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).

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

A major objective in recent computational materials research has been the search and discovery of novel materials with superior properties. However, prior to the availability of immense computational power, materials design was guided by conceptual frameworks for synthesis-structure-property relationships, such as Pauling’s Rules, the Hume-Rothery Rules, Pettifor Tables, Structure Maps, Ashby Tables, etc. Not only can these heuristic frameworks point us towards new and valuable materials, they also provide a satisfying conceptual foundation upon which to base our scientific intuition. In this talk, I will discuss how we can leverage unsupervised machine-learning algorithms to extract new heuristic relationships from modern large-scale materials databases. In order to extract meaningful synthesis-structure-property relationships, we will first need physically-relevant materials features. Many relevant materials features are not immediately available in current materials property databases. Determination of which features to construct will likely rely on domain knowledge and physical intuition, at least in the near-term future. We will demonstrate how these computational materials discovery and informatics tools can be used to survey, visualize, and explain stability relationships across the inorganic ternary metal nitrides.*

*W. Sun et al., "A map of the inorganic ternary metal nitrides", Nature Materials (2019)

We present a method to predict the crystal structure of any given composition using machine learning methods. Then, using the example of bismuth ferrite, we illustrate how crystal structure, decomposed into distortion modes, can be implemented as a feature to explore the energy surface leading to the identification of metastable polymorphs. Crystal structure plays a crucial role in determining the electronic structure and property of any composition. Therefore, it has always been of great interest to predict the crystal structure of any composition without requiring synthesis and characterization. To achieve this goal, we combine machine learning and density functional theory (DFT) calculations. Initially, a classification model predicts the point groups of the given stoichiometries. Based on the predicted point group, a series of high-throughput DFT calculations determine the ground state of non-centrosymmetric crystal structures. In addition to the ground state structure, identifying metastable polymorphs that might get stabilized by controlling the synthetic conditions is of great importance as they can exhibit different functionalities. Therefore, we studied BiFeO₃ as a multifunctional compound with a rich low-energy phase space. A training set is constructed by mapping the phase space based on possible distortion modes starting from the cubic perovskite structure. A machine learning model is built using the generated training set predicting the energy surface of BiFeO₃ to explore new metastable phases.

Predicting ground state and metastable crystal structures using elemental and phonon mode descriptors Aria Mansouri Tehrani, Bastien Grosso, Ramon Frey, Nicola A. Spaldin Materials Theory, ETH Zurich, Wolfgang-Pauli-Strasse 27, 8093 Zürich, Switzerland aria.mansouri.t@mat.ethz.ch

Do we know all conceivable crystal structures? This question appears naive at first, because crystallography is a mature field. But the list of reported inorganic crystal structures is not necessarily representative of all kinds of order that are possible on other scales. Atomic crystal structures are affected by the discreteness of the periodic table and the resulting constraints on chemical bonding. Molecular crystals, metal organic frameworks, nanoparticle superlattices, and other soft-matter assemblies are free from these chemical constraints and can exhibit entirely new types of crystallographic order distinct from those found with atoms. A universal list of all plausible crystal structures in systems of particles ranging from the angstrom to the micrometer scale would benefit the search for—and design of—new materials.

Here, we perform a data-driven simulation strategy to systematically crystallize one-component systems of particles interacting with isotropic multiwell pair potentials resembling Friedel oscillations and encoding and generalizing quantum mechanical interactions [1]. We investigate two tunable families of pairwise interaction potentials. Our simulations self-assemble a multitude of crystal structures ranging from basic lattices to complex networks. The goal is to discover crystal structures on the computer de novo, a strategy which has so far not been attempted on such a diverse set of systems. We perform a semi-automatic crystal structure analysis of simulation data. Our analysis reveals sixteen structures that have natural analogues spanning all coordination numbers found in inorganic chemistry. Fifteen more are hitherto unknown and occupy the space between covalent and metallic coordination environments. We describe the numerical search, the analysis technique, phase diagrams, and details of the known and previously unknown crystal structures. The discovered crystal structures constitute novel targets for self-assembly and expand our understanding of what a crystal structure can look like.

[1] Dshemuchadse, J., Damasceno, P.F., Phillips, C.L., Engel, M., Glotzer, S.C. (2021). Proc. Natl. Acad. Sci. U.S.A. 118, e2024034118.

Advances in synchrotron X-ray scattering experiments have greatly increased the acquisition rates of pair distribution function (PDF) data. The analysis and interpretation of the data, however, are lagging behind the experimental advances because PDF analysis is met by the challenge of finding the correct structure model to fit against the data, which is a time-consuming process. We aim to apply data-driven methods to accelerate the analysis process of PDF data and the characterization of local material structures. Principal component analysis (PCA) and non-negative matrix factorization (NMF) are used to separate different features and/or constituents from the sample PDF data. We first applied these two methods on in-situ PDF measurement during tin oxide synthesis and then on the simulated PDFs of defected anatase titanium dioxide (TiO₂). It is found that for the in-situ PDF of tin oxide synthesis, NMF is able to separate constituents during different stages of the synthesis process and their relative concentrations are consistent with the experiments. For the PDF dataset of defected anatase (TiO₂), we found that NMF can separate the PDF signal of the defects from that of the perfect phase. This technique provides a tool to identify and quantify the defects from PDF data of materials.

Computer simulations are being increasingly used to understand the diffraction phenomenon from nanomaterials. Typically, such simulations are performed with the goal of establishing a mathematical relationship between the diffracting material and its diffraction profile under certain assumptions. For simulation of powder diffraction, the famous Debye equation [1] is generally used which also relies on particular assumptions about the diffracting material such as all Bragg reflections being represented by enough number of particles in the ensemble [2]. In this talk we will describe an alternative methodology that relies only on the far-field diffraction formulation [3] and starts off from the scattering phenomenon of x-rays from individual atomic positions. This methodology will be shown to be powerful and more general than the Debye equation -by relaxing some of the implicit requirements imposed by the Debye formula- enabling direct connection between each diffracted spot on a 2D detector and the diffracting crystallites [4, 5]. Once the methodology is explained, example studies on nanodiffraction experiments will be introduced and new information obtained by the computational tool will be demonstrated [6]. Although the proposed computational methodology is quite time-consuming since large number of calculations need to be performed for simulating diffraction from relatively larger nanocrystals, parallellization algorithms combined with exponentially increasing computational power becoming much more available to most researchers will potentially popularize its use in nanocharacterization studies in the near future.

In the recent review it was point out that the crystal structures in the Cambridge Structural Database (CSD), collected together, have contribute to various fields of chemical research such as geometries of molecules, noncovalent interactions of molecules, and large assemblies of molecules. The CSD also contributed to the study and the design of biologically active molecules and the study of gas storage and delivery [1].

In our group we use analysis of the crystal structures in the CSD to recognize and characterize new types of noncovalent interactions and to study already known noncovalent interactions. Based on the data from the CSD we can determine existence of the interactions, frequency of the interactions, and preferred geometries of the interactions in the crystal structures. In addition, we perform quantum chemical calculations to evaluate the energies of the interactions. Based on the calculated potential energy surfaces for the interactions, we can determine the most stable geometries, as well as stability of various geometries. We also can determine the interaction energies for the preferred geometries in the crystal structures. In the cases where the most preferred geometries in the crystal structures are not the most stable geometries at the potential energy surface, one can find significant influence of the supramolecular structures in the crystals.

Using this methodology our group recognized stacking interactions of planar metal-chelate rings; stacking interactions with organic aromatic rings, and stacking interactions between two chelate rings. The calculated energies indicate strong stacking interactions of metal-chelate rings; the stacking of metal-chelate rings is stronger than stacking between two benzene molecules [2]. The data indicate influence of the metal and ligand type in the metal chelate ring on the strength of the interactions. Our results also indicate strong stacking interactions of coordinated aromatic rings [3]. Studies of interactions of coordinated water indicate stronger hydrogen bonds and stronger OH/π interactions of coordinated in comparison to noncoordianted water molecule [4,5]. The calculations on OH/M interactions between metal ion in square-planar complexes and water molecule indicate that these interactions are among the strongest hydrogen bonds in any molecular system [6].

The studies on stacking interactions of benzene molecules in the crystal structures in the CSD show preference for interactions at large horizontal displacements, while high level quantum chemical calculations indicate significantly strong interactions at large offsets; the energy is 70% of the strongest stacking geometry [7].

[1] Taylor, R., Wood P. A. (2019) , Chem. Rev. 119, 9427

[2] Malenov, D. P., Janjić, G. V., Medaković, V. B., Hall, M. B., Zarić, S. D. (2017) Cood. Chem. Rev. 345, 318.

[3] Malenov, D. P., Zarić, S. D. (2020) Cood. Chem. Rev. 419, 213338

[4] Andrić, J. M., Janjić, G. V., Ninković, D. B., Zarić, S. D. (2012) PhysChemChemPhys, 14, 10896.

[5] Andrić, J. M., Misini-Ignjatović, M. Z., Murray, J. S., Politzer. P., Zarić, S. D. (2016) ChemPhysChem. 17, 2035.

[6] Janjic, G. V., Milosavljević, M., Veljković, D. Ž., Zarić S. D. (2017) Phys. Chem. Chem. Phys., 19, 8657

[7] Ninković, D. B., Blagojević Filipović, J. P., Hall, M. B., Brothers, E. N., Zarić, S. D. (2020) ACS Central Science, 6, 420.

Keywords: Cambridge Structural Database; noncovalent interactions; ab initio calculations; aromatic molecules; metal complexes

This work was supported by the Serbian Ministry of Education, Science and Technological Development (Contract numbers: 451-03-9/2021-14/200168 and 451-03-9/2021-14/200288)

(NH₄)₂[FeCl₅(H₂O)] is a rare molecular magnet exhibiting coupled magnetic and ferroelectric properties as a function of temperature and applied magnetic field [1-4]. Unlike its counterpart compounds where NH₄ group is replaced by K, Cs, and Rb, (NH₄)₂[FeCl₅(H₂O)] is the only system in this family that exhibits magnetically induced ferroelectricity at low temperature, suggesting that NH₄ plays a critical role in the unusual properties of (NH₄)₂[FeCl₅(H₂O)]. Neutron scattering is a powerful tool to study the magnetism of a materials. In this talk, I will present results of neutron scattering studies on deuterated (NHD₄)₂[FeCl₅(D₂O)] single crystals that provide insights on the nature of the coupled phenomena. Both elastic and inelastic neutron scattering experiments were performed at the High Flux Isotope Reactor (HFIR) and the Spallation Neutron Source (SNS) at Oak Ridge National Laboratory to determine the magnetic structures and investigate the dynamics in this material. Our inelastic neutron scattering results also reveal the role the ion played in the intriguing properties observed in (NH₄)₂[FeCl₅(H₂O)].

[1] M Ackermann et al, New Journal of Physics 15, 123001 (2013).

[2] Jose Alberto Rodriguez-Velamazan, et al, Scientific Reports, 5:14475, DOI:10.1038/srep14475; Phys. Rev. B 95, 174439 (2017).

[3] W. Tian et al, Phys. Rev. B 94, 214405 (2016); Phys. Rev. B 98, 054407 (2018).

[4] Amanda J. Clune et al, npj Quantum Materials 4:44 (2019)

Acknowledgments: Research conducted at ORNL's Spallation Neutron Source and High Flux Isotope Reactor was sponsored by the Scientific User Facilities Division, Office of Basic Energy Sciences, U. S. Department of Energy.

In topological materials science, the aim is to find pronounced phenomena rooted in the concepts of topology in new materials, and harness them for novel and robust functions. Promising materials classes include magnetic materials hosting nanoscale magnetic skyrmions, or Dirac and Weyl semimetals, which are hallmarked by topological invariants in real- or reciprocal spaces, respectively. With recent attention focused on magnetic topological materials, here we consider the question if novel functionalities may be found in systems with electronic and magnetic structures that are both topologically nontrivial, and where they coexist and may be coupled.

In this context, I will present our recent experimental work on the polar tetragonal magnet CeAlGe [1]. This system was predicted recently to be an easy-plane ferromagnetic type-II Weyl semimetal, with the magnetic and electrical properties little-explored. We combine magnetometry, neutron scattering and electrical transport measurements to reveal CeAlGe as a host of incommensurately-modulated multi-k magnetic phases with a nanometric length-scale. Application of modern magnetic symmetry analysis methods for refining neutron diffraction data reveals the ground state magnetic structure contains topological merons and antimerons, which can be thought of as 'half-skyrmions' carrying half-integer topological charge. While the ground state carries no topological Hall effect, the effect emerges for a phase induced by an intermediate field along the polar c-axis, which may be generated by a magnetic structure containing anti-meron pairs. We discuss the implication for the existence of such magnetic phases in Weyl semimetals and the possibilities for new functionalities.

[1]. P. Puphal et al... and J.S. White, Phys. Rev. Lett. 124, 017202 (2020)

The magnetetoelectric CaBaCo₄O₇ compound offers an interesting scenario to study frustrated magnetic configurations. The Co²⁺ and Co³⁺ ions in tetrahedral oxygen coordination form a three-dimensional framework of interconnected triangular and kagome layered arrangements [1]. The compound becomes ferrimagnetic below 60 K, and displays a strong increase of electric polarization of 17 000 μC/cm², driven by exchange-striction. In this work, we present our results on the thermal evolution of magnetic and crystallographic properties of powder samples of Ca_1-xSr_xBaCo₄O₇ (x = 0, 0.02, 0.05, 0.07) to study the effect of substitution at the Ca site. We will show that low doping levels (<10 at.%) change quite dramatically the magnetic behavior of the compound, as observed in magnetization vs. temperature measurements. Combined with extensive use of Neutron Power Diffraction we analysed the evolution of the magnetic order as a function of temperature and composition of the samples. The reported non collinear ferrimagnetic order of the parent compound is only retained for the lowest doping level x = 0.02 and is accompanied by a strong unit cell distortion. In turn, further Sr doping blurs this distortion and favors other magnetic arrangements. In the temperature range 62 K < T < 82 K, samples with x ≥ 0.02 show a plateau in the magnetization. By using the superspace group theory and its implementation in the Rietveld refinement of neutron diffraction data, we have solved the incommensurate magnetic structure that appears at these intermediate temperatures. The magnetic order has a propagation vector k = (1/2, 1/2, g) with g ≈ 0.02 and it belongs to the superspace group Pna2₁1’(1/2, 1/2, g)qq0s. This phase corresponds to a modulated spin structure with distinct behaviors of the triangular and kagome cobalt sites and could explain previous findings reported in the literature for other substitution sites in the CaBaCo₄O₇ family.

