Electron diffraction is gradually becoming a broadly accepted alternative structure determination method to the established approaches like single crystal x-ray diffraction. Although electron diffraction was used for structure determination long time ago, the real breakthrough was obtained only thanks to the rapid development of the three-dimensional electron diffraction methods (3D ED). Several 3D ED experimental techniques exist, but they all share the basic principle of collecting three-dimensional diffraction information from a single very small crystal by tilting the crystal, continuously or in steps, and recording the diffraction patterns as the crystal is tilted [1].

In the early days of 3D ED, mostly inorganic materials were analysed, as these materials are less beam sensitive and therefore easier to measure. Nevertheless, soon first successful attempts to analyse organic materials appeared (reference). Gradually, over the past ten years, structure analysis of organic materials by 3D ED has become almost a routine technique.

Structure analysis of molecular materials by 3D ED has certain specifics. First, molecular crystals are, typically, much more beam sensitive than crystals of inorganic materials, although this rule is by far not strictly applicable. The beam sensitivity of organic materials calls for specific experimental techniques. These include: measurements at low-temperature conditions (usually cooling to liquid nitrogen temperatures) to limit the beam damage; use of modern direct electron detectors with low background and high sensitivity to maximize the signal-to-noise ratio; combination of partial data sets from several crystals; or application of serial diffraction techniques. The latter can include either scanning a large single crystal with a small probe, measuring each diffraction pattern on a fresh part of the crystal [2,3], or collecting single diffraction patterns from a large number of crystals and combining them in a manner similar to serial femtosecond crystallography [4].

Once suitable data are collected, the challenge continues in the structure analysis part. It is usually not complicated to solve the structure by ab initio structure solution methods. However, it is challenging to obtain a good quality refinement. The multiple scattering effects that are always present in electron diffraction break the kinematical nature of the diffraction. If the kinematical approximation is used in the refinement, the figures of merit of the refinement tend to be high and weak signals in the structure may be obscured. This makes, for example, the detection of hydrogen atoms difficult, although not impossible [5,6]. The fit to experimental data can be improved by employing the dynamical diffraction theory in the calculation of the model intensities [3, 6, 7]. Such calculation results in an improved fit to experimental data and, as a consequence, to higher accuracy of the refined parameters and better sensitivity to weak features. A very important advantage of using the dynamical diffraction theory in the refinement is the possibility to determine the absolute structure of the crystals [3].

Despite of al the challenges, 3D ED was already proved to be an extremely successful technique for structure determination of molecular crystals. The fact that it can routinely analyse crystals with sub-micrometre size makes it an attractive alternative to single crystal x-ray diffraction.

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

[2] Kolb, u., Mugnaioli, E., Gorelik, T. (2011). Cryst. Res. Technol. 46, 542.

[3] Brázda, P., Palatinus, L., Babor, M. (2019). Science 364, 667

[4] Smeets, S., Zou, X., Wan, W. (2018). J Appl Cryst. 51, 1262.

[5] Jones, C. G., Martynowycz, M. W., Hattne,, J. Fulton,T. J., Stoltz, B. M., Rodriguez, J. A., Nelson, H. M., Gonen, T. (2018). ACS Cent Sci. 4, 1587.

[6] Palatinus, L., Brázda, P, Boullay, P., Perez, O., Klementová, M., Petit, S., Eigner, V., Zaarour, M, Mintova, S. (2017). Science 355, 166.

[7] Palatinus, L., Petricek, V., Correa, C. A. (2015). Acta Cryst. A 71, 235.

This work was funded by the Czech Science Foundation, project number 21-05926X.

Rechargeable batteries enable switching to “green” energy production and consumption making a decisive impact in electromobility and integration of renewable energy sources into electric grids. Steadily rising demands in increasing specific energy, durability and lowering cost of electrochemical energy storage devices inspired extensive search for improved positive electrode (cathode) materials for advanced metal-ion batteries. Rational design of the cathode materials requires understanding of the intricate relationships between their crystal and electronic structures, as well as their evolution in course of reversible (de)intercalation of the alkali cations and through extended number of charge and discharge cycles. As the intercalation-type electrodes rely on long-range cationic diffusion reckoning on availability of the cation migration pathways with low energy barriers, the presence, spatial distribution, concentration and atomic structure of point and/or extended defects, which can block the ionic transport, have huge impact on capacity and rate capability of the metal-ion batteries. Polyanion cathode materials demonstrate extremely complex chemistry and crystallography of defects leading to exchange of the alkali and transition metal cations as a result of the synthesis or formed upon electrochemical cycling. Antisite cationic defects, heterovalent anionic defects and order-disorder in the alkali metal sublattice will be considered in relation with the electrochemical capacity, cycling stability and a competition between the solid-solution and two-phase (de)intercalation mechanisms in A₂MPO₄F (A – alkali cation, M – transition metal) and LiFePO₄ polyanion cathodes. Cationic disorder in the layered A_1+xM_1-xO₂ oxide cathodes is believed to play pivotal role in voltage fade and voltage hysteresis. The degree of this disorder will be characterized at different spatial scales using a combination of diffraction techniques and aberration-corrected transmission electron microscopy, both in the pristine materials and in the materials at different states of charge. Finally, the relationships between planar defects, such as twin boundaries and stacking faults, and electrochemical properties of the hierarchically-structured layered oxide cathodes will be demonstrated. The work is supported by RSF (20-13-00233).

This paper discusses, along with historical background, the principle and the proof-of-concept studies of crystalline sponge (CS) method, a new single-crystal X-ray diffraction (SCD) analysis that can analyze the structures of small molecules without sample crystallization. The method uses single crystalline porous coordination networks, called crystalline sponges, that can absorb small guest molecules into the pores. The absorbed guest molecules are ordered via molecular recognition in the pores and become observable by conventional SCD diffraction analysis. [[(ZnI2)3(tpt)2]•x(solvent)]n complex (tpt = tris(4-pyridyl)-1,3,5-triazine) was first proposed as a crystalline sponge and has been most generally used. The principle of the CS method can be described as “post-crystallization” of the absorbed guest, whose ordering is templated by the pre-latticed cavities. The method has been widely applied to synthetic chemistry as well as natural product studies, for which proof-of-concept examples will be shown here.

We have developed a novel approach called CrystalDirect that enables fully automated crystal mounting and cryo-coolingclosing the automation gap between crystallization and X-ray data collection. The CrystalDirect technology also allows the automated delivery of small molecules to crystals, giving access to large scale small molecule screening through X-ray crystallography. We have combined this approach with automated data collection at the ESRF and other synchrotrons to develop a fully automated, remote-controlled pipelines for macromolecular crystallography and an automated pipeline for large scale compound and fragment screening to support structure guided drug discovery programs. In order to facilitate high throughput data analysis, we have built a series of Application Program Interfaces (APIs) linking the Crystallization Information Management System (CRIMS) and the ISPyB system for automated synchrotron data collection with automated structure refinement and analysis, using software pipelines developed by Global Phasing. These pipelines effectively provide online access to crystallization and synchrotron diffraction and data analysis facilities and remove key bottlenecks in modern crystallography. They can contribute to the rapid progression of challenging projects in structural biology, to facilitate the access to protein crystallography for scientist of other disciplines and stimulate translation of basic research into biomedical applications. On the other hand, the large amounts of data generated pose new challenges, but also provide new opportunities to develop integrated systems for data acquisition, processing and analysis. The experience from the use of these pipelines as well as the new opportunities enabled by the integration of crystallization, X-ray data collection and analysis into continuous, fully automated workflows will be discussed.

Crystallographic fragment screening, which involves screening small-molecule libraries against crystals of a target protein, is an essential tool in modern drug discovery. The technique relies on the high-throughput generation of cryo-cooled, soaked crystals followed by fast and efficient data collection at a synchrotron beamline. Each campaign may generate hundreds or thousands of samples, and the most efficient strategy for acquiring data is to use unattended data collection followed by automatic data processing.

The macromolecular crystallography (MX) group at the Swiss Light Source operates a fast fragment and compound screening (FFCS) pipeline that uses Smart Digital User (SDU) software to collect data at the beamlines. This presentation will give an overview of SDU, describe how it has been implemented at the MX beamlines and present some recent case studies.

Structural Biology Research Center in the Photon Factory (PF), Japan, has five macromolecular crystallography (MX) beamlines at two synchrotron radiation rings, PF and PF-AR. The end stations of all the beamlines are equipped with sample exchange robots [1], high-precision diffractometers, and pixel array detectors, which are controlled by a common control software. This enables us to realize a fully automated and unattended data collection and a remote interactive data collection at all beamlines.

For a fully automated data collection, we developed a dedicated software SIROCC (Sophisticated Interface for Routine Operation with Crystal Centering). After mounting a new sample on the goniometer by the sample exchange robot, SIROCC recognizes a sample loop, and perform two raster scans over the loop regions. From a heatmap based on the number of diffraction spots below 4 Å resolution, SIROCC recognizes a shape and location of a protein crystal and places it to the X-ray beam position. By taking two snapshots, SIROCC evaluates the diffraction quality of the crystal, and if it exceeds a user’s defined threshold, SIROCC collects a complete diffraction data set. In a fully automated data collection beamtime, a beamline staff loads samples from users, and starts the automated data collection. Then all samples are mounted and diffraction measurements by SIROCC are performed in a fully automated manner. For a remote interactive data collection, NoMachine Workstation is installed on a workstation running the control software at each beamline. Furthermore, NoMachine Cloud Server, which federates the workstations at all beamlines, is installed on a gateway server which is accessible from outside the facility. At the beginning of a remote access beamtime, a beamline operating staff prepares the beamline, and give a permission for a user to access to the beamline through the gateway server. Then, the user connects through a NoMachine remote desktop software, allowing users to perform measurements remotely from outside the facility. All experimental information from the fully automated or remote data collection are recorded in the database system, PReMo [2]. PReMo also functions as a data processing and analysis pipeline, and users can obtain the experimental information and the result of data processing and analysis on the Web. Recently, a dedicated server for data download is opened, and users can download a diffraction data or data processing result to perform a further analysis with their own workstation immediately after the data collection.

In remote access or fully automated data collection, the user packs frozen samples in Uni-pucks and ships them to the PF using a dry sipper. The beamline staff receives the dry sipper and transfers to the beamline which the sample is assigned. The Uni-pucks are then taken out from the dry sipper and placed in the liquid nitrogen Dewar of the sample exchange robot. To prevent miss-match of the sample mount on the diffractometer in a fully automated measurement or/and remote experiment, the transportation of the dry-shipper and placing the Uni-puck must be performed without errors. Therefore, it is very important to establish a sample tracking system for the reliable operation of fully automated measurements and remote experiments. Recently, we developed a sample tracking system for those experiments. In this system, the user must attach QR code labels to items such as a dry shipper, hard disk drive and so on to be sent, and place a pin with a two-dimensional barcode into No. 16 of the Uni-puck. When the beamline staff takes any action on the shipped items, the QR code is always read, and the status of the item is updated. The status is stored in a database system and shared among beamline staff members, which helps to prevent miscommunication. The two-dimensional barcode on the pin on No. 16 is read by the sample exchange robot after the Uni-pucks are placed in the Dewar, and the robot recognizes automatically which Uni-puck is set in which position in the Dewar.

In 2020, due to the pandemic situation of COVID-19, approximately 75% of the beamtime in MX beamlines were used for remote experiments or/and fully automated measurements with users unattended.

[1] Hiraki, M., Yamada, Y., Chavas, L.M., Matsugaki, N., Igarashi, N. & Wakatsuki, S. (2013). J. Phys.: Conf. Ser. 425, 012014.[2] Yamada, Y., Matsugaki, N., Chavas, L.M., Hiraki, M., Igarashi, N. & Wakatsuki, S. (2013). J. Phys.: Conf. Ser. 425, 012017.

Keywords: Synchrotron, automation, remote access

This research was supported by Platform Project for Supporting Drug Discovery and Life Science Research (Basis for Supporting Innovative Drug Discovery and Life Science Research (BINDS)) from AMED.

Watching biomolecules in motion on biologically relevant time scales has been a long-standing goal of structural biology. Current methodologies allowing for time-resolved crystallographic data collection are mostly through serial methods using microcrystals - which are technically challenging experiments with elaborate synchrotron beamline setups, consumption of large amounts of sample, and requiring contributions from many researchers. Here, we propose an alternative methodological setup in order to collect time-resolved data in the millisecond time regime (>5ms), suitable for measuring relatively large structural changes that may be rate-limiting in particular cases. Our approach has been to leverage rapid freeze-quenching by robotically plunging our crystals of choice through a substrate film prior to hyperquenching in liquid nitrogen. This method affords many quality of life improvements over current time-resolved methods, such as the potential for a single crystal use per time-point, divorcing the reaction initiation from data collection, and the ability to use the standard mail-in remote data collection available at all synchrotron sources. In order to show proof-of-concept, we used a well characterized metabolic enzyme phosphoenolpyruvate carboxykinase which converts oxaloacetic acid to phosphoenolpyruvate. Our initial experiments uncovered a previously hypothesized state believed to occur directly after phosphoryl transfer and prior to product release. We hope that this method, with its simplicity and ease of access, can allow many structural biology labs to begin time-resolved exploration of suitable systems to uncover further molecular details of enzymes of interest.

MXAimbot is a neural network based tool, designed to automate the task of centering samples for macro-molecular X-ray crystallography experiments before exposing the sample to the beam.

MXAimbot uses a convolutional neural network (CNN) trained on a few thousands images from an industrial vision camera pointed at the sample to predict suitable crystal centering for subsequent data collection.

The motivation for this project is that the machine vision automated sample positioning allows X-ray laboratories and synchrotron beamlines to offer a more efficient alternative for the manual centering, which is time consuming and difficult to automate with conventional image analysis, and for the X-ray mesh scan centering, which can introduce radiation damage to the crystal. MXAimbot can be used to improve results of standard LUCID loop centering for fully automated data collection in fragment-screening campaigns. No need for sample rotation should be an additional advantage.

A few original approaches and CNN architectures were tested by authors in [1,2]. They were using X-ray data from mesh scans and not relying on manual annotations. Finally for a current production a more simple method inspired by a DeepCentering approach [3] from SPring-8, has been adopted. The original training dataset was manually annotated with bounding-boxes around each crystal and the new CNN architecture is using the annotated data. MXAimbot can be used by other systems via a REST API. The next step for the project was including MXAimbot into MXCuBE3 - the common data acquisition framework at several European synchrotron facilities. This allows collection of anonymised datasets from the sample vision camera in the BioMAX beamline at the MAX IV synchrotron which can be further used for training and optimisation of CNNs and later be seamlessly included as an additional option in the MXCuBE3 data collection pipeline.

To the authors knowledge CNNs have been implemented for crystal centering at least at two synchrotron facilities including MAX IV. So far the CNN approach has shown outstanding results in automatically positioning crystals. Work is currently underway to test and statistically compare the model predictions to the manual centerings by real users with the goal of integrating MXAimbot into the FragMAX [4] - fragment screening facility at the MAX IV sychrotron.

[1] SCHURMANN, Jonathan; LINDHÉ, Isak. Crystal Centering Using Deep Learning. LU-CS-EX 2019-25, 2019.

[2] SCHURMANN, Jonathan; LINDHÉ, Isak et al. Crystal centering using deep learning in X-ray crystallography. Asilomar Conference on Signals, Systems, and Computers, 2019, 978-983. doi: 10.1109/IEEECONF44664.2019.9048793

[3] ITO, Sho; UENO, Go; YAMAMOTO, Masaki. DeepCentering: fully automated crystal centering using deep learning for macromolecular crystallography. Journal of synchrotron radiation, 2019, 26.4: 1361-1366. doi: 10.1107/S160057751900434X

[4] LIMA, Gustavo MA, et al. FragMAX: the fragment-screening platform at the MAX IV Laboratory. Acta Crystallographica Section D: Structural Biology, 2020, 76.8: 771-777. doi: 10.1107/S205979832000889X

In macromolecular crystallography, radiation damage limits the amount of data that can be collected from a single crystal. It is often necessary to merge multiple data sets from one or more crystals, for example multiple small-wedge data collections on micro-crystals, in situ room temperature data collections, lipidic mesophase data collections or time-resolved crystallography. Whilst indexing and integration of individual data sets may be relatively straightforward with existing software, additional challenges are commonly encountered when merging multiple data sets. For novel structures, identification of a consensus symmetry can be problematic, particularly in the presence of a potential indexing ambiguity. The presence of non-isomorphous or poor-quality data sets may degrade the overall quality of the merged data set.

To facilitate and help optimise the scaling and merging of multiple data sets, we developed a new program, xia2.multiplex, which takes as input the results of data sets individually integrated with DIALS [1] and performs symmetry analysis [2], scaling [3] and merging of multi-crystal data sets, as well as analysis of various pathologies that typically affect multi-crystal data sets, including non-isomorphism, radiation damage [4] and preferred crystal orientation.

xia2.multiplex has been deployed as part of the autoprocessing pipeline at Diamond Light Source, including integration with downstream phasing pipelines such as DIMPLE [5] and Big EP [6].

Using data sets collected as part of in situ room-temperature fragment screening experiments on the SARS-CoV-2 main protease, we demonstrate the use of xia2.multiplex within a wider autoprocessing framework to give rapid feedback during a multi-crystal experiment, and how the program can be used to further improve the quality of final merged data set.

[1] Winter, G., Waterman, D. G., Parkhurst, J. M., Brewster, A. S., Gildea, R. J., Gerstel, M., Fuentes-Montero, L., Vollmar, M., Michels-Clark, T., Young, I. D., Sauter, N. K. & Evans, G. (2018). Acta Crystallographica Section D.

[2] Gildea, R. J. & Winter, G. (2018). Acta Crystallographica Section D, 74(5), 405–410.

[3] Beilsten-Edmands, J., Winter, G., Gildea, R., Parkhurst, J., Waterman, D. & Evans, G. (2020). Acta Crystallographica Section D, 76(4), 385–399.

[4] Winter, G., Gildea, R. J., Paterson, N. G., Beale, J., Gerstel, M., Axford, D., Vollmar, M., McAuley, K. E., Owen, R. L., Flaig, R., Ashton, A. W. & Hall, D. R. (2019). Acta Crystallographica Section D, 75(3), 242–261.

[5] http://ccp4.github.io/dimple/

[6] Sikharulidze, I., Winter, G. & Hall, D. R. (2016). Acta Crystallographica Section A, 72(a1), s193.

Using the tools of group theory we have mapped out the symmetry consequences of structural distortions in hybrid layered perovskites. These distortions include octahedral tilting and cation ordering within the inorganic layers as well as orientational ordering of organic cations in the organic layers. This analysis is coupled with synthesis and crystal structure determination of a wide variety Ruddlesden-Popper phases. The combined analysis shows that certain modes of octahedral tilting are strongly favored in large part because they lead to favorable hydrogen bonding interactions between the halide ions of the inorganic layers and the ammonium-type protons of the organic cations that sit between the layers. This information is used to guide our search for new lead-free ferroelectrics and multiferroics among this large class of compounds.

The A-site ordered quadruple perovskites AA’₃B₄O₁₂ can accommodate transition metal cations at the square-planar A’ site. When the B site is occupied by non-magnetic cations, the complex magnetic interactions between the spins at the orthogonally-oriented A’-sites can result in a wide variety of non-trivial magnetic orders. For example, A’-site Cu²⁺ (S = 1/2) spins can align either ferromagnetically (FM) in CaCu₃Sn₄O₁₂ or CaCu₃Ge₄O₁₂ (T_C = 10 and 13 K respectively), or antiferromagnetically (AFM) in CaCu₃Ti₄O₁₂ (T_N = 25 K) as a result of competition between direct exchange and superexchange interactions. A’-site Mn³⁺ (S = 2) in YMn₃Al₄O₁₂ yields a G-type AFM structure (T_N = 37 K) and Mn²⁺ (S = 5/2) spins in LaMn₃V₄O₁₂ break the symmetry to form a helix-type AFM structure (T_N = 44 K).

We recently revisited the material CaFe₃Ti₄O₁₂ with S = 2 (Fe²⁺) centers at the A’-sites for which initial studies did not find any long range magnetic order down to 4.2 K. This absence of magnetic ordering was notably unconventional. We discovered that the Fe²⁺ (S = 2) spins in CaFe₃Ti₄O₁₂ order in a complex triple-k AFM ground state at T_N = 2.8 K. In contrast to most magnetic insulating oxides, the Heisenberg superexchange between first- and second-neighbour spins are minimised by strong easy-axis anisotropy. Further-neighbour interactions yield the resulting spin ground state. On application of magnetic field, a canted FM spin structure is induced. This magnetic ordering is contrastingly different from those previously reported for A’-site magnetic quadruple perovskite materials. Furthermore, our results show that exotic long-range magnetically ordered ground states can emerge in large-spin systems when the symmetric exchange is quenched.

Charge ordering is prone to occur in crystalline materials with mixed-valence ions. It is often accompanied by a structural phase transition between a low-symmetry phase and a more symmetric high-temperature parent crystal structure. Such a structural transition may be absent if the mixed-valence ions are already located in inequivalent crystallographic sites in the parent structure. In this work, we investigate the representative case of the homometallic Co ludwigite (Co²⁺)₂(Co³⁺)O₂BO₃ (Pbam space group) with four distinct Co crystallographic sites surrounded by oxygen octahedra [Co(1)-Co(4)]. X-ray Absorption Near-Edge Spectroscopy provide experimental support for a Co²⁺/Co³⁺ mixed-valence scenario at all temperatures. X-ray and neutron diffraction confirm that the oxygen octahedron surrounding the Co(4) site is much smaller than those associated with the Co(1)-Co(3) sites at low temperatures, consistent with a localization of the Co³⁺ ions at the Co(4) site. The size differentiation of the Co(4)O₆ and Co(2)O₆ octahedra is continuously reduced upon warming above ~ 370 K, revealing a gradual charge redistribution along the Co(4)-Co(2)-Co(4) (424) ladder. In addition, small anomalies in specific Co-O bond lengths in the Co(3)-Co(1)-Co(3) (313) ladder are observed at 470 K and 495 K, respectively, matching the temperatures where sharp transitions were previously revealed by calorimetry and resistivity measurements. These bond length anomalies occur without an accompanying space group change within our sensitivity. An increasing structural disorder, clearly beyond a conventional thermal effect, is noted above ~ 370 K, manifested by an anomalous increment of some XRD Debye-Waller factors and broadened vibrational modes observed by Raman scattering. The local Co-O distance distribution, revealed by Co K-edge Extended X-Ray Absorption Fine Structure (EXAFS) data and analyzed with an evolutionary algorithm method, is similar to that inferred from the XRD crystal structure below ~ 370 K. At higher temperatures, the local Co-O distance distribution remains similar to that found at low temperatures, indicating that the size differentiation between smaller Co³⁺ ions and larger Co²⁺ions is maintained despite the growing oxidation-state disorder within the 424 ladder upon warming. This study provides insight into the physics of ludwigites and other related complex oxides at high temperatures.

Acknowledgments: This work was supported by CNPq Grants 134752/2016-3 and 308607/2018-0,
FAPESP Grant 2018/20142-8, and CAPES, Brazil.

Transition metal oxides are a platform for a plethora of exotic electronic phases where multiple degrees of freedom of correlated d-electrons, together with an underlying lattice topology, are at play. The ground states of these systems are governed by a subtle balance of relevant electronic parameters such as Coulomb repulsion, bandwidth, and crystal fields. 4d ruthenium compounds have been playing a significant role in providing novel electronic states such as unconventional superconductivity, metal-insulator transition and quantum magnetism.

Besides metallic or Mott insulating ground states, some ruthenium compounds exhibit a nonmagnetic ground state, which is accompanied by the formation of molecular orbitals generated by direct hopping between spatially extended 4d orbitals. A prominent example is the honeycomb ruthenate Li₂RuO₃, which undergoes dimerization of Ru atoms below ~ 550 K and forms a "molecular orbital crystal", where the 4d electrons are accommodated into the bonding and antibonding molecular orbitals localized on the dimers.

In heavy-transition-metal compounds such as ruthenates, another key ingredient for their exotic electronic states is spin-orbit coupling (SOC) which produces spin-orbit entangled J_eff pseudospins. Probably the most striking impact on magnetism is realised in Ru⁴⁺ ruthenates with a d⁴ configuration. While SOC produces a nominally non-magnetic J_­eff = 0 singlet, “excitonic” magnetism can arise via the interaction between excited states, and spin-orbit excitons may condense into an exotic long-range magnetic order. Up to date, excitonic magnetism has been only established in a layered perovskite Ca₂RuO₄ and remains unexplored in other ruthenates.

The competition between electronic phases including molecular orbital crystal and spin-orbit magnetism is expected to be more pronounced in ruthenates with a frustrated lattice, such as pyrochlore ruthenates A₂Ru₂O₇ (A: trivalent cation). The pyrochlore ruthenates have been regarded as S = 1 Mott insulators due to the presence of a trigonal distortion which may lift the degeneracy of the t_2g orbitals and thus competes with SOC. While most of them order magnetically at low temperatures, Tl₂Ru₂O₇ exhibits a metal to non-magnetic insulator transition at ~ 120 K. The origin of the nonmagnetic ground state has been attributed to the formation of a Haldane gap in the one-dimensional zigzag chains of Ru atoms on top of the pyrochlore lattice. The distinct behaviour of Tl₂Ru₂O₇ may be related to the covalency of Tl-O bonds, which has been discussed as playing a key role in the metal-insulator transition. The covalent character of A-O bonds thus may be an important parameter for the ground state of pyrochlore oxides. On the other hand, the role of spin-orbit coupling has not been fully investigated in pyrochlore ruthenates.

In an attempt to explore the novel phase competition in pyrochlore ruthenates, we discovered a new compound In₂Ru₂O₇ using high pressure synthesis. At high temperatures above ~ 450 K, In₂Ru₂O₇ crystallizes in a cubic pyrochlore structure, but adopts a weakly distorted tetragonal structure at room temperature as elucidated with single crystal x-ray and powder neutron diffraction. From the spectroscopic measurements, In₂Ru₂O₇ was found to host a spin-orbit-entangled J_eff = 0 -like state at room temperature, despite presenting the largest trigonal distortion among the family of pyrochlore ruthenates. The spin-orbit entangled singlet state is expected to display excitonic magnetism. Strikingly, through successive structural transitions likely associated with the covalent In-O bonds, the singlet state collapses and In₂Ru₂O₇ forms a non-magnetic state below ~ 220 K as evidenced by muon spin rotation. The non-magnetic ground state was found to originate from a molecular orbital formation in the semi-isolated Ru₂O trimer molecules decorating the pyrochlore lattice. Such molecular orbital formation, which involves not only the Ru⁴⁺ ions but the O^2- anions as well, has not been reported in other pyrochlore oxides.

In this talk we discuss the subtle competition between spin-orbit coupling and molecular orbital crystal formation in pyrochlore ruthenate In₂Ru₂O₇. We present the structural details of the Ru₂O trimer formation and its impact on the magnetism and electronic structure of In₂Ru₂O₇. We argue that the unique molecular orbital formation involving an oxygen atom, distinct from dimers with direct overlap of d-orbitals commonly found in other transition metal oxides, is assisted by the distortion of the In-O network. Our result demonstrates that bond covalency of constituent ions can be an additional key parameter in understanding phase competitions in complex transition-metal oxides.

The scheelites are a family of compounds with chemical formula ABO₄, and a characteristic crystal structure consisting of AO₈ dodecahedra and BO₄ tetrahedra. This structure is flexible and can accommodate a large variety of cations with a range of atomic radii and valence combinations. Scheelite-type oxides, such as CaWO₄, BiVO₄ and NaLa(MoO₄)₂ have been extensively studied due to their diverse range of physical and electronic properties [1]. In particular, Bi³⁺ containing molybdates have been found to be efficient photocatalysts due to the strong repulsive force of the 6s² lone pair of Bi³⁺, resulting in distortion of the BO₄ tetrahedra and alteration of the band gap [2, 3].

In 1974 Bi₃FeMo₂O₁₂ (BFMO) was reported as the first scheelite-type compound containing trivalent cations on the tetrahedral sites [4]. Interestingly, two different polymorphs of BFMO can be isolated by varying the synthesis conditions [5]. The tetragonal scheelite-type polymorph, described by space group I4₁/a with a = 5.32106(13) Å and c = 11.656(4) Å, can be prepared by a sol-gel route from aqueous solution of the constituent ionic species and has a disordered arrangement of the Fe and Mo cations. When heated above 500 °C, a 2:1 ordering of the Mo and Fe cations occurs, which lowers the symmetry to monoclinic (C2/c). The corresponding superstructure has a tripling of the a axis (a = 16.9110 (3) Å, b = 11.6489(2) Å, c= 5.25630(9) Å, β = 107.1395(11)°). The two structures are illustrated in Fig. 1.

In the present study, both polymorphs of BFMO were synthesized and their structure and magnetic properties characterized using a combination of powder diffraction, microscopy and magnetometry techniques. In situ neutron powder diffraction (NPD) measurements of the structural evolution of disordered tetragonal BFMO with increasing temperature showed that no amorphization takes place prior to the formation of the ordered monoclinic phase. The lack of a structural break-down, despite the substantial cation movement required in such a transformation, suggests that a certain degree of local cation order exists in the “disordered” tetragonal phase, facilitating the direct conversion to the fully ordered monoclinic structure. Instead of the expected amorphization and recrystallization, the conversion takes place via a 1^st order phase transition, with the tetragonal polymorph exhibiting negative thermal expansion prior to its conversion into the monoclinic structure. Zero-field-cooled/field-cooled and field-dependent magnetization curves of the monoclinic structure revealed the existence of a magnetic transition below 15 K. The long-range nature of the low-temperature magnetic structure in the monoclinic polymorph was verified by high-resolution NPD data, which revealed the emergence of an incommensurate magnetic structure. There is no evidence for long-range magnetic order in the tetragonal polymorph. This is, to the best of our knowledge, the first study of the phase transition mechanism and magnetic properties of this complex system and represents a milestone in the structural understanding and targeted design of Bi³⁺ containing molybdates as efficient photocatalysts.

[1] Brazdil, J. F. (2015). Catalysis Science & Technology 5, 3452-3458.

[2] Feng, Y., Yan, X., Liu, C., Hong, Y., Zhu, L., Zhou, M. & Shi, W. (2015). Appl Surf Sci 353, 87-94.

[3] Tokunaga, S., Kato, H. & Kudo, A. (2001). Chem Mater 13, 4624-4628.

[4] Sleight, A. W. & Jeitschko, W. (1974). Materials Research Bulletin 9, 951-954.

[5] Jeitschko, W., Sleight, A. W., Mcclellan, W. R. & Weiher, J. F. (1976). Acta Crystallogr B 32, 1163-1170.

A detailed account of the local atomic structure and disorder at 5 K across the phase diagram of the high-temperature superconductor K_xFe_2-ySe_2-zS_z (0≤z≤2) is obtained from neutron total scattering and associated atomic pair distribution function (PDF) approaches [1]. Various model-independent and model-dependent aspects of the analysis reveal a high level of structural complexity on the nanometer length scale. Evidence is found for considerable disorder in the c-axis stacking of the FeSe S slabs without observable signs of turbostratic character of the disorder. In contrast to the related FeCh (Ch = S, Se)-type superconductors, substantial Fe-vacancies are present in K_xFe_2-ySe_2-zS_z, deemed detrimental for superconductivity when ordered. Our study suggests that the distribution of vacancies significantly modifies the iron-chalcogen bond-length distribution, in agreement with observed evolution of the PDF signal. A crossover-like transition is observed at a composition of z≈1, from a correlated disorder state at the selenium end to a more vacancy-ordered (VO) state closer to the sulfur end of the phase diagram. The S-content-dependent measures of the local structure are found to exhibit distinct behavior on either side of this crossover, correlating well with the evolution of the superconducting state to that of a magnetic semiconductor toward the z≈2 end. The behavior reinforces the idea of the intimate relationship of correlated Fe-vacancy order in the local structure and the emergent electronic properties.

[1] P. Mangelis et al., (2019) Physical Review B 100, 094108.

Work at Brookhaven National Laboratory was supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences (DOE-BES) under Contract No. DE-SC0012704. Alexandros Lappas acknowledges support by the U.S. Office of Naval Research Global, NICOP Grant Award No. N62909-17-1-2126. This research used resources at the Spallation Neutron Source, a U.S. Department of Energy Office of Science User Facility operated by the Oak Ridge National Laboratory.

In order to understand the packing and orientation of organic semiconductor thin films, we make use of microcrystal electron diffraction (MicroED) and grazing-incidence wide-angle X-ray scattering (GIWAXS). These complementary techniques provide structural insights to the structure of these thin films and can be used with the same sample preparation methods that are used to create the functional films. This removes the need for time-consuming crystallization experiments that may not directly capture the same semiconductor structure found in the films. We will present the application of these methods on four organic semiconductor samples, some of which represent novel structures determined by MicroED.

Three-dimensional electron diffraction (3D ED) has matured into a method routinely employed by several worldwide-located laboratories for addressing crystallographic problems, which were considered intractable by X-ray diffraction [1]. The main advantage of ED is the ability to get diffraction data from volumes of few hundreds or even few tens of nanometers. This allows acquiring comprehensive 3D structural information from crystals too small for X-ray single-crystal methods, from coherent domains in pervasively twinned or disordered materials, from isolated domains embedded in inorganic or biological matrices and from minor constituents of powdered polyphasic mixtures.

From the beginning, the main shortcomings of 3D ED appeared connected with the deterioration of the sample induced by TEM vacuum or by beam damage. Moreover, organic crystals are typically affected by mosaicity and bending. In this contribution we will show different experimental protocols for data collection and analysis that can be employed in any experimental set-up, even for low-voltage TEMs. Beam damage is minimised by coupling STEM imaging for sample search and tracking, and a small-size low-intensity parallel electron beam for diffraction data acquisition [2]. The size of the beam is crucial for picking narrow areas of the sample, either when coherent crystal domains are very small or when there is a need for moving to fresh parts of the crystal in order to lessen beam damage effects.

According with the specific sample characteristics, 3D ED data acquisition can be performed in step-wise mode, coupled with beam precession [3], or by continuous rotation [4]. Both approaches strongly benefit by the disposal of a new-generation ultra-fast single-electron detector [5]. Moreover, background noise can be almost completely suppressed with an energy filter that cuts out the inelastic scattering. Structure solution is normally obtained ab-initio by direct methods. Still, global optimisation approaches, like simulated annealing [6], are valuable alternatives when data are affected by low resolution, preferential orientation or experimental errors that compromise the overall intensity reliability (e.g. beam damage, merohedric twinning, diffuse scattering).

We will thus discuss examples of recently published [7, 8] and forthcoming structure characterizations of pharmaceutical compounds, organic charge-transfer co-crystals and polycyclic aromatic hydrocarbons. For each case, specific problematics of the sample will be discussed, together with experimental solutions adopted for achieving structural solution and refinement.

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

[2] Kolb, U., Gorelik, T., Kübel, C., Otten, M. T. & Hubert, D. (2007). Ultramicroscopy 107, 507.

[3] Lanza, A., Margheritis, E., Mugnaioli, E., Cappello, V., Garau, G. & Gemmi, M. (2019). IUCrJ 6, 178.

[4] Gemmi, M. & Lanza, A. E. (2019). Acta Cryst. B75, 495.

[5] van Genderen, E., Clabbers, M. T. B., Das, P. P., Stewart, A., Nederlof, I., Barentsen, K. C., Portillo, Q., Pannu, N. S., Nicolopoulos, S., Gruene, T. & Abrahams, J. P. (2016). Acta Cryst. A72, 236.

[6] Burla, M. C., Caliandro, R., Carrozzini, B., Cascarano, G. L., Cuocci, C., Giacovazzo, C., Mallamo, M., Mazzone, A. & Polidori, G. (2015). J. Appl. Cryst. 48, 306.

[7] Andrusenko, I., Hamilton, V., Mugnaioli, E., Lanza, A., Hall, C., Potticary, J., Hall, S. R. & Gemmi, M. (2019). Angew. Chem. Int. Ed. 58, 10919.

[8] Das, P. P., Andrusenko, I., Mugnaioli, E., Kaduk, J. A., Nicolopoulos, S., Gemmi, M., Boaz, N. C., Gindhart, A M. & Blaton, T., (2021). Cryst. Growth Des. 21, 2019.

3D Electron Diffraction (3D ED) has reached a point where it has become a routine technique for single-crystal diffraction studies at the nanometre scale [1]. Recently, some acquisition softwares have been developed with the aim of automatization and universal application [2]. One of them is the Fast and Automated Diffraction Tomography (Fast-ADT) [3]. This acquisition module is based on two tilt scans of the goniometric stage over the desired tilt range; the first one to monitor the crystal displacement with respect to the tilt angle in order to interpolate the necessary electron beam shifts, and the second one to acquire the diffraction patterns while following the crystal automatically. This procedure allows reliable diffraction acquisitions for crystals down to 20 nm provided that the stage has been aligned for tomography experiments and the holder is kept in good mechanical conditions. Fast-ADT can work in both TEM and STEM mode, but STEM is preferred mainly because of its low dose to acquire scanned images and its clear visualization of tiny or layered crystals in such conditions [4]. Another difference to other 3D ED routines is the use of Nano-Beam Electron Diffraction (NBED) instead of selected area electron diffraction. The combination of Fast-ADT and NBED enables several approaches focused on the optimization of 3D ED experiments, such as the shift of the beam at different positions of the same crystal or different crystals during diffraction pattern acquisitions. This versatility is beneficial as it gives the needed flexibility to study beam sensitive specimens even with post TEM column charged-coupled devices.

As an example, Fast-ADT was used to acquire datasets from disperse red 1 (DRED1) crystals, an organic molecule that was recrystallized in toluene. The dye DRED1 is an azobenzene derivate, which are well known for their photochromatic properties and large optical and electro-optic properties in various polymeric films. The processing of six Fast-ADT datasets­­­­­­­­­­ with eADT [5] revealed a triclinic crystal system with unit-cell parameters of a = 7.72 Å, b = 11.14 Å, c = 19.58 Å, α = 73.8°, β = 83.0°, γ = 70.5° and V = 1523.5 ų and indicated four molecules per unit cell. The real space method simulated annealing, implemented in Sir2014 [6], was used to solve the structure and the positions of the azobenzenes were found using both P1 (Z = 4) and P-1 (Z’ = 2). The small difference between structure solutions performed in both space groups was taken as an indication that the crystal structure could be described in the centrosymmetric space group. However, the correct orientation of the flexible side chains was more difficult to retrieve because of their high degree of freedom. For this reason, on one hand, two datasets were merged to obtain a higher number of independent reflections (85%) and, on the other hand, an analytical description of the rocking curves was applied to enable a frame orientation refinement and an improved reflection intensity integration [7]. These processing tools allowed solving the new polymorph of DRED1 ab initio in P-1, directly revealing the 46 non-hydrogen independent atoms from the scattering density map. Finally, the structure model was refined based on X-ray powder diffraction data using the Rietveld method.

Electron diffraction makes it possible to obtain crystal structures at atomic resolutions, for both small and macro-molecules [1-2]. For this purpose, the same as in case of X-ray diffraction, it is necessary to use scattering factors model. After years of experience people learned that Independent Atom Model (IAM) is not the best choice for X-ray diffraction. It is not a surprise that also for electron diffraction it will not give the best results. Different aspherical models, already known for X-ray diffraction, can be implemented for electron diffraction. However, it is necessary to investigate their possibilities and limits, to verify correctness of obtained structures.

We present analysis of refinements of Transferable Aspherical Atom Model (TAAM) with parameters of multipolar model taken from MATTS databank (databank of Multipolar Atom Types from Theory and Statistical clustering) - successor of UBDB databank [3]. We used electron scattering factors implemented in DiSCaMB library[4] and interfaced with Olex2-1.3[5]. Such solution is available through .tsc files [6] and it requires little effort (Fig.1).

Numerous refinements were performed against experimental electron structure factors and theoretical electron structure factors so as to find optimum refinement strategy. We discuss, inter alia, possibility of refinement of atomic displacement parameters, both for hydrogen and non-hydrogen atoms or positions of hydrogen atoms. It is interesting how they change e.g. with resolution cut-off. To confirm that our conclusions could be transferred for different, but still organic structures, we made simulations for several pharmaceutical compounds, such as carbamazepine, paracetamol, 1-methyluracil.

Support of this work by the National Centre of Science (Poland) through grant OPUS No.UMO-2017/27/B/ST4/02721 and PL-Grid through grant ubdb2019 are gratefully acknowledged.

