symmetry elements and conditions of mechanical compatibility, which were found by Fousek, Vanocek [2] and later by Sapriel [3].

The goal of this work is to re-formulate the conditions of mechanical compatibility in the form that it is suitable for the analysis of split peaks in high-resolution X-ray diffraction. We inspect diffraction from multi-domain ferroelectric crystals accordingly and show the way to assign different peak components to the individual domains.

The experimental part of the work is done at the single crystal four-circle X-ray diffractometer in Tel Aviv University (Tel Aviv, Israel) and Swiss-Norwegian Beamlines at the European Synchrotron (Grenoble, France). We used the methodology outlined in [4] to accumulate three-dimension X-ray diffraction intensity distribution in the reciprocal space around split Bragg reflection diffracted from the domains in BaTiO₃ (BT) and Na_0.5Bi_0.5TiO₃ (NBT). The positions of individual sub-peaks in the reciprocal space can be marked and geometrical parameters of the peak groups (e.g. the inter-peak vectors) can be analyzed.

The theoretical part of this work involved the geometrical analysis of domain walls of different symmetry, where a “wall” is defined as a strain-free planar interface between the arbitrary pair of domains. We developed the algorithm and MATLAB-based computer program which predicts the list of mechanically compatible domains / orientation of the domain walls, angle between polarization vectors (if the direction of polarization vector is known) and the matrix of orientation of one domain relative to another.

Furthermore, we proved (analytically) that every pair of mechanically compatible domains produces a pair of Bragg sub-peaks, separated in the reciprocal space along the direction that is perpendicular to the domain wall. This remarkable result is used to recognize possible pairs of domains in the diffraction pattern directly.

We demonstrate such recognition for the simple case of tetragonal domains in BT crystal and use to investigate the formation of the domains in the course of the phase transition to the lower symmetry monoclinic phases in PZT and NBT.

[1] Damjanovic, D. Reports on Progress in Physics, (1999), 61(9), p. 1267, 1999.

[2] Fousek, J., Vanocek, V. J. Appl. Phys., (1969), 40(135), 135-142.

[3] J. Sapriel, “Domain-wall orientations in ferroelastics”, Physical Review B12, p. 5125, 1975. 1974

[4] Gorfman, S., Choe, H., Zhang, G., Zhang, N., Yokota, H., Glazer, A.M., Xie, Y., Dyadkin, V., Chernyshov, D., Ye Z.-G. J. Appl. Cryst. (2020), 53(4), 1039-1050.

Ferroelectricity for the ferroelectric perovskite oxides (ABO)₃have been investigated for decades [1]. In the ferroelectric BaTiO₃, it is well known that the electronic p-d hybridization between empty d orbitals of titanium and filled 2p orbitals of oxygen causes a large ferroelectric polarization [2]. In contrast, magnetic-ordering-induced ferroelectric materials (multiferroics) have also been extensively investigated since a large nonlinear magnetoelectric effect was found in the perovskite TbMnO₃[3]. In tetragonal perovskite BaMnO₃, it is proposed that a large ferroelectricity is induced by the distortion of the Mn and O ions originating from the p-d hybridization in the paramagnetic phase. Since the magnetic Mn⁴⁺ion contributes to the emergence of the ferroelectricity, a large magnetoelectric effect is expected. Sakai et al. grew the tetragonal perovskite Sr_1/2Ba_1/2MnO₃[4]. A large reduction in the ferroelectric polarization is observed below the magnetic transition temperature. The reduction mechanism of the ferroelectric polarization should be unveiled by dividing the ferroelectric polarization into the respective contributions from the p-d hybridization and that from the magnetic interaction.

Here, we report the atomic displacements in the ferroelectric and multiferroic phases of the tetragonal perovskite Sr_1/2Ba_1/2MnO₃determined by the crystal-structure analyses [5]. Using a first-principles calculation based on accurate crystal-structure parameters, we quantitatively elucidate the suppression mechanism of the ferroelectric polarization in the multiferroic phase. The synchrotron x-ray diffraction experiments were carried out in the ferroelectric (T = 225 K) and multiferroic (T = 50 K) phases of the tetragonal perovskite Sr_1/2Ba_1/2MnO₃. Using the observed diffraction spots, we performed crystal-structure analyses. Comparisons between observed and calculated structure factors are shown in Fig. 1(a, b). Schematic views of the atomic displacements in the ferroelectric and multiferroic phases are shown in Fig. 1(c, d). To understand the effect of the magnetic order on the ferroelectricity in the multiferroic phase, we simulate the ferroelectric polarization in the ground-state G-type antiferromagnetic (G-AFM) structure. In the multiferroic phase, we consider two mechanisms to induce the ferroelectric polarization: hybridization between Mn 3d and apical O2 2p states (P_hyb) and in-plane Mn-O1-Mn magnetic exchange striction (P_extr), as shown in Fig. 1(e). In G-AFM, the magnetic exchange striction prevents the atomic displacement of the side O1 ion, so that total ferroelectric polarization is reduced. We conclude that only positive P_hybcontributes to the large ferroelectric polarization in the paramagnetic phase. In stark contrast, the magnetic exchange striction induces negative P_extr, causing the suppression of the ferroelectric polarization in the multiferroic phase.

[1] M. Dawber, et al., Rev. Mod. Phys. 77, 1083 (2005).
[2] R. E. Cohen, Nature (London) 358, 136 (1992).
[3] T. Kimura, et al., Nature (London) 426, 55 (2003).
[4] H. Sakai, et al., Phys. Rev. Lett. 107, 137601 (2011).
[5] D. Okuyama, et al., Phys. Rev. Research 2, 033038 (2020).

Rare-earth nickelates (RNiO₃) are strongly correlated-electron materials with electronic, structural and magnetic instabilities, including a rare, spontaneous metal to insulator transition (MIT). The origin of the MIT and the correct description of the structural anomalies are source of intensive debate in the scientific community. Here we investigate the gap opening and the simultaneous charge ordering in PrNiO₃ in a temperature range from 1.5 K to 300 K by combining bulk transport and magnetic properties with high-resolution neutron and synchrotron X-ray powder diffraction. The structural information is analysed in terms of symmetry-adapted distortion modes, an unconventional, but illustrative formalism that reveals the existence of sharp anomalies in all mode amplitudes at the MIT[1] and the appearance of new modes below T_MIT. Our analysis also unravels a linear correlation between the breathing-mode amplitude, representing the charge order, and the staggered Ni magnetization below T_MIT, which in this nickelate coincides with the long-range antiferromagnetic ordering of the Ni magnetic moments. We also observe an intriguing anomaly at T ∼60 K (∼0.4×T_MIT), visible in some lattice parameters, mode amplitudes and the electrical resistivity. Possible origins of this anomaly will be discussed, among them the existence of a hidden symmetry in the insulating phase, which could be caused by polar distortions driven by the non-centrosymmetric magnetic order[2].

Materials with perovskite-type structure are well known for undergoing series of phase transitions during temperature or pressure change, wherein the tilt-scheme of the network of corner-connected octahedra typically changes with respect to an untilted cubic parent structure. Rare-earth scandate perovskites (REScO₃, RE = Pr–Dy) defy this trend, as they crystallize at temperatures above 2000 °C [1] in an orthorhombic structure (Pnma) and do not undergo any known phase transitions when cooled to room temperature. Due to their high chemo-physical stability and because their lattice parameters can be tuned by (partly) exchanging the RE [2], they are widely used as substrate materials for epitaxial growth of other perovskites.

The thermoelastic properties of substrates are of great importance as they can be used to estimate interfacial stress that may develop between substrate and thin-film during temperature change. Thus, we used resonant ultrasound spectroscopy and inductive gauge dilatometry to determine the elastic stiffnesses and thermal expansion coefficients of single crystal NdScO₃, SmScO₃, TbScO₃ and DyScO₃ in situ from 103 K to 1673 K [3]. The elastic stiffness coefficients are indicative of high internal consistency, e.g. c₁₁ > c₃₃ > c₂₂ and c₆₆ > c₄₄ > c₅₅ hold for all crystal species at room temperature. With increasing charge density caused by decreasing RE-radius, the crystal species become stiffer. The anisotropy of the elastic behavior approaches tetragonal symmetry with rising temperature, which is probably caused by decreasing structural tilt as the orthorhombic phases approach hypothetical tetragonal phases [3].