[1] V. Caignaert, V. Pralong, A. Maignan, B. Raveau. Solid State Communications 149 ,453 (2009)

In crystal engineering hydrogen and halogen bonds have proven to be very valuable crystal engineering tool for design of supramolecular architectures by self-assemblies of small building blocks, shaping their final architectures and determine the resultant topology and ultimately controlling many physical properties. [1] A number of supramolecular synthetic strategies to harness their potential have already been developed, but only for purely organic system. Although metal-organic supramolecular assemblies exhibit many technologically important properties, their design is often difficult to predict because introduction of metal cations and charge-balancing entities into metal-free solids commonly disrupt well-established connectivity of the key functional groups.[2] This is especially pronounced for magnetic metal-organic systems where magnetic behaviour not only depends on fine tuned parameters in the crystal packing but as well on the functional group, nature of the acceptor (A) and donor (D) atoms, lengths and angles of non-covalent interactions. When all of this is taken into account, targeting supramolecular architectures with desired magnetic properties becomes even more difficult and multiplex. Therefore, in those systems hydrogen and halogen bonds are rarely explored as magnetic exchange pathways or as a crystal engineering tool for directing magnetic behaviour. As well as molecular interactions, in field of molecular magnetism, metal-organic systems are not even approximately investigated as a miscellaneous copper oxide compounds, especially compounds with pyrazine and pyridine based ligands in which copper is bridged by halogen element. So far it is known that pyrazine and pyrazine derivates can be mediators of magnetic exchange within dimers, linear chains and two-dimensional lattices, and they are used in preparation of low-dimensional magnetic materials.[3] However, some insight in functional group effects on magnetic exchange of these systems in literature is not observed.

In order to understand the magnetic behaviour of crystalline coordination compounds with general formula (n-Rpz/pym/py)CuX₂and correlate structural features (in particular, functional groups, chemical linkages, bond length and angles) to magnetic exchange, we presented statistical and magneto-structural analysis of crystallography database and prepared a series of 1D polymeric chain copper(II) halides with pyrazine-, pyrimidine- and pyridine based ligands bearing the lactam or halogen functionality as a supramolecular synthetic vector. For all obtained coordination compounds ([CuCl₂(2-NH₂pz)₂]_n, [CuCl₂(2-pyz)₂]_n, [CuCl₂(4-pym)₂]_n, [CuBr₂(4-pym)₂]_n, [CuBr₂(3-Clpy)₂]_n, [CuBr₂(3-Brpy)₂]_n and [CuBr₂(3-Ipy)₂]_n) temperature dependence of magnetization M(T) was measured using SQUID magnetometer in the temperature range 2‒300 K. Linear dependence between magnetization and magnetic field allows usage of the linear magnetic susceptibility, χ. In accordance with crystal structure, we applied approach of Bonner–Fischer and modelled entire M(T) curves for all obtained compounds using spin chain of antiferromagnetically interacting neighbouring Cu²⁺ ions along structural chains. [3] These results are compared and discussed within structural features influence on magnetic superexchange J.

[1] Bernstein J.; Crystal growth, polymorphism and structure-property relationships in organic crystals properties, J. Phys. D: Appl. Phys. 1993, 26, B66

[2] Desiraju, G.R. Crystal engineering: a holistic view, Angew. Chem. Int. Ed. 2007, 46, 8342- 8356

[3] Herringer S. N.; Longendyke A. J.; Turnbull M. M.; Landee C. P.; Wikaira J. L.; Jameson G. B.; Telfer S. G. Synthesis, structure, and magnetic properties of bis(monosubstituted- pyrazine)dihalocopper(ii) Dalton Trans. 2010, 39, 2785–2797 [4] O. Kahn, Molecular magnetism, Wiley-VCH, 1992.

Keywords: supramolecular assemblies of copper(II) complexes, antifferomagnetic spin chains, intermolecular interactions, magneto-structural correlations

Lacunar spinel is a class of compounds that are derivative of the spinel family, AB₂X₄, with some vacancies at the A-site. They are very interesting both crystallographically and with respect to the physical properties as several members exhibit structural phase transition from F-43m to R3m and long-range magnetic ordering at low-temperature. Having R3m (C_3v symmetry) space group along with long-range magnetism make these compounds interesting in the aspect of spintronics, as they may host Néel-type skyrmions. One such very well-studied compound is GaV₄S₈ that hosts skyrmion with individual size of 22 nm. Here, we report a study on a different member of the lacunar spinel family, GaMo₄Se₈ that is expected to have smaller skyrmions size. We performed high-resolution powder neutron diffraction across the structural phase transition (T_S = 51 K). Through Rietveld refinement, it is found out that there are two coexisting low-temperature crystal structures with space group R3m (major phase) and Imm2 (minor phase), which is very unique only for GaMo₄Se₈. We propose an explanation for the coexisting of both crystal structures through mode-crystallographic and bond-valence sum analysis and postulate that the large strain in the rhombohedral structure is alleviated by the formation of the orthorhombic phase with larger displacive distortion amplitude. Furthermore, we have carried out magnetization measurements and performed magnetic critical behavior analysis. We find that the magnetic transition in GaMo₄Se₈ is close to a tricritical mean-field model, and the analysis of the magnetic phase diagram using magneto-entropic map revealed a positive phase-field which might be an indication of the presence of complex magnetic structures such as cycloid or skyrmions states.

The orthorhombic iron- and chromium-based perovskites (orthoferrites RFeO₃ and orthochromites RCrO₃, where R is a lanthanide) have been studied for a long time for their wide variety of magnetic properties [1, 2]. Given the flexibility in chemical composition allowed within the perovskite structure, there are plenty of opportunities for cation substitutions in the search for novel properties. In this work, several new quaternary perovskites were studied in an attempt to tune different magnetic properties. Most of these materials display a magnetic transition called spin reorientation (SR), which is outlined on Fig. 1. To evaluate the diverse magnetic transitions, neutron powder diffraction (NPD) experiments were performed in the instruments HRPT (Paul Scherrer Institute) and D1B and D2B (Institut Laue Langevin).

Among the studied compounds, the perovskites RCr_0.5Fe_0.5O₃ (R = Tb, Dy, Ho, Er, Tm, Yb, Lu) display magnetic properties which are mainly determined by the lanthanide cation, particularly at low temperatures. These materials also retain similarities with the corresponding orthochromites and orthoferrites, providing a framework to understand their magnetic properties. Other interesting findings in these perovskites include negative thermal expansion, metamagnetic transitions and magnetization reversal (MR) [3, 4]. The next step was assessing different strategies for the tuning of the magnetic transition temperatures, with substitutions in the A and B sites of the perovskite structure (Sm_1-xTm_xFeO₃ and TmCr_1-xFe_xO₃, respectively). Both systems enabled the tuning of their magnetic transitions as a function of composition. In the former, the SR transition was successfully shifted to room temperature, while in the latter, three different magnetic transition temperatures (T_SR, T_compensation of MR and T_Néel) could be tuned.

This work covers a wide compositional space within the mixed orthochromite-orthoferrite system, exploring many interesting and puzzling magnetic properties. In all cases, NPD was used along extensive magnetization measurements to understand the different magnetic transitions in detail.

The Symmetry Database (https://symmdb.iucr.org/) forms part of the online edition of International Tables for Crystallography and gives access to databases of crystallographic point and space groups. These online databases expand and complement the symmetry information provided in the print editions of International Tables for Crystallography Volume A, Space-Group Symmetry [1] or Volume A1, Symmetry Relations between Space Groups [2]. The information in the database can either be retrieved directly or generated ‘on-the fly’ using a range of programs. Help pages briefly explain the crystallographic data and the functionality of the programs. The data and programs that are currently available in the Symmetry Database are arranged into three sections:

(i) Space-group symmetry: The data in Volume A are extended to include the generators, general positions and Wyckoff positions of all 230 space groups, including the 530 settings for the monoclinic and orthorhombic space groups listed in Volume A. If data are not available for a particular setting directly, an arbitrary basis transformation can be specified and the data will be transformed to this new basis. The Wyckoff positions are specified by the Wyckoff letters, multiplicities, coordinate triplets and site-symmetry groups. Optionally, the symmetry operations of the site-symmetry groups of any point (within the unit cell or specified by its coordinates) can be calculated. Different types of notation are used for the symmetry operations: they are presented as coordinate triplets, in matrix form, using geometric symbols (indicating the type and order of the operations, and the location and orientation of the corresponding geometric elements, and screw or glide components if relevant) and as Seitz symbols. Information is also available for the Euclidean, chirality-preserving and affine normalizers of the space groups.

(ii) Symmetry relations between space groups: The maximal subgroup data given in Volume A1 are extended to subgroups of arbitrary index for all the space groups, and series of isomorphic subgroups are available for indices up to 50 for orthorhombic, tetragonal, trigonal and hexagonal space groups and for indices up to 27 and 125 for cubic space groups. Interactive contracted and complete graphs of chains of maximal subgroups, including basis transformations and origin shifts for each step, can also be generated. In addition, data for supergroups of arbitrary index of all the space groups are provided. In contrast to Volume A1, where only space-group types of supergroups are indicated, in the symmetry database each supergroup is listed individually and specified by the transformation matrix that relates the conventional bases of the group and the supergroup. The subgroup and supergroup data can be transformed to the basis of the group, left- and right-coset decomposition calculations can be carried out, and Wyckoff-position splittings can be obtained along with the relations between the coordinates of the positions within the group and subgroup.

(iii) 3D Crystallographic point groups: The data for the point groups, presented in an analogous way to the space-group data, include generators, and general and special Wyckoff positions. The data can be transformed to different settings, thus enhancing and extending the data tabulated in Volume A. Clear and instructive visualization of the symmetry elements of the crystallographic point groups and their stereographic projections, including interactive 3D polyhedra representations of idealized crystals, is also provided [3].

The Symmetry Database is available to all subscribers to the online version of International Tables for Crystallography. A Teaching Edition of the Symmetry Database, which can be used to obtain and explore the data for a selected set of space groups is also available online.

The Symmetry Database has been developed as part of an ongoing project between International Union of Crystallography, eFaber Soluciones Inteligentes SL. (Bilbao) and the Bilbao-Crystallographic-Server team. Most of the additional crystallographic data for the space groups, their subgroups and supergroups, and program algorithms have been provided by the Bilbao Crystallographic Server (www.cryst.ehu.es).

[1] International Tables for Crystallography (2016). Volume A, Space-Group Symmetry, 6th ed., edited by M. I. Aroyo. Chichester: Wiley.

[2] International Tables for Crystallography (2010). Volume A1, Symmetry Relations between Space Groups, 2nd ed., edited by H. Wondratschek & U. Müller. Chichester: John Wiley & Sons.

[3] Arribas, V., Casas, L., Estop, E. & Labrador, M. (2014). Comput. Geosci. 62, 53–61.

The ARP/wARP software provides automated model building in macromolecular crystallography and cryo-EM maps for structures of proteins, and their complexes with nucleic acids and small molecule ligands. The ARP/wARP remote service for macromolecular model building has been available since 2004 and was used to provide tens of thousands model building jobs remotely submitted by more than 4,000 users. A comprehensive description of the ARP/ARP web service, including a historical perspective will be provided. To allow the user a direct monitoring of the model building task, its progress and accumulated results are displayed graphically (e.g. the Wilson plot, the development of crystallographic R/Rfree-factors, the number of residues built) and in a tabular form as well as JavaScript-based cartoons of the built structures. The output files can also be downloaded when the job is completed. A user can rerun jobs with modified parameters and the results of these can be compared to each other. The analysis of the accumulated data and a number of take-home messages will be presented.

Macromolecular crystallography instruments around the world run more and more in a remote access or unattended configuration. This leads to less contact between humans and the hardware as well as less awareness of software and hardware states. Beamline failures that were in the past routinely reported by humans are now missed and lost in the noise of other issues. On another hand there is a need to have a chain of triggers from the beamline failure to the call out of a synchrotron staff that can assess and fix an issue. Finally, although most facilities have constant monitoring tools such has text messages or emails on catastrophic failures like loss of vacuum or cooling in the DCM, they tend to not monitor less important values due to the incapacity of a human being to deal with excessive amounts of information including false positives. Here we present a beamline monitoring software that intents to monitor EPICS PVs as well as other systems via HTTP restful interfaces, database connections or on disk file analysis and report in a configurable way to systems such as Slack, Email, Signal/WhatsApp or others. The use of a Slack bot allows update of configuration notifications as well as query some beamline states remotely before a support remote connection is required. Concepts as beamline mode as well as custom notifications for different staff members as well as a dependency chain of failures help reduce the number of notifications to a level which can be dealt with. The expectation is that this will be part of the on call / callout system, monitor the beamline live for upcoming possible problems as well as provide a log of the beamline states for the last day(s).

Machine learning can be justified only if input descriptors are crystal invariants independent of accidental choices. To use a household analogy, the average color of human clothes can be the easiest descriptor to extract from images but cannot be seriously considered for learning reliable information about people. Similarly, no properties of crystals can be reliably predicted from ambiguous parameters of a unit cell and a motif. Since crystal structures are determined in a rigid form, they should be considered equivalent modulo rigid motion or isometry, which preserves all interpoint distances. Then crystals can be justifiably distinguished only by isometry invariants that are independent of a unit cell and are preserved under any translations and rotations. Though Niggli’s reduced cell is unique, it is discontinuous under atomic perturbations, which are always present in real crystals. This continuity of invariants is important to quantify similarities between near identical crystals obtained by Crystal Structure Prediction as approximations to energy minima.

All machine learning approaches implicitly assume that a target property continuously depends on a given input, for example similar crystals should have close values of their lattice energy. We experimentally tested that the lattice energy is discontinuous with respect to the density, powder X-ray diffraction and packing similarity (root mean square deviation as computed by Mercury). For example, many crystals detected as similar by the above tools have very different energies. The AMD invariants are not only theoretically continuous under perturbations but also satisfy continuity for energy learning: we experimentally identified a distance threshold d and a constant c such that any distance between AMD invariants smaller than d guarantees an energy difference smaller than c times d.

Standard machine learning tools were trained on AMD invariants without chemical data for 10 min and predicted the lattice energy with a mean average error of less than 5KJ/mole on a CSP dataset of 5679 crystals containing about 250 atoms per unit cell.

Distances between AMD invariants are computed so fast that the pairs of all 229K organic molecular crystals from the Cambridge Structural Database were processed overnight on a modest desktop. The AMD invariants were recently extended to a complete isoset that uniquely and continuously represents any periodic crystal and allows an explicit reconstruction of a crystal.

For over 40 years, the Collaborative Computational Project Number 4 in Protein Crystallography (CCP4) has maintained, developed, and provided an integrated Suite [1] of world-class software that allows researchers to determine macromolecular structures by X-ray crystallography and other biophysical techniques.

Traditionally, the Suite is operated via CCP4i(2) graphical user interface, available for all major desktop platforms. More recent developments include interfaces that offer users the convenience of crystallographic computing on mobile devices and access to cloud-based resources. There are several good reasons for exploiting the distributed computing paradigm in crystallography.

First, cloud-based solutions have become particularly appealing given recent advances in automated structure solution methods. Such methods are demanding for both computing power and various databases, making them less convenient for offline setups.

Second, the cloud model of operations relieves researchers from the burden of maintaining software locally, providing 24/7 access to always ready, tested, and updated software setup.

Third, cloud computing streamlines data management and logistics. Collected data may be put in cloud-based projects directly from synchrotrons, bypassing offload to user devices. Cloud projects can be shared in real-time between a team of researchers working from various geographic locations. This aspect has been particularly helpful at the virtual CCP4 workshops during the pandemic.

CCP4 currently provides two interfaces for online work [2]. CCP4 Online, started from automatic Molecular Replacement service “BALBES” in 2008, is a web portal allowing users to run in the cloud the molecular replacement and experimental phasing pipelines in the CCP4 suite. In 2020, CCP4 released an advanced online platform, CCP4 Cloud, featuring a full desktop experience online. CCP4 Cloud includes an HTML5 interface for most crystallographic tasks and allows to develop and maintain structure solution projects completely online using common web browsers on any modern platform, including mobile devices.

