Conference Agenda

Overview and details of the sessions of this conference. Please select a date or location to show only sessions at that day or location. Please select a single session for detailed view (with abstracts and downloads if available).

Please note that all times are shown in the time zone of the conference. The current conference time is: 29th Mar 2024, 02:25:04am CET

 
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Session Overview
Date: Friday, 20/Aug/2021
9:00am - 9:50amKN-28: 4th generation SR and XFEL facilities: new era in crystallography and material science
Location: Terrace 2A
Session Chair: Elena Boldyreva

Aleksandr Blagov

 

Fourth-generation Synchrotron radiation and XFEL facilities: new era in crystallography and material science.

Alexander Eugenievich Blagov

National Research Center «Kurchatov Institute», Moscow, Russian Federation

The capabilities of 4th generation synchrotron radiation sources and X-ray free electron lasers such as high brightness, coherence and temporal structure of pulses open new horizons in the studies of structure, structural dynamics and properties of materials.

X-ray radiation coherent methods enable to get access to the 3D structure of non-crystalline samples, nanocrystals and nanostructures with a resolution theoretically limited only by the diffraction limit [1]. Such samples include, for example, various biological objects [2], biological cells, viruses and nanosized crystallites of bio macromolecules and their complexes which are difficult to crystallize.

Access to an atomic structure with ultra-high temporal resolution using ultrashort pulses of free electron lasers makes it possible to consider the different tasks of studying chemical reactions, self-organization and destruction of materials mechanisms, the formation of short-range and long-range orders, the study of phase transitions, and the complex dynamics of proteins and polymers at a fundamentally new level.

Novel scientific tasks cover a wide range of practical applications [3], including such priority areas as biotechnology and medicine, the creation of new functional materials (structural, composite, etc.), nanoelectronics and hybrid (sensors, biosensors, etc.).

Today most of the new synchrotron radiation sources have almost 100% transverse coherence, and the modernization of existing mega-facilities (for example, ESRF-EBS, PETRA IV, APS) focus on reducing the emittance (significantly less than 1 nm), increasing coherence, brightness and time resolution.

In the Russian Federation the development of coherent scattering and time resolving methods is becoming one of the priority tasks in connection with the implementation of the program for the development of the synchrotron-neutron infrastructure, including the construction of 4th generation sources: USSR-4 (synchrotron with a free electron laser) and SKIF project.

[1] J. Miao, T. Ishikawa, I. Robinson, M. Murnane Beyond crystallography: Diffractive imaging using coherent x-ray light sources. // Science. 2015. V. 348. 6234. P. 530.

[2] A. Mancuso, O. Yefanov, I. Vartanyants, Coherent diffractive imaging of biological samples at synchrotron and free electron laser facilities // Journal of Biotechnology, Volume 149, Issue 4, 2010, P. 229.

[3] H.Chapman, K. Nugent Coherent lensless X-ray imaging. // Nature Photonics. 2010. V. 4. P. 833.

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9:00am - 9:50amKN-29: Crystal engineering of adaptive smart materials: from mechanical bending to self-healing
Location: Terrace 2B
Session Chair: Masaki Kawano

Malla Reddy

 

Crystal engineering of adaptive smart materials: from mechanical bending to self-healing

C Malla Reddy

Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, 741246, India

High crystallinity, although desired in materials for a wide range of high-performance engineering applications, generally comes with undesirable attributes such as high brittleness and fragility [1]. This makes crystalline materials incompatible with many future technologies, such as flexible devices and soft-robotics. Recent progress in crystal engineering has brought into light many possible opportunities to address these issues, enabling the design of adaptive crystalline materials that respond to external stimuli with exceptional qualities [1-7]. For instance, crystals that bend (elastically or plastically), twist, curl, wind, jump, exfoliate, laminate, and explode, under external stresses, such as mechanical stress, pressure, light, heat, solvent, etc., have been shown. On the other hand, until very recent time, self-healing was observed only in soft and amorphous materials, mostly involving approaches that use chemical reactions, diffusion, solvent, vapour, electricity, etc., with typical healing time scales in minutes to weeks [8]. A new self-healing mechanism that we recently introduced [9] in materials science, enables ultrafast, near 100% autonomous diffusion-less repair in crystalline materials that uses electrostatic surface potentials generated on the freshly created fracture surfaces, inherent to certain types of polar single crystals. My talk will cover structure-property correlation for crystal engineering of adaptive materials.

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9:00am - 9:50amKN-30: Structure guided inhibitor discovery targeting a membrane receptor involved in atherosclerosis
Location: Club A
Session Chair: Julie Bouckaert

Arockiasamy Arulandu

 

Structure guided inhibitor discovery targeting a membrane receptor involved in atherosclerosis

Arockiasamy Arulandu1, Akanksha Tomar1, Azeem Khan1, Sibasis Sahoo1, Muthu Sankar Aathi1, Shobhan Kuila1, Anmol Chandele1, Jawahar L Mehta2, Kottayil I Varughese3

1International Centre for Genetic Engineering and Biotechnology, New Delhi, India; 2University of Arkansas for Medical Sciences and the Central Arkansas Veterans Healthcare System, Little Rock, Arkansas, United States; 3University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States.

Atherosclerosis is a major cause of cardiovascular diseases and stroke. Oxidized low-density lipoprotein (Ox-LDL) plays a key role in the initiation and progression atherogenic process. Lectin-like ox-LDL receptor-1 (LOX-1) [1], a scavenger receptor present on vascular endothelial cells, macrophages, smooth muscle cells, and platelets, facilitates internalization of ox-LDL leading to atherosclerotic plaque formation. Existing data points towards LOX-1 as a potential target for novel anti-atherosclerosis therapy [2-3]. However, no approved therapeutics targeting LOX-1 are known. Using computational tools, we first identified a potential druggable site on the extracellular C-terminal domain (CTLD) of LOX-1. Then, using structure-based screening and molecular dynamics we have identified and short-listed molecules from chemical libraries for further validation with a combination of surface plasmon resonance, cell-based ox-LDL uptake assay, and complex crystal structures. Our data clearly shows that LOX-1 is druggable. Further studies will be performed to decipher mechanistic details of ox-LDL uptake inhibition

[1] Sawamura, T., Kume, N., Aoyama, T., Moriwaki, H., Hoshikawa, H., Aiba, Y., ... & Masaki, T. (1997). Nature. 386(6620), 73.

[2] Mehta, J. L., Sanada, N., Hu, C. P., Chen, J., Dandapat, A., Sugawara, F., ... & Sawamura, T. (2007). Circ. Res. 100(11), 1634.

[3] Pothineni, N. V. K., Karathanasis, S. K., Ding, Z., Arulandu, A., Varughese, K. I., & Mehta, J. L. (2017). J. Am. Coll. Cardiol. 69(22), 2759.

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9:50am - 10:20amMorning break 6: Posters, coffee/tea
Location: Exhibition and poster area
10:20am - 12:45pmMS-73: Machine learning in biological and structural sciences
Location: Terrace 2B
Session Chair: Rita Giordano
Session Chair: Harold Roger Powell

Invited: Melanie Vollmar (UK), Sergei Grudinin (France)

 
10:20am - 10:25am

Introduction to session

Rita Giordano, Harold Roger Powell



10:25am - 10:55am

Predicting experimental phasing success for data triaging

Melanie Vollmar1, Irakli Sikharulidze1, Gwyndaf Evans1,2

1Diamond Light Source, Didcot, United Kingdom; 2Rosalind Franklin Institute, Didcot, United Kingdom

Over the recent years there have been large advances in technologies at synchrotron facilities. Photo-counting detectors with high frame rates (several hundred fps) allow for rapid data acquisition. Robotic sample exchangers combined with automated sample centring enable high-throughput sample screening. Fully automated and unattended data collection set-ups offer the possibility to rapidly gather data. Taken together, all these technologies produce vast amounts of data which need to be analysed and stored. Even for an expert crystallographer it can now be very challenging to assess the data gathered during an experimental session. For novel or non-expert users, the data amounts may even feel overwhelming. Additionally, many research groups do not have access to high-performance computing infrastructure or large storage space to keep their data and analyse it and for research facilities like synchrotrons this infrastructure is limited too.

Here we present some initial results for a machine learning-based triaging system which is currently being trialled at Diamond. The aim is to refine the current brute-force experimental phasing pipelines by introducing data driven triage and decision making. The system as it is in place, relies on data fulfilling certain metrics thresholds before being triggered and executing a number of experimental phasing programs in parallel. Each of these programs can run hours and up to a day before producing an output without a guaranteed success. Based on our initial results presented here, we now propose a machine learning-based decision maker which will estimate the chances of successful experimental phasing for the different software packages available within Diamond's automated data analysis pipelines. The outcome of the classification process is then used to execute subsets in the pipelines in a hieararchical fashion.

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10:55am - 11:25am

Deep learning entering the post-protein structure prediction era : new horizons for structural biology

Sergei Grudinin

Univ. Grenoble Alpes, CNRS, Grenoble INP, LJK, 38000 Grenoble, France

The potential of deep learning has been recognized in structural bioinformatics for already some time, and became indisputable after the CASP13 (Critical Assessment of Structure Prediction) community-wide experiment in 2018. In CASP14, held in 2020, deep learning has boosted the field to unexpected levels reaching near-experimental accuracy. Its results demonstrate dramatic improvement in computing the three-dimensional structure of proteins from amino acid sequence, with many models rivalling experimental structures. This success comes from advances transferred from several machine-learning areas, including computer vision and natural language processing. At the same time, the community has developed methods specifically designed to deal with protein sequences and structures, and their representations. Novel emerging approaches include (i) geometric learning, i.e. learning on non-regular representations such as graphs, 3D Voronoi tessellations, and point clouds; (ii) pre-trained protein language models leveraging attention; (iii) equivariant architectures preserving the symmetry of 3D space; (iv) use of big data, e.g. large meta-genome databases; (v) combining protein representations; (vi) and finally truly end-to-end architectures, i.e. single differentiable models starting from a sequence and returning a 3D structure. These observations suggest that deep learning approaches will also be effective for a range of related structural biology applications that will be discussed in this lecture.

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11:25am - 11:45am

How machine learning can supplement traditional quality indicators - and the human eye: A case study

Andrea Thorn1, Kristopher Nolte1, Yunyun Gao1, Sabrina Stäb1, Philip Kollmannsberger2

1Universität Hamburg, Germany; 2Julius-Maximilians-Universität Würzburg, Germany

Detecting the ice diffraction artifacts in single-crystal datasets can be very difficult once the data have been integrated, scaled and merged. Automatic tools are available in CTRUNCATE [1], phenix.xtriage [2] and AUSPEX [3]. Recently, the AUSPEX icefinder score was improved by Moreau and colleagues [4]. Automatic recognition of these artifacts would be highly beneficial as macromolecular structure determination can be negatively impacted or even completely hindered by ice diffraction, but remains difficult.

In 2017, we have shown that inspection of plots of merged intensities against resolution permit an easy identification of ice ring contamination in integrated data sets - by eye. However, this approach could be matched by automatic routines. This has led us to attempt identification using convolutional neural networks, which are exceptionally suited to classification of multi-dimensional arrays because they can retain spatial information of the input.

Here, we present our results to employ convolutional neural networks to detect ice artefacts in processed macromolecular diffraction data, resulting in a new automatic detection called “Helcaraxe”. which outperforms previous indicators. We will also discuss the scope this may offer for the structural biology community to tap into the vast amount of data the field has accumulated in 50 years of deposition to the Protein Data Bank.

Adams, P. D., Afonine, P. V., Bunkóczi, G., Chen, V. B., Davis, I. W., Echols, N., Headd, J. J., Hung, L.-W., Kapral, G. J., Grosse-Kunstleve, R. W., McCoy, A. J., Moriarty, N. W., Oeffner, R., Read, R. J., Richardson, D. C., Richardson, J. S., Terwilliger, T. C., & Zwart, P. H. (2010). PHENIX: A comprehensive Python-based system for macromolecular structure solution. Acta Cryst. D66, 213–221. https://doi.org/10.1107/S0907444909052925

Moreau, D. W., Atakisi, H., & Thorne, R. E. (2021). Ice in biomolecular cryocrystallography. Acta Cryst. D77, 540–554. https://doi.org/10.1107/S2059798321001170

Thorn, A., Parkhurst, J., Emsley, P., Nicholls, R. A., Vollmar, M., Evans, G., & Murshudov, G. N. (2017). AUSPEX: A graphical tool for X-ray diffraction data analysis. Acta Cryst. D73, 729–737. https://doi.org/10.1107/S205979831700969X

Winn, M. D., Ballard, C. C., Cowtan, K. D., Dodson, E. J., Emsley, P., Evans, P. R., Keegan, R. M., Krissinel, E. B., Leslie, A. G. W., McCoy, A., McNicholas, S. J., Murshudov, G. N., Pannu, N. S., Potterton, E. A., Powell, H. R., Read, R. J., Vagin, A., & Wilson, K. S. (2011). Overview of the CCP 4 suite and current developments. Acta Cryst. D67, 235–242. https://doi.org/10.1107/S0907444910045749

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11:45am - 12:05pm

Learning structure-energy relationships for the prediction of molecular crystal structures

Graeme M Day

University of Southampton, Southampton, United Kingdom

The discovery of new functional materials can be guided by computational screening, particularly if the structure of a material can be reliably predicted from its chemical composition. For this application, we have been developing the use energy-structure-function maps [1] of the crystal structures available to a molecule. These maps help understand the properties of predicted crystal structures and their energetic stabilities. However, the use of these methods is still limited by the computational cost of crystal structure prediction (CSP), most of which is associated with the calculation of the relative energies of predicted crystal structures using energy models that are sufficiently accurate to provide reliable energetic rankings. To accelerate these methods, we have been developing machine learning approaches to predict high quality energies (e.g. from solid state density functional theory) from structures that have been generated with computationally efficient energy models. These approaches rely on statistical models, in our case Gaussian Process Regression, to relate lattice energies to geometric descriptors of crystal structures. The talk will discuss two approaches that we have developed: learning of total energies calculated using solid state density functional theory [2,3], and a fragment-based approach [4] where we learn high level dimer energies, which are used to build up the total lattice energies of predicted structures.

[1] Day, G. M. and Cooper, A. I. (2018) Adv. Mater., 30, 1704944.

[2] Musil, F, De, S., Yang, J., Campbell, J. E., Day, G. M. and Ceriotti, M. (2018) Chem. Sci., 9, 1289-1300.

[3] Egorova, E., Hafizi, R., Woods, D. C. and Day, G. M. (2020) J. Phys. Chem. A, 124 , 8065–8078.

[4] McDonagh, D., Skylaris, C.-K. and Day, G. M. (2019) J. Chem. Theory Comput., 15, 2743–2758

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12:05pm - 12:25pm

New generalized crystallographic descriptors for structural machine learning

James Cumby, Sohan Seth, Ruizhi Zhang

University of Edinburgh, Edinburgh, United Kingdom

The ever-growing amount of crystallographic data offers the potential to uncover a range of scientific discoveries, from rapidly predicting physical properties to suggesting new materials with desirable functional behaviours. This is further enhanced by the current growth in machine learning (ML) algorithm development and implementation. There is, however, a significant obstacle to this goal; standard crystallographic information are not suitable inputs for ML algorithms. This arises due to the inherent flexibility of crystallography, such as non-unique unit cell definitions and symmetry. To overcome this problem, significant progress has been made in devising ‘descriptors’ for crystallographic ML, compressing and standardising crystallographic information into a smaller feature space. Much of the existing focus has been on molecular crystals, where the finite extent of individual molecules imposes a limit on the size of feature vector required. A large number of approaches have been proposed but do not easily extrapolate to extended (i.e. inorganic) materials. [1] The descriptors that are suitable for extended solids tend to be either hand-crafted for a specific problem, or have so many dimensions that extremely large datasets must be used to train reliable ML models. In addition, many do not scale well with variable numbers of atomic species.

Here, we present two new descriptors for crystallographic materials which are generally applicable and invariant to compositional complexity. The first is based on a real-space view of the structure, the second on a reciprocal (or diffraction) space view. Both descriptions are invariant to atomic permutations and unit cell choice, and can be considered as an ‘extended’ (i.e. more information-rich) version of the atomic radial distribution function (RDF) and powder diffraction pattern, respectively. The more complete features offered by these descriptors results in better physical property predictions. For example, our ‘extended’ RDF can predict bulk modulus from crystal structures obtained from the Materials Project [2] with a much lower error than the ‘simple’ RDF using linear ridge regression (Figure 1). It is notable that the error approaches current state-of-the-art results, [3] without any knowledge of the atom types involved.

[1] Rossi, K. & Cumby, J. (2020). Int. J. Quantum Chem., 120, e26151. [2] Jain, A., Ong, S. P., Hautier, G., et al. (2013). APL Mater., 1(1), 011002. [3] Chen, C., Ye, W., Zuo, Y. et al. (2019). Chem. Mater., 31, 3564.

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12:25pm - 12:45pm

Analysis of pre-edge XANES spectra of Fe:SiO4 system by using machine learning methods.

Danil Pashkov, Alexander Guda, Sergey Guda, Alexander Soldatov

Southern Federal University, Rostov-on-Don, Russian Federation

The x-ray absorption near-edge structure (XANES) spectra of some nano-structures exhibit small peaks when the incident x-ray energy is lower than the main absorption edge energy. The energies of these peaks depend on local environment, valency of chemical elements and density of electronic states. Advanced quantitative analysis of the local atomic geometry around active catalytic sites requires novel experimental method e.g. the pre-edge structure of X-ray absorption near edge spectra (XANES) measured in the high-energy resolution fluorescence detected mode, the so-called HERFD-XANES. However, there is no widely used ab initio theoretical method which could be routinely applied to the analysis of such experimental data except parametric multiplet calculations. To overcome the procedure of adjusting of parameters is the using of local DFT Hamiltonian constructed on the basis of Wannier orbitals – the so called multiplet ligand-field theory (MLFT) [1]. Pre-edge region of X-ray absorption spectra could be calculated using the XTLS code in the framework of multiplet ligand-field theory using maximally localized Wannier functions (MLWF).

Computation of pre-edge XANES spectra according to MLFT approach is a complicated process, which requires using a lot of software, such as: Wien2k, Wannier90, XTLS code and some additional programs and scripts. We developed «w2auto» program, which automates all process of pre-edge XANES computation. «w2auto» emulates work in w2web interface of Wien2k software and provides opportunity to run all necessary programs without user access. The launch of the necessary calculation steps is controlled through the configuration script in Python programming language. Also we developed a simple GUI for users who does not have any experience in programming in Python language. It helps to generate configure file in form of Python script.

In recent years machine learning has become a powerful instrument for solving scientific problems. It helps to classify and sort data, make approximations, find latent dependencies and features. In this work we have applied machine learning methods for analysis of the Fe:SiO4 pre-edge XANES spectra. As recently shown,

machine learning methods have been successfully applied to the quantitative analysis of spectroscopic data in general and of X-ray near edge spectroscopy (XANES) in particular [2-4].

In the present work we show applicability of machine learning methods to retrieve structural information in system Fe:SiO4. In this research we have collected 60 pre-edge XANES spectra in differrent coordination (from 2-fold to 6-fold) and oxidation states (Fe2+ and Fe3+) using «w2auto» program. We used this dataset to train and validate several machine learning methods (Decision Tree, ExtraTrees, SVM, Logistic regression and neural network) to determine both coordination number and oxidation state by spectrum.

Acknowledgment

The work was supported by grant of President of Russia for young scientists (MK-2730.2019.2).

References

[1] E. Gorelov, A.A. Guda, M.A. Soldatov, S.A. Guda, D. Pashkov, A. Tanaka, S. Lafuerza, C. Lamberti, A.V. Soldatov, MLFT approach with p-d hybridization for ab initio simulations of the pre-edge XANES, Radiation Physics and Chemistry, 2018, DOI: 10.1016/j.radphyschem.2018.12.025.

[2] A. Martini, S. A. Guda, A. A. Guda, G. Smolentsev, A. S. Algasov, O. A. Usoltsev, M. A. Soldatov, A. L. Bugaev, Y. V. Rusalev, A. V. Soldatov, PyFitit: the software for quantitative analysis of XANES spectra using machine learning algorithms, Computer Physics Communications, 2019

[3] A. A. Guda, S. A. Guda, K. A. Lomachenko, M. A. Soldatov, I. A. Pankin, A. V. Soldatov, L. Braglia, A. L.Bugaev, A. Martini, M. Signorile, E. Groppo, A. Piovano, E. Borfecchia, C. Lamberti, Quantitative structural determination of active sites from in situ and operando XANES spectra: From standard ab initio simulations to chemometric and machine learning approaches, Catalysis Today, V. 336, 2019, P. 3-21, DOI: 10.1016/j.cattod.2018.10.071.

[4] Guda, A.A., Guda, S.A., Martini, A., Bugaev A., Soldatov, M. A., Soldatov, A. V. & Lamberti, C. (2019). Machine learning approaches to XANES spectra for quantitative 3D structural determination: The case of CO2 adsorption on CPO-27-Ni MOF. Radiation Physics and Chemistry. 108430. DOI: 10.1016/j.radphyschem.2019.108430.

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10:20am - 12:45pmMS-74: Structural biology of receptors, signaling and membrane proteins
Location: Club A
Session Chair: SUSAN KAY BUCHANAN
Session Chair: Michael Parker

Invited:  Robert Keenan (USA), Isabel Moraes (UK)

 
10:20am - 10:25am

Introduction to session

Susan Kay Buchanan, Michael Parker



10:25am - 10:55am

Structures of the archaerhodopsin-3 transporter reveal that disordering of internal water networks underpins receptor sensitization

Isabel Moraes1, Peter J. Judge2, Juan F. Bada Juarez2, Danny Axford3, Tristan Kwan1, Anthony Watts2

1National Physical Laboratory, Teddington, TW11 0LW, UK; 2Biochemistry Department, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK; 3Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK

Like other photoreceptor proteins, the archaerhodopsin-3 (AR3) protein has a desensitized, inactive state which is formed in the prolonged absence of light. This dark-adapted (DA) state must be converted to the light-adapted (LA) or resting state, before the protein can generate a proton motive force. In general, receptor desensitization is commonly achieved through reversible covalent or non-covalent modifications, which typically modulate intramolecular bonding networks to stabilize a conformation that is distinct from the active resting or ground state.

Here, we present high-resolution crystal structures of the LA and DA states of AR3, solved to 1.1 Å and 1.3 Å resolution respectively [1]. We observe significant differences between the two states in the dynamics of internal water molecules that are coupled via H-bonds to the retinal Schiff base. These changes modulate the polarity of the environment surrounding the chromophore, influence the relative stability of 13-cis and all-trans retinal isomers and facilitate the conversion between the two forms. These crystal structures also allow us to gain a better understanding of the extent to which the conformation of the chromophore is coupled to the networks of internal water molecules, see Fig. 1. They highlight how minimal displacements of charged and hydrophilic groups within the low dielectric environment of the membrane can induce changes in ligand conformation and vice versa. Finally, these structures also provide high-resolution structural information that increases our understanding of the mechanism of H+ translocation by AR3, and will facilitate the design of further, more efficient AR3 mutants for applications in optogenetics.

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10:55am - 11:25am

An ER translocon for multi-pass membrane protein biogenesis

Philip T McGilvray1, S Andrei Anghel1, Arunkumar Sundaram1, Frank Zhong1, Michael J Trnka2, James R Fuller1, Hong Hu1, Alma L Burlingame2, Robert J Keenan1

1University of Chicago, Chicago, United States of America; 2University of California, San Francisco, United States of America

Membrane proteins with multiple transmembrane domains play critical roles in cell physiology, but little is known about the machinery coordinating their biogenesis at the endoplasmic reticulum. Here we describe a ~ 360 kDa ribosome-associated complex comprising the core Sec61 channel and five accessory factors: TMCO1, CCDC47 and the Nicalin-TMEM147-NOMO complex. Cryo-electron microscopy reveals a large assembly at the ribosome exit tunnel organized around a central membrane cavity. Similar to protein-conducting channels that facilitate movement of transmembrane segments, cytosolic and luminal funnels in TMCO1 and TMEM147, respectively, suggest routes into the central membrane cavity. High-throughput mRNA sequencing shows selective translocon engagement with hundreds of different multi-pass membrane proteins. Consistent with a role in multi-pass membrane protein biogenesis, cells lacking different accessory components show reduced levels of one such client, the glutamate transporter EAAT1. These results identify a new human translocon and provide a molecular framework for understanding its role in multi-pass membrane protein biogenesis.

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11:25am - 11:45am

To eat or not to eat: Cryo-EM structure of melanocortin receptor 4 reveals mechanism of a “hunger switch” initiating satiety signaling.

Oksana Degtjarik1, Hadar Israeli1,2, Li F. Chan3, Danny Ben-Zvi2, Masha Y. Niv4, Peter J. McCormick3, Moran Shalev-Benami1

1Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel; 2Department of Developmental Biology and Cancer Research, The Hebrew University-Hadassah Medical School, Jerusalem, Israel; 3Centre for Endocrinology, William Harvey Research Institute, Barts and the London School of Medicine, Queen Mary, University of London, Charterhouse Square, London, UK; 4Faculty of Agriculture, The Hebrew University, Israel

Obesity is a global epidemic causing increased morbidity and impaired quality of life. The melanocortin receptor 4 (MC4R) is a G protein-coupled receptor that plays a key role in regulation of food consumption and energy expenditure in the central nervous system, thus becoming a prime target for anti-obesity drugs. We present the cryo-EM structure of the human MC4R-Gs signaling complex bound to the agonist setmelanotide, a cyclic peptide recently approved for the treatment of obesity. The work reveals the mechanism of MC4R activation, highlighting a molecular switch that initiates satiation signaling. Coupled to signaling assays and molecular dynamics simulations, the structure demonstrates the role calcium plays in receptor activation, but not inhibition. Altogether, these results fill a gap in understanding MC4R activation and provide guidelines for a structure-based design of novel and more efficient weight management drugs.

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11:45am - 12:05pm

Unravelling the molecular architecture of the Commander assembly

Michael David Healy1, Joanna Sacharz2, Tristan Croll3, David A Stroud2, Brett M Collins1

1The University of Queensland, Brisbane, Australia; 2University of Melbourne, Melbourne, Australia; 3Cambridge Institute fo Medical Research, Cambridge, United Kingdom

The Commander complex is a conserved regulator of intracellular trafficking. This ancient complex consists of 15 core components as well as a number of associated proteins that can be sub-divided into 3 categories: the COMMD/Coiled coil domain containing protein (CCDC) 22/CCDC93 (CCC) complex, the Retriever complex (a distant relative of the Retromer complex) and a number of associated proteins. Functionally Commander couples to Sorting Nexin 17 (SNX17) to facilitate the recycling of over 100 cell surface proteins including key receptors such as, LDLR, LRP1, p-Selectin and the amyloid precursor protein. In addition, Commander dysfunction has been linked to various disease pathologies including X-linked intellectual disability. It is therefore crucial to understand the structure, mechanism and function of this complex, an understanding that has remain largely elusive to date.

In the work presented here I have followed on from our previously published work on the structure of individual COMMD proteins [1] by reconstituting the core COMMD protein complex in vitro. The successful reconstitution of this complex using a polycistronic E. coli vector has allowed for the identification of two distinct subcomplexes of the COMMD family, a result supported by in vivo experiments conducted using quantitative mass spectrometry and a panel of COMMD knockout eHAP cell lines.

Identification of these distinct subcomplexes also allowed for the resolution of a ~3.3 Å crystal structure of COMMD subcomplex B. Revealing an intimately assembled tetramer, with interfaces along the β-strands of the highly conserved COMM domain and more subunit specific interactions between the loops on the COMM domain and the more variable helical N-terminal domain (See Figure 1). Intriguingly despite the formation of distinct subcomplexes in in vitro expression there is sufficient evidence to suggest COMMDs exist as a decameric assembly in the endogenous cellular environment. With this in mind we have used the aforementioned structure to model this assembly, revealing a geometrically perfect star assembly (See Figure 2).

[1] Healy, M. D., Hospenthal, M. K., Hall, R. J., Chandra, M., Chilton, M., Tillu, V., Chen, K., Celligoi, D. J., McDonald, F. J., Cullen, P. J., Lott, J. S., Collins, B. M., Ghai, R. (2018). eLIFE. 7, e35895.

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12:05pm - 12:25pm

Two-component pore formation by the novel CDCL proteins ALY short and ALY long from Elizabethkingia anophelis

Bronte A Johnstone1, Sara L Lawrence2, Michelle P Christie1, Rodney K Tweten3, Craig J Morton1, Michael W Parker1,2

1Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3010, Australia; 2ACRF Rational Drug Discovery Centre, St. Vincent’s Institute of Medical Research, Fitzroy, VIC 3065, Australia
; 3Department of Microbiology and Immunology, University of Oklahoma, Health Sciences Center, Oklahoma City, OK 73104, USA

Cholesterol-dependent cytolysins (CDCs) are bacterial pore-forming toxins that are secreted as soluble monomers and oligomerise into large circular pre-pores on the surface of cholesterol-rich membranes. Various structural changes and transitions results in insertion of β-hairpins into the lipid bilayer, forming a large β-barrel pore that results in cell lysis. We have identified a widely distributed family of bacterial proteins that share substantial structural similarity with CDCs. We have the named these proteins the “CDC-like” (CDCL) proteins, which derive from predominantly Gram-negative bacterial phyla. Many of these CDLS exist as homologous pairs. One partner of the CDCL pair, termed CDCL long, consists of four domains: three similar to CDCs and a unique fourth domain. The other partner, CDCL short, possesses three domains, all similar to CDCs. One CDCL pair, referred to as ALY long (ALYL) and ALY short (ALYS), originate from the species Elizabethkingia anophelis; an emerging and opportunistic pathogen of unknown virulence and transmission. We have solved the crystal structure of ALYL, which consists of characteristic CDC domain 1 – 3 structure; however, domain 4 differs from that of CDCs significantly. In the presence of lipids, ALYS forms a circular oligomer, while ALYS in combination with ALYL forms a functional pore capable of inserting into membranes. Unlike CDCs, formation of these pores is not cholesterol dependent. To determine the atomic structure of ALY pores, cryo-EM single-particle analysis is currently being pursued. Further studies include HDX-MS and lipid binding analysis to study the conformational changes and lipid binding details of pore formation. An understanding of pore formation by ALY may yield new knowledge of Elizabethkingia anophelis virulence, in addition to providing a system that could be applied to biotechnological applications.

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12:25pm - 12:45pm

Mechanistic insights into the synergistic activation ofthe RXR–PXR heterodimer by endocrinedisruptor mixtures

Vanessa Delfosse1, Tiphaine Huet1, Deborah Harrus1, Meritxell Granell1, Maxime Bourguet2, Caroline Gardia-Parège3, Barbara Chiavarina3, Marina Grimaldi3, Sébastien Le Mével4, Pauline Blanc1, David Huang1, Jakub Gruszczyk1, Barbara Demeneix4, Sarah Cianférani2, Jean-Baptiste Fini4, Patrick Balaguer3, William Bourguet1

1Center for Structural Biology, Montpellier, France; 2Laboratoire de Spectrométrie de Masse Bioorganique, Strasbourg, France; 3Institut de Recherche en Cancérologie, Montpellier, France; 4Muséum National d'Histoire Naturelle, Paris, France

Humans are chronically exposed to mixtures of xenobiotics referred to as endocrine-disrupting chemicals (EDCs). A vast body of literature links exposure to these chemicals with increased incidences of reproductive, metabolic, or neurological disorders. Moreover, recent data demonstrate that, when used in combination, chemicals have outcomes that cannot be predicted from their individual behavior. In its heterodimeric form with the retinoid X receptor (RXR), the pregnane X receptor (PXR) plays an essential role in controlling the mammalian xenobiotic response and mediates both beneficial and detrimental effects. Our previous work shed light on a mechanism by which a binary mixture of xenobiotics activates PXR in a synergistic fashion. Structural analysis revealed that mutual stabilization of the compounds within the ligand-binding pocket of PXR accounts for the enhancement of their binding affinity. In order to identify and characterize additional active mixtures, we combined a set of cell-based, biophysical, structural, and in vivo approaches. Our study reveals features that confirm the binding promiscuity of this receptor and its ability to accommodate bipartite ligands. We reveal previously unidentified binding mechanisms involving dynamic structural transitions and covalent coupling and report four binary mixtures eliciting graded synergistic activities. Last, we demonstrate that the robust activity obtained with two synergizing PXR ligands can be enhanced further in the presence of RXR environmental ligands. Our study reveals insights as to how low-dose EDC mixtures
may alter physiology through interaction with RXR–PXR and potentially several other nuclear receptor heterodimers.

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10:20am - 12:45pmMS-75: Small- and Wide-Angle Scattering for industrial materials far from equilibrium
Location: Club D
Session Chair: Jan Ilavsky
Session Chair: Semra IDE

Invited: Masato Ohnuma (Japan), Elliot Paul Gilbert (Australia)

 
10:20am - 10:25am

Introduction to session

Jan Ilavský, Semra Ide



10:25am - 10:55am

Characterising Food Materials and the Case for Extended q Scattering

Elliot Paul Gilbert

ANSTO, NSW, Australia

When designing food products, it is important to understand and predict structure-function-property relationships within food constituents. This includes knowledge of not only the structure of native materials but also their structural changes across a wide range of length scales brought about by food processing. The inherent complexity of food systems therefore calls for an arsenal of techniques and instrumentation that can access a broad range of dimensions.