Electrons interact with matter 10⁶ times stronger than X-rays do, which makes it an ideal radiation source for diffraction and imaging experiments on submicron- and nano-sized crystals. During the last three decades, 3D electron diffraction (3D ED) has been developed into a regular and reliable technique for structure determination, which is complementary to single-crystal X-ray diffraction (SCXD) and single particle analysis. One issue for electron diffraction is inelastic scattering, which brings background in the diffraction patterns. This background is most obvious for electron diffraction patterns from protein crystals, especially at low angles. Even though modern diffraction data software (XDS, DIALS, MOSFLM) has sophisticated background removal algorithms to deal with this, the existence of inelastic scattering will still add errors in the diffraction experiment. The inelastically scattered electrons can be removed by energy filters. Here, we implemented energy-filtered 3D ED using a Gatan Energy Filter (GIF) in both TEM selected area electron diffraction mode and STEM micro/nanoprobe mode. We explained the setup in detail and this implementation can allow researcher to have better accessibility to energy-filtered 3DED experiments because more microscopes are equipped with a GIF than an in-column omega filter. We also proposed a crystal tracking method in STEM mode using live HAADF image stream. This method enables us to collect energy-filtered 3DED datasets in STEM mode with a larger tilt range without foregoing any frames. This can avoid crystal moving out of the beam during the tilting and the tilt range can always reach the maximum tilt range of the microscope (in our case ~150°). We acquired multiple datasets from different crystals and we further processed and refined the structures. We observed that the final R₁ will improve 20% to 30% for energy-filtered datasets compared with unfiltered datasets. We also discussed the possible reasons that lead to the improvement.

3D Electron Diffraction (3D ED) is a very powerful tool for the structural elucidation of nanocrystalline particles. After its Science nomination for “Breakthrough of the year 2018” [1], 3D ED, using the continuous rotation method [2-3], and well-established crystallographic software, is gaining a lot of attention in all areas of research. In the recent years, many achievements using electron diffraction techniques have been made in the fields of organic and inorganic molecules, polymorphism, geological sciences, natural products, biomolecules, material sciences, energetic materials, batteries, and many others [2-4]. Such experiments are currently done in a (modified) transmission electron microscope, thus requiring customized experimental and data-analysis protocols, which vary depending on each specific instrumental setup. Hence, 3D ED experiments are currently carried out only by specialized staff and require a remarkable investment in terms of time, expertise, knowhow transfer and resources.

A strong need has emerged in the crystallographic community for instrumentation specifically dedicated to 3D ED experiments.

Here we present an electron diffractometer: a new device developed and optimized exclusively for 3D ED which allows a time-effective, automated and standardized experimental workflow along with user-friendly operability. Furthermore, the electron diffractometer is conceived to make use exclusively of well-established crystallographic approaches and to interact seamlessly with readily available crystallographic software. Experimental examples of different kind of materials measured with this device will be showcased.

Rational and creative design of organic and metal building blocks has successfully enabled the genesis of a variety of coordination polymers or metal-organic frameworks (MOFs) that are of fundamental scientific importance as well as provide a myriad of practical applications including gas storage and separation, catalysis, and sensing. One of the most attractive features in MOFs is flexibility because they show distinctive properties that cannot be achieved with rigid MOFs and other porous inorganic materials. In this talk, we will present strategies that exploit flexible MOFs for effectively separating hydrogen isotopes through the dynamic pore change of flexible MOFs. Especially, a unique isotope-responsive breathing transition of the flexible MOF was studied, which selectively recognize and respond to only D₂ molecules through a secondary breathing transition, monitored by in situ neutron diffraction experiments.

Biomacromolecules, such as enzymes, are ubiquitous in nature and essential for maintaining basic life activities. Apart from the fundamental biological functions, biomacromolecules are also of great values in industrial applications, especially in food and pharmaceutical production. However, their industrial applications are often handicapped by low operational stability, poor robustness, difficult recovery and reuse. Incorporation of biomolecules within protective exteriors has been proved to be an effective method to promote their stabilities and applications. As new classes of crystalline solid-state materials, porous frameworks materials (such as covalent-organic frameworks, COFs and metal-organic frameworks, MOFs) feature high surface area, tunable pore size, high stability, and easily tailored functionality, which entitle them as ideal supports for encapsulation of biomolecules to form novel composite materials for various applications. Moreover, the formed composites can combine the properties of both constitutes, where crystalline frameworks materials and biomolecules are indeed mutually beneficial. Our researches mainly focus on their biocatalysis, separation and medicinal applications. This novel crystalline platform composed of biomolecules-incorporation and framework materials exhibited various functionality and superior poteintials in biocatalysis, bioseparation, and biopharmaceutical formulations.

Supramolecular chemistry places focus on the weak non-covalent interactions between molecules in the solution or solid phases. These “soft” interactions are reversible and allow one to build materials which are responsive to their chemical or physical environment, changing form and properties under the influence of heat, light, pressure or chemical probes.

Dynamic materials, capable of responding to their environment, require flexibility which may be achieved using interactions such as hydrogen- or halogen-bonding or through the use of suitable metals and ligands in coordination compounds. Frameworks may be made up of relatively strongly bound entities such as those that make up metal-organic frameworks (MOFs) or may be more loosely bound such as host-guest systems where the host molecules crystallise as independent entities but leave spaces which can accommodate guest molecules. The process of guest exchange within porous solids can be used in a range of applications, such as selective absorption or separation of gases and heterogeneous catalysis. Among the more interesting examples of dynamic processes in frameworks are those which result in thermochromic and/or mechanochromic effects. Materials of this type are particularly of interest if they are able to revert to their original state on application of another external perturbation signal. Rational design of such systems remains a challenge however, and is thus an exciting area for application of crystal engineering principles.

In this presentation, examples from recent work in our laboratory will be presented, including MOFs and 3D hydrogen bonded frameworks constructed from the same flexible ditopic ligands. The influence of halogen versus hydrogen bonding on a molecular host-guest system will also be described. Frameworks exhibit thermochromic and mechanochromic properties, depending on the application of external stimuli such as heat, grinding or exposure to solvent vapours. Further examples will include the selective inclusion of halogenated volatile organic compounds in a porous metal-organic framework (Fig. 1).

The use of mechanical bonds for the synthesis of catenanes is a challenging process because of the many factors controlling the interpenetration process.[1,2] We report the kinetic control in the presence of various aromatic solvents of a poly-[n]-catenane (1). The polymeric structure is composed of interlocked M₁₂L₈ icosahedral nanometric cages with internal voids of ca. 2500 ų.[3] Using the symmetric exotridentate tris-pyridyl benzene (TPB) ligand and ZnCl₂ with appropriate templating solvent molecules due to the good ligand aromatic interactions are used, the metal-organic nanocages can be synthesized very fast, homogeneously, and in large amounts as microcrystals (Figure 1). Synchrotron single-crystal X-ray data (100 K) allowed the resolution of nitrobenzene guest molecules at the internal walls of the M₁₂L₈ cages, while in the centre of the nanocages the solvent is disordered and not observable by X-ray diffraction data. The guest release occurs in two steps with the disordered nitrobenzene released in the first step (lower temperatures) because of the lack of strong cage-guest interactions. Solid-state quantum mechanics provided a rationalization of the results, in particular, solid-state approaches, showed theoretical evidence of the kinetic nature in the formation of the polycatenation of the M₁₂L₈ nanocages by the analysis of the packing energy considering monomeric and dimeric cages.

Figure 1. Synthesis of the M₁₂L₈ interlocked nanocages forming the poly-[n]-catenane 1 under aromatic control.

[1] J. F. Stoddart (2009). Chem. Soc. Rev. 38, 1802-1820.

[2] Frank, M., Johnstone, M. D. & Clever, G. (2016). Chem.- Eur. J. 22, 14104-14125.

[3] Torresi, S., Famulari, A. & Martí-Rujas, J. (2020). J. Am. Chem. Soc. 142, 9537-9543.

The synthesis and conception of coordination polymers and supramolecular networks based on gold(I) complexes used as metallo-ligands (especially dicyanoaurate) is an established procedure to obtain materials with exciting properties: phosphorescence, non-linear optical behaviour, vapochromism and non-classical response to temperature and pressure [1-2]. However, the appearance of these solid-state properties is often connected to the manifestation of aurophilic interaction. The Au(I)‧‧‧Au(I) interaction, an attraction between closed shell d¹⁰ metal centres, is a relativistic effect that has a strength comparable to that of classical hydrogen bond [3]. Therefore, the study of new functional materials based on gold(I) properties must encourage the formation of these contacts in the crystal environment. We prepared, by a judicious choice of chelating ligands and balance in coordination equilibria [4], a series of 12 new coordination polymers or supramolecular networks based on dicyanoaurate anion and copper complexes presenting aurophilic interactions. The choice of copper as metal centre to connect to [Au(CN)₂]^- makes the synthesis particularly predictable due to the Jahn-Teller effect in the case of Cu(II), and the appearance of Cu(I) compounds due to redox effect of specific ligands will be commented. These compounds have been tested for vapochromism, and their behaviour in presence of ammonia has been interpreted with Raman, Ir and Uv-Vis absorption spectroscopy. On the same time, the response to temperature (T= 100-420 K) and pressure (P= 0.1-1.5 GPa) of {Cu(bipy)₂[Au(CN)₂]}[Au(CN)₂] (bipy =2,2’-bipyridine), a prototypical bimetallic aurophilic supramolecular network, has been investigated. Both the dependence of structural and reticular parameters to thermal and compression stimuli has been studied, and a phase transition at 1.2 GPa has been revealed. Moreover, we investigated the possibility to modulate the structural behaviour with the cocrystallization with other d¹⁰ metal tectons, and we demonstrate the possibility to obtain inclusion compounds with the presence of Hg(CN)₂ with a 3D weakly interacting framework still presenting Au‧‧‧Au contacts.

The supramolecular compound catena-{[Co(amp)₃][Cr(C₂O₄)₃]·6H₂O}(I) was synthetized as reported earlier [1,2]. To get insight into the structural modifications of its architecture within the water sorption processes (see Fig.1 (a)), in situ powder X-Ray Diffraction (PXRD) measurements were performed on a Bruker D8 Advance Diffractometer in a Bragg−Brentano geometry, using Cu(Kα₁) radiation. The humidity was controlled by exposing the sample to a nitrogen flow heated at 40°C and having humidity rates ranging from 0 to 90% relative humidity (r.H.) and then from 90 to 0% r.H. The PXRD carpet plot diagram ((see Fig.1 (b)) and the refinements of the PXRD patterns coupled with the single crystal diffraction results were used. During the adsorption and desorption processes, only two phases are involved, that of the dehydrated phase ([Co(amp)₃][Cr(C₂O₄)₃] (I’), P 2₁/n, a= 12.0542, b=16.0920, c = 13.8841, β = 99.8013) and the hydrated phase (I, P 2₁/n; a= 13.2330, b=18.2611, c = 14.1396, β = 100.5016). For the adsorption process, during the first step (from 0 to 30% r.H) corresponding to an adsorption of ∼ 1 mol H₂O / mol of I’, only phase I’ is involved and the volume of its unit cell does not change significantly. During the second step (from 30 to 35% r.H.) corresponding to an abrupt adsorption of ∼5.6 mol H₂O / mol of I’, both phases are involved with different percentages (deduced from Rietveld refinements) progressing to the complete conversion of I’ to I. During the third phase where the quantity of water adsorbed shows a plateau (from 35 to 90 % r.H.), only phase I is present and the volume of its unit cell does not change significantly with the humidity. For the desorption process, the same observations apply. During the first step (from 90 to 20 % r.H.) only I is present and its volume decreases just slightly. During the deep desorption process (from 20 to 14 % r.H.), both phases are involved with different percentages and during the last step (from 14 to 0% r.H) at the contrary to the adsorption process, both phases are still present while the sorption isotherm in this region looks like a type-I isotherm in the IUPAC classification [4]. These results suggest a quick capillary condensation followed by a pore filling process that produces a type-V isotherm profile [4], in relation with the first order structural transition followed by insignificant changes of the unit cell volume. The adsorption and desorption branches in the S- shaped isotherms of H₂O-vapor for this compound occur at the values of relative humidity at which these phase transitions start. The conversion of I to I’ and vis-versa is followed by the cleavage and formation of the hydrogen bonds in the architectures of these materials.

The first stable binary icosahedral quasicrystals (iQCs) were found in Cd-Yb and Cd-Ca alloy systems [1, 2], which was followed by finding of nine isostructural iQCs in Cd-R (R = Y, Gd-Tm) [3] and Zn-Sc systems [4]. The structural type of these iQC is called Tsai-type, and it has been extended to ternary or quaternary alloys by atomic substitutions.

Higher-dimensional structure analysis of the Cd-Yb iQC by single-crystal X-ray diffraction revealed that the atomic structure consists of two main building blocks, rhombic triacontahedron (RT) and acute rhombohedron (AR) units [5]. In ternary iQCs, the structure analysis becomes more difficult because occupational disorder has to be taken into account in the 6D structure model. Furthermore, recent studies have shown that some sites are preferentialy occupied by the substituting elements [6,7], which indicates that the higher-dimensional structure model must be optimized to ternary iQCs. To build such model, knowledge of atomic structures in ternary quasicrystal approximants (APs) is quite important.

In the first part of my talk, I will present the superstructure and basic structure of ternary Yb-Cd-Mg 1/1APs with the compositions Yb_12.9Cd_78.4Mg_8.8 and Yb_13.3Cd_64.2Mg_22.5 [8]. The former was determined to have a face-centred packing structure comprising two distinguishable RT units (space group Fd3, a = 31.377(1) Å), while the latter was found to have a body-centred packing structure made of identical RT units (space group Im3, a = 15.7596(4) Å). The distinction between the two types of RT units in the superstructure is based on the positional disorder of the first tetrahedron shell and the relative Cd/Mg occupancy at sites (48h) in the fourth icosidodecahedron shell.

In the second part, I will introduce a Python package (PyQCstrc) for building the higher-dimensional models of iQCs [9] and present a modification of six-dimensional structural model for the primitive Tsai-type iQCs so as to incorporate the selective Cd/Mg occupation found in the Cd-Mg-Yb 1/1 APs [7].

[1] A.P. Tsai, J.Q. Guo, E. Abe, H. Takakura, and T.J. Sato, (2000), Nature, 408, 537–538.
[2] Guo, J. Q., Abe, E., Tsai, A. P. Phys. Rev. B. (2000), 62, R14605−R14608.
[3] Goldman, A. I., Kong, T., Kreyssig, A., Jesche, A., Ramazanoglu, M., Dennis, K. W., Bud’ko, S. L., Canfield, P. C., (2013), Nat. Mater, 12, 714−718.
[4] Canfield, P. C., Caudle, M. L., Ho, C. S., Kreyssig, A., Nandi, S., Kim, M. G., ... & Goldman, A. I. (2010), Phys. Rev. B, 81(2), 020201.
[5] Takakura, H., Pay Gómez, C., Yamamoto, A., de Boissieu, M., and Tsai, A.P., (2007), Nat. Mater. 6, 58–63.
[6] Pay Gómez, C. & Tsai, A. P. (2013). Comptes Rendus Physique, 15(1), 1–10.
[7] Yamada, T., Takakura, H., de Boissieu, M. and Tsai, A.-P., (2017), Acta Cryst. B73, 1125-1141.
[8] Yamada, T, (2021), Phil. Mag., 101(3), 257-275.
[9] Yamada, T, J. Appl. Cryst., in press.

Keywords: Quasicrystal, Approximant

This work was supported by JSPS KAKENHI grants (numbers JP18K13987, JP19H05818).

It has been known for some time now that normally a crucial element in QC formation, at least in soft matter, is the presence of two prominent wave numbers in the linear response behaviour to periodic modulations of the particle density distribution. This is equivalent to having two prominent peaks in the static structure factor or in the dispersion relation. In the first half of the talk, we demonstrate how the crucial pair of prominent wave numbers are connected to the length and energy scales present in the pair potentials. Whilst the ratio between the two length scales is important, we show here that for thermodynamically stable soft matter quasicrystals, the ratio of these wave numbers should be close to certain special values. We identify features in the particle pair interaction potentials which can suppress or encourage density modes with wave numbers associated with one of the regular crystalline orderings that compete with quasicrystals, enabling either the enhancement or suppression of quasicrystals. In the second half of the talk we look how to compute phase diagrams for a given interaction potential in an efficient manner. In order to do this, we focus on the representation of the density distribution in soft matter systems. The form of the average (probability) density distribution in solids is often represented as a sum of Gaussian peaks (or similar functions) centred on lattice sites or via a Fourier sum. Here, we argue that representing instead the logarithm of the density distribution via a Fourier sum is better. The advantage of this representation is that it excels both deep in the crystalline region of the phase diagram and also close to melting. Additionally, we show how a strongly nonlinear theory (SNLT) enables efficient computation of the phase diagram for a threedimensional quasicrystal-forming system using an accurate nonlocal density functional theory.

The atomic structure of the decagonal Al-Cu-Rh quasicrystal with a space group is refined based on five X-ray diffraction datasets, collected at 293 K, 1013 K, 1083 K, 1153 K and 1223 K with the use of a synchrotron radiation [1]. The real-space structure solution with the tiling-and-decoration approach based on the moment series expansion [2] is executed.

All the crystallographic – factors are ranging from 5.9% to 6.4% for the datasets of common 1460 symmetry-inequivalent peaks. What is the most intriguing is the correlation (Pearson correlation equal to 0.85) between lattice parameters (edge-length of rhombus and the interatomic layer distance) and the maximum of the residual electron density. The identical temperature dependence presented in figure 1 for the parameters implies the phase transformation. The residual density is agglomerated in the origin of the 4D unit cell what implies the phase transformation is related to the General Penrose Tiling (GPT). Additionally, we can observe a local minimum around the 1083-1153 K of the moments values being directly related to phasons. This is the temperature the structure is the most stable around. The existence of the local minimum in all the plots proves the phason disorder is related to the structure stability what was previously questioned due to insufficient quality of the refinement [1].

We modified the moment series approach to accommodate the existence of the 5^th atomic surface arising for the random-tiling model of the decagonal quasicrystal (figure 2). After the structural refinement with the updated model we obtained much better results in terms of the R-factors. Even more, up to the uncertainty estimated with Hesse matrix, we could prove the 5^th atomic surface existence is not only the artefact of the electron density calculation but the crucial feature of the structure in the 1083-1153 K. The calculations prove the random-tiling hypothesis of the structural stability is true for the decagonal quasicrystals and the structure is stabilized by phasons.

Beyond Golay-Rudin-Shapiro S. I. Ben-Abrahamshelomo.benabraham@gmail.com

I briefly recapitulate the necessary background about the original pseudorandom Golay-Rudin-Shapiro sequence (GRS) and its known generalizations [1-5]. The standard method to make the one-sided GRS based on a two-letter alphabet A₂ = {a, b} two-sided is by constructing a proto-GRS structure based on a four-letter alphabet A₄ = {a, b, c, d} and then reduce it to A₂. In order to generalize to higher dimensions one proceeds analogically. Here I extend GRS to eight symbols (alias letters, digits or colors). I also refine the terminology introducing the designation dD GRSn for a GRS structure based on n symbols and supported by Z^d.

The most natural support for 3D GRS8, that is a structure is based on A₈ = {0, 1, 2, 3, 4, 5, 6, 7} is Z³. The respective substitution is

(1)

The bottom matrix refers to 2D GRS8. The bottom line, in turn, refers to 1D GRS4, while the alphabet A₈ splits into two disjoint A₄'s. Thus 1D necessitates special treatment. As in the case of GRS4, the substitution must be applied twice.

Fig.1 shows an isometric projection of the hull of the second generation of 3D GRS8.

Figure 1. Aspect of hull of 3D GRS8 generation 2.The Fourier spectrum of all GRS structures is absolutely continuous [7, 8].

[1] Golay, M. J. E. (1949) J. Opt. Soc. Amer. 39 437-444.

[2] Rudin, W. (1959) Proc. Amer. Math. Soc. 10 855-859.

[3] Shapiro, H. S. (1951) Extremal problems for polynomials and power series, Master's thesis (MIT, Cambridge MA).

[4] Queffélec, M. (1995) Substitution dynamical systems – spectral analysis, LNM 1294, 2nd. ed. (Springer Verlag, Berlin).

[5] Ben-Abraham, S. I. and David, A. (2020) J. Phys.: Conf. Ser. (in press).

[6] Allouche J.-P. and Shallit J. (2003) Automatic Sequences: Theory, Applications, Generalizations, (Cambridge University Press.

[7] Baake, M. and Grimm, U. (2013) Aperiodic Order. Volume 1: A Mathematical Invitation, (Cambridge University Press).

[8] Barbé, A. and von Haeseler, F. (2003) J. Phys. A: Math. Gen. 38 2599-2622.

Keywords: Golay-Rudin-Shapiro structures

Developing realistic three-dimensional growth models for quasicrystals is a fundamental requirement. Uchida found a general principle for building crystal structures (the Uchida stacking motif) in complex alloys such as the μ-Al₄Mn phase [1]. Here, we investigated the Uchida stacking motif using molecular dynamics (MD) simulations to search for clues to the origins of the atomic arrangements in quasicrystals. We used the LAMMPS code for the MD simulations. Our MD simulation results well reproduce the Uchida stacking motif seen in the μ-Al₄Mn phase. The simulations also reveal the formation of a deformed icosahedron. Our results provide new insights into the growth mechanism and origin of complex alloys and quasicrystals.

[1] Uchida, M. & Matsui. Y. (2000). Acta Cryst. B56, 654.

The atomic-resolution holography (ARH) technique [1,2] offers the possibility to experimentally determine the local atomic-scale structure of quasicrystals. This method can selectively investigate specific elements and their 3-dimensional local atomic environment in a range of up to around 2 nm, without the need of a priori information on the structure. Therefore, it can provide a novel perspective for the visualization of the structure of aperiodic systems.

Recently, we have described the results of the ARH reconstruction for the Penrose lattice, which can be regarded as a reference system for decagonal quasicrystals. The resulting pattern of atomic images can be interpreted a projection of the average structure.[3] Using this framework, we can now describe how the experimental results for decagonal Al-Co-Ni quasicrystals compare with the projection of the average structure from a computational model.[4]

An example is shown in the Figure below, with exemplary data of an experimental hologram of an Al-Co-Ni quasicrystal (a). The intense lines in the hologram are the so-called X-ray standing wave lines, which indicate the 10-fold symmetry of the system. The reconstruction of the environment around the Co atoms from the holograms is illustrated in (b), and is compared with the corresponding projection from the computational model (c). Shown here is the quasi-periodic plane that includes the emitter atom at the origin. The atomic images at the vertices of the dashed polygons can be identified with transition metal atoms, while Al atoms are mainly distributed along the polygon edges.

We will also demonstrate the differences of the quasiperiodic structure versus a crystalline approximant and illustrate the ARH results for icosahedral structures.

Jana2020 is a new program for solving and refining regular, modulated and magnetic structures. The lecture will present new possibilities of this program in the field of magnetic structures.

In the last three years, a series of developments within the FullProf Suite [1], concerned with magnetic structures (both commensurate and incommensurate), have been performed. From the the first publication describing shortly the program FullProf [2] in 1993 many changes and re-writing of the code were done. In particular, the phase convention in the expression of the magnetic structure factor were changed. In 1993, we introduced for the first time the Simulated Annealing (SAnn) procedure for solving magnetic structures in a program called MagSan [2] that was later developed for incommensurate structures and embedded within FullProf. The method to make a symmetry analysis during many years was based in the Bertaut’s and Izyumov proposals [3-5] and we developed the program BasIreps to help the a priori construction of magnetic models to be refined. The use of magnetic space groups (MSG) was possible but, in the absence of appropriate tables or computing tools, the user had to construct the symmetry operators by hand. The treatment of incommensurate magnetic structures either was only possible by using basis vectors of irreducible representations or by constructing a series of 3D operators accompanied by a phase factor that was done by looking at the output of BasIreps and completing the information if the user was able to understand group theory.

The availability of new tools on the Web [6-8] and the creation of the Commission on Magnetic Structures of the IUCr has allowed the development of precise and unambiguous ways of describing magnetic structures using MSG and magnetic superspace groups (MSSG) [8, 9] by mean of magnetic CIF files. The team working in the FullProf Suite has accompanied these developments and created new tools to import these CIF files and convert them to input control files for FullProf. We have now the possibility of treating MSSG within FullProf with up to three independent modulation wave vectors, both for powders and single crystals, with automatic symmetry constraints determination for the amplitudes of modulations [10]. The displacement and thermal amplitudes are implemented but, for the moment, the calculation of structure factors using integration in internal coordinates is not yet available.

One important feature of FullProf is the use of SAnn, using the full powder diffraction pattern in which the components of the magnetic amplitudes are free parameters, in either crystallographic or spherical settings. This is very important for the powder case in which the loss of information may give rise to ambiguous or degenerate solutions. Moreover, the SAnn method may be used as an alternative to refinement because in such cases the least-squares refinement procedure diverges or it is unable to arrive to convergence.

In this talk, after summarizing the full set of changes performed during the last years (interoperability with the Bilbao Crystallographic Server [6, 7] and ISODISTORT [8], the use of magnetic Hall symbols [11], magnetic symmetry modes, etc.) I will present few recent examples of the use of FullProf in the magnetic structure determination of magneto-electric and multiferroic materials.

[1] https://www.ill.eu/sites/fullprof/

[2] Rodriguez-Carvajal J. (1993). Physica B. 192, 55.

[3] Bertaut E.F. (1968). Acta Cryst. A24, 217.

[4] Izyumov Yu. A., Naish V.E. and Ozerov R.P. (1991), Neutron Diffraction of Magnetic Materials, New York: Consultants Bureau.

[5] Rodriguez-Carvajal J. and Bourée F. (2012). EPJ Web of Conferences 22, 10, https://doi.org/10.1051/epjconf/20122200010.

[6] Aroyo M.I., Perez-Mato J.M., Capillas C., Kroumova E., Ivantchev S., Madariaga G., Kirov A. & Wondratschek H. (2006), Z. Krist. 221(1), 15.

[7] Aroyo M.I., Kirov A., Capillas C., Perez-Mato J.M. & Wondratschek H. (2006), Acta Cryst. A62, 115. http://www.cryst.ehu.es.

[8] Campbell B.J., Stokes H.T., Tanner D.E. & Hatch D.M. (2006), J.Appl.Cryst 39, 607. http://stokes.byu.edu/iso/isotropy.php

[9] Perez-Mato J.M., Ribeiro J. L., Petricek V. and Aroyo M. I. (2012), J. Phys.: Condens. Matter 24, 16320.

[10] Rodriguez-Carvajal J. and Villain J. (2019). C.R. Physique 20, 770, https://doi.org/10.1016/j.crhy.2019.07.004.

[11] González-Platas J., Katcho N.A. & Rodriguez-Carvajal J. (2021). J.Appl.Cryst 54, 338

Keywords: magnetic structures, simulated annealing, superspace groups

I thank my colleagues of the Diffraction Group at ILL and all the users of the FullProf Suite for the help in improving the programs.

MagStREXS is a crystallographic software dedicated to the analysis of resonant elastic X-ray scattering (REXS) diffraction data for the determination of magnetic structures that is under development at beamline P09 at PETRA III (DESY).

REXS is a powerful and element specific technique to study charge, spin, and orbital ordering in solids and thin films. Different types of data can be collected in a REXS experiment, although the analysis of these data is complex. The aim of MagStREXS is to facilitate this type of analysis to the non-specialist in this technique, and also to provide tools for the preparation of these experiments.

In this talk an overview of MagStREXS will be presented, together with some magnetic structures that have already been determined with it.

Lanthanide ions play a crucial role in various research fields. Much theoretical effort, that aims understanding and enhancing magnetic anisotropy in multiferroics and molecular magnetic materials, shows that the variation of magnetisation anisotropy is accompanied by important changes of 4f-electron, spin and orbital distributions. However, the experimental determination of the shape of these distributions is a non-trivial task especially in the case of unquenched orbital moment. Here, the procedure of magnetisation density reconstruction in lanthanides with unquenched orbital moment is developed, based on the iterative entropy maximization and the site susceptibility approach. The calculation were performed by recently developed code written as part of a crystallographic CrysPy library [1].

We illustrate the possibilities of the method by the first joint magnetisation density reconstruction and susceptibility refinement of locally anisotropic lanthanide pyrochlores RTi2O7 (R=Tb, Ho, Er and Yb) [2]. An oblate asphericity of Tb3+ density and prolate these of Ho3+ and Yb3+ was revealed (fig.1). Reconstructed distributions and refined susceptibility parameters are compared with these predicted by the crystal field theory in frame of single ion anisotropy model using McPhase software [3].

1. GitHub page of CrysPy library: https://ikibalin.github.io/cryspy/
2. H. Cao et al. Phys. Rev. Lett. (2009) 103, 056402
3. M. Rotter et al J. Phys.: Conf. Ser. (2011) 325 012005.

Magnetic x-ray standing waves (MXSW) - a combination of x-ray standing waves (XSW) [1] and x-ray magnetic circular dichroism (XMCD) - is a new method for direct investigation of magnetic structure of crystals and thin films on the atomic level. In the regular XSW technique a standing wave emerging in the region where incoming and Bragg reflected waves interfere is employed to study atomic positions in element specific manner. The standing wave has a periodicity of the lattice and moves by half of its period as the sample is rocked through the reflection domain. This movement across the lattice causes modulations in the amount of emitted fluorescence - their character is characteristic for a distribution of given atomic kind. This gives - in contrary to diffraction methods - a direct, element specific structural information. In MXSW, additional magnetic sensitivity is achieved by using circularly polarised incoming wave and magnetising the sample. The normalised difference between fluorescence yields recorded for each helicity/magnetic field orientation (XMCD signal) is proportional to the distribution of magnetic atoms and their magnetic moments. This makes MXSW site, element and magnetic sensitive method.

The theoretical framework of MXSW method is based on dynamical theory of x-ray diffraction and time-dependent perturbation theory. The first is used to describe the phenomena of the scattering of x-rays by the crystal lattice and yields a form of the wavefield inside the crystal for circularly polarised incident wave. The latter provides a tool to evaluate the absorption cross-section for the considered wavefield. What is obtained finally is an angular dependence of XMCD signal, which similarly as a single fluorescence yield in XSW method, exhibits variations dependent on the distribution of magnetic atoms.

The Fig. 1 shows an exemplary, simulated MXSW signal for the magnetite crystal, (004) reflection. The insets present schematically the magnetic structure and the positions of the standing wave at the low (marked by green colour) and high (blue) angular side of the reflection domain. Iron ions in the magnetite structure are arranged in two sublattices – octahedrally (marked by blue colour) and tetrahedrally (green) coordinated ones. Since the magnetic moment on each of two sublattices is different and oriented opposite, the contribution of the sublattices to the overall XMCD signal changes depending on the position of the nodes and antinodes of the standing wave. The variations are characteristic for this arrangement of the iron atoms and their shape would be different for any other one. Therefore, the MXSW signal directly provides information about the magnetic structure.

The first experiment aiming at proving the feasibility of the method and confirming the established theory was performed at PETRA III synchrotron on the single crystal sample of Pt₃Co alloy. The measurements were conducted at the Pt L₃ absorption edge. A clear variation in XMCD signal of the magnetic origin was observed. As a next step, an experiment on magnetite is planned to show the power of the method to probe the arrangement of the magnetic ions.

[1] Zegenhagen, J., Kazimirov, A., The X-Ray standing Wave Technique: Principles and Applications (2013).

The local minima of optimized non-linear functions are a reason for ambiguity of the obtained solutions in crystal structure analysis and magnetic structure analysis (Figure 1). In this study [1], semidefinite programming relaxation (SDR) was applied for the first time to the determination of magnetic structure. Use of SDR allows us the following things (i) completing the global optimization procedure in a very short time (less than several seconds in many cases), (ii) judging whether the obtained solution is truly global one, there are multiple good candidates, or the irreducible representations considered are wrong with 100 % probability. The solid foundation is provided by the duality theorem for convex optimization problems (Figure 2).

In general, the global optimization of SDR is applicable for estimating not only magnetic moment vectors but also atomic occupancies at a fixed set of coordinates x₁, …, x_m from the absolute values of structure factors. Therefore, the method can be also used to judge if x_i is an atomic site or a void.

In many cases, this problem has a unique minimum solution. In some cases, there are a few distinct solutions, all of which can be constructed from the output of SDR. In a very few cases, the existence of multiple solutions is suggested by the SDR result. This often occurs when the atomic coordinates x₁, …, x_m in the unit cell are periodic or almost periodic as in Figure 3. If the symmetry of the atomic coordinates is considered, the existence of such multiple solutions can be largely eliminated.

As a result, SDR can provide a numerical answer to the classical problem of the uniqueness of solutions in crystal structure analysis [2]. Global optimization of the SDR method is now being implemented into Z-Rietveld software [3] distributed for users of J-PARC (Japan Proton Accelerator Research Complex).

The idea for ptychography dates back to 1969, but its realization as a practical imaging method awaited the development of iterative phase retrieval algorithms. By now, it is firmly established for nanoscale studies of materials using X rays, both in transmission mode and also using Bragg diffraction. While focusing optics greatly aid its implementation, the spatial resolution is determined not by optics but by the finest length scales from which one can measure elastic scattering. On the experimental side, the hundredfold increases in quasi-time-continuous coherent flux provided by diffraction-limited storage rings will dramatically advance what ptychography can do. On the computational side, the application of nonlinear optimization approaches has allowed one to compensate for many experimental limitations, including errors in nanopositioning as well as partial coherence, and allow one to re-think how one might acquire ptychographic data. Thus far, x-ray ptychography has been applied to millimeter-size samples in 2D, and roughly 10 micrometer size samples in 3D. How far might that go? Can one combine the advantages of X rays of high penetration power and low multiple scattering to image even larger samples? Can one carry out nanoscale imaging of cubic centimeter volumes? I outline some of the opportunities this might provide, and some of the challenges in achieving this.

Recent developments in 4th generation light sources and high-speed detectors are leading to rapid growth in data rates and data volumes, increasing the demand for automated data collection, handling/reduction/storage, and analysis processes. In combination with limited in-person access to experimental setups in times of the pandemic, portable and user-friendly tools for remote access as well as improved workflows are critical for enabling scientists from various disciplines to leverage ptychographic imaging to answer scientific questions.

With the growing popularity of ptychography, a broad range of data formats, acquisition schemes, and algorithms has been developed over the years, e.g. [1-3]. Whereas this variety has been advantageous to tackle different real-world deviations from the ideal ptychographic model such as partial incoherence [4], positioning errors [5], broad-bandwidth radiation [6], or multi-scattering [7], it also complicates the comparability and reproducibility of results. With ptychography being established as an everyday workhorse technique at many instruments around the world, it is important to find common ground and establish standards to support reliable algorithm and collaborative software development addressing the big data challenges of today and the future.

In this presentation, I will cover recent cross-facility efforts [8] to develop and promote data standards for ptychography. Furthermore, I will give an overview of ongoing software development at the Advanced Light Source in collaboration with the other DOE light sources for building data acquisition and analysis tools leveraging existing python packages with an outlook for future progress in terms of remote access and workflows.

[1] Enders B., & Thibault P., (2016). Proc Math Phys Eng Sci. 472(2196) 20160640.

[2] Wakonig K., Stadler H.-C., Odstrčil M., Tsai E. H. R., Diaz A.,Holler M.,Usov I., Raabe J., Menzel A., & Guizar-Sicairos M. (2020). Journal of Applied Crystallography, 53(2) 574-586

[3] Favre-Nicolin V., Girard G., Leake S., Carnis J., Chushkin Y., Kieffer J, Paleo P. & Richard M.-I. (2020). J. Appl. Cryst. 53, 1404-1413

[4] Thibault P. & Menzel A. (2013). Nature 494, pages 68–71

[5] Maiden A.M., Humphry M.J., Sarahan M.C., Kraus B. & Rodenburg J.M., (2012). Ultramicroscopy, 120, 64-72

[6] Enders B., Dierolf M., Cloetens P., Stockmar M., Pfeiffer F. & Thibault P., (2014). Appl. Phys. Lett. 104, 171104

[7] M Kahnt, Grote L, Brückner B., Seyrich M., Wittwer F., Koziej D. & Schroer C. G., (2021). Sci Rep 11, 1500

[8] Data Solution Task Force Pilot https://www.bnl.gov/newsroom/news.php?a=216902

This work was supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Science, under the Data Solution Task Force Pilot.

The work was partially funded through the Center for Advanced Mathematics for Energy Research Applications (CAMERA), which is jointly funded by the Advanced Scientific Computing Research (ASCR) and Basic Energy Sciences (BES) within the Department of Energy’s Office of Science, under Contract No. DE-AC02-05CH11231.

This research used resources of the National Energy Research Scientific Computing Center (NERSC), a U.S. Department of Energy Office of Science User Facility located at Lawrence Berkeley National Laboratory, operated under Contract No. DE-AC02-05CH11231.

This work was supported by the Advanced Photon Source, a US Department of Energy (DOE) Office of Science User Facility operated for the DOE Office of Science by ANL under contract No. DE-AC02-06CH11357.

This research used resources of the National Synchrotron Light Source II, a U.S. Department of Energy (DOE) Office of Science User Facility operated for the DOE Office of Science by Brookhaven National Laboratory under Contract No. DE-SC0012704.

Cement manufacturing is responsible for ~7% of the anthropogenic CO₂ emissions and hence, decreasing the CO₂ footprint, in a sustainable, safe, and cost-effective way, is a top priority. It is also key to develop more durable binders as the estimated world concrete stock is 315 Gt which currently results in ~0.3 Gt/yr of concrete demolition waste (CDW). Moreover, models under development predict a skyrocketing increase of CDW to 20–40 Gt/yr by 2100. This amount could not be easily reprocessed as aggregates for new concretes as such volumes would be more than two times the predicted need. Furthermore, concretes have very complex hierarchical microstructures. The largest components are coarse aggregates with dimensions bigger than a few centimetres and the smallest ones are amorphous components and the calcium silicate hydrate gel with nanoparticle sizes smaller than a few nanometres. To fully understand the properties of current and new cement binders and to optimize their performances, a sound description of their spatially-resolved contents is compulsory. However, there is not a tomographic technique that can cover the spatial range of heterogeneity and features of concretes and mortars. This can only be attained within a multitechnique approach overlapping the spatial scales in order to build an accurate picture of the different microstructural features. Here, we have employed far-field and near-field synchrotron X-ray ptychographic nanotomographies to gain a deeper insight into the submicrometer microstructures of Portland cement binders. With these techniques, the available fields of view range from 40 to 300 mm with a true spatial resolution (not voxel sizes) evolving between ~50 nm to ~300 nm. It is explicitly acknowledged here that other techniques like X-ray synchrotron microtomography are necessary to develop the whole picture accessing to larger fields of view (millimetres and even centimetres) albeit with poorer spatial resolution and without the quantitativeness in the reconstructed electron densities.

After framing the problems which are being tackled, we plan to present here our recent results using X-ray ptychographic nanotomography. We will start introducing the outputs obtained using far-field ptychographic nanotomography to determine phase assemblages and mass densities of amorphous components [1,2]. Then, we will move to cover the secondary porosity induced by cement conversion with temperature [3]. Finally, we will present our ongoing work with near-field ptychographic nanotomography in Portland and Belite cements with a larger field of view, capillaries from 200 to 300 mm of diameter. Between other features, Hadley grains (hollow-shells hydrated particles) have been imaged in 3D and their properties are being statistically extracted, see Figure 1. Further details will be discussed and the comparison between far-field and near-field nanotomographies will be carried out.

[1] Cuesta, A., et al. (2017) Chemistry and Mass Density of Aluminum Hydroxide Gel in Eco-Cements by Ptychographic X‑ray Computed Tomography. J. Phys. Chem. C, 121, 3044−3054.

[2] Cuesta, A., et al. (2019) Quantitative disentanglement of nanocrystalline phases in cement pastes by synchrotron ptychographic X-ray tomography. IUCrJ, 6, 473–491.

[3] Shirani, S., et al. (2020) Calcium aluminate cement conversion analysed by ptychographic nanotomography. Cem. Con. Res. 137, 106201.