The shear resistance c₄₄ has anomalous positive temperature coefficients at low temperatures; the relevant temperature ranges are shifted to lower temperatures with increasing RE-radius (Fig. 1). This resembles the characteristic behavior of the critical parameter of an orthorhombic to monoclinic phase transition involving shear of the (100)-plane. c^[101] and c^[011] are two effective resistances of plane waves propagating parallel [101] and [011] with respective displacement vectors subparallel [-101] and [0-11] that have positive temperature coefficients at low temperatures in the case of TbScO₃ (Fig. 1). This is indicative of at least one additional competing structural instability for TbScO₃ which may activate a phase transition involving shear of the (120)-plane. Only magnetic phase transitions at very low temperatures are known for these REScO₃, so increasing pressures may be required to activate phase transitions associated with these instabilities [3].

[1] Christen, H. M., Jellison, G. E., Ohkubo, I., Huang, S., Reeves, M. E., Cicerrella, E., Freeouf, J. L., Jia, X. & Schlom, D. G. (2006). Appl. Phys. Lett. 88, 262906.

[2] Uecker, R., Klimm, D., Bertram, R., Bernhagen, M., Schulze-Jonack, I., Brützam, M., Kwasniewski, A., Gesing, T. M. & Schlom, D. G. (2013). Acta Phys. Pol. A 124, 295.

[3] Hirschle, C., Schreuer, J., Ganschow, S., & Schulze-Jonack, I. (2019). J. Appl. Phys. 126, 165103.

Hybrid halide perovskites are currently at the forefront of energy materials research for their appealing optical and electronic features, but applications in working devices are still hindered by chemical/structural stability. To enhance their properties, new hybrid compounds with a wide range of different organic cations have been proposed in the last years. The choice of bulky organic cations can reduce the dimensionality of the inorganic scaffold from 2D to 0D. These lower-dimensional perovskites, best defined as pseudo-perovskites, feature useful structural flexibility that can be further exploited to enhance the materials properties. We present here monodimensional hybrid iodide pseudo-perovskites, with Pb²⁺ and Bi³⁺ as B site cations, and (CH₃)₃SO⁺ (TMSO) in the A site. The Pb or Bi end members are isomorphic, and crystallize in the Pnma space group with wires of [BX₆] octahedra along the a direction. As shown in the figure, the chains are continuous for the Pb sample, or interrupted, for the Bi sample, with a B-site vacancy every third site to maintain charge balance. We prepared doped samples with general formula ((TMSO)₃Pb_3xBi_2(1-x)I₉ with complete miscibility between (0≤x≤1) ^[1]. In the a direction, the structure is especially sensitive to Bi and cation vacancy (whose stoichiometry is (1-x) in the formula above) content. Interestingly, the XRD patterns of the samples with high Bi content (e.g. x=0.33) feature a peculiar broadening of hkl peaks having h ¹ 0, while 0kl peaks remain sharp (Figure 1). This broadening points out to a short-range order in the sequence of Pb-Bi-vacancy of the doped structure chains that can be successfully modeled using a stochastic matrix approach to model the Pb/Bi/V probability sequences and reconstruct the experimental XRD traces. The influence of bismuth doping on the optical properties is also significant: even a few % loading of bismuth lowers the band gap by about 0.5 eV. Further characterization using X-ray spectroscopies (X-ray Raman scattering, XANES) to correlate the local electronic states to Bi content is underway. This work is a first insight into the effect of inorganic cation doping on short-range order and electronic properties of a 1D hybrid pseudo perovskite structure.

[1] C. Pipitone, F. Giannici, A. Martorana, S. Carlotto, M. Casarin, G. Garcìa-Espejo, A. Guagliardi, N. Masciocchi, J. Phys. Chem. C, in press.

This Stoichiometric rare earth nickelates (RNiO₃) are a textbook example of strongly correlated electron materials, which provide a notable opportunity to study the interplay between, lattice, charge, and spin degrees of freedom. Their most remarkable characteristic is the presence of spontaneous, temperature-driven metal-to-insulator transitions (MITs) at temperatures T_MIT that increase for smaller R ionic radii [1]. Since this happens in absence of Ni mixed valence or chemical disorder, nickelates are perfect, extremely clean model systems for the investigation of the boundary between localized and itinerant behaviour in theoretical studies. Although the existence of the MIT in RNiO₃ has been known since 1991 [2], the mechanism(s) at the origin of the spontaneous electronic localization is still the subject of lively debate. In particular, it is unclear how electronic correlations, lattice, and magnetic degrees of freedom interact and lead to the gap opening. Moreover, other interesting phenomena such as an unusual non-centrosymmetric antiferromagnetic ordering [3], superconductivity [4, 5] or multiferroelectricity [6, 7] have been either observed or theoretically predicted.

An important drawback for the advancement in the comprehension of the complex nickelate physics has been the limited amount of experimental information, needed to validate theoretical predictions. The reason behind is their challenging chemistry, which requires the use of high oxygen pressure and high temperature during synthesis. These extreme conditions, has prevented to date the growth of sizable bulk single crystals with R ≠ La, Pr and Nd. Here we present the first successful growth of RNiO₃ single crystals with R = Nd, Sm, Gd, Dy, Y, Ho, Er, and Lu with sizes up to ~100 μm, achieved by applying the solvothermal method in temperature gradient under 2000 bar oxygen pressure [8]. We also report a detailed structural and physical property characterization illustrating the excellent quality of the obtained bulk RNiO₃ crystals, long time considered impossible to growth.

[1] Gawryluk, D. J. Klein, Y. M. Shang, T. Sheptyakov, D. Keller, L. Casati, N. Lacorre, Ph. Fernández-Díaz, M. T. Rodríguez-Carvajal, J. Medarde, M. (2019). Phys. Rev. B 100, 205137.

[2] Lacorre, Ph. Torrance, J.B. Pannetier, J. Nazzal, A.I. Wang, P.W. Huang T.C. (1991). J. Solid State Chem. 91, 225.

[3] Alonso, J. A. García-Muñoz, J. L. Fernández-Díaz, M. T. Aranda, M. A. G. Martínez-Lope, M. J. Casais, M. T. (1999). Phys. Rev. Lett. 82, 3871.

[4] Chaloupka, J. Khaliullin, G. (2008). Phys. Rev. Lett. 100, 016404.

[5] Li, D. Lee, K. Wang, B. Y. Osada, M. Crossley, S. Lee, H. R. Cui, Y. Hikita, Y. Hwang, H. Y. (2019). Nature 572, 624.

[6] Giovannetti, G. Kumar, S. Khomskii, D. Picozzi, S. van den Brink, J. (2009). Phys. Rev. Lett. 103, 156401.

[7] Perez-Mato, J. M. Gallego, S. V. Elcoro, L. Tasci, E Aroyo, M. I. (2016). J. Phys.: Condens. Matter 28 286001.

[8] Klein, Y. M. Kozłowski, M. Linden, A. Lacorre, Ph. Medarde, M. Gawryluk D. J. (unpublished). arXiv:2104.09873.

Three-dimensional (3D) hybrid perovskites of Pb²⁺ halides have recently gained significant interest due to their use as sensitisers in perovskite solar cells [1]. However, the toxicity of Pb²⁺ has required researchers to look for an alternative to Pb²⁺ containing perovskites. Organic-inorganic (O-I) hybrid Cu²⁺ perovskites containing methylammoniumcations and Cl^- or Br^- halide anion have been studied, as an alternative to Pb²⁺halide perovskites for solar cell applications [2]. Hybrid perovskites of Cu²⁺ halides typically form two-dimensional (2D) layered perovskite structures, even with smaller cations like methylammonium, resulting in band gaps too large for solar cell applications [3]. Despite their large band-gap and low power conversion efficiency, recent studies have shown an improvement in performance of perhalocuprate(II) perovskites, creating opportunity for further research[3]. The 2D hybrid perovskites of Cu²⁺ are of interest as they are low-dimensional magnetic systems and can be used as models for high temperature superconductors [4]. The Cu²⁺ ion is a S = ½ ion, with quenched orbital angular momentum, simplifying the system magnetically, and is typically described by the S = ½ Heisenberg Hamiltonian.