The Australian Nuclear Science and Technology Organisation (ANSTO) commenced the ‘Food Materials Science Programme’ to explore opportunities for the utilisation of the nuclear based methods, including small and ultra-small angle neutron scattering ((U)SANS), in a quest to extend the understanding of complex food systems. This presentation will highlight the role of (U)SANS in the context of broader materials characterisation methods, using several examples1-8.

[1] Elliot Paul Gilbert, Current Opinion in Colloid & Interface Science 42 (2019) 55.

[2] Amparo Lopez-Rubio, Elliot Paul Gilbert, Trends in Food Science and Technology 20 (2009) 576.

[3] James Doutch, Mark Bason, Ferdi Franceshcini, Kevin James, Douglas Clowes, Elliot P. Gilbert, Carbohydrate Polymers 88 (2012) 1061.

[4] Constantinos V. Nikiforidis, Elliot Paul Gilbert, Elke Scholten, RSC Advances, 5 (2015) 47466.

[5] Zhi Yang, Xu Xu, Ravnit Singh, Liliana de Campo, Elliot P. Gilbert, Zhonghua Wu, Yacine Hemar, Carbohydrate Polymers, 212 (2019) 40-50

[6] Yaiza Benavent-Gil, Cristina M. Rosell and Elliot P. Gilbert, Food Hydrocolloids 112 (2021) 106316.

[7] Steven Cornet, Liliana de Campo, Marta Martinez-Sanz, Elke Scholten and Elliot Paul Gilbert, in manuscript

[8] https://www.ansto.gov.au/research/programs/other/food-science

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10:55am - 11:25am

"Slow operand" measurements by laboratory small-angle X-ray scattering

Masato Ohnuma1, Shigeru Kuramoto2, Isamu Kaneda3

1Hokkaido University, Sapporo, Japan; 2Ibaraki University, Hitachi, Japan; 3Rakuno Gakuen University, Ebetsu, Japan

Majority of recent small-angle X-ray scattering (SAXS) studies have been performed mainly in the large-facility, such as SPring-8 (JAPAN), APS (USA), and other synchrotron radiation facilities. Since high intensity of those source makes possible to realize time resolve measurements in a few seconds in non-distractive mode, "operand" measurements become popular and important to understand formation of nanostructures in many materials. In contrast, laboratory SAXS systems are usually regarded as the tool for static measurements. However, recent progress in source, optics (confocal mirror, low scattering slit) and detector makes us possible to measure nanostructure in a few minutes. Those systems can also be optimized for high energy source such as Mo solid or In-rich liquid metal targets. Combining these features, reaction continuing for a few days can be monitored non-destructively, which we call "slow operand" measurements. Two examples will give in this talk; First one is about low temperature aging (room temp., 65ºC, 120ºC) of Al-Zn-Mg-Cu alloys for 2 days. Second example is shape change of colloidal calcium phosphate (CCP) in real cheese for more than 5 days. In the former case, we have measured 1 mm thick aluminum sheet directly from solid solution treatment (SST) without any sample thinig using labo-SAXS with Mo source. We have also measured the sample with rolling following SST. Since all has been done in same room, the uncovered time before starting measurements are less than 5 minutes. Advantage in the second example is the physical distance between source and cheese factory. Since fresh curd (before salting) and cheese has been carried from real cheese factory in Rakuno Gakuen Univ. to labo. SAXS in Hokkaido Univ. with in 1 hour. Samples (curd or cheese) with 1.8 mm thick put into the glass cell and sealed. Shape of nanostructure of cheese corresponding to CCP changes from about sphere of 2.4 nm in diameter to disc like shape with 14 nm in diameter as shown in Fig.1.

Though there are many studies using SAXS [1, 2] including operand measurements in both case, such long time-span measurements have not been reported as far as we know. Nevertheless, there are several processes which are industrially important and occur slowly around room temperature. For those target, the slow operand technique with labo-SAXS must be very useful and important in addition to regular operand technique with large facilities.

Figure 1. Time evolution of SAXS profiles of curd and cheese from 1 hour to 5 days after production . [1] ex. Deschamps, A., De Geuser, F., Horita, Z., Lee, S. & Renou, G., (2014). Acta. Mater. 66, 105[2] ex. Ingham, B., Smialowska, A., Kirby, N. M., Wang, C. & Carr, A. J. (2018). Soft Matter. 14, 3336.

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11:25am - 11:45am

Breaking Bad: Towards Certifiable Additively Manufactured Alloys Using Post-Build Heat Treatment

Fan Zhang1, Carelyn E. Campbell1, Mark R. Stoudt1, Lyle E. Levine1, Andrew J. Allen1, Eric A. Lass2, Greta Lindwall3

1Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA; 2Department of Materials Science and Engineering, University of Tennessee, Knoxville, TN 37996, USA; 3Department of Materials Science and Engineering, KTH Royal Institute of Technology, Brinellvägen 8, 114 28 Stockholm, Sweden

Additive manufacturing (AM) of metals provides great flexibility in manufacturing parts with complex geometrical shapes and is fast becoming an attractive option for the fabrication of high-valued metal components in aerospace, oil & gas, and biomedical industries. The rapid heating and cooling during AM fabrication, which by nature is a highly nonequilibrium process, often leads to significant microstructural heterogeneity uncommon to wrought and cast alloys. Such heterogeneity creates tremendous challenge in the qualification and eventual certification of AM metal parts for many applications.

Using a combination of in situ synchrotron-based X-ray scattering and diffraction methods, ex situ electron microscopy, atom-probe tomography, and thermokinetic and thermodynamic modelling, we have focused on the development of post-build heat treatment protocols for AM alloys. Our established protocols recover the designed phase composition of two types of widely used commercial AM alloys, a major step towards their part certification. Specifically, our work on AM nickel-based superalloy Inconel 625 demonstrates the importance of understanding the effect of elemental microsegregation, a ubiquitous phenomenon in AM alloys resulting from rapid solidification, on the structure and microstructure evolution during post-build heat treatments [1]. Our simulation-constructed and experiment-validated time-temperature-transformation diagram clearly demonstrates the acceleration (by a factor of 100 – 1000) of formation kinetics of a phase deleterious to the fatigue performance of this alloy [2, 3]. Our work on nitrogen-atomized 17-4 stainless steel shows that the starting powder chemistry and compositional partition during solidification results in the as-fabricated 17-4 being fully austenitic, as opposed to being fully martensitic as designed. Our three-step heat treatment protocol successfully recovers the martensitic structure of parts fabricated using nitrogen-atomized 17-4 powders [4]. We also determined the optimal ageing heat treatment to yield optimal strength of this precipitation-hardening alloy.

Our work points to a common and important theme that post-build heat treatment is critical for producing AM alloys with predictable and reproducible microstructures and hence materials properties. The emphasis of proper post-build heat treatment cannot be overstated for the certification of many AM alloys. We also emphasize that rigorous and in situ bulk structure and microstructure measurements only available at synchrotrons are essential for modelers to validate AM simulations for the advancement of AM technologies [5].

References:

[1] Zhang, F., Levine, L. E., Allen, A. J., Stoudt, M. R., Lindwall, G., Lass, E. A., Williams, M. E., Idell, Y. & Campbell, C. E. (2018). Acta Materialia 152, 200-214.

[2] Stoudt, M. R., Lass, E., Ng, D. S., Williams, M. E., Zhang, F., Campbell, C. E., Lindwall, G. & Levine, L. E. (2018). Metallurgical and Materials Transactions A 49, 3028-3037.

[3] Lindwall, G., Campbell, C., Lass, E., Zhang, F., Stoudt, M. R., Allen, A. J. & Levine, L. E. (2019). Metallurgical and Materials Transactions A 50, 457-467.

[4] Lass, E. A., Zhang, F. & Campbell, C. E. (2020). Metallurgical and Materials Transactions A, 1-15.

[5] Zhang, F., Levine, L. E., Allen, A. J., Young, S. W., Williams, M. E., Stoudt, M. R., Moon, K.-W., Heigel, J. C. & Ilavsky, J. (2019). Integrating Materials and Manufacturing Innovation 8, 362-377

Acknowledgement:

Portions of this research were performed on beamline 9-ID-C, 11-ID-B, and 11-BM at 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.

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11:45am - 12:05pm

Time-evolution of Au and Ag nanofluids prepared by direct deposition of gas aggregated nanoparticles into the liquid polymer

Tereza Košutová1, Daniil Nikitin2, Pavel Pleskunov2, Renata Tafiichuk2, Andrei Choukourov2, Milan Dopita1

1Department of Condensed Matter Physics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 5, 121 16, Prague, Czech Republic; 2Department of Macromolecular Physics, Faculty of Mathematics and Physics, Charles University, V Holešovičkách 2, Prague, 180 00, Czech Republic

Nanofluids, i. e. liquids containing dispersed nanoparticles, are gaining increasing interest since the first use of this designation by Choi in 1995 [1]. The primary application for heat transfer as a thermally conductive fluid for cooling is nowadays expanding to sensors, lubricants, magnetic sealing or solar energy collectors. The unique properties of nanofluids arise from the synergy between nanoparticles and the surrounding medium. Our study concerns Ag and Au nanoparticles which belong to plasmonic nanoparticles with the localized particles plasmon resonance (LPPR) in the region of visible light which makes them and their colloidal suspensions attractive for optical applications.

There are numerous preparation methods of nanofluids, among them the very straightforward and solvent-free is magnetron sputtering of metals on the surface of vacuum-compatible liquids (oils, ionic liquids, and polymers). In this method nanoparticles are formed at the vacuum-liquid interface [2]. In our work, the nanoparticle synthesis takes place in the gas phase prior to their landing onto the liquid. Silver and gold nanoparticles were prepared using a magnetron-based gas aggregation cluster source and subsequently deposited into liquid polyethylene glycol (PEG).

The main aim of our study is to determine the stability of Ag and Au nanoparticle dispersions in PEG and to understand the post-deposition processes inside the nanofluids comprising nanoparticles prepared by aggregation from the gas phase. Solutions with different mass concentration of nanoparticles were prepared by controlling the deposition time reaching tens of mg/ml, a value typical for commercially-available Ag colloidal solutions. To investigate the size distributions and interactions between nanoparticles inside the colloidal suspensions the small angle x-ray scattering (SAXS) was used. We performed SAXS measurements repeatedly during six months to determine the suspension stability. The x-ray diffraction proved the crystalline nature of nanoparticles and also the changes in the amount of material dispersed in the suspension. The optical properties of individual suspensions were analyzed by UV-Vis spectroscopy. TEM and SEM measurements of nanoparticles separated from the suspensions were performed to validate the results obtained by the scattering methods.

Prepared Au nanoparticles have bimodal size distribution with mean sizes 13 nm and 40 nm and the corresponding absorption peak associated to the LPPR is observed around 550 nm in the UV-Vis spectrum. In the case of Ag nanoparticles dispersion, UV-Vis spectroscopy shows the maximum corresponding to the LPPR of individual separated nanoparticles around 410 nm and another maximum at larger wavelengths corresponding to nanoparticles aggregates for freshly prepared samples. This observation was further confirmed by SAXS, the mean size of single nanoparticles is around 10 nm and the nanoparticles interact through the hard-sphere interaction. The hard-sphere volume fraction however decreases in time and after two months is not detectable anymore. The resultant suspension exhibited characteristic plasmonic colour in the yellow/orange range and is expected to be stable over extended periods due to constrained mobility of PEG’s macromolecular chains.

[1] Choi, S. U. S., & Eastman, J. A. (1995). American Society of Mechanical Engineers, 231 (March), 99–105.

[2] Wender, H., Gonçalves, R. V., Feil, A. F., Migowski, P., Poletto, F. S., Pohlmann, A. R., Dupont, J., & Teixeira, S. R. (2011). Journal of Physical Chemistry C, 115(33), 16362–16367.

This study was financed by the Grant Agency of Charles University (grant 1546119), by the Czech Science Foundation (grant GACR 21-12828S) and by ERDF in the frame of the project NanoCent - Nanomaterials Centre for Advanced Applications (Project No. CZ.02.1.01/0.0/0.0/15_003/0000485).

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12:05pm - 12:25pm

XRD, USAXS, SAXS and WAXS Investigations of ferroelectric PZN-4.5PT nanoparticles thin Films

Rémi Ndioukane1, Abdoul Kadri Diallo1, Ndeye Coumba Yandé Fall1, Moussa Touré1, Diouma KOBOR1, Tabbetha Amanda Dobbins2, Jan Illavsky3, Laurent Lebrun4

1Laboratoire de Chimie et de Physique des Matériaux (LCPM), University Assane Seck of Ziguinchor (UASZ), Quartier Néma 2, BP 523, Ziguinchor, Senegal; 2Department of Physics & Astronomy, Provost Fellow (2019), Division of University Research, Rowan University, Oak Hall North 109, 201 Mullica Hill Road Glassboro, NJ 08028-1701; 3X-Ray Science Division, Advanced Photon Source, Argonne National Laboratory 9700 S. Cass Avenue, bldg 433A002, Lemont, IL 60439, USA; 4Univ Lyon, INSA-Lyon, LGEF, EA682 - 8 rue de la Physique, F-69621, Villeurbanne, France

The Pb(Zn1/3Nb2/3)O3-4.5PbTiO3 (PZN-4.5PT) single crystals showed very large ferroelectric and piezoelectric properties compared to traditional ferroelectric ceramics (BaTiO3 and PZT) used presently as active material in medical imaging, detection and sonars. However, despite these excellent properties, the greatest difficulty to use PZN-4.5PT single crystals on electronic devices is to achieve them in thin layers form because of their incongruent melting property. To overcome this difficulty, we deposit them as thin layers by dispersing their nanoparticles in a gel containing a matrix that can maintain at least their bulk properties. After this size reduction at nanoscale and the annealing process following the deposition, changes and structural transformations would occur. We fabricate with success thin films by dispersing these nanoparticles in a gel. The materials show some agglomeration at the surface of the silicon substrate films (from SEM images) and non-identified hexagonal microcrystals, which could be at the origin of their excellent properties.

In this paper we use the combined USAXS/SAXS/WAXS instrument at 9ID beamline at APS-ANL for in situ characterization of undoped and 1% Mn doped PZN-4.5PT inorganic perovskite nanoparticles thin films deposited on nanostructured silicon to understand the phases transitions and determine the observed hexagonal microcrystals structure. It revealed a hexagonal structure of the nanoparticles thin films, which could be explained by the new phase that can be assigned to the Pb3(PO4)2 based component. The peak at 31° indicates the presence of the rhombohedral phase perovskites assigned to the nanoparticles. XRD spectra, Raman and EDX mapping are compared to the USAXS, SAXS and WAXS results. WAXS characterization permitted to identify three phase transitions during thermal annealing confirming dielectric permittivity temperature phases transitions.

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12:25pm - 12:45pm

The nSoft Autonomous Formulation Laboratory: SANS/SAXS/WAXS Liquid Handling for Industrial Formulation Discovery

Peter A Beaucage, Tyler B Martin

National Institute of Standards and Technology, Gaithersburg, United States of America

Complex liquid mixtures are the foundation of industrial products from personal care products to biotherapeutics to specialty chemicals. While small- and wide-angle reciprocal space methods (SANS, SAXS, WAXS) are workhorse techniques for characterizing model formulations, the large number of components (10-100) in many real products often prevents rational mapping between component fractions, structure, and product stability. To enable rational design of these materials, we must leverage theory, simulation, multimodal characterization and machine learning (ML) tools to greatly reduce the expense of exploring the stability boundaries of a particular, desirable phase. Applying ML tools to scattering experiments requires a platform capable of autonomously synthesizing and characterizing samples with varying composition and chemistry. While there are numerous examples of robots which perform specific user facility operations, these systems tend to be bespoke and non-adaptable to new tasks. We have developed a highly adaptable platform that can be programmed to autonomously prepare and characterize liquid-formulations using neutron and X-ray scattering in addition to offline techniques such as optical imaging, UV/vis/NIR, viscometry, etc. Here we will highlight the design of the platform and our latest results in autonomous stability mapping of model formulations from personal care, biopharmaceutical, and alternative energy partner companies.

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10:20am - 12:45pmMS-76(59b): Crystal chemistry with emerging technology II
Location: Club C
Session Chair: Consiglia Tedesco
Session Chair: Toru Asahi
 
10:20am - 10:25am

Introduction to session

Consiglia Tedesco, Toru Asahi



10:25am - 10:55am

In situ study of chemical synthesis using high-energy X-ray diffraction on beamline I12 at Diamond Light Source

Oxana V. Magdysyuk, Thomas Connolley, Robert Atwood, Stefan Michalik

Diamond Light Source Ltd., Didcot, United Kingdom

The crystallisation of various materials from solution is an important area of study in the field of in situ X‑ray diffraction. Beamline I12 at Diamond synchrotron offers the improved experimental capabilities for in situ investigation of the large-scale synthesis process in unprecedented detail [1]. Time-resolved monochromatic high energy X-ray diffraction on the Beamline I12 is a fast and efficient method for investigation of crystallization allowing the detection of crystalline intermediates, formulating an idea about the crystallization mechanism, and the assessment of individual reaction parameters, i.e., reaction rate constants and activation energies. Thus, the optimization of the synthesis conditions of new compounds can be achieved. The high X-ray flux on the beamline I12 allows real-time monitoring the synthesis in the large containers, including standard laboratory metal autoclaves. Using monochromatic X-rays for the synchrotron experiments produces the high-quality diffraction data that permits the full structural refinements to be undertaken on metastable materials observed during the reaction.

The simplest experimental setup for low temperature in situ diffraction experiments is a metal heating block, which allows measurements during the synthesis from room temperature to approx. 90oC. It can be used with magnetic hotplate stirrer, allowing to mix substance during the measurements providing the homogeneous distribution of material in the reaction tube. For synthesis at temperatures close to the room temperature, the remotely controlled syringe pump can be used allowing simultaneous or sequential adding the reactants, thus permitting the investigation of the reaction in the controlled way from the very early stages [2].

Figure 1. Custom design metal heating block for in situ chemistry measurements with magnetic hotplate stirrer (left); ODISC furnace with quartz tube inside and magnetic stirrer below (middle); ODISC furnace with metal autoclave inside and magnetic stirrer below (right).

For more demanding in situ synthesis – at temperatures above 100oC or in metal autoclaves – the custom designed furnace ODISC was developed on the beamline I12 [3]. The furnace is very versatile with integrated heating, stirring, and precise sample centring and it can be used for a wide range of in situ experiments on the beamline. On the beamline I12, the furnace ODISC can be used in two configurations: 1) in situ measurements of reaction kinetic during solvothermal synthesis experiments, which performed at temperatures below boiling temperature of the solvent. In this case simple quartz tubes are used as a container during large-scale in situ synthesis [4]. 2) in situ measurements of reaction kinetic during hydrothermal synthesis, which should be performed in metal autoclaves. Despite measurements during the crystallization were performed in the metal autoclave, the data quality recorded on the beamline I12 allowed the refinement of the diffraction data and subsequent analysis of crystallization kinetic [5].The references should be in Heading 4 style (Times New Roman 9 pt, shortcut CTRL + NUM 4) and listed immediately at the end of the text without a heading.

[1] Drakopoulos M., Connolley T., Reinhard C., Atwood R., Magdysyuk O., Vo N., Hart M., Connor L., Humphreys B., Howell G., Davies S., Hill T., Wilkin G., Pedersen U., Foster A., De Maio N., Basham M., Yuan F., Wanelik K. J. (2015). Synchrotron Rad. 22, 828.

[2] Yeung H.H-M., Sapnik A.F., Massingberd-Mundy F., Gaultois M.W., Wu Y., Fraser D.A.X., Henke S., Pallach R., Heidenreich N., Magdysyuk O.V., Vo N.T., Goodwin A.L. (2019). Angew. Chem., Int. Ed., 58, 566.

[3] Moorhouse S.J., Vranješ N., Jupe A., Drakopoulos M., O’Hare D. (2012). Rev. Sci. Instr. 83, 084101

[4] Cliffe M.J., Castillo-Martínez E., Wu Y., Lee J., Forse A.C., Firth F.C.N., Moghadam P.Z., Fairen-Jimenez D., Gaultois M.W., Hill J. A., Magdysyuk O.V., Slater B., Goodwin A.L., Grey C.P. (2017). J. Am. Chem. Soc. 139, 5397.

[5] Cook D.S., Wu Y., Lienau K., Moré R., Kashtiban R.J., Magdysyuk O.V., Patzke G.R., Walton R.I. (2017). Chem. Mater. 29, 5053–2057.

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10:55am - 11:25am

The solid-state chemistry of rhodium(I) pincer complexes under extreme conditions.

Alexandra Longcake, Jeremiah P. Tidey, Mark S. Senn, Adrian B. Chaplin

University of Warwick, Coventry, United Kingdom

The activation of B-H bonds in σ-borane complexes is of interest not only due to their applications in catalysis (hydroborations, borylations), but because of the ambiguity of σ-borane coordination modes, which can be challenging to formerly define.[1] Because σ-borane complexes are intermediates to B-H activation, they can be difficult to study due to the transience of the highly reactive species.

The σ-borane complexes [Rh(PONOP)(ɳ2-HBR)][BArF4], (PONOP = 2,6-Bis(di-tert-butyl-phosphinito)pyridine; ArF = 3,5‑Bis(trifluoromethyl)phenyl; HBR = HBcat: 1; HBR = HBpin: 2) have been synthesised in good yields and have been established to undergo oxidative addition (OA) in solution at modest temperatures (< 75 °C). However, the OA products were unstable in solution, preventing their full characterisation using traditional solution-based methods. A single crystal high-pressure study of 1 was undertaken up to pressures of 25.8 kbar. An isomorphous phase transition was observed between the pressures of 4.8 and 8.8 kbar, which was accompanied by several geometrical rearrangements of the HBcat ligand with respect to the remainder of coordination complex. Most notably, the decrease in the N-Rh-B bond angle of ca. 6 ° across the phase transition suggests an increased overlap between the metal d orbital and the ‘empty’ boron orbital, indicating a stronger interaction between the metal centre and the σ-borane ligand. [2]

We aim to further the understanding of B-H bond activation by studying σ-borane complexes using high-pressure X-ray diffraction (HP-XRD) as the principal analytical tool. Precise structural determination and analysis of a systematic series of σ-borane complexes will ultimately allow for better modelling of their reactive transition states in associated catalytic cycles, ultimately enabling better targeted design of industrially relevant catalysts.

[1] Hebden, T. J.; Denney, M. C.; Pons, V.; Piccoli, P. M. B.; Koetzle, T. F.; Schultz, A. J.; Kaminsky, W.; Goldberg, K. I.; Heinekey, D. M. (2008) J. Am. Chem. Soc. 130, 10812–10820.

[2] Marder, T. B.; Lin, Z., Contemporary Metal Boron Chemistry I. Springer-Verlag: Berlin Heidelberg, 2008; Vol. 130, p 125-127.

Keywords: organometallic chemistry; B-H bond activation; pincer complexes; high-pressure crystallography

Alex Longcake acknowledges the Royal Society for a PhD studentship (RGFEA180160) and Diamond Light Source for time on Beamline I19 under proposal CY26847.

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11:25am - 11:45am

Insight into the Structural Variations of Fergusonite-Type Structures: Combined Experimental and Computational Studies

Bryce Mullens1, Maxim Avdeev1,2, Helen Brand3, Subrata Mondal4, Ganapathy Vaitheeswaran5, Brendan Kennedy1

1School of Chemistry, The University of Sydney, New South Wales 2006, Australia; 2Australian Nuclear Science and Technology Organisation, Lucas Heights, New South Wales 2234, Australia; 3Australian Synchrotron, 800 Blackburn Road, Clayton, Victoria 2168, Australia; 4Advanced Centre of Research in High Energy Materials (ACRHEM), University of Hyderabad, Prof. C. R. Rao Road, Gachibowli, Hyderabad 500 046, Telangana, India; 5School of Physics, University of Hyderabad, Prof. C. R. Rao Road, Gachibowli, Hyderabad 500 046, Telangana, India

The development of carbon-neutral energy-generation is critical to combatting climate change. One such technology is the development of next-generation ion conductors for solid-oxide fuel cells (SOFCs). SOFCs offer a much more efficient method to extract energy from hydrogen or hydrocarbon fuels than current combustion engines due to their one-step chemical process. However, a bottleneck to the large-scale uptake of SOFCs is the poor performance of the conducting electrolytes that separate the anode from the cathode. Various lanthanoid fergusonite structures (LnBO4) have recently been proposed as solid electrolyte candidates in solid-oxide fuel cells, with increased high-temperature ionic conductivity being measured in chemically doped lanthanum orthoniobates (LaNbO4) [1]. However, a phase transition from I2/a to I41/a within the operational temperature of SOFCs makes these structures non-ideal.

To understand the effects of chemical doping on the structure and electrochemical properties of these fergusonite structures, several complex fergusonites have been investigated [2-3]. Of interest is the substitution of NbV for TaV on the B-site, which has shown a decrease in the unit cell volume of the structure [4]. This is particularly remarkable, given the two metal cations have the same ionic radius and Ta has an extra 5d valence shell compared to the 4d shell of Nb. Such substitution has further shown to increase the I2/a to I41/a first-order phase transition temperature, highlighting the potential of the properties of these structures to be specifically ‘tailored’ to be used for SOFCs.

Various solid-solution series of Ln(Nb1-xTax)O4 (Ln = La-Lu) have been synthesised using conventional solid-state methods. Synchrotron X-ray and neutron powder diffraction methods have been used to investigate their structures, focusing on changes in both their unit cell volumes and the temperature of the I2/a to I41/a phase transitions. Whilst the fergusonite structure is a monoclinic structure derived of the tetragonal scheelite aristotype, it’s structure is based on BO6 polyhedra as opposed to BO4 scheelite polyhedra. These studies have revealed several anomalies, revealing that different structures can be isolated by controlling the size of the Ln ion and synthetic conditions, and that the volume of the BO6 polyhedra and length of the B–O bonds change depending on its surrounding Ln ion. This data surprisingly implies that the AO8 polyhedra act as a rigid framework in which the BO6 polyhedra respond. The experimental data has been further reinforced by ground state energy calculations performed using density functional theory. This is a landmark accomplishment that has not been previously used in similarly studied structures. These insights can be used in the development and engineering of novel and advanced electrolyte materials for SOFCs.

[1] - Cao, Y.; Duan, N.; Yan, D.; Chi, B.; Pu, J.; Jian, L.; Enhanced Electrical Conductivity of LaNbO4 by A-Site Substitution. Int. J. Hydrogen Energy, 2016, 41 (45), 20633-20639.

[2] - Arulnesan, S. W.; Kayser, P.; Kimpton, J. A.; Kennedy, B. J.; Studies of the Fergusonite to Scheelite Phase Transition in LnNbO4 Orthoniobates. J. Solid State Chem., 2019, 277, 229-239.

[3] - Ivanova, M.; Ricote, S.; Meulenberg, W. A.; Haugsrud, R.; Ziegner, M.; Effects of A- and B-Site (Co-)Acceptor Doping on the Structure and Proton Conductivity of LaNbO4. Solid State Ionics, 2012, 213, 45-52.

[4] – Mullens, B. G.; Avdeev, M.; Brand, H. E. A.; Vaitheeswaran, G.; Kennedy, B. J.; Insights into the Structural Variations in SmNb1-x­TaxO4 and HoNb1-xO4 Combined Experimental and Computational Studies. Under Revision for Dalton Transactions.

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11:45am - 12:05pm

Growth and spectroscopic studies of Na2W2O7 crystals doped with Ce+4 and Cr+3 ions, promising scintillation detectors of elementary particles

Veronika Grigorieva, Mariana Rakhmanova, Alexey Ryadun

Nikolaev Institute of Inorganic Chemistry SB RAS, Novosibirsk, Russian Federation

Studies of "dark matter" is an important fundamental branch of modern cosmology and theoretical physics. Cryogenic scintillation detectors based on single crystals of tungstates (ZnWO4, CaWO4, Na2W2O7) can be used to register "dark matter"; they register extremely rare signals of interaction of Weakly Interacting Massive Particles (WIMP) with the nuclei of the detector material [1].

The important requirements to scintillation materials for the search and registration of such rare events are luminescence, light yield, energy resolution, high level of radiation purity. Necessary radiation purity level and optical quality of scintillators require the development of special technologies for deep purification of starting materials and new approaches to crystal growth under conditions of low temperature gradients, the production of scintillation elements with a high utilization rate of the costly starting material. Scintillation bolometers based on Na2W2O7 must also be of high mechanical strength for their practical significance since bolometric elements of specified form will have to be cut from the crystals. To improve the mechanical and optical characteristics, charge with chromium Cr+3 and cerium Ce+4 doping was prepared, doped Na2W2O7 crystals were grown and their luminescent properties were investigated [2].

Na2W2O7 crystals were grown from melt by low-thermal-gradient Czochralski technique (LTG Cz) developed at NIIC SB RAS (Novosibirsk, Russia). Major difference from conventional Czochralski technique is in temperature gradients reduced by two orders of magnitude, below 1 K/cm. Main advantages of LTG Cz are reduced thermoelastic stresses in growing crystals so that they don’t influence crystal quality, and suppression of melt components decomposition and volatilization. By LTG Cz many scintillating crystals of record size and optical quality were obtained, such as BGO, CdWO4 and many other [3].

As precursors, Na2CO3, WO3, CeO2, TiO2 and Cr2O3 powders were used. Initial charge for crystal growth was prepared by solid-state synthesis at 400 °C in muffle furnace according to the reaction:

Na2CO3 + 2WO3 → Na2W2O7 + CO2

Completeness of synthesis was controlled by weight change due to CO2 volatilization. Crystallization rate was set at 1.5 mm/h, rotation velocity at 10 rev/min. Diameter of grown Na2W2O7 crystals was 30 mm, length up to 70 mm and 40 mm for pure and doped ones, correspondingly.

[1] Indra, Raj, Kim, H.J., Lee, H.S., Kim, Y.D., Lee, M.H., Grigorieva, V.D., Shlegel, V.N. (2018) Eur. Phys. J. C, 78, 973. [2] Ryadun, A.A., Rakhmanova, M.I., Grigorieva, V.D. (2020) Optical Materials, 99, 109537. [3] Shlegel, V.N., Borovlev, Yu.A, Grigoriev, D.N, Grigorieva, V.D. et al. (2017) JINST, 12, C08011.

Keywords: Na2W2O7; Czochralski technique; scintillators; elementary particles; luminescence

This work was supported by Russian Foundation for Basic Research (grant No. 20-43-543015).

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12:05pm - 12:25pm

Correlation between structural studies and third order NLO properties of three new semi-organic compounds

Rim Benali-Cherif1, Radhwane Takouachet1, El-Eulmi Bendeif2, Nourredine Benali-Cherif3

1Abbes Laghrour Khenchela University, Khenchela, Algeria; 2Laboratoire de Cristallographie, Résonance Magnétique et Modélisations (CRM2, UMR CNRS 7036). France; 3Houari Boumédiène (USTHB)-Member of Algerian Academy of Sciences and Technology (AAST) Algiers. Algeria

Correlation between structural studies and third order NLO properties

of three new semi-organic compounds

R. Benali-Cherif R1, R. Takouachet 1, E-E Bendeif2, N. Benali-Cherif R3

1Abbes Laghrour Khenchela University. Algeria, 2 Laboratoire de Cristallographie, Résonance Magnétique et Modélisations (CRM2, UMR CNRS 7036). France, 3 Houari Boumédiène (USTHB) and Member of Algerian Academy of Sciences and Technology (AAST) Algiers. Algeria Algeria

The study of semi-organic compounds has been of growing interest for a few years. In addition to their fundamental interest in the nature of the bonds occurring between inorganic anions and organic cations, these compounds also have remarkable physico-chemical and optical properties. Recently, the variety of semi-organic hybrid crystals has been developed for NLO applications. The combination of organic compounds, especially amino acids with mineral acids, gives rise to new hybrid crystals with strong NLO properties.Semi-organic compounds play an important role in cell metabolism; they intervene in transfer of energy because of their richness in hydrogen bonds. Inter-ionic interactions through the hydrogen bridges present in this type of semi-organic compounds can serve as mimes explaining some bio-inorganic mechanisms.

Measurement of nonlinear third order electrical susceptibilities was performed for three new compounds (Table 1) by the Third Harmonic Generation (THG) technique. Figure 1 shows the intensity of the THG signal as a function of the angle of incidence, it exhibits the same behavior as the silica.

Table 01. Experimental values of nonlinear susceptibility of the third order.

The third order nonlinear electrical susceptibility values of studied compounds are stronger than that of silica (reference material). The largest value is observed for the first compound, = 9,63×10-21 m2/V2 (Table 1) due to the increase in charge transfer and the large number of hydrogen bonding which increases the dipole moment of the compound .

Figure 1. Intensity of the third harmonic for the three samples

These optical measurements revealed different optical behaviors of the three compounds studied. It is therefore very interesting to analyze and discuss the different structural factors correlated with these interesting physical properties. Several structural parameters affect the physical and optical properties of these materials such as: atomic arrangement, intra- and intermolecular interactions, crystal symmetry and electron density distribution.

Keywords: semi-organic compounds - NLO properties - THG technique

[1] Publication of a book on May 05, 2017 entitled “Corrélations structures propriétés ONL de 3 nouveaux composés hybrides »in the “Éditions Universitaires Européennes »

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12:25pm - 12:45pm

Structural, magnetic and optical properties study of tellurium–based: Sr3–xPbxFe2TeO9 (0 ≤ x ≤ 2.25) double perovskites

Abdelhadi El Hachmi1, Bouchaib Manoun1,2, Mohammed Sajieddine3, Peter Lazor4

1Laboratoire Rayonnement Matière et Instrumentation, S3M, FST, University Hassan 1er, 26000 Settat, Morocco; 2Materials Science and nano–engineering (MSN), University Mohammed VI Polytechnic, Lot 660 Hay Moulay Rachid, 43150 Ben Guerir, Morocco; 3Material Physics Laboratory, Faculty of Sciences and Techniques, Sultan Moulay Sliman University, B.P. 523, 23000 Beni–Mellal, Morocco; 4Department of Earth Sciences, Uppsala University, SE–752 36, Uppsala, Sweden

Materials family of A3B’2B’’O9 (A = alkaline–earth metal ions with valence +2, B’ and B’’= transition metal ions with valences +3 and +6 respectively) were subjected to extensive studies, and have attracted significant interest owing to their physical properties and technological applications. The discovery of colossal magnetoresistance (CMR) in the ordered A2B’B’’O6 double perovskite oxides has given rise to many recent research [1–3].