We will discuss the latest developments, achieved results, and future directions. Providing a global computing infrastructure for protein crystallography is now a feasible task; are we ready to accept it in practice?

[1] M. D. Winn et al. Acta. Cryst. D67, 235-242 (2011)
[2] E. Krissinel, V. Uski, A. Lebedev, M. D. Winn, C. Ballard. Acta Cryst. D74: 143-151 (2018)

All biological processes rely on the formation of protein-ligand, protein-peptide and protein-protein complexes. Studying the affinity, kinetics and thermodynamics of binding between these pairs is critical for understanding basic cellular mechanisms. There are many different technologies designed for probing interactions between biomolecules, each based on measuring different signals (fluorescence, heat, thermophoresis, scattering and interference; among others). Evaluation of the data from the binding experiments and its fitting is an essential step towards the quantification of binding affinities. Here, we present user-friendly online tools to analyze biophysical data from steady-state fluorescence spectroscopy, microscale thermophoresis and differential scanning fluorimetry experiments. The modules from our data analysis platform (spc.embl-hamburg.de) contain classical thermodynamic models and clear user guidelines for the determination of equilibrium dissociation constants (K_ds) and thermal unfolding parameters such as melting temperatures (T_ms).

Since the discovery of quasicrystals in 1982, there has been a lot of progress in finding sufficient and necessary conditions for their mathematical counterparts such as point sets and measures to have pure point diffraction. A comparatively less tackled issue is the presence of absolutely continuous components. An inherent stochasticity or randomness of the underlying structure guarantees the presence of absolutely continuous spectrum, but is not the only mechanism that does so. There are deterministic examples arising from aperiodic tilings of the d-dimensional Euclidean space which also share this feature [3,4].
In this talk, we will present the mathematical requirements for such objects to give rise to absolutely continuous diffraction components [1,5], and we will give some deterministic examples which satisfy them. We will also briefly mention several sufficient criteria to conclude the singularity of the spectrum (i.e., absence of absolutely continuous components) [1,2].

This is based on joint works with Michael Baake, Natalie Priebe Frank, Franz Gaehler and Uwe Grimm.

1. M. Baake, F. Gaehler, N. Mañibo, Renormalisation of pair correlation measures for primitive inflation rules and absence of absolutely continuous diffraction, Commun. Math. Phys. 370 (2019) 591--635.

2. M. Baake, U. Grimm, N. Mañibo, Spectral analysis of a family of binary inflation rules, Lett. Math. Phys. 108 (2018) 1783-1805.

3. L. Chan, U. Grimm, I. Short, Substitution-based structures with absolutely continuous spectrum, Indag. Math. 29 (2018) 1072-1086.

4. N. P. Frank, Substitution sequences in Z^d with a non-simple Lebesgue component in the spectrum, Ergodic Th. & Dynam. Syst. 23 (2003) 519-532.

5. N. Strungaru, On the Fourier analysis of measures with Meyer set support, J. Func. Anal. 278 (2020) 108404.

Correlated disorder in crystalline materials gives rise to single crystal diffuse scattering. While the average structure determination via Bragg data analysis is considered a standard procedure, disorder analysis is thought of as a lengthy and complicated process. We present a mean field approximation to model single crystal diffuse scattering in molecular materials from a simple pair-interaction Hamiltonian.

Mean filed theory is a self-consistent field theory, which is widely used in statistical physics to model high-dimensional random systems. It has proven a valuable tool in the analysis of magnetic diffuse scattering data [1]. Here, the formalism is applied to describe orientationally disordered molecular crystals,

We present a computational study based on the mean field model suggested by Naya [2] and proof its applicability to strongly correlated disorder, where the local building block geometry dictates allowed and prohibited local configurations. The system that will be analysed in detail is a two-dimensional analogue of Hg(NH₃)₂Cl₂ as depicted in Figure 1 (a) [3]. The Hg atoms are disordered over the cubic face centres to form [H₃N - Hg - NH₃]²⁺ molecules. The local arrangement is strictly dictated by these building rules.

We compare the results of the diffuse scattering analysis using the mean field model as introduced by Naya [2] to the results of RMC modelling and ΔPDF models based on a Warren-Cowley short range order parameter refinement (see Figure 1 (b)). Finally, the stability of the mean field analysis on limited data availability is demonstrated: Diffraction experiments under pressure or electric field yield a limited reciprocal space coverage. Here, we demonstrate the robustness of the proposed method against incomplete data sets.

Figure 1. (a) Disordered Hg(NH₃)₂Cl₂ [3], where the Hg is disordered over the cubic face centres. (b) Simulated data for a two dimensional analogue compared to refinements using mean field theory (MF), DPDF analysis for the Warren-Cowley short-range order parameters (WC) and reverse Monte Carlo modelling (RMC).

[1] Paddison, J.A.M., Stewart, J.R. et al. (2013). Phys. Rev. Letters. 110, 267207.

[2] Naya S. (1974) J. Phys. Soc. Jap. 37, 340-347.

[3] Lipscomb, W. N. (1953) Analytical Chemistry 25, 737-739.

Kossel lines and X-ray localized conical modes

V.A.Belyakov

Landau institute for Theoretical Physics, Kosygin str.2 , 119334 Moscow,

Russiabel@landau.ac.ru

An alternative way to describe the X-ray Kossel lines [1] based at the localized conical X-Ray modes existing in perfect crystals is proposed. A theory of the X-ray Kossel lines is presented in the framework of two-wave dynamical diffraction approximation for the conical modes [2]. The theoretical results compared with the known experimental results show a good general agreement with the main experimental observation as for the X-ray [3], so for the optical [4] Kossel line patterns. The influence of crucial parameters of the crystal (absorption, perfection, sample size, the Borrmann Effect etc.) on the shape of Kossel lines are discussed. For confirming a direct connection of Kossel lines with the localized conical X-Ray modes is proposed to apply a time-delayed techniques in studying the Kossel lines.

[1] Kossel, W., Loeck, V. & Voges, H. (1935). Z. Fur Phys. 94, 139.

[2] Belyakov, V. A. (2019). Diffraction Optics of Complex Structured Periodic Media, 2nd. Ed. Springer, Chapts. 5-8.

[3] Belyakov, V. A. (2021). JETP, 132, 323.

[4] Belyakov, V. A. (2020). Crystals, 132, 323.

Keywords: localized X-ray modes; Kossel line patterns; optical Kossel lines

3DED (three-dimensional electron diffraction) is currently already routinely used for the characterization of the average structure from Bragg reflections, and recently its use for quantifying correlated disorder from electron diffuse scattering is also taken off [1,2,3].

In this work, we used a combination of 3DED, HAADF-STEM and STEM-EDX to quantify the correlated disorder in Ge₄Bi₂Te₇. Ge₄Bi₂Te₇ is reported to contain vacancy-layers along <11-1>_Fm3m and <1-1-1>_Fm3m with a higher Bi-concentration neighbouring these layers, which leads to the occurrence of streaks of diffuse scattering [4, 5].

Using the combination of advanced TEM techniques, we have not only confirmed the defects previously found by single crystal X-ray Diffraction but also observed and characterized a plethora of other forms of correlated disorder not reported before in literature for this material, including domains with locally different structure and composition, interstitial atoms and local periodicity between Ge and Bi. This diversity in correlated disorder results in 3D diffuse scattering and superstructure reflections that previously passed unnoticed to other techniques.

This work illustrates the large potential of TEM in characterizing correlated disorder from the analysis of diffuse scattering.

1. Zhao, Haishuang, et al. "Elucidating structural order and disorder phenomena in mullite-type Al₄B₂O₉ by automated electron diffraction tomography." Journal of Solid State Chemistry 249 (2017): 114-123.

2. Brázda, Petr, et al. "Mapping of reciprocal space of La_{0. 30}CoO₂ in 3D: Analysis of superstructure diffractions and intergrowths with Co₃O₄." Journal of Solid State Chemistry 227 (2015): 30-34.

3. Brázda, Petr, et al. "Calcium-induced cation ordering and large resistivity decrease in Pr_{0. 3}CoO₂." Journal of Physics and Chemistry of Solids 96 (2016): 10-16.

4. Urban, Philipp, et al. "Real structure of Ge₄Bi₂Te₇: refinement on diffuse scattering data with the 3D-ΔPDF method." Journal of Applied Crystallography 48.1 (2015): 200-211. 5. Callaert, Carolien. "Characterization of defects, modulations and surface layers in topological insulators and structurally related compounds." PhD thesis, University of Antwerp, 2020.

We acknowledge the financial support of the Research Foundation-Flanders (FWO), project G035619N, “Quantification of 3D correlated disorder in materials from electron diffraction diffuse scattering with application to lithium battery materials”.

Disorder is commonly used in chemistry for designing functional materials. For instance, preparation of solid solutions is nothing else than the introduction of a controlled number of point defects in a crystal. Disordered systems, though, provide more degrees of freedom: not only the number of defects, but also their distribution can be used to optimise the functional properties of materials, however up until now, defect distribution was hard to control and thus was rarely used in practice.

In this talk we will show how to precisely tune distribution of point defects by changing various chemical parameters during crystal growth and characterise it with the single crystal diffuse scattering.

We will use Prussian Blue Analogues (PBAs) as our model system. PBAs is a class of cyanide materials with the general formula M[M’(CN)₆]_1-δ * xH₂O where M and M’ are transition metals. Depending on the nature of transition metals, PBAs can accommodate a large number of vacancies on the M’(CN)₆ site (for instance δ=0.33 for M=Mn and M’=Co) which makes them highly porous and, as a result, attractive for hydrogen storage applications. Distribution of M’(CN)₆ vacancies is important for the performance of this material, since more disordered vacancy configurations provide more diffusion pathways through the structure, larger accessible volume, and easier transport.

[1] Simonov, Arkadiy, et al. "Hidden diversity of vacancy networks in Prussian blue analogues." Nature 578.7794 (2020): 256-260.

Reverse Monte Carlo (RMC) model is a powerful tool based on supercell approach, targeting at the structure model that explains comprehensive experimental datasets. Typically, the RMCProfile package can incorporate neutron/X-ray total scattering, Bragg and extended X-ray absorption fine structure (EXAFS) data. For practical implementation, apart from theoretical pattern calculation and structure model adjustment based on metropolis algorithm, there are various effects under certain circumstances that one needs to take into account to avoid artificial effects. Here we are going to introduce several different types of correction that we recently developed and implemented, in the framework of RMCProfile, namely, 1) the correction for nano-size effect concerning total scattering modelling for nano-systems from 0D nanoparticles to 2D nanosheets [1]. 2) the implementation of arbitrary Bragg peak profile in a tabulated manner, through interacting with Topas software [2]. 3) the correction for finite instrument resolution effect going beyond the conventionally used analytical approach based on Gaussian assumption for peak shape [2]. Through such development and implementation, we hope to extend the scope of application of RMCProfile package for solving structural problems from local perspective. Typically, the implementation of resolution correction enables the modelling to an otherwise-unreachable super-large length scale, e.g., 100 Å, following the supercell approach.

Although amorphous materials lack long-range translation order, they are strongly ordered at the length scale of single interatomic bonds, and retain some order into more distant coordination shells. One form of order is local, approximate rotational symmetry. For example, local five-fold rotational symmetry has been shown in simulations to correlate to slower dynamics in metallic liquids and greater strength in metallic glasses [1]. Local structural symmetry gives rise to symmetry in electron nanodiffraction speckle patterns acquired with sub-nanometer probes, but evaluating symmetries in patterns from amorphous materials is challenging. Only small clusters of atoms have symmetry, their symmetry is often distorted or imperfect, and the symmetric cluster is embedded in more atoms which are disordered. One method to assess symmetries in nanodiffraction is the angular power spectrum. We have used angular power spectrum data to demonstrate that Zr₆₅Cu_27.5Al_7.5 glasses exhibit increasing 4-fold and 5-fold structural symmetry with increasing stability in the glassy state and increasing hardness [2].

However, angular symmetry is subject to three artifacts that give rise to power that does not correspond to symmetries in the structure. First, aliasing transfers power from lower n to higher n. Second, electron nanodiffraction patterns without Friedel symmetry give rise to non-structural odd-order power. Third, the extra atoms surrounding the ordered cluster can create speckles which cause the power in rotational orders that are not present in the structure. We have proposed a different method to assess symmetries in amorphous nanodiffraction inspired by the Symmetry STEM method for crystals [3]. This method defines symmetry coefficients S_n which sample only the discrete angles associated with n-fold symmetry [4]. The discrete sampling avoids the aliasing and Friedel breakdown artifacts entirely, and it reduces the incidence of the structure overlap artifact. Electron scattering simulations in Figure 1(a) show that S_n is sensitive to nearest-neighbour icosahedral order in metallic glass atomic models. Experiments on Pd₄₃Ni₁₀Cu₂₇P₂₀ in Figure 1(b) result in symmetries consistent with dodecahedral structure found in previous studies.

Figure 1(c) demonstrates the use of symmetry coefficients for spatial mapping of high-symmetry clusters. It is derived from a 4D STEM data set acquired with a high sensitivity, high-speed direct electron detection camera recently developed by the Wisconsin Materials Research Science and Engineering Center and Direct Electron, Inc. These data were acquired at 7,000 frames per second (fps). The current maximum speed of the camera is 24,000 fps, and the ultimate design speed is in excess of 100,000 fps. These extremely high speed will enable time-resolved, in situ experiments using symmetry coefficients to track the evolution of local symmetries in supercooled liquids as they cool through the glass transition.

[1] Cheng, Y. Q. Q., Ma, E. (2011) Prog. Mater. Sci. 56, 379.

[2] Muley, S. V., Cao, C., Chatterjee, D., Francis, C., Lu, F. P., Ediger, M. D., Perepezko, J. H., Voyles, P. M. (2021). Phys. Rev. Mater. 5, 033602.

[3] Krajnak, M. & Etheridge, J. A (2020) Proc. Natl. Acad. Sci. 117, 27805.

[4] Shuoyuan, H., Francis, C., Ketkaew J., Schroers J., Voyles P. M. (in preparation)

The pair-distribution function (PDF) method is widely used to obtain structural information beyond the typical diffraction techniques together with standard structure refinement utilizing Bragg reflections [1]. PDF analysis using x-ray and neutron powder diffraction data is well established. Electron-based PDF (ePDF) analysis has drawn considerable attention in recent years [2,3,4]. In addition to the very strong electron-matter interaction (~10⁵ than x-ray), the main advantages of the electron-based over x-ray and neutron-based is to utilize modern electron microscopes, which offer (sub)nano-sized probe of the electron beam and various imaging and spectroscopy techniques simultaneously. Therefore, ePDF is particularly good for study nano-materials, disordered materials and specific region of interest in the specimens.

Although the procedures of ePDF analysis is similar to those obtained by x-ray and neutron, several parameters and steps, which are due to electron scattering and TEM practice, are crucial in the processing. For instance, Q_max is always important in all PDF experiments. However, Q_min, which is not considered in x-ray and neutron, should be carefully determined in ePDF. On the other hand, the shape factor can influence the ePDF results. The smaller the particles the stronger effect can be seen. Different stepwise atomic layer arrangement of the crystal surface can contribute significantly in the analysis [5]. In addition to experimental and analysis procedures different to those for x-ray or neutron-based, the uniqueness and possibility of ePDF analyses of some amorphous materials and nanostructures will be discussed.