The crystal structures, magnetic properties and magneto-structural correlations of eleven novel bis-(n- carboxyalkylammonium) tetrahalidecuprate(II) compounds, of the forumula ⁺(NH₃(CH₂)_nCOOH)₂[CuX₄]^2- are presented, with n = 2, 3, 4, 5 and 10 and X = Cl^- or Br^-. Thermotropic phase transitions were exhibited by two chlorido members of the series, namely bis-(3-carboxylpropylammonium) tetrachloridocuprate(II), ⁺(NH₃(CH₂)₃COOH)₂[CuCl₄]^2-, and bis-(5-carboxylpentylammonium) tetrachloridocuprate(II), ⁺(NH₃(CH₂)_nCOOH)₂[CuX₄]^2-. Dominant ferromagnetic (FM) interactions are displayed at high temperatures, while the systems shifted to an antiferromagnetic (AFM) state below the ordering temperature, T_c, as shown in Fig. 1. Hysteresis effects, zero field-cooled (ZFC)/field-cooled (FC) cool plots indicated the presence of coercive fields and rememerance effects in some of the compounds. The two-dimensional chlorido structures exhibited an in-plane J value of 14.332 K to 15.109 K and the bromido containing structures displayed an in-plane J value of 18.56 K to 23.65 K.

[1] Smith, I.C., Smith, M.D., Jaffe, A., Lin, Y., Karundadasa, H.I. Chem. Mater, 29 (2017), 1868. [2] S. F. Hoefler, G. Trimmel, T. Rath, Monatsh. Chem. 148. (2017), 795. [3] Cortecchia, D., Dewi, H.A., Yin, J., Bruno, A., Chen, S., Baikie, T., Boix, P.P., Gratzel, M., Mhaisalkar, S., Mathews, N.. Inorg. Chem. 55. (2016), 1044. [4] C.P. Landee, and M.M. Turnbull, J. Coord Chem 63:3 (2014), p. 375.

Hybrid halide perovskites have made a quite spectacular appearance in the field of photovoltaics, not only because device efficiency has shot over 25 % within 10 years of their development [1], but also because of their specific behaviour that is yet to be fully understood. In structural terms, these materials compare to the oxide perovskites ABO₃ in many respects [2] but also hold some features that are rather distinct and largely related to the molecular cation occupying the A-cation site. [3]

Therefore, a structural categorisation of these materials is greatly beneficial to understand the underlying principles of structure and property relationships. At the core of this work, we will present a fairly comprehensive group-subgroup relationship applied to halide perovskites and double perovskites deriving from the cubic perovskite aristotype in the form of a Bärnighausen tree [3] This is seconded with a discussion of the different distortion modes applying to halide perovskites: atom shifts, octahedral tilting and A-cation orientation, with the latter being a distinct mechanism in hybrid halide perovskites. Furthermore, we will elucidate the implications for the properties and phase transitions given the specific space group settings of the different crystal structures.

We will highlight why the consideration of group-subgroup relationships in halide perovskites materials is not only of structural-systematic interest, but allows direct assumptions on the device performance of perovskite solar cells. For this, we will uncover some of the physical implications of the structural relationships as they arise from the group-subgroup relationships – for instance twinning in the tetragonal phase of MAPbI₃ [4] and a potential crystallographic explanation for the possibility of ferroelectricity in MAPbI₃ [5].

[1] https://www.nrel.gov/pv/cell-efficiency.html, accessed 14/04/2021.

[2] Breternitz, J. & Schorr, S. (2018). Adv. Energy Mater. 8, 1802366.

[3] Breternitz, J. (2021). Crystallography in Materials Science, edited by S. Schorr, C. Weidenthaler, Berlin: de Gruyter, in press.

[4] Breternitz, J., Tovar, M. & Schorr, S. (2020). Sci. Rep. 10, 16613.

[5] Breternitz, J., Lehmann, F., Barnett, S. A., Nowell, H. & Schorr, S. (2020). Angew. Chem. Int. Ed. 59, 424.

The hexagonal perovskite-type oxide 6H-Ba₄Ta₂O₉ undergoes an unconventional symmetry lowering lattice distortion when cooled below 1100 K in the presence of atmospheric water. This temperature corresponds to the onset of hydration, which reaches a stoichiometric value 6H-Ba₄Ta₂O₉.½H₂O by ~500 K. In the study to be presented here, we used a combination of diffraction, ab initio calculations and spectroscopy to show that both processes are due to the incorporation of intact water molecules into the close-packed ionic lattice. The presence of very large Ba²⁺ cations in octahedral interstitial sites (perovskite B sites) forces adjacent vacant octahedral interstitial sites to also expand, making room for occupation by water molecules, while also destabilizing the structure in a way that cannot be adequately addressed by conventional symmetry-lowering pathways on cooling. This gives rise to a synergistic hydration-distortion mechanism, which, to the best of our knowledge, is unique among close-packed ionic compounds. We will discuss the implications of our model for protonic and oxide ionic conductivity in hexagonal perovskites as fuel-cell membrane materials, and for earth sciences given the possibility that more examples could exist under high-temperature and pressure conditions.

Recently, there has been considerable interest in developing high energy density solid-state energy storage systems, where Na_1/2Bi_1/2TiO₃-based materials have also received significant interest for the exceptional large-field electromechanical response. In addition, nonstoichiometric NBT has been reported to be an excellent oxygen-ion conductor. As such, NBT has gained significant interest as the potential new materials for solid-oxide fuel cells and oxygen separation membranes. In this contribution, the effect of Bi non-stoichiometry on the crystal structure has been investigated. Bi non-stoichiometric Na_0.5Bi_xTiO_3-y ceramics with x = 0.485–0.51 were prepared by a conventional solid-state reaction method. The chemical analysis of the 4 sintered samples were performed using ICP-OES. The effects of Bi non-stoichiometry on structural transition and ferroelectric stability of NBT ceramics were systematically investigated by the Neutron diffraction at room temperature (RT), in situ high-temperature X-ray diffraction (HTK-XRD up to 560 °C, see Fig. 1), dielectric analyses, and electromechanical measurements. For all compositions, the room temperature structure was found to be rhombohedral without secondary phases. Whereas at 250 °C and 500 °C, tetragonal phase and cubic were observed, respectively. These results are consistent with previous reports. [1-3] In this study, the temperature-dependent phase transition of nonstoichiometric NBT is presented. The changes in the tilt angle (ω) and octahedral strain (ξ) were calculated from distortion parameters after Megaw and Darlington [4]. An in-depth analysis of the temperature-dependent data shows that the Bi-nonstoichiometry does not alter the average crystallographic structure and phase transition temperatures of the investigated compositions.

[1] Vakhrushev, S. B., Isupov, V. A., Kvyatkovsky, B. E., Okuneva, N. M., Pronin, I. P., Smolensky, G. A. & Syrnikov, P. P. (1985). Ferroelectrics 63 (1), 153-160.

[2] Jones, G. & Thomas, P. (2002). Acta Crystallogr. Sect. B: Struct. Sci. 58 (2), 168-178.

[3] Jones, G. & Thomas, P. (2000). Acta Crystallogr. Sect. B: Struct. Sci. 56 (3), 426-430.

[4] Megaw, H. D. & Darlington, C. N. W. (1975). Acta Crystallographica A 31 (2), 161-173.