Polycrystalline samples of the series of triple perovskites Sr3−xPbxFe2TeO9 (0 ≤ x ≤ 2.25) were synthesized using solid state reaction [4]. These materials have been studied by a combination of XRPD, Mössbauer spectrometry, Raman and UV–Vis spectroscopies. The crystal structures were resolved by the Rietveld refinement method, and revealed that this Sr3−xPbxFe2TeO9 (0 ≤ x ≤ 2.25) system shows one space group change from tetragonal I4/m (0 ≤ x ≤ 1) to another tetragonal form I4/mmm (1.25 ≤ x ≤ 1.88) and a second transition to hexagonal R-3m (2.08 ≤ x ≤ 2.25). The valence state of iron in the Fe site was determined to be Fe(III) by Mössbauer spectrometry, which also revealed two sites in a concordance with the XRPD measurements. 57Fe Mössbauer spectra measurements show paramagnetic and magnetic ordering behaviors. The observed Raman spectra as a function of composition show obvious changes on the positions (wavenumbers), the FWHM and the intensities of the modes confirming the phase transformations observed by the XRPD results. These structural transitions led to a distinct change in the optical band gap energy, varying from 2.14 to 1.85 eV.

[1] K.I. Kobayashi, T. Kimura, H. Sawada, K. Terakura, Y. Tokura. Nature, 1998, 395, 677–680.
[2] M. García–Hernández, J.L. Martínez, M.J. Martínez–Lope, et al., Phys. Rev. Lett., 2001, 86, 2443.
[3] W.R. Branford, S.K. Clowes, Y.V. Bugoslavsky, et al., J. Appl. Phys., 2003, 94(7), 4714–4716.
[4] A. El Hachmi, F. El Bachraoui, S. Louihi, Y. Tamraoui, S. Benmokhtar, et al., J. Inorg. Organomet. Polym., 30, 1990–2006 (2020). https://doi.org/10.1007/s10904-020-01446-4

 
10:20am - 12:45pmMS-77(71b): Disordered materials: spectroscopic and scattering techniques II
Location: 223-4
Session Chair: Simon Billinge
Session Chair: Angela Trapananti

Invited: Lars G.  M. Pettersson (Sweden), Maxwell Terban (Germany)

 
10:20am - 10:25am

Introduction to session

Simon Billinge, Angela Trapananti



10:25am - 10:55am

SpecSwap-RMC: A Generalized RMC Approach to Structure, Combining Scattering and Spectroscopic Data

Lars G.M. Pettersson

Stockholm University, Stockholm, Sweden

Structure determination using Reverse Monte Carlo (RMC) relies on atomistic moves where, after each move, the target property is computed and compared to experiment. The move is accepted if improving the agreement and accepted only with a probability if not. Since of the order a few hundred million moves need to be performed, this requires very rapid evaluation of the property in question. Typical applications include X-ray and neutron scattering and EXAFS in single-scattering mode. Different experimental probes are sensitive to different structural aspects, however, and it can thus be advantageous to combine with, e.g., spectroscopic data to narrow down the range of solutions.

To this end we have developed SpecSwap-RMC [1-3] which performs RMC on a large library of potential structures with precomputed scattering and spectroscopic signals associated with each structure. A subset of structures is selected and all properties built from the selected structures and compared to the experimental data. The RMC is then performed by exchanging structures instead of moving atoms. A set of weights is then generated based on how often each structure is found in the sample set when probed. These SpecSwap-RMC weights can then be used to reweigh the library, to extract an average structure that is consistent simultaneously with all the supplied data.

I will give examples of applications to liquid water, where we combine X-ray diffraction (XRD) and multiple-scattering EXAFS [2], to ice where we use SpecSwap-RMC to analyse what structures have actually been measured in XAS on various samples [4], and discuss XRD, NMR, XAS and XES [5] data on liquid water.

[1] M. Leetmaa, K.T. Wikfeldt, L.G.M. Pettersson, J. Phys.: Cond. Mat. 22 (2010) 135001

[2] K.T. Wikfeldt et al., J. Chem. Phys. 132 (2010) 104513

[3] https://github.com/leetmaa/SpecSwap-RMC.

[4] I. Zhovtobriukh, P. Norman, L.G.M. Pettersson, J. Chem. Phys. 150 (2019) 034501

[5] I. Zhovtobriukh et al., Science China 62 (2019) 107010

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10:55am - 11:25am

Developing more precise structural descriptions of layered covalent organic frameworks using total scattering data

Maxwell W. Terban1, Lars Grunenberg1,2, Alexander M. Pütz1,2, Sebastian Bette1, Gökcen Savasci1,2,3, Robert E. Dinnebier1, Bettina V. Lotsch1,2,3

1Max Planck Institute for Solid State Research, Stuttgart, Germany; 2Department of Chemistry, Ludwig- Maximilians-Universität (LMU), Munich, Germany; 3Exzellenzcluster E-conversion, Garching, Germany and Center for NanoScience, Munich, Germany

Materials containing microporous networks are an important topic of study for the development of improved technologies for a wide variety of applications including catalysis and gas storage. Widespread interest in metal– and more recently covalent–organic frameworks (MOFs/COFs) endures due to wide-ranging topologies and functionalities imbued by apparently limitless combinations of structural building units. However, while the focus remains primarily on crystalline products, semantics of how to interpret said crystallinity can vary widely in different communities, sometimes leading to oversight of important aspects of the structure that have essential implications on the material properties, or help to understand formation and functionalization processes [1].

The characterization of layered COFs in particular is difficult due to the presence of only a few, low-angle peaks in their diffraction patterns. This has led to a longstanding, dichotomous relationship between expectations based on energetic calculations and the structures observed by diffraction. We have recently demonstrated an experimental resolution, by considering the total rather than just Bragg scattering, and pair distribution function (PDF) analysis, to show how high apparent symmetries can emerge from random, local offsets of the layers [2].

Equipped with a fresh tool-set to characterize these structures, this talk will discuss our on-going efforts in this area — leveraging different length-scale sensitivities of real- and reciprocal-space vantage points for building and fitting models to obtain a more precise depiction of the structural states contained within.

[1] Grunenberg, L., Savasci, G., Terban, M. W., Duppel, V., Moudrakovski, I., Etter, M., Dinnebier, R. E., Ochsenfeld, C. & Lotsch, B. V. (2021). J. Am. Chem. Soc. 143, 3430.
[2] Pϋtz, A. M., Terban, M. W., Bette, S., Haase, F., Dinnebier, R. E. & Lotsch, B. V. (2020). Chem. Sci. 11, 12647.

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11:25am - 11:45am

Order-disorder transitions in battery electrodes studied by operando X-ray scattering

Dorthe Ravnsbæk, Christian Kolle Christensen, Christian Lund Jakobsen, Martin Karlsen

University of Southern Denmark, Odense M, Denmark

Development of novel electrode materials for intercalation type batteries have in the past focused on highly crystalline materials with the capability to retain long-range order during cycling. However, recent years have seen an increased interest for disordered materials, e.g. with the discovery of multiple high capacity electrodes based on disordered rock-salt structures or even completely amorphous materials exhibiting higher capacities than their crystalline counterparts [1,2]. Furthermore, it was recently showed by Ceder and co-workers, that long-range order is not a prerequisite for maintaining percolating intercalation pathways [3]. Still very little is known about the structural mechanisms behind order-disorder transitions induced by ion-intercalation or about ion-storage mechanisms in disordered mate-rials. This is in spite that fact that understanding these processes may also provide enhanced insights about how disorder influences the properties of traditional ordered electrodes.

Using operando synchrotron X-ray total scattering with pair distribution function analysis, we have studied a series of battery electrode materials, which undergo severe disordering during charge or discharge, i.e. during ion-extraction or -intercalation [4]. This allows us to map out the structural evolution during battery charge and discharge at the atomic-scale, and begin to understand the ion-storage mechanisms in such materials. The studied materials cover both Li-, Na and Mg-ion electrode materials composed of transition metal (Tm) oxides and phosphates with both layered and 3D-framework structures, e.g. NaxTmO2, NaxFePO4, LixTiO2, LixV2O5 etc.[4] Our findings reveal that the order-disorder transition can occur both reversibly and irreversibly, via topotactic or completely reconstructive transitions and entail several disordering phenomena such as cation disorder, nano-crystallization, amorphization etc. This talk will illustrate the large variety in order-disorder phenomena within battery electrodes and highlight our methodology for the operando total scattering studies and pair distribution function analysis.

[1] Lee,, J., Kitchaev, D. A., Kwon, D.-H. Lee, J. K,. Papp, C.-W., Liu, Y.-S., Lun, Z., Clément, R. J., Shi, T., McCloskey, B. D., Guo, J., Balasubramanian, M., Ceder, G. (2018) Nature 556, 185-190.

[2] Uchaker, E., Zheng, Y. Z., Li, S., Candelaria, S. L., Hu, S., Cao, G. Z. (2014) J. Mater. Chem. A 2, 18208-18214.

[3] Lee, J., Urban, A., Li, X., Su, D., Mautier, G., Ceder, G. (2014) Science 343, 519-522.

[4] Christensen, C. K., Ravnsbæk, D. B. (2021) J Phys Energy DOI: 10.1088/2515-7655/abf0f1

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11:45am - 12:05pm

Insight into the structure of SiO2-supported Ni-Ga nanoparticles for catalytic application via X-ray absorption spectroscopy and total scattering

Nora K. Zimmerli, Paula M. Abdala, Christoph R. Mueller

ETH Zurich, Zurich, Switzerland

To close the carbon cycle, the direct hydrogenation of CO2 to methanol (CH3OH) plays a key role allowing to convert a major greenhouse gas into a valuable energy carrier and platform chemical.[1] Supported bimetallic catalysts are gaining increasing attention for CO2 hydrogenation reaction due to the possibility of tuning their catalytic properties by judicious choice of the ratio of the alloying elements. The development of highly active and selective catalysts for CO2 hydrogenation relies hence on obtaining a fundamental understanding of the relationship between a catalyst’s structure and its activity. However, heterogeneous catalysts are complex systems, typically composed of various phases and sites that exhibit different functionalities which requires the use of multiple and complementary techniques for their characterization. [2] X-ray absorption spectroscopy and atomic pair distribution function analysis (PDF) of X-ray total scattering data can provide detailed information on the structure of bimetallic supported nanoparticles. XAS, being element selective, allows to study the electronic state and geometry of each metal via XANES analysis (X-ray absorption near edge structure analysis) and their local atomic structure between ~1-5 Å by EXAFS (extended X-ray absorption fine structure) analysis. Probing the longer-range order (i.e. above ca. 5 Å) via EXAFS analysis is however challenging. PDF can interrogate the local to nanoscale structure of supported bimetallic nanoparticles, extending substantially the atomic length scale that can be studied, from ~1 Å up to several nanometers. In this presentation, we will show how XAS (Ni and Ga K-edges) and PDF analyses provide structural information of a series of NixGay nanoparticles supported on SiO2 (total metal loading of ca. 5 w.%). The PDF analysis was performed via a so-called differential PDF approach, i.e. subtracting the signal of the SiO2 support and, thus, allowing us to characterize the nanocrystalline phases (disordered or intermetallic alloys) of the supported nanoparticles. Ga K-edge XANES and EXAFS reveal the presence of GaOx species while Ni XANES and EXAFS confirm the presence of Ni0. Thus, combining the information obtained via XAS and PDF techniques is highly important to obtain a full atomic to nanoscale description of heterogeneous catalysts.

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12:05pm - 12:25pm

Tuneable Local Structure in Thermoelectric Crystals

Nikolaj Roth

University of Oxford, Oxford, United Kingdom

Crystalline phases are usually characterised by their periodic structures and space group symmetry. However, some crystalline materials have periodic structures only on average and deviate on a local scale. Several different locally ordered structures can exist with identical average periodic structure and space group symmetry, making them difficult to distinguish using regular crystallographic techniques.

Using high-quality single-crystal x-ray diffuse scattering the local order in thermoelectric half-Heusler Nb1-xCoSb is investigated, for which different local orderings are observed. Half-Heusler materials have been intensely studied for their thermoelectric properties, but a general issue is their high thermal conductivity due to their simple structure. The defective half-Heuslers such as Nb1-xCoSb have high vacancy concentrations (x=1/6), giving them much lower thermal conductivities than other half-Heusler compounds. From measurements on different samples of Nb1-xCoSb, it is shown that crystals with identical stoichiometry and average crystal structure, but with different locally ordered structures, can be made by changing the synthesis method. The local structures in these samples are analysed using the three-dimensional difference pair distribution function (3D-ΔPDF).

A new method is shown which allows isolation of the substitutional correlations in the 3D-ΔPDF, showing that the vacancy distributions follow a vacancy repulsion model. Furthermore, the local structural relaxations around vacancies are quantised from analysis of Bragg peaks and 3D-ΔPDF. From the found short-range correlations, a physical model of the system is simulated using Monte-Carlo methods, and it is shown that the different samples correspond to the ground state and simulated quenched states of the model.

Advanced x-ray scattering techniques can unravel hidden local structures and for Nb1-xCoSb these local structures can be controlled by the synthesis conditions. If the local structure of crystalline materials can be more generally related to the properties, then a new frontier in materials research will be available.

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12:25pm - 12:45pm

Structure of complex aluminosilicate oxide-glasses: the role of zinc intermediate element.

Andrea Bernasconi1,2, Monica Dapiaggi1, Daniel T Bowron3, Giovanni Agostini2,4, Alessandro Pavese5

1University of Milan, Milano, Italy; 2ESRF The European Synchrotron, Grenoble, France; 3ISIS Pulsed Neutron and Muon Source, Didcot, UK; 4ALBA Synchrotron, Barcelona, Spain; 5University of Torino, Torino, Italy

Aluminosilicate-based oxide-glasses are natural materials forming volcanic magmas [1] and frequently the main constituent of manufactured products like ceramic glazes, fiber optic materials and, more recently, biocompounds [2]. To characterise the atomic structure of these materials requires techniques sensitive to the very local structural environment, like spectroscopies (i.e. Nuclear Magnetic Resonance - NMR, Extended X-ray Absorption Fine Structure – EXAFS) and scattering methods (i.e. Total Scattering), due to their lack in periodic order that prevents the application of conventional crystallography. The oxide-glass structure is shaped by silicon centered corner-sharing tetrahedra, which can be combined, depending on composition, with aluminium centered motifs, while large cations like sodium, potassium and calcium tend to depolymerize the network, affecting, in this way, some of the glass properties, such as thermal expansion and glass transition temperature, as demonstrated in a previous study [3]. The glass structural complexity increases when their composition involves some intermediate element, like zinc and beryllium, whose role in the network can vary as a function of the bulk composition, see [4] for some examples. This is the case of the present study that is based on a structural modeling of 2 series of different aluminosilicate-based oxide-glasses with different zinc amounts (3 samples each series). These samples have been prepared by melt-quenching route at 1350°C and then measured by combining EXAFS spectroscopy (BM23 beamline, ESRF, France) with both neutron (SANDALS instrument, ISIS, UK) and synchrotron (ID11 beamline, ESRF, France) Total Scattering data. Zn K-edge EXAFS has been applied at the beginning, in order to evaluate some of the bond distances and the Zn geometrical environment, and this information is used later as constraints for total scattering data modelling, performed by the Empirical Potential Structure Refinement (EPSR) method [5]. The refinements show good residuals, as displayed in Figure 1 (on the left-hand side) and the results indicate that zinc is mostly 4-fold coordinated, but with some 3-fold, 5-fold and 6-fold species. In such complex glasses, therefore, the parameters describing the polymerization degree, like NBO (Non-Bonding-Oxygens), BO (Bonding Oxygens) and triclusters are not predictable by theoretical models, based on prior assumptions of the structural role of zinc. Figure 1 (on the right-hand side) shows the variations of NBO with ZnO mole fraction, comparing the results of this work and of theoretical calculations. Furthermore, the data modelling gave access to a wide number of structural parameters like bond angles, cluster size and cation charge compensating characteristics, that are valuable for further structure-properties studies.

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10:20am - 12:45pmMS-78: Science meets art: X-ray spectrometry and X-ray diffraction in art and archaeology
Location: Club H
Session Chair: Gilberto Artioli
Session Chair: Sebastian Bette

 Invited: Katrien Keune (Netherlands), Christoph Berthold (Germany)

 
10:20am - 10:25am

Introduction to session

Gilberto Artioli, Sebastian Bette



10:25am - 10:55am

Operation Night Watch: macro- and microscale X-ray imaging studies on the Rembrandts’ masterpiece The Night Watch in the Rijksmuseum.

Katrien Keune1, Victor Gonzalez1, Annelies Loon1, Frederique Broers1, Nouchka Keyser de1, Petria Noble1, Frederik VanMeert2, Steven DeMeyer2, Koen Janssens2

1Rijksmuseum, Amsterdam, Netherlands, The; 2AXES Research Group, NANOLab Centre of Excellence, University of Antwerp, Belgium,

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

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

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

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

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10:55am - 11:25am

X-ray Microdiffraction of Cultural Heritage: Potentials und Limitations

Christoph Berthold

University of Tuebingen, CCA-BW, Tübingen, Germany

to be announced

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11:25am - 11:45am

XRPD as a tool for the study of pigment-binder interactions: from metal formates to long-chain carboxylates

Silvie Švarcová1, Eva Kočí1, Petr Bezdička1, Silvia Garrappa1, Jiří Plocek1, Ruslan Barranikov1, Libor Kobera2

1Institute of Inorganic chemistry of the Czech Academy of Sciences, Husinec-Řež 1001, 250 68 Husinec-Řež, Czech Republic; 2Institute of Macromolecular Chemistry of the Czech Academy of Sciences, Heyrovského nám. 2, 162 06, Praha 6, Czech Republic

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

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

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

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

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

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

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

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11:45am - 12:05pm

Effects of soft tissue on the crystallographic changes to bone mineral upon heating

Hannah Louise Cross, Charlene Elizabeth Greenwood

Keele University, Liverpool, United Kingdom

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

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

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

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12:05pm - 12:25pm

A multidisciplinary study unveils the nature of a Roman ink of the I century AD

Chiaramaria Stani1, Lara Gigli2, Simone Pollastri2, Mirta Sibilia3, Alessandro Migliori3, Francesco D’Amico2, Chiara Schmid4, Sabina Licen5, Matteo Crosera5, Gianpiero Adami5, Pierluigi Barbieri5, Jasper R. Plaisier2, Giuliana Aquilanti2, Lisa Vaccari2, Stefano Buson6, Federica Gonzato6

1CERIC-ERIC, Basovizza, Trieste, Italy; 2Elettra Sincrotrone Trieste S.C.p.A, Basovizza, Trieste, Italy; 3Nuclear Science and Instrumentation Laboratory, Physics section, IAEA, Seibersdorf, Austria; 4Department of Engineering and Architecture, University of Trieste, Trieste, Italy; 5Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, Italy; 6Museo Nazionale Atestino, Este, Padova, Italy

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

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

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

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

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

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

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

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

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

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12:25pm - 12:45pm

A new tool for ancient artefact conservation studies: Electron Diffraction Tomography to study blue corrosion product in Chinese Bronze sample

Partha Pratim Das1, Enrico Mugnaioli2, Quanyu Wang3, Stavros Nicolopoulos1, Mauro Gemmi2

1NanoMEGAS SPRL, Rue Émile Claus 49 bte 9, 1050, Brussels, Belgium; 2Center for Nanotechnology Innovation@NEST, Istituto Italiano di Tecnologia, Piazza San Silvestro 12, 56127, Pisa, Italy; 3Institute of Cultural Heritage, Shandong University, 72 Jimo Binhailu, Qingdao 266237, China

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

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

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

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

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

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

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10:20am - 12:45pmMS-79(69b): Complex structures of minerals and inorganic materials
Location: Club B
Session Chair: Marie Colmont
Session Chair: Sergey V. Krivovichev
 
10:20am - 10:25am

Introduction to session

Marie Colmont, Sergei Krivovichev



10:25am - 10:55am

Tracing electron density changes in langbeinite under pressure

Roman Gajda1, Dongzhou Zhang2, Jan Parafiniuk3, Przemysław Dera4, Krzysztof Woźniak1

1Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, 101 Żwirki i Wigury, Warszawa, 02-089, Poland; 2APS, University of Chicago, 9700 S Cass Ave, Bldg 434A, Argonne, IL 60439, USA; 3Institute of Geochemistry, Mineralogy and Petrology, Department of Geology, University of Warsaw, Żwirki i Wigury 93, Warszawa 02-089, Poland; 4Hawaii Institute of Geophysics and Planetology, School of Ocean and Earth Science and Technology, University of Hawaii at Manoa, 1680 East West Road, Honolulu, Hawaii 96822, USA

Detailed studies of electron density changes in a mineral called langbeinite K2Mg2(SO4)3 under pressure have been performed. Single crystal X-ray data for this mineral under pressure (1GPa) were collected at the 13-BM-C beamline at the Advanced Photo Source (Argonne National Laboratory, USA). Additionally, complementary experiments at ambient conditions were performed on an in-house diffractometers. Experimental results were complemented by theoretical calculations within the pressure range up to 40 GPa.

From the point of view of mineralogical processes taking part in the Earth mantle (and the mantles of other even extraterrestrial planets), establishing detailed changes of electron density in minerals under pressure is absolutely crucial to understand the nature and mechanisms of mineralogical processes. Combining both experimental charge density studies and high pressure investigations is still a real challenge. This work is our continuation of our previous feasibility studies on experimental quantitative electron density investigations of electron density in grossular under 1GPa pressure [1].

Answering the questions how electron density distribution in langbeinite is affected by increasing pressure is obviously the main topic of this work. However there are also some other issues which we would like to address. Are there any differences between experimental and theoretical charge density distributions obtained on the basis of experimental data and theoretical dynamic structure factors? Are there any significant differences in properties of charge density distributions obtained for complete and incomplete high resolution X-ray diffraction data sets? Are there any differences in charge density distributions obtained for X-ray data collected with two different wavelengths of X-ray radiation? Should the data be absolutely complete to obtain reasonable experimental charge density distribution? When experimental data are impossible to be collected, is it reasonable to use theoretically calculated dynamic structure factors instead and refine theoretical models of electron density?

Langbeinite crystalizes in the cubic P213 space group. Its structure is composed of SO4 tetrahedra and MgO6 octahedra. Potassium cations which are placed in the voids between these polyhedra are surrounded by oxygen anions. Unfortunately due to significant deformation, one cannot say that KO12 is a regular icosahedron. Although mentioned polyhedra seem to completely fill in the space, this schematic way of presentation is not the best one when topology of electron density distribution must be described.

Investigating changes of electron density as a function of pressure, we are going to compare electron density properties at BCPs, integrated atomic basins, changes of thermal ellipsoids. Obviously, raising pressure will cause shrinking of the unit cell and consequently, changes of electron density distribution. However, the question is how exactly such changes will manifest.

No doubt that polyhedra commonly used in mineralogy and crystallography are not useful representation of electron density as they neither have full representation of electron density of the central ion nor any of the corners ions. So from time to time returns an old question: how big are atoms in crystals [2]. Here we will answer this question and the other ones already mentioned above at the level of quantitative electron density distributions in our model mineral.

[1] Gajda, R., Stachowicz, M., Makal, A., Sutuła, S., Parafiniuk, J., Fertey, P. & Woźniak, K. (2020). IUCrJ. 7, 383-392.

[2] Brown, I. D. (2017). Struct. Chem. 28, 1377-1387.

Keywords: high pressure; electron density; theoretical structure factors

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10:55am - 11:25am

Experimental Electron Density Distribution and QTAIM Topological Analysis for the Perovskite Mineral: Sulphohalite – Na6(SO4)2FCl

Agata Wróbel, Roman Gajda, Krzysztof Woźniak

Department of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Poland.

A quantitative experimental charge density study was undertaken for the double antiperovskite mineral – sulphohalite [Na6(SO4)2FCl]. High-resolution X-ray diffraction data was collected employing AgKα radiation (λ = 0.56087 Å) to a resolution of 0.3941 Å at 100K. Electron density (ED) distribution – ρ(r) was modelled, in compliance with the Hansen-Coppens formalism[1], by consecutive least-square multipolar refinements. Based on such experimental distribution of charge, QTAIM topological analysis[2] was undertaken. Full-volume property integration over delineated atomic basins (AB’s) yielded their appertaining charges [QAB-Cl = -0.836e-; QAB-S = 03.168e-; QAB-Na = 0.910e-; QAB-F = -1.334e-; and QAB-O = -1.227e-] and volumes [VAB-Cl = 38.920Å3; VAB-S = 5.656Å3; VAB-Na = 7.931Å3; VAB-F = 14.178 Å3 and VAB-O = 17.416 Å3]. The percentage of unaccounted electrons and volume per unit cell was respectively 0.010% and 0.406%. Within the uncertainty range of performed numerical integration, such percentages can be unheeded. A total of 6·BCP’s [∇2ρ(rCl···S) = 0.120e-·Å-5; ∇2ρ(rCl···Na) = 0.575e-·Å-5; ∇2ρ(rS-O) = -31.00e-·Å-5; ∇2ρ(rNa···O) = 1.931e- ·Å-5; ∇2ρ(rNa···F) = 3.022e-·Å-5 and ∇2ρ(rF···O) = 0.868e-·Å-5], 5·RCP’s [∇2ρ(rI) = 0.912e-·Å-5; ∇2ρ(rII) = 0.332e-·Å-5 and ∇2ρ(rIII,IV,V) = 0.201e-·Å-5] and 4·CCP’s [∇2ρ(rI,II) = 0.514e-·Å-5 and ∇2ρ(rIII,IV) = 0.401e-·Å-5] were identified (Figure 1). Hence, Morse’s ‘characteristic set’ condition was met[3]. The study of primary bundles (PB’s), as proposed by Pendás[4], revealed the interconnection between AB’s and CP’s onto basins of attraction or basins of repulsion. The nature of interatomic interactions was assessed through the dichotomous classification[3]. The S–O contact was acknowledged as a covalent with a shared-shell. The remaining contacts were characterized as non-covalent closed-shell (Cl···Na, Na···O and Na···F) or weak van der Waals closed-shell (Cl···S and F···O).

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11:25am - 11:45am

Direct observation of pressure induced charge density redistribution at ions in zeolite, hsianghualite

Marcin Stachowicz, Roman Gajda, Krzysztof Woźniak

University of Warsaw, Warsaw, Poland

Modern approaches of X-ray diffraction allow for detailed quantitative studies of electron density in crystals of minerals. They can be combined with high pressure studies [1] as we demonstrate in this work for model zeolite mineral hsianqhualite, Ca3Li2(Be3Si3O12)F2.

At the level of electron density analysis first order configurational components in crystal structure description (Fig. 1a) were replaced by Bader’s atomic basins [2] which quantitatively characterise electron density of particular ions in mineral structures as well as precisely defined space, they occupy (Fig 1b). Their anisotropic and highly non-spherical shape reflects interatomic interactions and is sensitive to applied pressure. According to our studies the charge of ions in the crystal lattice differ from the formal, integer values and when external pressure is applied a redistribution of charge among ions takes place. This redistribution changes the size and shape, mostly at the edges of ionic basins in nonbonding fragments (Fig. 1c, d).

Negative compressibility of the F ion was observed. It was caused by the flow of electrons increasing the total negative charge and, consequently, increasing the volume of F ion at 1.9 GPa pressure (Fig 1d). Also inside of atomic basins of atoms electron density redistributes notably due to pressure.

The quantitative characterization of minerals under high pressure at the subatomic level of electron density, rise possibilities to better understand the nature of mineralogical process, phase transitions and formation of new phases and also to study plastic deformations of minerals using diamond anvil cells.

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11:45am - 12:05pm

Structural studies of titanium and zirconium silicate ion-exchange materials for the treatment of nuclear waste

Jennifer Readman

University of Central Lancashire, Preston, United Kingdom

Zeolites are commonly used as ion-exchange materials for the remediation of nuclear waste; however, they have certain drawbacks. Unlike zeolites which contain SiO4 and AlO4 tetrahedra, microporous Ti-silicates can contain SiO4 tetrahedra and TiO6 octahedra and therefore structures are possible which have no traditional aluminosilicate analogues [1]. Microporous Ti-silicates such as sitinakite KNa2Ti4Si2O13(OH)·4H2O and the synthetic niobium doped analogue are used for the removal of Cs+ and Sr2+ from nuclear waste [2,3]. The work presented here will focus on the structures and thermal behaviour of the ion-exchanged Ti- and Zr-silicates. A clear understanding of both is fundamental in determining if these materials have potential as ion-exchangers within the nuclear industry.

Umbite is a naturally occurring small pore microporous Zr- silicate, found in northern Russia and synthetic analogues, K2ZrSi3O9·H2O, can be prepared in the laboratory [4]. Ion-exchange studies here have shown that umbite has a preference for common radionuclides, such as Cs+ and Sr2+and Ce4+ (as a surrogate for Pu), even in the presence of competing ions. In-situ studies show that these materials behave differently with temperature, indicating that the nature and location of the charge balancing cation plays an important part in determining which high temperature phases are formed and the phases formed do not fit previously reported structures.

Natisite is another material which has interesting ion-exchange chemistry and is a layered Ti-silicate with the formula Na2TiSiO5 [6]. The structure consists of square pyramidal titanium, with the sodium cations located between the layers. This coordination environment is highly unusual for Ti. Inclusion of zirconium or vanadium in the framework has a considerable effect on the ion-exchange properties, with changes in the exchange capacity and the rate of uptake for certain ions of interest.

A combination of techniques to probe long and short-range order (PDF and XAS) have been used to understand the ion-exchange and thermal behaviour of these materials.

References:

1) P. A. Wright, Microporous Framework Solids, The Royal Society of Chemistry, Cambridge, 2008. 2) D. M. Poojary, et al., Chem. Mater., 6, 2364 (1994). 3) A. Tripathi, et al., J. Solid State Chem., 175, 72 (2003). 4) D. M. Poojary, et al., Inorg. Chem., 36, 3072 (1997). 5) A. Ferreira, et al., J. Solid State Chem., 183, 3067 (2010). 6) D.G. Medvedev et al., Chem. Mater., 16, 3659 (2004).

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12:05pm - 12:25pm

Crystal and Magnetic structures and Dielectric phase transition of the novel Organic-Inorganic Hybrid Halometallate compound: (quinuclidine)[FeCl4]

Palmerina González-Izquierdo1,2, Oscar Fabelo1, Imanol de Pedro del Valle2, María Teresa Fernández-Díaz1, Laura Canadillas-Delgado1, Garikoitz Beobide3, Manuel Sánchez Andújar4

1ILL, Grenoble, France; 2CITIMAC, Universidad de Cantabria, Spain; 3Inorganic Chemistry, Universidad del Pais Vasco, EHU/UPV, Spain; 4Department of Chemistry, Universidade da Coruna, Spain

The synthesis of multifunctional materials is a hot focus of research in materials science. In this respect, the synthesis of complexes based on the combination of organic-inorganic building blocks provides a promising approach in the design of systems with tuneable properties. In this communication we will present the properties of a new compound based on quinuclidine as the organic cation and FeCl4 as the inorganic anion, with the formula (quinuclidine)[FeCl4]. Similar compounds derived of this heterocyclic cation have been found to present interesting ferroelectric properties.[1] In this context, the multifunctional behaviour of this novel molecular crystal is related to the electronic structure of the 3d5 configuration of the Fe(III) ions together with the ability of the counter-ions to change of orientation or even become disordered as a function of temperature.

The structural characterization of (quinuclidine)[FeCl4] compound shows two phase transitions. The first one, detected in the range from 100 to 300 K, was resolved by single-crystal X-Ray and neutron diffraction. At 300 K, the compound presents the orthorhombic space group Pbc21. At 100 K, the space group is Pbca, with a doubling of the a-axis, related to the rotation of the cations: two different orientations of the counterion are observed in the low temperature phase along the a direction, contrary to the high temperature phase, where it appears only one orientation.

Moreover, this compound presents long-range magnetic order below 3 K. The magnetic structure was solved using single-crystal and powder neutron diffraction data from D19 and D1B instruments (ILL, France), respectively. Our best model was found on the Shubnikov magnetic space group P21’21’21. Although the refined model present an antiferromagnetic structure, based on the symmetry analysis of the P21’21’21 Shubnikov group, a ferromagnetic component along the c direction is allowed. However, the refinement of this ferromagnetic component is beyond the precision of our measurements. Nevertheless, this can be fixed to the values derived from the macroscopic magnetometry measurements (SQUID). In order to provide a complete model these values were included in the magnetic model and fixed during the refinements.

At temperatures higher than R.T, there is a second structural phase transition which produces an important modification of the electric behaviour, as it has been reported on similar compounds.[1] The dielectric permittivity data collected shows a sharp phase transition around 390 K (also observed in DSC measurements). The value of the permittivity increases drastically with the increase of the temperature, reaching a maxima of 105 at 390 K (measured at 1 kHz). This value is notable larger than similar compounds of this family.[1] This interesting behaviour could be of interest for electrochemical applications.