[1] Egami, T. & Billinge, S. J. L. (2002). Underneath the Bragg Peaks: Structural Analysis of Complex Materials. Amsterdam: Elsevier Science.

[2] Abeykoon, M., Malliakas, C. D., Juhás, D., Božin, E. S., Kanatzidis, M. G. & Billinge, S. J. L. (2012). Z. Kristallogr. 227 248.

[3] Tran, D.-T., Svensson, G. & Tai, C.-W. (2017). J. Appl. Crystallogr. 50, 304.

[4] Gorelik, T. E., Neder, R., Terban, M. W., Lee, Z., Mu, X., Jung, C., Jacob T. & Kaiser, U. (2019). Acta Crystallogr. B 75, 532.

[5] Tran, D.-T., Svensson, G. & Tai, C.-W. (2016). arXiv:1602.08078.

The Knut and Alice Wallenberg (KAW) Foundation is acknowledged for providing the electron microscopy facilities and financial support under the project 3DEM-NATUR for the initial development. Swedish Research Council (project no. 2018-05260) is also acknowledged.

Correlated disorder is any type of deviation from the average crystal structure that is correlated over the range of a few unit cells only. As correlated disorder lies at the origin of the physical properties of a compound, many open questions in materials science are related to it. Unfortunately, the diffuse scattering analysis from single-crystal X-ray and neutron diffraction needs large crystals which are often not available. In the case of submicron sized crystals, pair distribution function analysis on powder samples could be applied. However, as an alternative we suggest to turn to single-crystal electron diffraction. While the quantitative analysis of diffuse X-ray and neutron scattering has already been done for different types of correlated disorder, we will present for the first time the quantitative analysis of diffuse electron scattering using an evolutionary algorithm in DISCUS [1].

In the electron diffraction patterns of Li_1.2 Ni_0.13Mn_0.54Co_0.13O₂ diffuse streaks are present, which are caused by stacking faults (i.e. variations in the stacking of subsequent Li-, O- and transition metal -layers). An evolutionary refinement algorithm in DISCUS was used to determine the stacking fault probability as well as the twin ratio in Li_1.2Ni_0.13Mn_0.54Co_0.13O₂ by a refinement of the intensity profile of the diffuse streaks_. The refinement algorithm was first tested on simulated data, after which it was applied to experimental electron diffraction data obtained by three-dimensional electron diffraction (3D ED).

Funding information

The research leading to these results has received funding from the Research Foundation Flanders (FWO Vlaanderen) (grant No. G035619N)

[1] Proffen, T., & Neder, R. B. (1997). J. Appl. Crystallogr. 30, 171-175.

Metal-organic frameworks (MOFs) are known for their versatile combination of inorganic building units and organic linkers, which offers immense opportunities in a wide range of applications. However, many MOFs are typically synthesized as multiphasic polycrystalline powders, which are challenging for studies by X-ray diffraction. Therefore, developing new structural characterization techniques is highly desired in order to accelerate discoveries of new materials. Here, we report a high-throughput approach for structural analysis of MOF nano- and sub-microcrystals by three-dimensional electron diffraction (3DED). A new zeolitic-imidazolate framework (ZIF), denoted ZIF-EC1, was first discovered in a trace amount during the study of a known ZIF-CO₃-1 material by 3DED. The structures of both ZIFs were solved and refined using 3DED data. ZIF-EC1 has a dense 3D framework structure, which is built by linking mono- and bi-nuclear Zn clusters and 2-methylimidazolates (mIm^-). The discovery of this new MOF highlights the power of 3DED in developing new materials.

In recent years, Electron Diffraction, and especially the 4D-STEM [2] is growingly becoming a routine part of structural characterizations of materials at the nano-scale. Its un-matched spatial resolution (down to sub-nm) enables the exploration of local variations within a sample, which alternatively is averaged over the entire irradiated sampled area, when explored, for example, by x-rays. As often shown in electron microscope, samples are often heterogeneous, and consequently their local properties, which then reflect on the average behavior of the material, composite, or device. Besides morphology and composition, the local structural order can vary, especially in evolving systems. In this study, we explore how far we can take electron diffraction when the interest is in the evolution of materials.

We challenge ourselves with mapping the local structure in a composite of crystalline Ni and amorphous Zr-Cu-Ni-Al Bulk Metallic Glass (BMG) that was fused into a composite via hot-rolling [2]. Using a fast camera looking through the fluorescence screen, we captured diffraction patterns in a 4D-STEM modality, where we captured diffraction patterns coupled with beam precession with 3 nm step size in a Ni/BMG/Ni cross-section sample that was cut from the composite - in total 131x289 diffraction patterns. Using the collected diffraction patterns and tailoring automated data reduction and analysis pipelines, such as auto-masking, azimuthal-integration, Fourier-transformation to get the electron Pair Distribution Function (ePDF) and various fittings of the PDF, we were efficiently deriving a large set of physically meaningful scalars, which we generalize as Quantities of Interest, or QoI of a scanning nano-structure electron microscopy (SNEM).

Using different QoI's (see Figure)- those derived directly from the images, such as virtual-dark-field and mostly from ePDF's, we could map out most clearly Ni/BMG boundaries, visualize inter-diffusion between Ni and BMG, extract regions of formed nano-crystals within the BMG, follow compositional changes via the average bond-distance (verified with EELS from the same area) and extract the distribution of atomic pairs. We were also able to map the deviation of each pixel within the BMG from an expected structural model, which exposed the BMG/Ni inter-diffusion front. Finally, we could estimate the effective local structure of the nano-crystalline inclusions within the BMG as FCC structures.

Using an assembly of these results we could learn that nano-crystalline inclusions within the BMG are located in regions where Cu is deficient and Zr is in excess. Most importantly, we learn the origin of success in forming the Ni/BMG composite via hot-rolling, which is nonetheless, a challenging goal. Hot rolling is found to be a challenging process due to the excessive formation of nano-crystallites at the Ni/BMG interface. Here, however, the assembly of SNEM results suggested that the metallic Ni amorphized instead of the BMG--Ni crystallize at the BMG/Ni interface. These results emphasize the richness SNEM experiments hide, and with the assistance of automated (and in the future - autonomated) pipelines can expose the story of evolving systems.

[1] Xiaoke Mu, Andrey Mazilkin, Christian Sprau, Alexander Colsmann, Christian Kübel, (2019). Microscopy. 3554, 301
[2] Sina Shahrezaei, Douglas C. Hofmann, Suveen N. Mathaudhu (2019). JOM. 71, 2

An information theory based method [1,2] for the classification of more or less 2D periodic images from real-world crystals with atomic resolution [3] into non-disjoint plane symmetry groups is briefly described and applied to three pairs of synthetic images. One image of these three pairs is free of noise by design. Gaussian noise of mean zero has been added to the other three images of these pairs. All three image pairs are also highly pseudo-symmetric so that it is, for human beings on the basis of a visual inspection alone, very difficult to identify the underlying plane symmetry of the noisy image correctly. This is because all genuine symmetries and pseudo-symmetries are broken by the added noise so that their differences are diminished. The new information theory based classification method, on the other hand, overcomes such challenges [4].

The method enables the objective, i.e. researcher independent, identification of the plane symmetry group that provides the best known separation of structure and generalized noise at the given noise level of a processed image. This identification enables the most meaningful averaging of the image in the spatial frequency domain in support of subsequent crystallographic analyses. This kind of averaging is over all correctly identified asymmetric units in the image and removes noise more effectively than traditional Fourier filtering. Ratios of numerically obtained geometric Akaike Information Criterion values, i.e. first-order geometric-bias corrected sums of squared residuals between the complex-valued Fourier coefficients of the raw image intensity and their counterparts from the applicable symmetry models of this data, are utilized for plane symmetry classifications within the appropriate symmetry hierarchy branch or intersecting branches. The symmetrized model of the noisy raw data that is the best representation of the 2D periodic structure in the Kullback-Leibler divergence sense will be found within such a single branch or at the crossing with other such branches in cases of more elaborate symmetries.

Numerically obtained confidence levels are assigned to the classification of noisy images into minimal supergroups over their translationengleiche maximal subgroups. The resulting plane symmetry classifications are always generalized noise level dependent, which allows for better classification results as noise decreases with future improvements to the imaging and image-processing procedures. The information theory based method delivers only probabilistic classifications as it is fundamentally unsound to assign an abstract mathematical concept, such as a plane symmetry group, with 100 % certainty to the record of a noisy real-world imaging experiment of an imperfect real-world crystal.

[1] P. Moeck, Symmetry 10, paper 133 (46 pages) (2018), open access, DOI: 10.3390/sym10050133

[2] P. Moeck, IEEE Transactions on Nanotechnology 18, 1166-1173 (2019), DOI: 10.1109/TNANO.2019.2946597, see also http://arxiv.org/abs/1902.04155, August 31, 2019 for an expanded version of this review

[3] P. Moeck, A. Dempsey, and C. Shu, Microscopy and Microanalysis 25 (Suppl. 2), 184–185 (2019), DOI: 10.1017/S143192761900165X

[4] P. Moeck and A. Dempsey, Microscopy and Microanalysis 25 (Suppl. 2), 1936–1937 (2019), DOI: 10.1017/S1431927619010419

Strontium iron oxide is a candidate for many different energy applications, including solid oxide fuel cells, chemical looping, and thermochemical energy storage. Upon the redox reactions, SrFeO_x cycles between two end forms: an oxygen deficient form SrFeO_2.5 with a brownmillerite structure and an oxidized form SrFeO_3-δ with a perovskite structure. Two intermediate structures are reported from ex situ and in situ X-ray and neutron powder diffraction [1–3]. However, in real applications, submicron sized crystals are used and X-ray and neutron diffraction techniques are not able to access structural information on an individual submicron crystal. In situ 3D electron diffraction (3D ED) performed on a transmission electron microscope (TEM) is the only way to obtain single crystal data on all structural changes occurring during the actual redox reactions. Due to the single-tilt design of the environmental holders combined with the complexity of these structures, in-zone electron diffraction and high resolution imaging on random crystallites are unrealistic, but 3D ED does not require in zone orientation and could thus be successfully applied to gather structural data on the different phases.

We performed in situ oxidation of a brownmillerite SrFeO_2.5 crushed single crystal upon heating in an oxygen atmosphere in TEM using the sealed commercial holder. By acquiring 3D ED data at different steps of the reaction, we confirmed the formation of the perovskite SrFeO_3-δ structure, which we were able to reduce back to brownmillerite in a hydrogen atmosphere. The obtained data allowed us to derive the structures formed at different reaction steps, including the intermediate phases, resulting in new information about their crystal structures and microstructures. In my talk, I will compare the results of in situ 3D ED with the published data from X-ray and neutron diffraction, discuss the limitations of the method, and the next steps in improving in situ 3D ED in gas environments.

[1] A. Maity, R. Dutta, B. Penkala, M. Ceretti, A. Letrouit-Lebranchu, D. Chernyshov, A. Perichon, A. Piovano, A. Bossak, M. Meven, W. Paulus (2015). J. Phys. D. Appl. Phys. 48, 504004. [2] D.D. Taylor, N.J. Schreiber, B.D. Levitas, W. Xu, P.S. Whitfield, E.E. Rodriguez (2016). Chem. Mater. 28, 3951–3960. [3] J.P.P. Hodges, S. Short, J.D.D. Jorgensen, X. Xiong, B. Dabrowski, S.M.M. Mini, C.W.W. Kimball (2000). J. Solid State Chem. 151, 190-209.

Keywords: brownmillerite; TEM; 3D ED; in situ

This work was supported by BOF 38689 - New method to acquire in situ information on crystal structures changed by chemical reactions

Timescales of dynamic processes in extended solids span many orders of magnitude owing to the large number of degrees of freedom. Additionally, scaling laws dictate that discrete temporal domains comprising the entire continuum consist of associated spatial domains within which specific dynamics are dominant. Ideally, one would be able to probe the entire spatiotemporal range on a single specimen spot with a single instrument. Modern TEMs are exceptionally versatile in this regard, providing access to spatial and energy ranges that span sub-Å to micrometres and sub-10 meV to 1,000s of eV, respectively. However, timescales of the associated physical phenomena span 100s of attoseconds (10^-18 s) to minutes and longer, a range that cannot be fully covered by even the fastest direct detectors. Indeed, dynamics faster than ~0.1 ms are largely inaccessible to detector-based TEM approaches.

Here, an overview will be provided of ongoing efforts aimed at pushing TEM temporal resolutions well beyond the limits imposed by detectors and by peak dose rates. Emphasis will be placed on laser-driven nanosecond single-shot and fs stroboscopic modalities, currently the two most widely used approaches (Figure 1) [1-3]. Common hardware configurations based on modified commercial TEM platforms will be described, and current state-of-the-art performance specifications will be discussed. This will be followed by a brief survey of discoveries and advances that have been made with imaging, diffraction, and spectroscopy. Particular focus will be placed on experiments that have led to deeper understanding of materials and to new physics [4]. The talk will conclude with a brief look toward new emerging approaches and expanded applications, such as pulsed-beam damage mitigation [5, 6].

[1] Park, S. T., Flannigan, D. J. & Zewail, A. H. (2011). J. Am. Chem. Soc. 133, 1730.

[2] Cremons, D. R., Plemmons, D. A. & Flannigan, D. J. (2016). Nat. Commun. 7, 11230.

[3] Plemmons, D. A., Suri, P. K. & Flannigan, D. J. (2015). Chem. Mater. 27, 3178.

[4] Barwick, B., Flannigan, D. J. & Zewail, A. H. (2009). Nature 462, 902.

[5] VandenBussche, E. J. & Flannigan, D. J. (2019). Nano Lett. 19, 6687.

[6] VandenBussche, E. J., Clark, C. P., Holmes, R. J. & Flannigan, D. J. (2020). ACS Omega 5, 31867.

At present report time resolved methods and measurements of rocking curves (RC) and reciprocal space maps (RSM) under external dynamic ultrasonic loads are described. These measurements were made by using adaptive X-Ray optic (ABXO) elements.

Conducting experiments with time resolution using x-ray and synchrotron radiation is one of the advanced modern scientific problems. Today, there are three main directions in the development of such experiments - the creation of new sources (synchrotrons and XFELs), the development of detecting equipment, and the rapid tuning of experimental parameters. The first two directions have gained significant development in recent years, and the last direction rests on the impossibility of quickly adjusting experimental parameters using existing goniometric systems. As a result, the existing hardware and methodological base practically does not cover the range of time resolutions from seconds to microseconds, in which many interesting physical processes occur.

One of possibilities to overcome these limitations of traditional approach is using of non-mechanical adaptive X-ray optic elements, such as X-ray acoustic resonators of longitudinal oscillations or bimorph piezo-actuators [1]. It allows fast and precise variation of X-ray diffraction parameters, varying the angular position of the X-ray beam and controlling its wavelength. An important feature of the method is the possibility of conducting experiments not only in laboratory conditions, but also at synchrotron stations.