Bulk nanocrystalline samples of La_0.65 Ce_0.05 Sr_0.3 Mn_1-x Cu_xO₃(0 <x < 0.15) manganites are prepared by the sol–gel based Pechini method. The effect of the substitution for Mn with Cu upon the structural and magnetic properties has been investigated by means of X-ray diffraction (XRD), Raman spectroscopy and dc magnetization measurements. The structural parameters obtained using Rietveld refinement of XRD ata showed perovskite structures with rhombohedral (R-3c) symmetry without any detectable impurity phase. Raman spectra at room temperature reveal a gradual change in phonon modes with increasing copper concentration. The analysis of the crystallographic data suggested a strong correlation between structure and magnetism, for instance a relationship between a distortion of the MnO₆octahedron and the reduction in the Curie temperature, Tc. Hence, a theoretical description of the second-order magnetic transition, as well as the magnetic entropy change of La_0.65 Ce_0.05 Sr_0.3 Mn_1-x Cu_xO₃ (x=0 and x=0.15) compounds is presented based on the Bean-Rodbell model of magneto-volume interactions. It is shown that the magnetocaloric properties obtained from initial magnetization isotherms data are in a good matching with the numerical simulations. Within the framework of this specific theoretical model, the magnitude of the spin-lattice interaction, as well as the spin value fluctuation are found to increase upon Cu-doping. These observations shall be taken in accordance with the disorder induced by Cu^2+/Cu³⁺ ions in the system.

Hybrid perovskites of the formula A₂MX₄, A: ammonium substituted organic cation, M: a divalent metal ion and X: a halogen (Cl, Br, I) have attracted considerable attention recently. Their applications include lead-free perovskite solar cell [1], optoelectronic, exitonic and self-assembly quantum well. The properties of these hybrid perovskites OIHs are functions of A, M and X and there are possibilities to tailor the structure, physical and chemical properties according to the application needed [2-3]. The Co hybrid perovskite is a promising material for lead-free perovskite solar cell applications. Mn organic-inorganic hybrid can be used as catalysis and ultraviolet absorbing materials. Cu hybrid can be used in the application of self-assembly quantum well as well as lead-free perovskite solar cell [4]. Some of these materials posses reversible phase transition that may find application as sensors and data storage devises. The presenter has deposited about 15 of these novel hybrid perovskite materials at Cambridge Crystallographic Data Center (CCDC). For further investigation and characterization of diammonium hybrid perovskite materials xrf/xafs has been performed.

Figure 1. Left panel crystal structure of [NH₃(CH₂)₅NH₃]MnCl₂Br₂ at 240 K and right panel layered structure of [NH₃(CH₂)₅NH₃]CoCl₂Br₂ at T = 300 K. [1] Abdel-Aal, S. K., Abdel-Rahman, A. S., Kocher-Oberlehner, G., Ionov, A. & Mozhchil, R. N. (2017). Acta Cryst. A73, C1116. [2] Abdel-Aal, S. K., Abdel-Rahman, A. S., Gamal, W. M., Abdel-Kader, M., Ayoub, H. S., El-Sherif, A. F., Kandeel, M. F., Bozhko, S., Yakimov, E. E. & Yakimov, E. K. (2019). Acta Cryst. B75, 880-886. [3] Abdel-Aal, S. K. & Abdel-Rahman, A. S. (2017) J. Cryst. Growth. 457, 282-288. [4] Abdel-Aal, S. K. & Abdel-Rahman, A. S. (2019) J. Elec. Mat. 48(3) 1686-1693

In this work, SrCo_1-xMo_xO_3-δ(0 ≤ x ≤ 1) powders were synthesized by the gel-combustion method in order to explore two major aspects: the synthesis method and the crystal structure of these systems upon the variation of the Co/Mo relation. Sample SrCo_0.95Mo_0.05O_3-δ, exhibiting a tetragonal phase (space group P4/mmm) at room temperature (RT) was used as the parent compound as it was reported to be a good cathode for intermediate-temperature solid-oxide fuel cells (IT-SOFCs) [1]. The amount of glycine used as fuel in the synthesis route was studied in order to obtain a single-phased material with high homogeneity and reproducibility. Afterward, the relationship between the Co/Mo ratio in the B site of the perovskite was also investigated with the aim of implementing these materials as potential electrodes for intermediate-temperature symmetrical solid-oxide fuel cells (IT-SSOFCs). Thus, both the crystal structure and the reducibility properties of the powders were investigated by X-ray powder diffraction (XPD) and temperature-programmed reduction under diluted H₂ (H₂-TPR) techniques respectively. Additionally, scanning electron microscopy (SEM) was performed for the SrCo_0.95Mo_0.05O_3-δsample in order to study its morphology.

The SrCo_0.95Mo_0.05O_3-δsample synthesized by the addition of a non-stoichiometric amount of glycine, was able to stabilize the desired tetragonal phase as shown in Fig. 1. On the other hand, the undoped SrCoO_3-δ sample showed the typical hexagonal structure corresponding to the R32 space group. Samples containing 0.1 ≤ x ≤ 1 Mo, prepared in air flow at RT, presented two additional tetragonal phases (space groups: I4/m and I4₁/a), which correspond to the Sr₂CoMoO_6-d double perovskite and the SrMoO₄ scheelite phase respectively, as depicted in Fig. 2. Recent research has shown that this double perovskite material can become a promising ceramic oxide for anode applications in IT-SOFC [2]. Samples calcinated in a 5 mol% H₂ in Ar flow (50 cm³ (STP) min^-1) during the H₂-TPR experiments showed that, those with the lowest Mo content presented some reduction peaks at 275, 390 and 825 ºC; and the ones with the highest Mo content were partially reduced at 900 ºC. In the latter, a cubic phase was stabilized at RT (Pm-3m space group), which has been considered an ideal phase for its use as IT-SOFCs anode materials [3], meaning a big possibility to obtain other materials at intermediate Co/Mo compositions with optimal properties for IT-SSOFCs electrodes.

The prototype antiferroelectric material PbZrO₃ (PZO) features a peculiar transition from cubic (Z=1, Pm-3m) to orthorhombic (Z=8, Pbam) phase in which off-centre shifts of Pb²⁺ cations are accompanied with rotations of oxygen octahedra. These two displacive modes are present already in the cubic phase giving rise to strong structured diffuse scattering. Their coupling is considered to be at the core of the antipolar modulation of the PZO’s ground-state structure.

Here we show that partial substitution of Zr⁴⁺ cations with Sn⁴⁺ adds another level of complexity to this system [1]. For 28% of Sn two new intermediate phases appear before crystal reaches the known orthorhombic structure. The higher-temperature one is characterized by ordered system of octahedral tilts and signatures of incommensurate modulation. The latter properly develops at lower temperatures in the second intermediate phase. We track changes in the diffraction patterns in the wide temperature range, showing how diffuse scattering signal transforms to orders of magnitude stronger signal marking a critical growth of displacive modes correlation. These changes are discussed in the context of modes coupling.

[1] I. Jankowska-Sumara, M. Paściak, M Podgórna, A. Majchrowski, M. Kopecký and J. Kub, APL Materials 9, 021101 (2021).