[1] (a) Jun Harada et al., Nat Chem, 2016 Oct; 8(10):946-52. (b) You-Meng You et al., Nat Commun. 2017, 8:14934. c) Ting Fang et al., Z. Anorg. Allg. Chem. 2019, 645, 3–7. d) Guang-Meng Fan et al., CrystEngComm, 2018,20, 7058-7061.

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10:20am - 12:45pmMS-80: 4th generation SR and XFEL Facilities
Location: Terrace 2A
Session Chair: Makina Yabashi
Session Chair: Sofia Diaz-Moreno

Invited: Jean Susini (France)

 
10:20am - 10:25am

Introduction to session

Makina Yabashi, Sofia Diaz-Moreno



10:25am - 10:55am

The ultra-low emittance synchrotron storage rings: a new paradigm for matter characterization.

Jean Susini

Synchrotron SOLEIL, Gif sur Yvette, France

Over the last few years, photon science community has been experiencing a revolution with the advent of ultra-low emittance storage rings based on Multi-Bend Achromat (MBA). In addition to green fields projects MAXIV (1), SIRIUS (2), and HEPS (3) in operation, commissioning, or construction, respectively, many third-generation facilities undertook major upgrades such as ESRF-EBS (4), APS-U (5), ALS-U (6), SLS-2 (7), DLS-2 (8), etc. All are aiming to achieve unparalleled performances in terms of average spectral brilliance, coherent flux, and nano-focusing capabilities.

After an introduction of the main concepts behind this new revolutionary concept, the new characterization techniques and their potential for new applications will be discussed, for two distinct examples, including the commissioning and operation of the ESRF-EBS (6 GeV) and the project SOLEIL (2.75 GeV) upgrade:

Since 2015 the ESRF has prepared the replacement of its old storage ring based on the double-bend achromat lattice by the EBS storage ring(9) based on the newly developed HMBA lattice with seven bending magnets per cell. During a long shutdown the EBS storage ring was installed in 2019 and went into its commissioning phase in December 2019. The EBS storage ring was successfully commissioned as the first fourth generation high energy synchrotron light source during the first six month in 2020. Nominal beam parameters could be confirmed early on in the process and the beamlines resumed user operation in September 2020 as planned. The expected improvement of the key beam parameters in terms brilliance, coherence and flux were confirmed across the entire beamline portfolio. Details on the commissioning of the beamlines and the performance reached will be presented together with early scientific results.

In 2019, SOLEIL launched a CDR (10) for an upgrade of its 20 years old storage ring with the ambition to produce round electron beams with a record low emittance of less than 50 pm.rad x 50 pm.rad, hence photon beams with an exceptional brilliance exceeding by two orders of magnitude the performances of the current source. The very broad spectral range of Soleil from THz to tens of KeV is a challenge but offers unique scientific opportunities which will be discussed and illustrated by examples in materials science and biology.

[1] Tavares, P. F., et al., “Status of the MAX-IV Accelerators”, IPAC 2019 proceedings, TUYPLM3, 1185-1190 (2019).

[2] Liu, L., “SIRIUS Commissioning Results”, IPAC 2020 (2020).

[3] Jiao Y., “The HEPS Project”, Journal of Synchrotron Radiation, 25, 1611-1618 (2018).

[4] Raimondi P., “Hybrid Multi Bend Achromat: from SuperB to EBS”, 8th International Particle Accelerator Conference, May 2017, Copenhagen, Denmark, 3670-3675,10.18429/JACoW-IPAC2017-THPPA (2017).

[5] Borland, M. et al., “The Upgrade of the Advanced Photon Source”, IPAC 2018 proceedings, THXGBD1, 2872-2877 (2018).

[6] Steier, C. et al., “Design Progress of ALS-U, the Soft X-Ray Diffraction Limited Upgrade of the Advanced Light Source, IPAC 2019 proceedings, 1639-1641 (2019).

[7] Streun, A., et al., “SLS-2: the Upgrade of the Swiss Light Source”, Journal of Synchrotron Radiation, 25, 631-641 (2018).

[8] https://www.diamond.ac.uk/Home/About/Vision/Diamond-II.html

[9] Orange Book: http://www.esrf.eu/home/orange-book.html

[10] CDR SOLEIL, https://www.synchrotron-soleil.fr, to be published

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10:55am - 11:15am

Ultrafast structural changes in matter induced by intense X-ray free-electron laser pulses

Ichiro Inoue1, Yuichi Inubushi1,2, Taito Osaka1, Toru Hara1, Eiji Nishibori3, Makina Yabashi1

1RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan.; 2Japan Synchrotron Radiation Research Institute, Kouto 1-1-1, Sayo, Hyogo 679-5198, Japan; 3University of Tsukuba, Tsukuba, Ibaraki 305-8571, Japan.

X-rays have become established as an invaluable probe for gaining an atomic insight into the structure of matter through various kinds of interaction processes, such as scattering, absorption, and emission of photoelectrons and fluorescence. Since these interactions were usually weak with the previous X-ray sources, X-ray irradiation was assumed not to modify matter. This situation has been altered by the recent advent of X-ray free-electron lasers (XFELs), which can generate brilliant femtosecond X-ray pulses.

When an XFEL pulse irradiates matter, photoelectrons and Auger electrons are emitted during or shortly after the irradiation of the pulse and trigger cascades of secondary electrons. If the radiation dose exceeds a critical value, the electron excitations strongly change interatomic potential surface and cause subsequent atomic disordering, and may even lead to the Coulomb explosion in the case of high X-ray dose. Given the time scale of electron cascading (typically, a few tens of fs) and inertia of atoms, the onset of atomic disordering is expected to take place behind the start of X-ray exposure. Indeed, it has been predicted that ultrafast X-ray pulse as short as ~10 fs with sufficient intensity can produce high-quality diffraction before the onset of substantial radiation damage, enabling structure determination of macromolecular nanocrystals and even individual biomolecule [1]. A deep understanding of transient XFEL interaction with matter is essential not only because of fundamental interest but for analyzing experiments with intense XFEL pulses.

Up to now, transient XFEL-matter interactions have been relying on theoretical modeling, validated by time-integrated measurements of charge states of ions and emitted fluorescence using a single XFEL pulse. To observe time-dependent X-ray interactions with matter, we developed a femtosecond X-ray pump-X-ray probe method [2] by combining nano-focusing optics [3] and twin XFEL pulses with controlled time separations [4] at SPring-8 Angstrom Compact free-electron LAser (SACLA) [5]. This method was applied to various materials (diamond [2,5], silicon [6], oxides, and protein crystals) and revealed the time scale of the electron excitations and the onset time of the structural changes.

In this talk, the XFEL-induced transient structural changes in matter revealed by the pump-probe experiments are discussed. In addition, preliminary results of the advanced pump-probe experiments using seeded-XFEL pulses [7,8] will be presented.

[1] Neutze, R., Wouts, R., Van der Spoel, D., Weckert, E., Hajdu, J. (2000). Nature 406, 752.[2] Inoue, I., Inubushi, Y., Sato, Y., Tono, K., Katayama, T., Kameshima, T., Ogawa, K., Togashi, T., Owada, S., Amemiya, Y., Tanaka, T., Hara, T., & Makina, Y. (2016). Proc. Natl. Acad. Sci. USA 113, 1492.[3] Mimura, H., Yumoto, H., Matsuyama, S., Koyama, T., Tono, K. et al., (2014). Nature Commun. 5, 3539.[4] Hara, T., Inubushi, Y., Katayama, T., Sato, T., Tanaka, H., Tanaka, T., Togashi, T., Togawa, T., Tono, K., Yabashi, M. & Ishikawa, T. (2014). Nat. Commun. 4, 2919.[5] Inoue, I., Deguchi, Y., Ziaja, B., Osaka, T., Abdullah, M. M., Jurek, Z., Medvedev, N., Tkachenko, V., Inubushi, Y., Kasai, H., Tamasaku, K., Hara. T., Nishibori, E. & Makina, Y. (2021). Phys. Rev. Lett. 126, 117403.[6] Hartley, N., Grenzer, L., Huang, L., Inubushi, Y., Kamimura, N., Katagiri, K. et al. (2021). Phys. Rev. Lett. 126, 015703.[7] Inoue, I., Osaka, T., Hara, T., Tanaka, T., Inagaki, T. et al. (2019). Nature Photon. 13, 319.[8] Inoue, I., Osaka, T., Hara, T. & Yabashi, M. (2020). J. Synchrotron Rad. 27, 1720.

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11:15am - 11:35am

Pink-beam serial femtosecond crystallography for accurate structure factor determination at an X-ray free electron laser

Karol Nass1, Camila Bacellar1, Claudio Cirelli1, Florian Dworkowski1, Yaroslav Gevorkov2, Daniel James1, Philip J. M. Johnson1, Demet Kekilli1, Gregor Knopp1, Isabelle Martiel1, Dmitry Ozerov1, Alexandra Tolstikova2, Laura Vera1, Tobias Weinert1, Oleksandr Yefanov2, Joerg Standfuss1, Sven Reiche1, Christopher J. Milne1

1Paul Scherrer Institut, Forschungstrasse 111, Villigen, 5232, Switzerland; 2Center for Free-Electron Laser Science, Notkestrasse 85, Hamburg, 22607, Germany

Serial femtosecond crystallography (SFX) at X-ray free-electron lasers (XFELs) enables essentially radiation damage-free macromolecular structure determination using microcrystals that are too small for synchrotron studies [1]. However, SFX experiments often require large amounts of sample in order to collect highly redundant data where some of the many stochastic errors can be averaged out and accurate structure factor amplitudes determined [2]. Recently, an improvement in native-SAD phasing of SFX data was demonstrated by utilizing longer wavelengths that increased the strength of the anomalous signal [3]. This reduced up to 10-fold the number of indexed images needed for successful de novo structure determination. Another approach to reduce the number of indexed images, applicable not only to de novo phasing but also to molecular replacement strategies, is to use polychromatic (pink) X-ray pulses for SFX. Theoretically, faster convergence rates of the Monte Carlo approach can be achieved by increasing the bandwidth or divergence of the X-ray pulses [4, 5].

We used the capability of the Swiss free-electron laser (SwissFEL) to generate large-bandwidth X-ray pulses (Δλ/λ = 2.2 % FWHM) and applied them in SFX with the aim of improving the partiality of Bragg spots and thus decreasing sample consumption while maintaining the data quality. Sensitive data-quality indicators such as anomalous signal from native thaumatin micro-crystals and de novo phasing results were used to quantify the benefits of using pink X-ray pulses to obtain accurate structure factor amplitudes. Compared to data measured using the same setup but X-ray pulses with typical, quasi-monochromatic XFEL bandwidth (Δλ/λ = 0.17 % FWHM), up to four fold reduction in the number of indexed diffraction patterns required to obtain similar data quality was achieved. This novel approach, pink-beam SFX, facilitates the yet underutilized de novo structure determination of challenging proteins at XFELs, thereby opening the door to more scientific break-troughs.

[1] Nass, K. (2019). Acta Cryst. D 75, 211-218.

[2] Nass, K., Meinhart, A., Barends, T. R., Foucar, L., Gorel, A., Aquila, A., Botha, S., Doak, R. B., Koglin, J., Liang, M., Shoeman, R. L., Williams, G., Boutet, S. & Schlichting, I. (2016). IUCrJ 3, 180-191.

[3] Nass, K., Cheng, R., Vera, L., Mozzanica, A., Redford, S., Ozerov, D., Basu, S., James, D., Knopp, G., Cirelli, C., Martiel, I., Casadei, C., Weinert, T., Nogly, P., Skopintsev, P., Usov, I., Leonarski, F., Geng, T., Rappas, M., Doré, A. S., Cooke, R., Nasrollahi Shirazi, S., Dworkowski, F., Sharpe, M., Olieric, N., Bacellar, C., Bohinc, R., Steinmetz, M. O., Schertler, G., Abela, R., Patthey, L., Schmitt, B., Hennig, M., Standfuss, J., Wang, M. & Milne, C. J. (2020). IUCrJ 7, 965-975.

[4] Dejoie, C., McCusker, L. B., Baerlocher, C., Abela, R., Patterson, B. D., Kunz, M. & Tamura, N. (2013). J. Appl. Cryst. 46, 791-794.

[5] White, T. A., Barty, A., Stellato, F., Holton, J. M., Kirian, R. A., Zatsepin, N. A. & Chapman, H. N. (2013). Acta Cryst. D 69, 1231-1240.

Keywords: Pink-beam; serial femtosecond crystallography; de novo protein structure determination; X-ray crystallography; SFX; SAD; single-wavelength anomalous diffraction; XFEL; large-bandwidth

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11:35am - 11:55am

Towards a structural biology at organism relevant temperature and chemical conditions

John Richard Helliwell

University of Manchester, Manchester, United Kingdom

The three probes of the structure of matter in biology (X-rays, neutrons and electrons) have complementary properties and strengths. The balance between these three structural research probes, within their strengths and weaknesses, is perceived to change, even dramatically so at times. Of course for understanding biological systems the required perspectives are:- physiologically relevant temperatures and relevant chemical conditions. These remain very tough challenges because e.g. cryoEM looks never to set foot in room temperature and crystallization often requires non-physiological chemical conditions. X-ray crystallography especially from the synchrotron has brought huge improvements in analytical capability and dominates the PDB. CryoEM has also brought great advantage for structural studies of non-crystallisable complexes. Overall, integrated structural biology techniques and functional assays make a package towards physiological relevance of any given study. X-ray laser serial fsec crystallography experiments aimed at structural dynamics and neutron macromolecular crystallography aimed at determining protonation states of ionisable amino acids are both, as a spin off, yielding room temperature structures, as well as being damage free. Comparisons between room and cryo biological structures are increasing as the X-ray laser and neutron facilities expand in number and grow in capability; structural differences are being increasingly described in many papers. We need to expand these facility provisions for room temperature studies. Likewise the extremely bright sources such as ESRF2 ie "EBS" will bring a larger number of room temperature results through the serial crystallography approach but with X-ray radiation damage effects yet to be quantified.

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11:55am - 12:15pm

Ultrafast dynamical diffraction wavefronts in strained Si imagined with Tele-ptychography

Angel Rodriguez-Fernandez1, Ana Diaz2, Anand H. S. Iyer3, Mariana Verezhak2, Klaus Wakonig2, Magnus H. Colliander3, Dina Carbone4

1Eu XFEL GmbH, Schenefeld, Germany; 2Paul Scherrer Institute, Villigen PSI, Switzerland; 3Chalmers University of Technology, Gothenburg, Sweden; 4MAX IV, Lund University, Lund, Sweden

Dynamical diffraction effects, also known as echoes, produced in thin crystals in both forward and diffracted directions are of highest importance for X-ray optics at ultrafast sources, as XFELs, and for the study of ultrafast phenomena in micron-sized single crystals. These echoes present delays of few fs between each other and the transmitted beam (similar as it happens with sound echoes, but in this case of electromagnetic nature and therefore with the speed of light). The delay relates to a displacement of the monochromatic diffracted beams in the transverse direction to the X-ray beam propagation [1,2]. Such echoes are used in self-seeding forward monochromators at hard xFELs.

We would like to present our work performed at NanoMAX, MAX IV laboratory, Sweden, in which we image the dynamical diffraction wavefront from a 100 um thick Si wafer [3]. The work uses the full coherence and high flux of NanoMAX, together with the technique known as tele-ptychography [4], to image the forward diffracted wavefront at a pinhole located 3 mm downstream the sample. As presented in figure 1, the data collected is reconstructed using a ptychography algorithm in the pinhole plane, obtaining amplitude and phase of the wavefront. The wavefront is propagated back to the focus where, combined to the small size of the X-ray beam provided by NanoMAX, provides a high- resolution (55 nm) image for the detection of forward diffracted echoes.

The work underline how this effect must be taken into account in the imaging and study of samples with thickness of the order of the X-ray extinction length. We also show that a strain induced in the surface can modulate the temporal delay of the dynamical diffraction waves as presented in the second figure attached. All the work is accompanied with the simulation of the effect using a self-written code, that can be used to model both temporal and static strains in single crystal samples, as well as in micro-pillars in which these dynamical effects are also present [5].

[1] A. Rodriguez-Fernandez et al., ActaCryst. A74, 75 (2018);

[ 2] Y. Shvydko and R. Lindberg, Phys. Rev. ST Accel.Beams15, 100702 (2012);

[3] A. Rodriguez-Fernandez et al., "Imaging ultrafast dynamical diffraction wavefronts in strained Si with coherent X-rays" arXiv:2012.08893 (2020)

[4] E. H. R. Tsai et al, Optics Express 34 (2016) 6441;

[5] M. Verezhak et al. "X-ray ptychographic topography, a new tool for strain imaging" PRB (2021);

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Advances with EIGER2 (CdTe) detectors for Synchrotron and Laboratory

Stefan Brandstetter, Max Burian

Dectris Ltd, Baden-Daettwil , Switzerland

Hybrid photon counting (HPC) X-ray detectors are crucial ingredients for cutting-edge synchrotron research [1] by providing noise-free detection with advanced acquisition modes. In this regard, the latest HPC detector generation EIGER2 is setting new performance standards that push current horizons in X-ray science. These detectors combine all advantages of previous HPC detector generations while offering (i) 75 µm × 75 µm pixel size, (ii) kilohertz frame rates, (iii) negligible dead time (100 ns) and (iv) count rates of 107 photons per pixel.

Recently, EIGER2 detectors are available both with silicon and with CdTe sensors to provide high quantum efficiency at energies up to 100 keV. Two separately adjustable energy thresholds allow for reduction of high-energy background such as from cosmic radiation or higher harmonics radiation. For one, this active background suppression significantly improves signal-to-noise in laboratory applications where weaker signals are expected. For the other, these benefits advance established methods like crystallography and small angle X-ray scattering and empower new fields of research, such as X-ray photon correlation spectroscopy and coherent studies.

Here, we present results from detector characterization and application experiments, highlighting key properties such as count rate capability, readout and spatial resolution. We will further show the potential capabilities of newly released detector features, such as the double-gating acquisition mode for shot-to-shot background correction. Combined with characterization measurements at beamlines and in the laboratory, these results evidence how the EIGER2 detector systems will advance static and time-resolved X-ray experiments.

[1] Förster, A., et al. (2019) Philos. Trans. R. Soc. Math. Phys. Eng. Sci. 377, 20180241.

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12:45pm - 2:45pmLunch 6: Posters, lunches
Location: Exhibition and poster area
1:00pm - 2:30pmECA - SIG-11: ECA - SIG-11 Crystallography under Extreme Conditions
Location: Club A
1:00pm - 2:30pmECA - SIG-13: ECA - SIG-13 Molecular Structure and Chemical Properties
Location: virtual
1:00pm - 2:30pmECA - SIG-14: ECA - SIG-14 Dynamics, Disorder, Diffuse Scattering
Location: Club D
1:00pm - 2:30pmECA - SIG-2: ECA - SIG-2 Quantum Crystallography
Location: Club H
1:00pm - 2:30pmECA - SIG-9: ECA - SIG-9 Crystallographic Computing
Location: virtual
1:00pm - 2:30pmECA-1: ECA EC meeting 2
Location: Club C
Session Chair: Udo Heinemann
Session Chair: Arie van der Lee

ECA EC meeting

1:45pm - 2:45pmECA - SIG-7: ECA - SIG-7 Molecular Interaction and Recognition
Location: virtual
2:45pm - 3:50pmSMS-6: Spectroscopy applied to electrochemistry: operando studies
Location: Club C
Session Chair: Jasper Rikkert Plaisier
Session Chair: Dibyendu Bhattacharyya

Invited: Moniek Tromp (The Netherlands), Mahalingam Balasubramanian (USA)

 
2:45pm - 2:50pm

Introduction to session

Jasper Rikkert Plaisier, Dibyendu Bhattacharyya



2:50pm - 3:20pm

Operando X-ray Absorption Spectroscopy probing Dynamic Processes in Batteries

Moniek Tromp

University of Groningen, Groningen, Netherlands, The

An important element in the reduction of CO2 is the change of vehicles with internal combustion engines to electric battery powered vehicles. The as such produced renewable energy can be used for individual mobility as well as for a temporary intermediate storage of excess energy. A viable electric mobility concept requires however stable cycle batteries with high specific energy (minimising weight, maximising driving range).

Li ion batteries are widely used in applications such as mobile phones and laptops, and will likely be key to future electromobility. An alternative promising battery is the lithium sulfur battery with a potential twofold energy density increase. The requirements for such batteries present major challenges; e.g. energy capacity, deactivation/stability and safety. A detailed understanding of the charge, discharge and deactivation mechanisms are thus required, preferably quantitative and spatially resolved. X-ray absorption spectroscopy (XAS) is a characterisation technique which provides detailed electronic and structural information on the material under investigation, in a time- and spatially resolved manner.

Here, I will explain the strengths and limitations of XAS for battery research. A novel operando XAS cell design will be described [1], including the challenges to perform reliable experiments (electrochemically and spectroscopically). The cell allows time and spatial resolved XAS, providing insights in the type, location and reversibility of the intermediates formed in electrodes and electrolyte separately. Obtained insights in cycling and deactiviation mechanisms for the different battery types will be discussed [1-6] and future research directions described.

[1] Y. Gorlin, A. Siebel, M. Piana, T. Huthwelker, H. Jha, G. Monsch, F. Kraus, H.A. Gasteiger, M. Tromp, J. Electrochem. Soc. 162(7): A1146-A1155, 2015.

[2] Y. Gorlin, M. U. M. Patel, A. Freiberg, Q. He, M. Piana, M. Tromp, H. A. Gasteiger, J. Electrochem. Soc. 2016, 163(6), A930-A939.

[3] J. Wandt, A. Freiberg, R. Thomas, Y. Gorlin, A. Siebel, R. Jung, H. A. Gasteiger, M. Tromp, J. Mater. Chem. A 2016, 4, 18300-18305.

[4] A. T. S. Freiberg, A. Siebel, A. Berger, S. M. Webb, Y. Gorlin, H. A. Gasteiger, M. Tromp, J. Phys. Chem. C 2018, 122, 10, 5303-5316.

[5] A. Berger, A. T. S. Freiberg, R. J. Thomas, M. U. M. Patel, M. Tromp, H. Gasteiger, Y. Gorlin, J. Electrochem. Soc. 2018, 165(7), A1288-A1296.

[6] R. Jung, F. Linsenmann, R. J. Thomas, J. Wandt, S. Solchenbach, F. Maglia, C. Stinner, H. A. Gasteiger, M. Tromp, J. Electrochem. Soc. 2019, 166(2): A378-A389.

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3:20pm - 3:50pm

Operando diagnostics of cathode materials based on novel sodium iron titanites

Victor Vasilevich Shapovalov1, Alexander Alexandrovich Guda1, Vera Valerevna Butova1, Abdelaziz Mohamed Aboraia1, Igol Leonidovich Shukaev2, Alexander Vladimirovich Soldatov1

1Smart Materials Research Institute, Southern Federal University, Rostov-on-Don, Russian Federation; 2Department of Chemistry, Southern Federal University, Rostov-on-Don, Russian Federation

A set of sodium iron titanite samples with general formula NaxFe+2x/2Ti2–x/2O4 was prepared using solid-state synthesis in an inert atmosphere to test for application as cathode materials for Na-ion batteries. These materials have several advantages over analogues with Fe3+, demonstrating better sodium ion conductivity and higher Na+ ions capacity without phase transition or destruction of the structure. [1] In the course of the investigation, several compositions of a new compound were obtained with NSIT-like structure type similar to Na0.9Fe3+0.9Ti1.1O4. Among them, composition with x = 0.9 was selected due to its electrochemical performance and structural peculiarity. From the crystallographic point of view, formation of phases in NaxFe+2x/2Ti2–x/2O4 system with Na0.9Fe3+0.9Ti1.1O4 structure (having Fe3+ ions mixed with Ti4+ ions) is rather unusual due to different radii of mixing ions (Fe2+ = 0.92 Å, Fe3+ = 0.785 Å, Ti+4 = 0.745 Å (CN=6) [2]).

The Na0.9Fe3+0.9Ti1.1O4 was further studied by operando XANES spectroscopy. The sample was placed as a cathode inside custom electrochemical cell with glassy carbon X-Ray transparent windows. Li foil was used as anode and 1M LiPF6 in 1:1 EC:DMC commercial solution (Sigma) was used as electrolyte. The cell was cycled in 1.6 to 4.5 V range with current of C/20. Operando Fe K-edge XANES spectra were measured with the R-XAS Looper (Rigaku, Japan) laboratory X-Ray absorption spectrometer.

In total 200 spectra were collected for NaxFe+2x/2Ti2–x/2O4 sample with x = 0.9 during 10 consecutive cycles, which were further analyzed by PCA to extract spectra of phases participating the electrochemical process and corresponding phase content diagrams. 2 components were successfully extracted (fig. 1). Component corresponding to a Fe2+ phase shows good agreement with FeTiO3 reference in terms of absorption edge position and overall profile of the spectrum. On the other hand, agreement with the spectrum of as-prepared sample is far from decent. Component corresponding to a Fe3+ phase shows good agreements with a reference compound (reference sample, fully oxidized in air). Comparison with theoretical spectra for various structural models have shown decent agreement of Fe2+ phase with the spectrum of freudenbergite. Fig. 2 shows the cell potential and phase concentrations from PCA as a function of time. One can clearly see the decrease in Fe2+/Fe3+ conversion rate during first 3 cycles, after that the rate remains stable and conversion is highly reversible. This decrease in conversion rate, as well as lack of agreement between Fe2+ phase from PCA and as prepared sample, might be accounted by electrochemical substitution of Na with Li that takes place during cycling in Li-based cell, which causes the change in local atomic and electronic structure of material, possibly leading to partially blocked or collapsed ion transfer channels. The degree and details of such substitution are subject for study by operando XRD and Mössbauer spectroscopy.

[1] Rajagopalan et al., (2017) Adv. Mater. 29

[2] Shannon, R.D. (1976), Acta Crystallogr. Sect. A 32, 751-767

Authors would like to acknowledge the financial support of Russian Foundation for Basic Research in the framework of grant 20-32-70227

 
2:45pm - 5:10pmMS-81: Nucleic acids and binding proteins structure and function
Location: Club A
Session Chair: Stephen Neidle
Session Chair: Charles Bond

Invited: Millie Georgiadis (USA), Liliya Yatsunyk (USA)

 
2:45pm - 2:50pm

Introduction to session

Stephen Neidle, Charles Bond



2:50pm - 3:20pm

Non-canonical DNA structures and their interactions with small molecule ligands

Liliya A. Yatsunyk, Dana Beseiso, Sawyer McCarthy, Erin Chen, Elizabeth Gallagher, Joanne Miao

Swarthmore College, 500 College Ave, Swarthmore, PA, United States of America

Non-canonical DNA structures, notably G-quadruplexes and i-motifs, draw significant attention because biological evidence suggests that they play crucial roles in a variety of disease-related biological processes. G-quadruplex DNA is composed of planar guanine tetrads which are engaged in efficient p-p stacking and are further stabilized by monovalent central cation (e.g. K+ or Na+). Sequences with G-quadruplex forming potential are present in telomeres and in oncogene promoters, according to bioinformatics studies. I-motifs are intercalated hemi-protonated cytosine-rich structures formed in the C-rich sequences. Naturally, such sequences are present in the regions complimentary to the G-rich parts of genome.

In this work we have investigated nine variants of telomeric DNA with the repeat (TTGGGG)n from the organism Tetrahymena thermophila using biophysical and x-ray crystallographic studies. Biophysical characterization showed that all sequences folded into stable GQs which adopted a variety of conformations, most commonly parallel and hybrid. Native PAGE suggested that most of the sequences form multiple species in the presence of potassium. All species, but one, are monomolecular. We successfully crystallized two variants, TET25 (resolution 1.56 Å) and TET26 (three crystal forms with resolution 1.99 and 1.97 Å) and solved the structures via molecular replacement. TET25 adopted a hybrid (3+1) conformation with a four G-tetrad core, three lateral loops, one propeller loop, and 5’ snapback. TET26 fold into a parallel GQ conformation with a four G-tetrad core and three TT propeller loops. We have also investigated binding of N-methylmesoporphyrin IX (NMM) to all sequences and crystallized three variants with NMM. NMM induces parallel fold in all sequences. Both crystal structures display 5’-5’ dimers of parallel GQs with NMM bonded to the 3’ G-tetrad. NMM binds GQ with one of its faces and another NMM molecule with another. Our structural data demonstrate great plasticity of the telomeric sequence from the telomeric region of T. thermophila where small variation in the overhang length and composition leads to drastically distinct GQ structures.

I will also share our progress toward the structure an i-motif DNA from the HRAS oncogene promoter as well as the structure of repetitive DNA (CAGAGG)n from difficult-to-replicate regions of the mouse genome implicated in replication stress. Our findings have potential to contribute to the development of new and efficient anticancer therapies.

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3:20pm - 3:50pm

Structural properties of Alien DNA, an alternative genetic system

Millie M. Georgiadis1, Shuichi Hoshika2, Steven Benner2

1Indiana University School of Medicine, Indianapolis, Indiana, United States of America; 2Foundation for Applied Molecular Evolution, Alachua, Florida, United States of America

The simple elegance of the Watson-Crick DNA model reported in 1953[1] belies an underlying complexity that is central to all life. However, about thirty years then elapsed before the true complexity of DNA was revealed in high resolution crystals structures of oligonucleotides. In these structures, DNA was captured in three distinct helical forms, Z [2], B [2], and A [3], providing the first evidence for the remarkable ability of DNA to adopt different stable conformations influenced by nucleobase sequence. Since then, our understanding of the fundamental properties of DNA has been challenged further with efforts to expand the genetic code through the creation of unnatural nucleobases. These new entities include nucleobases that pair strictly through hydrophobic interactions [4, 5] and those that pair through hydrogen bonding interactions [6]. The latter nucleobases were created by Benner and coworkers and are referred to as the Artificially Expanded Genetic Information System (AEGIS) [7]. AEGIS takes advantage of alternative hydrogen bonding arrangements between Watson-Crick like pairs, a large purine-like nucleobase and a small pyridimine-like nucleobase that exclusively pair to one another rather than natural nucleobases. This concept has produced an expanded genetic code, Hachimoji DNA [8] comprising 8 letters, 4 natural and 4 unnatural, and most recently Alien DNA, comprising 4 unnatural nucleobases. These systems including unnatural base pairs (UBPs) expand the structural landscape of DNA through the creation of duplexes that do not conform to known helical forms.

In previous work, we have reported structures including up to 6 UBPs within 16 bp duplex DNA structures [9]. Our most recent work on Alien DNA includes structures with 12 UBPs of 16 base pairs (almost Alien DNA) contained within the structure captured in B-like and A-like helical forms. The B-like structures were obtained through the use of our host-guest system, which is selective for DNA sequences that can adopt helical forms that are more similar to B than A-form DNA. In this system, the N-terminal fragment of Moloney murine leukemia virus reverse transcriptase serves as the host and a 16-mer DNA duplex as the guest [10]. Using this system, we have determined structures of numerous DNA sequences at relatively high resolution (1.6-1.8 Å) including now one with 12 UBPs. One of the almost Alien DNA sequences including 12 UBPs has crystallized in three different crystal forms, two that diffract to 1.2 Å, providing the first very detailed structural information for these UBPs including sugar conformations. These latest structures of almost Alien DNA will be presented here along with comparative analyses with natural and other less Alien DNA structures including UBPs.

[1] Watson, J.D. and F.H. Crick, (1953). Nature 171, 737-8.

[2] Wang, A.H., G.J. Quigley, F.J. Kolpak, J.L. Crawford, J.H. van Boom, G. van der Marel and A. Rich, (1979). Nature 282, 680-6.

[3] Heinemann, U., H. Lauble, R. Frank and H. Blocker, (1987). Nucleic Acids Res 15, 9531-50.

[4] Leconte, A.M., G.T. Hwang, S. Matsuda, P. Capek, Y. Hari and F.E. Romesberg, (2008). J Am Chem Soc 130, 2336-43.

[5] Hirao, I., M. Kimoto, T. Mitsui, T. Fujiwara, R. Kawai, A. Sato, Y. Harada and S. Yokoyama, (2006). Nat Methods 3, 729-35.

[6] Yang, Z., D. Hutter, P. Sheng, A.M. Sismour and S.A. Benner, (2006). Nucleic Acids Res 34, 6095-101.

[7] Sefah, K., Z. Yang, K.M. Bradley, S. Hoshika, E. Jimenez, L. Zhang, G. Zhu, S. Shanker, F. Yu, D. Turek, W. Tan and S.A. Benner, (2014). Proc Natl Acad Sci U S A 111, 1449-54.

[8] Hoshika, S., N.A. Leal, M.J. Kim, M.S. Kim, N.B. Karalkar, H.J. Kim, A.M. Bates, N.E. Watkins, Jr., H.A. SantaLucia, A.J. Meyer, S. DasGupta, J.A. Piccirilli, A.D. Ellington, J. SantaLucia, Jr., M.M. Georgiadis and S.A. Benner, (2019). Science 363, 884-887.

[9] Georgiadis, M.M., I. Singh, W.F. Kellett, S. Hoshika, S.A. Benner and N.G. Richards, (2015). J Am Chem Soc 137, 6947-55.

[10] Cote, M.L., S.J. Yohannan and M.M. Georgiadis, (2000). Acta Crystallogr D Biol Crystallogr 56, 1120-31.

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3:50pm - 4:10pm

APE1 Exonuclease Distinguishes Various DNA Substrates by an Induced Space-Filling Mechanism.