Wiring diagrams of neural circuits are of central importance in delineating mechanisms of computation in the brain (1). Hereby, the individual parts of neurons - axons, dendrites and synapses - need to be densely identified in 3-dimensional volumes of neuronal tissue. This is typically achieved by volume electron microscopy (2), which requires ultrathin physical sectioning or ablation, using high precision slicing techniques or ion beams, either before or during the image acquisition process (3-6). Here, we demonstrate that cryogenic X-ray ptychographic tomography (7-9), a coherent diffractive X-ray imaging technique, can acquire 3-dimensional images of metal-stained mouse neuronal tissue with sufficient resolution to densely resolve axon bundles, boutons, dendrites and synapses without physical sectioning. We show that the tissue volume can be subsequently imaged in 3D using high-resolution, focussed ion beam-scanning electron microscopy (FIB-SEM). This suggests that metal-stained neuronal tissue can be highly radiation-stable. Using FIB-SEM as ground truth, we could show that X-ray ptychography reliably resolves 60% of the synaptic contacts in the mouse olfactory bulb external plexiform layer with an 80% precision. Ongoing improvements in synchrotron, X-ray and detector technologies (8, 10, 11) as well as further optimization of sample preparation and staining procedures (12, 13) could lead to substantial improvements in acquisition speed. Combined with laminography (14) and nano-holotomography (15, 16) it could allow for non-destructive x-ray imaging of synapses and neural circuits in increasingly larger volumes.

Catalysts are ubiquitous materials that play a major role in many areas of economy and everyday life. The development and study of catalysts is important for progress in areas such as environment, energy, and fuels, with the main goal being to improve the performance and efficiency of catalysts, especially at the industrial scale. Therefore, a thorough analysis is crucial to understand the relation between structure and performance, the deactivation process and the reasons for the loss of efficiency over the lifetime. This analysis is challenging, because technical catalysts are complex multicomponent bodies, ranging from dozens of μm to several cm, consisting of active phases, supports and additives in shaped forms suitable for their application. One of the most important conversion processes in petroleum refineries is Fluid Catalytic Cracking (FCC) in which heavy hydrocarbon fractions of crude oil are converted into valuable products such as olefins and aromatics [1]. For this process, FCC particles of 50 - 100 µm diameter are used in an up-flow reactor, where they move up, whereas the feed flows downward. During the short contact time, catalyst and feed can react. During this reaction the catalyst is partially deactivated by coke formed during the cracking and a subsequent regeneration cycle is required [2]. Thus, the characterization of the microstructure at different length scales with a spatial resolution at the nanometer length scale and a large field of view is necessary, but also the investigation of the location and chemical state of the active metallic sites in the structure.

The imaging of a large field of view with a resolution of ~ 30 - 100 nm is possible with ptychography, even for low absorbing samples. To get spatial resolved spectral information, spectro-ptychography can be used, where the measurements are repeated at different energies, including the absorption edge of a specific element. This method has already been applied for the nanoscale chemical imaging and structural analysis of a heterogeneous catalyst [3].

We investigated a FCC catalyst containing 10 wt.% Mn₂O₃ at different lifetimes by means of spectro-ptychography. Ptychographic scans are repeated at 40 different energies around the Mn K-edge. We show here the results of the experiment carried out at the beamline ID16B at ESRF, where this method has never been used before. The absorption is weak due to the low concentration of Mn and the small thickness of the samples, and hence we work with the phase contrast images. The phase contrast can be associated with the anomalous scattering factor f’, which is energy dependent in the proximity of absorption edges. The f’ spectra can be extracted by comparing the reconstructed phase contrast images recorded at different energies. The work includes the preparation of the instrumentation, the development of the algorithms for the data preparation and the python programs for the spectral analysis. We show the methodological developments necessary for the extraction of the information from the obtained measurements, starting from the phase retrieval and normalization of the phase images, to the alignment of the images of different energies, to the extraction of the f’ spectra and the search for the Mn signature in the sample.

[1] W. Letzsch,Handbook of Petroleum Processing, Springer Int. Publishing, Cham 2015, 216-316.

[2] A. Corma, et al., Catalysis Science & Technology 2017, 7, 12.

[3] M. Hirose, et al., Angew. Chem. Int. Ed. 2017, 56, 1-6.

Three-dimensional X-ray microscopy by ptychographic tomography is usually per formed by separating the steps of acquiring two-dimensional ptychographic reconstructed projection images at different projection angles and afterwards performing the three-dimensional tomographic reconstruction. Recently it has been suggested that those two separate steps can be coupled / joined together, allowing for the sharing of information between angular views during the ptychographic reconstruction step [1, 2, 3]. We performed such a coupled X-ray ptychographic tomography reconstruction for the first time on an experimental dataset, improving the achieved resolution in the process [4]. Furthermore we validated the predicted relaxation of the overlap criterion between adjacent scan positions in the tomographic plane by successively leaving out columns of recorded diffraction patterns and achieving robust reconstructions even beyond the point of no
overlap between neighboring scan points.

References:

[1] D. Gürsoy, “Direct coupling of tomography and ptychography,” Opt. Lett., vol. 42, pp. 3169–3172, Aug 2017.
[2] T. Ramos, B. E. Grønager, M. S. Andersen, and J. W. Andreasen, “Direct three-dimensional tomographic reconstruction and phase retrieval of far-field coherent diffraction patterns,” Phys. Rev. A, vol. 99, p. 023801, Feb 2019.
[3] S. Aslan, V. Nikitin, D. J. Ching, T. Bicer, S. Leyffer, and D. Gürsoy, “Joint ptycho-tomography reconstruction through alternating direction method of multipliers,” Opt. Express, vol. 27, pp. 9128–9143, Mar 2019.
[4] M. Kahnt, J. Becher, D. Brückner, Y. Fam, T. Sheppard, T. Weissenberger, F. Wittwer, J.-D. Grunwaldt, W. Schwieger, and C. G. Schroer, “Coupled ptychography and tomography algorithm improves reconstruction of experimental data,” Optica, vol. 6, pp. 1282–1289, Oct 2019.

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)

Ample

Martin Karlsen, Berrak Ozer, Peter Strickland, Simon Westrip, Nicola Ascroft, Brian McMahon, Dave Holden, Song Sang Koh and Simon J. L. Billinge

https://simbad.readthedocs.io/en/latest/

Protein conformational dynamics play an important role in numerous biological processes. Markov State Models (MSMs) provide a powerful approach to study these dynamic processes by predicting long time scale dynamics based on many short molecular dynamics (MD) simulations. To improve the efficiency of MSMs, we recently developed quasi-MSM (qMSM) that encodes the non-Markovian dynamics in a generally time-dependent memory kernel. We successfully applied qMSMs to elucidate molecular mechanisms of DNA loading into a bacterial RNA polymerase complex via flexible loading gate (consisting of the clamp and β-lobe domain), a process occurs at millisecond. Using qMSMs, we showed that the opening of β-lobe is orders of magnitude faster than that of the clamp, which depends on the structure of the Switch 2 region. Strikingly, opening of the β-lobe is sufficient geometrically to accommodate DNA loading even when the clamp is partially closed. These two observations highlight β-lobe’s critical role allowing DNA loading during initiation. In my talk, I will also present our recent results in elucidating molecular mechanisms of 1′-Ribose cyano substitution allows Remdesivir to effectively inhibit nucleotide addition of the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp).

COVID-19 pandemic is a great threat to the general and global public health and economy. The rapid development of new antiviral compounds and vaccines is needed to control the current pandemic as well as to prepare for the emergence of new variants. Among the proteins encoded by the SARS-CoV-2 genome, M^pro is one of the primary drug targets due to its essential role in maturation of the viral polyprotein. In this study, we describe a high-density acoustic droplet ejection (ADE) method for co-crystallization of M^pro-ligand complexes using only 40 nL M^pro solution. Also, we will briefly describe crystallographic data from crystals obtained using ADE and other methods as evidence that three clinically approved anti hepatitis C virus (HCV) drugs are capable of covalent binding to the M^pro Cys145 catalytic residue in the active site (Fig. 1). Activities of the National Virtual Biotechnology Laboratory (NVBL) for the design and development of new antiviral inhibitors for SARS-CoV-2 is briefly discussed.

The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the causative agent of COVID-19 illness is responsible for more than half a million deaths in the United States alone. The SARS-CoV-2 nsp16/nsp10 enzyme complex modifies the 2’-OH of the first transcribed nucleotide (N₁ base) of the viral mRNA by covalently attaching a methyl group to it. This single RNA modification event converts the status of the mRNA cap from Cap-0 (^m7GpppA) to Cap-1(^m7GpppAm) and helps the virus evade immune surveillance in the host cell. Here, we report three high-resolution crystal structures of nsp16/nsp10 heterodimer representing substrate (Cap-0)-bound state, and pre- and post-release states of the RNA product (Cap-1). The binding of Cap-0 induces large conformational changes. This ‘induced fit’ model provides new mechanistic insights into the 2’-O methylation of the viral mRNA cap. We reveal the structural basis for the RNA specificity of nsp16/nsp10. We also discover an alternative ligand-binding site unique to SARS-CoV-2 [1]. We also observe overall widening of the enzyme upon product formation, and an inward twisting motion in the substrate-binding region upon product release. These changes reset the enzyme for the next round of catalysis, and may be the structural basis of dissociation nsp10 from nsp16. The structures also identify a unique binding mode of a divalent metal ion in nsp16, which aligns the first two bases of the viral RNA in the catalytic pocket for efficient Cap-1 formation. Using LC/MS-based intact mass analysis, we show dramatic perturbations in Cap-1 formation by an emerging clinical variant of SARS-CoV-2, previous SARS-CoV outbreak strain, and their altered sensitivity to divalent metal ions [2]. Such reliance and preference for metals also suggests that an imbalance in cellular metal concentrations could differentially alter the RNA capping and thus, host innate immune response to infections by various CoVs. Altogether, our work provides a revised framework from which new therapeutic modalities may be designed for the treatment of COVID-19 and emerging coronavirus illnesses.

SARS-CoV-2 is a novel coronavirus and causative agent of the zoonotic disease Covid-19, which has been responsible for over 3 million deaths globally. Although the rapid development of several highly efficacious vaccines is proving effective in reducing the spread and severity of the disease, the development of novel, low cost and globally available anti-viral therapeutics remains an essential goal, both for this pandemic and for future outbreaks of related coronaviruses.

To identify starting points for such therapeutics, the XChem team at Diamond Light Source, in collaboration with various international colleagues, have performed large crystallographic fragment screens against 7 key SARS-CoV-2 proteins including the Main protease, the Nsp3 macrodomain and the helicase Nsp13 [1-3]. The expeditious collection and dissemination of data from these screens has been enabled by the well-established platform at Diamond and by the implementation of various new tools in the XChem pipeline.

This work has identified numerous starting points for the development of more potent inhibitors as exemplified by the ongoing work from the open science drug discovery project, the Covid Moonshot [4]. By merging fragment hits from the initial XChem screen and harnessing crowdsourced medicinal chemistry designs from the global community we have been able to rapidly develop potent inhibitors of the Main protease that exhibit promising antiviral activity.

[1] Douangamath, A., et al., Nature Communications, 11, 2020.

[2] Schuller, M., et al., Science Advances, 7, 2021.

[3] Newman, J., et al., BioRxiv, 2021.

[4] The COVID Moonshot Consortium, BioRxiv, 2021.

Human coronaviruses such as SARS-CoV, MERS and SARS-CoV-2 continue to emerge as significant threats to public health. Other human coronaviruses such as NL63, HKU1, 229E and OC43 continue to persist in the population but are significantly less deadly. Since the SARS-CoV epidemic emerged in 2003, we have worked to develop small-molecule inhibitors of coronavirus 3C-like protease (3CLpro, also known as main protease or Mpro) and the papain-like protease (PLP or PLpro). Initially, we focused on the proteases from SARS and then on NL63 and MERS. However, the differences in inhibitory potencies of our compounds and the taxonomic distance of the alpha and beta coronavirus genera taught us that approach of studying one virus at a time was too slow and provided to little molecular information to inhibit multiple coronaviruses. Moreover, it was not allowing us to predict how to inhibit emerging coronavirus pathogens. In the interest of pandemic preparedness, we are now taking what we call a taxonomically-driven approach to the structure-based design of coronavirus protease inhibitors. We targeted 12 different 3CLpros from the alpha-, beta- and gamma-coronavirus genera with a series of 50 compounds that we designed and synthesized using the Automated Synthesis and Purification platform at Eli Lilly. We identified inhibitor templates that potently inhibit the enzymes from the alpha and beta genera but not the gamma genus. To ascertain the structural basis of the selectivity, we utilized LS-CAT and LRL-CAT beamlines at the APS and performed a sparse-matrix sampling approach and determined multiple X-ray structures of 3CLpro from the different coronavirus genera in complex with different inhibitors. We identified precise structural regions that define inhibitor selectivity for different inhibitor scaffolds and we are now extending this approach to PLpro. We have been able to design and synthesize over 350 additional compounds against SARS-CoV-2 3CLpro. These compounds include potent non-covalent inhibitors, reversible-covalent and covalent inhibitors with low nanomolar to picomolar potency including inhibitors with broad-spectrum, i.e. pancoronavirus, activity against 12 different alpha, beta and gamma coronavirus.

This work was supported in part by funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under Contract No. HHSN272201700060C.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) papain-like protease (PLpro) is essential for the virus replication and covers multiple functions (1,2). In this context, PLpro is an interesting drug target to identify compounds that inhibit the activity and can further be optimized towards drugs to cure Covid-19 in the future. Beside the cysteine-protease activity, PLpro has the additional and vital function of removing ubiquitin and ISG15 (Interferon-stimulated gene 15) from host-cell proteins to aid coronaviruses in their evasion of the host innate immune responses. Therefore, in terms of drug discovery investigations PLpro is thus an excellent drug target allowing a two-fold strategy, to identify compounds that inhibit viral replication and strengthen the immune response of the host in parallel. To establish a framework allowing an efficient and high throughput screening of compounds to identify inhibitors, we first expressed, purified and crystallized PLpro (Fig.1), determined and refined the native crystal structure to atomic resolution of 1.42 Å (Fig.2, pdb code: 7NFV).

Further, we initiated screening via co-crystallization utilizing a library of 2.500 selected natural compounds, obtained from ICCBS Karachi, and identified first potential inhibitors binding to a site that has been previously shown to bind to the ISG15 molecule, refined structures were deposited with pdb codes: 7OFS, 7OFT, 7OFU. Comparing the PLpro-ligand complex structures with the PLpro-ISG15 complex crystal structure (pdb code: 6XAA) clearly shows that several regions of the Ubiquitin fold domain move dynamically, showing functional flexibility to accommodate the ligands (Fig. 3). Corresponding structural data and details, as well as on-going structural efforts to identify new antiviral compounds to combat the coronavirus spread will be presented.

Small Angle Neutron Scattering is a low-resolution technique enabling to probe the solution structure of individual biomacromolecules possibly in complex with its partners. In particular, concerning membrane proteins, the membrane-like environment can be made invisible in order to see only the protein. Here, we combined SANS with X-ray crystallography, cryoEM, H/D exchange coupled with mass spectrometry and limited proteolysis to reveal the flexibility and ligand-induced conformational changes of the multidrug ABC transporter BmrA.

Limited proteolysis revealed an important flexibility of BmrA WT in most steps of its catalytic cycle. Cryo-EM provided high-resolution of the closed conformation by analysis of an artificially monodisperse sample, and X-ray crystallography data enabled to build homology models of other conformations, which constituted the starting point of SANS analysis. H/D X-MS pinpointed the flexible part along the transporter sequence and SANS revealed the extent of this flexibility.

Together, these techniques enable us to describe the ABC transporter cycle in term of successive conformational equilibria, a much more realistic and accurate vision of this biological process [1].

Figure 1. A: Main steps of the enzymatic cycle of ABC transporters (from [2]); B: Structural definition of these steps in solution by sequential conformational equilibria [1].

[1] Javed et al. in preparation

[2] Wannes Dermauw, Thomas Van Leeuwen, The ABC gene family in arthropods: Comparative genomics and role in insecticide transport and resistance, Insect Biochemistry and Molecular Biology, Volume 45, 2014

Molecular dynamics (MD) is crucially important for protein functions. MD simulation is a powerful computational tool for investigating molecular dynamics of proteins in atom detail. However, due to the time-scale limitation of MD simulation, conformational samplings in MD simulation are occasionally insufficient. Thus, to validate simulation structures, the comparison of the simulation structures with experimental results is useful.

Small-angle x-ray scattering (SAXS) experiments is a powerful method to measure protein structures in solution. Although the resolution of SAXS is limited to low because of the orientational and conformational averaging, the information of protein conformations in solution can be obtained. Therefore, the comparison of simulation results with SAXS data serves to obtain the protein solution structures consistent with experiments.

We have developed a hybrid method of MD simulations and SAXS (MD-SAXS) [1­–3]. The first example of MD-SAXS applications was EcoO109I, a type II restriction endonuclease [1]. The enzyme was revealed to be substantially flexible, and the intrinsic flexibility was found to be closely related to the structural changes upon DNA binding.

Ion effects on SAXS data were investigated using MD-SAXS [2]. At a series of ion concentrations from 0 to 1 M, the MD-SAXS analysis for lysozyme was performed. The SAXS excess intensities were strongly dependent on ion concentrations. Based on the MD-SAXS, we developed a fast method to handle ion effects.

MD-SAXS was also applied to the drug target protein [4]. Vitamin D receptor (VDR) is a member of the nuclear receptor family, and functions as the control of the expression of genes through Vitamin D binding. The VDR ligand binding domain (LBD) is expected to undergo conformational changes upon agonist or antagonist binding. However, the crystal structures of VDR-LBD share a similar structure even with bound agonist or antagonist. The crystal structure of VDR-LBD in the ligand-free state has not been determined. The SAXS experiments suggest that both the ligand-free and antagonist-bound structures in solution are different from the crystal structure. Thus, the MD-SAXS analysis was performed to elucidate the solution structures of VDR-LBD in both the states. In the ligand-free and antagonist-bound state, the obtained solution structures were in good agreement with their SAXS data. Their structural features were consistent with the function of VDR.

Sampling capability of all-atom MD simulations is occasionally insufficient for very flexible and large molecules. To overcome the limitation, we developed a hybrid method of a coarse-grained MD simulations and SAXS (CG-MD-SAXS) [5]. Even in the coarse-grained models (e.g., Cα only), SAXS data were accurately reproduced from the structure models. CG-MD-SAXS was applied to the three types of nucleosomes (canonical, CENP-A, and H2A.B nucleosomes), and revealed the substantial difference in the dynamics of DNA around histones.

[1] Oroguchi, T., Hashimoto, H., Shimizu, T., Sato, M., Ikeguchi, M. (2009) Biophys. J. 96, 2808.

[2] Oroguchi, T., Ikeguchi, M. (2011) J. Chem. Phys. 134, 025102.

[3] Oroguchi, T., Ikeguchi, M. (2012) Chem. Phys. Lett. 541, 117.

[4] Anami, Y., Shimizu, N., Ekimoto, T., Egawa, D., Itoh, T., Ikeguchi, M., Yamamoto, K. (2016) J. Med. Chem. 59, 7888.

[5] Ekimoto, T., Kokabu, Y., Oroguchi, T., Ikeguchi, M. (2019) Biophys. Physicobiol. 16, 377.

: The RNA transcription complex (RTC) from the virus, SARS-CoV-2, is responsible for recognizing and processing RNA for two principal purposes. The RTC copies viral RNA for propagation into new virus and for ribosomal transcription of viral proteins. To accomplish these activities the RTC mechanism must also conform to a large number of imperatives including RNA over DNA base recognition, base pairing, distinguishing viral and host RNA, production of mRNA that conforms to host ribosome conventions, interface with error checking machinery and evading host immune responses. In addition, the RTC will discontinuously transcribe specific sections of viral RNA to amplify certain proteins over others. Central to SARS-CoV-2 viability, the RTC is therefore dynamic and sophisticated. We have conducted a systematic structural investigation of three components that make up the RTC: Nsp7, Nsp8 and Nsp12 (also known as RNA dependent RNA polymerase (RdRp)). We have solved high resolution crystal structures of the Nsp7/8 complex providing insight into the interaction between the proteins. We have used small angle X-ray and neutron solution scattering (SAXS and SANS) on each component individually as pairs and higher order complexes and with and without RNA. Using size exclusion chromatography and multi-angle light scattering coupled SAXS (SEC-MALS-SAXS) we defined which combination of components form transient or stable complexes. We used contrast matching neutron scattering to mask specific complex forming components to test whether components change conformation upon complexation. Altogether, we find that individual Nsp7, Nsp8 and Nsp12 structures vary based on whether other proteins in their complex are present. Combining our crystal structure, atomic coordinates reported elsewhere, SAXS, SANS and other biophysical techniques we provide greater insight into the RTC assembly, mechanism and potential avenues for disruption of the complex and its functions.

Correct formation of disulfide bonds is critical to the folding of a wide variety of proteins. Bacterial virulence factors are one class of proteins containing disulfide bonds, thus, an approach to disarm virulent bacterial might involve shutting down the machinery involved in the formation of disulfide bonds. The suppressor of copper sensitivity (Scs) proteins form part of the disulfide bond forming machinery in bacteria, and it is hoped that determining the structure of molecules such as this may lead to the development of new classes of antibiotics. There are four Scs proteins (ScsA, B, C and D) present in numerous Gram-negative bacteria, and few have been structurally characterised. In this work we show that the ScsC protein from Proteus mirabilis is trimeric and flexible, where the high level of flexibility is afforded by a glutamine rich motif. We also show that the protein interacts with ScsB and that this interaction rigidifies the ScsC protein.

Despite their importance in function, the conformational states and changes of proteins are often poorly understood mainly because of the lack of an efficient tool. MurD, a 47-kDa three-domain protein enzyme responsible for peptidoglycan biosynthesis, is one of those proteins whose conformational states and changes during its catalytic cycle are not well understood. The previous crystallographic studies have identified two major conformational states of MurD, open and closed conformations, in which the domain 3 has distinct orientations with respect to the other two domains. The conformational difference between the two crystal structures suggested that MurD can undergo drastic conformational changes in solution. However, the details about the conformational states and changes of MurD in solution coupled with the binding with the ligands or the inhibitors remained to be elucidated.

In our study, we exploited multiple biophysical methods including nuclear magnetic resonance (NMR), electron paramagnetic resonance (EPR), small-angle X-ray scattering (SAXS), and molecular dynamics (MD) simulation to demonstrate evaluation of the conformational states and distribution of MurD. We exploited paramagnetic lanthanide ions that can be attached to the specific position(s) on the protein by the use of the lanthanide tags [1]. In NMR, the effects of the paramagnetic lanthanide ions are observed as pseudo-contact shifts (PCSs) that can provide long-range (< ~40 Å) distance and angular information of each of the observed nuclei in the protein [1]. The lanthanide ion was fixed on the domain 2 of MurD and PCSs were observed from the resonances derived from the domain 3. Analysis of PCSs achieved estimation of conformational states of MurD in solution and detection of the conformational changes of MurD induced by its ligands and inhibitors [2]. The paramagnetic lanthanide ions, especially gadolinium ions, can be exploited by EPR and double electron–electron resonance (DEER) measurement that provides inter-gadolinium distance and population (distance distribution) [1]. The distance distributions obtained from DEER measurement were consistent with the information derived from PCS-NMR, SAXS, and MD simulation.

Our study highlights several biophysical methods to investigate the overall conformational states of a multi-domain protein. The integrated use of these methods can be an efficient strategy to evaluate the conformational states and distribution of proteins in solution.

[1] Saio, T., Ishimori, K. (2020) Biochim. Biophys. Acta. Gen. Subj. 1864.

[2] Saio, T., Ogura, K., Kumeta, H., Kobashigawa, Y., Shimizu, K., Yokochi, M., Kodama, K., Yamaguchi, H., Tsujishita, H., Inagaki, F. (2015) Sci. Rep. 5, 16685.

Small-angle X-ray scattering (SAXS) experiments provide an estimation of biological macromolecule geometry on the level of domain structure. The reliability of structural inference drawn from SAXS data is dependent on the accurate measurement as well as the proper post-processing procedure. The methods improving raw data quality and gaining more information are widely explored. Among those innovations, size-exclusion chromatography small-angle X-ray solution scattering (SEC-SAXS) has become a standard method for modern bio-SAXS synchrotron light sources (Ryan et al. 2018; Brennich et al. 2016; Blanchet et al. 2015). However, the principle of data post-processing for SEC-SAXS remains rather unclear. This includes background correction and averaging of the raw data. Several statistical tools have been developed to assess solution SAXS data quality (Rambo and Tainer 2013; Franke et al. 2015). These are mostly useful for “rejecting” significantly different data points or data frames, based on the assumption that the rest of the data are close to the “truth”. But this can lead to a situation where mediocre data, for example data contaminated with radiation damage, are not correctable or simply cannot be evaluated before any interpretation is done.

To alleviate this problem, an objective metric, correction-state score (CSS) is proposed. CSS can be used to both verify the data quality and identify the optimal data correction procedure for post-processing of SEC-SAXS data. CSS can be represented as a numerical likelihood with a scale of 0 to 1. Using this objective score it is possible to quantitatively assess the “goodness” or appropriateness of a background correction for SEC-SAXS data. Under the guidance of CSS, the metadata recorded during a SEC-SAXS experiment can be used to maximise the fidelity of the post-processing as well as reduce the ambiguity in further data interpretation.

References
Blanchet, C.E., Spilotros, A., Schwemmer, F., et al. 2015. Versatile sample environments and automation for biological solution X-ray scattering experiments at the P12 beamline (PETRA III, DESY). Journal of Applied Crystallography 48(Pt 2), pp. 431–443.
Brennich, M.E., Kieffer, J., Bonamis, G., et al. 2016. Online data analysis at the ESRF bioSAXS beamline, BM29. Journal of Applied Crystallography 49(1), pp. 203–212.
Franke, D., Jeffries, C.M. and Svergun, D.I. 2015. Correlation Map, a goodness-of-fit test for one-dimensional X-ray scattering spectra. Nature Methods 12(5), pp. 419–422.
Rambo, R.P. and Tainer, J.A. 2013. Accurate assessment of mass, models and resolution by small-angle scattering. Nature 496(7446), pp. 477–481.
Ryan, T.M., Trewhella, J., Murphy, J.M., et al. 2018. An optimized SEC-SAXS system enabling high X-ray dose for rapid SAXS assessment with correlated UV measurements for biomolecular structure analysis. Journal of Applied Crystallography 51(1), pp. 97–111.

Water plays a critical role in many steps of the pharmaceutical development as this small molecule has the ability to interact with compounds in numerous ways and may therefore significantly affect manufacturing processes and finally the quality of (pharmaceutical) products. The formation of a molecular compound (hydrate), where water becomes a part of the crystal lattice, is mostly accompanied with a significant change in the solid-state properties, and therefore this type of interaction must be seen as critical [1]. Hydrate formation itself is a widespread phenomenon and is known to occur for at least one third of drug molecules [2,3], and this trend is increasing significantly for new drug substances. Nevertheless, we are still not able to predict hydrates, their stability and dehydration mechanisms based on the molecular diagram only.

This talk will emphasise on the efforts that are sometimes required to identify solid forms of complex hydrate forming systems. Examples from our research will be used to illustrate how the combination of a variety of experimental techniques, covering temperature- and moisture-dependent stability, and computational modelling allows to generate sufficient kinetic, thermodynamic and structural information to understand hydrate formation and its impacts on relevant physicochemical properties.

The solid form landscape of brucine sulphate was elucidated, resulting in three hydrate forms and amorphous brucine sulphate. HyA was produced from water and the other two by dehydration starting from HyA. Removal of the essential water molecules stabilising the hydrate structures causes a collapse to the amorphous state [4]. Eight hydrate forms were verified for the related compound, strychnine sulphate. Three of the hydrates were found to be stable at ambient conditions. The other five hydrates are only observable at low(est) relative humidity (RH) levels at room temperature. Some of the hydrates can only exist within a very narrow RH range and are therefore regarded as intermediate phases. The specific moisture and temperature conditions of none of the applied drying conditions yielded a crystalline water-free form, highlighting the essential role of water molecules for the formation and stability of crystalline strychnine sulphate [5].

Despite their structural similarity, marked differences in the formation of solid forms are seen for brucine and strychnine. One anhydrous form and 1,4-dioxane solvates were crystallized for strychnine, whereas two non-solvated polymorphs, four hydrates, an isostructural dehydrate, twelve solvates and two hetero-solvates are known to exist for brucine [6-8]. One of the brucine hydrates shows a non-stoichiometric (de)hydration behaviour, one collapses to an amorphous phase, and the third one to the polymorph which is stable at room temperature. Interestingly, each of the three hydrates may become the most stable form depending on temperature and water activity.

To conclude, this study demonstrates the importance of applying complimentary analytical techniques and appropriate approaches for understanding the stability ranges and transition behaviour between the solid forms of compounds with multiple hydrates.

[1] Khankari, R. K. & Grant, D. J. W. (1995). Thermochim. Acta, 248, 61.

[2] Stahly, G. P. (2007). Cryst. Growth Des, 7, 1007.

[3] Reutzel-Edens, S. M., Braun D. E. & Newman A. W. (2019). Polymorphism in the Pharmaceutical Industry: Solid Form and Drug Development, edited by R. Hilfiker & M. Von Raumer: Wiley-VCH, pp. 159-188.

[4] Braun, D. E. (2020). CrystEngComm, 22, 7204.

[5] Braun, D. E., Gelbrich, T., Kahlenberg, V. & Griesser, U. J. (2020). Cryst. Growth Des., 20, 6069.

[6] Braun, D. E. and Griesser, U. J. (2016). Cryst. Growth Des., 16, 6405.

[7] Braun, D. E. and Griesser, U. J. (2016). Cryst. Growth Des., 16, 6111.

[8] Watabe, T., Kobayashi, K., Hisaki, I., Tohnai, N. & Miyata, M.Bull. (2007). Chem. Soc. Jpn., 80, 464.

We have recently studied a diarylamine compound, tolfenamic acid (TFA), and examined its solution chemistry, crystallization kinetics, and molecular interactions. The polymorphic system typically crystalizes as From I or Form II, or both concurrently, with Form I being the most stable at room temperature. Both polymorphs are composed of hydrogen-bonded, carboxyl homodimers as the supramolecular synthon in their respective crystal structures. One interesting kinetic phenomenon that we experimentally discovered was an intermediate or transitional retraction of the mass composition of Form I in crystallized samples over the course of concomitant crystallization. The composition retraction bears two characteristic attributes, the retraction depth and the onset fraction. The former quantifies the maximal extent to which the Form I composition retracts prior to elevation, whereas the later attribute characterizes the initially measured Form I composition. Conversely, during solvent-mediated phase transformation, the mass composition of Form I monotonically increases and only Form II nucleates initially. We further learned through population balance simulations that this characteristically kinetic phenomenon is a sufficient condition indictor of concomitant crystallization of polymorphic systems. Interestingly, when experimental observation is made at a later time after the kinetic retraction, it seems unlikely to kinetically differentiate the two crystallization pathways.

In recent years, considerable investment has been made towards advancing pharmaceutical development and manufacturing through Digital Design approaches.¹ Industrial scientists are moving away from time and resource intensive screening techniques to more rapid in silico methods to inform key decisions throughout the drug manufacturing process.

The links between solid form and structural properties are well developed,² but our understanding of the relationship between particle and surface properties and downstream manufacturability of an Active Pharmaceutical Ingredient (API) are considerably less established. By providing new methods for visualising and describing these key attributes, we can gain a deeper insight into properties that contribute to the way particles flow or how they form tablets under compression.

Since describing these approaches and their application to the drug lamotrigine,³ we have continued to develop and refine the way that we can describe a particle and its properties. This presentation will discuss those advances and the challenges that lie ahead.

References

1. www.addopt.org

2. P.T.A Galek et al., CrystEngComm 2012, 14, 2391–2403

3. M.J. Bryant et al., Cryst. Growth Des. 2019, 19, 9, 5258–5266

Pharmaceutical industries have witnessed an increasing trend towards poor aqueous solubility and according to a report 75% of the marketed drugs belong to BCS class II or IV. Efforts to improve aqueous solubility by modifying the chemical structures are carried out during lead optimization in early drug discovery stage while trying to maintain desired potency and ADME properties. However, experimental aqueous solubility assays available during lead optimization are prone to overestimate solubility to a variable extent. This overprediction of aqueous solubility can result in overly optimistic view of developability with negative implications for compounds differentiation and candidate selection for development. On the other hand, failure to improve aqueous solubility could lead to inadequate evaluation of safety and efficacy profile of candidates and resource intensive formulation approaches. With the advancement of computations as well as due to immense pressure to shorten development timelines, in-silico approaches to predict aqueous thermodynamic solubility are of greater importance. In this presentation a physics-based ensemble modeling approach consisting of high-fidelity cloud-based crystal structure prediction (CSP) methodology optimized for computational cost and a novel free energy perturbation (FEP+) workflow is discussed to predict aqueous thermodynamic crystalline solubility of chemically structurally related compounds during lead optimization stage using just the 2-D structure as an input.

The various aspects of drug design or catalysis is compartmentalized within defined research fields, i.e. bioactivity testing versus pure synthetic chemistry; homogeneous versus heterogeneous catalysis. These are independent and often non-interactive specialities which have developed along parallel pathways with a common objective. The world economic drive towards the 4^th industrial revolution captures the idea of the confluence of new technologies and their cumulative impact on our world. Hence the ability to merge, bridge and remove boundaries will result in the establishment of interoperable research.

Drug design, particularly the development of target specific radiopharmaceuticals which involves the selective receptor binding of a radioactive organometallic complex to a possible disease site involves multiple facets. Simple manipulation of the ligand system bound to the metal centre can significantly alter parameters such as steric and electronic character, chirality, stability, biological and hydro/lipophilicity properties. Our organometallic research utilising the group 7 transition metal triad of manganese, technetium and rhenium for nuclear medical imaging and therapeutic agents, includes the interactions with proteins using protein crystallography. This provides valuable structural information in a similar vein to fragment based drug discovery (FBDD). The domain of chemical versus macromolecular crystallography has resulted in multiple discipline variations, such as incompatible software, data formatting and terminology. A key challenge which hinders research advancement is the lack of interoperability between chemical and biological crystallographic data.

This perspective will highlight the opportunities of harvesting both small molecule and macromolecular structural data, the joint usage of the CSD and PDB databases, as well as the advantages of software which can convert organometallic small molecule structural data for use in protein refinement software. This multidiscipline approach to radiopharmaceutical development will include kinetic reactivity studies highlighting how subtle structural changes can significantly affect chemical reactivity and hence the protein coordination in macromolecular structures. Trends similarly witnessed in catalysis research.

Multiple scattering in 3D electron diffraction (3D ED) experiments is responsible for deviations of diffracted intensities from intensities expected from kinematical diffraction theory [1]. Though this is usually considered a disturbing factor in routine structure determinations, these deviations also contain valuable information on the absolute structure [2]. Analysing 3D ED measurements from different laboratories around the world, we demonstrate that the absolute structure of single submicrometric crystals can be reliably and easily determined in a routine way if dynamical diffraction effects are incorporated in the refinement of the structure model.

We investigated and reinvestigated data sets of non-centrosymmetric samples recorded with beam-precession (precession-assisted 3D ED) and with continuous-rotation 3D ED (IEDT, MicroED, cRED) to determine the absolute structure, which directly determines the absolute configuration of chiral molecules in the unit cell. Dynamical effects are very sensitive to the absolute structure due to the interference of multiple beams contributing to each reflection [3]. In comparison to X-ray diffraction-based methods, the requirements for a successful determination of the absolute structure are strongly reduced. We demonstrate that with a completeness as low as 25% (Figure 1), a limited resolution d_min > 1 Šand only a preliminary structure model the correct chirality can still be identified. The low requirements also allow significantly reducing the number of refinement parameters so that the computationally demanding calculations applying dynamical diffraction theory are only a matter of minutes even for unit cells with a volume of several thousand ų. The determination is based on a simple comparison of residual factors (R_obs and wR_all) of the refined, inversion-related models (Figure 1). With this approach, the routine determination of the chirality of molecules in submicrometric crystals is ready to be implemented in any laboratory with access to 3D electron diffraction measurements. Considering ongoing developments, improvements and increasing level of automatization of data acquisition and analysis [1], we believe that especially the pharmaceutical industry will strongly benefit from the presented approach.

[1] Gemmi, M., Mugnaioli, E., Gorelik, T., Kolb, U., et al. (2019). ACS Cent. Sci. 5, 1315−1329.

[2] Brázda, P., Palatinus, L., Babor, M. (2019). Science. 364, 667−669

[3] Spence, J.C.H., Zuo, J.M., O'Keeffe, M., Marthinsen, K., Hoier, R. (1994). Acta. Cryst. A50, 647−650

Support by the Czech Science Foundation (project number 21-05926X), and by Operational Programme Research, Development and Education financed by European Structural and Investment Funds and the Czech Ministry of Education, Youth and Sports (Project No. SOLID21 CZ.02.1.01/0.0/0.0/16_019/0000760) is highly appreciated.

Propertios of halogen (X), chalcogen (E) and pnictogen (Pn) bonds can be modulated by changing (i) the nature of the X, E and Pn, (ii) the chemical environment of the X, E and Pn, and (iii) properties of the electron donor. Apart from small molecular complexes, this has been demonstrated in protein-ligand complexes, e.g. on a series of aldose reductase inhibitors. The counterintuitive ability of heteroboranes to form strong σ-hole interactions was found and attributed to the multicenter bonding. It breaks the classical electronegativity concept and results highly positive σ-holes on heterovetices that are incorporated into the skeleton via multicenter type of bonding. X, E and Pn elements in neutral heteroboranes can thus have highly positive σ-holes that are responsible for strong σ-hole interactions. The E···π, X···π, Pn···π and Pn···H-B types of σ-hole interactions of heteroboranes have been observed in the corresponding crystal packings. σ-Hole interactions can be used for designing protein-ligand interactions as well as for crystal engineering.

Materials which switch their optical spectroscopic properties (i.e., color, fluorescence) upon physical external stimulation (i.e., pressure, temperature) arouse much interest owing to their potential applications in fields as varied as sensing, construction, recording, display technologies or rewritable paper [1]. In the quest for new organic stimuli responsive materials, the 2,1,3-benzothiadiazole moiety (BTD) have emerged as a promising building block, since the absorption and emission properties of this moiety is strongly influenced by its external environment. In the last few years several BTD-based chromogenic and fluorogenic materials have been reported, but although there are some recent exceptions, in most examples crystalline-to-amorphous transitions are in the origin of this behaviour. This fact prevents an in-depth study of the mechanism behind this process and limits the rational development of new chromophores with predesigned properties.

Herein we present a variety of BTD-derivatives, which crystallizes in different polymorphs with layer-like organization, exhibit distinct light emitting properties under UV illumination and can be readily interconverted by means of external stimuli [2, 3]. Through a joined crystallographic, spectroscopical and theoretical approach we have been able to unravel the origin of the polymorphic transformation and fluorogenic behavior.

In this communication we will discuss interesting design principles, to obtain novel BTD stimuli-responsive organic materials that we have been able to establish as a result of this study. A special emphasis will be placed on the role of “2S–2N” square synthon [4] in the supramolecular arrangement and switchable light emission properties of BTD derivatives.

[1] Roy, B.; Reddy, M. C.; Hazra, P. (2018) Chem. Sci. 9, 3592 [2] Echeverri, M.; Ruiz, C.; Gámez-Valenzuela, S.; Martín, I.; Delgado, M. C. R.; Gutiérrez-Puebla, E.; Monge, M. Á.; Aguirre-Díaz, L. M. & Gómez-Lor, B. (2020) J. Am. Chem. Soc. 142, 17147. [3] Echeverri, M.; Ruiz, C.; Gámez-Valenzuela, S.; Alonso-Navarro, M.; Gutierrez-Puebla, E.; Serrano, J. L.; Ruiz Delgado, M. C. & Gómez-Lor, B. (2020) ACS Appl. Mater. Interfaces 12, 10929. [4] Ams, M. R.; Trapp, N.; Schwab, A.; Milić, J. V.; Diederich, F. (2019) Chem. A Eur. J 25, 323.