A quantitative experimental charge density study was undertaken for the double antiperovskite mineral – sulphohalite [Na₆(SO₄)₂FCl]. High-resolution X-ray diffraction data was collected employing AgKα radiation (λ = 0.56087 Å) to a resolution of 0.3941 Å at 100K. Electron density (ED) distribution – ρ(r) was modelled, in compliance with the Hansen-Coppens formalism[1], by consecutive least-square multipolar refinements. Based on such experimental distribution of charge, QTAIM topological analysis[2] was undertaken. Full-volume property integration over delineated atomic basins (AB’s) yielded their appertaining charges [Q_AB-Cl = -0.836e^-; Q_AB-S = 03.168e^-; Q_AB-Na = 0.910e^-; Q_AB-F = -1.334e^-; and Q_AB-O = -1.227e^-] and volumes [V_AB-Cl = 38.920ų; V_AB-S = 5.656ų; V_AB-Na = 7.931ų; V_AB-F = 14.178 ų and V_AB-O = 17.416 ų]. The percentage of unaccounted electrons and volume per unit cell was respectively 0.010% and 0.406%. Within the uncertainty range of performed numerical integration, such percentages can be unheeded. A total of 6·BCP’s [∇²ρ(r_Cl···S) = 0.120e^-·Å^-5; ∇²ρ(r_Cl···Na) = 0.575e^-·Å^-5; ∇²ρ(r_S-O) = -31.00e^-·Å^-5; ∇²ρ(r_Na···O) = 1.931e^- ·Å^-5; ∇²ρ(r_Na···F) = 3.022e^-·Å^-5 and ∇²ρ(r_F···O) = 0.868e^-·Å^-5], 5·RCP’s [∇²ρ(r_I) = 0.912e^-·Å^-5; ∇²ρ(r_II) = 0.332e^-·Å^-5 and ∇²ρ(r_III,IV,V) = 0.201e^-·Å^-5] and 4·CCP’s [∇²ρ(r_I,II) = 0.514e^-·Å^-5 and ∇²ρ(r_III,IV) = 0.401e^-·Å^-5] were identified (Figure 1). Hence, Morse’s ‘characteristic set’ condition was met[3]. The study of primary bundles (PB’s), as proposed by Pendás[4], revealed the interconnection between AB’s and CP’s onto basins of attraction or basins of repulsion. The nature of interatomic interactions was assessed through the dichotomous classification[3]. The S–O contact was acknowledged as a covalent with a shared-shell. The remaining contacts were characterized as non-covalent closed-shell (Cl···Na, Na···O and Na···F) or weak van der Waals closed-shell (Cl···S and F···O).

The anharmonicity of the lead-halide bond influences the optoelectronic properties of hybrid perovskites. Since many optoelectronic properties undergo large changes during the orthorhombic/tetragonal phase transformation, this temperature range is the focus of our investigation. The aim of this study was to determine the anharmonicity of the lead-halide bond in chlorine-substituted MAPbI₃ by combining temperature-dependent synchrotron XRD and Pb L3-edge EXAFS measurements from 20 K to 265 K. The partial negative thermal expansion (NTE) behavior of the [PbX₆] octahedra observed with XRD is related to the negative tension effects of the lead-halide bond in MAPbI₃ and MAPbI_2.94Cl_0.06 observed with EXAFS, whereas in MAPbCl₃ the positive bond expansion towards higher temperatures is predominant. The experimentally observed EXAFS parameters showed clear effects at 100 % chlorine substitution. The lead-halide bond in the orthorhombic phase of MAPbCl₃ was much less anharmonic than in pure MAPbI₃. However, after the phase transition to the room temperature phase, MAPbCl₃ showed much greater anharmonicity, indicating a significantly changed state of the lead-chlorine bond. At 2 % chlorine substitution, smaller changes became apparent compared to MAPbI₃. But significant differences between MAPbI₃ and MAPbI_2.94Cl_0.06 could be observed in the degree of anisotropy γ and the asymmetry parameter C₃/C₂^3/2. By determining the structural parameters that are required for the conversion of the effective force constants k₀ and k_3, into the Morse potential parameters α and D, we found our results to be in conformance with other experimental findings.

Catalytic processes are indispensable in energy research. It is essential to enhance their environmental friendliness and resource‑efficiency by exploring and optimizing new reaction routes for future sustainability. One major topic in this context is the chemical energy storage using eg. hydrogen, in a pure state or hydrogen-carrier molecules. The release of hydrogen from carrier molecules, such as ammonia (NH₃), is achieved by a catalytic reaction. Among others, promising catalysts for ammonia decomposition are nickel-based catalysts [1]. Perovskites, eg. LaNiO₃, can serve as catalyst precursors.

The synthesis of LaNiO₃ was conducted via incipient wetness impregnation of mesoporous carbon spheres and subsequent sintering [2]. Detailed microstructure analysis was performed via transmission electron microscopy that enabled the identification of Ruddlesden-Popper faults. These [LaO]-[LaO] shear faults have been reported in the past to be present in LaNiO₃ thin films grown on various substrates [3, 4]. With this information, a Rietveld refinement of synchrotron powder diffraction data could be performed using a stacking fault model based on the superstructure, space group Pm-3m, of the original LaNiO₃ crystal structure, space group R‑3cH (Fig. 1 a). In addition, the local structure of the perovskite was investigated by total scattering neutron and synchrotron experiments and subsequent pair distribution function analysis.

The aim of this work is the correlation of structure properties with the catalytic performance of perovskites with different chemical compositions. The catalytic performance of the synthesized material was tested during NH₃ cracking experiments. For LaNiO₃, a conversion of 70% could be achieved at 550°C with a gas flow of 15000 ml/g^-1h^-1 of 100% NH₃. The structural behavior during the reaction was investigated by in situ synchrotron diffraction experiments at the high-resolution powder diffraction beamline P02.1 (PETRA III, DESY). A decomposition of the perovskite via intermediate states and the reduction to the active phase of metallic Ni on La₂O₃ could be observed (Fig. 1 b).

We investigated the pulsed-laser deposition of epitaxial layers of hexagonal LuFeO₃ by measuring the x-ray diffraction intensity in the quasi-forbidden reflection 0003 in situ during deposition. For this purpose we used a growth chamber attached to the NANO beamline at KARA storage ring of Karlsruhe, Germany.

The dependence of the diffracted intensity exhibited characteristic oscillating behaviour, the period of the oscillation is inversely proportional to the growth rate and the decay of the oscillation visibility is connected with the growth kinetics, especially to the transition from two-dimensional to three-dimensional growth mode.

The experimental data were compared to numerical simulations, for which we developed a novel growth model. The model is based on the solution of equations describing the time evolution of monolayer coverages and numbers of mobile particles at surface terraces. From the model it follows that the widths of the monolayer coverage profiles exhibit a power law dependence on the deposition time and the exponent of this law sensitively depends on the width of the diffuse Ehrlich-Schwoebel barrier, as well as on the effective temperature of two-dimensional gas of mobile molecules on the growing surface.

[1] Bauer, S., Lazarev, S., Molinari, A., Breitenstein, A., Leufke, P., Kruk, R., Hahn, H., Baumbach, T. (2014) J. Synchr. Rad. 21, 386.

[2] Holý, V., Bauer, S., Rodrigues, A., Horák, L., Jin, X., Schneider, R., Baumbach, T. (2020) Phys. Rev. B 102, 125435.

[3] Bauer, S., Rodrigues, A., Horák, L., Jin, X., Schneider, R., Baumbach, T., Holý, V. (2020) Materials 13, 61.

The work was supported by the Czech Science Foundation (project No. 19-10799J) and by the project NanoCent financed by European Regional Development Fund (ERDF, project No. CZ.02.1.01/0.0/0.0/15.003/0000485). The additional funding by the German Research Foundation within the framework of the projects SCHN 669/11 and BA 1642/8-1 is gratefully acknowledged.

The steady-state in the field of software allowing the application of different approaches for crystal structure determination [1,2] could give the impression that the determination of the crystal structure from the powder diffraction data is a common and straightforward task that does not deserve additional attention. However, looking at crystal structures determined from powder diffraction data, one can estimate the limit of the method. In the words of degrees of freedom, the current limit is around 40. The two most complex crystal structures found in the CSD database [3,4], and also many others, were solved using the direct-space methods [5]. Simply said, the direct-space methods find the structural model by changing the position and shape of the molecular fragments in the asymmetric part of the unit cell. They allow defining additional conditions for the studied crystal structure, which is handled as additional observation. For example, the model can be restricted by several specifying torsion angles or by rigid groups as it is already implemented in existing software [6,7]. All these additional observations aim to make it possible to find a solution or at least significantly reduce the calculation time.