Tung-Chang Liu2, Chun-Ting Lin1, Kai-Cheng Chang1, Kai-Wei Guo2, Shuying Wang3, Jhih-Wei Chu4, Yu-Yuan Hsiao2

1Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan; 2Institute of Molecular Medicine and Bioengineering, National Chiao Tung University, Hsinchu 30068, Taiwan; 3Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan, Taiwan; 4Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 30068, Taiwan

Apurinic/apyrimidinic endonuclease 1 (APE1) is a well-known endonuclease specifically targeting an AP site to initiate base excision repair. Interestingly, APE1 also bears 3′-to-5′ exonuclease activity that shows very different catalytic properties and cellular functions. The 3'-to-5' exonuclease activity of APE1 is responsible for processing matched/mismatched terminus of duplex DNA in various DNA repair pathways, as well as for nucleoside analogs removal associated with drug resistance. Due to the limited information of APE1’s exonucleolytic catalysis, its fundamental roles in various DNA repair pathways and in drug resistance are poorly understood. In addition, how APE1 exonucleolytically recognizes and processes the terminus of duplex DNA without base preference remain unclear. We determined the first two APE1-dsDNA complex structures, which displayed a dsDNA end-binding mode. Integration of our structures, biochemical assays, and molecular dynamics simulation reveals the general rules of APE1 in handling various dsDNA substrates. The DNA binding-induced RM (Arg176 and Met269) bridge formation in active site and DNA-binding modes transition between matched and mismatched termini of dsDNA compose the exquisite machinery for substrate selection, binding, and digestion. Our studies pave the way for understanding the dsDNA terminal-processing-related cellular functions and drug resistance mechanisms of APE1.

(Ref: Nat Commun. 12, 601 (2021). https://doi.org/10.1038/s41467-020-20853-2. )

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4:10pm - 4:30pm

Structural characterization of clinically reported missense mutations identified in BRCA1

Neha Mishra, Suchita Dubey, Ashok K Varma

Tata Memorial Centre Advanced Centre for Treatment, Research and Education in Cancer, Mumbai, India

Structural characterization of clinically reported missense mutations identified in BRCA1

Neha Mishra1, 2, Suchita Dubey1, 2 Ashok K Varma1, 21Advanced centre for Treatment, Research and Education in cancer, Kharghar, Navi Mumbai, Maharashtra – 410210, INDIA, 2Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai, Maharashtra – 400094, INDIA nmishra@actrec.gov.in

Germline loss of function mutations in Breast Cancer Susceptibility gene 1 (BRCA1) and Breast Cancer Susceptibility gene 2 (BRCA2) are known to be responsible for Hereditary Breast and Ovarian Cancer Syndrome (HBOCS). BRCA1 encodes 1863 amino acids consisting of N-terminus RING domain, intrinsically disordered central DNA binding region and highly conserved two tandem repeats of BRCTs constituting the C-terminus domain (CTD)[1]. The RING domain forms a heterodimer with BRCA1-associated RING domain protein 1 (BARD1) and acts as E3- Ubiquitin ligase. However, C-terminal of the BRCA1 is known to interact with proteins containing the consensus sequences of pS-X-X-F motif to mediate different complex formation at the time of Double Strand Break Repair (DSBR). Majority of the missense mutations are found in the BRCT, RING domain and few in the central domain of BRCA1. Several studies have been performed to classify such variants of uncertain significance (VUS) in BRCA1 as pathogenic or neutral but the exact molecular mechanism of pathogenicity still remains to be deciphered[2, 3]. The aim of the present study is to evaluate the structural significance of these missense mutations located in the central and C-terminus functional domains of BRCA1 using biophysical, biochemical and in-silico tools. It was found that BRCA1 Arg866Cys in the central region, Thr1691Arg and Gly1801Asp in the BRCT domain show conformational alterations. The central non-specific DNA binding domain has also been evaluated for its conformational changes in the presence and absence of super-coiled DNA. However, a reduced DNA binding ability was observed for the mutant as compared to the wild- type protein. Further, the central region of BRCA1 has been assessed for its intrinsically disordered behaviour. Addition of 2,2,2-trifluoroethanol (TFE) led to gain of structure of the central region and therefore, less susceptibility towards proteolysis. The mutations have been characterized with the help of Size exclusion chromatography (SEC), Circular Dichroism spectroscopy, nano DSF, EMSA. With this information we would further extend our studies for protein-protein interactions of the wild type and mutant proteins using ITC, SPR and co-crystallization. The reported results will enhance our understanding towards the fundamental structural differences arising due to cancer predisposing missense mutations.

Keywords: Hereditary Breast Cancer; BRCA1; secondary structural changes; BRCT; Intrinsically disordered protein regions (IDPRs); DNA binding regions

Acknowledgement-Funding for this study was supported by Annual Scientific Fund from ACTREC-TMC. The authors thank the XRD facility at ACTREC for providing necessary support to this study.

[1] R. Roy, J. Chun, and S. N. Powell, “BRCA1 and BRCA2 : different roles in a common pathway of genome protection,” Nat. Rev. Cancer.

[2] R. W. Anantha et al., “Functional and mutational landscapes of BRCA1 for homology-directed repair and therapy resistance,” pp. 1–21, 2017.

[3] P. Bouwman, H. Van Der Gulden, I. Van Der Heijden, R. Drost, and C. N. Klijn, “RESEARCH ARTICLE A High-Throughput Functional Complementation Assay for Classifi cation of BRCA1 Missense Variants,” 2013.

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4:30pm - 4:50pm

Solid-solid phase transition in adenine riboswitch crystals driven by large conformational changes induced by ligand

Jason R. Stagno1, Saminathan Ramakrishnan1, William F. Heinz2, Valentin Magidson2, Xiaobing Zuo3, Yun-Xing Wang1

1Center for Structural Biology, Centre for Cancer Research, National Cancer Institute, Frederick, MD-21702, USA.; 2Optical Microscopy and Analysis Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA.; 3X-ray Science Division, Argonne National Laboratory, Lemont, IL 60439, USA

A solid-solid phase transition (SSPT) occurs between distinguishable crystalline forms. SSPTs have been studied extensively in metallic alloys, inorganic salt or small organic molecular crystals, but much less so in biomacromolecular crystals. In particular, SSPTs involving large-scale molecular changes that are important to biological function are largely unexplored, yet may enhance our understanding of conformational space. Here, we report a systematic study of the ligand-induced SSPT in crystals of the adenine riboswitch aptamer RNA (riboA) using a combination of polarized video microscopy (PVM), solution atomic force microscopy (AFM), and time-resolved serial crystallography (TRX). The SSPT, driven by large conformational changes induced by ligand, transforms the crystal lattice from monoclinic (apo), to triclinic (intermediate lattice in a ligand-bound conformation), to orthorhombic (final bound conformational and lattice state). Using crystal structures of each state, we mapped out the changes to the crystal packing interfaces, which define the interplay between molecular conformation and crystal phase, which were corroborated by solution AFM. Using PVM to monitor changes in crystal birefringence, we characterized the kinetics of the SSPT in crystals of different sizes and ligand concentration. Together, these studies illustrate a practical approach for characterizing SSPT in biomacromolecular crystals involving large conformational changes, and provide useful spatiotemporal data for informing time-resolved crystallography experiments.

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Molecular mechanism of self-antigen recognition by the ligand binding domain of B cell inhibitory co-receptor CD72

Nobutaka Numoto1, Kunio Hirata2, Chizuru Akatsu3, Takeshi Tsubata3, Nobutoshi Ito1

1Department of Structural Biology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan; 2RIKEN SPring-8 Center, Hyogo, Japan; 3Department of Immunology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan

CD72 is an inhibitory co-receptor that negatively regulates B cell antigen receptor (BCR) signalling. The ligand-binding domain of CD72 at the extracellular region belongs to the C-type lectin-like domain (CTLD) superfamily. We have demonstrated that it recognizes the nuclear autoantigen Sm/RNP composed of proteins and RNA, and suppresses autoimmune diseases such as systemic lupus erythematosus [1]. The crystal structure of the ligand-binding domain of mouse CD72a, a lupus-resistant allele, has been determined at 1.2 Å resolution. Electrostatic potential analysis of the molecular surface of CD72a-CTLD suggest that charge distribution at the putative ligand-binding site may affect the binding affinity between CD72 and Sm/RNP.

We have determined the crystal structure of the ligand-binding domain of mouse CD72c, a lupus-susceptible allele with reduced affinity to Sm/RNP. The obtained crystals were large enough for X-ray diffraction experiments of about 200 µm cubic, but clusters of hundreds or thousands of microcrystals (Fig. 1). Development of the micro focus X-ray beam and rapid automated data collection [2] and processing [3] systems at SPring-8 enabled us to obtain a full data set that allowed the successful structure determination and refinement at 2.5 Å resolution (Fig. 2). We took 1,400 of small-wedge (10 degree) data from 14 crystals. The data were classified based on the unit-cell dimensions or correlation coefficient between data and merged to a full data set for structure determination. Analysis of the hierarchical clustering of the small-wedge data shows that the crystal packing varies along with the c-axis direction, but no significant conformational variations were observed among the crystal structures.

The obtained structure reveals that substitutions of amino acids at the ligand-binding site do cause the inversion of the charge distribution of the molecular surface as we hypothesized. Charge repulsion between CD72c-CTLD and strong negative charges of RNA of Sm/RNP would be the molecular mechanism of reduced affinity.

[1] Akatsu, C., Shinagawa, K., Numoto, N., Liu, Z., Ucar, A. K., Aslam, M., Phoon, S., Adachi, T., Furukawa, K., It,o N. & Tsubata, T. (2016) J. Exp. Med. 213,2691.

[2] Hirata, K., Yamashita, K., Ueno, G., Kawano, Y., Hasegawa, K., Kumasaka, T. & Yamamoto M. (2019) Acta Cryst. D75, 138.

[3] Yamashita, K., Hirata, K. & Yamamoto, M. (2018) Acta Cryst. D74, 441.

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2:45pm - 5:10pmMS-82: Handling of big data in crystallography
Location: 223-4
Session Chair: Wladek Minor
Session Chair: Brinda Vallat
 
2:45pm - 2:50pm

Introduction to session

Wladek Minor, Brinda Vallat



2:50pm - 3:20pm

IRRMC (https:// proteindiffraction.org): Impact on quality of structures in PDB

Marek Grabowski, Marcin Cymborowski, David Cooper, Wladek Minor

UNIVERSITY OF VIRGINIA, Charlottesville, United States of America

Preservation and public accessibility of primary experimental data are cornerstones necessary for the reproducibility of empirical sciences. Many crystallography journals recommend that authors of manuscripts presenting a crystal structure deposit their primary experimental data (X-ray diffraction images) to one of the dedicated resources created in recent years. We present the Integrated Resource for Reproducibility in Molecular Crystallography (IRRMC). In its first five years, several hundred crystallographers have deposited over 9000 datasets representing more than 5,700 diffraction experiments performed at over 60 different synchrotron beamlines or home sources all over the world. We describe several examples of the crucial role that diffraction data can play in improving previously determined protein structures. In addition to improving the resource and annotating and curating submitted data, we have been building a pipeline to extract or generate the metadata necessary for seamless, automated processing. Preliminary analysis shows that about 95% of the data received by our resource can be automatically reprocessed. A high rate of reprocessing success shows the feasibility of automated metadata extraction and automated processing as a validation step that ensures the correctness of raw diffraction images. The IRRMC is guided by the Findable, Accessible, Interoperable, and Reusable data management principles. Data from IRRMC have already enabled several novel research projects.

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3:20pm - 3:50pm

A Gold Standard for the archiving of macromolecular diffraction data

Herbert J. Bernstein1, Andreas Förster2, Aaron S. Brewster3, Graeme Winter4

1Ronin Institute for Independent Scholarship, c/o NSLS II, Brookhaven National Laboratory, Upton, NY, USA; 2DECTRIS Ltd., Täfernweg 1,5405 Baden-Dättwil, CH; 3Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA; 4Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK

Macromolecular crystallography (MX) is the dominant means of determining the three-dimensional structures of biological macromolecules. Over the last few decades, most MX data have been collected at synchrotron beamlines using a large number of different detectors produced by various manufacturers and taking advantage of various protocols and goniometry. These data came in their own formats, some proprietary, some open. The associated metadata rarely reached the degree of completeness required for data management according to Findability, Accessibility, Interoperability and Reusability (FAIR) principles. Efforts to reuse old data by other investigators or even by the original investigators some time later were often frustrated.

In the culmination of an effort dating back more than two decades, a large portion of the research community concerned with High Data-Rate Macromolecular Crystallography (HDRMX) agreed in 2020 to an updated specification of data and metadata for diffraction images produced at synchrotron light sources and X-ray free electron lasers (XFELs) [1]. This Gold Standard builds on the NeXus/HDF5 NXmx application definition and the International Union of Crystallography (IUCr) imgCIF/CBF dictionary and is compatible with major data processing programs and pipelines. It will ensure effortless automatic data processing, facilitate manual reprocessing of data independent of the facility at which they were collected, and enable data archiving according to FAIR principles, with a particular focus on interoperability and reusability.

Direct consequences of the Gold Standard are an unambiguous definition of the experimental geometry, a record of the synchrotron and beamline where the data were collected, and additional optional metadata that will make subsequent submission of the structural model to the PDB more straightforward. Just as with the IUCr CBF/imgCIF standard from which it arose and to which it is tied, the Gold Standard is intended to be applicable to all detectors used for crystallography. In particular, the application of the Gold Standard does not require the use of HDF5. Corresponding metadata definitions exist in CBF/imgCIF. All hardware and software developers in the field are encouraged to adopt and contribute to the standard.

The Gold Standard provides a convenient and consistent way to record the essential minimal data and metadata needed to process a wide range of macromolecular diffraction experiments including single axis, single crystal rotation experiments using single-module detectors, XFEL serial crystallography experiments using powerful multi-module detectors producing tens of thousands of images from huge numbers of small crystals, as well as synchrotron experiments producing large number of wedges from micro-crystals. Examples from all of these and more will be discussed.

[1] Bernstein, H.J., Förster, A., Bhowmick, A., Brewster, A.S., Brockhauser, S., Gelisio, L., Hall, D.R., Leonarski, F., Mariani, V., Santoni, G., Vonrhein, C. and Winter, G. (2020). Gold Standard for macromolecular crystallography diffraction data. IUCrJ, 7(5) 784 -- 792.

The work was supported in part by funding from Dectris Ltd., from the U. S. Department of Energy (BES KP1605010, KP1607011, DE-SC0012704), from the U. S. National Institutes of Health (NIGMS P30GM133893, R01GM117126).

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3:50pm - 4:15pm

Data evaluation on the fly: Auto-Rickshaw at the MX beamlines of the Australian Synchrotron

Santosh Panjikar

Australian Synchrotron, ANSTO, Clayton, Australia

Auto-Rickshaw [1,2] is a system for automated crystal structure determination. It provides computer coded decision-makers for successive and automated execution of a number of existing macromolecular crystallographic computer programs thus forming a software pipeline for automated and efficient crystal structure determination.

Auto-Rickshaw (AR) is freely accessible to the crystallography community through the EMBL-Hamburg AR Server [3].

Recently, it has been installed at the ASCI cluster at the Australian Synchrotron which uses Docker and Kubernetes system for launching AR jobs in high-throughtput manner. The synchrotron AR server is accessible to users from the MX beamline computers.

AR at the MX beamlines can be invoked through command line or a web-based graphical user interface (GUI) for data and parameter input and for monitoring the progress of structure determination. It can be also invoked via automatic data processing if the parameter inputs have been pre set at the AR-GUI during X-ray diffraction experiment.

A large number of possible structure solution paths are encoded in the system and the optimal path is selected as the structure solution evolves. The platform can carry out experimental (SAD, SIRAS, RIP or various MAD) and MR phasing or combination of experimental and MR phasing. The system has extended extensively for evaluation of multiple datasets for various phasing protocols as well as for evaluation of ligand binding and fragment screening.

The new implementation and features will be discussed during the presentation.

References

[1] Panjikar, S., Parthasarathy, V., Lamzin, V. S., Weiss, M. S. & Tucker, P. A. (2005). Auto-Rickshaw - An automated crystal structure determination platform as an efficient tool for the validation of an X-ray diffraction experiment. Acta Cryst. D61, 449-457.

[2] Panjikar, S., Parthasarathy, V., Lamzin, V. S., Weiss, M. S. & Tucker, P. A. (2009). On the combination of molecular replacement and single-wavelength anomalous diffraction phasing for automated structure determination Acta Cryst. D65,1089-1097.

[3] http://www.embl-hamburg.de/Auto-Rickshaw

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4:15pm - 4:40pm

Rapid response to biomedical challenges and threats

Wladek Minor1, Mariusz Jaskolski2, Alexander Wlodawer3, Zbigniew Dauter3, Joanna Macnar4, Dariusz Brzezinski5, David Cooper1, Marcin Kowiel7, Miroslaw Gilski2, Ivan Shabalin1, Marek Grabowski1, Bernhard Rupp6

1University of Virginia, Charlottesville, United States of America; 2A. Mickiewicz University, Poznan, Poland; 3National Cancer Institute, United States of America; 4University of Warsaw, Warsaw, Poland; 5Poznan University of Technology, Poznan, Poland; 6k.-k Hofkristallamt, United States of America; 7Polish Academy of Sciences, Poland

Structural information, mainly derived by X-ray crystallography and Cryo-Electron Microscopy, is the quintessential prerequisite for structural-guided drug discovery. However, accurate structural information is only one piece of information necessary to understand the big picture of medical disorders. To provide a rapid response to emerging biomedical challenges and threats like COVID-19, we need to analyze medical data in the context of other in-vitro and in-vivo experimental results. Recent advancements in biochemical, spectroscopical, and bioinformatics methods may revolutionize drug discovery, albeit only when these data are combined and analyzed with effective data management framework like Advanced Information System proposed in 2017. The progress on AIS is too slow, but creating such a system is a Grand Challenge for biomedical sciences. By definition, a Grand Challenge is a challenging and extremely difficult long-term project that is not always appreciated by those looking for immediate returns.

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4:40pm - 5:05pm

Development of an on-the-fly data processing with information-lossless compression for CITIUS detectors at SPring-8

Toshiyuki Nishiyama Hiraki1, Toshinori Abe1,2, Mitsuhiro Yamaga1,2, Takashi Sugimoto1,2, Kyosuke Ozaki1, Yoshiaki Honjo1, Yasumasa Joti1,2, Takaki Hatsui1

1RIKEN SPring-8 Center, Hyogo, Japan; 2Japan Synchrotron Radiation Research Institute, Hyogo, Japan

Diffraction-limited synchrotron radiation sources (DLSRs) using the advanced accelerator technologies deliver high-brilliance X-rays at high repetition rates. The DLSRs are expected to provide X-ray diffraction (XRD) measurements with benefits such as a reduction of the total time required for a complete scan and an improvement of temporal resolution. At the proposed SPring-8-II facility [1], one of the DLSRs, anticipated experiments using XRD techniques require X-ray imaging detectors with a frame rate over 10 kHz, high pixel count, a count rate over 100 Mcps/pixel, and single-photon sensitivity. To meet these demands, we have been developing a high-speed X-ray imaging detector CITIUS (Charge Integration Type Imaging Unit with high-Speed extended-Dynamic-Range Detector) [2] for SPring-8 and SACLA. As for SPring-8, our first milestone is to install a 20M-pixel CITIUS detector in 2023. It has a frame rate of 17.4 kHz and a raw data rate of 1.4 TB/s. Such a high raw data rate demands the careful design of the data handling scheme from the transfer, on-the-fly processing, storage, to post-analysis.

In this presentation, we describe our plan on the data acquisition and analysis scheme and the current status of the development. Our baseline implementation of the data-processing flow is composed of two steps. At the first step, detector images are processed by on-the-fly processing such as accumulation and a veto mechanism, which reduces the peak data-stream rate from 1.4 TB/s to ~400 GB/s. The processing algorithms are implemented onto custom PCB boards (Data Framing Board, DFB). Each DFB has three field-programmable gate arrays (FPGAs). Then generated processed data are transferred via PCI Express 3.0 bus to PC server memory. The second step is to compress the images by PC servers. We are investigating several information-lossless compression algorithms including the one presented in [3]. The peak data rate after the compression is further reduced to ~10 GB/s. The compressed images are to be stored in cache storage with a capacity of about 4-day measurements. The cached data are transferred to the high-performance computing system for post-analysis, and long-term storage. We also present the results of the experiment using an X-ray photon correlation spectroscopy technique. We also present the infrastructure in detail to execute this flow.

[1] “SPring-8-II Conceptual Design Report” (Nov. 2014) http://rsc.riken.jp/eng/pdf/SPring-8-II.pdf. [2] T. Hatsui, “New opportunities in photon science with high-speed X-ray imaging detector Citius, and associated data challenge”, Presentation at the 2nd R-CCS International Symposium (2020) [3] R. Roy et al., the proceedings of CCGrid2021, accepted.

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2:45pm - 5:10pmMS-83: High pressure crystallography
Location: Terrace 2A
Session Chair: Lars Ehm
Session Chair: Jon Henry Eggert
Session Chair: Vitali Prakapenka
Session Chair: Przemyslaw Dera

Merged sessions
Invited: June Wicks (USA)Rachel Husband (Germany)

 
2:45pm - 2:50pm

Introduction to session

Lars Ehm, Jon Henry Eggert, Vitali Prakapenka, Przemyslaw Dera



2:50pm - 3:20pm

Experimental measures of the orientation dependence of the B1-B2 transformation in shock-compressed MgO

June Ki Wicks

Johns Hopkins University, Baltimore, United States of America

Of the over 6,000 confirmed and candidate extrasolar planets discovered to date, those 1-4 times the radius of the Earth are found to be most abundant. MgO (periclase), is expected to be a major component of the deep mantles of terrestrial planets and exoplanets. Its high-pressure transformation from a rocksalt (B1) structure to the B2 (CsCl) structure is expected to occur in rocky exoplanets greater than about 5 Earth masses in size. In this work, the structure and temperature of MgO upon shock compression over the 200-700 GPa pressure range was examined at the Omega-EP Laser facility. Laser drives of up to 2 kJ over 10 ns were used to shock compress single-crystal MgO. At peak compression, the sample was probed with He-α X-rays from a laser-plasma source. Diffracted X-rays were recorded on image plates lining the inner walls of a box attached to the target package. For each shot we measure pressure (velocity interferometry), density (x-ray diffraction) and shock temperature (pyrometry). We also probe orientation-dependence of the shock Hugoniot by conducting laser-driven decaying shock measurements of single crystal MgO [100], [111] and [110], and will discuss the importance of single crystal experiments to better improve phase diagram models of materials at extreme conditions.

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3:20pm - 3:50pm

Simultaneous imaging and diffraction of phase transitions at intermediate compression rates

Rachel J. Husband1, Zsolt Jenei2, Johannes Hagemann1, Earl F. O'Bannon2, William J. Evans2, Andreas Schropp1, Konstantin Glazyrin1, Hanns-Peter Liermann1

1DESY, Notkestrasse 85, 2260 Hamburg, Germany; 2Lawrence Livermore National Laboratory, 7000 East Avenue, L-041 Livermore, CA 94550, USA

Fast compression in the dynamic diamond anvil cell (dDAC) allows for the study of materials at intermediate strain rates that are not accessible using traditional static and dynamic compression techniques [1]. Previous dDAC studies revealed compression-rate dependent phenomena such as rate-dependent phase transformation pathways [2], the formation of metastable phases [3], and shifts in phase transition boundaries from their equilibrium positions [2,3,4]. The fast diffraction set-up at the Extreme Conditions Beamline (P02.2) at PETRA-III offers time-resolved X-ray diffraction with kHz data collection rates, which allows for phase transition boundaries to be accurately determined at compression rates up to ~1000 GPa/s. Future experiments at the European XFEL will allow for data collection rates up to 4.5 MHz, which will extend these studies to compression rates >100 TPa/s.

In order to develop a full understanding of phase transitions under dynamic compression, it is necessary to investigate sample behaviour on both atomistic (crystal structure) and microscopic (crystal morphology) length scales. This allows for kinetic parameters such as nucleation and growth rates to be determined. When crystallite of the high pressure phase have well-defined phase boundaries, imaging techniques can be used to visualize the growth of the new phase. The X-ray phase contrast imaging platform at P02.2 allows for the visualization of samples that are opaque to visible light, where the simultaneous X-ray diffraction measurements allow for pressure determination, phase identification, and structural refinement. Phase contrast imaging allows us to resolve phase boundaries for grains of similar Z, where conventional absorption-based imaging typically fails.

Here, we present results from X-ray imaging experiments on dynamically-compressed Ga (Fig. 1), where we have successfully imaged pressure-induced melting (Ga-I/liquid) and solidification (liquid/Ga-III). Using an imaging configuration in which the sample is positioned upstream from the focal spot of a CRL-focussed X-ray beam allows for the collection of ‘clean’ diffraction patterns with minimal contribution from the gasket material, and produces clearly-defined solid/liquid phase boundaries in the X-ray images.

[1] Jenei, Zs. et al. Rev. Sci. Instrum. 90, 065114 (2019). [2] Lee, G. W., Evans, W. J. & Yoo, C. S. Phys. Rev. B 74, 134112 (2006). [3] Chen, J. Y & Yoo, C. S. PNAS 108 7685-7688 (2011). [4] Husband. R. J. et al. ‘Compression-rate dependence of pressure-induced phase transitions in Bi’, submitted.

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3:50pm - 4:10pm

Phase Changes in Dynamically Compressed Water

Michael G Stevenson1, Lisa M V Zinta1, Benjamin Heuser1, Zhiyu He1, Divyanshu Rajan1, Mandy Bethkenhagen1, Martin French1, Armin Bergermann1, Ronald Redmer1, Thomas Cowan2, Oliver Humphries2, Julian Lütgert2, Katja Voigt2, Anja Schuster2, Tommaso Vinci3, Emma E McBride4, Nicholas J Hartley4, Arianna Gleason- Holbrook4, Siegfried Glenzer4, Silvia Pandolfi4, Adrien Descamps4, Benjamin Ofori-Okai4, Christopher Schoenwaelder4, Griffin Glenn4, Luke B Fletcher4, Bob Nagler4, Hae Ja Lee4, Eric Galtier4, Dimitri Khaghani4, Jean-Alexis Hernandez5, Alessandra Ravasio3, Dominik Kraus1,2

1University of Rostock, Rostock, Germany; 2Helmholtz-Zentrum Dresden-Rossendorf, Dresden, Germany; 3Laboratoire LULI, Ecole Polytechnique, Palaiseau, France; 4SLAC National Accelerator Laboratory, Menlo Park, USA; 5University of Oslo, Oslo, Norwa

Extreme conditions are ubiquitous in nature. Much of the matter in the universe exists under high pressures and temperatures. Of interest, are the planetary interiors of the icy giants, Uranus and Neptune. Which have particularly complex magnetic fields [1].

To understand these complex magnetic fields the conditions and composition of icy giant planetary interiors need to be determined. The interiors of these planets are understood to contain mixtures of water, ammonia and hydrocarbons [2].

Under compression the phase diagram of ice is rather complex. With several phases determined and predicted under high pressure and temperature conditions [3]. High pressure ice above ~1500K and 50 GPa is predicted to undergo a superionic transition, where the hydrogen atoms diffuse into the oxygen sub- lattice [4,5]. These superionic phases are a possible source of the complex magnetic fields of both Uranus and Neptune.

Several high-pressure phases of water have been observed in the superionic region of the phase diagram. A body-centred cubic (bcc) phase, which if superionic would be analogous to ice X structure and with increasing pressure a phase transition to a face centred cubic (fcc) phase has been reported [5].

Experiments carried out at the MEC end station at the LCLS XFEL in December 2020, utilised reverberating shocks to compress water into Off-Hugoniot states within the superionic region of the ice phase diagram [6]. Liquid water samples were confined between a diamond ablator and a rear window, reaching P-T states ranging from ~40 GPa and 1200K to ~200 GPa and 4000K.

The bcc phase of ice has been observed from ~50 GPa and ~1200 K. A mixed phase region starting at ~90 GPa and ~2500 K, has been of observed with the bcc phase and a second phase. With increasing pressure the second phase becomes more prominent with the loss of the initial bcc phase.

The higher-pressure ice initially appears to be the fcc phase as described by Millot et al. However, further examination of the diffraction revealed misfits to the fcc lattice and a lack of refinement has suggested that that this may in fact be a different structure. The structure of this phase has yet to be determined. However, several candidates are proposed from predicted high pressure ices [7].

Ongoing work aims to determine these structures of ice under superionic P-T conditions and with comparison with simulation, understand the magnetic field behaviour of icy giant type planets.

Acknowledgements: The work was supported by the Helmholtz Association under VH-NG- 1141 and ERC-RA-0041. Use of the Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, is supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences under Contract No. DE-AC02-76SF00515. The MEC instrument is supported by the U.S. Department of Energy, Office of Science, Office of Fusion Energy Sciences under Contract No. SF00515.

[1] W.J. Nellis, J. Phys.: Conf. Ser. 950, 042046 (2017)

[2] M. D. Hofstadter et al., Ice Giants: Pre- Decadal Survey Mission Study Report, NASA-JPL report JPL-D-100520 (2017)

[3] C. G. Salzmann, J. Chem. Phys 150, 06091 (2019)
[4] I. A. Ryzhkin, Sol. Stat. Com. 56, 1 (1985)

[5] M. Millot et al., Nat. 569, 7755 (2019)

[6] M. Millot et al., Nat. Phys. 14, 3 (2018)

[7] A. Hermann et al., PNAS 109, 3 (2012)

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4:10pm - 4:30pm

Investigations of the high-pressure, high-temperature behaviour of Au using laser-driven dynamic compression

Amy Coleman, Raymond Smith, Tom Lockard, Damian Swift, James McNaney

Lawrence Livermore National Laboratory, Livermore, United States of America

Au has long been regarded as an important calibration standard in the high-pressure diffraction community, especially for experiments involving diamond anvil cells. The face centred cubic phase of Au is believe to be stable for hundreds of GPa at room temperature [1,2]. Recent dynamic-compression work has shown that the high-pressure behaviour of Au is not as simple at higher temperatures, and under laser-driven shock-compression, Au was found to transform, on-Hugoniot, from its ambient face centred cubic phase to a body centred cubic phase at 223 GPa before melting around 320 GPa [3].

As well as being used as a calibration standard, Au is also a commonly used material in target packages for laser-driven, dynamic-compression experiments. For experiments that explore the behaviour of various materials at the highest pressures and temperatures achievable (such as the experiments conducted at the National Ignition Facility or at the Omega laser facility) a layer of Au may be placed before the material of interest to act as a shield to prevent x-ray heating of the material of interest before the compression wave has reached the sample. For many of these experiments, the compression wave is not necessarily a shock wave, but the target may instead be ramp-compressed meaning that the compression state does not lie on the Hugoniot.

Given the frequent use of Au in diffraction experiments at extreme conditions, it is important that its high-pressure, high-temperature behaviour is well constrained off-Hugoniot so that we may correctly identify its contribution to diffraction data collected in this regime. To this end, a series of shock and ramp compression experiments have been conducted across various laser-compression platforms to explore the extent of the high-pressure bcc phase of Au. These experiments involve the compression of Au to previously unexplored pressures and temperatures, utilizing diffraction and velocity interferometry as the primary diagnostics. This talk presents a discussion of these results and reconciles this new, unpublished data with existing findings within the field.

This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.

[1] Dubrovinsky, L., Dubrovinskaia, N., et al. (2007). Phys. Rev. Lett. 98, 045503
[2] Boettger, J.C. (2003) Phys. Rev. B. 67, 174107
[3] Briggs, R.J., et al., (2019) Phys. Rev. Lett. 123, 045701

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4:30pm - 4:50pm

Mineral inclusions as models to characterize deviatoric stress in single crystals

Marta Morana1, Ross J. Angel2, Alice Girani1, Mara Murri1, Frederico Alabarse3, Matteo Alvaro1

1University of Pavia, Pavia, Italy; 2Istituto di Geoscienze e Georisorse, Padua, Italy; 3Elettra Sincrotrone, Basovizza, Trieste, Italy

Non-hydrostatic stress is known to change the evolution of unit cell parameters [1] and the compression of bond lengths and angles in the structures of crystals, e.g. [2]. The resulting modifications in the structures can lead to changes in the physical and thermodynamic properties of crystals, and thus change their thermodynamic stability. As a consequence, both reconstructive phase transitions [3] and displacive-type symmetry-breaking phase transitions [4] under deviatoric stress can occur at different temperatures and different mean stress than under hydrostatic pressure. Despite its importance, the effect of non-hydrostatic stress on crystal structures is still poorly understood, because it is challenging to perform experiments under controlled deviatoric stress conditions. On the other hand, mineral host-inclusion systems composed of a mineral entrapped inside another mineral provide the perfect example to characterize a crystal under deviatoric stress. Because the inclusion is entrapped inside another crystal, it will not be under hydrostatic pressure and the deviatoric stress imposed on it will be the result of the difference in the elastic properties of the two crystals and their mutual crystallographic orientations. In this contribution, we describe a methodology to characterize the effect of deviatoric stress on inclusion crystal structures using synchrotron x-ray diffraction, including how to deal with the experimental challenges in the collection of intensity data from a host-inclusion system, and the evaluation of the quality of the results. The quartz in garnet system is an ideal candidate for this study. Quartz has a simple and well-known structure, whose variation with pressure and temperature has been widely characterised, while garnet, being cubic, imposes an almost isotropic strain on the inclusions, thus providing a relatively simple case study. Furthermore, quartz is one of the most common mineral inclusions in different types of rocks, so it qualifies as an interesting case for geological applications.