In the pharmaceutical area, the screening of multicomponent forms of a drug is a well-known strategy to assess new crystalline forms with improved physicochemical properties, such as solubility, dissolution, absorption, and others [1-3]. Among the possible multicomponent forms, co-crystals, salts, and solvates are obtained from the inclusion of other suitable molecules (co-formers) within the target molecule‘s crystalline structure. The process to obtain multicomponent crystalline forms of a drug could be an expensive and long-term process, since there is an infinity of possible co-former molecules, in addition to the large number of crystallization techniques that can be used [4]. Thus, it is necessary a strategy to help in the screening of new multicomponent forms of a target molecule through the rationalization of co-former selection, associated with lower consumption of materials and other costs, such as the final disposal of toxic waste. Aiming this, it is proposed a new methodology to optimize and to rationalize the co-former selection using knowledge-based supramolecular chemistry [5]. This new methodology aims to predict the formation of a multicomponent form through the evaluation of the molecular complementarity and the possible intermolecular interactions between the target molecule and the co-former through the use of three statistical tools developed by the Cambridge Crystallographic Data Centre (CCDC) [6]. The SFIMP (Statistical Analysis of Frequency of Interaction for Multicomponent Prediction) method [7] was developed based on the optimization of three CCDC tools – Molecular Complementarity (MC), Coordination Value likelihood calculation (CV), and H-Bond Propensity (HBP) [4, 8-10] – to perform a multicomponent analysis and to allow the combination of their results to obtain a single multicomponent score. Nevirapine (NVP), an antiretroviral drug that exhibits low-aqueous solubility, was used as the target molecule in this study. A bunch of 470 possible co-former molecules was evaluated and the multicomponent score obtained for each one was used to rank these molecules according to the possibility of forming a NVP multicomponent. The SFIMP method was validated through an experimental screening of new multicomponent forms of NVP. The results obtained from the prediction were used in the experimental screening and it enabled the obtention of four new co-crystals of NVP with benzoic acid, 3-hydroxybenzoic acid, 4-hydroxybenzoic acid, and 2,5-dihydroxybenzoic acid [5, 11]. The crystalline structures of these new co-crystals were characterized through single-crystal and powder X-ray diffraction, and differential scanning calorimetry. The SFIMP method shows improvements compared to what is currently available in the CSD system for the analysis and prediction of multicomponent forms. Besides, the results show this methodology as a promising strategy to evaluate the possibility of multicomponent formation in new systems.

The distribution of the electron density at the outer regions of bonded atoms is anisotropic. This feature was first proposed for explaining the noncovalent interactions formed by bonded atoms early nineteen nineties [1] and now it is successfully used for rationalizing interactions of elements of all groups of the p block of the periodic table [2]. This mindset began to be extended to d block elements four years ago, being first applied to elements of group 11, then to elements of groups 10 and 12 [3]. For instance, some theoretical studies and experimental results have shown that gold can behave as an effective acceptor of electron density in some of its derivatives, e.g., attractive interactions, named coinage bond (CiB) [3], can be formed between donors of electron density and regions of most positive electrostatic potential at the outer surface of gold nanoparticles and halides.

In this communication we describe that gold can function as acceptor of electron density not only in neutral species, as mentioned above, but also in negatively charged species. It will be proven that the Au(III)∙∙∙nucleophile supramolecular synthon is quite robust and effectively controls the packing of ionic crystals. This synthon may complement the opportunities offered by the aurophilic interactions which are now dominating the interactional landscape of gold. Specifically, we report single crystal structures wherein AuCl₄ˉ anions act as self-complementary tectons, chlorine and gold atoms functioning as donors and acceptors of electron density, respectively. Au and Cl atoms of different units form short Au∙∙∙Cl contacts and construct supramolecular anionic polymers (Figure) wherein gold forms a second CiB with a lone pair possessing atom (the oxygen of an ester group). The electrophilic role of gold and the attractive nature of Au∙∙∙Cl/O interactions will be proven by some modelling. A survey of the Cambridge Structural Database (CSD) will be reported suggesting that this behaviour is quite general. Indeed, a non-minor fraction of CSD structures containing the AuCl₄ˉ anion show the presence of the Au∙∙∙nucleophile supramolecular synthon and the same holds for structures containing the AuBr₄ˉ and Au(CN)₄ˉ anions.

Crystal engineering requires precise insight into intermolecular interactions, which results in the crystal symmetry enabling the emergence of desired physical properties [1, 2]. Such a process is based on structural and thermodynamic information, and should also consider the possibility of polymorphism or phase transitions of engineered crystals [3, 4]. Therefore, the controlled synthesis and development of new multifunctional materials and pharmaceuticals should involve the understanding of the dynamics of their interaction networks. One of the most important and abundant intermolecular interactions in crystalline systems are the hydrogen bonds. Several classifications are available for H-bond description, which are based on geometrical parameters, spectroscopic features and charge density calculations. The analysis of different molecular arrangements formed via H-bonds is crucial to understand the stability of crystal phases and the origins of their physical properties [3-5].

In this investigation, the dynamics of complicated H-bond systems in selected crystals were studied using Born-Oppenheimer molecular dynamics (BOMD) simulations. Ab initio molecular dynamics computations provide on the flight evaluation of atomic force evolution using first-principles DFT calculations at every time step. BOMD simulations enable the characterization of solid-state phase dynamics in several statistical ensembles. The insight into crystal entropy and energy is given by the appropriate ensemble averages. The canonical ensemble (NVT) gives the possibility to study the temperature influence on the molecular motion, elastic properties as well as spectroscopic features. In addition, BOMD features allow considering the influence of anharmonicity and quantum effects at the vibrational spectra of examined materials.

In our computations, different cluster sizes were used for investigated H-bonded systems. The system dynamics were studied at different temperatures mainly in the NVT ensemble. Time and space correlations between molecular motions were analysed through the detailed study of interaction network changes along the obtained trajectories. The power spectra were used to investigate the spectroscopic features and the dynamics of considered H-bond systems. Additionally, the structural analysis based on X-ray diffraction experiments was performed, including H-bond propensities and coordination scores. These methods were used to assess the likelihood of specific H-bond formation, and the efficiency of entire H-bond systems according to donor and acceptor expected saturation.

[1] Tiekink, E. R. T., Vittal, J., Zaworotko, M., Ed. (2010). Organic Crystal Engineering: Frontiers in Crystal Engineering. Chichester: John Wiley & Sons, Ltd.
[2] Nangia, A. K. & Desiraju, G. R., (2019). Angew. Chem. Int. Ed. 58, 4100.
[3] Bernstein, J., Davey, R. J. & Henck, J.-O., (1999). Angew. Chem. Int. Ed. 38, 3440.
[4] Price, S. L., (2013). Acta Crystallogr. B69, 313.
[5] Aakeröy, C. B., Forbes, S. & Desper, J., (2014). CrystEngComm. 16, 5870.

Presented computations were performed using PL-Grid Infrastructure and resources provided by ACC Cyfronet AGH. The research was supported by the Polish National Science Centre, project PRELUDIUM 15 number 2018/29/N/ST3/00703 “Study of dynamics in the interaction networks of selected co-crystals”.

There has been a growing interest in mechanically responsive molecular crystals that show reversible and unusually large positive and negative thermal expansion triggered by external stimuli, a property which could be applied to the design of actuators for soft robotics, artificial muscles, and microfluidic and electrical devices [1]. However, controlling molecular motion to execute sufficiently larger and practically useful thermal expansion in crystals remains a formidable challenge, and strong deformation of such crystals usually results in their destruction [2]. Here we report a single crystal of simple organic compound which exhibits giant thermal expansion due to collective reorientation of molecules in the crystal lattice which is reversible after more than fifty heating and cooling cycles. Such atypical molecular motion, revealed by single crystal X-ray diffraction and microscopy analyses, drives an exceptionally large expansion of the crystal. The applicability of the material as an actuator with electrical properties is demonstrated by dielectric, capacitance, conductance and current measurements. The large shape change of the crystal, combined with remarkable durability and electrical properties, suggest that this material is a strong candidate for microscopic multifunctional thermal actuating devices.

Laser Powder bed fusion (L-PBF) has attracted a lot of interest in recent years, not only for its profound advantage of producing metallic components of complex geometries but also for the possibility of manipulating microstructures and crystallographic textures. Additionally, recent observations on wrought austenitic steels have revealed the strong dependence of the transformation induced plasticity (TRIP) effect in metastable stainless steels on the crystallographic texture [1–3]. Taking the aforementioned observations into consideration, we can now process TRIP steels such as 304L by L-PBF, in order to produce differently textured specimens and manipulate the TRIP effect. In this contribution, in situ uniaxial tension and compression tests with neutron diffraction, are utilized for monitoring of the microstructural evolution during deformation. The present study highlights how different microstructures, produced by L-PBF, lead to different deformation behavior in austenitic stainless steels and paves the way for tailored microstructures in different types of steels and for studies under different loading conditions.

References

[1] E. Polatidis et al., “The interplay between deformation mechanisms in austenitic 304 steel during uniaxial and equibiaxial loading,” 2019, doi: 10.1016/j.msea.2019.138222.

[2] E. Polatidis et al., “Suppressed martensitic transformation under biaxial loading in low stacking fault energy metastable austenitic steels,” Scr. Mater., vol. 147, pp. 27–32, Apr. 2018, doi: 10.1016/j.scriptamat.2017.12.026.

[3] E. Polatidis, J. Čapek, A. Arabi-Hashemi, C. Leinenbach, and M. Strobl, “High ductility and transformation-induced-plasticity in metastable stainless steel processed by selective laser melting with low power,” Scr. Mater., vol. 176, pp. 53–57, Feb. 2020, doi: 10.1016/j.scriptamat.2019.09.035.

Phase transformations in a single crystal of a metastable β titanium alloy (Ti-15Mo in wt %) were investigated in situ during heating by synchrotron x-ray diffraction. Metastable β titanium alloys contain such type and amount of alloying elements that the high‑temperature β phase (body-centred cubic) can be retained in a metastable state during fast cooling to room temperature; i.e. the formation of low-temperature α phase (hexagonal close-packed) is prevented. Ti alloys from this class generally undergo a wide range of phase transformations due to their metastable nature. First, nano-sized particles of metastable ω phase form in this class of Ti alloys during fast cooling by a difusionless displacement mechanism, which can be characterized as a collapse of neighbouring (111)_β planes into their intermediate position. During ageing or heating, ω particles grow by a combined displacement and diffusion process which is accompanied by rejection of alloying elements from the ω phase into the surrounding β matrix. At higher temperatures, lamellae of the thermodynamically stable α phase precipitate in the material; this process can be assisted either directly or indirectly by the previous β+ω microstructure.

In situ x-ray diffraction was measured using 60 keV photons at the high-energy beamline ID11, ESRF, Grenoble, France. This experiment was performed using an oriented single crystal of Ti-15Mo prepared in an optical floating zone furnace. A slice of the single-crystalline material with the [100]_β crystallographic axis parallel to the primary beam was placed in a special quartz chamber furnace which allowed measuring in a high vacuum. X-ray diffraction patterns were acquired in situ during heating with a constant heating rate of 5 °C/min.

Fitting of the temperature dependence of intensity of selected representative single-crystalline diffraction spots showed that at the beginning of linear heating, up to approximately 350°C, the volume of ω phase decreased, which is likely connected with displacement-accompanied ω to β reversion. Between 350°C and 420°C, the volume fraction of ω particles increased which is the consequence of diffusion-driven coarsening of ω phase particles. Subsequently, as the temperature approached the stability limit of the ω phase, the volume of ω decreased. A complete dissolution was observed at 560°C. Finally, a rapid growth of the α phase commenced at about 580°C. It was also verified that during linear heating, none of the crystallographic variants of ω and α phase is preferred.

Many mechanical structures are submitted to repeated loadings during their life span and can break under stress lower than the ultimate tensile stress. This phenomenon, called fatigue of materials, has attracted the scientific community attention due to its effect in many industrial sectors, such as the transport, aeronautic and energy. Fatigue design is thus crucial in engineering and it requires the accurate characterization of material behavior under cyclic loadings to ensure the safety and reliability of structures throughout their life. It is presently common to find mechanical systems subjected to several billion cycles, in what is called the gigacycle fatigue domain or very high cycle fatigue (VHCF) domain [1]. The characterization of the fatigue behavior of materials have been largely investigated with fatigue tests requiring long testing time with standard laboratory. To overcome this inconvenient new approaches using ultrasonic fatigue machines have been developed during the last decades. In particular, the present research group developed recently a new method for the fast determination of fatigue behavior interpreting diffraction patterns with a temporal resolution of ∼1 µs during an ultrasonic fatigue test and loading frequency of about 20 kHz. The present study points on the estimation of the amount of energy stored by the specimen during its deformation due to an ultrasonic fatigue loading. This energy is a crucial parameter as it is strictly related to the fatigue damage and can be estimated from the intrinsic dissipation and the mechanical work supplied to the specimen. X-ray diffraction analysis were performed to measure the supplied work by integrating over one fatigue cycle of the product of the strain rate by the stress. In particular, pure copper and steel specimens were loaded using a 20 kHz ultrasonic fatigue machine mounted on the six-circle diffractometer available at the DiffAbs beamline on the SOLEIL synchrotron facility in France. Then, in order to obtain the mechanical work: 1) from the shift of Bragg peaks is possible to estimate the total stress applied to the sample, 2) from both the broadening and shift of peaks one can measure the mean elastic lattice strain distribution, and 3) from the peak broadening the fluctuation of elastic strain is deduced, providing information about intragranular strain heterogeneity and dislocation density.

[1] Bathias, C. & Paris, P. (2005). Gigacycle Fatigue in Mechanical Practice. New York: Marcel Dekker.

Important problem studied in this work is the anisotropy of mechanical properties for textured polycrystalline materials. The mechanical behaviour during in-situ loading tests for magnesium AZ-31 alloy was studied using neutron diffraction. The lattice strains were measured during tensile by using angle-dispersive neutron diffraction (TKSN 400 at NPI in Řež, Czech Republic) and changing sample orientation with respect to the scattering vector. The measurements were done for sets of poles corresponding to different orientations of the grains in strongly textured Mg alloy. Subsequent experiment was performed using time of flight (TOF) neutron diffraction at the pulsed reactor IBR-2 in Joint Institute for Nuclear Research (Dubna, Russia), using EPSILON-MDS instrument equipped with 9 detectors. The experiments allowed to develop an experimental methodology based on the so-called crystallite group method in order to determine the evolution of the stresses localised in polycrystalline grains having different crystallographic orientations. The components of stress tensor were determined directly from measured lattice strains corresponding to chosen orientations of crystallite lattice.It was found that the crystallites having two main orientations, named A and B, are harder when compared with other ones. For these orientations the basal slip system cannot be activated because the load is applied in direction parallel to the basal plane. Orientation B was completely transformed to twins (having T orientation) during the compression test. In the case of the soft orientations C and D, the direction of the load is inclined from the basal plane, i.e. the basal system can be activated. Using the experimental data the evolution of stress tensor and von Mises stress were determined for selected groups of grains. A large difference in the hardness of crystallites having different lattice orientations was found. The highest von Mises stress appeared on twins, which was compensated by low stresses localised on soft orientations C and D.

The novelty of our study is in original methodology used for direct determining of stress tensor for groups of polycrystalline grains having different orientations (especially for preferred texture orientations). The stress evolution measured during sample loading allowed us to find out the critical resolved shear stress (CRSS) values for different slip systems and twinning process.

Research on lead-free piezoceramics is a trending topic [1]. A significant component of this search is the characterization of the effect of texture on the properties of polycrystalline electroceramics. The present contribution describes an integrated methodology, systematized in a software package, to solve the following tasks: (a) interpretation by numerical simulation of XRD patterns produced by textured samples; (b) forecast of the effective elasto-electrical properties of piezoceramics, starting from the knowledge of the corresponding single-crystal tensors and the texture determined in (a).

Part (a) considers 1D and 2D diffraction experiments, with Bragg-Brentano, grazing incidence and transmission geometries. The inverse pole figure of the symmetry axis of fiber-textured piezoceramics is proposed and refined by a Rietveld-type procedure [2].

The calculations in part (b) are performed using a variant of the Voigt-Reuss-Hill approximations. Particular precautions are taken with regard to the selection of the quantities considered as independent variables [3].

The computer programs developed to solve the proposed tasks are shown, the use of the MPOD database [4] in this type of work is described, and representative case studies are presented.

Fig. 1 shows as an example the computerized modelling of the variation of the representative longitudinal surfaces of the elastic compliance s(h) and the charge constant d(h) of the lead-free piezoceramic 0.95(Na_0.5Bi_0.5)TiO₃-0.05BaTiO₃ (BNBT5) as the texture evolves from relatively sharp to a random distribution.

Figure 1. Modelled effect of axial texture on elastic compliance and piezoelectric charge constant of lead-free BNBT5 piezoceramic. As the width of the orientation distribution (Ω) increases, the elasticity tends to isotropic and the piezoelectricity collapses to zero.

[1] Villafuerte-Castrejón, M. E., Morán, E., Reyes-Montero, A., Vivar-Ocampo, R., Peña-Jiménez, J. A., Rea-López, S. O., & Pardo, L. (2016). Materials 9, 21. [2] Burciaga-Valencia, D. C., Villalobos-Portillo, E. E., Marín-Romero, J. A., Del Río, M. S., Montero-Cabrera, M. E., Fuentes-Cobas, L.E. & Fuentes-Montero, L. (2018). J. Mater. Sci: Mater. Electron. 29, 15376. [3] Villalobos-Portillo, E. E., Fuentes-Montero, L., Montero-Cabrera, M. E., Burciaga-Valencia, D. C. & Fuentes-Cobas, L. E. (2019). Mater. Res. Express 6, 115705. [4] Fuentes-Cobas, L. E., Chateigner, D., Fuentes-Montero, M. E., Pepponi, G & Grazulis, S. (2017). Adv. Appl. Ceram. 116, 428.

Sponsorship by the Consejo Nacional de Ciencia y Tecnología (México), Projects 257912 and 270738, is appreciated. Support from the Project MAT2017-86168-R“Piezocerámicas ecológicas para la generación de ultra-sonidos” (CSIC, Spain), is acknowledged.

Production of nanostructures of extended covalent systems has remained a long-standing challenge, mainly due to the elevated activation energies required for their crystallization.[1] Such solids tend to exhibit outstanding mechanical properties, i.e. superhardness, the most illustrative case being diamond. Moreover, if nanostructuration is achieved (ideally in the ≈10 nm size range), further enhancement of the hardness can be obtained. For instance, diamond nanorods show an increase of the hardness by 86% compared to the bulk (from 80 GPa to 150 GPa).[2] Superhard materials are of great industrial importance, with applications as cutting and polishing tools, coatings and abrasives. Diamond is indeed the traditional choice for such purposes, but it has well-known limitations: it is brittle, oxidizes to carbon dioxide at 800–900 °C in air and reacts with Fe‑containing solids during cutting, not to mention the difficulty and cost of its production associated to the high-pressure machinery needed.

While several possible diamond substitutes have been suggested, boron carbide (B_4+δC) stands as one of the few superhard phases that can be reached at room pressure. Boron carbide crystallizes in the R-3m spacegroup and its network is based on B icosahedra linked to each other through both direct B-B bond and CBC chains, as depicted in Figure 1. B_4+δC exhibits an intrinsic hardness of 38 GPa, yet far from the industrially profitable range. Plenty of effort has been devoted to the optimization of boron carbide’s particle size and consequent amelioration of its mechanical properties. Approaches using different reactants, lower temperatures (down to 600°C) and/or liquid-phase reactions have not been able to enable further lower the B_4+δC particle size. In this work, instead of using pristine reagents, we demonstrate the capacity to produce 10 nm B_4+δC nanoparticles from a nano-precursor, namely NaB₅C. The structure of this cubic compound (space group Fd-3c) resembles that of perovskites, where B₅C octahedra form an anionic network that leaves cavities filled by Na⁺ cations (Figure 1 left). 5-7 nm NaB₅C nanoparticles were synthesized by using a high temperature liquid-phase procedure in molten salts.[3] The intrinsic carbon and boron mixture in a composition lying well within the range of the B_4+δC solid solubility makes it an interesting precursor to yield boron carbide. Indeed, upon calcination, the NaB₅C nanostructures are transformed to B_4+δC with nanostructuration preservation at circa 10 nm. After hot-pressing densification, the synthesized powders show enhancement of their mechanical properties above any previous record. We have used powder X-ray diffraction to shed light on the transformation from NaB₅C to B_4+δC at the atomic level. The implications of the new morphology of B_4+δC on the mechanical properties will be discussed as well as the importance of the templating effect remaining from the original NaB₅C nanostructures.

(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.

A proposal for a high brilliance upgrade to the SOLEIL synchrotron radiation source is expected to increase the beam brightness by > 50 times on beamlines used for life sciences. The combined expertise of the life sciences beamline teams at SOLEIL form the HelioBiology section, which has been, for the last 4 years, developing a post-upgrade approach to structural biology. This approach will be presented, paying particular attention to facilities that are novel to SOLEIL including in-vivo crystallisation [1] , microfluidic devices and their synchrotron applications [2], and concrete efforts towards an integrated approach to structural problems. Initial proposals for structural biology facilities (including an on- and off- beamline portfolio of instruments) will be presented, drawing on recent examples to illustrate the approach.

This work is presented on behalf of the members of the HelioBio scientific section at SOLEIL (https://www.synchrotron-soleil.fr/en/research/house-research/biology-health-heliobio).

References

[1]. Banerjee, S., Montaville, P., Chavas, L.M.G., Ramaswamy, S. "The New Era of Microcrystallography" Journal of the Indian Institute of Science., 98(3): 273–281. (2018).

[2]. Chaussavoine, I., Beauvois, A., Mateo, T., Vasireddi, R., Douri, N., Priam, J., Liatimi, Y., Lefrançois, S., Tabuteau, H., Davranche, M., Vantelon, D., Bizien, T., Chavas, L.M.G., Lassalle-Kaiser, B. "The microfluidic laboratory at Synchrotron SOLEIL" Journal of Synchrotron Radiation., 27(1): 230-237. (2020).

The global need to collect diffraction data from micro-crystals has been reflected by the development of dedicated microfocus beamlines for macromolecular crystallography worldwide. The increased intensity and brightness of these beamlines imposes a fundamental limitation however which precludes successful structure determination from a single microcrystal: radiation induced damage. X-ray induced radiation damage means that data must often be merged from many crystals to yield a complete dataset for structure solution [1, 2]. This is frequently the case for challenging projects when only crystals of limited size are available. Increasing the X-ray energy beyond the typical 10-15 keV range promises to provide a solution to this problem via an increase in the amount of information that can be obtained per unit absorbed dose or ‘diffraction efficiency’ [3-5].

To date however hardware limitations have negated any possible high energy gains. Typically the sensor material of detectors used in macromolecular crystallography is silicon. With its low atomic number, silicon becomes transparent as the X-ray energy is increased and the detector quantum efficiency falls rapidly as a function of energy. Recently, detectors using cadmium telluride as a sensor material have been developed; resulting in a quantum efficiency of 90% below the cadmium absorption edge (26.7 keV) and nearly 80% up to energies of 80 keV [6].

Through use of a new cryogenic permanent magnet undulator and a Cadmium Telluride Eiger2 detector high photon fluxes at high energies (>20 keV) can be generated and resulting microcrystal diffraction efficiently detected. Our results show that at higher energies fewer crystals will be required to obtain complete data, as the diffracted intensity per unit dose increases significantly between 12.4 and 25 keV. In an additional gain for the crystallographer, we observe that data collected at higher energies typically extend to higher resolution. Taken together our results illustrate that the use of high energies allows the best possible data to be collected from small protein crystals pointing to a high energy future for synchrotron-based macromolecular crystallography.

During the last decades, structural biology had a major impact in understanding the structure-functional aspects of some of the most important biological machineries. The new ESRF Extremely Brilliant Source opened a new age in microcrystallography and permitted to extend further the capabilities of the macromolecular crystallography beamlines and will open new pathways in the study of time-dependent structural changes. This is the scope of the upgrade of the ID29 beamline.

The new beamline combined cutting edge instrumentations to fully exploit serial crystallography experiments at room temperature. This presentaition will present the the beamline design with particular relevance to the new instrumentations and present the new scientifc opportunities that it will offer to the structural biology user community.

To study the effect of high pressure on any sample property, suitable pressure devices are a fundamental requirement. Their design has to be tailored to the experimental demands regarding the intended pressure, the employed instrumentation and the expected scientific results. Our work presents the development of high pressure cells for neutron scattering on polycrystalline and single-crystalline samples at low temperatures and with applied magnetic fields.

One of the most common devices for high-pressure neutron experiments is the clamp cell [1], where the pressure is applied ex situ and which can be used independently in various setups. Our cell design [2] has been specifically developed for neutron scattering experiments at low temperatures in the closed-cycle cryostats on the instruments DNS (diffuse scattering neutron spectrometer), MIRA (cold three axes spectrometer), and POLI (polarized hot neutron diffractometer) at the Heinz Maier-Leibnitz Zentrum (MLZ) in Garching, Germany. Two variants of the compact monobloc cell (Fig. 1) were produced, one from CuBe alloy and from NiCrAl “Russian Alloy”, working up to about 1.1 GPa and 1.5 GPa, respectively. The low paramagnetic moment of both alloys allows also measurements of magnetic properties.

First tests of the cell with neutron radiation were performed to calibrate the load/pressure-curve of the CuBe cell (up to 1.15 GPa) (at POLI), to estimate its neutron absorption and background (at MIRA), and to measure magnetic reflections (at MIRA). In addition, the thermal response in the cryostat of DNS was measured, and the experimental findings were complemented by simulations.

Ultimately, these cells are intended as standard cells for high pressure measurements on different instruments at MLZ suitable for all available magnets and cryostats down to 1.5 K. Further tests under various conditions (temperature, pressure, magnetic field) as well as simulations are planned for both cells in the near future. The results will help both to establish the present cells and to optimise the design of subsequent cells to achieve higher pressures, to fit into smaller cryostats and to enable neutron-independent pressure calibration.

Figure 1. Schematic drawing of the clamp cell.

[1] Klotz, S. (2013). Techniques in High Pressure Neutron Scattering. CRC Press.

[2] Eich, A., Hölzle, M., Su, Y., Hutanu, V., Georgii, R., Beddrich, L. & Grzechnik, A. (2020). High Press. Res. 41[1], 88–96.

High-end x-ray scattering techniques such as BIO-SAXS (e.g. SEC-SAXS), non-ambient SAXS and GISAXS rely heavily on the x-ray source brightness for resolution and exposure time. Traditional solid or rotating anode x-ray tubes are typically limited in brightness by when the e-beam power density melts the anode. The liquid-metal-jet technology has overcome this limitation by using an anode that is already in the molten state.

We have previously demonstrated prototype performance of a metal-jet anode x-ray source concept with unprecedented brightness in the range of one order of magnitude above current state-of-the art sources. Over the last years, the liquid-metal-jet technology has developed from prototypes into fully operational and stable X-ray tubes running in many labs over the world. Small angle scattering has been identified as a key application for this x-ray tube technology, since this application benefits greatly from high-brightness and small spot-sizes, to achieve a high flux x-ray beam with low divergence. Multiple users and system manufacturers have since installed the metal-jet anode x-ray source into their SAXS set-ups with successful results. With the high brightness from the liquid-metal-jet x-ray source, time resolved and in-situ SAXS studies can be performed – even in the home laboratory.

This presentation will review the current status of the metal-jet technology specifically in terms of flux and brightness and the impact of SAXS measurement. Such as the influence of the size of the x-ray source and its distance to the x-ray optics on the divergence will be discussed, and how to minimize the divergence and maximize the flux in SAXS experiments targeted to specific applications. It will furthermore refer to some recent SAXS and GISAXS data from users of metal-jet x-ray tubes.

For the first time, holistically optimized laboratory x-ray absorption spectroscopy (XAS) systems enable XAS measurements of most elements in the periodic table (Z>13) in minutes with energy resolution better than 0.7 eV, approaching capabilities of XAS facilities using bending magnet beamlines at second generation synchrotron light sources. The optimizations include:

• High brightness x-ray source with high thermal conductivity target incorporating diamond substrate, multiple target materials providing smooth spectrum free from characteristic x-ray lines, x-ray source size and shape optimized for using low miller index diffraction planes of cylindrically bent Johannsson crystal analyzers at low-medium Bragg angles, which provides optimal tradeoff between x-ray energy resolution and flux.
• Making use of dispersion of cylindrically bent Johannsson crystal analyzers in both tangential and sagittal directions for efficient use of source x-rays.
• 2D photon counting detector for recording x-rays dispersed by the crystal analyzer in tangential and sagittal directions and rejecting harmonics reflected by a crystal analyzer.

With those options, we have developed laboratory XAS systems operating from 1.7 keV to 25 keV, providing monochromatic x-ray flux over 2*10^7/s, and achieved energy resolution better than 0.7eV. The design and performances of the systems will be presented.

In scanning transmission electron microscopy (STEM), real space image quantification allows the counting of the number of atoms in a crystallographic projection, perpendicular to the electron probe. Atom counting is an established method in high-angle annular dark-field (HAADF) imaging and has applications that include the estimation of 3D shapes in metallic nanoparticles [1-2], or local composition variations in high-Z materials with known, constant thickness [3]. The incoherent nature of the HAADF contrast yields a monotonic increase of the image counts with Z, and this allows us to directly interpret image contrast at atomic columns positions as the number of atoms in projection. However, HAADF is only valid for atom counting of heavy elements that scatter strongly at high-angle. Phase imaging techniques are more appropriate for counting light elements because they ensure the collection of weak scattering signals at low angles. Phase methods recover the phase of the electron wavefunction scattered by both light and heavy elements; however, this phase is not directly quantifiable due to coherence [4]. Here, we present a novel approach to phase quantification, based on the combination of HAADF atom counting and electron ptychography. Electron ptychography is a 4D STEM phase technique whereby we recover the complex exit wavefunction from a set of 2D coherent electron diffraction patterns collected over a 2D image grid. Unlike other phase recovery techniques, electron ptychography has the unique advantage that it can be performed simultaneously with HAADF imaging. This allows for atom counting of heavy elements which can be used as means to rescale the ptychographic phase and count the light elements [5-6]. Herein, we apply this novel quantitative ptychographic approach to determine the local sub-stoichiometric composition of CeO_2-x nanoparticles. Fig. 1 (a) illustrates a schematic of the 4D STEM ptychographic method, where the Ce atom count in (b), obtained from the simultaneously recorded HAADF image, is used to calibrate the ptychographic phase in (c) to count O atoms.

[1] L. Jones et al., Nano Lett. 14 (2014) 6336.
[2] S. Van Aert et al., Phys. Rev. B 87 (2013) 064107.
[3] A. Rosenauer et al., Ultramic. 109 (2009) 1171.
[4] D. Van Dyck et al., Nature 486 (2012) 243.
[5] H. Yang et al., Nat. Comm. 7 (2016) 12532.
[6] A. De Backer et al., Ultramic. 171 (2016) 104.

Knowing the 3D atomic structures of materials or biomolecules is crucial for understanding their functions. X-ray diffraction is currently the most important technique for determination of 3D atomic structures, but requires large crystals which are often difficult to obtain. Electrons, similar to X-rays and neutrons, are powerful source for diffraction experiments. Due to the strong interactions between electrons and matter, crystals that are considered as powder in X-ray crystallography can be treated as single crystals by 3D electron diffraction methods [1]. This enables structure determination of materials and organic molecules from micron- to nanometer-sized 3D crystals that are too small for conventional X-ray diffraction. Furthermore, by taking the advantages of the unique properties of electron scattering, it is possible to determine the charge states of atoms/ions [2] and the absolute structure of chiral crystals [3].

Over the past decades, a number of 3D ED methods have been developed for structure determination. At the early stages of 3D ED method development, tilting of the crystal was done manually, while diffraction patterns were collected on negative film. It could take years before sufficient data were obtained and processed in order to determine the crystal structure. The computerization of TEMs and the development of CCD detectors allowed software to be developed that can semi-automatically collect 3D ED data in less than an hour [1]. Thanks to the recent advancement in CMOS and hybrid detector technology, it is now feasible to collect diffraction data in movie mode while continuously rotating the crystal (continuous rotation election diffraction, cRED, also known as MicroED [4] in structural biology). Benefiting from these technological advances, structure determination can now be accomplished within a few hours. Recently, fully automated serial rotation electron diffraction data collection and processing has been realized by our group [5].

By using 3D ED / MicroED methods, we have solved more than 200 novel crystal structures of small inorganic compounds [6] (including zeolite, MOF, COF and minerals) and biomolecules [7,8] (pharmaceuticals, small organic molecules, peptides and proteins) in the past 7 years. Recently, we have solved two novel protein [9,10] structures with 3D ED/MicroED and shown that it is feasible to use MicroED for structure based drug discovery [11]. We aim to further improve these methods, develop new methods and more importantly spread them to labs around the world.

[1] Gemmi M., Mugnaioli E., Gorelik T. E., Kolb U., Palatinus L., Boullay P., Hovmöller S. & Abrahams J. P. (2019). ACS Cent. Sci. 5, 1315–1329.

[2] Yonekura K., Kato K., Ogasawara M., Tomita M. & Toyoshima C. (2015). Proc. Natl. Acad. Sci. 112, 3368–3373.

[3] Brázda P., Palatinus L. & Babor M. (2019). Science. 364, 667–669.

[4] Shi D., Nannenga B. L., Iadanza M. G. & Gonen T. (2013). eLife. 2, e01345.

[5] Wang B., Zou X. & Smeets S. (2019). IUCrJ. 6, 854–867.

[6] Huang Z., Willhammar T. & Zou X. (2021). Chem. Sci. 12, 1206–1219.

[7] Clabbers M. T. B. & Xu H. (2020). Drug Discov. Today Technol., S1740674920300354.

[8] Clabbers M. T. B. & Xu H. (2021). Acta Crystallogr. Sect. Struct. Biol. 77, 313–324.

[9] Xu H., Lebrette H., Clabbers M. T. B., Zhao J., Griese J. J., Zou X. & Högbom M. (2019). Sci. Adv. 5, eaax4621.

[10] Clabbers M. T. B., Holmes S., Muusse T. W., Vajjhala P., Thygesen S. J., Malde A. K., Hunter D. J. B., Croll T. I., Flueckiger L., Nanson J. D., Rahaman H., Aquila A., Hunter M. S., Liang M., Yoon C. H., Zhao J., Zatsepin N. A., Abbey B., Sierecki E., Gambin Y., Stacey K. J., Darmanin C., Kobe B., Xu H. & Ve T. Nat. Commun. (In Press)

[11] Clabbers M. T. B., Fisher S. Z., Coinçon M., Zou X. & Xu H. (2020). Commun. Biol. 3, 417.

The project is supported by the Knut and Alice Wallenberg Foundation (2018.0237, X.Z.), the Swedish Research Council (2017-05333, H.X.; 2019-00815, X.Z.) and the Science for Life Laboratory through the pilot project grant Electron Nanocrystallography, and MicroED@SciLifeLab.

Quantitative convergent-beam electron diffraction (QCBED) has become renowned for its accuracy and precision when it comes to measuring bonding electrostatic potentials and electron densities [1 – 3]. Density functional theory (DFT) needs no introduction because of its ubiquity in materials science and crystallography. It is efficient but compromised in accuracy by the approximations needed to make it less computationally expensive than many-body wave-function calculations. It is also feared by some that DFT is becoming over-parametrised in the bid to deal with the shortcomings of approximations and is therefore “straying from the path toward the exact functional” [4].

We have integrated DFT into QCBED in such a way that allows DFT model parameters, including parameters associated with density functionals, to be refined by fitting DFT-calculated convergent-beam electron diffraction (CBED) patterns to experimental CBED patterns from a real material. We call this QCBED-DFT [5] and illustrate the basic principle of the method in Fig. 1 below.

We will present a number of experimental measurements of density functional parameters such as the Hubbard energy, U, in some strongly correlated electron materials, NiO and CeB₆, from our recently published work [5], as well as some new, unpublished trials.

[1] Zuo, J. -M., Kim, M., O’Keeffe, M. & Spence, J. C. H. (1999). Nature 401, 49.

[2] Nakashima, P. N. H., Smith, A. E., Etheridge, J. & Muddle, B. C. (2011). Science 331, 1583.

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

[4] Medvedev, M. G., Bushmarinov, I. S., Sun, J., Perdew, J. P. & Lyssenko, K. A. (2017). Science 355, 49.

[5] Peng, D. & Nakashima, P. N. H. (2021). Phys. Rev. Lett. 126, in press.

We thank the late Prof. Andrew Johnson. We are grateful to the Monash Centre for Electron Microscopy where the CBED data were collected. Many thanks to Prof. Joanne Etheridge for her valuable advice throughout this work. PN thanks the Australian Research Council for funding (FT110100427 & DP210100308).

3D electron diffraction (3D ED) undergoes rapid development in the past years. Structure solution is relatively easy, dynamical refinement provides accurate structure models and also absolute structure determination [1], but the accuracy of the lattice parameters remains a problem despite some effort. Lattice parameters obtained by 3D ED have at least an order of magnitude lower accuracy than single crystal x-ray data and the comparison is even worse with powder x-ray data. The reasons causing this poor accuracy are instrument-induced geometrical distortions present in the data and, in case of beam sensitive samples, crystal damage induced by the electron beam. In 2D diffraction patterns, distortions caused by aberrations of electromagnetic lenses are well known and have been analysed several times [2], but the precession assisted data collection induces new distortion, which were never analysed and we quantify and describe them for the first time. For mathematical description, we split the total in-plane difference between the expected and observed position of the diffraction maxima into radial and tangential (Dr and Dt) contributions, which are then described by circular harmonics - function of diffraction vector length r and azimuth j of the diffraction maximum (eq. 1).

Parameters j_r,n, j_t,n, r_n,m and t_n,m need to be determined either by the calibration of the microscope or by the refinement against the diffraction data. This general approach allowed us to compensate for all observed distortions, not only the classical pincushion-barrel, spiral and elliptical. The distortions depend on excitation of the lenses and can be calibrated. Tools for distortion refinement are incorporated in software PETS 2 [3] and distortion refinement workflow may be found in Jana Cookbook example Borane [4].

The effects of geometrical distortions in 3D ED data was so far only marginally analysed [3]. Here we analyse the effects of both the distortions in the plane of diffraction image and also the errors in the crystal orientation. The effect of the accumulated electron dose is also significant (Figure 1). Measurements of anti-B₁₈H₂₂ molecular crystal shows that the beam damage results in lattice parameters increase by about 1.5(5)‰ per accumulated dose of 1 e^-.Å^-2.

Recent developments in the ability to control the shape of metal nanocrystals using wet chemistry synthesis techniques have drawn significant attention for potential applications in plasmonics, photonics and catalysis. It is conjectured that shape control can be achieved by controlling the nanocrystal surface structure, primarily using surfactants and metal additives. For example, various shapes of Au nanoparticles, including rods, cubes, decahedra and octahedra, can be grown selectively using a trace amount of Ag [1] or Cu [2] additives. Understanding the underlying mechanisms of shape control by metal additives is therefore vital for the further engineering of nanocrystals. However, the establishment of atomic structure models of metal additives on the nanocrystal surface, that are just a few atoms wide, is still challenging.

For this aim, there are three essential requirements of the characterisation technique: (1) sufficient chemical sensitivity to distinguish surface additives; (2) spatial resolution at the atomic scale; (3) avoidance of damage to the surface structure from the probe.

Scanning transmission electron microscopy (STEM) has been widely used as a powerful means of resolving atomistic structures of nanocrystals. In this study, we studied the structure of Cu additives on the surface of Au nanocubes using conventional energy dispersive X-ray spectroscopy STEM (EDX-STEM) and high-angle annular dark filed STEM (HAADF-STEM), as well as four-dimensional STEM (4D-STEM) tuned specifically for the detection of surface adatoms.

EDX-STEM mapping reveals the presence of Cu on the {100} surfaces of Au nanocubes. However, the high electron dose required to achieve meaningful statistics can damage the structure during acquisition so a quantitative, high resolution analysis of an undamaged surface is not possible.

HAADF-STEM collects electrons at high angles by an annular detector and presents intensity sensitive to the atomic number (Z), however, it is also sensitive to other material parameters such as thickness and local environments (such as vacuum) [3,4]. We observe the intensity to drop at the nanoparticle atomic surface layer in the HAADF-STEM image but cannot distinguish whether this is due exclusively to the presence of (lower Z) Cu atoms or just fewer atoms on the surface layer. Furthermore, this is a dose-inefficient technique, using only those electrons scattered to high angles, and surface modification can be observed during acquisition.

4D-STEM using a fast pixelated detector records the full diffraction patterns at each probe position during the STEM experiment. The collected 4D datasets enable us to investigate features in diffraction patterns that are specifically related to different material parameters [4]. This method has the advantages of a lower dose than EDX-STEM and access to much more specimen information than HAADF-STEM. In this work, we developed an iterative method by starting with an ideal nanocube model with uniform thickness and with/without surface Cu layers. Dynamic diffraction conditions and scattering angles sensitive to the presence of Cu additives were identified based on the comprehensive dynamical scattering 4D-STEM simulations of this initial model. We then collected experimental 4D-STEM datasets using our optimised imaging conditions, from which Cu adatoms on the surface were evident with excellent contrast. In the next step, a matching of experimental diffraction patterns with simulated diffraction patterns was conducted to determine the realistic surface thickness profile. These allowed us to further refine the nanocube model using the observed surface structure of Cu adatoms and fitted thickness profile for the ultimate 4D-STEM simulations. Excellent agreement was achieved in both qualitative and quantitative comparisons between 4D-STEM simulations and 4D-STEM experiments over various imaging models (which each correspond to different diffraction physics). This suggests that the refined nanocube surface model represents the actual structure of Cu additives on the surface of Au nanocubes. This provides an approach for identifying the type and arrangement of the critical surface atoms that play an important role in controlling the growth and shape of nanoparticles.