Another observation that may increase the probability of finding the correct solution is the information about intermolecular distances in the crystal structure. This information can be obtained by performing a specific ssNMR measurement which usually offers a list of short-range interactions between atoms. We decided to implement such a possibility to the already existing software FOX [5], and we tested it on several compounds. First of all, we tested it on the already solved crystal structures. We defined intermolecular distances between several selected atoms with various precisions, and we used them as additional restrictions that influenced the final cost function. We then tested it on a compound with an unknown crystal structure, for which we obtained estimated intermolecular distances from the ssNMR. We used these additional observations for the structure solution process from X-ray powder diffraction data.

1. David, W.I.F.; Shankland, K. Structure Determination from Powder Diffraction Data. Acta Crystallogr. A 2008, 64, 52–64, doi:10.1107/S0108767307064252.

2. Meden, A.; Radosavljevic Evans, I. Structure Determination from Powder Diffraction Data: Past, Present and Future Challenges: Structure Determination from Powder Diffraction Data: Past, Present and Future. Cryst. Res. Technol. 2015, 50, 747–758, doi:10.1002/crat.201500048.

3. Husak, M.; Jegorov, A.; Czernek, J.; Rohlicek, J.; Zizkova, S.; Vraspir, P.; Kolesa, P.; Fitch, A.; Brus, J. Successful Strategy for High Degree of Freedom Crystal Structure Determination from Powder X-Ray Diffraction Data: A Case Study for Selexipag Form I with 38 DOF. Cryst. GROWTH Des. 2019, 19, 4625–4631, doi:10.1021/acs.cgd.9b00517.

4. Fernandes, P.; Shankland, K.; Florence, A.J.; Shankland, N.; Johnston, A. Solving Molecular Crystal Structures from X-Ray Powder Diffraction Data: The Challenges Posed by γ-Carbamazepine and Chlorothiazide N,N,-Dimethylformamide (1/2) Solvate. J. Pharm. Sci. 2007, 96, 1192–1202, doi:10.1002/jps.20942.

5. Černý, R.; Favre-Nicolin, V. Direct Space Methods of Structure Determination from Powder Diffraction: Principles, Guidelines and Perspectives. Z. Für Krist. - Cryst. Mater. 2007, 222, doi:10.1524/zkri.2007.222.3-4.105.

6. Černý, R.; Favre-Nicolin, V.; Rohlíček, J.; Hušák, M. FOX, Current State and Possibilities. Crystals 2017, 7, 322, doi:10.3390/cryst7100322.

7. David, W.I.F.; Shankland, K.; van de Streek, J.; Pidcock, E.; Motherwell, W.D.S.; Cole, J.C. DASH : A Program for Crystal Structure Determination from Powder Diffraction Data. J. Appl. Crystallogr. 2006, 39, 910–915, doi:10.1107/S0021889806042117.

Soft crystals transform into another polymorphic forms by macroscopic gentle stimuli at room temperature and show remarkable changes in luminescence and optical properties [1]. In order to control and analysis the phenomena of soft crystals, it is important to determine the polymorphs and clarify mechanism of the polymorphic transitions. We have developed computational techniques for crystal structure prediction (CSP) and provided successful results in a past blind test of CSP [2]. Recently, we reported a new method related to the CSP technique with measured powder X-ray diffraction (PXRD) data [3]. The method can find the observed crystal structure among a number of computationally suggested structures by using the measured PXRD data and crystal energy, while it is often difficult to find that by only an energy evaluation even with advanced calculations. Therefore, the method can provide candidate structures to experimental crystal structure analyses of unknown crystal structures from the PXRD data.

In this presentation, this new method is applied to flexible organic molecules including the soft crystal materials where the structure analysis from the PXRD data is often difficult, and it is demonstrated that the appropriate crystal structures can be determined by using the CSP technique with PXRD data. We also show that this method is useful for polymorphism analysis.

[1] Kato, M., Ito, H., Hasegawa, M. & Ishii, K. (2019). Chem. Eur. J. 25, 5105.

[2] Reilly, A. M. et al. (2016). Acta Cryst. B72, 439.

[3] Ishii, H., Obata, S., Niitsu, N., Watanabe, S., Goto, H., Hirose, K., Kobayashi, N., Okamoto, T. & Takeya, J. (2020). Sci. Rep. 10, 2524.

Creating an automated XRPD analysis is often hampered by either a complex GUI (setting it up is difficult) or because the analysis itself is too complicated and requires decisions, loops or other non-linear elements.

In our HighScore(Plus) V4.9 [1] release we have solved both obstacles at once by providing a graphical Flowchart alike design & execution Interface, that can contain decision steps as well as any number of loops. The automation batch is simply put together by dragging and connecting action and decision step boxes.

In addition, supervised and unsupervised learning features are greatly improved, by adding the very popular t-SNE method [2] to cluster (neighborhood) analysis, and by enhancing the automatic optimization of pre-processings [3] and automated variable selection [4] to the PLSR [5,6] implementation. The cross-validation is sped up by a factor of 100 by using multi-threading and algorithm optimizations. All in all, these additions allow creating better, more accurate predictive models in a much shorter time.

[1] T. Degen, M. Sadki, E. Bron, U. König & G. Nénert, The HighScore Suite, Powder Diffr. Vol. 29, (2014), Supplement S2, 13-18.

[2] L.J.P. van der Maaten and G.E. Hinton, Visualizing High-Dimensional Data Using t-SNE. Journal of Machine Learning Research 2008, 9, 2579-2605.

[3] Jan Gerretzen, Ewa Szymańska, Jeroen J. Jansen, Jacob Bart, Henk-Jan van Manen, Edwin R. van den Heuvel, Lutgarde M. C. Buydens, Simple and Effective Way for Data Preprocessing Selection Based on Design of Experiments, Anal. Chem. (2015), 87, 12096-12103.

[4] Loann David Denis Desboulets, A Review on Variable Selection in Regression Analysis, Econometrics 2018, 6(4), 45

[5] Wold, Herman, (1966). Estimation of principal components and related models by iterative least squares, in P.R. Krishnaiaah, Multivariate Analysis. New York: Academic Press. (1966), pp. 391-420.

[6] S. de Jong, SIMPLS: An alternative approach to partial least squares regression, Chemometrics Intell. Lab. Syst., (1993), 18(3), 251-263.

Electrical, optical and magnetic properties of phosphates related in the literature made interesting the study of these materials. Specifically, many structures of phosphates are stables at high temperature [1]. Co(II) phosphates avoid some deficiencies detected when cobalt oxides or other cobalt salts are used as raw materials in the synthesis of ceramic pigments [2]. Cobalt violet phosphate, Co₃P₂O₈, is included in the DCMA Classification of the Mixed Metal Oxide Inorganic Coloured Pigments (DCMA-8-11-1) [3]. Melting point in Co₃P₂O₈ compound at 1160 ºC could be increased from the formation of solid solutions with Mg₃P₂O₈ with melting point at 1240 ºC. The stable polymorph of Co₃P₂O₈ compound presents Mg₃P₂O₈ structure with monoclinic symmetry, so the formation of these solid solutions seems possible in a partial or total compositional range. Unit cell parameters are a = 5.064 Å, b = 8.371 Å, c = 8.794 Å, β = 121.01 in Co₃P₂O₈ compound (ICSD-38259) and a = 5.077 Å, b = 8.230 Å, c = 8.833 Å, β = 120.94 in Mg₃P₂O₈ compound (ICSD-31005). The variation of the unit cell parameters with composition will confirm the formation of these solid solutions. Structural characterization of the Mg_xCo_3-xP₂O₈ compositions with temperature, position of the Co(II) absorption bands in Visible spectrum and measurement of the CIEL*a*b* colour parameters [4] give us information about the composition and temperature in which the desired colour is developed.

Figure 1. Rietveld refinement from Co₃P₂O₈ composition fired at 1000 °C (L* = 32.12, a* = +25.99, b* = -25.56)

[1] Tena, M. A., Mendoza, R., García, J. R. & García-Granda, S. (2017). Results in Physics, 7, 1095-1105.

[2] Tena, M. A., Mendoza, R., Trobajo, C., García, J. R. & García-Granda, S. (2018). J. Am. Ceram. Soc., 00, 1-10.