[1] Bassett, W. A. (2006). J. Phys.: Condens-Mat., 18(25), S921.
[2] Gatta, G. D., Kantor, I., Ballaran, T. B., Dubrovinsky, L., & McCammon, C. (2007). Effect of non-hydrostatic conditions on the elastic behaviour of magnetite: an in situ single-crystal X-ray diffraction study. Phys, Chem. Miner., 34(9), 627-635.
[3] Richter B., Stünitz H. & Heilbronner R. (2016) J. Geophys. Res. -Solid Earth, 121, 8015-8033.
[4] Bismayer U., Salje E. & Joffrin C. (1982) J. Phys., 43, 1379-1388.

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4:50pm - 5:10pm

High-pressure low-temperature phase transitions and structural development in quasi-two-dimensional transition metal oxychlorides

Achim Mathias Schaller1, Maxim Bykov2,3, Elena Bykova2, Konstantin Glazyrin4, Sander van Smaalen1

1University of Bayreuth, Laboratory of Crystallography, Bayreuth, Germany; 2Carnegie Institution of Washington, Geophysical Laboratory, Washington DC, USA; 3Howard University, Washington DC, USA; 4Photon Sciences, Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany

The strong interest in MOCl (M = Ti, V, Cr, Fe) compounds stems from their nonlinear optical properties in the IR band (CrOCl) [1], their use as intercalation compounds for cathode materials (FeOCl) [2], their use as parent structures for van der Waals heterostructures [3] and especially from their low-dimensional magnetic phenomena [4-6].

MOCl-type compounds are isostructural at ambient conditions with the space group Pmmn and consist of double layers of distorted MO4Cl2 octahedra, which are connected by van der Waals forces. It has been shown that the magnetic behaviour and the dimensionality of MOCl-type compounds is determined by orbital order of the 3d electron of the transition metal [4-6]. For M = V, Cr, Fe orbital order leads to strong intra- and interchain exchange couplings, which results in quasi-two-dimensional (2D) magnetic systems that exhibit antiferromagnetic (AFM) order at low temperatures [4,5]. The transition to the AFM state is characterized by a magneto-elastic coupling in the form of a monoclinic lattice distortion that lifts the geometric frustration of the magnetic order on the orthorhombic crystal structure as well as by the formation of an incommensurate modulation of the structure [4,5].

Applying hydrostatic pressure to those compounds allows us to continuously adjust the intra- and interchain exchange parameters through the modification of the octahedral geometry and the metal-to-metal distances. This provides a unique opportunity to study the interplay between magnetic order and pressure-induced structural changes in dependence of the electronic configuration of the transition metal within one single structure type. Pressurizing MOCl compounds to approximately 15 GPa leads to a normal-to-incommensurate phase transition, characterized by an optimization of the interlayer packing, which is not associated with changes in the electronic or magnetic structure [7]. This gives us, in addition, the possibility to investigate the effect of the high-pressure structural transition on the magnetic order and vice versa.

The high-pressure (HP) low-temperature (LT) single crystal X-ray diffraction experiments, which were conducted at P02.2/PETRA III above and below TN,1bar for pressures up to 40 GPa and temperatures down to 6 K, provides an insight into the HP-LT mechanisms of FeOCl: The magneto-elastic coupling is governed by a monoclinic lattice distortion below TN,1bar, whereas an interplay between lattice distortion and significant structural changes takes place above TN,1bar. These changes enhance, from a geometrical perspective, superexchange interactions up to a pressure of ≈ 15 GPa where the structural HP phase transition gets superimposed on the further structural development. We will present the sequence of phase transitions and the structural development of FeOCl in detail and compare it, where applicable, with the quasi-2D compound CrOCl.

With the described approach and an in-depth analysis of structural changes, we aim at disentangling the magneto-structural correlations in the model system of MOCl as a function of composition, temperature and pressure in order to facilitate the understanding of low-dimensional magnetic systems in general.

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2:45pm - 5:10pmMS-85: Science meets art: Crystallography and cultural heritage
Location: Club H
Session Chair: Alicja Rafalska-Lasocha
Session Chair: Petr Bezdicka

Invited: Koen Janssens (Belgium), Sebastian Bette (Germany)

 
2:45pm - 2:50pm

Introduction to session

Alicja Rafalska-Lasocha, Petr Bezdička



2:50pm - 3:20pm

Fingerprinting Natural Ultramarine in 15th-17th century Netherlandish paintings

Koen Henri JANSSENS1,4, Steven De Meyer1, Stijn Legrand1, Frederik Vanmeert1,2, Veronique Buecken3, Annelies van Loon4, Katrien Keune4

1University of Antwerp, Antwerp, Belgium; 2Royal Institute for Cultural Heritage, Brussels, Belgium; 3Fine Arts Museum, Brussels, Belgium; 4Rijksmuseum, Amsterdam, The Netherlands

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

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

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

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

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

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

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

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

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

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

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

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

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

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3:20pm - 3:50pm

The variety of calcium bearing efflorescence phases - An explanation by crystal chemistry

Sebastian Bette1,2, Gerhard Eggert2, Robert E. Dinnebier1

1Max-Planck-Institute for Solid State Research, Stuttgart, Germany; 2State Academy of Art and Design, Stuttgart, Germany

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

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

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

References

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

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

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

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

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

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

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

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

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

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

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

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

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3:50pm - 4:10pm

Why is heptagonal symmetry so rare in art and architecture?

Arie van der Lee

Institut Européen des Membranes, Université de Montpellier, ENSCM, CNRS, Montpellier, France

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

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4:10pm - 4:30pm

Crystallography vs. human masterpiece: Li20Mg6Cu13Al42, Mg9Ni6Ga14 and Mg3Ni2Ga structures vs. ivory puzzle balls

Grygoriy Dmytriv1, Nazar Pavlyuk1, Volodymyr Pavlyuk1,2, Helmut Ehrenberg3

1Ivan Franko National University of Lviv, Lviv, Ukraine; 2Częstochowa Jan Długosz University, Częstochowa, Poland; 3Karlsruhe Institute of Technology, Karlsruhe, Germany

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

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

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

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

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

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

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

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4:30pm - 4:50pm

Information theory based symmetry classifications of more or less 2D periodic patterns in Islamic building ornaments and Hans Hinterreiter’s graphic art

Peter Moeck

Portland State University, PORTLAND, Oregon, USA

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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4:50pm - 5:10pm

Laboratory X-ray powder diffraction as a useful tool for identification of pigments and degradation products in portrait miniatures painted on ivory

Eva Kočí1, Petr Bezdička1, Silvia Garrappa1, David Hradil1, Janka Hradilová2, Michal Pech2

1Institute of Inorganic chemistry of the Czech Academy of Sciences, ALMA Laboratory, Husinec-Řež 1001, 250 68 Husinec-Řež, Czech Republic; 2Academy of Fine Arts in Prague, ALMA Laboratory, Veletržní 65, 170 00 Praha 7, Czech Republic

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

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

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

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

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

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

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2:45pm - 5:10pmMS-86: Modular structure of inorganic and mineral compounds
Location: Club D
Session Chair: Isabella Pignatelli
Session Chair: Berthold Stöger

Invited: Olivier Perez (France), Marie Colmont (France)

 
2:45pm - 2:50pm

Introduction to session

Isabella Pignatelli, Berthold Stöger



2:50pm - 3:20pm

Designing Composite Spin Chain Structures Built up of Dimeric and Trimeric Polyhedral Units: The oxides A1+y[(Mn1-xCox)1-zz]O3 (A=Ca, Sr; x = 3/8).

Olivier Perez1, Vincent Caignaert1, Bernard Raveau1, Vincent Hardy Hardy1, Nahed Sakly1, MD Motin Seikh2

1CRISMAT, CNRS-ENSICAEN,6 Bd du Maréchal Juin, 14050 Caen Cedex, France; 2Department of Chemistry, Visva-Bharati University, Santiniketan 731235, West Bengal, India

Spin chain oxides containing cobalt and manganese whose structure is closely related to the 2H hexagonal perovskite [1-5] offer a very attractive field for the investigation of magnetic and multiferroic properties. The structure of the prototypic one-dimensional manganate and cobaltate Sr4Mn2CoO9 consists of chains of face-sharing MnO6 octahedra and trigonal CoO6 prisms. According to the very important study performed by Perez-Mato et al [2], these spin chain oxides can be described as a composite 2H hexagonal perovskite family A1+x(Mn1-Cox)O3. Recently the possibility of extra oxygen incorporation during synthesis has been evidenced leading to a large family aperiodic chain structures [6] expressed by the simple formal formula Sr1+x(Mn1-xCox)O3+δ; it induces a decrease of the proportion of the number of trigonal prismatic sites (NP) with respect to the octahedral sites (NO) within the chains as δ increases and concomitantly the formation of cobalt vacancies on the trigonal prismatic sites. Therefore the structural formula of these oxides must be expressed as Sr1+y[(Mn1-xCox)1-zz]O3.]

The air-synthesized oxide x=3/8-Sr1+x(Mn1-xCox)O3+δ is of great interest, since by decreasing the oxygen over stoichiometry to δ=0, one should obtain the oxide “Sr11Mn5Co3O24”(x=y, z=0) expected to be built up of trimeric and dimeric polyhedral units according to the sequence [Sr4Mn2CoO9]2.[Sr3CoMnO6]. Such an oxide containing exclusively strontium was never synthesized in air due to the partial oxidation of Co2+ into Co3+, imposing δ>0. We then have investigated the substitution of calcium for strontium in the pure Sr-phase x=3/8 (δ~0.09). The objective was to design composite structures built up of trimeric and dimeric units by decreasing δ down to zero through Ca for Sr substitution in order to finally obtain the stoichiometric oxide A11Mn5Co3O24 (A=Sr,Ca). We report herein on a series of A11/8(Mn5/8Co3/8)O3+δ oxides with composite structures, commensurate or incommensurate, built up of trimeric M3O9 and dimeric M2O6 units (M= Mn, Co, o) with cationic vacancies on the trigonal prismatic sites. We also show the possibility to synthesize the quasi commensurate stoichiometric composite Sr4.2Ca6.8[Mn2CoO9]2.[MnCoO6] (δ=0.002).

[1] J. Darriet, M.A. Subramanian, J. Mater. Chem. 5 (1995) 543-552.

[2] J.M. Perez-Mato, M. Zakhour-Nakhl, F. Weill, J. Darriet, J. Mater. Chem. 9 (1999) 2795-2807.

[3] K. Boulahya, M. Parras, J.M. Gonzalez-Calbet, J. Solid State Chem. 145 (1999) 116-127.

[4] K.E. Stitzer, J. Darriet, H.-C. zur Loye, Curr. Opin. Solid State Mater. Sci. 5 (2001) 535-544.

[5] H.-C. zur Loye, Q. Zhao, D.E. Bugaris, W.M. Chance, Cryst. Eng. Commun. 14 (2012) 23-39.

[6] Caignaert V, Perez O, Boullay P, Seikh MM, Sakly N, Hardy V, Raveau B, J. of Mater Chem. C 8 (2020) 14559-14569

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3:20pm - 3:50pm

Diffraction enhancement of symmetry and modular structures

Akihiro UMAYAHARA1,2, Bernd Souvignier1, Massimo Nespolo2

1Radboud University, Faculty of Science, Mathematics and Computing Science, Institute for Mathematics, Astrophysics and Particle Physics. Postbus 9010, 6500 GL Nijmegen, The Netherlands.; 2Université de Lorraine, Vandoeuvre lès Nancy, France

Diffraction enhancement of symmetry (DES) is a phenomenon by which the space-group symmetry suggested by the diffraction pattern of a crystal is higher than the space-group symmetry of the structure that has produced it [1-5]. The most well-known example is that of Friedel’s law, which is however realized only when resonant scattering is not taken into account. In modular structures, DES does occur also when considering resonant scattering. We address this phenomenon in monoarchetypal modular structures [6]. The condition for DES to occur is that both the module and the vector set (set of all interatomic vectors) [7] are invariant under an isometry that is not a symmetry operation for the structure. Only τ-isometries [8], i.e. isometries that do not reverse the polarity of the stacking vectors, can lead to DES once resonant scattering is taken into account. The example of SiC polytypes, where the phenomenon has been confirmed experimentally, is studied in detail. The SiC layer has symmetry p6mm (diperiodic group); the stacking of SiC layer leads to many polytypes, rapidly increasing in number with the number of layers defining the period along to stacking direction. These polytypes can occur in four types of space group: F-43m, R3m P63mc and P31m. If the vector set exhibits hexagonal symmetry, than the space group of the polytype can be either of type P63mc or of type P31m. In both cases, the diffraction pattern shows hexagonal symmetry although in the latter case the structural symmetry is only trigonal: DES is thus observed. The number of polytypes showing DES increases rapidly with the number of layers, but the fraction of these polytypes with respect to the total number of polytypes decreases. These conclusions apply as well to all modular structures built by layers of the same symmetry, like ZnS.

[1] Iwasaki, H. (1972). On the Diffraction Enhancement of Symmetry. Acta Cryst. A28, 253-260.

[2] Perez-Mato, J. M. and Iglesias, J.E. (1974). Acta Cryst. A33, 466-474.

[3] Sadanaga, R. and Ohsumi, K. (1975). Proc. Japan Acad. 51, 179-183.

[4] Sadanaga, R. and Ohsumi, K. (1979). Acta Cryst. A35, 115-122.

[5] Iglesias, J. E. (1979). Z. Kristallogr. 150, 279-285.

[6] Ferraris, G.. Makovicky E. and Merlino, S. (2008). Crystallography of Modular Materials. Oxford: Oxford University Press, 384 pp..

[7] Buerger, M. J. (1950). Acta Cryst. 3, 87-97.

[8] Dornberger-Schiff, K. and Grell-Niemann H. (1961). Acta Cryst. 14, 167-177.

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3:50pm - 4:15pm

Polytypism in cronstedtite; how various stacking sequences of layers affect diffraction pattern

Jiří Hybler

Institute of Physics of the Czech Academy of Sciences, Prague 8, Czech Republic

Polytypism in cronstedtite; how various stacking sequences of layers affect diffraction pattern Jiří Hybler1,

1Institute of Physics of the Czech Academy of Sciences, Na Slovance 2, CZ-18224 Prague 8, Czech Republic

hybler@fzu.cz

The 1:1 layered silicate cronstedtite (Fe2+3-x Fe3+x)(Si2-xFe3+x)O5(OH)4, of the serpentine-kaoline group forms relative large amount of polytypes. They are subdivided into four OD subfamilies, or Bailey’s groups A, B, C, D according to different stacking rules of identical (structure building) 1:1 layers (equivalents of OD packets) with trigonal protocell a=5.5, c=7.1 Å. Distributions of so called subfamily reflections along the reciprocal lattice rows [2l]* / [11l]* / [2l]* in (lhex)* / (hhlhex)* / (2hlhex)* planes of diffraction pattern is used for subfamily determination. Similarly, distributions of characteristic reflections along [10l]* / [01l]* / [1l]* rows in (h0lhex)* / (0klhex)* / (hlhex) planes allow determination of particular polytypes. For this purpose, graphical identification diagrams simulating distribution of reflections along named rows are used [1]. Owing modern diffractometers with area detectors and appropriate software, and/or Electron Diffraction Tomography (later EDT) technique, precession-like images of Reciprocal Space (later RS) sections corresponding to above listed planes can be easily and quickly obtained.

Lot of specimens of cronstedtite from various terrestrial localities and synthetic run products were studied by the author [1-5]. RS sections were recorded, and selected ones are presented in the lecture in order to demonstrate the variability of diffraction pattern.

In the subfamily A, the stacking rule comprises ±ai/3 shifts of consecutive layers. The most common is the 3T, relatively rare are 1M and 2M1 polytypes. They usually occur in 3T+1M, 3T+2M1, 1M+2M1 mixed crystals. Monoclinic polytypes might be affected by twinning by reticular merohedry with 120º rotation as twinning operation. Six-layer 6T2 and three-layer triclinic 3A polytypes are rare. Another possible twinning by 60º rotation changes obverse setting of the subset of subfamily reflections into the reverse one [1, 4].

In the subfamily D, the stacking rule is characterized by alternating 180º rotations of consecutive layers, combined by ±b/3 (of the orthohexagonal cell) or zero shifts. The most common polytypes are 2H1 and 2H2, occurring either isolated or in mixed crystals. Rarely, several six-layer polytypes were found. They usually occur in mixed crystals containing more polytypes, up to six! Diffraction patterns of such crystals are, of course, confusing. Fortunately, in many cases polytypes were isolated simply by cleaving crystals into smaller fragments, later studied separately. Hall et all. [6] derived 24 possible sequences of six-layer polytypes of subfamily D serpentines, valid also for cronstedtite. Their diffraction patterns were modelled, and compared with real RS sections. This simulation revealed, that five pairs of sequences (No. 4+6, 7+18, 8+10, 9+13, 11+12) provided identical diffraction patterns. Polytypes really found correspond to following sequences: 1 (Hall’s 6T1), 5 (proposed 6T3), 8+10 (6T5), 11+12 (6T4), 24 (6T6) (trigonal polytypes), 22 (6R1), 23 (6R2), (rhombohedral polytypes). The hexagonal polytype 6H2 corresponding to the sequence 14 was also found. However, the identical diffraction pattern can be produced by the obverse-reverse twin of the rhombohedral polytype 6R2 (sequence 23).

Mixed crystals of polytypes belonging to different subfamilies were rarely found. 1M+1T mixed crystal of subfamilies A and C, respectively, was identified by EDT in the synthetic material [1]. The C subfamily is characterized by mere ±b/3 or zero shifts, without any rotation. The mixed crystals of A+D subfamilies were found in some terrestrial samples. Sometimes, the A and D parts of such crystals were separated by cleaving into smaller fragments.

Many RS sections showed diffuse streaking of characteristic reflections along c* due to partial stacking disorder. In extreme cases, reciprocal lattice rows are completely replaced by diffuse streaks.

The total number of ascertained polytypes of cronstedtite, recognized in RS sections, is 15 (+ one questionable).

[1] Hybler, J., Klementová, M., Jarošová, M., Pignatelli, I., Mosser-Ruck, R., & Ďurovič, S. (2018). Clays and Clay Minerals 66, 379–402.

[2] Hybler, J., Sejkora, J., & Venclík, V. (2016). European Journal of Mineralogy, 28, 765–775.

[3] Pignatelli, I., Mugnaioli, E., Hybler, J., Mosser-Ruck, R., Cathelineau, M., & Michau, N. (2013). Clays and Clay Minerals 61, 277–289.

[4] Hybler, J., Števko, M., & Sejkora, J. (2017). European Journal of Mineralogy, 29, 91–99.

[5] Hybler, J., Dolníček, Z., Sejkora, J., & Števko, M., (2020). Clays and Clay Minerals 68, 632-645.

[6] Hall, S. H., Guggenheim, S., Moore, P., & Bailey, S. W. (1976). Canadian Mineralogist 14, 314-321.

Keywords: cronstedtite; polytypism; layer stacking; X-ray diffraction; electron diffraction tomography

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4:15pm - 4:40pm

Binary beryllium pnictides: ordered and disordered coloring variants of the diamond structure

Alexander Feige, Marvin Michak, Maxim Grauer, Daniel Günther, Lennart Staab, Christopher Benndorf, Oliver Oeckler

Leipzig University, Faculty of Chemistry and Mineralogy, Leipzig, Germany

Even after decades of solid-state research, there are intriguing binary systems lacking investigation, even exclusively with main group elements. For instance, there are significantly fewer investigations on beryllium compounds than on any other class of light-element materials, even though beryllium-containing phases feature interesting properties for basic and applied research.[1] Owing to its toxicity, efforts to understand the chemistry of Be are rather rare. However, the limited knowledge present promises a rich and unusual structural chemistry. The few results concerning Be compounds with group 15 elements include the disordered diamond-like structure of BeP2.[2] Yet, the true building blocks, i.e. the arrangement of polyphosphide anions, remained elusive with respect to the description of the average structure. Preliminary work on BeAs2 and BeSb2 indicates related structures for both compounds;[3] however, this information is only based on qualitative evaluation of powder X-ray diffraction data. Precise structural data require very accurate diffraction data due to the large difference in scattering factors. Despite the simple stoichiometry, a complete structural analysis proved difficult as the crystals obtained are by far too small for data collection using laboratory diffractometers. We now employed a combined approach using microfocused synchrotron radiation, electron diffraction and HRTEM.

Synchrotron data of a microcrystal of BeSb2 reveal a coloring variant of the cubic diamond structure (Fig. 1). The corresponding tetragonal superstructure contains twisted chains of Sb atoms interconnected by Be atoms with all atoms showing a distorted tetrahedral coordination. The conformation of the polyanion corresponds to the Ge substructure in Li~3AgGe2.[4] This indicates chemical bonding according to a Zintl phase with a “sulfur-like” Sb- polyanion (comparable to Ge2-). Yet, BeSb2 can also be viewed as a Grimm-Sommerfeld semiconductor with an average valence electron concentration of 4. Compared to Be13Sb, which features Be12 icosahedrons in analogy to the NaZn13 type, the bonding situation changes from quasi-molecular entities to typical semiconductors upon varying the relative Be content. Hypothetical intermediate structures may exhibit rather unusual chemical bonding.

For BeP2 and BeAs2, our investigations have confirmed the disordered diamond-like / sphalerite-like structures according to the average structures in literature, which can be refined in space group I41/amd.[2,3] Diffraction patterns (both with X-rays and electrons, Fig. 2) exhibit pronounced diffuse streaks that indicate stacking disorder. Synchrotron data were collected from microcrystallites on TEM grids that were pre-characterized by electron microscopy. Both the evaluation of synchrotron diffraction data and HRTEM imaging reveal the nature of the disorder and the local structure of the polyanions. Stacking probabilities were derived by simulation diffraction patterns. The degree of ordering varies: diffuse streaks can be almost uniform but, especially in the case of BeAs2, they may also approach a superstructure.

[1] M. R. Buchner, R. Pöttgen, H. Schmidbaur (2020). Z. Naturforsch. 75b, 403.

[2] P. L’Haridon, J. David, J. Lang, E. Parthé (1976). J. Solid State Chem. 19, 287.

[3] R. Gerardin, J. Aubry (1976). J. Solid State Chem. 17, 239.

[4] A. Henze, V. Hlukhyy, T. F. Fässler (2015). Inorg. Chem. 54, 1152.

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2:45pm - 5:10pmMS-87: Topological materials
Location: Terrace 2B
Session Chair: Yugui Yao
Session Chair: Wenhui Duan
Session Chair: Avadh B. Saxena

Invited: Tomasz Dietl (Poland)Xiang Li (China)

 
2:45pm - 2:50pm

Introduction to session

Catherine Pappas, Yugui Yao, Wenhui Duan, Avadh B Saxena



2:50pm - 3:20pm

Phase separations and nematicity of transition metal impurities

Tomasz Dietl1,2

1International Research Centre MagTop, Insitute of Physics, Polisha Academy of Sciences, Warsaw, Poland; 2WPI-Advanced Institute for Materials Research, Tohoku University, Sendai 980-8577, Japan

Phase separations and nematicity of transition metal impurities

Tomasz Dietl1,2

1International Research Centre MagTop, Institute of Physics, Polish Academy of Sciences, PL-02668 Warsaw, Poland

2WPI-Advanced Institute for Materials Research, Tohoku University, Sendai 980-8577, Japandietl@MagTop.ifpan.edu.pl

Semiconductors [1] and topological materials [2] doped with transition metal elements attract considerable attention due to the fascinating physics and nonospintronic functionalities associated with exchange coupling between band carries and localized spins. However, there is a growing amount of pieces of evidence that d-shells of magnetic impurities contribute also to bonding, which can affect their spatial distribution and modify key properties, such as magnetic ordering temperature [3]. It has recently been experimentally demonstrated that the resulting phase separation (spinodal decomposition) can be anisotropic and result in the hitherto puzzling rotational symmetry breaking (i.e., nematic characteristics) revealed in a certain class of dilute magnetic semiconductors [4]. This finding put in a new light a possible origin of nematicity in other systems, such as unconventional superconductors and modulation-doped semiconductor quantum wells, in which rotational symmetry breaking has so far been assigned to the unidirectional spontaneous ordering of spin, orbital or charge degrees of freedom.

[1] T. Dietl and H. Ohno, Rev. Mod. Phys. 86, 187–251 (2014).

[2] Y. Tokura, K. Yasuda, and A. Tsukazaki, Nature Rev. Phys. 1, 126–143 (2019).

[3] T. Dietl, K. Sato, T. Fukushima, A. Bonanni, M. Jamet, A. Barski, S. Kuroda, M. Tanaka, Phan Nam Hai, H. Katayama-Yoshida, Rev. Mod. Phys. 87, 1311–1376 (2015).

[4] Ye Yuan, R. Hübner, M. Birowska, Chi Xu, Mao Wang, S. Prucnal, R. Jakieła, K. Potzger, R. Böttger, S. Facsko, J. A. Majewski, M. Helm, M. Sawicki, Shengqiang Zhou, and T. Dietl, Phys. Rev. Materials 2, 114601 (2018).

Keywords: crystallographic phase separation, chemical phase separation, spinodal decomposition, nematicity, dilute magnetic semiconductors

This work has been supported by the Foundation for Polish Science through the IRA Programme financed by the EU within SG OP Programme.

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3:20pm - 3:50pm

Pressure-induced phase transitions and superconductivity in a black phosphorus single crystal

Xiang Li

Beijing Institute of Technology, Beijing, China, People's Republic of

A high-pressure study of a black phosphorus crystal leads to a rich phase diagram,
including a Lifshitz-type semiconductor-semimetal transition, a Weyl semimetal, and
superconductivity as well as structural phase transitions. Transport properties and
quantum oscillations under high pressure provide critically valuable information to
understand the physics behind these new phases. These properties have been measured
reliably under hydrostatic pressure and magnetic field with a large-volume apparatus.
Superconductivity in the A7 phase has been found to exhibit the largest
magnetoresistance effect in its normal state so far. The BCS superconductivity in the A7
phase as identified by the experiment can be accounted for by a first-principles
calculation.

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3:50pm - 4:10pm

Unconventional states and topological defects in Fe-langasite

Maxim V. Mostovoy, Evgenii O. Barts

Zernike Institute for Advanced Materials, University of Groningen, The Netherlands

Topology of defects in ordered states of matter is determined by dimensionality and symmetry properties of the order parameter. Larger number of variables needed to describe an ordered state gives rise to a greater diversity and complexity of topological defects, a prominent example being the A-phase of superfluid 3He. The order parameter describing non-collinear antiferromagnetic orders in the swedenborgite, CaBaCo2Fe2O7, and Fe-langasite, Ba3TaFe3Si24O14, is an SO(3) matrix [1,2]. The iron langasite spin lattice is built of triangles formed by antiferromagnetically coupled Fe3+-ions (S = 5/2). The orientation of three co-planar spins added into the zero total spin is described by three Euler angles. This amazing material is both chiral and magnetically frustrated. It shows a non-collinear 120o spin ordering at the scale of one unit cell, a spiral with a period of 7 lattice constants and complex spin superstructures at the scale of 1000 Å. Lifshitz invariants allowed by the lack of inversion symmetry give rise to interesting modulated magnetic phases and stabilize particle-like topological defects previously discussed in very different physical contexts, e.g. nuclear physics and superfluid 3He.

References:

[1] J. D. Reim, E. Rosén, O. Zaharko, M. Mostovoy, J. Robert, M. Valldor, and W. Schweika, Phys. Rev. B 97, 144402 (2018).

[2] M. Ramakrishnan et al., npj Quantum Materials 4, 60 (2019).

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4:10pm - 4:30pm

Magnetic excitations and structure of the topological semimetal YbMnSb2

Siobhan Maeve Tobin1, Jian-Rui Soh2, Hao Su3, Bachir Ouladdiaf4, Andrea Piovano4, Yang-Feng Guo3, Dharmalingam Prabhakaran1, Andrew Timothy Boothroyd1

1University of Oxford, Oxford, United Kingdom; 2Institute of Physics, École Polytechnique Fédéral de Lausanne, Switzerland; 3School of Physical Science and Technology, ShanghaiTech University, China; 4Institut Laue Langevin (ILL), France

Topological semimetals have high carrier mobility in the form of quasiparticles resembling relativistic fermions. Experimental realisations of magnetic topological semimetals are relatively thin on the ground. Here we probe both the magnetic structure and interactions of the topological semimetal candidate YbMnSb2 using neutron scattering.

YbMnSb2 belongs to the P4/nmm space group and shows evidence of a magnetic ordering transition involving the Mn moments at ~350 K [1]. This is a relatively high Néel temperature among the family of materials AMnSb2 (A = Ca, Sr, Ba, Yb, Eu), which has demonstrated characteristics of the topological semimetals. The quasi-2D plane formed by the Sb ‘square’ may host Weyl or Dirac fermions [1-3]. YbMnSb2 has previously been studied via quantum oscillations, magnetometry, optical spectroscopy, ab initio band structure calculations, and angle-resolved photon emission spectroscopy [1, 4, 5]. Interestingly, these studies reached different conclusions as to the magnetic structure of YbMnSb2, and hence its semimetal nature: the jury is out on whether it is a Dirac [4], nodal-line [5], or Weyl semimetal [1].

In this presentation I shall report the magnetic structure of YbMnSb2 found by neutron diffraction, which is different to any previously proposed structures: C-type antiferromagnetism with the spins pointing along the c axis. This magnetic structure is shared by YbMnBi2 [6]. Dirac physics is also seen in such AMnBi2 materials; however, Bi rather than Sb layersresults in stronger spin-orbit coupling. This widens the band gap at any nodes and makes the resulting quasiparticles more massive [1]. We have also measured the spin wave spectrum of YbMnSb2 and the results of this measurement will be described and compared with the spin dynamics in related materials. The implications for the topology of the electrons will be discussed.

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4:30pm - 4:50pm

Occupancy disorder and magnetism in tetradymite based topological insulators

Laura Christina Folkers1,2,3, Anna Isaeva3,4

1Technical University Dresden, Dresden, Germany; 2Institute for Solid State and Materials Physics, TU Dresden, Germany; 3Leibniz Institute for Solid State and Materials Research, Dresden, Germany; 4University of Amsterdam, Amsterdam, The Netherlands

Magnetic topological insulators (MTIs) are a hot topic of materials science, promising future availability of spintronics with low energy consumption, quantum computing and phenomena like the Quantized Anomalous Hall Effect (QAHE) [1-2]. MTIs are chemically and structurally akin to the original non-magnetic topological insulators. Of those, the tetradymites Bi2Te3 and Sb2Te3 have recently proven to allow the introduction of a third magnetic element resulting in magnetically active, topologically non-trivial compounds. A magnetic element can be incorporated either via substitution on the Bi/Sb position in (Bi, Sb)2Te3, or by adding a third element which introduces a new crystallographic site, resulting for example in MnBi2Te4. (Bi, Sb)2Te3 itself and all members of its family exhibit the rhombohedral Rm1 space group (No. 166) [2]. Therein interchanging sheets of Mn, (Bi, Sb) and Te build septuple layers with the central sheet being Mn (Wyckoff position 3a). Situated between the respective layers is a van der Waals gap (Fig. 1).

Our group was the first to successfully grow single crystals, and conduct an in depth study of the physical properties of MnBi2Te4 [4-5]. Single crystal diffraction experiments reported in that study showed intermixing of Mn and Bi and since then several studies have reported intermixing of the two elements (MnBi2.14Te3.96 [6], Mn1.01Bi1.99Te4 and Mn0.98Bi2.05Te4 [7]). While a lot of attention has been given to MnBi2Te4, MnSb2Te4 proved to be synthetically achievable too. Similar to MnBi2Te4, MnSb2Te4 features intermixing of Mn and Sb (Mn0.852Sb2.296Te4 [8]). For MnSb2Te4, a recent study by Murakami et al. uncovers the impact of finding a certain amount of the magnetic Mn on the position of the non-magnetic Sb [9]. According to their discoveries, this changes the magnetic order from antiferromagnetic to ferrimagnetic.

These compounds are known to react sensitively to synthesis procedure and tempering history. Hence, our studies aim at understanding the greater connection between synthesis aspects and the resulting structural and physical properties. More precisely we studied MnBi2Te4 and MnSb2Te4 containing various amounts of Mn and other analogues of these systems. In these studies we uncovered, that the magnetism in MnSb2Te4 is even more sensitive to annealing procedures than previously expected.

[1] Y. Ando, Journal of the Physical Society of Japan, (2013), 82, 102001

[2] I. I. Klimovskikh, M. M. Otrokov, D. Estyunin, et al., Quantum Materials, (2020), 54.

[3] Y. Feutelais, B. Legendre, N. Rodier, V. Agafonov, Materials Research Bulletin, (1993), 28, 591-596

[4] A. Zeugner, F. Nietschke, A. U. B. Wolter, et al., Chemistry of Materials, (2019), 31, 2795-2806.

[5] M. M. Otrokov, I. I. Klimovskikh, H. Bentmann, et al., Nature, (2019), 576, 416-422.

[6] H. Li, S. Liu, C. Liu, et al., Physical Chemistry Chemical Physics, (2020), 22, 556-563.

[7] M.-H. Du, J. Yan, V. R. Cooper, M. Eisenbach, Advanced Functional Materials, (2020), 2006516.

[8] L. Zhou, Z. Tan, D. Yan, et al., Physical Review B, (2020), 102, 85114.

[9] T. Murakami, Y. Nambu, T. Koretsune, et al., Physical Review B, (2019), 100, 195103.