[1] Personick, Michelle L., et al. Nano letters 11.8 (2011): 3394-3398. [2] Sun, Jianhua, et al. Crystal Growth and Design 8.3 (2008): 906-910.[3] LeBeau, James M., et al. 100.20 (2008): 206101. [4] Cowley, John. M. Surface Science 114.2-3 (1982): 587-606.[4] Ophus, Colin. Microscopy and Microanalysis 25.3 (2019): 563-582.

Keywords: Metal nanocrystals; Metal additives; Surface structure; 4D-STEM; STEM simulation

This work was carried out on the microscopes at the Monash Centre for Electron Microscopy funded by ARC grant number (LE0454166). This work was supported by ARC funding Discovery Project number DP160104679.

One of major crystallographic challenges is how to determine the structure of severely distorted crystal lattices, such as at a dislocation core and in high entropy alloys where distortion is non-uniform. Here we propose a new 4D scanning transmission electron microscopy (4D-STEM) based technique, called Cepstral STEM, for imaging disordered crystals using electron diffuse scattering. Local fluctuations of diffuse scattering are captured by scanning electron nanodiffraction (SEND) using a coherent probe. The harmonic signals in electron diffuse scattering are detected through Cepstral analysis and used for imaging. By integrating Cepstral analysis with 4D-STEM, we demonstrate that information about the distortive part of electron scattering potential can be separated and imaged at nm spatial resolution. We apply our technique to the analysis of a dislocation core in SiGe and lattice distortions in high entropy alloy [1].

[1] Yu-Tsun Shao, Renliang Yuan, Haw-Wen Hsiao, Qun Yang, Yang Hu, and Jian-Min Zuo, "Cepstral scanning transmission electron microscopy imaging of severe lattice distortions", Ultramicroscopy, 113252 (2021).

The recent surpassing of 1 million structures in the Cambridge Structural Database [1] offered a moment for celebration and an opportunity to reflect. Achieving this significant milestone is a testament to the exemplary initiatives and engagement emanating from the crystallographic community over many decades. The development of semantic representation formats [2], the cultivation of joined-up publishing workflows, and the broad adoption of standards all pre-empted the principles, guidelines and practices that have come to dominate the discourse around research data preservation and reuse today [3]. We cannot however rest on our laurels. The curation activities of organisations such as the Cambridge Crystallographic Data Centre remain of critical importance and must continue to evolve. We must ensure that our data resources remain relevant and can be readily utilised by the data-driven approaches being applied to the complex scientific problems of today.

This presentation will offer reflections on the successes of the crystallographic community that have been critical in ensuring the outputs of the past can conform to the expectations and demands of the future. It will highlight how these have enabled a wealth of structural chemistry knowledge to be applied across industry and academia to innovate and educate [4]. Additionally, it will look at the challenges and opportunities presented by an evolving research publication landscape, new experimental and computational methods, and the desire for greater reproducibility and richer reuse of structural chemistry data.

[1] Groom C. R., Bruno I. J., Lightfoot M. P. & Ward S. C. (2016). Acta Crystallogr. Sect. B Struct. Sci. Cryst. Eng. Mater. 72(2), 171.

[2] Hall S. R. & McMahon B. (2016). Data Sci. J. 15(3), 1.

[3] Wilkinson M. D., Dumontier M., Aalbersberg IjJ., et al. (2016). Sci Data. 3(1), 1.

[4] Taylor R., Wood P. A. (2019) Chem Rev. 119(16), 9427.

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), the US data center for the global PDB archive and a founding member of the Worldwide Protein Data Bank partnership, serves tens of thousands of data depositors in the Americas and Oceania and makes 3D macromolecular structure data available at no charge and without restrictions to millions of RCSB.org users around the world, including > 800 000 educators, students and members of the curious public using PDB101.RCSB.org. PDB data depositors include structural biologists using macromolecular crystallography, nuclear magnetic resonance spectroscopy, 3D electron microscopy and micro-electron diffraction. PDB data consumers accessing our web portals include researchers, educators, and students studying fundamental biology, biomedicine, biotechnology, bioengineering, and energy sciences. During the past two years, the research-focused RCSB PDB web portal (RCSB.org) has undergone a complete redesign, enabling improved searching with full Boolean operator logic and more facile access to PDB data integrated with > 40 external biodata resources. New features and resources will be described in detail using examples that showcase recently released structures of SARS-CoV-2 proteins and host cell proteins relevant to understanding and addressing the COVID-19 global pandemic.

The Inorganic Crystal Structure Database (ICSD) has been collecting published crystal structures for more than 40 years. In addition, the database offers the structures in curated and extended form. In the process of adding a structure to the database, a series of tests are run to verify data integrity and correctness. Furthermore, the data is enriched with additional or missing information, which can help to detect possible discrepancies. Some of the procedures used will be explained here, and examples will be given to show how careful evaluation of crystallographic parameters and the addition of missing parameters improves the quality of the crystal structure entry.

The Powder Diffraction File™ (PDF®) is a comprehensive materials database containing data for inorganic materials including minerals (natural and synthetic), metals and alloys, and high-tech ceramics, as well as organic materials such as pharmaceuticals, excipients and polymers. Databases, including the PDF, that provide structural details can be used for a range of materials characterization analyses, including (but not limited to) phase identification, quantitative analysis, and structure modelling for Rietveld refinement and whole-pattern fitting. As a result, structural databases are one of the key tools used in the crystallographic community [1]. Though these databases do tend to have some common applications, they often differ in content, format, and functionality. ICDD’s PDF databases primary purpose is to serve as a quality reference tool for the powder diffraction community.

Historically, the PDF has contained entries constructed as d-spacing and intensity (d-I) reduced diffraction pattern representations for phase identification. These condensed entries reduced storage space requirements, and increased search speed capabilities. With the advancement of computer hardware and software, and the transition of the PDF to a relational database format, storage space and speed capabilities have become less limiting [2]. Over time the PDF has grown exponentially, and has evolved to where it is now common practice to construct entries of full digital patterns. In addition to being a powerful characterization database used for the analysis of single and multi-phase X-ray diffraction data, the ICDD has systematically been adding raw data digital pattern references for crystalline and non-crystalline materials since 2008; with an emphasis on excipients and polymers [3]. The addition of full digital patterns has enabled the analysis and identification of disordered and amorphous materials using a combination of the raw data pattern and d-I lists, or whole pattern similarity searching. The evolution of raw data archiving in the Powder Diffraction File will be discussed in this presentation, with emphasis on the benefits and increased capabilities for characterization of materials in both research and industrial applications including pharmaceutical, forensic, and energy sectors.

[1] Kuzel, R. and Danis, S. (2007). Mater. Struct. Chem., Biol., Phys. Technol. 14, pp.89–96.

[2] Gates-Rector, S., & Blanton, T. (2019). Powder Diffraction, 34(4), pp. 352-360.

[3] Fawcett, T., Gates-Rector, S., Gindhart, A., Rost, M., Kabekkodu, S., Blanton, J., & Blanton, T. (2019). Powder Diffraction, 34(2), pp. 164-183.

Protein Data Bank Japan (PDBj) accepts and processes regional 3D structure data of biological macromolecules since 2000. We celebrated our 20th anniversary of our regional Data-in activities last year. Our Data-out service has a much longer history, dating back to before the establishment of PDBj. The first protein structure from Asia was determined at the Institute for Protein Research (IPR) in 1971 at 4 Å [1] and a subsequent structure at 2.3 Å solved in 1973 [2] was deposited to the PDB in 1975 as the 21st entry in PDB. Based on these early contributions to the crystallographic community, IPR founded the Crystallographic Research Centre and installed several 4-circule diffractometers, and developed the Imaging Plate detectors of R-axis series later [3] together with Rigaku. In addition to above activities, IPR was assigned as the National Affiliated Centre of Cambridge Crystallographic Data Centre from 1978 and keep serving until now (http://www.protein.osaka-u.ac.jp/CSD/, Fig.1). Distribution of the PDB data from IPR started in 1979 as a regional data centre, initially by magnetic tape and later by CD-ROM, until the installation of an official mirror site of Brookhaven PDB in 1998. Since 2001, we have provided our newly developed online Data-out services freely and publicly through our own web site (https://pdbj.org; Fig.2), which includes our molecular graphics viewer, Molmil; a molecular surface database for functional sites, eF-site; and a database of protein dynamics calculated via normal mode analysis, Promode Elastic [4], and we have served since 2003 as a founding member of the worldwide PDB (https://wwpdb.org). During the COVID-19 pandemic, we have provided a COVID-19 featured page in three Asian languages (Japanese, Chinese and Korean) and have started a new service archiving raw X-ray image data directly related to deposited PDB entries (XRDa, https://xrda.pdbj.org; Fig.3) [5]. Since we already have BMRBj (formerly PDBj-BMRB) and EMPIAR-PDBj on-site, XRDa completes the regional experimental raw data archives of the related PDB, BMRB and EMDB entries from the three major experimental methods; Macromolecular Crystallography, NMR spectroscopy and 3D Electron Microscopy.

[1] Ashida, T., Ueki, T., Tsukihara, T., Sugihara, A., Takano, T. & Kakudo, M. (1971) J. Biochem. 70, 913–924. [2] Ashida, T., Tanaka, N., Yamane, T., Tsukihara, T. & Kakudo, M. (1973) J. Biochem., 73, 463–465.

[3] Sato, M., Katsube, Y. & Hayashi, K. (1993) J. Appl. Cryst., 26, 733-735.

[4] Kinjo, A.R., Bekker, G.-J., Wako, H., Endo, S., Tsuchiya, Y., Sato, H., Nishi, H., Kinoshita, K., Suzuki, H., Kawabata, T., Yokochi, M., Iwata, T., Kobayashi, N., Fujiwara, T., Kurisu, G. & Nakamura, H. (2018) Protein Sci., 27, 95-102.

[5] Bekker, G.-J. & Kurisu, G. in preparation

One often observes small but measurable differences in diffraction data measured from different crystals of a single protein. These differences might reflect structural differences in the protein and potentially reflect the natural dynamism of the molecule in solution. Partitioning these mixed-state data into single-state clusters is a critical step to extract information about the dynamic behavior of proteins from hundreds or thousands of single-crystal data sets. Mixed-state data can be obtained deliberately (through intentional perturbation) or inadvertently (while attempting to measure highly redundant single-crystal data). To the extent that different states adopt different molecular structures, one expects to observe differences in the crystals; each of the polystates will create a polymorph of the crystals. After mixed-state diffraction data are measured, deliberately or inadvertently, the challenge is to sort the data into clusters that may represent relevant biological polystates. Here we address this problem using a simple multi-factor clustering approach that classifies each data set using independent observables, thereby assigning each data set to the correct location in conformation space. We illustrate this method using two independent observables – unit cell constants and intensities – to cluster mixed-state data from chymotrypsinogen (ChTg) crystals. We observe that the data populate an arc of the reaction trajectory as ChTg is converted into chymotrypsin.

The XtaLAB Synergy Flow turns any Synergy cabinet diffractometer into an automated, high-throughput machine by incorporating a 6-axis UR3 Universal Robot and a 3-puck dewar. The Flow system can automatically screen and collect 48 crystal samples with minimal human intervention. CrysAlisPro has been upgraded with tools to control all aspects of robotics and sample queuing. A unique X-ray safe dewar-drawer system allows loading and unloading of pucks without opening the X-ray enclosure or disturbing data collection. Ultimately, the XtaLAB Synergy Flow system is the perfect solution to allow full-time use of your diffractometer during a time when human interaction and contamination must be minimized.

For half a century the refinement of atomic model parameters to best explain the observed diffraction pattern has been fundamental to the process of crystallographic structure solution. This process has traditionally been carried out by the optimization of individual atomic parameters, with the use of stereochemical restraints to maintain plausible model geometry, particularly when data resolution is poor. However the data are often too poor to reliably indicate how individual atoms should be moved, and as a result the refinement calculation becomes a protracted battle between the noisy data pulling atoms in different directions and the restraints which are trying to maintain model geometry. This limits both the speed and radius of convergence of the calculation.

Shift field refinement is a new approach in which shifts to the calculated electron density are determined over extended regions of the unit cell, where the region size may be varied according to the resolution of the data and the type of feature (from whole domain to individual atom) being refined. The enables refinement to capture large domain shifts at low resolution, and to be applied at any resolution with rapid convergence. We have already demonstrated improved molecular replacement results when incorporating this step. We now demonstrate how the method can be used to refine a map against a set of diffraction observations, even in the absence of an atomic model.

We also demonstrate how the incorporation of a separate regularization step can be used to improve the refinement results by allowing more cycles of refinement to be run without the risk of model degradation due to accumulated model distortions. This in turn leads to further improvements in the refinement results.

High-end x-ray diffraction techniques such as macromolecular crystallography rely heavily on the x-ray source brightness for resolution and exposure time. As boundaries of technology are pushed forward samples are becoming smaller, weaker diffracting and less stable which put additional requirements on ever brighter sources. With bright enough compact sources, even the toughest challenges can be solved in the home laboratory. Traditional solid or rotating anode x-ray tubes are typically limited in brightness by when the e-beam power density melts the anode. The liquid-metal-jet technology (MetalJet) has overcome this limitation by using an anode that is already in the molten state thus e-beam power loading above several megawatts per mm are now feasible.

Over a decade ago the first prototypes of liquid-metal-jet x-ray sources were demonstrated. These immediately demonstrated unprecedented brightness in the range of one order of magnitude above current state-of-the art sources. Over the last years, the liquid-metal-jet technology has developed from prototypes into fully operational and stable X-ray tubes running in more than 100 labs over the world. X-ray crystallography is naturally considered a key application for the x-ray tube technology, since this application benefits greatly from small spot-sizes, high-brightness in combination with a need for stable output. To achieve a single-crystal-diffraction (SCD) platform addressing the needs of the most demanding crystallographers, multiple users and system manufacturers has since installed the MetalJet x-ray source into their SCD set-ups with successful results.

This contribution reviews the evolvement of the MetalJet technology specifically in terms of flux and brightness and its applicability for pushing boundaries of what is possible in the home lab. Recent user examples will illustrate how the MetalJet has enabled faster turnaround time of research and also enabled easy and convenient 24/7 access to the highest quality of crystallography data.

Carbohydrates are central to many biological processes. As protein glycosylation, they mediate interactions in recognition processes in cancer, viral infection, fertilisation. For example, the surfaces of viruses and antibodies are often covered in carbohydrates, which has been exploited in the development of vaccines and therapies. To further such efforts, it is important to have a good understanding of their 3D structure.

A software, Sails (Software for Automated Identification of Linked Sugars), has been developed to build sugars into electron density/potential maps automatically. It currently works for N-glycosylation and ligands, with plans to expand it for O-glycosylation. Sails uses a database of sugar fingerprints. These fingerprints are generated by superposing sugars from high-resolution structures in the PDB in their minimal-energy conformation, with correct anomeric forms and stereochemistry. The resulting fingerprints contain a set of coordinates of the atoms, plus a set of peaks and voids. Peaks represent map places where the electron density/potential of the fingerprint is expected to be high, while voids are places where map density values are likely to be close to zero. Figure 1 represents examples of sugars detected with Sails. As part of this presentation, I will discuss the fingerprinting method, its application to sugars and real world results from using Sails on published datasets.

Deep UV laser ablation is a technique to improve diffraction data quality from cryocooled macromolecular crystals by removing non-crystalline portion of the sample in the cryoloop or fabricating the crystal into symmetrical shape such as sphere [1]. It has been shown particularly effective for native single-wavelength anomalous dispersion (SAD) phasing in macromolecular crystallography (MX), where very accurate data is required to detect week anomalous signals from light atoms [2]. The systematic errors due to the beam absorption by the sample itself are reduced which is problematic in performing diffraction experiment using long wavelength X-ray. The application is straightforward, however, time consuming with human intervention, and even difficult in case the crystal is hard to identify by visual inspection, such as membrane protein crystals in lipidic cubic phase.

We are developing an unattended system to shape large number of samples based on the 3D map constructed by visual images or by X-ray raster images. In the case of using X-ray raster images, the map is automatically created from the raster images collected at several orientations at a synchrotron MX beamline in a standard, unattended manner. The map is then transferred to the laser shaping machine, allowing to visualize the envelope of the crystal on the mounted, ready-to-shape sample. By specifying the type of processing, e.g., ‘removing non-crystalline region’ or ‘fabricating into inscribed sphere’, the system automatically defines the orbit of the laser and repeats processing until the sample converges to the target shape. It is quite useful in preparing large number of shaped samples, typically in native SAD phasing experiment where high-redundant diffraction data is required.

XALOC is a tunable MX beamline, in user operation since 2012, located at the 3^rd generation synchrotron ALBA (Barcelona). XALOC has been designed to deal with automatable X-ray diffraction experiments of micrometer-sized crystals, including a variety of crystal sizes, unit-cell dimensions and crystals with high mosaic spread and/or poor diffraction. The aim for a reliable all-in-one beamline is equaled by the aim to maximize ease-of-use and automatization. Mail-in data collection is now in routine operation and dewar transport expenses are covered for users from Spain and abroad. To achieve a high-throughput MX beamline, we have implemented a new double gripper at the CATS sample changer that allows sample interchange in less than 20 seconds. Besides, an improvement in the CATS dewar allows to allocate up to 6 Unipucks (96 samples). EMBL/ESRF pucks are also acceptable with a capacity of 30 samples. In addition, MXCube and ISPyB software platforms for data collection and sample tracking/experiment reporting are routinely used at the beamline, allowing automated centering and the possibility to download the results obtained with the EDNA automated data processing pipeline through a web browser (https://ispyb.cells.es/). The beamline allows “in-situ” diffraction and serial crystallography experiments have been carried out successfully. XALOC is continuously open to new proposals providing beamtime within a few weeks. The latest updates and efforts and future developments on automation will be presented

Small-angle X-ray and neutron scatterings (SAXS and SANS; collectively called SAS) offer overwhelming opportunities for structural analysis of a biomacromolecule in solution. Modern SAS analysis with a computational simulation provides a three-dimensional structural model, whereas it is essential for the high-quality analysis to obtain the scattering profile surely corresponding to a target molecule. However, an undesirable aggregate, even at the low weight fraction, deteriorates the scattering profile of the target molecule and then lead to failure of the structural analysis. To overcome the aggregation-problem, we have developed the integrated approach with analytical ultracentrifugation (AUC) and SAS, namely “AUC-SAS”[1].

Figure 1 demonstrates the aggregation-removal with AUC-SAS for a bovin serum albumin (BSA) solution including the aggregates. AUC revealed the weight fractions of the monomer and their aggregates in the solution (Figure 1a). Because SAS offered the scattering profile ensemble-averaged over the monomer and their aggregates (open circles in Figure 1b), the simple experimental scattering profile led to the incorrect structural model as the monomer. AUC-SAS derived the scattering profile of the monomer (closed circles in Figure 1b) from the simple experimental one utilizing the information of AUC. Consequently, the derived profile led to the reasonable structural model as the monomer. In the recent progress, AUC-SAS succeeded for the solution including aggregates up to 20 % of weight fraction.

AUC-SAS does not require a large amount of sample nor very high intensity beam compared with size exclusion chromatography-SAXS (SEC-SAXS). Therefore, AUC-SAS has a potential as a complementary method for laboratory-based SAXS and standard SANS. The software for AUC-SAS data reduction is available at http://www.rri.kyoto-u.ac.jp/NSBNG/activity.html.

Proteins are bio-macromolecules that are responsible for various biological phenomena. Their functional expression takes place in the intracellular environment, i.e., the solution environment, which is a multi-component system with multiple proteins. Solution scattering is an effective method for structural analysis in such an environment. Particularly, in order to selectively analyze the structure of a specific protein in a multi-component system, the "inverse contrast matching small-angle neutron scattering (iCM-SANS)" method is valuable utilizing the characteristics of neutron scattering, in which the scattering lengths of hydrogen and deuterium differ greatly. In this method, when deuterated and hydrogenated proteins are observed in D₂O solvent, the deuterated proteins become scatteringly invisible due to contrast matching, and only the scattering of the hydrogenated proteins be observed. For this analysis, it is necessary to prepare the proteins whose the degree of deuteration is precisely controlled to 75%.

We have prepared 75% deuterated proteins using E. coli expression system and established a simple and rapid method to measure the degree of deuteration of proteins by mass spectrometry using MALDI-TOF MS. We also established a precise and simple method to measure the D₂O/H₂O ratio of the solvent using the measurement by Fourier transform infrared spectroscopy (FT-IR).

By using these techniques, we were able to obtain the accurate degree of deuteration of the proteins and D₂O/H₂O ratio in the solvent, and match out the deuterated protein very well.

Both the preservation of transparency and high refractive index is indispensable for the maintenance of normal function of eye lens. Especially, its high refractive index is attained by high protein concentration (~300 mg/mL in human eye lens). Since there exists no turnover in the eye lens, the eye lens is always at the risk of onset of aggregation. However, the long-term transparency in eye lens is preserved at least for several tens years. Then, how can eye lens maintain a long-term transparency? Key protein retarding the onset of abnormal aggregation is chaperone activity of alpha-crystallin, which exists as oligomers consisting of approximately 20~40 subunits of two homologues: alphaA-crystallin and alphaB-crystallin. Aiming at the elucidation of mechanism of its chaperone function, clarification of its quaternary structure has been challenged through crystallography techniques for long time. However, its quaternary structure has not been solved due to the availability of its crystal. To overcome such a situation, experimental trials revealing its quaternary structure have been tackled through state-of-the art experimental techniques. However, no consensus conclusions on such revealed structure have been drawn at present. We then reached one assumption that alpha-crsytallin intrinsically lacks robust quaternary structure (dynamic quaternary structure) to understand such diverse experimental results without inconsistency. It is also considered that such dynamic quaternary structure must be originated from subunit exchange between alpha-crsytallin oligomers.
To prove our expectation, we then try to apply deuteration assisted small-angle neutron scattering technique for visualizing subunit exchange in alpha-crsytallin oligomer. At the presentation, we will also discuss the effect of concentration on mechanism of subunit exchange in alpha-crsytallin oligomer.

The small angle X-ray scattering (SAXS) profile of a biomolecule reflects its meso- and nano- scale structure. Since the profile is contributed by all molecules in solution, the SAXS is a powerful method to study structural ensemble of the protein. We are establishing methods to elucidate structural ensemble of proteins at near-atomic resolution by combining SAXS and molecular dynamics simulations.

In this study we focused on structure and dynamics of multi-domain protein ER-60. ER-60 is a member of Protein disulfide isomerase family, which promote correct protein folding via isomerization of disulfide bonds. The ER-60 is composed four domains, a, b, b’, and a’. Both a and a’ domain have active Cys-Gly-His-Cys (CGHC) motif. In each CGHC motif, two cysteines take either S-S (oxidized) or -SH (reduced) states. We have obtained SAXS profiles of ER-60 with both all CGHC oxidized (oxidized ER-60) and CGHC reduced (reduced ER-60). Our SAXS profiles did not match known crystal structure, and the SAXS profiles of the two states were slightly different from each other.

To investigate behavior of ER-60 in solution, we performed multi-scale molecular dynamics simulations. First, fluctuation of each domain was examined by atomistic MD simulations. The fluctuation around active site differed between oxidized and reduced ER-60, but no significant difference was seen in the other regions. It suggests that the difference of SAXS profile between two states is not due to the difference of intra-domain dynamics.

Second, motion of full-length ER-60 was examined by coarse-grained molecular dynamics (CGMD) simulations with CG Martini model, where each amino acid is represented by one to six particles. We have successfully obtained simulation trajectory which reproduce our SAXS profile. From the simulation trajectory, we analyzed inter-domain interface and frequency of binding/dissociation of each pair of the four domains.

Third, structural difference between oxidized ER-60 and reduced ER-60 was studied by coarser CGMD simulations with AICG2+ model, which enable extensive structural-sampling. We compared simulation snapshots which reproduce SAXS profile of oxidized ER-60 with simulation snapshots which reproduce that of reduced ER-60. Our simulation showed that the difference of two SAXS profiles reflect the difference in position of a’ domain.

Detergents are commonly used to disrupt noncovalent interactions of proteins, leading to detergent-protein complex or stabilized recombinant proteins. In past, many methods have been used to investigate conformational changes of proteins and protein-detergent complexes to understand their interactions, polarity and stability in varied detergent concentrations. The local structure of such protein/detergent complex could be resolved by spectroscopies; however, resolving the corresponding stoichiometric protein unfolding conformation requires separating the effects contributed by the coexisted protein/detergent complex and SDS micelles in the solution.

Figure 1. R_g and I₀ profiles extracted from the SAXS data measured along the chromatogram I_{UV280 nm} of the BSA/SDS solution in SDS buffer. Bottom shows the DAMMIF models of the complexes at the states indicated. (Shown models are assumed as single phase and further analysed by two-phase MD simulation.).

In this work, we show that sodium dodecyl sulfate (SDS), a frequently used surfactant in purification of membrane proteins, can bind to bovine serum albumin (BSA) for multistage unfolding. The on-line protein purification system of high performance liquid chromatography (SEC-HPLC) incorporated to the beamline 13A synchrotron BioSWAN instrument of the Taiwan Photon Source at the National Synchrotron Radiation Research Center, allows separating the scattering contributions from the BSA/SDS complexes and SDS micelles. Together with integrated observations of UV-vis absorption and refractive index (RI), we have resolved the stoichiometric unfolding conformations of BSA by SDS monomers to micelles. Offline SEC-MALS (multi angle light scattering (MALS) results are also consistent. In Figure 1, the corresponding protein-SDS association numbers along the unfolding process are determined uniquely from a combined analysis of UV-Vis absorption, refractive index, and zero-angle SAXS intensity measured in one sample elution. WAXS features (not shown) revealed the conformational change of complex inter-domain motions.

A cataract is a common disease for the aged people and has a very high chance to lead blindness. Instead of the surgery of replacing the clouding eye lens with an artificial one, it’s important to develop a non-surgical therapy. But it’s difficult to be carried out due to the lack of understanding on mechanism of cataract.

In the vertebrate eye lens, alpha-crystallin(α-crystallin) is the major structural protein and consists of two subunits, αA and αB, which are used to maintain lens transparency throughout life. As a member of the small heat shock protein family (sHsp), α-crystallin exhibits chaperone-like activity to prevent misfolding as well as aggregation of key proteins in the lens associated with cataract diseases. The previous studies reported that binding capacity of α-crystallin to lens lipids increases with age, and high molecular complex, comprising α-crystallin and misfolding protein, showed higher association with membrane. Recent evidences showed that sterols compounds can improve lens transparency. Due to the strong interaction between sterols with membranes, we proposed a model based on the membrane-mediated sterol-crystallin interaction.

In this study, we used αA and αB crystallin proteins, ergosterol and membranes as a model system to study the interactions between proteins, sterol molecules, and membranes. First, the influence of membrane on chaperone-like activity of αA and αB were checked by the assays of insulin, lysozyme and alcohol dehydrogenase (ADH). Circular dichroism (CD) was used to monitor the secondary structure changes of crystallin proteins induced by binding to membranes. Lamellar X-ray diffraction (LXD) was used to probe crystallin-induced structural change of membranes. Furthermore, small-angle X-ray scattering (SAXS) was used to probe structural changes of membranes with and without ergosterol induced by protein binding. The effects of ergosterol on the interaction between crystallin proteins and membranes will be discussed.

Neural precursor cells expressed developmentally downregulated protein 4– 2 (Nedd4-2) plays a key role in the ubiquitination process, which leads to the endocytosis and degradation of its downstream target molecules such as membrane proteins. Nedd4-2 belongs to the HECT ubiquitin ligase family, which regulates signal transduction through interaction with other proteins including 14-3-3 proteins. 14-3-3s are evolutionarily conserved proteins, which negatively regulate Nedd4-2 in cAMP- dependent manner through phosphorylation by protein kinase A (PKA). This regulation is performed by providing scaffolding for Nedd4-2, thereby preventing the interaction with Nedd4-2 and other membrane proteins. Though this is known, the molecular mechanism of this regulation remains unknown and is under scientific scrutiny. We aim to understand the structural and functional basis of 14-3-3 mediated regulation of Nedd4-2 using combined structural biology and biophysical approaches such as fluorescence spectroscopy, protein crystallography and chemical crosslinking coupled with mass spectroscopy

Possible mechanism of the 14-3-3 mediated inhibition of pNedd4-2 includes stabilization of inactive conformation of Nedd4-2 in which, HECT and C2 domains are involved in the intramolecular interaction and steric masking of WW domains surfaces. To test this hypothesis, we performed the time resolved fluorescence spectroscopy measurements using phosphorylated Nedd4-2 variants labelled by extrinsic fluorophore and monitor their interaction with 14-3-3 protein. Fluorescence spectroscopy provided basic information on the dynamics of the interaction between Nedd4-2 ligase and 14-3-3 protein. Measuring of rotational correlation time and determination of the mean lifetime values of excited fluorophore in Nedd4-2 alone and in the complex with 14-3-3 protein allow us to trace the microenvironment of one particular cysteine ​​amino acid, which is located at different positions within Nedd4-2 construct.

We also crystallized the complex of 14-3-3γΔC with the peptide containing phosphorylated Ser³⁴², solved its structure using molecular replacement and refined it at 1.61 Å resolution.

1. J. A. Manning and S. Kumar, Trends Biochem. Sci. 43, (2018), 635–647.

2. P. Goel, J. A. Manning, and S. Kumar, Gene, 557, (2015), 1–10.

3. Nagaki K, Yamamura H, Shimada S, Saito T, Hisanaga S, Taoka M, Isobe T, Ichimura T,

Biochemistry, 45, (2006), 6733-40.

4. Ichimura T, Isobe T, J Biol Chem., 280, (2005), 13187-94.

This study was supported by the Czech Science Foundation (Projects 20-00058S), the Czech Academy of Sciences (Research Projects RVO: 67985823 of the Institute of Physiology) and by Grant Agency of Charles University (Project No.348421).

The TIR superfamily includes membrane receptors, Interleukin-1 receptors (IL-1Rs) and Toll-like receptors (TLRs) and also TIR-containing cytoplasmic adaptor proteins such as MAL and MyD88. These proteins play a major role in immune signalling and are vital to innate host defense, inflammation, injury and stress [1]. IL-1R8, also known as single immunoglobulin interleukin-1 receptor-related protein (SIGIRR) is an inhibitory receptor from IL-1R family which regulates signalling of both IL-1Rs and TLRs. The mechanism of inhibition is not yet known, but the only available genetic evidence suggests that the conserved intracellular TIR domain of IL-1R8 alone is necessary to inhibit LPS-induced TLR4 signalling [2]. The recent cryo-EM structure of the MAL protofilament has revealed the molecular mechanism of TIR-TIR interactions in the MAL and MyD88 dependent TLR4 signalling [3]. Based on this, we hypothesize that a similar TIR:TIR interaction between the TIR domain of IL-1R8 and the TIR domains of either TLR4/MAL/MyD88 would be involved in the inhibition mechanism.

The TIR domain of human IL-1R8 was cloned, expressed and purified using E. coli host system. Turbidity assays, negative-stain electron microscopy (EM) and single-molecule fluorescence spectroscopy (SMFS) analysis indicated a potential interaction between IL-1R8^TIR and MAL^TIR. MAL^TIR forms filamentous assemblies when incubated with IL-1R8^TIR (Fig. 1). We are currently focusing on solving the 3D structure of MAL^TIR/IL-1R8^TIR filaments using negative-stain EM and cryo-EM to obtain molecular insights into the interaction interfaces and binding sites of IL-1R8^TIR and MAL^TIR. This study will eventually lead to an understanding of how TLR4 signalling is regulated by IL-1R8 and can potentially pave way in development of new therapeutic agents in future.

Figure 1. Left: Model representing the inhibition of TLR4 signalling by IL-1R8. Right: Negative-stain EM image of MAL^TIR/IL-1R8^TIR filaments taken using Hitachi HT 7700 TEM.

[1] Boraschi, D. et al. (2018). Immunol Rev. 281, 97-232[2]. Qin, J. et al. (2005). J Biol Chem. 280, 25233-25241[3]. Ve, T. et al. (2017). Nat. Struc. Mol. Biol. 24, 743-751

Paratellurite TeO₂ crystals under the application of a strong electric field demonstrate significant changes of the shape of allowed reflections, which are associated with the migration of oxygen vacancies to the surface layers [1]. Similar effect was found earlier in strontium titanate SrTiO₃ and got the name of “migration-induced field-stabilized polar phase” [2].

An experiment was carried out at P23 beamline of PETRA III synchrotron, devoted to the study of the changes in the forbidden reflections 002 and 100 in TeO₂ under applied electric field. These reflections are forbidden in conventional X-ray scattering, but can be observed at the energies close to absorption L-edges of Te, due to appearance of dipole-dipole resonant contribution to the atomic factor of Te. The experiment was carried out at the incident radiation energy, close to L₁ edge of Te 4938 eV. For both reflections the azimuthal dependence and energy spectrum were measured with and without application of electric field. For 002 reflection electric field magnitude was 500 and 750 V/mm, for 100 reflection it was 750 and 1050 V/mm.

We have observed a change of azimuthal dependence (Fig.1) caused by the violation of a symmetry in electric field in accordance with the predictions of preliminary theoretical calculations. Also we have observed a change of the energy spectrum at the field magnitude of 500 V/mm. It is assumed that this change is caused by appearance of oxygen vacancies in the environment of Te. For reflection 100 this change of the energy spectrum was even more obvious. This is justified because in this experimental geometry migration of vacancies is more pronounced.

[1] A. G. Kulikov, A. E. Blagov, N. V. Marchenkov, et.al. // JETP Letters, 107:10 (2018), 646–650 [2] J.Hanzig, M.Zschornak, F.Hanzig, et.al // Physical Review B 88, 024104 (2013)

A new biological small-angle X-ray scattering (BioSAXS) beamline is developed with the 3.0 GeV Taiwan Photon Source (TPS), for studies of biological structures in a wide range of length and time scales. The beamline provides a high flux (4 x10¹⁴ photons/s) for time-resolved and synchronized small- and wide-angle X-ray scattering (SAXS-WAXS), and offers new opportunities for ultra-SAXS (USAXS) to resolve the hierarchical structures of bio-machinery assemblies in solution, gel or condensed forms and anomalous SAXS/WAXS for metal or mineral distributions and compositions in an organelle or drug carrier. The beamline application extends to microbeam SAXS/WAXS for correlated crystal and nanostructural mappings in natural fibril tissues and synthetic biomaterials under tailored environmental controls. Concomitant SAXS-WAXS data collections are realized with a unique detecting system comprising an Eiger X-9M detector for SAXS and a custom-designed Eiger X-1M detector for simultaneous WAXS. These two X-ray detectors (75 mm pixel resolution) move independently with multi-degrees of freedom inside a large vacuum vessel of 12 m long and 1.5 m dia., providing dynamic and fast changes in detecting configuration for optimized data collections. Solution SAXS and WAXS of biomacromolecules are facilitated with an integrated system of online sample purification system of HPLC, strengthened by onsite UV-vis absorption followed by refractive of index measurement in one sample elution. The beamline has been opened to users since September 2020.

The Centre of Molecular Structure (CMS) provides services and access to state-of-art instruments, which cover a wide range of techniques required by not only structural biologists. CMS operates as part of the Czech Infrastructure for Integrative Structural Biology (CIISB), and European infrastructures Instruct-ERIC and MOSBRI. CMS is organized in 5 core facilities: CF Protein Production , CF Biophysics, CF Crystallization of proteins and nucleic acids, CF Diffraction techniques, and CF Structural Mass Spectrometry.

CF Diffraction techniques employs two laboratory X-ray instruments equipped with high flux MetalJet X-ray sources: a single crystal diffractometer D8 Venture (Bruker) and a small angle X-ray scattering instrument SAXSpoint 2.0 (Anton Paar). The configurations of both instruments represent top tier of possibilities of laboratory instrumentation. Apart from standard applications, the instruments are also extended for advanced experiments: the diffractometer is equipped with the stage for in-situ crystall diffraction and crystal dehydration, SAXS is equipped with in-situ UV-Vis spectroscopy and liquid chromatography system for SEC-SAXS. The setups enable easy access and fast turn-around of samples under different conditions, but also collection of high quality end-state data without further need for synchrotron data collection in many cases. CF Diffraction provides services in synergy with the other CFs on-site, therefore scientific questions can be quickly answered as they emerge from the experiments.

The Centre of Molecular Structure is supported by: MEYS CR (LM2018127); project Czech Infrastructure for Integrative Structural Biology for Human Health (CZ.02.1.01/0.0/0.0/16_013/0001776) from the ERDF; UP CIISB (CZ.02.1.01/0.0/0.0/18_046/0015974), and ELIBIO (CZ.02.1.01/0.0/0.0/15_003/0000447).

Type I collagen solution (bovine skin based) is studied using the biological small- and wide-angle X-ray scattering beamline at the 3.0 GeV Taiwan Photon Source of the National Synchrotron Radiation Research Center. Concomitant SAXS-WAXS data are collected from the sample elution with an online size exclusion column (SEC) of HPLC, incorporated with UV-vis absorption followed by refractive of index measurements. SEC-SAXS result indicates a relatively monodisperse size distribution of the tropocollagen, which comprises three left-handed helices of polypeptide strands that are twisted together into a right-handed coiled coil for a triple helix. The SAXS-revealed gyration R_g of 195 Å and elongated shape together with the molecular mass and the hydrodynamic radius R_h measured from dynamic light scattering and multi-angle laser light scattering, together, indicate a dimer form of the tropocollagen. Interestingly, these dimers can gradually form visible networks in solution upon adding short peptides; further, circular dichroism result indicates that these peptides are fond to reserve better the secondary structure of tropocollagen in solution upon UV illumination. The network formation mechanism of tropocollagen will be discussed in terms of the interaction of tropocollagen with the short peptides.

In response to emergence of global COVID-19 pandemic, studies of SARS-CoV-2 have been well underway with an unprecedentedly fast phase particularly for vaccine development. While spike proteins and proteases Mpro and PLpro are getting much of attention as therapeutic drug targets against COVID-19, however, the progress in developing drugs is still lagging behind. Non-structural protein 15 (Nsp15) is another SARS-CoV-2 protein demanding researchers’ attention as a critical drug target. Nsp15 is an endoribonuclease and an essential enzyme for SARS CoV-2 with a role of interfering host immune response. It has been reported that Nsp15 is evading melanoma differentiation-associated gene 5 (MDA5) activity which is triggered by ds/ssRNA molecular pattern produced by replication-transcription complex by trimming replication produced (-) strand polyU track. We characterized Nsp15 by crystallography, biochemical, and whole-cell assays. Several structures of Nsp15: the Apo-form and several ligands bound forms are determined. Our Nsp15 structures with nucleotide-base ligands elucidated how Nsp15 recognizes uridine base specifically. The structure with a transition state analog, uridine vanadate, confirms interactions key to catalytic mechanisms which is mimicking that of RNaseA. We also found an uracil analog Tipiracil, an FDA approved drug that is used in the treatment of colorectal cancer, as a potential anti-COVID-19 drug. These findings can be new insights for the development of uracil scaffold-based therapeutic drugs.

The PDBe-KB COVID-19 data portal, developed by the team at Protein Data Bank in Europe Knowledge Base (PDBe-KB), aggregates all the available structure data from SARS-CoV-2 structures in the PDB, to help researchers easily identify important structural features to support the development of treatments and vaccines.

Since the beginning of the COVID-19 pandemic, an unprecedented number of scientific efforts have taken place worldwide in order to help combat the SARS-CoV-2 virus. One of the biggest challenges during this fast-moving situation was to share data and findings in a coordinated way and ensure this was available to any researchers who needed it.

To support research efforts to understand more about the SARS-CoV virus and the structures of its proteins, we created dedicated PDBe-KB pages to highlight important structural features of PDB entries and allow easy download of all relevant data files. These pages highlight ligand binding sites and residues involved in protein-protein interactions through visualisation tools, including a new structure superimposition feature. These pages help researchers to easily identify common features from all the available structure data, supporting drug and vaccine development.