The method has been successfully applied to the study of processes occurring in crystals under dynamic ultrasonic loads. Using this method, studies of a silicon crystal subjected to quasistatic mechanical load were carried out [2]. The studies of the evolution of the defective structure of lithium fluoride (LiF) and TeO₂ single crystals under the conditions of dynamic ultrasonic loading in a wide range of amplitudes have also been studied [3]. It is shown that the diffraction pattern (shape and FWHM of rocking curves) under the action of ultrasound can differ significantly from the original, and the proposed method allows monitoring its changes with a temporal resolution of up to 10 μs, inaccessible when using mechanical goniometric systems. Studies of the evolution of the defective structure using the new method showed its significant (at least 3 orders of magnitude on a laboratory source) superiority in speed over existing methods.

The technique was also successfully applied for conducting experiments in a three-crystal X-ray diffraction scheme. It was shown that with its help it is possible to carry out fast (several minutes even with laboratory X-ray source) measurements of the reciprocal space maps from the studied samples under dynamic ultrasonic loads, as well as studying the distribution of ultrasonic vibrations in resonator crystals.

The reported study was funded by RFBR and DFG 19-52-12029 and by RFBR according to the research project №18-32-20108.

1. Blagov A.E., Bikov A.S and etc // IET. 2016. № 5. С. 109
2. Eliovich I.A., Akkuratov V.I. and etc. // Crystallography reports, 2018, Vol. 63, № 5, p. 708
3. Blagov A.E., Pisarevskii Yu.V. and etc. // PSS. 2017. Vol. 59. № 5. p. 947.

Many phase transformations associated with solid-state precipitation look structurally simple, yet take place with great difficulty. Classic cases of surprisingly difficult phase transformations can be found in alloy systems forming the basis for a broad range of high-strength lightweight aluminium alloys. In these systems, the difficult nucleation of strengthening phases, which are usually semi-coherent, is often preceded by the easy nucleation of another phase with strong structural similarities, typically a coherent precipitate. It is therefore of interest to investigate the reasons behind the difficult transformation from coherent to semi-coherent precipitate phases.

Using scanning / transmission electron microscopy (S/TEM) techniques both ex situ and in situ, combined with atomic scale simulations (density functional theory and semi-empirical potentials) we examined phase transformations in several alloy systems, including the textbook Al-Cu and Al-Ag systems. We show that certain microalloying additions, or different processing conditions applied to samples in bulk or nanoscale form, result in previously unreported precipitate phases [1-2] – see Figs. 1-2, or promote the nucleation of existing phases [3-4]. The nucleation mechanisms of these phases involve structural templates provided by coherent precipitates [1-3] and depend critically on the availability of vacancies [1-2,4]. Based on our observations atomic-scale mechanisms are proposed for phase transformation pathways. We also characterised the surface structure and growth mechanisms of voids, uncovering a crystallographic relationship necessary for the growth of high-aspect ratio voids [5]. These findings suggest several approaches to not only stimulate known precipitate transformations, but also discover new phases and transformation pathways.

The sensitiveness to the electron beam of nanocrystalline metal-organic frameworks (MOFs) has always posed an objective criticality for the accurate determination of their structure by single crystal electron diffraction. The reversible atomic displacement caused by the high flexibility of the organic linkers further complicates the characterization of the framework and the understanding of their complex functional properties at the atomic level ^[1]. Although standard diffraction experiments can elucidate dynamic phenomena ^[2,3], an analysis of the anisotropic displacement parameters (ADPs) obtained after refining MOFs against electron diffraction data has never been performed. In this study, we solved and refined the structures of UiO-67 /MIL-140C, coexisting in mixture, by using continuous rotation electron diffraction (cRED). For both structures, restricted small-angle librations of the linker were revealed by analysing the ADPs at room temperature and in cryogenic conditions (98 K). Our work shows that continuous rotation electron diffraction (cRED) not only provides reliable and accurate crystallographic models as that obtained by single crystal X- ray diffraction (SCXRD), but it represents a powerful tool to investigate the dynamic in the molecular fragments of the framework.

[1] Bennett, T.; Cheetham, A.; Fuchs, A.; Coudert, F.-X. (2017) Nature Chem., 9, 11–16

[2] Smeets, S.; Parois, P.; Burgi, H- B; Lutz, M. (2011) Acta Cryst, B67, 53-62

[3] Lock, N.; Wu, Y.; Christensen, M.; Cameron, L. J.; Peterson, V. K.; Bridgeman, A. J.; Kepert, C. J.; Iversen, B. B. (2010) J. Phys. Chem. C, 114, 16181− 16186

The GPR52 receptor is a Class-A orphan G protein-coupled receptor (GPCR) whose endogenous ligand remains elusive. Highly expressed in the brain, it represents a promising therapeutic target for treating psychiatric disease and Huntington’s disease. However, tool ligand and drug discovery have been largely hampered by a lack of structural information due largely to the low homology (<20%) of GPR52 to any known GPCR structure. We reported three high resolution human GPR52 structures with and without a bound ligand. According to the structures, we observed a unique configuration of extracellular loop 2 (ECL2) that occupies the orthosteric pocket, a novel side pocket and a special winding mode for Transmembrane helix 5 (TM5). Mutagenesis and functional assay suggested the self-activation by ECL2. These findings provide unprecedented insights into the structural basis of GPR52 ligand recognition that will be valuable for GPR52 deorphanization and will guide the design of diverse ligands with distinct pharmacological properties that have not yet been possible.

Integrative modeling is an increasingly important tool in structural biology, providing structures by combining data from varied experimental methods and prior information. As a result, molecular architectures of large, heterogeneous, and dynamic systems, such as the ~52 MDa Nuclear Pore Complex, can be mapped with useful accuracy, precision, and completeness. Key challenges in improving integrative modeling include expanding model representations, increasing the variety of input data and prior information, quantifying a match between input information and a model in a Bayesian fashion, inventing more efficient structural sampling, as well as developing better model validation, analysis, and visualization. In addition, two community-level challenges in integrative modeling are being addressed under the auspices of the Worldwide Protein Data Bank (wwPDB). First, the impact of integrative structures is maximized by PDB-Dev, a prototype wwPDB repository for archiving, validating, visualizing, and disseminating integrative structures. Second, the scope of structural biology is expanded by linking the wwPDB resource for integrative structures with archives of data that have not been generally used for structure determination but are increasingly important for computing integrative structures, such as data from various types of mass spectrometry, spectroscopy, optical microscopy, proteomics, and genetics. To address the largest of modeling problems, a type of integrative modeling called metamodeling is being developed; metamodeling combines different types of input models as opposed to different types of data to compute an output model. Collectively, these developments will facilitate the structural biology mindset in cell biology and underpin spatiotemporal mapping of the entire cell.

Axonal degeneration is responsible for disease progression and accumulation of disability in many neurodegenerative conditions. Sterile alpha and Toll/interleukin-1 receptor motif-containing 1 (SARM1) is a nicotinamide adenine dinucleotide (NAD⁺)- cleaving enzyme whose activation triggers axon destruction [1-4]. Loss of the biosynthetic enzyme NMNAT2, which converts nicotinamide mononucleotide (NMN) to NAD⁺, activates SARM1 via an unknown mechanism. Using crystallography, cryo-EM, NMR and biochemical assays, we demonstrate that SARM1 is activated by an increase in the ratio of NMN to NAD⁺ and show that both metabolites compete for binding to the autoinhibitory N-terminal armadillo repeat (ARM) domain of SARM1 [5]. We show that NMN binding disrupts ARM-TIR interactions in the full-length SARM1 octamer, enabling its TIR domains to self-associate and form a catalytic site capable of cleaving NAD⁺ [5]. These structural insights identify SARM1 as a metabolic sensor of the NMN/NAD⁺ ratio, define the mechanism of SARM1 activation, and may enable a path to the development of allosteric inhibitors that block SARM1 activation.

[1] Essuman, K. et al.(2017). Neuron 93, 1334-1343.

[2] Essuman, K. et al. (2018). Curr. Biol. 28, 421-430.

[3] Horsefield, S. et al. (2019). Science 365, 793-799.

[4] Wan, L. et al. (2019). Science 365, 799-803.

[5] Figley, M. et al. (2021). Neuron 109, 1118–1136.

De novo cysteine biosynthesis is a pathway responsible for metabolizing inorganic sulfur to produce L-cysteine, which holds significance in the cellular activities of several organisms, majorly plants and microbes. Absence of this pathway in humans, accompanied by differential roles of accumulated L-cysteine in aiding adaptation of microbes in the harsh host environment, promoting toxin inactivation, biofilm formation, and development of antimicrobial resistance (AMR), make this pathway a lucrative target for novel therapeutics. The pathway is fuelled by a bienzyme complex, the Cysteine Synthase Complex (CSC), made up of CysE and CysK enzymes, where a hexameric CysE binds two CysK dimers, one on either end, to further cysteine production in a two-step fashion from L-serine. Recognition of industrial value in addition to the therapeutic potential of this pathway urges the need for further molecular investigations for its optimal exploitation. However, the large size of the molecular complex has put to question the feasibility of resolving its 3-D structure, partially reasoning the inability to obtain a 3-D structure even after nearly three decades of the complex’s discovery. Klebsiella pneumoniae, a pathogen with its multi-drug resistance (MDR) recognized in WHO’s list of six extensively MDR pathogens grouped as ES‘K’APE group of pathogens. Targeting the CSC of K. pneumoniae is a promising approach to up our armamentarium against the growing menace caused by the pathogen.

The success of rational structure-based drug discovery is driven by the availability of a crystal structure of the target protein complex. With a recent study reporting the SAXS-modelled CSC from E. coli, we aim to model the CSC complex using the K. pneumoniae CysE structure previously made available by our group, adopting a knowledge-based approach. The present poster reports the purification and characterization of recombinant CSC from K. pneumoniae, as an essential first step in progressing towards understanding its structure and biochemical function. Purified recombinant CSC was obtained and subjected to - (i) gel filtration chromatography to separate and estimate molar mass of the complex, (ii) dynamic light scattering for determining hydrodynamic radius and verifying homogenous population, and (iii) negative stain electron microscopy to visualize the purified complex. Simultaneous utilization of in silico tools integrated with techniques of structural biology is being carried to predict the 3-D structure of CSC, and identify residues involved in protein-protein interface stabilization. Following physical analysis and attempts to crystallize the CSC complex obtained from K. pneumoniae we observed heterogeneity in the CSC preparation, with a flexible/dynamic nature of the association between the two interacting proteins posing considerable challenges. Additionally, identification of interacting residues using in silico predictions would facilitate a better understanding of useful molecular recognition inferences within CSC, which presently are far from being well-understood.

Arsenic is a widely distributed toxic metalloid that poses a significant threat to human health by contaminating ground water systems [1]. Arsenic can exist in both organic and inorganic forms, with arsenite (AsO₃^3-) and arsenate (AsO₄^3-), being toxic species. Although arsenic is hazardous to human health, some prokaryotes have developed unique mechanisms that utilise arsenite (AsO₃^3-) and arsenate (AsO₄^3-) for respiration and therefore as energy sources.

The organism Rhizobium sp. NT-26, respires with arsenite and employs the arsenite oxidase enzyme (Aio) for its crucial respiratory activity, which catalyzes the oxidation of arsenite (AsO₃^3-) to arsenate (AsO₄^3-). The Aio enzyme consists of a large catalytic subunit (AioA), which contains a molybdenum centre and a 3Fe-4S cluster, and a small subunit (AioB) containing a Rieske 2Fe-2S cluster. Arsenite is oxidized to arsenate at the Mo site,concomitantly reducing Mo(VI) to Mo(IV) [2]. The electrons are then passed to the 3Fe-4S cluster, the Rieske cluster in AioB and finally to an electron acceptor, which is cytochrome c₅₅₁ (cyt c₅₅₁) [2, 3]. Structures of interprotein transfer complexes are interesting as they form via extensive electrostatic interactions, which are highly transient. Structural flexibility at the protein-protein interface promotes fast dissociation of the complex following electron transfer [4]. To date, the structure of the Aio and cyt c₅₅₁ complex has not been investigated, and the kinetics and thermodynamics of the Aio to cyt c₅₅₁ interaction are unknown. In this study, we describe the structure of the Aio/cyt c₅₅₁ complex, determined by X-ray crystallography. The structure provides insight into various types of interactions (hydrogen bonding, salt bridges and electrostatic interactions) of the complex that can be studied further to understand the mechanism and specificity between the partner proteins during electron transfer.

[1] H. V. Aposhian, and M. M. Aposhian, “Arsenic toxicology: five questions,” Chem Res Toxicol, vol. 19, no. 1, pp.1-15, Jan, 2006.

[2] T. P. Warelow, M. Oke, B. Schoepp-Cothenet, J. U. Dahl, N. Bruselat, G. N. Sivalingam, S. Leimkühler, K.

Thalassinos, U. Kappler, and J. H. Naismith, “The respiratory arsenite oxidase: structure and the role of residues surrounding the rieske cluster,” PLoS One, vol. 8, no. 8, pp. e72535, 2013.

[3] P. J. Ellis, T. Conrads, R. Hille, and P. Kuhn, “Crystal structure of the 100 kDa arsenite oxidase from Alcaligenes faecalis in two crystal forms at 1.64 Å and 2.03 Å,” Structure, vol. 9, no. 2, pp. 125-132, 2001.

[4] D. Leys, and N. S. Scrutton, “Electrical circuitry in biology: emerging principles from protein structure,” Curr Opin Struct Biol, vol. 14, no. 6, pp. 642-7, Dec, 2004.

α-L-Fucosidases (EC 3.2.1.51) catalyse hydrolysis of the α-L-fucosyl moiety from the non-reducing terminus of oligosaccharides and glycoconjugates. New representatives are sought for their unique functional properties or particular specificity, especially in connection with the transglycosylation ability to enable targeted modification of compounds for biomedical applications. They belong to several glycosyl hydrolase families, GH29, GH95, GH139, GH141, and GH151, and utilize either the retaining or inverting mechanism. While members of some families, e.g. GH29, have been studied thoroughly, the structural information and mechanistic details for other families, including GH151, are missing.

In our previous studies [1,2] and our more recent results we bring structural and functional insights into the mechanism, active site complementation and specificity of two isoenzymes from bacterium Paenibacillus thiaminolyticus. The proteins were characterised using a range of biophysical techniques, small angle X-ray scattering, X-ray crystallography, and in silico analysis (substrate docking), together with assays of α-L-fucose hydrolysis and transglycosylation ability. The crystal structure of α-L-fucosidase isoenzyme 1 (GH29) showed a new and unusual organization of the enzyme in a hexamer, with the active sites exposed to the surrounding environment and suggested active site complementation. Mutagenesis and catalytic assays confirmed the first case of active site complementation in α-L-fucosidases [2]. Our recent crystal structure of isoenzyme 2 from the same bacterium brings the first structural insight into the GH151 family, with unexpected oligomerization, enclosure of the active site inside the oligomer, and, again, proven active site complementation. Mutations modifying the complemented amino acid lead to changes in the catalytic properties of both enzymes. The comparison on the level of structure, functional, and biophysical data for the two isoenzymes brings answers to some principal questions regarding α-L-fucosidase substrate specificity and raises new questions about the functionality and stability of complemented active sites within these families of α-L-fucosidases.