[3] Dry Color Manufacturer’s Ass. (1982). DCMA Classification and Chemical description of the Mixed Metal Oxide Inorganic Coloured Pigments. 2^nd ed. Metal Oxides and Ceramics Colours Subcommittee, Washington DC.

[4] Commission Internationale del’Eclairage (1971) Recommendations on Uniform Color Spaces, Color Difference Equations, Phychometrics Color Terms. 1978. Supplement nº 2of CIE Publication Nº 15 (E1-1.31). Bureau Central de la CIE, Paris

We gratefully acknowledge the financial support provided by Spanish Ministerio de Ciencia, Innovación y Universidades, project MAT2016-78155-C2-1-R.

Symmetry considerations are vital in chemistry and even more so in crystallography [1-2]. Typically, students first come into contact with this during their studies in the context of stereochemistry or spectroscopy where usually the Schönflies notation is used. Learning and teaching about molecular symmetry naturally requires spatial imagination. To develop and refine this, models and model kits are of outmost importance and are readily available for a broad range of purposes [3].

The description of crystalline matter from a crystallographer’s point of view naturally requires translational symmetry to be considered. Therefore, the applied framework to learn and discuss about molecular symmetry needs to be extended, also leading to the introduction of the Herman-Mauguin notation. From our teaching experience this transition and especially the introduction of translational symmetry components is difficult and something students struggle with. These difficulties typically culminate when it comes to the combination of symmetry elements and their assembly to give space groups. The connotation in the International Tables for Crystallography, section A [4] is not particularly intuitive to understand and to apply without the help of models.

We herein present large scale (i. e. typically 50 x 50 x 50 cm), physical 3D models of complete space groups (Figure 1) to promote student’s spatial imagination and to help understanding the construction of space groups by symmetry elements. The models were designed and built to fulfil three basic requirements: (1) to be accurate space group representations containing the symmetry symbols, (2) to visually resemble the conventional 2D space group notation if viewed along the respective crystallographic axis and, (3) to allow students to assemble asymmetric units within the unit cell by themselves.

Grabbing fosters grasping!

[1] Jaffé, H. H. (2013). Symmetry in Chemistry; New York: Dover Publications.
[2] Glasser, L. (1967). J. Chem. Educ. 44, 502.
[3] Flint, E. B. (2011). J. Chem. Educ. 88, 907–909.
[4] Brock, C. P.; Hahn, T.; Wondratschek, H.; Müller, U.; Shmueli, U.; Prince, E.; Authier, A.; Kopský, V.; Litvin, D. B.; Arnold, E.; Himmel, D. M.; Rossmann, M. G.; Hall, S.; McMahon, B.; Aroyo, M. I. (2016). International Tables for Crystallography, Volume A; International Union of Crystallography: Chester, England.

The authors would like to thank the Ministry of Science and Culture of Lower Saxony, Germany for funding. We are very grateful for the help of our workshop in constructing the models and the help of Xiaobai Wang in taking the photographs.

Structure solution in macromolecular crystallography is not always a straightforward process and it may be rather difficult for structural biologists without advanced training. A trained crystallographer exploits an extended set of approaches and tricks, based on the analysis of several indicators, general assessment of the case, and developed strategies for dealing with a particular class of problems. If such an approach, used by an expert, can be formalised in terms of an algorithm, then it can be implemented as a computer program or automated user advice system to help users solving structures quicker and with a higher success rate. It is not surprising then, that programs for macromolecular crystallography are moving towards full automation, taking off burden from researchers and lowering the entry barriers for novice users.

During the last few years, substantial progress has been made towards automation of the whole macromolecular structure determination process. There are a number of examples of successful automatic solutions for various stages of structure determination, such as molecular replacement, experimental phasing, and refinement [1-5].

In this communication, we report two novel automation features implemented in CCP4 Cloud [6], the new system for solving macromolecular structures online, released with CCP4 Software Suite 7.1 in 2020. Automated user advice framework, named Verdicts, provides simple graphical representation of results quality with detailed analysis of points for improvement as part of every task (e.g., refinement) report. The analysis includes suggestions on what could be done in order to improve the result (i.e., which parameters could be optimised). Then, the task can be re-run with the suggested parameters, which can be further adjusted by the user as appropriate.

Another automation feature, Workflows, was designed for unfolding structure solution Projects, or their parts, automatically using user-supplied data. Such automatically initiated and unfolded Projects may include a number of tasks, arranged in branching Project Trees as if this were done by the user themselves. In common cases without complications, this may result in structure solved, and if not, then a starting Project is offered to the user for analysis and further manipulations, where simple, first-order structure solution attempts are already performed. Any task or branch of the starting Project may be cloned and re-run with optimized parameters, and new tasks may be added as needed. Workflows combine automation and human expert skills, and, therefore, represent an excellent starting point for users with different level of expertise, ranging from novices to experienced crystallographers. Workflows are particularly useful in a common case of processing large sets of isomorphous crystals, because, once structure is solved in one crystal, the process is well-repeatable in systems with moderate modifications.
[1] Winter, G., Lobley, C. M. & Prince, S. M. (2013). Acta Crystallogr D Biol Crystallogr 69, 1260.
[2] Long, F., Vagin, A. A., Young, P. & Murshudov, G. N. (2008). Acta Crystallogr D Biol Crystallogr 64, 125.
[3] Keegan, R. M., Long, F., Fazio, V. J., Winn, M. D., Murshudov, G. N. & Vagin, A. A. (2011). Acta Crystallogr D Biol Crystallogr 67, 313.
[4] Minor, W., Cymborowski, M., Otwinowski, Z. & Chruszcz, M. (2006). Acta Crystallogr D Biol Crystallogr 62, 859.
[5] Wojdyr, M., Keegan, R., Winter, G., Ashton, A., Lebedev, A. & Krissinel, E. (2014). Acta Crystallographica Section A 70, C1447.
[6] Krissinel, E., Uski, V., Lebedev, A., Winn, M. & Ballard, C. (2018). Acta Crystallographica Section D 74, 143.

The celebration of the International Year of Crystallography (IYCr2014) in Argentina was an unforgettable experience, with a lot of academic, educational and dissemination activities all over the country including exhibitions, science fairs, art or photo contests, and outreach talks, among other events. Many members of the Argentinian Association of Crystallography (AACr) participated enthusiastically and, in this way, it was possible to bring Crystallography to all provinces in our country. The most important activity launched by the AACr for the IYCr2014 was the “National Crystal Growing Contest for High Schools”, which also involved the organization of 38 short courses on Crystallography and Crystal Growth for training of primary and secondary school teachers all over the country. The students, organized in teams of a maximum of three or individually, had to perform a crystal growing project, guided by their teachers, and submit a short video or written essay presenting their results and conclusions. The contest was a complete success, receiving about 500 projects of high scientific quality and creativity. Through this exciting, funny and hands-on scientific experience, Crystallography and other related scientific fields were promoted along the Argentinian high school community, being also a way to encourage young students to continue exploring Science and developing their scientific skills.

Considering the great success of the first edition, the AACr decided to continue this activity annually in the frame of the “Legacy of the IYCr2014” initiative. The Contest continued to arouse great enthusiasm, with the participation of hundreds of schools and training more than one thousand teachers every year. It is worth to mention that many of them also participated in the “IUCr Crystal Growing Competition for Schoolchildren”, the international contest organized by the IUCr, with great success. As such, Argentina has been the country with the highest number of projects submitted in every edition.

The COVID-19 pandemic has represented a global challenge since March 2020 and many congresses, courses and outreach activities could not take place or had to be postponed. However, as 2020 progressed, some of these difficulties were overcome. Many virtual courses were organized and some of them, thanks to the online modality, reached new regions or countries. Therefore, the AACr decided to continue with the Contest, this time proposing students to work from home with simple and inexpensive materials, without any danger. In addition, bibliographic research works related to Crystallography were also accepted in the 2020 edition, allowing the participation of students that could not grow crystals at home or school but that were interested in joining our activity. Many students accepted the challenge and 90 works were received. Many of them involved the growth of single or polycrystals, but others were interesting research projects related to the history of Crystallography and some of the great milestones of our science field. The short courses on Crystallography and Crystal Growth, taught in a new virtual format, were very successful too, receiving a large number of new participants not only from Argentinian cities not visited by AACr members in the previous years, but also from all over Latin America. In this way, 15 online short courses were organized, with the participation of over 4,000 teachers. The year finished with a virtual awards ceremony, opened to the general public, in which the finalists selected by the jury had the opportunity to share their experience.