To view the PDBe-KB COVID-19 Data Portal, please visit PDBe.org/covid19.

3DBionotes-WS, an ELIXIR recommended interoperability resource, is a set of web services that provides multiple annotations oriented to structural biology analysis. It can be accessed through a website interface that features a fully interactive 3D viewer for macromolecular structures and functional, genomic, proteomic and structural feature annotations.

Motivated by COVID-19 pandemic, we present a new section (https://3dbionotes.cnb.csic.es/ws/covid19) dedicated to SARS-CoV-2 viral protein structures that have been provided by X-ray crystallography, cryo-EM, NMR and various modelling and structural predictions approaches.The aim of this section is collecting and providing centralized access to all available structural information on the SARS-CoV-2 viral proteins, as well as other related viruses or interacting molecules. In addition, when validation and quality information is available from PDB-REDO [1] and the Coronavirus Structural Task Force [2], special tags are incorporated for every entry, pointing to the re-refined models.

Among the new annotations added are functional mappings for ligand binding sites and protein-protein interaction sites. Functional mapping annotations allow to locate the residues that are likely to constitute binding sites between SARS-CoV-2 proteins and other viral or human proteins [3] and for multiple candidate inhibitors already identified for SARS and MERS homologous proteins. Of particular interest are ligands tested in large-scale studies searching for potential drugs, like the one performed against the SARS-CoV-2 main protease using the PanDDA method [4] at the Diamond synchrotron, Oxford (https://www.diamond.ac.uk/covid-19/for-scientists/Main-protease-structure-and-XChem).

Regarding the genomic context, SARS-CoV-2 variants compiled at the China National Center for Bioinformation (https://bigd.big.ac.cn/ncov/variation) have been summarized in a new annotation track. Also, some methods to evaluate the quality of cryo-EM maps and the fit to their atomic models was incorporated. These methods are deepRes [5], that analyse the map local resolution and FSC-Q [6] and map Q-score [7], that inform about the fit and resolvability of the built atomic model.

[1] Joosten, R. P., Long F., Murshudov, G. N. & Perrakis, A. (2014). IUCrJ, 1, pp. 213–220

[2] Croll, T. I., Diederichs, K., Fischer, F, Fyfe C. D., Gao, Y., Horrell, S., Joseph, A. P, Kandler, L., Kippes O., Kirsten, F., Müller, K., Nolte, K., Payne, A. M., Reeves, M., Richardson, J.S., Santoni, G., Stäb, S., Tronrud, D. E., von Soosten, L. C., Williams C. J. & Thorn, A. (2021). Nat Struct Mol Biol 28, pp. 404–408

[3] Srinivasan, S., Cui, H., Gao, Z., Liu, M., Lu, S., Mkandawire, W., Narykov, O., Sun, M. & Korkin, D. (2020). Viruses, 12(4)

[4] Pearce, N.M., Krojer, T., Bradley, A. R., Collins, P., Nowak, R.P., Talon, R., Marsden, B.D. Kelm, S., Shi, J., Deane, C.M. & von Delft, F. (2017). Nat Commun., 8, 15123

[5] Ramírez-Aportela E., Mota J., Conesa P., Carazo J. M. & Sorzano C. O. S. (2019). IUCrJ, 6, pp. 1054-1063

[6] Ramírez-Aportela, E., Maluenda, D., Fonseca, Y. C., Conesa P., Marabini, R., Heymann, J. B., Carazo J.M. & Sorzano C.O.S. (2021) Nat Commun, 12(42)

[7] Pintilie, G., Zhang K., Su Z., Li S., Schmid M. F. & Chiu W. (2020) Nat Methods. 17(3), pp. 328-334.

We acknowledge financial support from: CSIC (PIE/COVID-19 number 202020E079), the Comunidad de Madrid through grant CAM (S2017/BMD- 3817), the Spanish Ministry of Science and Innovation through projects (SEV 2017-0712, FPU-2015/264, PID2019 104757RB-I00 / AEI / 10.13039/501100011033), the Instituto de Salud Carlos III: PT17/0009/0010 (ISCIII-SGEFI / ERDF-) and the European Union and Horizon 2020 through grant EOSC Life (INFRAEOSC-04-2018, Proposal: 824087). Contributions from the Coronavirus Structural Task Force were supported by the German Federal Ministry of Education and Research [grant no. 05K19WWA] and Deutsche Forschungsgemeinschaft [project TH2135/2-1]. The authors acknowledge the support and the use of resources of Instruct, a Landmark ESFRI project.

Tailed bacteriophages are one of the most widespread biological entities on Earth. Their singular structures, such as spikes or fibers are of special interest given their potential use in a wide range of biotechnological applications. In particular, the long fibers present at the termini of the T4 phage tail have been studied in detail and are important for host recognition and adsorption. Although significant progress has been made in elucidating structural mechanisms of model phages, the high-resolution structural description of the vast population of marine phages is still unexplored.

Our group studies the marine flavobacterium Bizionia argentinensis JUB59, a psychrotolerant Gram-negative microorganism isolated from surface seawater in Potter Cove, Antarctica, and whose genome has been sequenced. This bacterium constitutes a relevant source for the discovery of new proteins showing biological activity in extreme conditions of low temperature. In recent years, we have developed a medium-throughput structural genomics project to functionally classify B. argentinensis JUB59 proteins annotated with unknown function. We set up a screening protocol based on bioinformatics analysis, NMR and crystallography to identify and characterize suitable targets for structure determination [1-4]. In this context, and amongst other members, we selected a 277-residue protein named C24, whose sequence lacks homology to proteins of known function.

In the present work, we crystallized and solved the structure of C24 at 1.82 Å resolution by means of the single-wavelength anomalous diffraction method (manganese peak) with excellent statistics [5]. The protein folds as an 89-kDa homotrimer with a rocket shape. It bears a total length of 160 Å and a varying diameter along the particle axis, with a maximum value of 60 Å at its base. The structure of C24 closely resembles that of the receptor-binding tip from the bacteriophage T4 long tail fiber [6], although there are notorious differences in their domain organization, sequence, molecular dimension and number and type of bound structural divalent cations. We then confirmed the viral origin of C24 by bioinformatic and experimental approaches: (i) the C24 sequence is located inside a detected prophage by the ACLAME Prophinder tool, and (ii) the antibiotic mitomycin C induces the lytic cycle of a virus present in the bacterial genome, which was able to be isolated and visualized by transmission electron microscopy, revealing a morphology that is compatible with the order Caudovirales and, more importantly, these viral particles carry the nucleotide sequence of C24 in their genome.

As a general conclusion, the crystal structure of C24, together with induction and electron microscopy experiments, reveal that this protein may be the receptor-binding tip of a novel uncharacterized tailed bacteriophage present as a lysogen in B. argentinensis JUB59. These findings bring new avenues for the discovery of novel viral structures and provide valuable information to expand our current knowledge on the viral machinery prevalent in the oceans.

[1] Aran, M., Smal, C., Pellizza, L., Gallo, M., Otero, L. H., Klinke, S., Goldbaum, F. A., Ithurralde, E. R., Bercovich, A., Mac Cormack, W. P., Turjanski, A. G. & Cicero, D. O. (2014). Proteins 82, 3062-3078.

[2] Pellizza, L., Smal, C., Ithurralde, E. R., Turjanski, A. G., Cicero, D. O. & Aran, M. (2016). FEBS J. 283, 4370-4385.

[3] Cerutti, M. L., Otero, L. H., Smal, C., Pellizza, L., Goldbaum, F. A., Klinke, S. & Aran, M. (2017). J. Struct. Biol. 197, 201-209.

[4] Pellizza, L., Smal, C., Rodrigo, G. & Aran, M. (2018). Sci. Rep. 8, 10618.

[5] Pellizza, L., López, J. L., Vázquez, S., Sycz, G., Guimarães, B. G., Rinaldi, J., Goldbaum, F. A., Aran, M., Mac Cormack, W. P. & Klinke, S. (2020). J. Struct. Biol. 212, 107595.

[6] Bartual, S. G., Otero, J. M., García-Doval, C., Llamas-Saiz, A. L., Kahn, R., Fox, G. C. & van Raaij, M. J. (2010). Proc. Natl. Acad. Sci. USA 107, 20287-20292.

Keywords: Protein structure; Prophage; Mitomycin C; Flavobacteriaceae; Caudovirales

This work was supported by the Argentinian Ministry of Science and the University of Buenos Aires. We are grateful for access to the SOLEIL Synchrotron in France.

Since one and a half years the world has been fighting a COVID-19 pandemic, which caused unprecedented crisis all over the world. And, the full evolutionary potential of SARS-CoV-2 has yet to be revealed. A super-virus with features of the highly transmissible SARS-CoV-2 and the deadly SARS and MERS viruses could lead to more catastrophic loss of life. What is more, a new serious onslaughts due to (corona)viruses and other pathogens are inevitable.

Structural biology has been at the centre of the efforts of development of effective therapeutics. It helps to „see” 3D protein structures of invisible viruses and their interactions with host proteins, and potential ligands, knowing molecular mechanisms driving the viral evolution and shape biomedicinal research field [Barcena et al., 2021; Lynch et al., 2021]. Only through structural biology can we gain a deeper insight into the new variants of viruses and effect of mutations on the proteins. The ongoing outbreak has pushed numerous structural studies, using crystallography, cryoelectron microscopy, structural virology and vaccinology, structural bioinformatics, dynamics, and omics, leading to either revolutionary progress of structural biology or understanding of pandemic evolution leading to therapeutic findings. Here, we should mention about some examples.

The basic biomolecules, amino acids, and short peptides, as constituents of proteins associated with RNA, are crucial elements in the pandemic`s puzzles. Amino acid variations in the spike of SARS-CoV-2 affects the shape, binding, and function of the protein. The virus can escape neutralizing antibodies through only a single amino acid replacement. Thanks to structural studies, we found evidence how amino acids and short peptides drive mutations, which is critical in predicting emergent strains and their deadly potential in the context of designing effective pan-vaccines and preventing the spread of disease [In preparation]. Some studies have found evidence that coevolving amino acids play a pivotal role in increasing the affinity of the spike protein against ACE2, leading to more successful infection, with some of these amino acids under more evolutionary pressure than others [Priya et al, 2021]. On the other hand, other viral proteins, such as the non-structural protein 1, contribute to immune evasion. The coevolution impact on interaction patterns of proteins among a growing number of variants should not be neglected.

Short peptides are naturally suited to treating infectious disease as they can disrupt protein-protein interactions [Apostolopous et al, 2021; Bojarska et al., 2021]. Notably, these inter-contacts are the heart of most important cellular processes and primary targets for smart drug discovery but are ”undruggable” by small-molecules due to the large and flat contact surfaces characteristic of protein-protein interactions. Notably, there are a plethora of disease-relevant protein-protein interactions, but most of them have so far been unexplored. More specifically, viral proteins take over cellular host functions through short peptide interaction motifs (in unstructured regions) that bind to defined pockets on globular host domains. These motifs evolve by mutation, enabling viruses to interact with novel host factors. An understanding of these peptide-mediated protein-protein interactions can predict viral tropism and molecular processes within host cells. They could be targets for novel antiviral inhibitors, such as integrin-targeted drugs in controlling COVID-19 [Kruse et al, 2021].

The design of suitable antiviral drugs became possible by thorough knowing the composition of the binding site pocket of virus (SARS-CoV-2) main protease [Dai et al, 2020].

Structural mapping a protein network, that enables studying suitable protein interactions with other proteins, can identify repurposed drugs that could target disease relevant processes. This new tactic has identified cyclic depsipeptide (PF-07321332), a known anticancer drug, which is more potent than remdesivir in COVID-19. This idea could be used for other pathogens [White et al, 2021].

The concept of smart vaccines using machine learning, structural modelling, to precisely predict the binding between viral peptides and host proteins from the adaptive immune system or other evolutionary peptides, leading to an increase in the speed of vaccine development in future health crises [Alam et al, 2021].

Thus, advanced structural biology is a valuable tool to gather information helpful in controlling current and next outbreaks of deadly pathogens as well as rapid progress in the development of drugs and vaccines.

We will discuss key cutting-edge approaches in detail, highlighting their strengths and weaknesses, and indicating the important gaps as well as the further advances in bio-informatics methodology needed to fill them.

References

* A. Alam, A. Khan, N. Imam et al. Briefings in Bioinformatics, 22, 1309 (2021)

* V. Apostolopoulos, J. Bojarska, T.T. Chai et al. Molecules 26, 430 (2021)

* M. Bárcena, C.O. Barnes, M. Beck et al. Nat. Struct. Mol. Biol., 28, 2 (2021)

* J. Bojarska, R. New, P. Borowiecki et al. Front. Chem. 9, 679776 (2021)

* W. Dai, B. Zhang, X.M. Jiang et al. Science, 368, 1331 (2020)

* T. Kruse, C. Benz, D.H. Garvanska et al. bioRxiv 19, 2021. 10.1101/2021.04.19.440086

* M.L. Lynch, E.H. Snell, S.E.J. Bowman. IUCrJ 8, 335 (2021)

* P. Priya, A. Shanker. Infect, Genet. & Evol. 87, 104646 (2021)

* K.M. White, R. Rosales, S. Yildiz et al. Science, 371, 926 (2021)

Polymorphism in cocrystals is gaining interest because of the increasing interest in pharmaceutical cocrystals [1,2]. In this work, we report a 1:1 cocrystal of a BCS class 2 NSAID drug, niflumic acid (NIF), with caffeine (CAF) which exists in two polymorphic forms. Liquid Assisted Grinding (LAG) was used as a mechanochemical synthetic tool. Attempts to produce cocrystals by LAG led to the formation of polycrystalline material. Both the polymorphs were characterized in the solid state by diffractometric, spectroscopic and thermal methods. Recrystallization by slow solvent evaporation was carried out when the above-referred techniques strongly suggest the formation of a new solid form. In those cases where crystals were obtained, single crystal X-ray diffraction experiments were performed. Crystal structure analysis suggests that the NIF molecules in both polymorphs adopt different conformations but exhibits a common hydrogen bonding motif. Thermal analysis suggests that the polymorphs are related enantiotropically. Our work is completed with additional stability studies performed at controlled relative humidity conditions and followed by PXRD.

[1] Aitipamula, S., Chow, P. S., Tan, R. B. H. (2014) CrystEngComm, 16, 3451.

[2] Prohens, R., Barbas, R., Portell, A., Font-Bardia, M., Alcobé, X., Puigjaner, C. (2016) Cryst. Growth Des., 16, 1063.

Keywords: Cocrystal polymorphism; Niflumic acid; Mechanochemistry; Crystal structure

This research was funded by Spanish Research Agency of the Spanish Ministry of Science and Innovation, cofunded with FEDER (UE): “Bioscaffold project” grant number PGC2018-102047-B-I00 (MCIU/AEI/FEDER, UE).

Halogen bond has been the focus of crystallography and chemical engineering for many decades. The effect of intramolecular halogen bonds on adjacent intramolecular hydrogen bonding has hardly been investigated. O-hydroxy sulfonyl Schiff bases are a suitable class of compounds to shed light on these bonding aspects. Series of halogen bonded sulfonyl Schiff bases were synthesized and characterized spectroscopically using mass, FTIR, and NMR methods. The three-dimensional molecular structures of all the sulfonyl Schiff base compounds were confirmed through single-crystal X-ray diffraction studies. The crystal structures of Schiff bases exhibit both inter and intramolecular hydrogen bond interactions. Packing of the structures shows hydrogen bonded 1D chain and π---π interaction generates 2D supramolecular structure. O–H···N intramolecular interactions form the five-membered pseudo chelate rings. The Schiff base structures are also stabilized by C–O···π, N–O···π, π···π interactions and leads to the 3D network through supramolecular synthons. The intermolecular interactions were then quantified using Hirshfeld surface analysis. Further, the density functional theory calculations were employed using B3LYP hybrid functional with a 6-311+G (d, p) level basis set to optimize the structural coordinates. The chemically active regions of the Schiff base molecules were identified from the plot of the molecular electrostatic potential surface. Furthermore, the atoms in molecules (AIM) and their applications to chemical bonding based on Bader's theory have been studied to understand the molecular interactions.

In the last decades, pharmaceutical cocrystallization has being recognized as an interesting approach to modulate the physicochemical properties of active pharmaceutical ingredients (APIs) [1]. Ethenzamide is an anti-inflammatory and analgesic drug, which major drawback is the low solubility in aqueous medium. On the other hand, polyphenols have been widely studied due to their antioxidant properties and their implication in the prevention of degenerative diseases, particularly cardiovascular diseases. These molecules are also “generally recognized as safe” (GRAS), which gives the opportunity to use them as coformers in pharmaceutical cocrystallization [2].

In this study six new ethenzamide-based cocrystals were obtained by mechanochemical synthesis. A complete solid-state characterization was carried out by X-ray diffraction, spectroscopic and thermal techniques. Accelerated aging conditions (40ºC and 75% of relative humidity) were used to evaluate their stability. To complete the study, in vitro cytotoxicity essays were performed by co-culture of mesenchymal stem cells (MSCs) with the new multicomponent materials. The results will be discussed to evaluate the influence of the position of the -OH groups, in the coformer molecule, on the physicochemical properties of the new cocrystals.

Separation of Lutidine Isomers by Selective Enclathration

Molecular selectivity by host-guest procedures is an increasing method to help in the separation of isomers¹. The separation of a component from a mixture may be carried out by exploiting the physico-chemical properties of the compounds in that mixture. The most common techniques, viz. distillation, crystallization, liquid−liquid extraction, and various forms of chromatography, rely on differences in solubility and vapor pressure of the components. In the case of molecular isomers, their macro-properties are often similar, rendering the traditional separation techniques inefficient. In such cases the process of enclathration by a suitable host compound is a useful technique.^2,3,4

In this study, the host compound 3,3′-bis(9-hydroxy-9-fluorenyl)-2−2′-binaphthyl, H1, has been employed to separate the six isomers of lutidine. Competition experiments showed that the preference for enclathration is in the sequence 3,4-LUT > 2,6-LUT > 2,3-LUT > 2,5-LUT > 2,4-LUT ≈ 3,5-LUT. The structures yielded results that agree with the ¹H NMR analyses and with the thermal analysis. The effects of mixed hosts and vapor-phase competitions were briefly explored with two extra hosts, namely, 2,2′-bis(1-hydroxy-4,5-dihydro-2:3,6:7-dibenzocycloheptadien-1-yl)biphenyl (H2) or 3,3′-bis(di-p-olylhydroxymethyl) -1,1′-binaphthyl (H3). Following this study, 2,2’bis(1-hydroxy-4,5-dihydro-2,3:6,7-dibenzocycloheptatrien-1-yl)-biphenyl, H2, was then employed to discriminate between all the pairs of lutidine isomers. The preference for guest enclathration follows the sequence 3,4-LUT>2,4-LUT≈3,5-LUT>2,5-LUT>2,3-LUT>2,6-LUT. This has been confirmed by guest-release endotherms measured by DSC. Four extra diol host compounds with similar structures were tested on pairs of lutidine isomers which were poorly separated by H2.

References:

[1] Nassimbeni, L. R. In Separations and Reactions in Organic Supramolecular Chemistry; Toda, F., Bishop, R., Eds.; Wiley: Chichester, 2004; Chapter 5.

[2] Yang,Y., Bai, P., Guo, X., Separation of xylene isomers: a review of recent advances in materials Ind. Eng. Chem. Res., 56 (2017), pp. 14725-14753.

[3] B. Barton, E.C., Hosten, P.L., (2016) Tetrahedron, 72, 8099-8105.

[4] Nassimbeni, L.R., Bathori, N.B., Patel, L.D., Su, H. & Weber E. (2015) Chem. Commun., 51, 3627-3629.

The distribution of the electron density on the surface of molecules is typically anisotropic. This leads to regions featuring positive potential that can behave as electrophilic sites in attractive interactions involving regions in surrounding molecules having a negative electrostatic potential. Based on this mindset, a systematic rationalization of intermolecular interactions began in the 1990s, when on the surface of halogen atoms a region of positive electrostatic potential, the so called σ-hole,[1] was identified and explored as a new tool in supramolecular chemistry.

Analogous σ-holes were then found on other elements of p-block of the periodic table (elements of groups 14,[2] 15,[3] and 16[4]), and at the same time the awareness grew that also chemical interactions can be rationalized as periodic properties. Nowadays, the attractive interactions occurring between these positive regions and nucleophilic sites are now topics of intense research.

Although in adducts involving d-block elements the identification of electrophilic and nucleophilic moieties is generally nontrivial, some σ-holes have been identified on metals in some of these adducts. This is the case, for instance, of positive σ-holes on the group 11 metals in respective halides[5].

Here, we report the crystal structures of adducts between nitrogen (pyridine derivatives) or oxygen (pyridine N-oxide derivatives) nucleophiles and tetroxides of osmium, showing short noncovalent contacts involving Os. Theoretical evidences suggest that these contacts are σ-hole interactions, and that similar adducts of other group 8 elements behaves in a similar way.[6] We propose the term “osme bond” (OmB, Om=Os, Ru, Fe) for naming the noncovalent interactions wherein group 8 elements behave as electrophile.

In this work, I have analyzed the distribution of the shortest periods in homomolecular crystals of organic compounds, in which there are aromatic bonds, the influence of halogen atoms on this distribution was revealed, and energy analysis was carried out for several substances belonging to the group of 4 Å-structures, according to the method described in [1]. Сrystal structures investigated at normal pressure were extracted from the CSD version 5.41 (November 2019) + 3 updates using combinations of querries in ConQuest and the pre-defined best room temperature list [2].

As shown in Fig. 1a, at a large bin size, the histogram for reduced cell a values of all crystals under consideration (set I) can be well described by a single normal distribution function. As the bin size decreases, additional maxima begin to appear on the histogram (Fig. 1b), the position of which remains almost constant when the bin size changes from 0.3 to 0.03 Å. Similar distributions were plotted for molecules in which there are halogen atoms in any position (set II) and halogen atoms associated with a non-metal atom forming an aromatic bond (set III).

The position of the minimum following the maximum at 3.9 Å for all the above-mentioned sets corresponds to about 4.3 Å. It turned out that the parts of substances with the shortest period up to 4.3 Å of the total number of substances in each set are 1.9% for I, 2.8% for II, and 3.5% for III. A reliably determined substance with the shortest period (3.6021 Å) in all sets is 1,3,4,5,6,8-hexafluoronaphthalene-2,7-diamine (DAFMUV), in which the contribution of two strongest (E₁) translational molecular contacts to the total packing energy (PE) of the crystal (calculated with Mercury) is 55% (the energy coordination number, N_E, is two). At the other end of all sets is 2-bromo-4-chloro-6-[(2,4-dimethylphenylimino)methyl]phenol (EHUHIZ) with the reduced cell a equal to 4.2995 Å, N_E = 2, 2·E₁/PE = 0.48.

[1] Grineva, O. V. (2017). J. Struct. Chem. 58, 373.

[2] Streek van de, J. (2006). Acta Cryst., B 62, 567.

The work is a part of researches on the theme No. 121031300090-2.

Electrostatic self-assembly of organic crystals from charged macrocycles

K. Kravets¹, M. Kravets¹, V. Sashuk¹, O. Danylyuk¹

¹Institute of Physical Chemistry, Polish Academy of Sciences

kkravets@ichf.edu.pl

Macrocyclic host molecules are versatile building blocks in the supramolecular chemistry and crystal engineering. Depending on their structure and properties, macrocycles have found numerous applications in the host-guest systems, sensing, catalysis, design of porous materials, etc. Here we describe our approach towards design of molecular crystalline assemblies using oppositely charged macrocyclic building blocks, anionic p-sulfonatocalix[4]arene and cationic pillar[n]pyridiniums. P-Sulfonatocalix[4]arene with electron-rich basket-like cavity is well-known water-soluble supramolecular host, capable of forming various types of assemblies, such as bilayer clay-type structures, capsules, nanometer tubules, spheres or Russian-doll assemblies.[1] Pillar[n]pyridiniums are new family of water-soluble inherently cationic host molecules of prismatic electon-deficient cavities.[2] These two types of macrocyclic hosts are complementary in terms of charge, size and shape. Their self-assembly is guided mainly by the electrostatic attraction between anionic sulfonate groups of calix[4]arene and positive charge on the pyridinium rings of the cationic macrocycles. The crystallization in gel and liquid-liquid diffusion methods have been used for the obtaining suitable crystals build from mixed macrocycles for single crystal X-ray diffraction analysis. The structural aspects of the supramolecular architectures and main non-covalent interactions guiding the assembly will be discussed.

[1] Scott, J., Dalgarno, M.J., Hardie, J., Mohamed, M., Colin L. R. (2003). Chem. Eur. J. 9, 2834.

[2] Kosiorek, S., Butkiewicz, H., Danylyuk, O., Sashuk, V. (2018). Chem. Commun. 54, 6316.

Keywords: p-sulfonatocalix[4]arene; pillar[n]pyridinium; complex.

National Science Center for funding the research Grant 2019/35/O/ST4/01865 .

Spin-crossover (SCO) materials can change their spin state in response to a variety of stimuli such as temperature, light and guest molecules. These transitions are accompanied by changes in magnetic properties and often a colour change, making them attractive as smart materials.¹

Octahedral metal complexes containing iron(II) are known to be SCO active when certain ligands, often N-donors, are bound to the metal.² In framework and coordination polymer based spin-crossover materials, the cooperativity of the transition is aided by the covalent interactions present. However, in molecular complexes, the cooperativity of a transition relies on the elastic interactions that are present in the crystal structure.³ Therefore, designing molecular SCO materials with specific properties is very challenging due to the vast number of structure-directing intermolecular interactions that need to be considered. The difficulty of design becomes even more complex due to the potential for solvate and polymorph formation.^4,5

Thus, we have used crystal engineering concepts in the design and syntheses of a series of structurally-related SCO materials. We have used variable temperature single crystal X-ray diffraction analysis to obtain SCO curves, by following the octahedral volume at the Fe(II) center (Fig. 1). This variable temperature analysis has also provided valuable insight into the subtle structural changes such as distortions as well as the more drastic crystallographic symmetry-breaking phase transitions that we have seen in our materials.⁶ This work demonstrates design tools that will greatly benefit and evolve the way in which new and desirable SCO materials will be discovered.

1. A. Bousseksou, G. Molnár, L. Salmon and W. Nicolazzi, Chem. Soc. Rev., 2011, 40, 3313–3335.

2. J. Olguín and S. Brooker, Coord. Chem. Rev., 2011, 255, 203–240.

3. W. Nicolazzi and A. Bousseksou, Comptes Rendus Chim., 2018, 21, 1060–1074.

4. M. Hostettler, K. W. Törnroos, D. Chernyshov, B. Vangdal and H. B. Bürgi, Angew. Chemie - Int. Ed., 2004, 43, 4589–4594.

5. J. Tao, R. J. Wei, R. Bin Huang and L. S. Zheng, Chem. Soc. Rev., 2012, 41, 703–737.

6. L. Birchall and H. Shepherd, Manuscript in Preparation.

The single crystal of barium dihydrogenomonophosphate, Ba(H₂PO₄)₂ was prepared by the direct method. This compound exists in two forms: one orthorhombic, the other triclinic. In this work, we are interested in the triclinic form from the vibrational and crystalline sides too.X-ray crystallography showed that this compound crystallizes in the triclinic centrosymmetric with space group P-1 (Z=2) with a = 6.9917(5)Å,b = 7.1929(5)Å,c = 7.9667(9)Å,α = 104.517(8)°,β = 95.918(7)° and γ = 109.459(6). The structure was solved from 3444 independent reflections with R = 0.0198 with wR= 0.0633.The bands observed in the infrared and Raman spectra of Ba(H₂PO₄)₂ are assigned based on the literature results and the theorical group analyses carried out in the group of factors Ci. We were based on density functional theory (DFT / B3LYP) methods with the LanL2DZ base set for the calculation of Optimal molecular geometry, harmonic vibration frequencies, infrared intensities and Raman scattering activities. The HOMO-LUMO properties and geometries of this compound have been determined and discussed. The computational structural parameters are generally in agreement with the experimental investigations. The theoretical infrared and Raman spectra for the title compound have been constructed.

Le interazioni σ-Hole sono una sottoclasse di interazioni non covalenti in cui un'area di potenziale elettrostatico positivo sull'estensione di un legame covalente forma un'interazione netta attraente con un sito ricco di elettroni. Il legame tetrel (TtB) è un'interazione σ-foro in cui l'atomo elettrofilo è un elemento del gruppo 14 della tavola periodica. Il forte interesse per questa interazione è legato al ruolo fondamentale del carbonio nella chimica organica e bio [1].

Tuttavia, la ridotta polarizzabilità del carbonio rende questo elemento il meno incline nel Gruppo a essere coinvolto nella formazione dei TtB. In relazione al nostro lavoro sui derivati ​​del metonio come donatori di TtBs [2], proponiamo sali di metilene bis -piridinio come secondo sistema modello per studiare le caratteristiche geometriche ed energetiche di questa forza sui derivati -CH ₂ -. Le strutture cristalline ottenute presentano contatti brevi e lineari tra il metilene carbonio e vari nucleofili; la formazione di queste interazioni è interpretata come il risultato del forte effetto di ritiro degli elettroni degli atomi di azoto positivi legati direttamente al carbonio.

Le strutture cristalline sono state studiate con vari strumenti per valutare la natura del contatto, ottenendo la conferma inequivocabile che le interazioni presentate dovrebbero essere considerate TtB, completando così il nostro precedente studio sui derivati ​​dell'acido barbiturico [3]. I TtB su questi composti si sono rivelati abbastanza robusti da essere in grado di guidare l'impaccamento cristallino di addotti specifici e costruire architetture distintive.

A σ-hole interaction can be defined as a net attractive interaction between an area of positive electrostatic potential generated on the outer surface of an atom by one of the covalent σ-bonds it is involved in and an electron rich site (Lewis base, e.g., a lone-pair possessing atom or an anion) in the same or another molecular entity. According to the formalism of naming these interactions from the group of the periodic table the atom bearing the σ-hole belongs to, an interaction between a Lewis base and an atom of the Group 14 functioning as the electrophilic site is dubbed Tetrel Bond (TtB).

The N-methylammonium residue is ubiquitous in biology and chemistry, and many N-methylammonium bearing compounds are often used in crystal engineering for the designed formation of crystal architectures.

We propose here a series of 1,6-bis-trimethylammonium hexane crystal structures displaying a close contact between one carbon atom of an N-methylammonium moiety and a neutral and lone-pair-possessing atom or an anion. The geometrical features of these interactions are those typical for a TtB (i.e., linearity of the N⁺ ̶ C···electron-rich site angle, distance between C and the electron-rich site shorter than the sum of VdW radii of involved atoms) and are maintained when both charged and neutral species approach the N-methylammonium carbon.

Hirschfeld Atom Refinement (HAR) and Atom In Molecules (AIM) computational analyses have also been carried out to asses if the interaction occurring in the crystal packing between the N-methylammonium moiety and the electron rich sites are in fact hydrogen bonds (HB) or TtBs. The latter hypothesis is indeed confirmed by these analyses.

In conclusion, the reported experimental and theoretic results indicate that the close contacts between the carbon atom of an N-methylammonium residue and an electron-rich site are TtBs and that the interaction can be robust enough to be employed as an additional tool in the design of crystalline architectures involving this moiety. It can be expected the interaction plays a role in driving or influencing recognition processes involving biomolecules containing the N-methylammonium residue.

At the moment, single-crystal diffraction remains the most popular and widespread method for solving spatial structures of varying complexity for coordination chemistry and biology. Using a synchrotron radiation source for conducting this type of experiment allows one to achieve high resolution in the shortest time.

Despite the daily increase in demand for solving coordination chemistry problems and, accordingly, working with small molecules, the number of synchrotron beamlines for single crystal diffraction by small molecules is quite small, and protein crystallography stations are given priority.

The main ones are stations I19 on Diamond, 11.3.1 on ALS, BM01 on ESRF, XRD on Elettra, while the quantity of beamlines specialized for macromolecular objects are an order of magnitude larger. This is mainly due to the popularity of biological problems in the modern world, as well as the peculiarities of macromolecule crystals, because of which data collection at a laboratory source becomes almost impossible.

To make it easier for Russian users and provide an additional opportunity for foreign users to access this type of synchrotron beamline and to quickly collect high-resolution diffraction data from a wide range of samples, one of the installations of the Kurchatov synchrotron radiation source was optimized for working with crystalline samples in mass flow measurements, which allowed it to become a device that has no analogues in Russia for conducting this type of experiment [1]. Subsequently, to increase the quality of the data obtained, the diffractometer from the Belok station was transferred to the XSA beamline (Fig. 1). In addition, due to an increase in the intensity of the photon beam and the quality of the data collected, the number of experiments on the study of protein crystals has increased several times.

Raytracing of the XSA station was carried out and a noticeable increase in the photon flux on the sample was shown in comparison with the Belok station, where the hight-throutput single-crystal small-molecular crystallography experiments had previously been started [2]. The optimization of all stages of the structure solution and the demonstration of the quality of the data obtained were carried out using various classes of compounds as an example.

Serial femtosecond X-ray crystallography (SFX) involves the collection of thousands to up to millions of images in a few minutes. Being able to process these data at speeds that match the data collection rate is critical for scientists who need fast feedback on their data quality. Doing this while simultaneously creating data that fits FAIR standards (Findability, Accessibility, Interoperability, and Reusability) is challenging, and has been the focus of the High Data-Rate Macromolecular Crystallography (HDRMX) working group. We have recently published a consensus best-practice NeXus representation of a complex, multi-panel detector, the Jungfrau 16M from the SwissFEL Bernina endstation [1-2]. 256 individual panels are described and positioned in real space using a vector transformation system that is standard in NeXus, is machine readable, and completely specifies the experimental geometry.

We have implemented this approach during a subsequent data collection at the EuXFEL on the AGIPD detector, similar in geometry to the Jungfrau 16M [3]. Here we collected data at 2kHz and demonstrated the ability to process these data at these speeds with the software package DIALS on the Maxwell computing cluster at DESY, using 96 nodes, 80 cores per node. This required careful attention to how the data were laid out on disc. These methods and the NeXus framework for SFX will be presented.

[1] Bernstein, H.J., et. al. (2020). Gold Standard for macromolecular crystallography diffraction data. IUCrJ, 7(5) 784–792.

[2] Ingold, G., et.al. (2019). Experimental station Bernina at SwissFEL: condensed matter physics on femtosecond time scales investigated by X-ray diffraction and spectroscopic methods. J. Synchrotron Rad. 26, 874–886.

[3] Allahgholi, A., et. al. (2015). AGIPD, a high dynamic range fast detector for the European XFEL. JINST 10 C01023.

The work was supported in part by funding from Dectris Ltd., from the U. S. Department of Energy (BES KP1605010, KP1607011, DESC0012704), from the U. S. National Institutes of Health (NIGMS P30GM133893, R01GM117126).

We present a new, highly efficient metric for comparison of crystallographic lattices based on the Dirichlet cell (or Wigner-Seitz cell) which provides a very similar topology to that obtained with the G⁶ and S⁶ metrics, but without the combinatorial explosions sometimes seen with those metrics. As with G⁶, DC⁷ begins with Niggli reduction, but instead of comparing the G⁶ parameters, [a.a, b.b, c.c, 2 b.c, 2 a.c, 2b.c] or the S6 parameters [b.c, a.c, a.b, a.d, b.d, c.d], the squares of the 13 lengths of the Niggli cell edges, face diagonals and body diagonals considered in finding the Dirichlet cell, [||a||, ||b||, ||c||, ||b+c||, ||b-c||, ||a+c||, ||a-c||, ||a+b||, ||a-b||, ||a+b+c||, ||a+b-c||, ||a-b+c||, ||-a+b+c||] are sorted and the seven shortest taken as an identifying spectrum, corresponding to the distances between the pairs of faces forming the general Dirichlet cell. It is conjectured that the seven shortest of the thirteen lengths are sufficient to characterize the Niggli reduced cell from which they came, but at present it is best simply to retain the original cell along with the derived spectrum rather than try to recover the cell from the spectrum.

Work supported in part by supported by funding from the U.S. National Institutes of Health NIGMS (grant No. P30GM133893), and by the U. S. Department of Energy Office of Biological and Environmental Research (grant No. KP1607011), Office of Basic Energy Sciences (contract No. DE-SC0012704).

Efficient 1-dimensional seed-skewness algorithm adapted for X-ray diffraction signal detection together with signal integration procedure are presented. The method was shown to work well for both the standard single-crystal X-ray diffraction data, as well as, for more specific photocrystallographic time-resolved Laue data collected at Advanced Photon Source and European Synchrotron Radiation Facility. It enables reasonable separation of signal from the background in single 1-dimentional data vectors, it is capable of determining small changes of reflection shapes and intensities resulting from exposure of the sample to laser light, and allows for extracting relatively weak reflections from the background. The last is possible through adjusting of “trust level” and “signal level” parameters in the algorithm. Otherwise, the procedure is objective and does relay only on skewness computation and its subsequent minimization, which enable the best possible background estimation. The intensities of strong reflections are determined comparably as via the Kruskal-Wallis test method, whereas weak reflections are more sensitive to the algorithm setting parameters. In turn, both methods estimate the background level equally-well.

R.K., D.S. and P.Ł. would like to thank the SONATA grant (2016/21/D/ST4/03753) of the National
Science Centre in Poland for financial support. The time-resolved X-ray diffraction experiments
were performed at the ID09 beamline of the European Synchrotron Radiation Facility (ESRF),
Grenoble, France. The research used resources of the Advanced Photon Source, a U.S. Department
of Energy (DOE) Office of Science User Facility operated for the DOE Office of Science by
Argonne National Laboratory under contract No. DE-AC02-06CH11357. Use of BioCARS was
also supported by the National Institute of General Medical Sciences of the National Institutes of
Health (NIH) under grant No. R24GM111072 (note: the content is solely the responsibility of the
authors and does not necessarily represent the official views of NIH). Time-resolved set-up at
Sector 14 was funded in part through collaboration with Philip Anfinrud (NIH/NIDDK).

The Cambridge Structural Database (CSD)¹ is a database of over 1.1 million small molecule organic and metal-organic crystal structures. Each structure added to the database is curated to ensure important details about the structure are recorded alongside the entry. This curation process is particularly important for structures submitted directly to the CSD as a CSD Communication, with no accompanying journal article. As the CSD continues to grow and new techniques emerge it is essential that information is recorded consistently to ensure the data is findable. Consistency also allows the CSD to be utilised in data-driven approaches, such as machine learning, reducing the need for curation before it is ingested into models.

In addition to processing new data each year, the CCDC undertakes a series of improvement projects to assess the data stored in the CSD, ensure it is consistent and correct any errors. Ongoing projects also aim to capture additional information about the structure, such as if a specialist refinement technique is used. In addition, the CCDC is working towards updating the underlying format of the database, allowing new metadata about the structure to be stored. This poster will present highlights from work to continue to improve and grow the CSD.

1. Groom, C., Bruno, I., Lightfoot, M., & Ward, S. (2016). Acta Cryst. B 72, 171-179.

Reliable knowledge about structure and properties of chemical compounds is essential for pharmacology, food safety, environment preservation, design of new materials and understanding of functions of small molecules in living organisms. The number of unique substances known to humanity currently exceeds 100 million [1], and only the use of computers makes coping with the amount of available information possible.

The most accurate data about the structure of molecules are obtained from X-ray crystallographic (XRC) analyses. Currently, about 1 million crystal structures are known and the use of this information is enabled by crystallographic databases [2‑4]. These data, however, are not immediately usable by chemists. XRC determines accurate 3D coordinates of each atom in a crystal, and, in extreme cases, electron densities along chemical bonds, but it does not detect atomic charges, bond types or the presence of lone electrons in radicals. All such information needs to be inferred from the crystallographic data based on current chemical knowledge, either manually [5], or using heuristics, implemented as computer programs [6‑7]. However, the existing programs rarely consider information other than the coordinates. What is more, heuristics are usually specifically tailored for organic molecules. As a result, the derivation of chemical annotations by these programs is not always reliable, especially for metal-organic complexes.

Nevertheless, atomic coordinates in crystal structure reports are usually accompanied by additional chemical information. Systematic chemical names are often provided or derivable from publication titles or texts. Connectivity details in machine-readable formats may follow as well, albeit usually in forms not suitable for automated overlaying on the coordinate data. All this information could be employed to annotate crystallographic data with chemical details provided the mapping between different representations is known.