This work was supported by the Czech Academy of Sciences (86652036), by the European Regional Development Fund (CZ.02.1.01/0.0/0.0/15_003/0000447, CZ.02.1.01/0.0/0.0/16_013/0001776, CZ.1.05/1.1.00/02.0109), by the Ministry of Education, Youth and Sports of the Czech Republic (LM2015043 and LM2018127, support of Biocev-CMS – Crystallization, Biophysics and Diffraction facilities of CIISB, part of Instruct-ERIC).

1. Benešová E, Lipovová P, Krejzová J, Kovaľová T, Buchtová P, Spiwok V & Králová B (2015) α-L-Fucosidase isoenzyme iso2 from Paenibacillus thiaminolyticus. BMC Biotechnol. 15, 36.

2. Kovaľová T, Kovaľ T, Benešová E, Vodičková P, Spiwok V, Lipovová P, Dohnálek J (2019) Active site complementation and hexameric arrangement in the GH family 29; a structure–function study of α-L-fucosidase isoenzyme 1 from Paenibacillus thiaminolyticus. Glycobiology, 29(1), 59–73.

Operation Night Watch is the largest research and conservation project that Rembrandt’s masterpiece The Night Watch (1642, oil on canvas, h 378.4 x w 453 cm) has ever undergone. In the summer of 2019, the Rijksmuseum embarked on this multi-year project with the goal of thoroughly studying the condition and painting technique to determine the best treatment plan for the large canvas painting. The Night Watch was researched in situ in the gallery inside an ultra-transparent glass chamber in full view of the public (Fig. 1). The multi-disciplinary team of Operation Night Watch includes scientists, conservators and art historians, and collaborates with museums and universities in the Netherlands and abroad. Together they work alongside each other on the acquisition and interpretation of the research data.

The latest and most advanced research techniques are being used, ranging from digital imaging and scientific and technical research to computer science and artificial intelligence. The non-invasive macroscale imaging technologies that have been employed include macro X-ray fluorescence, macro X-ray powder diffraction, reflectance imaging spectroscopy, optical coherence tomography, high resolution photography and 3D scanning. The combined approach was essential to gain insight into the complex (art)historical and material information to answer the (technical) art history, conservation, and scientific questions. Parallel to this, microscale imaging analyses were carried out on embedded and loose microsamples making use of light microscopy, imaging-ATR-FTIR, scanning electron microscopy combined with X-ray elemental analyses, micro-Raman and synchrotron-based X-ray fluorescence and diffraction techniques in 2D and 3D mode.

During the lecture, examples will be given of the lead and arsenic sulphide-containing pigments that Rembrandt used in The Night Watch. The use, distribution, condition, and degradation products of these pigments will be discussed on both a macro and micro scale and the implications for the ensuing conservation treatment will be outlined.

Figure 1. The Night Watch (1642) by Rembrandt van Rijn was investigated inside the glass chamber in the Gallery of Honour, Rijksmuseum, Amsterdam, The Netherlands

to be announced

Pigment-binder interactions occurring in paint layers of artworks can either contribute to the stability of paint films as well as they can cause their degradation, seriously affecting the appearance and stability of paintings. Depending on intrinsic (i.e., composition of pigments and/or binders, presence of additives etc.) or extrinsic factors (i.e., relative humidity, temperature, conservation treatment etc.), formation of metal carboxylates can fulfil both aspects. Metal carboxylates result from reactions between metal-based pigments with carboxylic acids originating from a fatty medium. In paint layers, the reactive metal pigments are represented especially by lead-based pigments (e.g., lead white, red lead, lead-tin yellows etc.) or zinc white while fatty binder usually means drying oils (e.g., linseed oil, poppy-seed oil, walnut oil etc.) or even egg yolk. [1, 2] On one hand, these pigments accelerate drying of paint layers but, on the other hand, the neo-formed crystalline phases tend to aggregate, resulting in formation of inclusions, protrusions, crusts, blisters or efflorescence. Moreover, reacting with atmospheric gases and pollutants, metal carboxylates can induce the cascade degradation, often accompanied by changes in the tonality of paint layers. Understanding the processes in paint layers is essential for the development of suitable conservation strategies which are necessary to prevent these types of degradation. Since the paintings comprise complicated multi-layered systems in which each particular layer consists of numerous inorganic and organic components, the experimental studies performed on simplified model paint systems are reasonable for identification and description of the pigment-binder interactions. Complementing vibrational spectroscopies, XRPD represents and effective tool for detection of crystalline phases, especially if unexpected product such as metal formates occur. [1] On the other hand, usually robust XRPD meets certain limits in case of metal carboxylates with undetermined crystal structure. [3] Finally, XRPD can be also beneficial for the description of metal carboxylates adopting ionomer structures. Within the contribution, the advantages and limits of XRPD for study of pigment-binder interactions in paint layers will be discussed.

Figure 1. Time-dependent XRD patterns of model paint consisting of minium and linseed oil (LO). The XRD patterns between 0 hours (0H) and 5 days (5D) were collected every 12 hours and, further on, every week. The detected phases: F – lead formate, Pb(HCOO)₂; M – minium – Pb₃O₄; S – Pb-soap/ionomer.

[1] Švarcová, S., Kočí, E., Bezdička, P., Garrappa, S., Kobera, L., Plocek, J., et al. (2020). Dalton Trans. 49, 5044.

[2] Švarcová, S., Kočí, E., Plocek, J., Zhankina, A., Hradilová, J., Bezdička, P. (2019). J. Cul. Herit. 38, 8.

[3] Kočí, E., Rohlíček, J., Kobera, L., Plocek, J., Švarcová, S., Bezdička, P. (2019). Dalton Trans. 48, 12531.

Keywords: metal carboxylates; pigment-binder interactions; paintings; XRPD

The study was supported by the Czech Academy of Sciences in the frame of the programme Strategy AV21 no. 23 - City as a Laboratory of Change; Historical Heritage and Place for Safe and Quality Life.

Upon the recovery of burnt remains in a forensic or archaeological context, bone is often fragmented and comingled, making differentiation between human and non-human samples extremely challenging and subjective. Due to thermal degradation of the organic component, biological techniques, such as DNA analysis, often render futile and so attention is drawn to the final surviving component of bone, the mineral hydroxyapatite.

Exploring the physicochemical modifications that occurs to hydroxyaptite upon heating has shown promise in differentiating between species based on characteristic changes within its crystal lattice structure, and the presence of extraneous mineral phases [1]. However, the effects soft tissue has on the heat induced changes are not fully understood, yet are of paramount importance as most bodies are intact, not skeletonised, during a burning event. This study aims to explore the effect heating has on fleshed bone, specifically investigating modifications to the nanocrystalline structure of bone mineral, and whether this has a significant impact on species differentiation.

Varying weights (5g, 7g and 10g) of muscle and fat, and one layer of skin were tested separately to understand their individual affect. A combination of the three tissue types was also considered. The samples were heated for two hours at various temperatures (200°C, 400°C, 600°C and 900°C) which are representative of those temperatures reached in historical forensic and archaeological cases. Powder X-ray diffraction (pXRD) analysis was utilised to calculate coherence length and lattice parameter values and the weight percentages of extraneous mineral phases to identify species differentiating characteristics. Coherence length, which gives an indication on crystallite size and strain, was calculated using the Scherrer equation and the full width half maximum (FWHM) peak values. Spectroscopic techniques including Fourier Transform Infrared (FTIR) and Raman spectroscopy were utilised to collaborate the XRD data and to further our understanding of the relationship between the degradation of the organic matrix and the crystallographic changes.

The purpose of this work was to uncover the real nature and composition of a dry black ink powder found in a bronze inkwell (Fig.1) of the 1st century A.D. It was discovered during the excavation of a cemetery in the locality of Morlungo, Palazzina-Capodaglio, in the municipality of Este in 1878 [1]. Since 2500 BC and up to the thirteenth century AD [2] the carbon-based inks were the most common used. They were mainly composed of amorphous carbon obtained from soot charcoal, or bone black [3,4] usually dissolved in a binder, mixed with a small amount of water. During the IV century AD, a new kind of ink, called iron-gall ink, emerged. It was obtained by mixing gall-nuts, iron or copper metal sulphates, water and Arabic gum. From the early Middle Ages onwards, it became the most common ink in the history of the western world [2]. However, some recent studies on the chemical composition of inks, already spread on their ancient writing supports (papyri, parchment or paper) [5–7], have changed this perspective. The importance and the novelty of this work resides principally in the opportunity of directly studying the ink powder, avoiding the interference from the writing support, as well as analysing its container that was fundamental for a correct interpretation of the experimental results. The investigation was conducted through a multi-technical approach, combining several and complementary synchrotron radiation (SR)-based techniques allowing us to confirm the ink nature of the sample and to distinguish its original formulation from the contaminants.

In particular, XRPD, XAS and FTIR measurements showed a substantial presence of silicates and common clay minerals in the ink along with cerussite and malachite, Pb and Cu bearing-carbonates, respectively. These evidences support the hypothesis of an important contamination of the ink by the burial environment (soil) and the presence of degradation products of the bronze inkpot. Moreover, the combined use of IR, Raman, and GC-MS evidenced that the black ink was mainly composed of amorphous carbon deriving from the combustion of organic material mixed with a natural binding agent, Arabic gum. This work also wants to underline how the intrinsic multidisciplinary approach based on SR experimental techniques represents the most efficient way to obtain a complete overview of complex materials such as archaeological artefacts.

Figure 1. a. The bronze inkwell (front view); b. internal view of the inkwell with the black powder on the bottom and top view of the lid; c. the ink black powder residue collected from the bottom of the inkwell

[1] Presdocimi, A. Guida sommaria [2] Aceto, M., Agostino, A., Fenoglio, G., Gulminie, M., Bianco, V., Pellizzi, E. (2012). Spectrochim Acta Part A Mol. Biomol. Spectrosc.91, 352.

[3] Christiansen, T., Buti, D., Dalby, K. N., Lindelof, P. E., Ryholt, K., & Vila, A. (2017). J. Archaeol. Sci. Reports 14, 208.

[4] Lucas, A. & Harris, J. R. Ancient Egyptian Materials and Industries. (1962)

[5]. Ferrer, N. & Vila, (2006). Anal. Chim. Acta 555, 161.

[6] Tack, P., Cotte, M., Bauters, S., Brun, E., Banerjee, D., Bras, W., Ferrero, C., Delattre, D., Mocella, V. & Vincze, L., (2016). Sci. Rep.6, 1.

[7] Brun, E., Cotte, M., Wright, J., Ruat, M., Tack, P., Vincze, L., Ferrero, C., Delattre, D., and Mocella, V., (2016). Proc. Natl. Acad. Sci. U. S. A. 113, 375

The in-depth understanding of properties, manufacturing process and conservation of archaeological artefacts very often requires a reliable structural characterization. Non-destructive techniques, like X-ray diffraction and different kinds of spectroscopies (Raman, IR etc.), are usually employed to the study such materials. In recent years, the scientific community has also shown a renewed interest in characterization methods based on Transmission Electron Microscope (TEM); like High Resolution Transmission Electron Microscopy (HRTEM), Electron Diffraction (ED), Energy Dispersive X-ray Spectroscopy (EDX) and Electron Energy Loss Spectroscopy (EELS); which provide structural and chemical information at nm scale using very small quantities of material. In particular, we have shown how emerging diffraction techniques like Electron Diffraction Tomography (EDT) and Phase & Orientation mapping in TEM can be applied for the study of nanocrystalline phases present in Greek amphorisks, Roman glass tesserae and several Maya pigments [1, 2].

We are now working on the structural characterisation of corrosion products from different archaeological artefacts using TEM. In most cases, due to the very small quantity of existing corrosion products, conventional diffraction methods (single crystal X-ray diffraction or powder X-ray diffraction) are not suitable for a proper structural characterization. In particular, the pale blue corrosion products that form on ancient copper alloy artefacts have been subject of research for past several years, though the exact nature of such corrosion products have not yet been determined. Here, we present an innovative study based on EDT of a blue corrosion product forming on the surface of a Chinese Bronze artefact of the Shang dynasty (British Museum Collections).

For this study, a thin electron beam-transparent lamella (8 x 10 micron) was prepared from a larger poly-crystalline sample (100 x 200 micron) using Focused Ion Beam (FIB). Subsequently, EDX data was collected by a Scanning Electron Microscope (SEM). A very high quantity of Cu was observed, together with other elements like Ca, P and O. The thin lamella was then used for EDT study using TEM. EDT data was collected by stepwise rotation of the crystal around an arbitrary axis coupled with beam precession [Fig. 1]. From the EDT data, a monoclinic unit cell (a = 23.0 Å, b = 5.4 Å, c = 10.3 Å, b = 94.1°, space group P2/c) was determined. Interestingly the obtained unit cell does not match with any of the blue corrosion products reported in literature. Using the extracted intensity from EDT data, a preliminary structure was determined, which closely resembles one of the blue mineral, nissonite.

We believe that novel structural characterisations using EDT in future may not only help in the understanding of corrosion processes in ancient artefacts, but also can contribute to their optimum conservation and eventually provide information about their provenance.

[1] Zacharias, N., Karavassili, F., Das, P. P., Nicolopoulos, S., Oikonomou, A., Galanis, A., Rauch, E., Arenal, R., Portillo, J., Roque, J., Casablanca, J. & Margiolaki, I. (2018) Microchemical Journal, 138, 19.

[2] Nicolopoulos, S., Das, P. P., Pérez, A. G., Zacharias, N., Cuapa, S. T., Alatorre, J. A. A., Mugnaioli, E., Gemmi, M. & Rauch, E. F. (2019) Scanning.

In order to create a painting, an artist must carefully select his painting materials and especially those materials that convey color to the painting and help create other optical effects. In the 15^th-17^th century, most colored pigments were inorganic in nature, many of them powdered minerals Among painters’ pigments, commonly available materials are present such as earth colours, and bone black, but also fairly rare ones such as the red pigment vermillion/cinnabar or the blue pigment ultramarine.

The most expensive pigment of many historical periods is without any doubt natural ultramarine, sometimes referred to by its mineral names lazurite or lapis lazuli [1]. Lazurite is an alumino-silicate mineral containing zeolite cages in which sulphur polyanions are present that give it its characteristic blue colour. In the 15-17^th century, natural ultramarine was a material more expensive than gold. It derived its scarcity and hence its very high price from the fact that the only known mines of natural ultramarine were located in a remote northeastern Afghan province called Badakhshan. In the 15-17^th century, most natural ultramarine was transported along the silk road and reached Europe via Venice [2]. What was traded in this manner were either large lumps of the blue/white lazurite-rich rocks (that also contain other minerals) or already (partially) purified lazurite powder. In Venice and other locations in Europe, by means of the application of various crushing and particle selection techniques [3], the purity of the blue pigment was then improved, creating different grades of ultramarine of widely different price.

By means of Macroscopic X-ray powder diffraction (MA-XRPD), it is possible to record the distribution of crystalline materials in historical paintings and thus to identify which inorganic pigments were employed by an artist to create a specific work of art. In recent years, this method has been employed by our group to identify the inorganic pigments present in masterworks by artists such as Vincent Van Gogh [4],(19^th century), Johannes Vermeer [5] (17^th century) and Jan Van Eyck [6] (15^th century).