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4:50pm - 5:10pm

Topological analysis of local heteropolyhedral substitutions in the eudialyte-related structures

Sergey Aksenov1,2, Natalia Kabanova1,3, Nikita Chukanov4,5, Vladislav Blatov3, Sergey Krivovichev6,7

1Laboratory of Nature-Inspired Technologies and Environmental Safety of the Arctic, Kola Science Centre, Russian Academy of Sciences, Apatity, Russian Federation; 2Geological Institute, Kola Science Centre, Russian Academy of Sciences, Apatity, Russian Federation; 3Samara Center for Theoretical Materials Science, Samara State Technical University, Samara, Russian Federation; 4Institute of Problems of Chemical Physics, Russian Academy of Sciences, Chernogolovka, Russian Federation; 5Faculty of Geology, Moscow State University, Vorobievy Gory, Moscow, Russian Federation; 6Nanomaterials Research Centre, Kola Science Center, Russian Academy of Sciences, Apatity, Russian Federation; 7Department of Crystallography, Institute of Earth Sciences, St Petersburg State University, St Petersburg, Russian Federation

Eudialyte-group minerals (EGMs) are of a scientific and industrial interest as important concentrators of rare and strategic elements (mainly, Zr and REE) in agpaitic alkaline rocks. The general crystal chemical formula of EGMs is [N(1)3N(2)3N(3)3N(4)3N(5)3]{M(1)6M(2)3M(3)M(4)Z3(Si9O27-3x(OH)3x)2(Si3O9)2Ø0–6}X(1)X(2) where M(1) = VICa, VIMn2+, VIREE, VINa, VIFe2+; M(2) = IV,VFe2+, V,VIFe3+, V,VIMn2+, V,VINa, IV,VZr; M(3) and M(4) = IVSi, VINb, VITi, VIW6+; Z = VIZr, VITi; Ø = O, OH; N(1)–N(5) are extra-framework cations (Na, Н3О+, K, Sr, REE, Ba, Mn2+, Ca) or H2O; X(1) and X(2) are extra-framework water molecules, halide (Cl, F) and chalcogenide (S2–) anions, and anionic groups (CO32–, SO42–); x = 0–1 (Rastsvetaeva & Chukanov, 2012).

The crystal structure of EGMs is based on a heteropolyhedral framework (Chukanov et al., 2004) which makes these minerals similar to zeolite-like materials and molecular sieves. The first topological analysis of the eudialyte-type structures (eudialyte, kentbrooksite, oneillite, and khomyakovite) was performed using the approach of coordination sequences {Nk} (k = 1–12), using the representation of crystal structure as a finite ‘reduced’ graph (Ilyushin & Blatov, 2002). As an invariant of the eudialyte-type structure and its derivatives the MT-layer [Zr3Si24O72]∞∞ (PBU: primary building unit, an elementary component of an MT-framework) was chosen.

Topological analysis of the heteropolyhedral MT-framework in the eudialyte-type structure and its derivatives was performed based on a natural tiling (Blatov et al., 2007) (partition of the crystal space by the smallest cage-like units) analysis of the 3D cation nets using the ToposPro software (Blatov et al., 2014). According to the modern topological classification, it is necessary to use the standard representation to determine the topological type of the net. For the topological analysis carried out in this work, atomic nets for each of the 12 structure types were simplified and the corresponding underlying nets, which characterize the connectivity of the primary structural units as well as their point symbols, were obtained. The 0-1-2-free representation was used for topological analysis of cages within the tiling approach because it represented the cages in more detail. To analyze the migration paths of sodium cations in these structures, the Voronoi method was used.

The parental eudialyte-type MT-framework is formed by isolated ZO6 octahedra, six-membered [M(1)6O24] ring of edge-shared M(1)O6 octahedra, and two types of rings of tretrahedra, [Si3O9] and [Si9O27]. Different occupancies of additional M(2), M(3), and M(4) sites with variable coordination numbers by Q, T*, and M* cations, respectively, result in 12 types of the MT-framework. Corresponding point symbols for the cationic 3D-nets of the MT-frameworks as well as tiles’ sequences have been calculated.

Based on the results of natural tilings calculations as well as theoretical analysis of migration paths, it was found that Na+ ions can migrate through six- and seven-membered rings, while all other rings are too small. In eight types of the MT-frameworks, Na+-ion migration and diffusion is possible at standard temperature and pressure, while in four other types cages are connected by narrow gaps and, as a result, the Na+ diffusion in them is complicated at ambient conditions but may be possible either at higher temperatures or under mild geological conditions during long times. This conclusion is in a good agreement with numerous examples of the transformation of initial EGMs into their hydrated Na-deficient counterparts as a result of natural processes of sodium leaching and hydrolysis under hydrothermal conditions.

The relationships between heteropolyhedral substitutions and topological features of the derivative framework structures have been also discussed for alluaudite supergroup (Aksenov et al., 2021) minerals and related synthetic compounds. However, in the case of eudialyte-type structures such relationships look more complicated because of multiple variants of their derivative structures. Moreover, in the case of so-called “megaeudialytes” (Rastsvetaeva et al., 2012), i.e. EGMs which are characterized by modular structures and doubling of the c parameter (c ~ 60 Å), different modules regularly alternating in the structure can represent different types of the framework, which increases the amount of topological variations. Similar influence of modularity on the topological features of zirconium silicates have been described for the lovozerite-type structures (Pekov et al., 2009), where different ways of stacking of the lovozerite modules define the unit cell parameters, symmetry, and topology of the derivative structures (Krivovichev, 2015).

This work was financially supported by the Russian Science Foundation, project No. 20-77-10065, Ministry of Education and Science of the Russian Federation for financial support within grant No. 0778-2020-0005 , and state task, state registration number ААAА-А19-119092390076-7.

References:

Aksenov, S. M., Yamnova, N. A., Kabanova, N. A., Volkov, A. S., Gurbanova, O. A., Deyneko, D. V., Dimitrova, O. V. & Krivovichev, S. V. (2021). Crystals. 11, 237.

Blatov, V. A., Delgado-Friedrichs, O., O’Keeffe, M. & Proserpio, D. M. (2007). Acta Crystallogr. Sect. A Found. Crystallogr. 63, 418–425.

Blatov, V. A., Shevchenko, A. P. & Proserpio, D. M. (2014). Cryst. Growth Des. 14, 3576–3586.

Chukanov, N. V, Pekov, I. V & Rastsvetaeva, R. K. (2004). Russ. Chem. Rev. 73, 205–223.

Ilyushin, G. D. & Blatov, V. A. (2002). Acta Crystallogr. Sect. B Struct. Sci. 58, 198–218.

Krivovichev, S. V. (2015). Proc. Steklov Inst. Math. 288, 105–116.

Pekov, I. V., Krivovichev, S. V., Zolotarev, A. A., Yakovenchuk, V. N., Armbruster, T. & Pakhomovsky, Y. A. (2009). Eur. J. Mineral. 21, 1061–1071.

Rastsvetaeva, R. K. & Chukanov, N. V. (2012). Geol. Ore Depos. 54, 487–497.

Rastsvetaeva, R. K., Chukanov, N. V. & Aksenov, S. M. (2012). Minerals of Eudialyte Group: Crystal Chemistry, Properties, Genesis Nizhniy Novgorod: University of Nizhni Novgorod.

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2:45pm - 5:10pmMS-88: Quantum crystallography research
Location: Club B
Session Chair: Yu-Sheng Chen
Session Chair: Katarzyna N. Jarzembska

Invited: Sophie E. Canton (Hungary), Simon Grabowsky (Switzerland)

 

 
2:45pm - 2:50pm

Introduction to session

Yu-Sheng Chen, Katarzyna N. Jarzembska



2:50pm - 3:20pm

Synchrotron experiments revealing the similarities and differences between crystal and enzyme environmental effects on the electron densities of protease inhibitors and ibuprofen derivatives

Simon Grabowsky

University of Bern, Bern, Switzerland

Non-covalent intermolecular interactions polarize a drug molecule in the biological environment to prepare it for the recognition and binding process with a related enzyme. In a crystal structure of the same drug molecule, the crystal packing is defined by the same kind of non-covalent interactions. This means that in both a biological as well as a crystalline environment, the small molecule will conformationally adapt its shape to the prevailing intermolecular binding forces, so that the resulting bound state reflects both its inherent flexibility and the environment. Electrostatic complementarity between an enzyme binding site and an active molecule is an aspect that goes beyond geometry and molecular conformation since the electrostatic potential is inherently related to the electron density distribution. We ask to which extent small-molecule crystal structures can be used to predict the conformation and interaction density of the same molecule in the enzyme.

The first compound class investigated is related to loxistatin acid E64c. These compounds are cysteine protease inhibitors, and the active site is an electrophilic epoxide ring.[1] It took us many years to solve the small-molecule crystal structure of E64c,[2] and experimental electron-density studies were only possible for related model compounds.[3] Recently, however, we were able to perform a full quantum-crystallographic, molecular-dynamics and QM/MM study of the active site of E64c co-crystallizing in a system that closely resembles the binding situation of E64c in the cysteine protease cathepsin B.[4]

The second compound class investigated refers to ibuprofen derivatives. We used the umpolung principle to tune the properties of ibuprofen by carbon-silicon exchange, which in turn impacts on the electrostatic complementarity relationships when ibuprofen binds to cyclooxygenases.[5] Again, we investigated the enzyme and crystal environmental effects on ibuprofen and sila-ibuprofen by quantum crystallography, molecular dynamics and QM/MM calculations.[6]

Every low-temperature high-resolution single-crystal X-ray diffraction experiment utilized in this study was conducted at a synchrotron beamline at either DESY, APS or SPring-8. Without access to large infrastructure, such studies on weakly scattering pharmaceutically active compounds would not be possible. I will therefore not only report the biochemically relevant results, but also the importance of synchrotron experiments for our field.

[1] Mladenovic, M., Ansorg, K., Fink, R. F., Thiel, W., Schirmeister, T. & Engels, B. (2008). J. Phys. Chem. B, 112, 11798.
[2] Shi, M. W., Sobolev, A. N., Schirmeister, T., Engels, B., Schmidt, T. C., Luger, P., Mebs, S., Dittrich, B., Chen, Y.-S., Bąk, J. M., Jayatilaka, D., Bond, C. S., Turner, M. J., Stewart, S. G., Spackman, M. A. & Grabowsky, S. (2015). New J. Chem. 39, 1628.
[3] Grabowsky, S., Schirmeister, T., Paulmann, C., Pfeuffer, T. & Luger, P. (2011). J. Org. Chem. 76, 1305.
[4] Kleemiss, F., Wieduwilt, E. K., Hupf, E., Shi, M. W., Stewart, S. G., Jayatilaka, D., Turner, M. J., Sugimoto, K., Nishibori, E., Schirmeister, T., Schmidt, T. C., Engels, B. & Grabowsky, S. (2021). Chem. Eur. J. 27, 3407.
[5] Kleemiss, F., Justies, A., Duvinage, D., Watermann, P., Ehrke, E., Sugimoto, K., Fugel, M., Malaspina, L. A., Dittmer, A., Kleemiss, T., Puylaert, P., King, N. R., Staubitz, A., Tzschentke, T. M., Dringen, R., Grabowsky, S. & Beckmann, J. (2020). J. Med. Chem. 63, 12614.
[6] Kleemiss, F., Duvinage, D., Puylaert, P., Fugel, M., Sugimoto, K., Beckmann, J. & Grabowsky, S. (2021). Acta Cryst. B, in preparation.

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3:20pm - 3:50pm

Visualizing the multiscale structural dynamics of photoexcited molecular complexes with ultrafast hard X-rays

Sophie Canton

European XFEL, Schenefeld, Germany

Visualizing on the atomic scale the full extent of the electronic and structural changes that are triggered by charge separation and subsequent charge transport is crucial for developing the rational design of novel sensitizers and catalysts. The rapid progress of ultrafast X-ray techniques, both at synchrotrons (100 ps) and at X-ray free electron laser facilities (sub-ps) have equipped the scientific community with novel analytical tools that are capable of delivering unique feedback with spin and elemental sensitivity about the highly-correlated nonadiabatic dynamics that follow photoabsorption. The present talk will review the technical state-of-the art and the ongoing developments that are currently taking place. The talk will also highlight several of the recent results that have been obtained for intramolecular and interfacial processes of relevance for the function and optimization of advanced materials.

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3:50pm - 4:10pm

Ultrafast photocrystallographic and spectroscopic studies of selected coinage-metal coordination compounds

Piotr Łaski1, Jakub Drapała2, Radosław Kamiński1, Krzysztof Durka2, Katarzyna Natalia Jarzembska1

1University of Warsaw, Warsaw, Poland; 2Warsaw Institute of Technology, Poland

Photoactive materials are among the most commonly researched and engineered functional materials, due to the multiplicity of applications they find in research and industry. Investigating of the dynamics of short-lived excited states in crystal structures allows us to extract information on how such materials could be designed on the molecular level in order to obtain desired properties. Coordination compounds containing group XI transition-metal atoms, such as copper (I), silver(I), or gold(I), are excellent examples of compounds with interesting and diverse photoactive properties, and thus were chosen for this study.

Time-resolved photocrystallographic methods allow us to investigate structural changes occurring due to formation of short-lived laser-induced excited-state species in crystals. For the following study, several coinage-metal mononuclear and multinuclear coordination compounds were examined using time-resolved X-ray-pump / laser-probe Laue experiments, conducted at the 14-ID-B BioCARS APS synchrotron beamline. The studied complexes include the literature-reported Ag(PP)(PS) (PP = 1,2-bis(diphenylphosphino)ethane, PS = 2-(diphenylphospaneyl)pyridine) and newly-synthesised Ag2Cu2(PS)4 systems, both exhibiting bright luminescence in the solid state. The time-resolved data were processed with our home-made software and the photodifference maps were generated and analysed.

In order to comprehensively understand excitation-induced effects occurring in crystals, the abovementioned photocrystallographic measurements were supplemented with time-resolved luminescence spectroscopy experiments (355 nm excitation wavelength) and quantum computations yielding the nature of studied exited states and predicting the geometry changes (TDDFT and QM/MM methods) upon excitation. Results will be presented, and their accordance with photocrystallographic results assessed.

The authors thank NSC (2016/21/D/ST4/03753, 2014/15/D/ST4/02856) and WCSS (grant No. 285) in Poland, EU programme (POIG.02.01.00-14-122/09) and APS, USA (DOE: DE-AC02-06CH11357, NIH: R24GM111072) for financial support and access to facilities.

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4:10pm - 4:30pm

Electronic structure of (MePh3P)2[NiII(bdtCl2)2] . (CH3)2SO and (MePh3P)[NiIII(bdtCl2)2], (bdtCl2 - 3,6-dichlorobenzene-1,2-dithiolate)

Jozef Kozisek

STU Bratislava, Bratislava, Slovak Republic

High-resolution X-ray diffraction experiments, theoretical calculations and atom-specific X-ray absorption experiments are applied to investigate two nickel complexes [Ni(II) (A) and Ni(III) (B)] (Figure 1a, 1b) with the non-innocent 3,6-dichlorobenzene-1,2-dithiolate ligand. Combining the techniques of metal K-, L-edge and sulphur K-edge X-ray absorption spectroscopy with high-resolution X-ray charge density studies, the experimental assessment of oxidation states of the central Ni atoms is studied and compared with theoretical predictions. Furthermore, the experimentally derived X-ray charge density (obtained via the multipole model) and the electron density from theoretical calculations are provided to further explore the contrast and contest of both approaches employed.

Figure 1. Compounds(a) (A), (b) (B), (c) Laplacian of electron density

The oxidation state of the central atom will be discussed [1] (Figure 1c).

[1] Machata, P., Herich, P., Lušpai K., Bučinský, L., Šoralová, S., Breza, M., Kožíšek, J. & Rapta, P. (2014). Rev. Sci. Instrum. 70, 3554.

Organometallics 33 (18), 4846.

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4:30pm - 4:50pm

Unusual carbonyl interactions in co-crystals of urea and dicarboxylic acids

Anna Malgorzata Krawczuk1, Mariusz Mitoraj2

1University of Göttingen, Göttingen, Germany; 2Jagiellonian University in Krakow, Krakow, Poland

Carbonyl…carbonyl interactions have been identified in biologically active systems such as small biomolecules, proteins or protein-ligand complexes. Their contribution into molecular assembly was proven to be comparable to moderate hydrogen bonds, thus they can be considered as organic synthons playing crucial role in determining three-dimensional crystal packing or even stabilizing the secondary structure motifs of proteins. In the literature one can find many examples of C=O…C=O interactions between the same molecules, however to the best of our knowledge, only one case where such a pattern was characterized between different molecules (urea and oxalic acid co-crystal) [1].

Here we report a series of co-crystals of urea and dicarboxylic acid, where antiparallel carbonyl…carbonyl motif [2] between heteromolecules is observed and acts as a “glue” between 2D layers built of strong hydrogen bonds. In order to get inside into the nature and mechanism of the synthons, experimental and theoretical electron density studies were engaged as well as ETS-NOCV method (Extended Transition State. Natural Orbitals for Chemical Valence) was applied [3]. NCI analysis [4] and interaction energies calculated with EP/MM (Exact Potential and Multipole Method) method [5] indicate a correlation between the strength of carbonyl interactions and the number of carbon atoms in the main chain of the acid molecules.

Literature:

[1] A. Krawczuk, M. Gryl, M. Pitak, K. Stadnicka Cryst. Growth Des. (2015), 15, 5578−5592.

[2] F.H. Allen, I.J. Bruno Acta Crystallogr., Sect. B: Struct. Sci. (2010), 66, 380−386.

[3] F. Sagan, M. P. Mitoraj J. Phys. Chem. A (2019), 123, 21, 4616–4622

[4] E.R Johnson, S. Keinan, P. Mori-Sánchez, J. Contreras-Garciá, A.J. Cohen, W. Yang, J. Am. Chem. Soc. (2010), 132, 6498−6506.

[5] A. Volkov, T. Koritsanszky, P. Coppens, Chemical Physics Letters (2004), 391 (1–3), 170–175.

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4:50pm - 5:10pm

Testing various variants of Hirshfeld atom like refinement.

Michał Chodkiewicz, Magdalena Woińska, Sylwia Pawlędzio, Leonid Patrikeev, Krzysztof Woźniak

University of Warsaw, Warszawa, Poland

Hirshfeld atom refinement (HAR)[1,2] is one of the most successful methods for the accurate determination of structural parameters for hydrogen atoms from X-ray diffraction data. It employs atomic scattering factors based on atomic densities obtained via Hirshfeld partition of theoretically determined electron density.

There are various ways of calculating the electron density with theoretical methods. For example, among others, we can independently change (1) a method of quantum chemistry (2) basis set and (3) a representation of molecular environment. This a leads to obvious question – which set of settings is the best for HAR refinement?

An another dimension was recently added to the space of settings by introducing generalization of HAR to other electron density partitions [3] (so called generalized atom refinement (GAR)). This makes the optimal choice of settings even more challenging.

Another factor further complicates the situation – computational cost of GAR. Usually unfavorable scaling of quantum chemical calculations with size of a system may lead to long refinement time for large molecules. While computational chemistry brings here some solutions, we still have to figure out how to handle trade-off between computational cost and accuracy of refinement.

In this contribution we will analyze effects of various settings of GAR on accuracy of the method (assessed by comparison to neutron data). We will also try to find optimal solution for performing accurate refinement with optimized computational cost.

[1] Jayatilaka, D. & Dittrich, B. (2008). Acta Cryst. A64, 383–393.

[2] Capelli, S. C., Bürgi, H.-B., Dittrich, B., Grabowsky, S. & Jayatilaka, D. (2014). IUCrJ, 1, 361–379

[3] Chodkiewicz, M. L., Woińska, M. & Woźniak, K. (2020). IUCrJ, 7, 1199–1215.

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2:55pm - 5:55pmSF-6: Software Fayre 6
Location: 221-2
Session Chair: Martin Lutz
Session Chair: Claudia Millán
 
2:55pm - 3:40pm

AUSPEX: Finding pathologies in macromolecular X-ray data

Yunyun Gao

University Hamburg, Hamburg, Germany

AUSPEX

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3:40pm - 4:25pm

winPSSP: solving organic materials from powder diffraction

SILVINA PAGOLA

Old Dominion University, Williamsburg, United States of America

http://users.uoi.gr/nkourkou/winpssp/

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4:25pm - 5:10pm

Eval15: Intensity integration of area detector images

Martin Lutz

Utrecht University, Utrecht, Netherlands, The

http://www.crystal.chem.uu.nl/distr/eval/

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5:10pm - 5:55pm

Yell: Diffuse scattering analysis in single crystals

Arkadiy Simonov

ETH Zurich, Zurich, Switzerland

https://github.com/YellProgram/Yell

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3:55pm - 5:25pmSMS-5: Advances in data and model validation in biomolecular Small-Angle Scattering: Impacts on data and meta-data recording and data archiving
Location: Club C
Session Chair: Javier Perez
Session Chair: Thomas Weiss

Invited: Dina Schneidman (Israel)Thomas Grant (USA)

 
3:55pm - 4:00pm

Introduction to session

Javier Perez



4:00pm - 4:30pm

Representing low-resolution electron density maps from solution scattering data

Thomas Grant

University at Buffalo, Buffalo, United States of America

Many computational algorithms devoted to the interpretation and modeling of small angle scattering (SAS) data have been developed over the last several decades. In addition to the commonly used ASCII text files containing fits to data, real space transforms, modeling parameters, etc., modeling algorithms often generate coordinate files containing 3D coordinates of atomic or coarse-grained models to describe the object. Due to their versatility and community acceptance, coordinate files have become popular for representing models from a variety of different algorithms including bead modeling, rigid body modeling, ensemble modeling, flexible fitting, molecular dynamics, etc. and have found wide spread adoption in the SAS community. As novel algorithms are developed, new representations of particles are often required that may not be compatible with conventional coordinate models. Here I will describe the program DENSS1 which generates low-resolution 3D density maps from 1D solution scattering data using a novel ab initio reconstruction algorithm. The primary output of DENSS is an MRC file, commonly used in the electron microscopy community (and similar to the CCP4 format used in crystallography), which represents objects on a 3D grid of voxels where each voxel has a value corresponding to the density at that location. DENSS offers advantages over conventional algorithms that are implicit to its use of density to represent particles. Accurate and unbiased interpretation of a density map requires understanding how visualization programs graphically represent the 3D grid of values and how the low-resolution nature of the reconstruction affects this visualization. This includes tasks such as selecting appropriate contour thresholds and how to accurately and unbiasedly display such low-resolution density maps in publication figures and archives. Community engagement in this area will help to generate a set of standards for accurately publishing low-resolution density maps to avoid overinterpretation, as has previously been done for validation of conventional SAS models2.

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4:30pm - 5:00pm

Integrative modeling of structure and dynamics of macromolecules based on SAXS profiles and cross-linking mass spectrometry

Dina Schneidman

The Hebrew University of Jerusalem, Jerusalem, Israel

Proteins generally populate multiple structural states in solution. Transitions between these states are important for function, such as allosteric signaling and enzyme catalysis. Structures solved by X-ray crystallography provide valuable, but static, atomic resolution structural information. In contrast, cross-linking mass spectrometry (XLMS) and small angle X-ray scattering (SAXS) datasets contain information about conformational and compositional states of the system. The challenge lies in the data interpretation since the cross-links in the data often comes from multiple structural states. We have developed a novel computational method that simultaneously uncovers the set of structural states that are consistent with a given dataset (XLMS or SAXS). The input is a single atomic structure, a list of flexible residues, and an experimental dataset. The method finds multi-state models (models that specify two or more co-existing structural states) that are consistent with the data. The method was applied on multiple SAXS and XLMS datasets, including large multi-domain proteins and proteins with long disordered fragments. The applicability of the method extends to other datasets, such as 2D class averages from Electron Microscopy, and residual dipolar couplings.

 
5:10pm - 6:10pmAfternoon break 6: Poster session C2, coffee/tea
Location: Exhibition and poster area
5:10pm - 6:10pmPoster - 41 Receptors: Structural biology of receptors, membrane proteins
Session Chair: SUSAN KAY BUCHANAN
Session Chair: Michael Parker

 

 

Poster session abstracts

Radomír Kužel



Structural anomalies in the Eph receptor due to clinically relevant mutations and the subsequent effect on kinase domain

Shubhashish Chakraborty1,2, Ashok Kumar Varma1,2

1Advanced centre for Treatment, Research and Education in cancer, Kharghar, Navi Mumbai, Maharashtra – 410210,INDIA; 2Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai, Maharashtra – 400094 ,INDIA.

Eph (erythropoietin producing hepatocellular) receptor constitutes the largest family of receptor tyrosine kinase. Based on sequence homology and binding partners, Eph receptor and Ephrin ligand are classified into EphA/EphrinA and EphB/EphrinB complexes [1]. Eph-ephrin as a family is ubiquitously expressed in almost all tissue [2]. Both are membrane-bound structures and regulates key physiological events such as cell-cell interaction, cell migration, partitioning and cell adhesion [3]. Eph receptors constitute an extracellular ligand binding domain, a cysteine-rich sushi domain and fibronectin repeat domains. Followed by a transmembrane domain lies the intracellular region of the receptor - juxtamembrane domain, kinase domain (KD) and SAM or PDZ binding domain [4]. Mutations reported in Kinase domain (KD) can affect the overall functionality of the receptor and downstream signalling pathways. Among the different Eph receptors, EphA7 has been recently regarded as a cancer driver gene (cancer gene census, COSMIC database). Similar to other Eph receptors, EphA7 also hold a dual functionality were it can act both as an oncogene and as a tumor suppressor [5, 6]. This dual functionality relate to its varied expression in different cancers. Many clinically important mutations have been reported in EphA7 (cbioportal, cosmic database), among which KD specifically holds hot spot mutations. In the present study, EphA7 mutations, Gly656Arg, Gly656Glu and Asp751His, were selected on the basis of in-silico analysis presented in the cbioportal. Gly656Glu and Gly656Arg are the hotspot mutations and present in the loop connecting two conserved beta sheets at the N – lobe of kinase. The third mutant Asp751His is present on the helix of C – lobe near to the catalytic loop. G656R, G656E, D751H have been crystallized and the structure is solved at a resolution of 3.1Å, 2.6Å, 3.05Å with the Rfactor/Rfree – 0.244/.280, 0.181/0.21, 0.199/0.247 respectively. Significant alterations in kinase domain has been observed due to the mutations that can affect binding affinity of ATP as well as catalytic efficiency of the Kinase Domain. Changes at the secondary structure levels were also observed in the hinge region for Gly656Arg and Asp751His mutants. This can adversely affect the transition of Kinase Domain from open to closed or closed to open confirmations.

[1] U. Nomenclature and T. Ligands, “Unified nomenclature for Eph family receptors and their ligands, the ephrins. Eph Nomenclature Committee.,” Cell, vol. 90, no. 3, pp. 403–404, 1997.

[2] H. Taylor, J. Campbell, and C. D. Nobes, “Ephs and ephrins,” Current Biology. 2017.

[3] E. Stein et al., “Eph receptors discriminate specific ligand oligomers to determine alternative signaling complexes, attachment, and assembly responses,” Genes Dev., vol. 12, no. 5, pp. 667–678, 1998.

[4] J. P. Himanen and D. B. Nikolov, “Eph signaling: A structural view,” Trends in Neurosciences. 2003.

[5] V. Modi and R. L. Dunbrack, “Defining a new nomenclature for the structures of active and inactive kinases,” Proc. Natl. Acad. Sci. U. S. A., vol. 116, no. 14, pp. 6818–6827, 2019.

[6] M. Anderton, E. van der Meulen, M. J. Blumenthal, and G. Schäfer, “The role of the eph receptor family in tumorigenesis,” Cancers (Basel)., vol. 13, no. 2, pp. 1–15, 2021.

[7] N. N. Phan et al., “Overexpressed gene signature of EPH receptor A/B family in cancer patients-comprehensive analyses from the public high-throughput database.,” Int. J. Clin. Exp. Pathol., vol. 13, no. 5, pp. 1220–1242, 2020.

Keywords: RTKs; crystal structure; secondary structural changes; mutations; cancer; change in intramolecular interaction

Acknowledgement – Funding for this study was supported by Annual Scientific Fund from ACTREC-TMC. S.C. is thankful to Council for scientific and industrial research (CSIR) for fellowship. The authors thank the XRD facility at ACTREC for providing necessary support to this study.

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Influence of glycosylation on the structure of human natural killer cell receptor NKp30 in complex with its tumor ligand B7-H6

Tereza Skalova1, Ondřej Skořepa2, Barbora Kalousková2, Jan Bláha2, Celeste Abreu2, Jan Dohnálek1, Ondrej Vaněk2

1Institute of Biotechnology CAS, v.v.i., Vestec, Czech Republic; 2Department of Biochemistry, Faculty of Science, Charles University Prague, Hlavova 8, 128 40 Praha, Czech Republic

NKp30 is an activating receptor on the surface of human natural killer (NK) cells. Its crystal structure has been published previously by Joyce et al. [1], PDB code 3NOI. B7-H6 is an activating immunoligand expressed by some tumor cells. Its structure in complex with NKp30 has been described by Li et al. [2], PDB code 3PV6.

In this study, we present a new crystal structure of NKp30:B7-H6 at resolution 3.1 Å using homogenously glycosylated proteins produced in HEK293S GnTI- cell lines. The structure has been deposited in the Protein Data Bank under code 6YJP and published [3].

For the structural study, NKp30 was used with complete glycosylation, while B7-H6 was deglycosylated after the first GlcNAc for better crystallization. The new structure showed the same NKp30:B7-H6 interaction interface as observed by Li et al. (3PV6). Similarly, as in the structure of Joyce et al. (3NOI), NKp30 form dimers. However, the dimers of glycosylated NKp30 are different (the glycan presence hinders the formation of the dimers observed in PDB 3NOI), and according to Pisa server validation, the new dimers are more likely biologically relevant.

Furthermore, the asymmetric unit of the new crystal structure contains a dimer of NKp30 placed among two B7-H6 molecules (contacts of chains A-C and B-Dsymm). The illustration taken from our paper [3] shows a hypothesis of NKp30 dimer bound between two B7-H6 ligands during contact of the NK cell and the tumor cell.

[1] Joyce, M.G., Tran, P., Zhuravleva, M.A., Jaw, J., Colonna, M., Sun, P.D. (2011) Proc. Natl. Acad. Sci. USA 108, 6223–6228.

[2] Li, Y., Wang, Q., Mariuzza, R.A. (2011). J. Exp. Med. 208, 703–714.

[3] Skořepa, O., Pazicky, S., Kalousková, B., Bláha, J., Abreu, C., Ječmen, T., Rosůlek, M., Fish, A., Sedivy, A., Harlos, K., Dohnálek, J., Skálová, T., Vaněk, O. (2020). Cancers 12, 1998.

This research was funded by Czech Science Foundation (18-10687S), MEYS of the Czech Republic (LTC17065, CZ.02.1.01/0.0/0.0/16_013/0001776), BIOCEV (ERDF CZ.1.05/1.1.00/02.0109), and Charles University (GAUK 927916, SVV 260427/2020). CIISB research infrastructure project LM2015043, funded by MEYS CR, is gratefully acknowledged for the financial support of experiments at the CMS. The authors also acknowledge the support and the use of Instruct-ERIC resources (PID: 1314) and iNEXT (PID: 2322) infrastructures. The Wellcome Centre for Human Genetics is supported by Wellcome Trust grant 203141/Z/16/Z. O.S. and O.V. received short-term scientific mission support from COST Action CA15126.

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CD4+ T cell recognition of pneumolysin, a pore-forming cytolysin derived from Streptococcus pneumoniae presented by a common HLA allotype

Lisa Ciacchi1, Martijn D. B. van de Garde2, Jan Petersen1, Carine Farenc1, Martien C. M. Poelen2, Hugh H. Reid1, Kristin Ladell3, David A. Price3, Cecile A. C. M. van Els2, Jamie Rossjohn1

1Monash Biomedicine Discovery Institute, Monash University, Clayton, Australia; 2Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands; 3Cardiff University School of Medicine, Cardiff, United Kingdom

Infection with the pathobiont Streptococcus pneumoniae (pneumococcus) can cause life-threatening invasive pneumococcal diseases (IPD), including pneumonia, sepsis, and meningitis [1-3]. With the emergence of new pneumococcal strains, there is an urgent need for vaccines that elicit broader population coverage against conserved pneumococcal antigens, irrespective of capsular serotype. Pneumolysin (Ply) is a key pneumococcal virulence factor belonging to a family of cholesterol-dependent cytolysins (CDCs) that disrupts host cell defence mechanisms and immune cell function. This cytotoxin is expressed by virtually all pneumococcal strains and pneumococcal carriage and infection induce natural immunity to Ply. A detoxified form of this protein has therefore been tested as a potential serotype-independent vaccine candidate to protect against IPD [4-6].

In this study, we identified a highly immunogenic human CD4+ T cell epitope in pneumolysin, widely presented by a common HLA allotype. The nature of the Ply-specific T cell receptor (TCR) repertoire was evaluated in healthy HLA-typed individuals. HLA-Ply-specific tetramer+ CD4+ TCRs were cloned, expressed, and purified. The ternary structures of three TCRs, including examples of near-public (B1) and private sequences (B5 and 5F), were solved in complex with HLA-Ply.

All of these TCRs formed stabilizing contacts with solvent-exposed residues in the central region of the peptide via their hypervariable CDR3 loops. The immunodominance of this epitope can therefore be explained by the preferential selection of TCRs capable of this ubiquitous mode of recognition.

[1] Adams, W., Bhowmick, R., Bou Ghanem, E. N., Wade, K., Shchepetov, M., Weiser, J. N., McCormick, B. A., Tweten, R. K. & Leong, J. M. (2020). J. Immunol. 204, 101.