The largest open access crystallographic database, the Crystallography Open Database (COD, [2]), contains computer readable chemical descriptions for nearly half of its entries [5]. Currently, these descriptions are not linked to particular atoms in crystals, thus studies that require the combined crystallographic and chemical information have to infer the correspondence on their own. This task is tedious, involves repetition of work, and disregards readily available high-quality chemical descriptions.

Graph-based algorithms can be used to determine the links between the crystallographic and chemical data in the COD. Establishment of isomorphism between graphs derived from atomic coordinates and graphs derived from chemical descriptions enables the assignment of chemical attributes to individual bonds and atoms. Open-access nature of the COD allows dissemination of this information under FAIR (Findability, Accesibility, Interoperability and Reusability [8]) principles on the Web, immediately enabling numerous computational searches and research by pharmaceutical companies and academic groups. Thus, publishing and maintaining chemical annotations for crystallographic data in the COD would enhance research capabilities in pharmaceutical science, bio- and cheminformatics, materials science.

[1] CAS REGISTRY, https://www.cas.org/support/documentation/chemical-substances

[2] Gražulis et al. (2012). Nucleic Acids Research, 40. doi:10.1093/nar/gkr900

[3] wwPDB consortium (2019). Nucleic Acids Research, 47. doi:10.1093/nar/gky949

[4] Groom & Allen (2014). Angewandte Chemie International Edition, 53, 3. doi:10.1002/anie.201306438

[5] Quirós et al. (2018). Journal of Cheminformatics, 10, 1. doi:10.1186/s13321-018-0279-6

[6] O'Boyle et al. (2011). Journal of Cheminformatics, 3. doi:10.1186/1758-2946-3-33

[7] Willighagen et al. (2017). Journal of Cheminformatics, 9, 1. doi:10.1186/s13321-017-0220-4

[8] Wilkinson et al. (2016). Scientific Data, 3. doi:10.1038/sdata.2016.18

The development of new classes of high energetic materials (HEM) with high efficiency and low impact sensitivity is in the focus of numerous experimental and theoretical studies [1]. However, the high efficiency of HEM molecules is usually related to the high sensitivity towards detonation [2]. It is known that the sensitivity of HEM molecules towards detonation depends on many factors, including oxygen balance, energy content, and positive values of electrostatic potential above the central regions of the molecular surface. Analysis of positive values of molecular electrostatic potentials (MEP) showed to be an excellent tool in the assessment of impact sensitivities of high energetic molecules since positive values of MEP above the central regions of molecules are associated with high sensitivity towards detonation of HEM molecules [2]. Here we analysed the influence of hydrogen bonding on the values of the electrostatic potentials of fragments of HEM molecules extracted from crystal structures [3].

Crystal structures of three selected high energetic molecules were extracted from Cambridge Structural Database (CSD) and analysed in terms of non-covalent interactions. Three well-known HEM molecules were selected for the analysis: 1,3,5-Trinitrobenzene (TNB), 2,4,6-Trinitrophenol (TNP), and 2,4,6-Trinitrotoluene (TNT). Geometries of these molecules were used for electrostatic potentials calculations and for the design of model systems for interaction energies calculations. Electrostatic potential maps were calculated for TNB, TNP, and TNT geometries extracted from crystal structures for free molecules and molecules involved in hydrogen bonding. Values of electrostatic potentials above the central regions of molecules were analysed and compared for non-bonded HEM molecules and HEM molecules involved in hydrogen bonding.

Analysis of crystal structures showed that selected HEM molecules are involved in three types of hydrogen bonds: O-H…O-N interactions, C-H…O-H interactions, and in the case of TNP molecule O-H…O-H interactions. Analysis of positive values of the electrostatic potentials showed that hydrogen bonds have a significant influence on the values of the electrostatic potential in the central regions of HEM molecules. Calculations performed at M06/cc-PVDZ level showed that in the case when HEM molecules are involved in hydrogen bonding as hydrogen atom donors, positive values of electrostatic potentials in the centres of molecules decreased by 20 – 25%. In the case when HEM molecules were involved in hydrogen bonding as hydrogen atom acceptors, positive values of electrostatic potentials in the centres of HEM molecules increased by 10%.

Results presented in this study show that hydrogen bonds could be used as a tool for the modification of positive values of MEP above the central regions of HEM molecules and for the modification of their sensitivities towards detonation. Moderate change of positive electrostatic potential values above the central regions of HEM molecules upon formation of hydrogen bonds provide an opportunity for fine-tuning of sensitivities of HEM molecules towards detonation.

This research was supported by the Science Fund of the Republic of Serbia, PROMIS, #6066886, CD-HEM. This work was supported by the Serbian Ministry of Education, Science and Technological Development (Grant No. 451-03-9/2021-14/200026, 451-03-9/2021-14/ 200288 and 451-03-9/2021-14/200168).

[1] Liu, G., Wei & S.-H., Zhang, C., (2020). Cryst. Growth Des. 20, 7065.

[2] Politzer, P. & Murray, J. S., (2015). J Mol Model, 21, 1.

[3] Kretić, D. S., Radovanović, J. I. & Veljković, D. Ž., (2021). Phys. Chem. Chem. Phys., 23, 7472.

Crystallography Open Database (COD) [1] is the largest open-access FAIR [2] collection of small-molecule crystal structures that currently contains over 475 000 entries. In recent years, several notable improvements have been made to enhance the data curation process as well as expand the data search capabilities.

Data curation tasks of the COD heavily rely on the Crystallographic Information Framework (CIF) therefore recent CIF-related IUCr innovations stipulated the appropriate changes to the COD software. The F/LOSS cod-tools software package was updated to support the CIF2 data format [3] and the DDLm [4] dictionary language thus enabling the routine formal validation of all COD CIF files against the latest generation of CIF dictionaries [5]. The collected validation results were compiled in a publicly available CIF validation issue database that has already proven useful in data maintenance and ontology development tasks. A set of programs intended to aid in the dictionary migration from the now deprecated DDL1 language to the novel DDLm language was also created.

Effective search is another aspect of the COD database that has been greatly improved. Efficient chemical structure search in a crystallographic database requires that certain properties of the crystallised materials, such as molecular connectivity and other chemical features, be described in a machine-readable way. However, completely automated derivation of such information from CIF files is difficult and often provides suboptimal results. With this in mind, a set of high-quality manually curated SMILES that cover more than 40% of all COD entries have been made publicly available and can be used for chemical substructure search in the COD or for any other purpose on an open-access basis. The conventions that have been followed to represent various types of compounds as well as description of the semi-automatic SMILES derivation pipeline have also been extensively described [6] to improve the reusability and reproducibility of the data.

The COD data search capabilities were even further enhanced by implementing the OPTIMADE application programming interface (API) [7, 8] that aims to improve the interoperability between materials databases. It is extremely beneficial to be able to access information from multiple materials databases as they often differ in fidelity and focus across material classes and properties. However, retrieving data from multiple databases is difficult as each database has its own specific API. Moreover, as the APIs of individual databases inevitably evolve, existing clients must also evolve and are required to translate the responses from the new API to the internal representation of the client, which can require significant effort. The OPTIMADE consortium aims to alleviate most of these problems by providing a common RESTful API based on the JSON:API specification [9].

These recent changes to the COD are aimed at improving the data quality assurance process as well as ensuring that the data remain open, FAIR and readily available for a diverse range of applications in fields such as cheminformatics and materials science.

[1] Gražulis, Saulius et al. (2012). Nucleic Acids Res. 40, D420. doi: 10.1093/nar/gkr900

[2] Wilkinson, Mark D. et al. (2016). Scientific Data, 3. doi: 10.1038/sdata.2016.18

[3] Bernstein, Herbert J. et al. (2016). J. Appl.Crystallogr, 49, 277. doi: 10.1107/S1600576715021871

[4] Spadaccini, N. & Hall, S. R. (2012). J. Chem. Inf. Model. 52, 1907. doi: 10.1021/ci300075z

[5] Vaitkus, Antanas et. al. (2021). J. Appl. Crystallogr. 50, 661. doi: 10.1107/S1600576720016532

[6] Quirós, Miguel et. al. (2018). J. Cheminformatics 10. doi: 10.1186/s13321-018-0279-6

[7] Andersen, Casper W. et al. (2020). The OPTIMADE Specification. doi: 10.5281/zenodo.4195050

[8] Andersen, Casper W. et al. (2021). OPTIMADE: an API for exchanging materials data. url: https://arxiv.org/abs/2103.02068

[9] JSON:API v1.0. url: https://jsonapi.org/format/1.0/

During macromolecular crystallography (MX) data collection one or more crystals are exposed to a high flux of ionising radiation, which even at cryo-temperatures can damage the crystal(s), causing structural and chemical changes. If sufficiently severe, this damage can prevent solution of the crystal structure. However, even when structure solution remains possible, specific damage artefacts can confuse the biological conclusions drawn from a structure: hence their identification is important. Traditionally however the detection of specific radiation damage artefacts within crystal structures has proven difficult.

To address this problem, previously the Garman group developed the B_Damage metric^[1], calculated by the CCP4^[2] program RABDAM^[3]. B_Damage is a per-atom metric that highlights potential sites of specific radiation damage as atoms with high B-factor values as compared to other atoms in a similar local environment in the parent crystalline structure. Whilst this metric is useful at identifying damage artefacts in individual structures, unfortunately B_Damage values can not be compared between different structures. To address this limitation, here we present a derivative of the B_Damage metric, B_net, a per-structure metric that can be used to compare the relative damage suffered by different protein crystal structures. After validating that B_net is an appropriate metric on a dataset of structures known to contain specific damage artefacts, we use B_net to analyse the specific radiation damage present in a dataset of 94,145 protein crystal structures in the Protein Data Bank (PDB). Notably, many of the structures identified as damaged by B_net, and which on closer inspection contain obvious damage artefacts, have reasonable or excellent values for the metrics typically reported for PDB structures.

[1] Gerstel, M., Deane, C. M. & Garman, E. F. (2015). J. Synchrotron Rad. 22, 201–212.

[2] Winn, M. D. et al. (2011). Acta Cryst. D67, 235–242.

[3] Shelley, K. L., Dixon, T. P. E., Brooks-Bartlett, J. C. & Garman, E. F. (2018). J. Appl. Cryst. 51, 552–559.

The Taiwan Photon Source (TPS) 13A biological small-angle X-ray scattering (SAXS) beamline at the National Synchrotron Radiation Research Center was recently opened to users. The beamline is designed for probing biological structures and kinetics in wide length and time scales, from angstrom to micrometer and from microsecond to minutes. A 4-m IU24 undulator provides high flux X-rays in the energy range of 4.0 to 23.0 keV. MoB₄C double-multilayer and Si-(111) double-crystal monochromators (DMM/DCM) are combined on the same rotating platform for a smooth transition from high flux beams (~4x10¹⁴ photons/s) to a high-energy-resolution beam ((delta E)/E^­ ~ 1.5x10^-4). USAXS and microbeam modes are also available through a series of carefully designed optical components. An X-ray detecting system comprising two in-vacuum detectors was designed to perform synchronized small- and wide-angle X-ray scattering data collections at the endstation.

TPS 13A beamline adopts the Experimental Physics and Industrial Control System (EPICS) for integrated hardware and software controls, including all motors of the optical components and their corresponding sensing and cooling systems. Communication among local systems was achieved via defined process variables (PVs) provided by the EPICS Input/Output Controller (IOC) program. We have integrated two main clients of PVs: (1) Control-System Studio (CSS) GUI and (2) command-line system SPEC for beamline control. The data acquisition on TPS 13A is based on a synchronous operation of all detectors, ms-shutter, and intensity monitors. With the high frame rate of the detectors and a large number of pixels, a typical protein solution SEC-SAXS experiment can generate a few GB of data. The data storage, remote data access, and data treatment problems become essential if the user community continues to grow and even more critical for future high-throughput screening applications. Here we collaborate with Academia Sinica Grid-computing Center to create an online platform called Distributed Cloud Operating System (DiCOS)-BioSAXS platform (https://bioswan.twgrid.org/). It provides TPS 13A BioSAXS beamline users a friendly interface to access their experimental data, analyze data, and submit SAXS simulation jobs.

MicroMAX at the first 4th generation storage ring [1] at MAX IV Laboratory is a new beamline providing the macromolecular crystallography field with a new powerful tool. The main applications are serial crystallography, time-resolved science, and micro-crystallography.
The X-ray beam at the sample, provided by a 156-period in-vacuum undulator, will have 1013 photons/second in monochromatic mode (5-25 keV energy range) and up to 1015 photons/second using a wider energy bandpass mode (10-13 keV energy range). The beam focusing will use compound refractive lenses with final focusing by either lenses or mirrors to give a focused beam down to 1 micrometer but flexible and easily tailored to the experimental needs.
The beamline will offer different sample delivery systems for serial crystallography, in particular fixed-target and injector-based systems but be flexible to accommodate other setups. In addition, the experiment setup will also provide a highly automated mode for oscillation data collection including a robotic sample changer. The setup will include a chopper providing short X-ray pulses (down to microseconds) and instrumentation for different time-resolved experiments. The detector stage will host two area detectors, a photon-counting and an integrating detector.
The possibility to combine all these different modes and instrumentation in a flexible way will allow to cater a wide range of experiments in structural biology including methods not yet developed.
The beamline will use the same experimental control system, MXCuBE3, and information management system, ISPyB, as the existing BioMAX beamline [2].
MicroMAX will have a laboratory for working with different sample environments and a laboratory for sample preparation. Additional infrastructures including a bio-laboratory and resources for data handling and analysis are shared with other beamlines. The beamline has a second experiment hutch that will be taken in operation at a later stage. It will allow preparation of specialized setups while experiments are done in the first hutch.
X-ray commissioning of MicroMAX is planned to start in 2022. MicroMAX is funded by the Novo Nordisk Foundation.
The MAX IV Laboratory macromolecular crystallography facilities include the BioMAX beamline in user operation since 2017 and the FragMAX fragment screening facility [3].
[1] Tavares, P. F., Al-Dmour, E., Andersson, A., Cullinan, F., Jensen, B. N., Olsson, D., Olsson, D. K., Sjöström, M., Tarawneh, H., Thorin, S. & Vorozhtsov, A. (2018). J. Synchrotron Rad. 25, 1291–1316. DOI:10.1107/S1600577518008111
[2] Ursby, T., Åhnberg, K., Appio, R., Aurelius, O., Barczyk, A., Bartalesi, A., Bjelčić, M., Bolmsten, F., Cerenius, Y., Doak, R. B., Eguiraun, M., Eriksson, T., Friel, R. J., Gorgisyan, I., Gross, A., Haghighat, V., Hennies, F., Jagudin, E., Norsk Jensen, B., Jeppsson, T., Kloos, M., Li-don-Simon, J., de Lima, G. M. A., Lizatovic, R., Lundin, M., Milan-Otero, A., Milas, M., Nan, J., Nardella, A., Rosborg, A., Shilova, A., Shoeman, R. L., Siewert, F., Sondhauss, P., Talibov, V., Tarawneh, H., Thånell, J., Thunnissen, M., Unge, J., Ward, C., Gonzalez, A. & Mueller, U. (2020) J. Synchrotron Rad. 27, 1415–1429. DOI:10.1107/s1600577520008723
[3] Lima, G.M.A., Talibov, V.O., Jagudin, E., Sele, C., Nyblom, M., Knecht, W., Logan, D.T., Sjögren, T. & Mueller, U. (2020) Acta Crystallogr D Struct Biol. 76, 771-777. doi: 10.1107/S205979832000889X

P11 at PETRA III in Hamburg is a versatile beamline for macromolecular crystallography (1). The photon energy can be adjusted between 5.5 - 28 keV with the possibility of using a CdTe-detector for higher energies (> 22 keV). Beam sizes are available between 200 x 200 μm and 4 x 9 μm with a maximum photon flux of 1e13 ph/s at 12 keV.

P11 is optimized for high-throughput crystallography. EIGER2 X 16M detector is fully integrated since spring 2021 and sample cycle of less than 2 min can be reached. The automatic sample changer at P11 is based on the unipuck format with a total capacity of 23 pucks (368 samples) and a mounting cycle of 20 s.

Remote access was established in spring 2020 and enabled fast-track access for SARS-CoV2 related projects (e.g. 1-4) and since May 2020, almost normal user operation, despite the pandemic restrictions.

The P11 setup in the experimental hutch is very flexible and allows to accommodate various non-standard experiments e.g. via the long term proposal (LTP) scheme. Serial crystallography at P11 is enabled with sample delivery through various types of solid supports or the tape-drive setup, which also enables time-resolved experiments by the mix-and diffuse method (5). Serial data collections are implemented as fast 2D scans or as series of rotation wedges in the graphical user interface; full integration of tapedrive experiments is in progress. OnDA (6) is available for real time evaluation of SSX data and implementation of real-time SSX processing is in progress within an LTP.

1. Rut et al. (2020) Nat. Chem. Biol., 2020
2. Qiao et al. (2021) Science 10.1126/science.abf1611
3. Oerlemans et al. (2021) RSC Medicinal Chemistry
4. Günther et al. (2021) Science 10.1126/science.abf7945
5. Beyerlein et al. (2017) IUCrJ 4:769
6. Mariani et. al. (2016) J. App. Cryst. 49:1073

Unattended X-ray data collection of macromolecules is in increasing demand by an ever more diverse research community, both academic and industrial, especially under the current situation of restricted access to research facilities due to the global pandemic. To better serve the user’s needs, and to allow automated and high-throughput operation, a sample changer that can perform autonomous crystal screening and data collection of up to 48 samples per session has been developed. The SCOUT sample changer centers the sample initially by means of visual loop centering in conjunction with feature recognition algorithms. In the case of opaque samples, centering by means of orthogonal X-ray scans can also be performed. The samples are kept safe in a custom designed, twin dewar system to minimize ice buildup upon storage and operation, while the six-axis, collaborative robotic arm is mounted on the enclosure ceiling to ensure a minimal footprint during manual operation. The system can be fitted to any D8VENTURE platform providing an exciting upgrade path to existing laboratory hardware. A comprehensive software package completes the system providing fully customizable, automatic routines for crystal screening, strategy determination, data collection and further downstream data processing.

Macromolecular crystallography instruments around the world are mostly set on a single or handful of configurations. These makes them more predictable and more reliable. At the same time, current throughput demand on MX beamlines squeezes more and more the time for a careful regular maintenance and calibration of the instrument. The latter is extremely important to maximize data quality, protect equipment from failure and detect degradation that can lead to both degradation of performance and unexpected component breakdown down the track with consequence loss of beam hours. Across the world instrument scientists and software engineers have, with success, automated the daily setup & calibration but often neglected the need for quality control (QC) database recording. Proper QC systems allow a maintenance record of checks with numerous advantages namely: optimizing time by not doing all tests everyday but also guaranteeing that certain tests are done in regular intervals; plot beamline degradation or improvements particularly when new software or hardware is implemented; guarantee that beamline performance is not dependent of synchrotron staff doing the checks because they are all done the same way and recorded the same way; help train new staff into instrument scientist positions and many others. Here we present the next generation of a software tool initially developed at the Australian Synchrotron [1] in Python 2 and using QT 4 but recently re-written with more modern software with Python 3 and QT 5 (DLS internal Gitlab). It is currently in beta tests at Diamond Light Source i04 [2] beamline. The tool attempts to represent the checks currently done (Figure 1a) using visual cues pointing to when the check was last performed as well as provide some guidance on how to do the step-by-step checks. It will then database and file record the result of that check for future reference, tracking and baseline QC (Figure 1 b-c).

The DanMAX beamline [1] located at the diffraction limited storage ring at the MAX IV synchrotron facility [2] and is under commissioning. The beamline is designed to be highly versatile and perform both PXRD and full-field imaging experiments in the energy range 15-35 keV. The very brilliant X-ray source (3m IVU16) and a flexible optics system allows for three different band pass modes, ∆E/E ~ 10^-4, 5*10^-3 & 10^-2, and focusing of the beam from ~10 µm up to ~ 1 mm.

DanMAX will have two instruments for PXRD. The first one is equipped with a DECTRIS PILATU3 X 2M CdTe area detector and a silicon drift detector for simultaneous diffraction and X-ray fluorescence spectroscopy. The detector positioning stage will offer large flexibility in both sample to detector distance and in detector tilt to increase the attainable Q range. The instrument is built around a Symétrie Breva hexapod that can accommodate bulky sample environments weighing up to 200 kg. A wide range of sample environments will be available at the beamline. Open standards will be available, both mechanical and software, for fast and easy integration of custom-built sample environments at the beamline. This instrument is expected to be available to users in 2021.

A high resolution instrument will be added in 2022. This instrument will use microstrip detectors and have a large angular coverage. This will enable fast experiment with high resolution. It is planned to start a mail in program for rapid access to this instrument. The instrument will thus be equipped with a robotic sample changer and use computer vision to align the samples, thus ensuring the optimal data quality.

[1] www.maxiv.lu.se/danmax

[2] Tavares, P. F., Leemann, S. C., Sjöström, M. and Anderson, Å. J. Synchrotron Rad., 2014, 21, 862-877.

The structure determination on ever smaller and weakly diffracting crystals is one of the biggest challenges in the development of in-house X-ray analytical equipment for chemical and biological crystallography, which continuously raises the requirements for modern X-ray sources and detectors. Nowadays, modern low power microfocus X-ray sealed tube sources define the state-of-the-art for most in-house X-ray diffraction equipment, as they deliver intensities in the range of rotating anodes, yet maintain all the comfort of a sealed tube system.

Throughout the past years, we have continuously explored the physical limitations of impact ionization sources in order to find ways to push or even overcome some of the limitations, such as the heat transfer in the anode, leading to brighter X-rays sources with solid targets. The brightness of an X-ray tube is mainly limited by the thermal conductivity of the bulk anode material. As the thermal conductivity of diamond is up to about 5 times higher than that of copper and the highest known conductivity of all bulk materials [1], industrial diamond is increasingly replacing traditional materials for the thermal management in challenging applications [2], in which a high local heat load needs to be dissipated, such as in heat sinks for high-power microelectronic devices [3, 4]. In X-ray sources, diamond can be used as a heat sink directly coupled to the anode material, resulting in a significantly higher thermal conductivity compared to a conventional metallic anode and, hence, allowing for an increase in tube brilliance by applying a higher power load on the anode [5].

As a result of our efforts, we recently introduced a unique new class of microfocus sealed tube X-ray sources that uses a novel anode technology, the diamond hybrid anode [6]. It consists of a thin layer of metal deposited onto a bulk industrial diamond which acts as a heat spreader and significantly improves the heat dissipation in the anode. Consequently, the anode can accept a higher power density in the focal spot on the target without damaging the surface of the target layer. The balanced heat management allows the source to be air-cooled, while assuring that the intensity loss over time is only a few percent over 10,000 h of full power operation, which is significantly lower than the intensity degradation observed for microfocus rotating anodes [7, 8]. Along with this, optimizing the take-off angle of the anode and the filament parameters of the cathode to match the requirements of the X-ray optics enables a significant increase in the intensity on the sample. In combination with the latest developments in multilayer mirror technology, the IµS delivers an intensity in the range of 1·10¹¹ phts/s/mm² with a divergence that matches the typical mosaicity of weakly diffracting samples. Therefore, the IμS DIAMOND combines the performance of a modern 1 kW microfocus rotating anode with all the comfort of a conventional microfocus sealed tube source.

We will be reviewing the latest innovations in microfocus sealed tube X-ray sources and multilayer optics and be presenting selected results from protein and pharmaceutical crystallography that demonstrate the impact of these recent developments on the data quality.

[1] Moore, A.L. & Shi L. (2014). Materials Today 17, 163.

[2] Dischler B. & Wild C. (1998). Low-Pressure Synthetic Diamond Manufacturing and Applications. Berlin: Springer.

[3] Obeloer T., Bolliger B., Han Y., Long Lau B., Tang G. & Zhang X. (2015). IMAPS, 1.

[4] Pu S., Luo W., Shuai Y., Wu C. & Zhang W. (2016). ICMIA, 184.

[5] Li X., Wang X., Li Y. & Liu Y. (2020). Materials 13, 241.

[6] Durst R. D., Michaelsen C., Radcliffe P. & Schmidt-May J. (2020). US Patent 10,847,336.

[7] Mehranian A., Ay M. R., Riyahi Alam N. & Zaidi H. (2010). Med. Phys. 37, 742.

[8] Kákonyi R., Erdélyi M. & Szabó G. (2010). Med. Phys. 37, 5737.

In-situ synchrotron powder diffraction experiments under a gas atmosphere are one of the most powerful tools used to investigate the crystal structure and to characterize materials function or the applications of gas storage and separation materials. However, in most cases, the information of crystal structures was limited to the static conditions. To understand the overall materials functions to improve thermodynamic and kinetic gas separation properties and storage capacity, it is important to observe continuous structural changes under gas adsorption, desorption and reaction processes. Therefore, we developed new gas handling system [1]. This system can control gas- and vapor-pressure synchronized with the continuous data acquisition of millisecond temporal-resolution high-resolution powder diffraction measurements. However, for the high-speed powder diffraction measurement, it is difficult to obtain uniform Debye-Scherrer ring intensity data if the powder sample has large size and/or non-uniform particles. This difficulty is come from an instrumental limitation that the gas cell mounted on diffractometer cannot be rotated during the measurement due to stainless tube to introduce gas to the sample.

To solve this problem, we have developed a new high-speed spinner for in-situ powder diffraction under controlling gas pressure at the beamline BL02B2 at SPring-8 [2]. The high-speed spinner mainly consists of a gas cell to hold the glass capillary with double O-rings, a contactless magnetic fluid seal, a brushless motor, and the bearings. The translation and tilt stages are also equipped on the spinner for the alignment of glass capillary sample. The rotation speed can be set to 200 r.p.m. for standard use, and further development of the spinner is currently underway to achieve up to 1000 r.p.m. The various gas species except water and oil are available, and absolute pressure from 1 Pa to 130 kPa can be controlled.

Using the developed high-speed capillary spinner cell and gas handling system, we have demonstrated in-situ and time-resolved powder diffraction measurements for a nanoporous Cu coordination polymer [3], which has a pillared layer structure containing one-dimensional nanochannels with dimensions of 0.4 nm x 0.6 nm along the a-axis, with large particle size of approximately 20 microns. A two-dimensional flat-panel detector (XRD3025) was used as X-ray detector, and 50 frames of continuous powder diffraction data was obtained in temporal resolution of 0.33 seconds. We tested the evaluation of the diffraction intensity during spinning of capillary sample. On the conditions of high rotation speed with 200 r.p.m., the difference of 5 % between maximum and minimum peak intensity was observed. On the other hand, on the conditions of low rotation speed with 25 r.p.m, twice variation of the peak intensity was observed in diffraction data of 50 frames. In this case, the measurement was performed for a sample with large particles. Moreover, we collected time-resolved diffraction patterns in the Ar gas adsorption process for nanoporous Cu coordination polymers with different particle sizes of approximately 1, 5, and 20 microns, respectively. As a result, this developed spinner allows to give uniform Debye-Scherrer ring intensity even in sub-second time-resolved data, where the particle size is possibly smaller than that of 5 microns. The results also show that the transition speed from desorption to adsorption phase is highly dependent on the particle size as well as the introduction of gas pressure and temperature. In this presentation, we will show that the mechanism and concept of high-speed capillary spinner cell for in-situ powder diffraction under control of gas atmosphere, and will display the results of the time-resolved powder diffraction measurements for nanoporous Cu coordination polymers under various Ar gas adsorption processes.

[1] Kawaguchi, S., Takemoto, M, Tanaka, H., Hiraide, S., Sugimoto, K., & Kubota, Y. (2020). J. Synchrotron Rad. 27, 616-624.
[2] Kawaguchi, S., Takemoto, M., Osaka, K., Nishibori, E., Moriyoshi, C., Kubota, Y., Kuroiwa, Y. & Sugimoto, K. (2017). Rev. Sci. Instrum. 88, 085111.
[3] Kitaura, R., Matsuda, R., Kubota, Y., Kitagawa, S., Tanaka, M., Kobayashi, C. T. & Suzuki, M. (2005). J. Phys. Chem. B, 109, 23378–23385.

This research was supported by KAKENHI Grant Nos. (20H04466, 20H02575, 19KK0132). The synchrotron radiation experiments were performed at beamline BL02B2 of SPring-8 with the approval of the Japan Synchrotron Radiation Research Institute (JASRI) (Proposal Nos. 2019B2094, 2020A2132, and 2021A0068). The authors thank Professor K. Otake and Professor S. Kitagawa for their assistance with the preparation of the samples.

Molecular structure determination plays an important role both in fundamental and applied sciences such as organic chemistry, inorganic chemistry, biochemistry, drug discovery, and material chemistry, etc.

A number of analytical methods are routinely used to determine molecular structure: nuclear magnetic resonance (NMR), mass spectrometry (MS), infrared absorption spectroscopy (IR), X-ray diffractometry (XRD), and so on. In particular, single-crystal X-ray structure (SC-XRD) analysis is the most effective method to obtain a detailed and overall three-dimensional molecular structure of a molecule. However, it is generally believed that single crystal analysis takes a relatively long time, and requires a large crystal and information of elemental composition.

A combination of "PhotonJet-R (rotating anode X-ray generator + newly designed optic)" and "HyPix-6000HE (Hybrid Photon Counting detector)" has achieved high brightness and noise-free shutterless data collection in an in-house instrument for the latest SC-XRD analysis.

By the recent progress of the elemental technology, we came to be able to get structure of a single crystal in the order of a few mm in an in-house instrument. Furthermore, evolution of the software enabled automatic measurement and analysis without any expertise.

We determined precise crystal structure of agrochemical products microcrystalline powders using “What is this?” (WIT) experiment without any elemental information[1]. The WIT combined with the latest SC-XRD system provides the best way to obtain unambiguous structural information from microcrystalline powders (Fig. 1).

The capillary mounting of single crystals can be necessary under some circumstances prior to X-ray diffraction experiments. When crystals are air-sensitive or may undergo a desolvation, a deterioration of the samples may be observed over time which will affect the data quality during measurements. Using protective vacuum oil and working at low temperature help slowing down crystal quality decay, however capillary mounting offers a better air protection by isolating the samples [1-2]. This kind of mounting may also offer a protection of the experimenter when the crystalline compounds exhibit health hazard, it is then relevant for a better respect of hygiene and safety rules in lab workspaces.

Capillary mounting requires patience and dexterity, and so can be a matter of apprehension. Its success rate will strongly depend on the capillary size and the operator’s experience. Some methods have been suggested in literature [3-4]. However, to prepare a series of samples, the required work is time demanding and a significant fraction of crystals may be lost.

In this work, a home-made setup for capillary mounting is described. A crystal sample mounted on the top of a glass fibre can be slid in a capillary with an inner diameter smaller than 1 mm. The capillary mounting is manually performed thanks to a micrometric translation stage and a goniometer head with five degrees of freedom Rx, Ry, X, Y, Z. The operation is monitored using a small numerical microscope with its output displayed on computer screen by a simple program written in Python.

Materials under extreme conditions of radiation and temperature, as in nuclear facilities, need to be tested and analysed to understand the neutron-induced microstructural defects that might affect their mechanical properties at macroscale and thus affect the material performance. X-ray diffraction (XRD) is a widely use technique for structural characterization of materials in a bulk or powder form. Special care must be taken when manipulating radioactive material, specially in a powder form, since it can lead to unwanted radioactive contamination [1, 2]. Therefore, the handling and milling of radioactive materials (e.g. minerals-rocks, concrete) is carried inside of a hermetically sealed shielded glovebox under negative pressure [3]. Milling in ethanol of the bulk material was performed using an oscillating ball mill, producing a fine powder (after air-drying) with an average particle size of 4 microns, “wet” milling offers the advantage to produce a powder with an homogeneous size distribution and also to avoid the dispersion of the radioactive dust into the air. Radioactive samples for XRD analysis must fulfil two requirements: 1) small size to avoid excessive irradiation, and 2) a contention barrier between the sample and its surroundings to avoid radioactive contamination due to leaking of powder. To meet those requirements a drop-casting of material (approx. 15 mg) onto PEEK foil (6 µm) has been chosen as a suitable option. After air-drying of the sample, it is covered with a second layer of foil and sealed with fast-drying glue to avoid powder leaking. The thus prepared sample is now ready for XRD analysis in transmission mode [4]. The data collection is performed using a multipurpose diffractometer (Empyrean from Malvern-PANalytical) with a Co X-ray tube, the diffractometer posses a magazine and a robotic arm for automatic loading of samples, besides it can be operated remotely reducing the exposition to radiation of the operator. With the described procedure phase identification, quantification of amorphous content using the internal-standard method, and monitoring of changes in lattice parameters of the identified crystalline phase can be safely performed on radioactive samples.

One applicative example was the study of aggregates (majorly quartz, > 90 wt.%) under different levels of neutron fluences (up to 10²⁰ n/cm²). Where it was observed a progressive amorphization of quartz from 9 wt.% to 76 wt.%, at the same time volumetric expansion of the unit cell was observed (up to 11%), as both axes a and c increased with the neutron fluence. Crystal density (g/cm³), calculated from the previously calculated lattice parameters, decreases (-10%) with the increase of neutron fluence irradiation.

In summary, the developed methodology represents an easy and affordable way to study the irradiated materials at laboratory scale.

X-ray based analysis techniques play a crucial role in a vast range of academic and industrial research areas. These include fields as diverse as pharmaceutical research, geology, building materials, materials science, specialty chemicals, and the life sciences. X-ray based methods can be advantageous over complementary methods such as electron microscopy due to the minimum need for sample preparation, the non-destructive nature of X-rays, and the possibility to work under both ambient and non-ambient conditions (in-situ studies). In addition, different techniques such as XRD and SAXS may both be used together to give complementary information which allows a more in-depth understanding of the sample in question and its properties.

As a manufacturer of X-ray sources, advanced X-ray optics, XRD equipment, and SAXS instruments, this poster will present the latest developments in X-ray analysis equipment from Anton Paar which further extend the capabilities of in-house X-ray based measurements under both ambient and non-ambient conditions.

About 100 years ago, one of the first non-ambient studies was done on resistively heated wires to observe property changes with regard to the transition from α- to β-iron [1] using X-ray diffraction (XRD). At this time, the first ever high-temperature camera was developed for this purpose. This milestone opened the fascinating discipline of non-ambient XRD and since then the changing physical, chemical and mechanical material properties from standard to non-ambient conditions could be studied in-situ.

When exposing sample materials to non-ambient conditions, their properties (chemical, physical,..) may significantly change, frequently leading to a completely different behavior of the material. Due to this, intensive studies have to be performed in order to obtain material properties over the complete range of possible non-ambient conditions.

Non-ambient X-ray diffraction is a versatile tool to study processes linked to variable non-ambient conditions (temperature, pressure, gas environments, relative humidity, electrical and magnetic fields, mechanical load,…). Besides its relevance for conducting research, this knowledge is essential for optimizing technical processes and performing quality control in industry.

Anton Paar is the market leader in non-ambient XRD instrumentation and is continuously striving to optimize the design and set-up of commercially available non-ambient XRD stages. This poster will highlight the possibilities of setting up non-ambient XRD experiments, how to enhance the data quality of your experiment, and what needs to be considered when performing a non-ambient XRD experiment.

[1] Westgren, A., Lindh, A. E. (1921). I. Z. Phys. Chem. 98, 181.

In 2016 at Helmholtz-Zentrum Berlin, an X-ray user lab with various powder diffraction methods was founded and subsequently extended. The lab covers X-ray methods for standard powder diffraction, thin film analysis (grazing incidence, texture and epitaxial analysis) and diffraction experiments under non-ambient conditions (vacuum, nitrogen, temperatures from 12 K up to 1400 K). Besides experimental options the lab hosts X-ray diffraction schools for beginners (two weeks) consisting of general introduction into X-ray diffraction combined with hands-on experiments, and newly, a Rietveld school for advanced users (one week) covering introduction into crystallography, databases, and structural analysis applying the Fullprof suite [1]. The lab is open to users of all materials research disciplines and free of charge for non-profit organisations. The proposed contribution will illustrate the possibilities of the lab.

Materials Growth and Measurement Laboratory (MGML) is the open research infrastructure in Prague, Czech Republic. MGML offers an open access for external users to the instrument suite dedicated to preparation, characterization and measurement of physical properties of materials. The MGML technology facilities are enabling controlled synthesis of high-quality samples (single crystals and polycrystals) of various types of materials, detailed phase and structural characterization using a unique suite of X-ray diffractometers and measurements of a rich spectrum of physical properties of materials in a wide range of temperatures, magnetic and electrical fields, and hydrostatic uniaxial pressures.

MGML provides to its users advanced structural analysis in a wide tempreature range, focused on studies of single-crystals, bulk, polycrystalline, nanocrystalline, amorphous and organometallic materials, as well as on the investigation low-dimensional system as thin polycrystalline and epitaxial layers, multilayers, quantum dots, wires and tubes.

Researchers interested in using the MGML instrumentation are invited to submit experimental proposals via the User Portal on mgml.eu. The discussion with local contact(s) is recommended prior to submission. The proposals will be evaluated by the MGML Panel.

As a result of the TEAM-TECH Core Facility Project from the Foundation for Polish Science, we have established the Core Facility for Crystallography and Biophysics (CFCB) at the Biological and Chemical Research Centre, University of Warsaw, under the supervision of Professor Krzysztof Woźniak (Head) and Jan Kutner, Ph.D. (Deputy Manager).

The Core Facility services (Figure 1) are focused on the analysis of proteins and small molecule compounds leading to crystallization trials for academic and commercial users. The project enables studies of challenging biochemical and pharmaceutical problems, with an emphasis on drug development. Research at CFCB is carried out in an interdisciplinary way, including both wet biology (“BIO”) and chemical crystallography (“CHEM”) techniques as well as theoretical approaches including structure modelling, bioinformatics and computational methods. Biology and chemistry team members work in synergy complementing their knowledge, skills and experience. Apart from services and collaborations, postdoctoral and Ph.D. researchers carry out their research projects dedicated either to small-molecule or protein crystallography.

Figure 1. The main pipelines of the CFCB

Work in the Facility includes collaboration with other research groups and biotech/pharmaceutical companies, such as the WPD Pharmaceuticals, Cellis, Leaderna Biostructures, OncoArendi Therapeutics, Pikralida, Bio-Rad and Innvigo.

Moreover, we cooperate with Dr. Sebastian Glatt and Dr. Przemysław Grudnik (Structural Biology Core Facility, Jagiellonian University, Cracow) under the TT CF extension concerning the commercial aspects (The Integrative Platform for Accelerated Drug Discovery – IPADD).
We are open to different forms of collaborations with individual researchers, research groups, or biotech/pharma companies.

Acknowledgments
The project is supported by Foundation for Polish Science/European Union under the European Regional Development Fund (TEAM TECH CORE FACILITY/2017-3/4, POIR.04.04.00-00-31DF/17-00)"

The first generation of the SmartLab XRD multipurpose diffractometer was launched in 2008. It involved immense effort from Rigaku engineers, X-ray scientists and application experts aiming to deliver a multifunctional XRD instrument to cover wide range of X-ray scattering techniques in the lab environment. 10 years later, after the success of the first SmartLab, Rigaku released the new generation of SmartLab, implementing newest solutions and technologies based on scientific and industrial demands fulfilling users’ needs and requests. This overview presentation provides an update of the new solutions implemented in the second generation of SmartLab resulting in substantial extension of applicability of the instrument.

In addition to standard Powder and Thin Film XRD applications, the new SmartLab has been updated with a new family of Cross Beam Optics (CBO), Goebel’s mirror equivalent, which includes elliptical mirror CBO-E, and flat mirror CBO-α for different wavelengths including Cu, Mo, and Ag. In addition, an X-ray polycapillary unit CBO-f and confocal mirror set CBO-μ has been designed for micro-area testing utilizing focused beams of 400 μm and 50 μm respectively.

Furthermore, newly designed sample attachments along with the appropriate optical set, enable uncompromised SAXS, WAXS, GISAXS and GIWAXS measurements that require utilization the large 2D acquisition area. The requirement of 2D data collection over large angular space is fulfilled with in-house development and manufacturing of HyPix400 and HyPix3000 2D detectors characterized by outstanding dynamic range (>2Mcps/pixel), read out speed (zero dead-time) and robustness. Due to their unique technology HyPix detectors do not require primary X-ray beam attenuation and can be safely used with strong beams, including exposure to the direct beam from a 9kW X-ray source.

The Differential Scanning Calorimetry (DSC) and reaction sample chamber (Reactor X) for in-situ studies is of particular interest to research scientists. This instrument set-up is ideal for examining phase transitions under alternating temperature and humidity as the results can be directly observed when combining XRD and DSC in one experiment. Materials transformations in an atmosphere of reactive gases (mixtures of gases, or also in air or vacuum) may be studied using Reactor X which is capable to elevate temperature up to 1000^oC with ultra-rapid ramp rate. Additionally, following high demand in investigations of energy storage materials, Rigaku has designed a set of battery attachments for reflection and transmission geometries for in-operando experiments.