Of particular usefulness for highly specific pigment mapping of oil paintings is reflection mode MA-XRPD. Although dependent on the diffraction characteristics of the pigments studied and on the measurement conditions, in this mode, the detection limit of scanning MA-XRPD is of the order of 2-5%. Next to allowing for a direct identification of the pigment mixtures that constitute the paint of a particular hue, this ability to detect and identify minor components in a complex mixture makes it also possible to employ MA-XRPD to record fingerprints of specific pigments and highlight art historically relevant differences between pigment subtypes. For example in Vermeer’s Girl with the Pearl Earring, it was possible to establish that Vermeer used at least two distinctly different subtypes of lead white to paint the Girl’s face: one hydrocerussite-rich (2PbCO₃.Pb(OH)₂) to paint the lighter/highlighted facial areas and another, poorer in hydrocerussite and richer in cerussite (PbCO₃) which is used in the shadow areas [5,7].

Since natural ultramarine pigment powder is invariably prepared by purification of (heat-)crushed lazurite-rich Afghan rocks, the resulting powder not only contains microcrystals of the blue mineral lazurite, but also of its accessory minerals such as albite, sodalite, diopside, pyrite, quartz, sanidine etc. Some of these share the structure and overall chemical composition of the blue alumino-silicate mineral while others are quite different. All of these accessory minerals, however, lack the intense blue color of lazurite and thus alter the color intensity and tone of the blue pigment when they are (too) abundantly present.

Through MA-XRPD mapping of blue areas of a series of Netherlandish paintings by well-known 15^th and 17^th century artists from various museums in Belgium and the Netherlands, we have made a non-exhaustive survey of the presence of the pattern of accessory minerals that are present in 15^th and 17^th century natural ultramarine. The aim of the survey was to answer questions such as: (a) does the fingerprinting pattern of the accessory mineral change with time?, (b) and if so, does it change gradually or erratically? and (c) is the pattern significantly affected by the application of the purification methods? In the presentation, preliminary answers to some of these questions will be discussed by means of examples from the oeuvre of 15^th-17^th century artists Petrus Christus, Albrecht Bouts, Jan Steen and Johannes Vermeer.

[1] Kirby, J., Nash, S., Cannon, J. (eds.) (2010) Trade in Artists’ Materials. London: Archetype Publications.

[2] Matthew, L. and Berrie, B., in [1], pp. 245-252.

[3] Gambardella A. et al. (2020). Science Advances 6, eaay8782.

[4] Vanmeert et al. (2018). Angewandte Chemie Int. Ed. 57, 7418-7422.

[6] De Meyer et al. (2019). Science Advances 6, eaax1975.

[7] Van der Snick et al. (2020). Science Advances 6, eabb3379.

[8] Van Loon A. et al. (2019). Heritage Science 7, 102.

Cultural heritage objects are affected by various corrosion processes during decades and centuries of storage in museums and collections. Atmospheric gases like CO₂, moisture or - as wood emits significant amounts of formic and acetic acid¹ - the storage furniture itself can induce corrosion. Calcareous heritage objects like historic Mollusca shells², eggs³, ancient pottery (Figure 1, a) or marble reliefs (Figure 1, c, d) are very sensitive to acetic and formic acid vapours. The corrosion process leads to the formation of efflorescence crystals sometimes crystallizing in pores and cracks, which can cause severe damage to the artifacts. This phenomenon has been known as “Byne’s disease” since the end of the 19^th century.⁴ Both, simple salts like Ca(CH₃COO)₂∙H₂O⁵ or Ca(CH₃COO)₂∙½H₂O⁶ and complex compounds like calclacite (Ca(CH₃COO)Cl·5H₂O)⁷ or thecotrichite (Ca₃(CH₃COO)₃Cl(NO₃)₂·6H₂O)^8-9 were found as corrosion phases on calcareous historic objects. Many of these efflorescence phases, however, still remain poorly characterized due to their microcrystalline character and the occurrence of polyphase mixtures.

Our work focuses on the characterization of unknown or hitherto poorly characterized efflorescence phases found on herriatge objects. As the amount of substance that can be removed from the artifacts is usually very small, we also describe the synthesis of the corrosion phases by model experiments. In this study we present the characterization and structure elucidation of complex efflorescence salts like Ca₂(CH₃COO)(HCOO)(NO₃)₂·4H₂O¹⁰, Ca(CH₃COO)(HCOO)·2H₂O and Ca₃(CH₃COO)₄(HCOO)₂· 4H₂O¹¹ that were found on ancient amphorae (Figure 1, a) or historic birds eggs⁵ and seemingly simple corrosion phases like Ca(CH₃COO)₂∙½H₂O¹² which crystallizes on marble reliefs (Figure 1, c, d) or ceramics⁶. A systematic structural investigation of these efflorescence phases revealed calcium carboxylate zig-zag chains (Figure 1, b) as the common structural motif, which shows the crucial role of the carboxylic acids in the corrosion processes and explains the great chemical variety of these compounds. The seemingly simple Ca(CH₃COO)₂·½H₂O was found to crystallize in a 11794.5(3) ų unit cell with a triple helix motif (Figure 2, e) analogous to the collagen proteins.

In summary, the investigations on corrosion phases found on cultural heritage objects led to the discovery of many hitherto unknown or only poorly characterized solid phases with complex crystal structures. In addition, global structural motifs that were revealed in these studies indicate that a lot more compounds are to be discovered.

References

(1) Gibson, L. T.; Watt, C. M., Acetic and formic acids emitted from wood samples and their effect on selected materials in museum environments. Corrosion Science 2010, 52 (1), 172-178.

(2) Tennent, N. H.; Baird, T., The deterioration of Mollusca collections: identification of shell efflorescence. Stud. Conserv. 1985, 30 (2), 73-85.

(3) Bette, S.; Mueller, M. X.; Eggert, G.; Schleid, T.; Dinnebier, R. E., Efflorescence on calcareous objects in museums: crystallisation, phase characterisation and crystal structures of calcium acetate formate phases. Dalton Trans. 2019, 48, 16062-16073.

(4) Byne, L. F. G., The corrosion of shells in cabinets. Journal of Conchology 1899, 9, 172-178.

(5) Tennent, N. H.; Baird, T., The deterioration of Mollusca collections: identification of shell efflorescence. Studies in Conservation 1985, 30 (2), 73-85.

(6) Boccia Paterakis, A.; Steiger, M., Salt efflorescence on pottery in the Athenian Agora: A closer look. Studies in Conservation 2015, 60 (3), 172-184.

(7) Giuseppetti, G.; Tadini, C.; Ungaretti, L., La struttura cristallina della calclacite/ Crystalline structure of a triclinic phase of the compound corresponding to calclacite, Ca(CH3COO)​Cl.5H2O. Periodico di Mineralogia 1972, 41, 9-21.

(8) Gibson, L. T.; Cooksey, B. G.; Littlejohn, D.; Linnow, K.; Steiger, M.; Tennent, N. H., The Mode of Formation of Thecotrichite, a Widespread Calcium Acetate Chloride Nitrate Efflorescence. Studies in Conservation 2005, 50 (4), 284-294.

(9) Wahlberg, N.; Runčevski, T.; Dinnebier, R. E.; Fischer, A.; Eggert, G.; Iversen, B. B., Crystal Structure of Thecotrichite, an Efflorescent Salt on Calcareous Objects Stored in Wooden Cabinets. Crystal Growth & Design 2015, 15 (6), 2795-2800.

(10) Bette, S.; Eggert, G.; Fischer, A.; Stelzner, J.; Dinnebier, R. E., Characterization of a new efflorescence salt on calcareous historic objects stored in wood cabinets: Ca 2 (CH 3 COO)(HCOO)(NO 3 ) 2 ·4H 2 O. Corrosion Science 2018, 132, 68-78.

(11) Bette, S.; Müller, M. X.; Eggert, G.; Schleid, T.; Dinnebier, R. E., Efflorescence on calcareous objects in museums: crystallisation, phase characterisation and crystal structures of calcium acetate formate phases. Dalton Transactions 2019, 48 (42), 16062-16073.

(12) Bette, S.; Stelzner, J.; Eggert, G.; Schleid, T.; Matveeva, G.; Kolb, U.; Dinnebier, R. E., Corrosion of heritage objects: collagen-like triple helix found in the calcium acetate hemihydrate crystal structure. Angewandte Chemie International Edition 2020.

Seven and fivefold point symmetries are incompatible with three-dimensional translation symmetry and thus very rare as symmetry elements of building blocks in tilings and pavings. Heptagonal symmetry elements as local symmetry elements in isolated objects in art, architecture and nature appear surprisingly much less frequently than pentagonally shaped designs. This presentation aims to give some objective, but also subjective reasons why architects, designers and artists rarely choose for local heptagonal symmetry in their creations. It is argued that reasons that are commonly put forward as explanation for the choice for heptagonal symmetry are too simplistic and probably not true. A number of examples is presented where the designer has chosen for heptagonal symmetry as a key element for creation and reasons for these choices are proposed where possible. Special emphasis will be given to two outstanding heptagonal religious edifices in French Occitany and larger heptagonal urban geometries in the low countries.

Beauty of our world we can see everywhere, but always two points of view are among scientists and artists, who is better: nature or human in the process of creativity. In our work we present three-shell clusters in intermetallic compounds and compare it with ivory puzzle balls. The crystal structures of all these intermetallic compounds were studied by single crystal method and confirmed by X-ray powder diffraction. Li₂₀Mg₆Cu₁₃Al₄₂ [1] (sp. gr. Im-3, a = 13.8451(2) Å) crystallizes as an ordered version of Mg₃₂(Al,Zn)₄₉, Mg₉Ni₆Ga₁₄ (sp. gr. Fd-3m, a = 19.8621(1) Å) and Mg₃Ni₂Ga (sp. gr. Fd-3m, a = 11.4886(17) Å) crystalizes in the own structure types. All these structures can be described as three-shell clusters: [CuAl₁₂@Li₂₀Cu₁₂@Al₆₀] (fig. 1a) for the Li₂₀Mg₆Cu₁₃Al₄₂, [Ni₆Ga₆@Mg₂₀@Ni₁₈Ga₄₂] (fig. 1b) for the Mg₉Ni₆Ga₁₄ and[Mg₆@Ni₁₂Ga₆@Mg₃₆] (fig. 1c) for the Mg₃Ni₂Ga. Very easy to see, that the kind of packing of core shells for all these clusters is very similar to well-known human masterpiece ivory puzzle balls which are very popular in China (fig. 1d), but also known in Europe as “contrefait Kugeln” (fig 1e), which are created on the base of Johannes Kepler’s Platonic Solids model of the Solar system from Mysterium Cosmographicum (fig 1f) [2]. The last one consists as second and third spheres octahedron and icosahedron like in first and second spheres of [Mg₆@Ni₁₂Ga₆@Mg₃₆] cluster and as forth spheres dodecahedron with pentagons and hexagons which also form third sphere of [CuAl₁₂@Li₂₀Cu₁₂@Al₆₀] and [Ni₆Ga₆@Mg₂₀@Ni₁₈Ga₄₂] clusters.

Figure 1. Atomic structure of a three-shell clusters [CuAl₁₂@Li₂₀Cu₁₂@Al₆₀] (a), [Ni₆Ga₆@Mg₂₀@Ni₁₈Ga₄₂] (b), [Mg₆@Ni₁₂Ga₆@Mg₃₆] (c), Chinese ivory puzzle ball (d), Ivory puzzle ball from German workshop (e), Johannes Kepler’s Platonic Solids model of the Solar system (f).

The results of electronic structure calculations for Li₂₀Mg₆Cu₁₃Al₄₂, Mg₉Ni₆Ga₁₄ and Mg₃Ni₂Ga confirm the three-shell clusters.

[1] Pavlyuk, N., Dmytriv, G., Pavlyuk, V., Ehrenberg, H. (2019). Acta Crystallogr. B75, 168.

[2] Sparavigna, A. C. (2018). hal-01825008.

Keywords: three-shell cluster; single crystal; intermetallic compound; lithium; magnesium

Funding for this research was partially provided by National Science Centre, Poland (No. 2017/25/B/ST8/02179).

Possibly for recreational purposes, the very well established crystallographer Emil Makovicky has for the last 30 to 40 years turned his formidable analytical skills to the classification of the symmetries that underlie patterns of Islamic building ornaments and Hans Hinterreiter’s graphical art. These patterns can be characterized as being more or less periodic in two dimensions (2D), see e.g. [1-5]. He stated in [2] that “in performing the symmetrological analysis, we should stay on the same level of accuracy on which the creator of the pattern worked”. He had to concede, however, more than 30 years ago that this “certainly brings a certain subjectivity into the process: we should not shun away from it because such a degree of abstraction from imperfections of certain degrees and kinds underlies the entire practice of natural sciences wherefrom the science of symmetry originated” [2]. Utilizing recently developed information theory based approaches to crystallographic symmetry classifications in 2D [6,7], one can now replace that subjectivity with the objectivity that comes from calculations that involve all pixel intensity values of digital images of such patterns.

These information theory based approaches to crystallographic symmetry classifications utilize geometric Akaike Information Criteria (G-AICs), which are in essence first-order geometric bias corrected sums of squared residuals between the raw image data and symmetrized versions of this data. G-AIC value ratios are used for the selection of symmetry models to represent the raw data, whereby the need to estimate the level of the “generalized noise“ is removed by algebraic means whenever non-disjoint models are involved. Performing the symmetry model selection in reciprocal/Fourier space and basing it exclusively on the structure-bearing complex-valued Fourier coefficients of the image intensity has the advantage of suppressing much of the generalized noise just by calculating the discrete Fourier transform, which is the first step of translation averaging. Symmetrizing the Fourier coefficients and transforming them back into direct space is equivalent to averaging over the asymmetric units.

A simple definition of generalized noise is that it sums up all variations of the intensities of all individual image pixels that are left unexplained by a correct plane symmetry classification. This type of noise is the sum total of all effects of the recording and processing of the digital image and also includes all disturbing effects of “structural defects” in the underlying patterns. For the methods to work (at their current state of development), this kind of noise needs to be considered as approximately Gaussian distributed. Given that there are many sources of that kind of noise with different distributions and that the contribution of none of these sources dominates, this assumption is justified by the central limit theorem.

The new methods allow for objective, i.e. researcher independent, classifications of the full range of crystallographic symmetries, i.e. Bravais lattice type, Laue class, and plane symmetry group, of “noisy” real-world patterns. The identification of the plane symmetry group that can with the highest likelihood, i.e. minimized Kullback-Leibler information loss [6,7], be assigned to a noisy digital 2D periodic image of that pattern by an information theory based method enables the most meaningful crystallographic averaging in the spatial frequency domain.

Considering that it is fundamentally unsound to assign an abstract mathematical concept such as a single symmetry type, class, or group with 100 % certainty to a piece of art or the work of artisans, the information theory based approaches to crystallographic symmetry classifications deliver probabilistic (rather than definitive) classifications. This means that numerically derived confidence levels of the classifications within individual symmetry hierarchy branches are provided with each classification result so that the researcher is presented with objectively derived information, which may be used at the researcher’s discretion.