In conclusion, even though 2020 has been a very difficult year, the AACr has continued with the dissemination of Crystallography, and similar activities are nowadays in progress in the frame of the 2021 edition of the National Crystal Growing Contest.

Acknowledgements: We are grateful to the following institutions for supporting in the National Crystal Growing Contest: IUCr, Argentinian Research Council (CONICET) through its VocAr Initiative (Programa de Promoción de Vocaciones Científicas), Balseiro Foundation, and Argentinian Ministry of Science, Technology and Innovation. Special thanks to the AACr members, regional representatives and local Education Ministries that help us organize this federal activity.

Alarm sounded for lack of bringing and building crystallography in Ethiopia

Alebel N.Belay^1
1Department of Chemistry, Bahir Dar University, P.O.Box 79, Bahir Dar, Ethiopia.
Email: crossispower@gmail.com or alebel.nibret@bdu.edu.et

As you know the current population of Africa is 1,374,451,375 as of Monday, July 26, 2021, based on the latest United Nations estimates. Africa population is equivalent to 16.72% of the total world population. Africa ranks number two among regions of the world (roughly equivalent to "continents"), ordered by population. With over 110 million inhabitants, Ethiopia is one of the most populous landlocked countries in the world, as well as the second-most populous nation on the African continent after Nigeria.

Bahir Dar University is now among the largest universities in the Federal Democratic Republic of Ethiopia, with more than 52,830 students in its 219 academic programs; 69 undergraduate, 118 masters, and 32 PhD programs. The vision of Bahir Dar University is to become one of the ten premier research universities in Africa by 2025. For instance, basic and in-depth skill and knowledge in introduction to Crystallography, Crystal Chemistry, Chemical crystallography, etc., and most favoured technique for structure determination of proteins and biological macromolecules for undergraduate and postgraduate students will be compulsory in future. Currently, BDU students’ and the rest part of Ethiopia still have had many challenges to start the extensive practical classes in crystallography using equipment like Single-crystal X-ray diffraction. Because of problems associated with potential future Ethiopian Crystallographic Association (EthCA) and working it for most advanced technology and many other emerging applications are evident [1, 2]. Indeed, a senior scientist helping young scientists to achieve their potential is important but it is often difficult to establish exactly when a scientific multidiscipline began. This is also true when trying to identify the moment when a particular field of research got a foothold in a new geographical region like Ethiopia.

Therefore, the main goal of this presentation is too aware and build knowledge, scientific research work and acquire experience to promote science through crystallography as a vehicle further in Ethiopia (my home country, Bahir Dar University, Ethiopia), Africa and beyond. Due to this we are trying to continue the thrust to establish a Steering Committee for a potential future establishment of an Ethiopian Crystallographic Association (EthCA). Moreover, experiences I got from different conference start with IUCr2014 in Bloemfontein, South Africa, the PCCr1 meeting in Dschang, Cameroon, in 2016, IUCr meeting in Hyderabad, India, in 2017 and so on were helped us to achieve our objective [2-5]. But the African Crystallographic Association’s (AfCA) 2017 report shown to pursue a follow-up meeting of all potential members of the AfCA Steering Committee, or representatives, to determine further actions for the immediate future, but still nothing to did it and see any on-going progress practically regarding to establishing crystallography in Ethiopian. This might be effect of COVID-19 in financial crises.

Keywords: Challenges; crystallography; Establishing, Young scientist, Ethiopia

My thanks and appreciation go to the following institution for supporting me: Crystallographic team of the University of the Free State for the PhD training and fund supported by South Africa’s National research Foundation (NRF) and the World Academy of Science (TWAS) (UIDs 99782). And also UFS, BDU, UNESCO and IUCr for travel grants of various international conferences (real and virtual) since 2014 to present.

The 17^th conference of the Asian Crystallographic Association (AsCA) will be held in Jeju island, Republic of Korea, from October 30th to November 4. The conference venue is the Lotte Hotel, located on the beautiful seaside hill. The conference is planned to be held offline only at this moment. However, depending on the situation of Covid-19, mix of on- and offline meeting will be considered. The local organizing committee welcomes not only Asian crystallographer but also scholars from all over the world to the AsCA conference.

At the Chemistry Department of the Moscow M. V. Lomonosov State University, the compulsory course “Crystal Chemistry” and numerous elective courses for undergraduate and postgraduate students (devoted to the in-depth study of several crystallographic and crystallochemical topics) do not include extensive practical classes that can be performed only in specially equipped rooms. Therefore, in principle, they can be done remotely without significant changes in content. In fact, remote learning at the Department in the last three semesters differs significantly from the option of education that was called distance learning before the COVID-19 pandemic. Classical distance learning assumes that the student can become acquainted with the teaching materials and perform test tasks conveniently within a specified period. The current procedure of remote learning at the Department may be called classroom-like: there is a schedule of lectures and seminars, while teachers are obliged to conduct live seminars, and live lectures are highly desirable.

Although before the pandemic, in most of the lectures and seminars on the general course “Crystal Chemistry”, the teachers demonstrated space models (polyhedra, individual molecules, Bravais lattices, models demonstrating the effect of symmetry elements, unit cells of inorganic and organic substances), and for some students, this facilitated the perception of the material, but strictly speaking, such demonstrations are not mandatory for a successful understanding of the course. Since 2009, the course includes acquaintance with structure visualization programs, and students have access to cif files for the structures on the must-have list. Before the pandemic, work with such programs was mainly done in the classroom, but students were recommended to download demo versions of the Diamond and Mercury programs for deeper insight, so the teachers already had some experience, which is difficult for students. During the “pandemic” semesters, the work with these programs was done completely at home, and most of the students coped with it successfully. Unfortunately, independent searches according to different criteria in the CSD, which were previously done by students of one of the specialized groups, were not implemented (due to licensing restrictions and a very large database). Demonstration of searches from the teacher’s computer were not quite complete in Zoom when using the usual option of screen sharing since inner windows in ConQuest were not visible, and the setting in Zoom allowing to see everything was undesirable when working with students. Therefore, it was necessary to make additional slides for the presentations. Nevertheless, because the use of computer programs became part of the “Crystal Chemistry” course long before the pandemic, difficulties in the transformations to remote learning were mainly due to the suddenness of the jump and technical problems among some students and teachers (the lack of devices allowing to set up necessary programs and to work with them, as well as with remote resources, poor Internet connection).

The advantages of the remote format for students include watching videos (teachers were required to record both lectures and seminars) as many times as they need to understand. In addition to the videos, many teachers shared other materials. Unfortunately, this format fostered complacancy for some students, but overall, the students’ responses after completing the courses were not worse than in the face-to-face studies.

For teachers, the distance format makes it generally easier to carry out current control of knowledge using computer tests (Moodle is the main program at the Department for these purposes), although, of course, preparing good tests takes a lot of time. Unfortunately, computer tests cannot adequately assess students’ knowledge for all sections of the “Crystal chemistry” course, and in those cases, when students placed the answers to the tasks in the form of pictures, their verification took significantly longer than checking traditional paper forms.

For me, the most inconvenient and time-consuming part of fully remote learning compared to the face-to-face format was exams using Zoom and MS Teams. This is partly due to imperfect programs (for example, in MS Teams, it is inconvenient to draw, much more often than in Zoom, there was the poor quality of communication), but more importantly, it is impossible to determine with absolute certainty whether the student really has a bad connection or is deliberately wasting time and creating interference to somehow find the answer to the question asked.