New optics, sample attachments and developments in detector technology have enabled the SmartLab to achieve best-in-class experiments for Powder XRD and Thin Film structural analysis, phase transitions, Small- and Wide-Angle X-ray Scattering, PDF, micro-area testing, pharmaceutical research, applications for steels, alloys, and multifunctional materials.

The demand for fast and reliable data storage is strongly rising, with the IoT and Cloud Computing sectors being big drivers. This is reflected by the estimated global next-generation data storage market size in 2018 was 53.1 billion USD with an expected compound annual growth rate of 12.5% until 2025 [1]. Coming to automotive applications (elevated temperatures), the current state of the art for non-volatile data storage employing flash technology (e.g. in SSDs), is reaching fundamental limits because of its physical principle. Owing to their properties, phase change materials (PCMs) can solve the problem. PCMs can be reversibly switched between an amorphous and a crystalline phase through controlled (local) heating, e,g, by lasers or by an electrical current. Thus, PCMs open the path to Phase Change Random Access Memories (PCRAM), a very promising alternative to replace flash technology [2]. In this contribution investigations on the PCM GST-theta a Ge-rich material within the Ge-Sb-Te ternary system are presented. GST-theta reaches crystallization temperatures above 350°C, which is needed in automotive applications [3]. In a previous study on 50 nm thick films of GST-theta [4], we have shown that the crystallization of that PCM proceeds in two steps (fig 1). Ge crystallization precedes the crystallization of Ge₂Sb₂Te₅, a cubic, metastable phase [5]. In the present work we aim at investigating the effects of N-doping and H₂-treatment on the structural evolution of GST-theta (crystallization temperatures, evolution of grain sizes, elastic strains). Therefore, a series of annealing experiments was performed and followed by in-situ X-ray diffraction at the DiffAbs beamline of SOLEIL synchrotron. All samples are annealed up to 500°C under N₂-atmosphere using an Anton Paar® heating stage mounted on the six-circle diffractometer. The diffraction patterns were recorded with an XPAD hybrid pixel detector and corrected and transformed into 1D patterns following previously developed procedures [6]. The 1D patterns are then indexed and diffraction peaks are fitted. A fitting procedure was developed in-house to find and handle also very weak peaks on a strong background. We will discuss here the influence of H₂-treatment, N doping and lateral confinement on the crystallization and microstructure development in GST-theta thin films and nanostructures. It is worth mentioning that some investigated samples are very close to final products (several metallization layers on top), which demonstrate the capability of synchrotron X-ray diffraction to investigate the PCM in its “real” environment.

Here should be a figure.

Fig 1. areas of the Ge 111 and Ge₂Sb₂Te₅ 200 reflections upon heating of an amorphous film show a phase separation

[1] https://www.grandviewresearch.com/industry-analysis/next-generation-data-storage-market

[2] M. Gallard, PhD thesis, Aix Marseille Univ. (2019)

[3] P. Zuliani, E. Palumbo, et al. (2015). Solid State Electronics. 111, 27

[4] O. Thomas et al. (2021). Microelectronic Engineering

[5] T. Matsunaga, N. Yamada, and Y. Kubota (2004). Acta Crystallogr. Sect. B Struct. Sci. 60, 685

[6] C. Mocuta, M.I. Richard, et al. (2014). J. Appl. Crystallogr. 47, 482

Keywords: chalcogenides; data storage; in-situ synchrotron X-ray diffraction; phase change materials; nanostructures

Acknowledgments We would like to thank SOLEIL synchrotron for allocating beamtime on DiffAbs beamline. Ph. Joly (Synchrotron SOLEIL, DiffAbs) is thanked for technical support. IPCEI/Nano 2022 program is acknowledged for partial funding of this work.

In the case of alloy films and multilayers, measure of composition may be hard, since the volume of film is far less than that of substrate. Therefore, the surface sensitive measurements, such as X-ray photoelectron spectroscopy (XPS) and Auger electron spectroscopy (AES), are employed frequently. Alterative way is the chemical etching of film followed by the concentration analysis of the aqueous solution. However, all these methods are destructive and can be performed only under ex-situ condition. Also, diffraction stress analysis of alloy films may be difficult, since the composition is required for estimating the diffraction elastic constants.
Considering the situation described above, we proposed the self-consistent diffraction stress analysis method for analysing composition and stress (Fig. 1) [1]. This method is based on the strain-free lattice parameter, which is generally treated as a by-product of diffraction stress analysis and receives less attention. However, we here tried to utilize it, since it contains the information of composition. The main concept of the proposed method is the feedback of the strain-free lattice parameter in the form of composition. Due to the feedback, the diffraction stress analysis can be performed even when the exact composition is unknown. After the convergence of feedback calculation, the final results are composition and stress; they have self-consistency.
The validity of this analysis method was experimentally confirmed using example specimens of (111) fibre-textured palladium cobalt (PdCo) alloy films with different composition. Note that PdCo alloy films are expected as the next generation magnetism-based hydrogen sensor, since they absorb hydrogen and show both perpendicular magnetic anisotropy and large magnetostriction constant [2-4]. The lattice spacings measured at the different tilt angles are analysed using the proposed method. It was revealed that the self-consistent calculation converged well and the resultant composition is in a good agreement with the result of AES. The difference of composition is 1 at.%, even though this method only provides the estimated composition from the strain-free lattice parameter. The resultant stress also shows an agreement with one of the conventional diffraction stress analysis.
The proposed self-consistent method is suitable for cases, such as in-situ measurement, where the measure of composition is difficult. This method expands the applicability of diffraction stress analysis.

Scandium nitride (ScN) has attracted a great deal of attention in recent years due to its promising properties as high hardness, temperature stability and high electrical conductivity [1], [2]. Twin domains have been already studied in this interesting material for some other configurations including ScN crystalline and polycrystalline growth on different substrates[3]–[5]. Five epitaxial (001) ScN films from 145 nm to 1080 nm thicknesses were deposited at the same conditions on MgO (001) substrate by DC reactive magnetron sputtering. The presence of twins has been analyzed through 2theta scans, 002, 022 and 111 pole figures and 2D reciprocal space maps (RSM). Four twin domains are present in all samples being (111) the twining plane. This gives rise to twelve distinguished peaks of 002 reflection (labelled on the inset pole figure for the thickest sample in Figure 1). Special care must be taken for thinner samples, since the presence of twins can be hidden under the strong contribution arisen from the epitaxial layer. The twins/epitaxial layer diffracted intensity ratio seems to rise with the layer thickness. Further research must be done to elucidate if there is a limiting layer thickness for twin formation.

The tungsten carbide films were deposited by reactive magnetron sputtering in an industrial-scale coating chamber at different bias voltages and gas (argon/acetylene) flows. As substrate materials, silicon wafers and 100Cr6 steel sheets were used. The films were characterized using electron probe microanalysis with wavelength-dispersive X-ray spectroscopy (EPMA/WDX) and in situ high-temperature X-ray diffraction (HTXRD). EPMA revealed the chemical composition of the films; HTXRD gave overview over the thermally activated phase transformations and stabilization of metastable phase through the microstructure defects. The as-deposited films contain metastable phases WC_1-x and W₂C with distorted crystal structures. With increasing temperature and/or longer annealing time, the crystal structure of the high-temperature W₂C phase recovered, although the annealing temperature was below the temperature, which is required to make W₂C thermodynamically stable. The density of the microstructure defects in W₂C was reduced, but some defects persisted. The structure relationships between individual phases will be discussed. Further heat treatment resulted in a decomposition of W₂C, which was accompanied by the formation of metallic tungsten. The EPMA results confirmed that this decomposition is accelerated by the reaction of carbon with oxygen impurities in the annealing atmosphere. When the 100Cr6 steel is used as substrate material, W₃Fe₃C forms at the interface between the substrate and the coating. The presence of this carbide influences the decomposition of W₂C.

Recently the rocking curve imaging (RCI) technique has been transferred from synchrotron to laboratory set-ups. RCI is an X-ray diffraction technique which combines full-field X-ray digital topography and Bragg-diffraction rocking curve recording. A large almost parallel monochromatic beam irradiates a crystalline sample with a misorientation distribution characterized by local tilt angles. Series of digital topographs are measured by a two-dimensional detector at different sample orientations from which peak characteristics of millions of local Bragg peaks from each series are extracted. The field of view and lateral resolution is given by the camera size, its pixel size and the Bragg angle, while the angular resolution is given by the rocking curve width being typically much smaller than the misorientation angles of the studied crystal. Simultaneous high spatial resolution provided by the two-dimensional detector and high angular resolution (0.001°) allows to quantify crystalline structure perfectness over large sample area which scales with the area of the detector. Therefore the rocking curve imaging is an imaging method with faster recording compared to usual scanning area diffractometry which requests measurement of the rocking curve at each surface point.

Synchrotron RCI [1,2] profits from large parallel beam, high flux and small detector pixel size downto one micrometre. For small misorientations, detector can have any distance from the sample, while larger misorientations due to inherent focusing/defocusing of the diffracted (micro)beams require a dedicated reconstruction procedure.

Laboratory RCI [3] with a slightly divering beam requires small misorientation angles and very small sample to detector distance, thus a home-made extension for a commercial diffractometer is necessarily. Current two-dimensional detectors available at laboratory diffractometers have typical spatial resolution downto 0.1 mm which make it possible to analyze a large sample area at once. On several examples, we will show suitability of the method for a characterisation of several large-area semiconductor wafers. In particular, we demonstrate application of the method on mapping of local lattice tilt distortion of large array of SiGe microcrystals epitaxially grown on silicon.

[1] P. Mikulík, et al. (2003) Journal of Physics D: Appl. Phys. 36, A74–A78.

[2] D. Lübbert, et al. (2005) Journal of Applied Crystallography 38, 91–96.

[2] M. Meduňa, et al. (2021) Journal of Applied Crystallography 54.

Titanium alloys are material that is often used in aerospace industry and in biomedical engineering for their excellent properties as low density, high tensile strength and corrosion resistance in some common environments. On the other hands the disadvantages of these materials are in general poor performance in sliding, hardness and wear. Enriching the surface area of pure titanium by nitrogen lead to improve hardness, corrosion resistance and abrasion resistance. Moreover, the required low modulus of elasticity of bulk material is maintained which is susscesfully used for example in joint replacements and dental crowns.

In our contribution we would like to present the study of surface area of alfa-titanium after implantation of nitrogen ions. The X-ray diffraction and x-ray reflectivity were used for characterization of these surfaces. The special cheap home-made improvement of incident beam that enable to reach lower angles during reflectivity measurements will be presented.

Zr/Nb nanometric multilayers deposited on Si substrate by magnetron sputtering, having a periodicity from 6 to 167 nm were subjected to room temperature irradiation by carbon, silicon and copper ions. The mechanical proprieties, ion profiles, and disordering behavior have been investigated by Secondary Ion Mass Spectrometry - SIMS, nanoindentation, X-ray diffraction - XRD, and scanning transmission electron microscopy - STEM. The damaged regions are clearly visible on STEM bright field micrographs of cross-section lamellae prepared by focused ion beam technique - FIB. Damage starts from the surface side of the multilayer, and the most damaged and disordered zone is located close to the maximum ion concentration. Near the substrate, no damage was observed. The C and Si concentration profiles detected by SIMS were not affected by the nanolayers periodicity. This agrees with the Stopping and Range of Ions in Matter - SRIM software simulations. Diffraction analyses – selective area electron diffraction, and XRD suggest a structural evolution in relation to the multilayer periodicity. For the multilayer with a periodicity of 6 nm, and 27 nm, Si, C and Cu-ion irradiation led to a tensile strain in Nb layers and compressive strain in Zr layers. In contrast, for periodicity higher than 27 nm, both Zr and Nb layers are subjected to compressive out-of-plane strain.

Metals and alloys used in daily applications are submitted to deformations repeated for a very large number of cycles during their lifespan and can break under stresses amplitude lower than their ultimate tensile stress (fatigue of materials). Evaluating the evolution of the microstructure during deformation can provide insights into the mechanisms responsible for the observed mechanical behaviour and produce useful input to design materials ensuring the safety and reliability of the structures throughout their life service. Several techniques, including transmission electron microscopy (TEM), synchrotron x-ray diffraction and neutron diffraction techniques, and electron backscattered diffraction (EBSD), were used to evaluate the dislocation density in plastically deformed materials. However, all these techniques are affected from several limitations in distinguishing the influences of domain size and dislocation density. During the last two decades, Groma et al.[1] developed a new method for the evaluation of the dislocation density and its fluctuation in plastically deformed specimens with the only limitation of the coherent domain size that should be larger than 1μm. This method is based on the asymptotic behavior of the second- and fourth-order restricted moment in the tail portion of the x-ray diffraction peak.
The present research aims to use the variance method for estimating dislocation density when a very large number (~10⁹) cyclic loadings is applied on the single crystal with an applied stress significantly lower than the yield stress so that deformation is almost entirely elastic. The monocrystalline copper specimen was loaded using a 20 kHz ultrasonic fatigue machine mounted on the six-circle diffractometer available at the DiffAbs beamline on the SOLEIL synchrotron facility (France). Since we are interested to investigate the very high cycle fatigue domain, the amplitudes of the cyclic stresses range from 7 to 91 MPa. The diffraction patterns were acquired with a 2D hybrid pixel X-ray detector (XPAD S140) which integration time has been synchronized with the fatigue rig. The diffraction data are analysed with the k-order restricted moments method of the tail portions of individual Bragg peaks, for estimating the microstructure evolution in terms of dislocation density and spatial distribution of the dislocations. The results of these experimental data show an increase in the dislocation density with the external loading. Detailed results will be presented and discussed.

[1] Groma. (1998) Physical Rev. B, 57(13), pp. 7535–7542.

Important advancements in the field of powder X-ray scattering aim at improving the reach and accuracy of pattern analysis methods. Pair distribution function and other methods based on the Debye scattering equation (DSE) are the most straightforward as they directly compute the interference between couples of atoms. All interatomic distances for all grains in the powder have however to be computed. Whole powder pattern and pair distribution function modelling methods solve, instead, the same problem by considering whole objects in place of atoms. Even if not as general, they provide the same result but faster [1, 2].
Common volume functions (CVFs) are used to model the scattering contribution from crystalline domains of any shape. However, CVFs are readily available for a limited set of regular shapes. Allegra and Wilson [3] computed the scattering line profile of deformed shapes applying a linear transformation. Although reprised multiple times, such approach is not suitable for techniques based on the CVF formalism. We generalized the paper of Allegra and Wilson considering the effects on the powder diffraction pattern of a deformation applied to the shape (i), to the underlying lattice (ii) or to both (iii).
Here we discuss the transformation of the CVF to account for the scattering contribution of domain shape and crystal structure deformations (Fig. A), and shape-structure relative orientation (Fig. B). As an example, starting from the CVF for a sphere (cube) domain and a cubic crystal structure, the transformation allows the analysis of (i) ellipsoid (parallelepiped) domains in a cubic lattice, (ii) sphere (cubic) domains in a triclinic lattice and (iii) ellipsoid (parallelepiped) domains in a homologous triclinic lattice. The presence of size and shape deformation dispersions are also considered. The resulting profiles are used to model both the intensity scattering contributions and the small-angle shape function used to correct numerical pair distribution function profiles. Finally, we analysed pattern simulated via DSE to assess the possibility of extracting the deformation information from real powder scattering data.

Nano-structuring is a crucial step in optimizing permanent magnet materials, where both the size and morphology of the individual particles heavily affect the properties of the compacted bulk magnet. The size is tuned to ensure magnetic single-domain particles, which is crucial for optimizing the coercivity of the magnet (the field strength required to flip the magnetic orientation), as this is lowered by the mobility of walls between domains. Generally, the minimum required coercivity of a permanent magnet is half of the saturation magnetization, at which point the remanence (the magnetization at zero field) is the limiting factor. The remanence, in turn, is primarily tuned by the alignment of the particles, i.e. the texture of the bulk magnet.

One way to control the alignment is through the morphology of the nano-particles, as the right particle shape leads the powder to self-alignment during compaction and sintering into dense pellets, thus optimizing the alignment of the magnetic domains in the resulting bulk magnet^[1].
The overall figure-of-merit for permanent magnets is evaluated from the volume-weighted energy product (a.k.a. the BH_max), reported in kJ/m³ (MGOe in cgs-units). It follows that the density of the final bulk magnet is an important parameter, which again is correlated with the particle microstructure. The combination of crystallite size, texture, and density emphasizes the compaction process when going from powder to bulk, which also often includes a sintering step. Powder diffraction is a powerful technique for studying the compaction and sintering processes, as proper refinement of the data can provide valuable information about phases, crystallite size, texture, and, in the case of neutron diffraction, the magnetic moments, as they develop during the compact. Neutron powder diffraction also comes with the benefit of a large probing volume, which is useful for studying bulk behavior.

The rapid improvements in both detectors and sources allow for faster and faster data collection, but the accompanying large data quantities require robust and efficient data treatment strategies. One such strategy is sequential refinement, where each pattern in the dataset is refined one after the other (typically) in chronological order, using the final model of the previous refinement as a starting model for the next.

Taking it a step further gives us parametric refinement. Here, a single overall model is used to describe an entire dataset simultaneously, while still allowing some individuality between patterns. This is accomplished by describing suitable parameters using functions or constraints across all N patterns. In this way, the remaining unconstrained parameters are allowed to more freely refine towards physically sensible minima. As an example, a given phase formation might be known to follow a certain kinetic model, and so the scale factor can be parameterized to follow that model. Likewise, the unit cell parameters for a compound known to exhibit linear thermal expansion might be described by two parameters (slope and intercept), rather than N times unit cell parameters. This is clearly a significant reduction in the total number of refined parameters, especially for large in situ datasets. The ability to refine across several patterns makes parametric refinement a powerful tool for disentangling correlating parameters such as intensity-dependent parameters or peak profile parameters, as it allows us to impose physically meaningful time-dependent constraints.

Using parametric refinements allows us to get the most out of our neutron powder diffraction data!

^[1] Stingaciu, Marian, et al. "Optimization of magnetic properties in fast consolidated SrFe 12 O 19 nanocrystallites." RSC advances 9.23 (2019): 12968-12976.

Polycrystalline layers of organic perovskites such as CH3NH3PbI3 (MAPbI3) are intensively studied in order to achieve high performance of solar cells. The final efficiency correlates with the defect density, size and morphology of the crystallites. These materials exhibit tendency to form strongly oriented layers with sharp fibre multi-component texture. In order to correlate the relevant physical properties of the layers with their crystallographic orientation, it is highly desirable to easily measure the present texture.

As a classical and well-established approach, one can use pole figure measurement to fully determine the texture of the layers, however here the task is complicated by the fact that the low-symmetry unit cell of this material is rather large. Consequently, the number of observable peaks is high and their diffraction angles are partially overlapping. In order to resolve them, the resolution in diffraction angle has to be increased at the expense of the intensity making the pole figure measurement to be a time consuming. Another specific problem can be a presence of some possible strain influencing the peak positions.

Fortunately, fast 2D detectors are more and more available also in standard laboratory diffractometers that makes it possible to measure reciprocal-space maps very quickly. In this presentation, the measurements with 2D detector placed closely behind the sample are presented. Using the shorter sample-detector distance, the resolution is partially sacrificed while the reciprocal space area observed by the detector is dramatically extended. In this configuration, the continuous theta-2theta scan fully probes a long stripe in a reciprocal space. By measuring several such stripes, it is easy to reveal the full planar cut of the reciprocal space, and surprisingly the total acquisition time can be only tens of minutes for strongly oriented layers. Moreover, such measurement can be performed for different sample azimuth in order to obtain different planar cuts. This is desirable for single-crystal substrates, for which the surface symmetry can be followed.

The obvious advantage of this approach is a possibility to quickly visualise the intensity in reciprocal space and to compare the obtained images with the simulations based on some expected phase/texture model giving semi-quantitative results. Therefore it is very suitable for the first-try characterization of the unknown samples.

We reveal the novel result about the residual strain distribution as a function of depth in alumina/ stainless steel brazing joint using synchrotron XRD in transmission geometry. The evolution of the residual strain distribution in the joint during cooling is in-situ measured using an in-house developed brazing equipment. The residual strain in the joint is low at relatively high temperature and with the decrease of the temperature, the residual strain increases and becomes compressive. The residual strain is found to be increasing from the surface to the interface in a nonlinear fashion. The microstructure of the joint is characterised and the effect of the pores and the fillet on the residual strain distribution is studied by image based modelling.

Electronic devices are becoming more and more present in our daily life and their relevance will increase even more in the future. These gadgets evolve aiming at higher performance, lower energy consumption and better portability. This continuously creates a demand for miniaturised components. Such devices contain many elements whose properties are based on ferroelectricity. Barium titanate is the model ferroelectric system. In addition, its properties are highly temperature and grain size dependent. It has excellent properties with grain sizes of approximately 1 µm, but undergoes marked weakening as the grain size decreases. A wide range of unimodal grain size distribution between 0.4 µm and 15 µm was successfully sintered, avoiding abnormal grain growth. Samples with intermediate grain size, showed excellent electromechanical and dielectric properties. They possess a balance between microstructural strain, existence and mobility of domain walls, which in turn allows the field induced crystal phase transformation. The samples, under application of external electric field, were subjected to in situ high energy X-ray diffraction analysis. To resolve the angular resolution a high‑resolution multianalyser detector was used. By means of STRAP the field induced phase transformations were quantified. This induced phase transformation is stronger in samples whose grain size distribution curve is located around 1 µm. These results contribute to the understanding of fundamental questions about the ferroelectric effect in barium titanate and consequently other similar systems.

In our contribution we will present feasibility of using a high resolution three axis neutron diffractometer performance for elastic and plastic deformation studies of metallic polycrystalline samples. The method consists of unconventional set up employing bent perfect crystal (BPC) monochromator and analyzer with a polycrystalline sample in between (see Fig. 1). After realization of focusing conditions in real and momentum space at the neutron wavelength of 0.162 nm, a high angular resolution down up to FWHM(Δd/d)=2x10^-3 and FWHM(Δd/d)=3x10^-3 which was achieved on the standard α-Fe(110) samples 2 mm diameter in the vertical position and 8 mm diameter for 10 mm irradiated length in the horizontal position, respectively. It opens the possibility for mea-surements of small lattice parameter changes even on bulk samples. The drawback of theperformance shown in Fig. 1 consists in the necessity step-by-step analysis by rocking the BPC-analyzer. However, in the case of residual strain/stress measurements, position sensitive detector can by employed (see Fig. 1b) and partly eliminate the former drawback. In the latter case, bulk samples e.g. in the tension/compression rig can be studied with a high resolution. The feasibility of both instrument performances for macro- and microstrain as well as grain size studies is demonstrated on the polycrystalline samples of standard and low carbon shear deformed steel wires.

Figure 1.

Figure caption:

Fig. 1. Three axis diffractometer set-ups employing BPC monochromator and analyzer as used in the experimental feasibility studies (R_M, R_A - radii of curvature, θ_M, θ_A - Bragg angles) with a point detector – (a) and/or with a position sensitive detector (PSD) – (b).

Due to their excellent mechanical properties and high specific mass, tungsten heavy alloys are used in demanding applications, such as kinetic penetrators, gyroscope rotors, or radiation shielding [1]. However, their composite structure, consisting of hard tungsten particles embedded in a soft matrix [2], makes the deformation processing a challenging task. This study focused on the characterization of deformation behaviour during thermomechanical processing of a W-Ni-Co tungsten heavy alloy (produced by powder metallurgy) via the method of rotary swaging (aimed at still improving properties) at ambient temperature and at 900°C.

Swaging changed mechanical properties, and - as an important step to optimize microstructure and mechanical properties is to understand the underlying processes - the aim of the neutron diffraction study was to determine texture and to characterize microstrain, dislocations as well as the active slip system. The strength of neutron diffraction method lies in the information provision from the bulk of the sample, i.e. not only from its near-surface region. This advantage is still amplified for materials with very high X-ray absorption (like tungsten alloys) and/or with large grains.

First, phase identification was done from the diffraction patterns. The detected main phase was corresponding to the original tungsten powder grains of bcc structure, the second (in fact matrix) phase, was Ni-Co solid solution with fcc structure [3]. Peak broadening after swaging was visible in the soft matrix phase.

Further, texture measurement using neutron diffraction was done, which shows that the original as sintered material had for the tungsten phase no texture. It also shows that there were very large grains of Ni-Co matrix phase in the as sintered bar, without any clear preferential orientation. During rotary swaging, the large grains of Ni-Co are fractioned to fine-grained microstructure. A strong texture formed in both phases after rotary swaging [4]. Both bcc phase and fcc phase, after rotary swaging, have the same texture type as for wire drawing. It can be thus concluded that the primary deformation mechanism for rotary swaging was the same as for wire drawing. The textures for cold and hot swaging are qualitatively the same, but stronger for cold swaging which indicates that secondary deformation mechanisms are also active for the hot swaging. The deformation was also connected with formation of residual macrostresses [4,5].

The peak broadening was evaluated for the neutron-diffraction peaks of the relatively soft Ni-Co matrix phase [3]. The modified Williamson-Hall plot shows that the microstrain increased approximately 3 times after rotary swaging. In accord with the texture measurement, the edge dislocations with <110> {111} slip system (typical in fcc) provide such contrast factor, that the integral breaths of the individual reflections fit very well to straight lines. Interesting is the Ni-Co matrix in non-deformed as-sintered bar where the contrast factor for screw <111> dislocation fits best with the measured integral breaths. The dislocation densities from the slope of the modified Williamson-Hall plot were estimated. The dislocation density increased approximately 5 times after rotary swaging, which is linked with the mechanical properties: swaged samples exhibited substantial strengthening - primarily caused by the increase in dislocation density. Further, the dislocation density is 15% higher for the sample swaged at room temperature than for the sample deformed at 900°C, which fits the trend observed in stress-strain curve.

[1] Kocich, R.; Kunčická, L.; Dohnalík, D.; Macháčková, A. & Šofer, M. (2016) Int. J. Refract. Met. Hard Mater. 61, 264–272.

[2] Durlu, N.; Caliskan, N.K. & Sakir, B. (2014) Int. J. Refract. Met. Hard Mater 42, 126–131.

[3] Strunz, P.; Kunčická, L.; Beran, P.; Kocich, R. & Hervoches, C. (2020). Materials 13, 208, doi:10.3390/ma13010208

[4] Strunz, P.; Kocich, R.; Canelo-Yubero, D; Macháčková A.; Beran, P. & Krátká, L. (2020) Materials 13, 2869; doi:10.3390/ma13122869

[5] Canelo‑Yubero, D.; Kocich, R.; Hervoches, Ch.; Strunz, P.; Kunčická, L. & Krátká, L. (2021) Metals and Materials International, https://doi.org/10.1007/s12540-020-00963-8

Keywords: tungsten heavy alloys; rotary swaging; neutron diffraction; dislocations; microstrain; texture

The authors acknowledge support for this research by Czech Science Foundation, grant No. 19-15479S. Measurements were carried out at the CANAM infrastructure of the NPI CAS Řež. The presented results were obtained also with the use of infrastructure Reactors LVR-15 and LR-0 financially supported by the Ministry of Education, Youth and Sports - project LM2018120.

Deformation behavior of ZN11 magnesium alloy in a form of extruded profile has been investigated with respect to different loading directions. The samples were compressed at room temperature with a constant strain rate of 10^-3s^-1 along extrusion (ED), transversal (TD) and normal direction (ND). X-ray diffraction technique was employed to follow the development of texture during loading. The twinning activity was studied by the subsequent analysis of microstructure using scanning electron microscopy (BSD, EBSD). The deformation behavior of the extruded profile was also investigated by the acoustic emission (AE) technique, where the AE signal analysis correlates the microstructure and the stress-time curves to the active deformation mechanisms. Compression along the ND (i.e. compression perpendicular to the basal planes) is not favorable for twinning, while during compression along the ED and TD twinning activity is observed.

Three-dimensional electron diffraction 3DED has turned nowadays into a reliable and promising method used worldwide for the crystal structure analysis of nanoparticles [1]. Since the first attempts to fine scan the electron diffraction space and use the reconstructed reciprocal volume for single crystal structure analysis [2] the method has been adapted in great variety in several labs. In comparison to traditionally applied 3DED methods, where series of oriented diffraction patterns are collected and indexed individually, automated diffraction tomography (ADT) provides major improvements of diffraction data. Scanning the diffraction space while tilting the crystal delivers non-oriented diffraction patterns with reduced dynamical scattering effects, allows to collect the full diffraction information throughout the acquisition range thus providing an enhanced coverage of the expected diffraction intensities as well as improved diffraction intensity determination. The subsequent three dimensional reconstruction of electron diffraction data provides all information necessary for single crystal structure solution [3]. Dedicated data acquisition strategies and data processing routines allow the investigation of highly beam sensitive material as well as complicated crystallographic features such as the detection and quantitative description of diffuse scattering effects, twinning, superstructures or modulations.

Crystal structures solved “ab initio” with ADT run through a large number of scientific areas and range from the first structural analysis of barite [3] to complex minerals [4], from the first small organic molecule [5] to large organometallic networks [6], from ZSM-5 single crystals [7] to stacked zeolites and layered silicates [8], from the first pseudo symmetric chalcogenide [9] to complicated oxides covering twinned and modulated materials. Many hitherto unknown crystal structures could be solved by 3DED, several of them new and unexpected structures of often metastable compounds [10].

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

[2] Kolb, U., Gorelik, T., Otten, M. (2008). Ultramic. 108, 763.

[3] Mugnaioli, E., Gorelik, T., Kolb, U. (2009) Ultramic. 109, 758.

[4] Rozhdestvenskaya, I., Mugnaioli, E., Czank, M., Depmeier, W., Kolb, U., Reinholdt, A., Weirich, T. (2010) Mineralogical Magazin,74(1), 159.

[5] Kolb, U., Gorelik, T., Mugnaioli, E., Stewart, A. (2010) Polymer Reviews, 50, 385.

[6] Rhauderwiek, T., Zhao, H., Hirschle, P., Doblinger, M., Bueken, B., Reinsch, H., De Vos, D., Wuttke, S., Kolb, U., Stock, N. (2018) Chem. Sci. 9, 5467.

[7] Mugnaioli, E., Kolb, U. (2014) Microporous and Mesoporous Materials, 189, 107. [8] Krysiak, Y., Maslyk, M., Silva, B.N., Plana-Ruiz, S., Moura, H.M., Munsignatti, E.O., Vaiss, V.S., Kolb, U., Tremel, W., Palatinus, L., Leitão, A.A., Marler, B,, Pastore H. O. (2021), Chem. Mater. 33, 3207.

[9] Birkel, C., Mugnaioli, E., Gorelik, T., Panthöfer, M., Kolb, U., Tremel, W. (2010) J.A.C.S. 132(28) 9881.

[10] Zou, Z., Habraken, W.J.E.M., Matveeva, G., Jensen, A.C.S., Bertinetti, L., Hood, M.A., Sun, Ch-Y. Gilbert, P.U.P.A, Polishchuk, I., Pokroy, B., Mahamid, J., Politi, Y., Weiner, S., Werner, P., Bette, S., Dinnebier, R., Kolb, U. Zolotoyabko, E., Fratzl, P. (2019), Science, 363, 396.

Modern electron crystallography started off in the 1960-ies by the work of Aaron Klug and collaborators in Cambridge, UK. At that time the resolution was around 25 Ångström - enough for showing the icosahedral envelopes of spherical viruses. In 1975 Nigel Unwin and Richard Henderson solved the first structure of a membrane protein, bacteriorhodopsin, using Fourier analysis of EM images of 2D crystals of the protein. The resolution was 7 Å.

In parallel, but essentially without contact with the molecular biologists, inorganic structures were also studied by electron microscopy. The resolution of 3.5-4 Å in the 1970-ies was just enough to see metal atoms in oxides. In 1984 we determined the atomic positions of metal atoms in an Nb/W-oxide by EM to an accuracy of about 0.1 Å.

Because of a confused nomenclature regarding the word "phase", the two communities biological and physical, hardly spoke to each other for decades. Crystallographers consider "phase" as crystal structure factor phases, which describe standing waves of electron density in crystals. These waves have wavelengths that correspond to the d-spacings of reflections. In contrast, the physicists studying inorganic compounds by EM, talked about the phases of the electron waves propagating through the crystals. The wavelengths of these waves are determined by the acceleration voltage of the electron microscope used. For 100 kV to 300 kV, these wavelengths are about 0.037 to 0.025 Å. Already by comparing the wavelengths, it is obvious that the two types of phases are different.

Furthermore, the “structure factor phases” are relative to the fixed position of an origin in the unit cell; a position specific for each of the 230 space groups and listed in the International Tables for Crystallography. The “electron wave phases” are relative to the electron wave as it propagates through the crystal at about half the speed of light. Most importantly, the “structure factor phases” are present in the EM images, as Aaron Klug had already explained in the 1960-ies. These phases can be read out from the Fourier transform of an EM image. In contrast, the “electron wave phases” are lost in the EM images. The phases are always lost in diffraction patterns, whether X-ray or electron diffraction.

The confusion as to the presence or not of the phases in EM images was so large that I wasn’t invited as a speaker at the first Electron Crystallography Schools organized by IUCr in Beijing 1993 and Bristol 1994, because “Hovmöller confuses the students”. As a reaction to this, Xiaodong Zou and I started our own schools of electron crystallography in Stockholm. From a very modest scale with just a dozen participants, these schools grew and became annual. The greatest honour was when we were invited by Lodovico Riva de Sanseverino to arrange one of the IUCr schools in Erice. This has since become a tradition every seven years.

X-ray crystallography has been done in 3D right from the start, when the structure of NaCl was solved by Bragg & Bragg in 1912. But electron crystallography for minerals and other inorganic crystals remained in 2D, limiting the structures that could be investigated. In the 1980-ies, we developed the software program CRISP, based on the methods developed in Cambridge for Fourier analysis of EM images. At that time, the great concern about distorted intensities in electron diffraction patterns due to multiple scattering, hampered the development.

A major breakthrough was the invention of the precession electron diffraction technique by Roger Vincent and Paul Midgley in Bristol 1994. It was obvious already by just looking at the electron diffraction patterns that the intensities now were much closer to kinematical. However, it was still only in 2D. The step into 3D came as a result of improved instrumentation combined with software developments. The electron microscopes could be programmed to take series of hundreds of diffraction patterns in just minutes. The diffraction patterns were recorded on very fast detectors (cameras). Systems with different geometries, but fundamentally similar, were then developed independently by Ute Kolb and her group in Mainz (ADT) and by our group in Stockholm (RED). Data collection that previously required days or weeks, was speeded up first to hours and now to minutes or even seconds.

With the new techniques RED (rotation electron diffraction) and ADT (automatic diffraction tomography), the data quality was also substantially improved. The intensities obtained by electron diffraction are now approaching those by X-ray diffraction. Perhaps even more important than reliable intensities, is the fact that these modern ways of electron diffraction give us (nearly) complete 3D data.

Today, 3D electron diffraction has become a fast and highly reliable method for crystal structure determination. Data is collected as fast as with synchrotrons. Because of the very strong interaction of electrons with matter, even the finest powder diffracts like single crystals. Hundreds of structures have now been solved by electron diffraction. From zeolites and metal-organic frameworks (MOF) to quasicrystal approximants, pharmaceutics and proteins are solved from sub-micrometer sized crystals, too small even for synchrotrons.

Finally, after half a century of efforts, electron crystallography is no longer a peculiar young brother from the countryside (compared to X-ray crystallography) but a mature science in its own right.

A particular family of stable organic radicals, the 1,2,3,5-dithiadiazolyls (DTDAs), has been the focus of much research due to their potential as building blocks for molecular materials, in particular materials with interesting magnetic or conducting properties [1]. However, DTDAs frequently dimerise in the solid state via an interaction known as pancake bonding (Fig. 1 left) [2], rendering them diamagnetic. Our various efforts to understand and overcome this pancake bonding interaction will be presented.

The potential of co-crystallisation as a means to overcome dimerisation in DTDAs has been investigated [3]. Thus far, all DTDA-DTDA co-crystals characterised crystallise as pancake-bonded dimers. This has been probed computationally. In related studies, control of polymorph and crystal morphology of a monomeric DTDA by co-sublimation has been demonstrated.

A DTDA has been included in a porous metallocyclic host in an effort to produce materials with interesting magnetic behaviour through interaction between the radical and the host (Fig. 1 right) [4]. The coordination of DTDAs to metalloporphyrins has also been extensively investigated. One particularly interesting DTDA-porphyrin polymer will be discussed [5]. In these systems, dimerisation has been overcome either by restriction of space available for the radical, or by formation of a DTDA-metal bond.

In order to gain a deeper understanding of pancake bonding, experimental charge density analysis has been carried out on a number of DTDA homodimers, heterodimers and monomers [6]. These data, as well as various computational results, have been assessed to probe the nature of the pancake bonds in DTDAs, and reveal how pancake bonds differ from both covalent bonds and conventional intermolecular interactions.

It is clear that DTDAs show great potential as building blocks in the construction of molecular materials.

Figure 1. (left) A DTDA pancake-bonded dimer. (right) DTDA included in a porous metallocycle.

[1] Haynes, D. A. (2011). CrystEngComm 13, 4793. [2] (a) Beneberu, H. Z., Tian, Y.-H. & Kertesz, M. (2012). Phys. Chem. Chem. Phys. 14, 10713. (b) Cui, H., Lischka, H., Beneberu, H. Z. & Kertesz, M. (2014). J. Am. Chem. Soc. 136, 12958. (c) Preuss, K. (2014). Polyhedron 79, 1-15. [3] (a) Alan,C., Haynes, D. A., Pask, C. M. & Rawson, J. M. (2009). CrystEngComm, 11, 2048. (b) Robinson, S. W., Haynes, D. A. & Rawson, J. M. (2013). CrystEngComm, 15, 10205. [4] Nikolayenko, V. I., Barbour, L. J., Arauzo, A., Campo, J., Rawson, J. M. & Haynes, D. A. (2017) Chem. Commun., 53, 11310. [5] Haynes, D. A., van Laeren, L. J. & Munro, O. Q. (2017). J. Am. Chem. Soc., 139, 14620. [6] (a) Domagała, S., Kość, K., Robinson, S. W., Haynes, D. A. & Wozniak, K. (2014). Cryst. Growth Des. 14, 4834. (b) Domagała, S. & Haynes, D.A. (2016). CrystEngComm, 18, 7116. (c) Voufack, A. B., Claiser, N., Dippenaar, A. B., Esterhuysen, C., Haynes, D. A, Lecomte, C. & Souhassou, M. Manuscript in preparation.

Hybrid structural methods to probe atomic features of the Type III Secretion Injectisome of Pathogenic Bacteria

Natalie C.J. Strynadka, Dept of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada V6T1Z3

Bacteria have evolved several sophisticated assemblies to transport proteins across their biological membranes, including those required specifically for pathogenicity. Recent advances in our understanding of the molecular details governing the molecular action of these protein secretion systems has benefited from an integrated toolbox of x-ray crystallography, NMR, mass spectroscopy, molecular modelling and increasingly and most dramatically, cryo electron microscopy. A syringe like nanoassembly, the Type III Secretion system injects multiple virulence “effector” proteins from the bacterial cytosol through to the infected host cell. These effectors manipulate host cell processes in varying ways to the benefit and subsequent pathogenicity of the bacteria. An essential element of disease in several of the most notorious Gram negative bacterial pathogens including the causative agents of food and water borne disease, hospital sepsis, cholera, typhoid fever, bubonic plague and sexually transmitted disease, a molecular understanding of the Type III Secretion systems being garnered from these structural studies provides the foundation for the development of new classes of antibacterials and vaccines to combat infection in the clinic and community. Highlights of recent advances in our structure/function analysis of the multi-membrane spanning Type III Secretion system “injectisome” will be presented emphasizing cryoEM focused refinements of the symmetry mismatched components of the core Type III Secretion System basal body complex spanning the inner through outer membranes of the prototypical Gram negative Salmonella typhimurium bacterial variant. These studies highlight a remarkable set of unexpected interactions including localized recruitment of protomers to allow symmetric coupling interactions between the inner and outer membrane components and a nanodisc like interaction of the inner membrane rings with the multicomponent export apparatus complex “gate”, T3SS proteins previously predicted to be membrane spanning in nature, but clearly sitting atop the membrane bilayer in the assembled structures.

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