The paper demonstrates the objective classification of a few Islamic building ornaments and examples of Hans Hinterreiter’s graphical art. It is hoped that this will be helpful to the recreation of busy conference participants at the 25^th World Congress and General Assembly of the International Union of Crystallography. Using some of Emil Makovicky’s words from the second direct quote above, information theory based crystallographic symmetry classifications are poised not only to help resolve controversies in the symmetrology of art and cultural artifacts field [8], but also in the “natural sciences wherefrom the science of symmetry originated” [2].

[1] E. Makovicky, The crystallographic art of Hans Hinterreiter, Zeits. für Kristallogr. 150 (1979) 13–21.

[2] E. Makovicky, Symmetrology of art: coloured and generalized symmetries, Computers Math. Applic. 12B (1986) 949–980.

[3] E. Makovicky, Ornamental Brickwork, Theoretical and applied symmetrology and classification of patterns, Computers Math. Applic. 17 (1989) 955–999.

[4] E. Makovicky, Symmetry through the eyes of the old masters, Berlin: De Gruyter, 2016.

[5] E. Makovicky and M. Ghari, Neither simple nor perfect: from defect symmetries to conscious pattern variations in Islamic ornamental art, Symmetry: Culture and Science 29 (2018) 279–301.

[6] P. Moeck, Towards generalized noise-level dependent crystallographic symmetry classifications of more or less periodic crystal patterns, Symmetry 10, paper 133 (46 pages) (2018), DOI: 10.3390/sym10050133, open access.

[7] P. Moeck, On classification approaches for crystallographic symmetries of noisy 2D periodic patterns, IEEE Transactions on Nanotechnology 18 (2019) 1166–1173, DOI: 10.1109/TNANO.2019.2946597, see also http://arxiv.org/abs/1902.04155, August 31, 2019 for an expanded version of this review.

[8] E. Makovicky, Comments on decagonal and quasi-crystalline tilings in medieval Islamic architecture, Science 318, Art. no. 1383a, (2 pages) 2007, DOI: 10.1126/science.1146262.

Fully non-invasive multi-analytical approach combining spectroscopic (FT-IR, Raman) and X-ray-based (MA-XRF, XRPD) techniques was used to study a number of miniature portraits from Czech collections.

The portrait miniatures of the late sixteenth to the nineteenth century represent a highly specific and significant field of European fine art. After 1700, ivory plates were introduced and became the most frequent support of the eighteenth and the nineteenth centuries. Watercolour and gouache were the most common techniques; however, the use of oil has also been recorded.

It is the ivory-painted miniatures that are a special challenge for XRPD - not only because the painting layers are very thin and the ivory signal can interfere the signal from the phases in the painting layer, but also because ivory is a hygroscopic material whose dimensions and curvature respond to changes in environmental conditions (temperature, relative humidity) even during the measurements. We have therefore created a special methodological procedure for measuring miniatures painted on ivory, which we plan to present together with the most interesting results. XRPD helped to identify rare pigments, degradation products and even the binder used thanks to the evidence of metal soaps’ formation in paint layers.

Figure 1 X-ray pattern measured in yellow-green curtains in the background. The XRPD identified lead white (H), mixed Pb-Sb-Sn yellow (Y), earth pigments represented by mica (M) and kaolinite (K) and lead soaps (S) formed by interaction of fatty binder (oil) with Pb-based pigments.

Keywords: X-ray diffraction, X-ray microdiffraction, non-invasive analysis, miniature painting, metal soaps

The study was supported by the Ministry of Culture of the Czech Republic, NAKI II programme, project No. DG18P02OVV034.

Crystallography research in Latin America started with the pioneering work of Prof. Ernesto Galloni in Buenos Aires, Argentina, during the 1940s. The progress in several countries was very fast and, during the 1950s and 1960s, courses on crystallography were given regularly in Argentina, Brazil, Chile and Mexico. The first international crystallography course in Latin America was probably the “Latin American course on Pure and Applied Crystallography” held in Santiago, Chile, in 1959, which was the birth of the Ibero American Crystallographic Group. This group organized several meetings and courses during 35 years. Unfortunately, due to economic problems and the long distances among the countries involved, this group was finally dissolved. The Latin American Crystallographic Association (LACA) was founded in October 2013 in Córdoba, Argentina, and recognized as a Regional Association of the IUCr during the 22nd IUCr Congress and General Assembly (Montreal, Canada, August 2014). At present, this association has seven full members (Argentina, Brazil, Mexico, Chile, Costa Rica, Uruguay and Venezuela) and organizes several meetings, schools and OpenLabs. The International Year of Crystallography 2014 (IYCr2014) was an excellent opportunity to increase the work related to education and outreach throughout Latin America and several activities were carried out, including exhibitions, science fairs, art or photo contests, outreach talks, etc. In addition, very successful national crystal growing contests were organized in Argentina, Chile and Uruguay, which also involved short courses on crystallography and crystal growth for primary and secondary school teachers. Most of these activities were organized during several years with great success.

Nowadays, there are an important number of regular local, national or international courses in Latin America, covering all kind of topics: single crystal X-ray diffraction, powder diffraction, fundamental crystallography, protein crystallography, crystallization methods, synchrotron radiation techniques, neutronic techniques, small-angle X-ray scattering, X-ray absorption spectroscopies, etc. Many of them are organized by national crystallographic associations, while LACA has a regular regional Crystallography school. In most of the cases, the topics taught in these courses involve applications in a wide variety of areas, resulting in interdisciplinary activities that are enriching for all the participants.

The COVID-19 pandemic was a global challenge and many congresses, schools, courses and outreach activities in Latin America had to be postponed or cancelled. However, as 2020 progressed, some of these difficulties were overcome. For example, the 3rd LACA school on Small Molecule Crystallography, planned to be held in Mexico in March 2020, was postponed, but it was finally held in a virtual modality in November/December 2020 with great success. Many virtual courses were also organized and some of them, thanks to the online modality, reached new regions or countries. Such was the case of the short courses on crystallography and crystal growth organized by the Argentinian Association of Crystallography (AACr), that in 2020 had to be taught in a new virtual format. These courses received a large number of new participants not only from Argentinian cities not previously visited by AACr members, but also from all over Latin America.

Finally, it is worth to mention that the crystal growing contests organized in Argentina and Uruguay continued in 2020, this time proposing that students work from home with simple and inexpensive materials, without any danger. In the case of the contest organized by the AACr, 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. Once again, both contests were highly successful and are planned to be continued in 2021.

African countries, especially Sub-Saharan Africa, suffers from a severe deficit of engineers and scientists and relies heavily on imported expertise for several reasons including poor quality of education, limited research facilities, and lack of practical experience among graduates. According to the UNESCO’s second engineering report, Africa continues to have the lowest number of engineering professionals per capita of all regions of the world [1]. Hence, developing inclusive high-tech education and research facilities is an efficient way to bridge this gap. That is the purpose of the X-TechLab.

X-TechLab is a regional training platform that aims to provide the region with skills and tools to use X-ray techniques for developing innovative solutions to critical issues in Africa. The initiative is the result of an interaction between the Lightsources for Africa, the Americas, Asia, Middle East, and the Pacific (LAAAMP) and the Sèmè City hub, one of Benin Government’s flagship projects, which aims to create a world-class knowledge and innovation centre in Africa. The goals are to: 1) provide hands-on experience with the use of cutting-edge X-ray equipment, 2) develop X-ray-based problem-solving skills targeting specific socioeconomic issues, 3) meet the requirement for Feeder Facilities that allow the preparation of samples to be studied at world advanced light sources and 4) contribute to the emergence of a community of experts who will be active users of the future African Synchrotron.

Learners participating in the X-TechLab are trained around 2 parallel, interrelated yet distinct, tracks: Crystallography and X-ray diffraction techniques, including both single and powder diffraction applied to structural studies; and Absorption and phase contrast X-ray imaging (Microtomography) using mathematical tools for research on sustainable and ecological materials. Started in 2019, X-TechLab training sessions gathered many scientists from several countries and scientific disciplines. As shown in the figure below, 84 participants with 1/3 of women from 12 African countries (Benin, Burkina Faso, Burundi, Cameroon, Congo-Brazzaville, Côte d’Ivoire, Democratic Republic of Congo, Ethiopia, Ghana, Nigeria, Senegal, Togo) have been trained [2]. About 20 Experts from several academic institutions worldwide (Africa, Europe, USA) are involved in the training sessions. This will emphasize the unique potential of X-ray techniques as a multidisciplinary tool for development in Africa.

Modern crystallography, as an umbrella of techniques and methods, reaches out to almost everyone interested in the basic question: how are atoms or molecules arranged in a material. This inherent interdisciplinarity of crystallography is further supported by availability of various schools for aspiring crystallographers. On one hand, a well-curated content, good choice of lecturers, and offered sponsorships, make it possible to reach out to students from various backgrounds, interests, regions and economic status. On the other, on-site presence and a good social program ensure interactions between lecturers, students and organizers. Having all this in mind, the success of these schools is not a coincidence. Their interdisciplinarity seems to rely on three factors: content, outreach and interactivity.

In the last year, COVID19 has forced many of crystallographic schools and initiatives to undergo a digital transformation. Emergence of virtual schools has removed many restraints imposed by physical presence in real space: costs, time and geographical limitations, and recruitment of lecturers and speakers. However, it also opened up new questions. What are the needs of a modern researcher/crystallographer? Can crystallography get more interdisciplinary by adopting new fields, such as didactics, communications and economics? Can modern technology be used to enforce interdisciplinarity by improving interactivity, outreach and content?

This presentation looks back to the past and then turns to the future in order to examine possible ways that could be taken to optimize content, outreach and interactivity in both real and virtual schools. Examples are focused on building and maintaining crystallographic communities and include use of social media, industry-academia collaborations, and online interaction tools.

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From December 2010 till December 2020, I have been involved in over a dozen schools and short courses in different countries of Latin America where I -alone or as part of a group of Lecturers- have been teaching crystallographic symmetry and the International Tables for Crystallography Volume A: Space Group Symmetry (ITC-A). I was not new to teaching symmetry in 2010 since I have taught an undergraduate course of Crystallography for Chemists at my institution since 1995. However, the first of these international schools, and the one I have been involved in more times (the International School on Fundamental Crystallography with MaThCryst Commission [1]), has pushed me to teach symmetry in many other schools devoted to single crystals and/or powder X-rays and/or neutron diffraction, that have recently evolved to virtual schools (such as the 3^rd LACA School on Small Molecule Crystallography [2]). This lecturing has allowed me to meet all sorts of students/researchers of very different backgrounds from most of the countries of the region, as well as interacting with many colleagues working in different areas of crystallography, solid-state physics/chemistry, and materials science. With the aim of improving the learnings of students over the years, I have tried to make systematic observations of the background, difficulties, and outcomes of participants in the different kinds of schools. It is significantly different to evaluate the outcome of learning symmetry in very different course formats having a total time of symmetry lectures of 40, 15, or 4 hours. Moreover, it could be argued that nobody could learn any significant concept about crystallographic symmetry in 4 hours. However, the need of students and users/practitioners of crystallography coming from different disciplines, of having at least the minimal rudimentary tools to deal with symmetry in everyday work makes it worth it. Figure 1 shows two extracts of the many evaluation forms I have collected in the last decade. In this presentation, I will show the main conclusions of the evaluations regarding the fundamental part of the courses, and more specifically symmetry and the ITC-A, and share some of the strategies I have developed to give students with common or varied background the best tools I consider could make a difference for their understanding of symmetry, even in the very unfavourable conditions of teaching 2 hours of theoretical and 2 hours practical sessions. Luckily this will help other colleagues improve their teaching work, as well as giving me feedback for my next 10 years of teaching symmetry.

[1] https://www.crystallography.fr/mathcryst/meetings.php (scroll down to Schools in Latin America).

[2] https://www.iquimica.unam.mx/LACA/

I would like to acknowledge M.I. Aroyo and M. Nespolo from MaThCryst Commission and J. Ellena and H. Napolitano from LACA for pushing me to organize schools and Open-labs in Montevideo, Uruguay that have eventually made me specialize in teaching crystallographic symmetry in local and international schools in the Latin American region. I would also like to thank all the colleagues that have shared the heavy but rewarding task of organizing and Lecturing in the Schools I have been involved in over the years. I would finally want to dedicate this abstract to the memory of Prof. Dr. Graciela Punte from LANADI, Universidad Nacional de La Plata, Argentina for being an inspiring crystallographer and teacher and selflessly contributing to the current development of the Latin American and particularly the Uruguayan community of Crystallographers.

Resources to develop high impact skills in diffraction data collection and interpretation can be limited by facility access, expert availability, and the budgetary requirement to meet a critical mass of participants before it becomes practical to offer instruction. At the local level, shared resources between institutions, as well as curriculum approaches that incorporate scaffolding practices from first year general chemistry to senior undergraduate capstone courses, can be employed to equip trainees with skills in structural science.¹ Looking to the regional and (inter)national level, the Canadian National Committee for Crystallography (CNCC)¹ sponsors the annual Canadian Chemical Crystallography Workshop (CCCW) and the Canadian Powder Diffraction Workshop (CPDW), both which have now past their first decades of instruction. Several hundred trainees from Canada, and well beyond (for example, the US, UK, and Brazil) have participated in these opportunities.

As a university instructor, the organizer for CCCW2019 – 2021, and an administrative supporter of CPDW, this presentation will highlight (1) the diversity of experiences that attendees have, (2) logistical aspects of organizing and teaching in these various ventures, with a look at the transition to remote delivery for CCCW2020 and 2021, amid the current pandemic, and (3) I will share some insights and results from past trainees whose research practices have been transformed as a result of these learning opportunities.

1. Gražulis, S.; Sarjeant, A. A.; Moeck, P.; Stone-Sundberg, J.; Snyder, T. J.; Kaminsky, W.; Oliver, A. G.; Stern, C. L.; Dawe, L. N.; Rychkov, D. A.; Losev, E. A.; Boldyreva, E. V.; Tanski, J. M.; Bernstein, J.; Rabeh, W. M.; Kantardjieff, K. A. Crystallographic Education in the 21st Century. J. Appl. Crystallogr. 2015, 48, 1964–1975. https://doi.org/10.1107/S1600576715016830.

2. Canadian National Committee for Crystallography: https://xtallography.ca/

We are privileged in crystallography that every published crystal structure is shared through established databases and that scientists worldwide can gain new insights from these collections. The Cambridge Crystallographic Data Centre (CCDC) was set up to curate and distribute one of these databases, the Cambridge Structural Database (CSD), a resource containing over one million experimental crystal structures.

As a non-profit organisation sharing data from crystallographers worldwide the CCDC has always had a keen interest in developing material to help others to use structural data to teach both chemical concepts and crystallography. More recently we have realised that we also need to use our position in the scientific community to engage students and researchers to help promote interdisciplinarity in research.

This presentation will highlight some of our efforts to cultivate more interdisciplinarity in science from the establishment of new guidelines, partnerships, links and community initiatives. We will explore recent activities to engage scientists across research areas and ages through our involvement in a variety of schools, workshops and science festivals globally. We will also share our experiences in creating more virtual resources including a new series of CCDC virtual workshops and on-demand training courses through CSD University.

Finally, we will reflect on some of the challenges we have faced, what we have learnt from our experiences and look at what more could be done to increase interdisciplinarity in science.