[2] Backhaus, E., Berg, S., Andersson, R., Ockborn, G., Malmström, P., Dahl, M., Nasic, S. & Trollfors, B. (2016). BMC Infect. Dis. 16, 367.

[3] Kaur, R., Surendran, N., Ochs, M. & Pichichero, M. (2014). Infect. Immun. 82, 5069.

[4] Salha, D., Szeto, J., Myers, L., Claus, C., Sheung, A., Tang, M., Ljutic, B., Hanwell, D., Ogilvie, K., Ming, M., Messham, B., van den Dobbelsteen, G., Hopfer, R., Ochs, M. M. & Gallichan, S. (2012). Infect. Immun. 80, 2212.

[5] van de Garde, M. D. B., van Westen, E., Poelen, M. C. M., Rots, N. Y. & van Els, A. C. M. (2019). Infect. Immun. 87, e00098.

[6] Rossjohn, J., Gilbert, R. J. C., Crane, D., Morgan, P. J., Mitchell, T. J., Rowe, A. J., Andrew, P. W., Paton, J. C., Tweten, R. K. & Parker, M. W. (1998). J. Mol. Biol. 284, 1223.

We wish to acknowledge Josien Lanfermeijer from the RIVM/IIV for technical support, Frans Reubsaet from RIVM/IDS for providing clinical bacterial isolates, Sanofi-Pasteur for providing the peptide, and the NIH Tetramer Core Facility. We thank the staff at the Monash Macromolecular Crystallisation Facility and the Australian Synchrotron (beamlines MX1 and MX2) for assistance with crystallisation and data collection, respectively.

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Molecular characterization of the native (non-linked) CD160-HVEM protein complex revealed by initial crystallographic analysis

Simona Lenhartová1, Marek Nemčovič2, Radka Šebová1, Mário Benko1, Dirk Zajonc3,4, Ivana Nemčovičová1

1Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovak Republic; 2Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia; 3Division of Immune Regulation, La Jolla Institute for Immunology, La Jolla, CA, USA; 4Cancer Immunology Discovery, Pfizer Inc., San Diego, CA, USA

An increasing number of surface-exposed ligands and receptors acting on immune cells are being considered as a starting point in drug development applications. As they are dedicated to manipulate a wide range of immune responses, accurately predicting their molecular interactions will be necessary for the development of safe and effective therapeutics to enhance immune responses and vaccination. Here, we focused on characterization of human CD160 and HVEM immune receptors whose mutual engagement leads to bidirectional signaling (e.g., T cell inhibition, natural killer cell activation, or mucosal immunity). In particular, our study report on the molecule preparation, characterization and initial crystallographic analysis of CD160-HVEM complex and both HVEM and CD160 in ligand-free form. Despite the importance of the CD160-HVEM immune signaling and its therapeutic relevance, the structural and mechanistic basis underlying CD160-HVEM engagement has some controversial evidence. Some newer studies reported CD160 molecule in monomeric form [1-3], while older reports provided evidence on multimeric form acting on immune cells [4, 5]. In our study, the native non-linked CD160-HVEM complex was co-expressed in the baculovirus-insect host; purified to homogeneity by anion-exchange chromatography to provide missing evidence of trimeric form in solution. The CD160-HVEM crystallized in orthorhombic space group with unit cell parameters that could accommodate one trimeric complex (3:3) in asymmetric unit. Crystals of CD160-HVEM complex, CD160 trimer and HVEM monomer (reported in two space groups) diffracted to a minimum Bragg spacing of 2.8, 3.1 and 1.9/2.1 Å resolution, respectively.

[1] Liu, W.; Garrett, S. C.; Fedorov, E. V.; Ramagopal, U. A.; Garforth, S. J.; Bonanno, J. B.; Almo, S. C. Structure (2019), 27 (8), 1286-1295 e4.

[2] Kojima, R.; Kajikawa, M.; Shiroishi, M.; Kuroki, K.; Maenaka, K. J Mol Biol (2011), 413 (4), 762-72.

[3] Stiles, K. M.; Whitbeck, J. C.; Lou, H.; Cohen, G. H.; Eisenberg, R. J.; Krummenacher, C. J Virol (2010), 84 (22), 11646-60.

[4] Anumanthan, A.; Bensussan, A.; Boumsell, L.; Christ, A. D.; Blumberg, R. S.; Voss, S. D.; Patel, A. T.; Robertson, M. J.; Nadler, L. M.; Freeman, G. J. J Immunol (1998), 161 (6), 2780-90.

[5] Maiza, H.; Leca, G.; Mansur, I. G.; Schiavon, V.; Boumsell, L.; Bensussan, A. J Exp Med (1993), 178 (3), 1121-6.

Keywords: CD160/BY55; HVEM/TNFRSF14; immune receptor; immunological synapse; receptor-ligand interaction

This research was funded by the contribution of the Slovak Research and Development Agency under the project APVV-14-0839 and continuous project APVV-19-0376; and the contribution of the Scientific Grant Agency of the Slovak Republic under the grant VEGA-02/0020/18 and VE-GA-02/0060/21. IN was Marie Curie Fellow financed by programme SASPRO co-funded by European Union and the Slovak Academy of Sciences. The part of the research team was supported by Interreg V-A SK-AT cooperation programme by project CAPSID under the contract No. NFP305010V235 co-financed by European Regional Development Fund.

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Structure-based drug discovery enabled for membrane protein targets

Michael Hennig

leadXpro AG, Villigen, Switzerland

Integral membrane proteins suchg as GPCR’s, ion-channels or transporters are drug targets for more than 60% of all approved drugs. Structure based drug discovery on soluble proteins is managed well within the project timelines and portfolio changes in pharmaceutical industry, but transmembrane proteins are still underexplored because of their challenges to be expressed, purified and made them work for high resolution structure determination and ligand characterization by biophysical methods.

The presentation includes recent advances in the technologies and their application to relevant drug targets.

Construct engineering, application of in meso in situ serial X-ray crystallography (IMISX) is exemplified with the GPCR structure of CCR2 in complex with an antagonist ligand. This study is combined with detailed binding characterization using grating-coupled interferometry (GCI, Creoptix) to facilitate drug design with binding kinetic, affinity. Furthermore, the crosstalk between allosteric and orthosteric ligand binding could be investigated.

The structure of the human TRPV4 ion-channel with bound small molecule agonist shows activation of the channel opening with a significant structural change enabling direct observation of agonist pharmacology by high resolution cryo-EM analysis. Next example is LPTDE, a clinically validated antibiotics drug target. Due to limited size of 120 kDa and the monomeric b-sheet transmembrane architecture, the leadXpro proprietary tool of Pro-Macrobodies was essential for the successful EM structure at 2.9 A resolution.

The outlook at future perspectives includes further advances in cryo-EM and the application of serial X-ray crystallography using femtosecond pulsed Free Electron Lasers (FEL) for determination of room temperature structures and observation of structural dynamic of ligand binding and associated conformational changes. All new developments in structural biology will further enhance the impact to the design of candidate drug compounds.

Selected references:

Botte M. et al. Cryo-EM structural studies of the agonist complexed human TRPV4 ion-channel reveals novel structural rearrangements resulting in an open-conformation (2020), https://doi.org/10.1101/2020.10.13.334797

Nass, K., et al. Advances in long-wavelength native phasing at X-ray free-electron lasers. IUCrJ, 2020

https://doi.org/10.1107/S2052252520011379

Cheng, R.K.Y., Towards an optimal sample delivery method for serial crystallography at XFEL, Crystals, 2020, 10, 215;

Rufer, A, Hennig, M., Biophysical assessment of target protein quality in structure‐based drug discovery. https://onlinelibrary.wiley.com/doi/book/10.1002/9781118681121

Apel, A-C., Crystal structure of CC chemokine receptor 2A in complex with an orthosteric antagonist provides insights for the design of selective antagonists, Structure 27, (2019)

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Optimization of the NZ-1 labeling technique for the application to 3D structure analysis

Rie Aruga1, Risako Tamura-Sakaguchi1, Mika Hirose2, Toru Ekimoto1, Rika Oi1, Mika K. Kaneko3, Yukinari Kato3,4, Mitsunori Ikeguchi1,5, Kenji Iwasaki6, Terukazu Nogi1

1Graduated School of Medical Life Science, Yokohama-city University, Japan; 2Institute for Protein Research, Osaka University, Japan; 3Department of Antibody Drug Development, Tohoku University Graduate School of Medicine, Japan; 4New Industry Creation Hatchery Center, Tohoku University, Japan; 5Center for Computational Science, RIKEN, Japan; 6Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Japan

Antibody labeling has become a useful tool for determining three-dimensional (3D) structures of protein molecules and their complexes. Antibody fragments such as antigen-binding fragments (Fabs) serve as crystallization chaperones to promote lattice formation in X-ray crystallography. On the other hand, Fabs can be used as fiducial marks to aid the particle picking and alignment in cryo-electron microscopy (EM), which is difficult to apply to small protein molecules. However, establishing antibodies that bind stably to their respective targets is a prerequisite for utilizing the antibody labeling. To expand its applicability, we have developed an alternative strategy by inserting an exogenous epitope into targets and subsequently preparing complexes with antibody fragments. Specifically, we utilized a monoclonal antibody NZ-1, which has been established by immunizing rat with a 14-residue peptide segment (PA14) from human podoplanin.It has been shown that a 12-residue peptide segment (PA12) lacking two N-terminal residues of PA14 binds to NZ-1 with an extremely high affinity.[1] In addition, a previous crystallographic analysis of the NZ-1 Fab complexed with the PA14 peptide has revealed that the PA12 part adopts a bent loop-like conformation within the antigen-binding pocket of NZ-1. Based on these observations, we first attempted to develop the NZ-1 labeling technique using the PA12 tag. We inserted the PA12 tag into the PDZ tandem (PDZ-N and PDZ-C) located in the periplasmic region of intramembrane protease. In fact, the PA12-inserted PDZ tandem formed a stable complex with the NZ-1 Fab.[2] However, our structural analysis also showed that the complex formation through the inserted PA12 tag inevitably caused structural changes around the insertion site on the target. Therefore, we next attempted to utilize the PA14 tag, instead of PA12, which contains Glu-Gly residues upstream of PA12. We expected that the two additional residues could serve as a buffer region to tolerate structural changes on the target because they are flexible in the above-mentioned crystal structure of the NZ-1 Fab complexed with the PA14 peptide. As a result, the PA14-inserted PDZ tandem also produced co-crystals with the NZ-1 Fab, where the complex formation had less impact on the folding of the target PDZ domains as compared to the NZ-1 labeling with the PA12 tag.[3] In addition, molecular-dynamics (MD) simulations have also suggested that PA14-inserted PDZ domains stably bind to the NZ-1 Fab with no significant structural changes. To demonstrate that our improved NZ-1 labeling technique could be applied to EM analysis, we also performed negative stain EM on the NZ-1-labeled full-length intramembrane protease. We actually obtained 3D models of the complex and succeeded in approximating the spatial arrangement of the PDZ domains based on the docking mode of the NZ-1 Fab.

[1] Fujii, Y., Kaneko, M., Neyazaki, M., Nogi, T., Kato, Y. & Takagi, J. (2014). Protein Expr. Purif. 95, 240-247.

[2] Tamura, R., Oi, R., Akashi, S., Kaneko, M., Kato, Y. & Nogi, T. (2019). Protein Sci. 28, 823-836.

[3] Tamura-Sakaguchi, R., Aruga, R., Hirose, M., Ekimoto, T., Miyake, T., Hizukuri, Y., Oi, R., K.Kaneko, M., Kato, Y., Akiyama, Y., Ikeguchi, M., Iwasaki, K. & Nogi, T. (2021). Acta Cryst. D77, 645-662

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Structure, function and evolution of the orally active insecticidal toxin complex, YenTc

Sarah Piper1,2, Lou Brillault1,2, Joseph Box1, Yu Shang Low1, Irene Chassagnon1, Gabriel Foley1, Nadezhda Aleksandrova1, Lauren Hartley-Tassell4, Cassandra Pegg1, Ben Schulz1, Thomas Ve4, Shaun Lott3, Mark Hurst5, Michael Landsberg1,2

1School of Chemistry and Molecular Bioscience, The University of Queensland, St Lucia, Australia; 2Institute for Molecular Bioscience, The University of Queensland; 3School of Biological Sciences, The University of Auckland; 4Institute for Glycomics; 5AgResearch NZ

Yersinia entomophaga is a naturally occurring, Gram negative insect pathogen, first isolated from the diseased larvae of the New Zealand grass grub C. zealandica a decade ago [1]. Its main virulence determinant is YenTc, a heterogenous 2.4 MDa toxin complex that is a prototypical example of the ABC or Tc family of predominantly insecticidal toxins. YenTc is unique amongst members of this family, in that it is the only member of this class of toxins characterised to date that has a broad target host range, and which exhibits potent oral activity towards susceptible hosts without relying on a nematode symbiont for delivery. This has positioned YenTc as a potentially high value target for the development of novel biopesticides based on this class of toxins.

Previous work from our lab has yielded structures of the pore-forming A component determined by cryo-EM [2,3], the toxin-encapsulating BC cage [4] of YenTc determined by X-ray crystallography, as well as the co-expressed chitinase enzymes Chi1 and Chi2 also determined by X-ray crysatllography [4,5], the latter of which we show are structurally incorporated into the complex. Moreover, these chitinases exhibit significant structural mobility and appear to play a role in glycan recognition at the host cell surface. Our most recent work has led to the determination (using cryo-EM) of structures for the complete YenTc holotoxin assembly in both pre-pore and pore states. Comparing these structures to those of related toxins (primarily derived from the nematode symbiont Photorhabdus luminescens), has helped us to elucidate the overall mechanism of toxin packaging, translocation and delivery. We used the knowledge derived from these structures to guide a Hidden Markov Model-based bioinformatic analysis that led to the identification of more than 800 putative toxin complexes in diverse bacterial genome sequences. Phylogenetic analysis of these putative toxins led us to conclude that ABC toxins cluster into 4 subtypes, and illuminate a model for the evolution of these subtypes in response to host adaptation. Finally, as part of this analysis, we identified an orphan subunit located outside the pathogenicity island of YenTc, and solved the structure of the cytotoxic effector encoded within this subunit using X-ray crystallography. This is, to our knowledege, the first cytotoxic effector associated with an ABC toxin to have it's structure determined.

[1] Hurst, M.R.H. et al. (2011) Int J Syst Evol Microbiol, 61(4) 844-849.

[2] Landsberg, M.J. et al. (2011) PNAS, 108(51) 20544-20549

[3] Piper, S.J. et al. (2019) Nature Commun, 10(2019) 1952.

[4] Busby, J.N. et al. (2013) Nature, 501(7468) 547-550.

[5] Busby, J.N. et al. (2011) J Mol Biol, 415(2) 359-371.



Understanding the structural basis of TIR-domain assembly formation in TRAM- and TRIF- dependent TLR signalling

Mengqi Pan, Andrew Hedger, Jeff Nanson, Bostjan Kobe

the University of Queensland, St Lucia, Australia

Toll-like receptors (TLRs) detect pathogens and endogenous danger, initiating immune responses that lead to the production of pro-inflammatory cytokines. At the same time, TLR-mediated inflammation is associated with a number of pathological states, including infectious, autoimmune, inflammatory, cardiovascular and cancer-related disorders. This dual role of the pathways has attracted widespread interest from pharmaceutical industries. Cytoplasmic signaling by TLRs starts by their TIR (Toll/interleukin-1 receptor) domain interacting with TIR domain-containing adaptor proteins MyD88, MAL, TRIF and TRAM. Combinatorial recruitment of these adaptors via TIR:TIR domain interactions orchestrates downstream signaling pathways, leading to induction of the pro-inflammatory genes. Although many constituents of the TLR pathways have been identified, the available information on their coordinated interactions is limited. Such information is crucial for a mechanistic understanding of TLR signaling, development of therapeutic strategies, and understanding of the molecular basis of the consequences for human disease of adaptor polymorphic variants. We have discovered that TIR domains can form large assemblies. We hypothesized that TIR domain signaling occurs through a mechanism involving higher-order assembly formation. In this study we aim to determine the molecular architecture of higher-order assemblies formed by TIR domains with a focus on TRAM-TRIF assemblies in the TLR4 and TLR3 pathway.

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Structural basis of higher-order assembly formation in Toll-like receptors 1,2 and 6 signaling pathway

YAN LI

The University of Queensland, St Lucia, Australia

Innate immunity represents a typical and widely distributed form of immunity. Innate immune responses are the first line of defense against pathogens, which can help destroy invaders invertebrate animals, invertebrates, and plants. The innate immune system recognizes microorganisms via pattern-recognition receptors (PRRs). The family of Toll-like receptors (TLRs) is a distinct group of PRRs. They detect the microbial components known as pathogen-associated molecular patterns (PAMPs), activate downstream transcription factors such as nuclear factor-κB (NF-κB), resulting in a pro-inflammatory response [1]. 10 TLRs has been identified in the human TLR family. In humans, TLR2 can form heterodimers with TLR1 and TLR6 when binding different types of ligands. The cytoplasmic Toll/interleukin-1 receptor (TIR) domain can be found in all TLRs and is responsible for transmitting extracellular signals to intracellular cytoplasmic TIR domain-containing adaptor proteins through TIR: TIR domain interactions, thus initiating downstream signaling. Two TIR-domain containing adaptor proteins, Myeloid differentiation primary response 88 (MyD88) and MyD88 adaptor-like (MAL) mediate downstream signaling in TLR2-TLR1/6 signaling pathway. It has been previously demonstrated that higher-order assembly formation occurs in the TLR4 signalling pathway [2]. The mechanism, which is known as signaling by cooperative assembly formation (SCAF), may occur in all TLR signal transduction. To date, the transduction mechanisms of TLR2-TLR1/6 signalling are still unclear. My project is to determine the structural basis of higher-order assemblies formed by TIR domains with a focus on assemblies in the TLR2-TLR1/6 signalling.

 
5:10pm - 6:10pmPoster - 42 Enzymes: Structural biology of enzymes
Session Chair: Mirjam Czjzek

 

 

Poster session abstracts

Radomír Kužel



Structural characterisation of mitochondrial complex IV assembly factors

Shadi Magool1, Luke Formosa2, Dinesha Cooray3, David Stroud4, David Aragão5, Michael Ryan2, Megan Maher1

1School of Chemistry and The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Australia; 2Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800, Australia; 3Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne 3086, Australia; 4Department of Biochemistry and Molecular Biology and The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria 3010, Australia; 5Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK

Cytochrome c oxidase or mitochondrial respiratory chain complex IV catalyses the transfer of electrons from cytochrome c in the intermembrane space, to molecular oxygen in the matrix and therefore contributes to the proton gradient that drives mitochondrial ATP synthesis. Complex IV dysfunction is a significant cause of human mitochondrial disease. Complex IV requires the incorporation of three copper ions, heme a and heme a3 cofactors for the assembly and activity of the complex. Complex IV assembly factors are required for subunit maturation, co-factor incorporation and stabilization of intermediate assemblies of complex IV in humans. Loss-of-function mutations in several genes encoding complex IV assembly factors have been shown to result in diminished complex IV activity and severe pathologic conditions in affected infants [1].

Our study focuses on two mitochondrial complex IV assembly factors, Coa6 and Coa7, that are located in the intermembrane space of mitochondria and contain intramolecular disulfide bonds. Coa6 binds copper with femtomolar affinity and has been proposed to play a role in the biogenesis of the CuA site of complex IV [2,3]. The W59C pathogenic mutation in Coa6 does not affect copper binding or import of the protein into mitochondria but affects the maturation and stability of the protein [3]. The precise role of Coa7 in the biogenesis of complex IV is not completely understood. However, patients with Coa7 pathogenic mutations suffer from mitochondrial diseases owing to complex IV deficiency. This presentation will describe the crystal structures of the Coa7 and Coa6 (wild-type and the W59C mutant) proteins and implications for their roles in complex IV assembly and function.

References:

[1] Timon-Gomez, A., Nyvltova, E., Abriata, L. A., Vila, A. J., Hosler, J., and Barrientos, A. (2018) Mitochondrial cytochrome c oxidase biogenesis: Recent developments, Seminars in cell & developmental biology 76, 163-178.

[2] Stroud, D. A., Maher, M. J., Lindau, C., Vögtle, F. N., Frazier, A. E., Surgenor, E., … Ryan, M. T. (2015). COA6 is a mitochondrial complex IV assembly factor critical for biogenesis of mtDNA-encoded COX2. Human molecular genetics, 24(19), 5404–5415. doi:10.1093/hmg/ddv265

[3] Maghool, S., Cooray, N., Stroud, D. A., Aragão, D., Ryan, M. T., & Maher, M. J. (2019). Structural and functional characterization of the mitochondrial complex IV assembly factor Coa6. Life science alliance, 2(5), e201900458. doi:10.26508/lsa.2019004583.

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Chemical biology and structural studies on the mechanism of regulation of phosphoinositide-dependent protein kinase 1 (PDK1)

Lissy Z. F. Gross1, Mariana Sacerdoti1, Alejandro E. Leroux1, Abhijeet Ghode4, Ganesh S. Anand4, Jörg O. Schulze2, Melissa A. Graewert5, Dmitri I. Svergun5, Sebastian Klinke3, Ricardo M. Biondi1,2

1IBioBA - CONICET - Partner Institute of the Max Planck Society, Buenos Aires, Argentine Republic; 2Department of Internal Medicine I, Universitätsklinikum Frankfurt, Germany; 3Leloir Institute - CONICET, Buenos Aires, Argentine Republic; 4Department of Biological Sciences, National University of Singapore, Singapore; 5European Molecular Biology Laboratory (EMBL), DESY Hamburg, Germany

Phosphoinositide-dependent protein kinase 1 (PDK1) is a master AGC kinase of the PI3K signalling pathway that phosphorylates at least other 23 AGC kinases, being PKB/Akt the most relevant substrate for growth and cell survival, and therefore a potential drug target for cancer treatment. Over the years, our laboratory used a chemical and structural biology approach to study and characterize in detail the allosteric regulation of the catalytic domain of PDK1. We developed small compounds that bind to a regulatory site we termed the PIF-pocket and activate PDK1, mimicking the mechanism of activation of AGC kinases by phosphorylation.

Using an integrative approach between biochemistry, crystallography and molecular dynamics, we showed how PS653, a small compound that binds to the active ATP-Binding site, displaces through a reverse allosteric mechanism the in vitro interaction between the PIF-pocket and PIFtide, which is a peptide derived from the hydrophobic motif of a PDK1 substrate. Thus, we not only demonstrated an allosteric regulation from a regulatory site to the active site, but also showed experimentally the existence of the reverse process [1]. This bidirectional allosteric mechanism of regulation between both pockets can therefore be modulated by small molecules that bind to their specific orthosteric site and either enhance or inhibit interactions at the allosteric site. Taking this into consideration, it is not surprising that while the pharmaceutical industry has been developing compounds that bind at the ATP-binding site of kinases, they unwillingly developed drugs that affect protein–protein interactions [2]. Moreover, we now provide further evidence of the bidirectional system using hydrogen/deuterium exchange (HDX) experiments and present a rather complete model for a kinase that can be modulated bidirectionally with small compounds. This concept of bidirectional allostery in kinases can be exploited to produce drugs that enhance or disrupt the formation of multi-protein complexes. Could this mechanism be already in use physiologically? We found out that adenosine binds at the ATP-binding site and allosterically enhances the interaction between PIFtide and PDK1, which demonstrates that bidirectional allostery is a phenomenum that can also be modulated by metabolites. But interestingly, adenine, AMP, ADP, or ATP do not produce this effect. The findings open the possibility that the physiological regulation of the kinase complexes may be modulated by metabolites and implies that the metabolic state of cells could be linked to the regulation of cell signalling.

As a master kinase tightly regulated, PDK1 possesses a selective activation of substrates such as SGK or S6K, which in order to be phosphorylated require a docking interaction of their C-terminal hydrophobic motifs with the PIF-Pocket of PDK1. However, this is not the case of Akt/PKB, since it can be activated in a PIF-Pocket independent way. In this line, we and others showed that small compounds that bind to the PIFpocket of PDK1 block the phosphorylation of S6K, but do not affect the phosphorylation of PKB/Akt by PDK1[3]. However, up to date little is known about the mechanistic and structural details of PDK1 full length. We are currently using an interdisciplinary approach to understand how the full-length protein is regulated and if this regulation mechanism can be manipulated to specifically inhibit the activation of PKB/Akt. As a result of a medium-scale screening of small compounds, we validated a series of “hits” that modulate PDK1 structure by interaction at different sites on PDK1. We here present a series of results obtained using HDX and SAXS experiments on full length PDK1, as well as the crystal structure of the catalytic domain of PDK1 bound to a small compound that stabilizes a particular PDK1 conformation.

The new data is used to present an updated model on the molecular mechanism of regulation of full length PDK, in which we not only show the existence of bidirectional allostery but also the existence of 3 different conformations of full length PDK1.

[1] Schulze, J.O., Saladino, G., Busschots, K., Neimanis, S., Suess, E., Odadzic, D., Zeuzem, S., Hindie, V., Herbrand, A.K., Lisa, M.N., Alzari, P.M., Gervasio, F.L. and Biondi, R.M. Bidirectional Allosteric Communication between the ATP-Binding Site and the Regulatory PIF Pocket in PDK1 Protein Kinase. Cell Chem Biol, 2016. 23(10): p. 1193-1205.

[2] Leroux, A.E. and Biondi R.M, Renaissance of Allostery to Disrupt Protein Kinase Interactions. Trends Biochem Sci, 2020.

[3] Busschots, K., Lopez-Garcia, L.A., Lammi, C., Stroba, A., Zeuzem, S., Piiper, A., Alzari, P.M., Neimanis, S., Arencibia, J.M., Engel, M., Schulze, J.O. and Biondi, R.M., Substrate-Selective Inhibition of Protein Kinase PDK1 by Small Compounds that Bind to the PIF-Pocket Allosteric Docking Site. Chem Biol, 2012. 19(9): p. 1152-63

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Structure of the Caulobacter Crescentus suppressor of copper sensitivity protein C

Guillaume A. Petit1, Karrera Y. Djoko2, Jennifer L. Martin1,3, Maria A. Halili1

1Griffith Institute for Drug Discovery, Griffith University, Nathan, QLD, Australia; 2Department of Biosciences, Durham University, UK; 3Vice-Chancellor’s Unit, University of Wollongong, NSW, Australia

Bacterial oxidoreductase enzymes are found in the periplasm of bacteria and are involved in protein thiol oxidation, reduction and isomerisation. These proteins contribute to folding and correcting disulfide bonds in a wide range of substrates, including virulence factors. Among oxidoreductases, the disulfide bond forming protein A (DsbA) for example, has been thoroughly studied, characterised and shown to be involved in the virulence of multiple pathogenic bacteria. More recently, other oxidoreductases have received attention too. This is the case for the suppressor of copper sensitivity proteins (SCS). One member of this family, ScsC, has been found to contribute to copper resistance in Salmonella enterica serovar Typhimurium (Subedi et al., 2019), and, is involved in disulfide bond isomerisation in the periplasm of the bacterium Proteus mirabilis (Furlong et al., 2018). The C-terminal catalytic domain of ScsC has an architecture similar to that of DsbA, displaying a conserved thioredoxin fold, including a CXXC catalytic motif and an embedded α-helical domain, however the N-terminal domain, responsible for the quaternary structure of the protein, varies strongly in between the proteins from different bacteria species. In S. Typhimurium the protein is monomeric while in P. mirabilis, it is trimeric. More interestingly, the catalytic activity of the protein seems to depend on these C-terminal oligomerisation domains. Here we report the crystal structure of a new trimeric ScsC protein from the model bacterium Caulobacter crescentus, termed CcScsC. The trimerization domain of CcScsC is comprised of a long N-terminal α helix, which assemble via hydrophobic contact between the helices of the different protomers as well as a number of electrostatic interactions between their charged residues. In addition CcScsC is shown to bind copper (I) with picomolar affinity and to have isomerase activity comparable to the known bacterial isomerase E. coli DsbC. In conclusion, we report the structure of a trimeric bacterial oxidoreductase, with a role in protein thiol isomerisation and copper binding.

Furlong, E. J., Choudhury, H. G., Kurth, F., Duff, A. P., Whitten, A. E. & Martin, J. L. (2018). The Journal of biological chemistry 293, 5793-5805.

Subedi, P., Paxman, J. J., Wang, G., Ukuwela, A. A., Xiao, Z. & Heras, B. (2019). The Journal of biological chemistry 294 15876-15888

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The structural panorama of L-asparaginases includes an alien from nitrogen-fixing bacteria

Mariusz Jaskolski1, Joanna Loch2, Mirek Gilski1, Barbara Imiolczyk3

1Faculty of Chemistry, A.Mickiewicz University, Poznan, Poland, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland; 2Faculty of Chemistry, Jagiellonian University, Cracow, Poland; 3Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland

L-Asparaginases from bacterial periplasm (e.g. EcAII) have high L-asparagine affinity and are used as potent antileukemic drugs. Plants possess a different, Ntn class of asparaginases, which are also found in bacteria (e.g. EcAIII). It was predicted ~20 years ago that Rhizobium etli, a bacterial symbiont of legume plants that is capable of nitrogen fixation, will possess yet another, R.etli-type L-asparaginase. The crystal structure of this enzyme, ReAII, reveals a dimeric protein that is indeed completely different from the EcAII and EcAIII prototypes, with structural resemblance to some serine β-lactamases and glutaminases. The presumed active site is organized around S48, which is surrounded by three tightly H-bonded water molecules and is further H-bonded to N134. Near-by there is a tandem of Cys residues coordinating a zinc cation. The coordination sphere is completed by a water molecule and a Lys side chain. Another Lys residue penetrates the active site to provide an H-bond link to S48. C225 of this Cys-rich protein also bears an unknown posttranslational modification.

Version:1.0 StartHTML:0000000183 EndHTML:0000038935 StartFragment:0000038461 EndFragment:0000038895 SourceURL:file:///Z:/home/mariusz/Dysk-E/mariusz/ABSTRACTS/IUCr-2020-mj.docx which is surrounded by three tightly H-bonded water molecules and is further

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Structures of a DYW domain shed first light on a unique plant RNA editing regulation principle

Mizuki Takenaka1, Sachi Takenaka1, Tatjana Barthel2, Brody Frink1, Sascha Haag3, Daniil Verbitskiy3, Bastian Oldenkott4, Mareike Schallenberg-Rüdinger4, Christian Feiler2, Manfred S. Weiss2, Gottfried J. Palm5, Gert Weber2

1Department of Botany, Graduate School of Science, Kyoto University, Kyoto, Japan; 2Helmholtz-Zentrum-Berlin (HZB), Berlin, Germany; 3Molekulare Botanik, Universität Ulm, Germany; 4IZMB – Institut für Zelluläre und Molekulare Botanik, Abt. Molekulare Evolution, University of Bonn, Bonn, Germany; 5University of Greifswald, Molecular Structural Biology, Greifswald, Germany

Pentatricopeptide (PPR) proteins with a C-terminal DYW domain have been characterized as site-specific factors for C to U RNA editing in plant mitochondria and plastids. While substrate recognition is conferred by the repetitive pentatricopeptide (PPR) tract, the exact role of the DYW domain, which can be also recruited to an editing site in trans, has not been clarified. The DYW domain, which was named by the highly conserved last three amino acids, aspartate, tyrosine, and tryptophan, has been proposed as the best candidate to elicit deamination employing a HxE(x)nCxxC zinc ion binding signature. Since DYW domains share a low sequence conservation with known deaminase structures (from 5 to 19% residue identities), modelling attempts have been conducted albeit with a limited reliability. Lastly, missing structural information has left the exact function and catalytic properties of DYW domains within the RNA editosome open.

We present structures and functional data of a DYW domain in an inactive ground state and a catalytically activated conformation. DYW domains harbour a cytidine deaminase fold and a C-terminal DYW motif, with catalytic and structural Zn atoms, respectively. The deaminase fold is interrupted by a conserved domain, which regulates the active site sterically via a large-scale conformational change and mechanistically via the Zn coordination geometry. Thus, we coined this novel domain 'gating domain' and the accompanying unusual metalloprotein regulation principle of DYW proteins 'gated Zn-shutter'. An autoinhibited ground state and its activation by the presence of either ATP, GTP or the inhibitor tetrahydro uridine is consolidated by differential scanning fluorimetry as well as in vivo and in vitro RNA editing assays. Our observations explain three decades of prior failed attempts to establish an in vitro RNA editing assay and impaired nucleotide binding of DYW domains. In vivo, the framework of an active plant RNA editosome triggers the release of DYW autoinhibition to ensure a controlled and coordinated deamination likely playing a key role in mitochondrial and chloroplast homeostasis.

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Seeing is believing: glycosylation in the crystal structure of human myeloperoxidase

Lucas Krawczyk1, Shubham Semwal1, Goedele Roos1, Pierre Van Antwerpen2, Julie Maria Jozefa Bouckaert1

1Centre National de REcherche Scientifique, Villeneuve d'Ascq, France; 2Laboratory of Pharmaceutical Chemistry and Analytical Platform, Faculty of Pharmacy, Université libre de Bruxelles, CP205/05, Boulevard du Triomphe, 1050 Brussels, Belgium

Human myeloperoxidase (MPO) was first isolated in 1941 from purulent pleuritis fluid from tuberculosis patients. When neutrophilic polymorphonuclear leukocytes (neutrophils) entrap microbial or other invasive particulates, they release MPO during degranulation. In a respiratory burst of highly reactive oxygen species, MPO catalyzes the production of hypohalous acids, primarily hypochlorous acid in physiologic situations, from hydrogen peroxide. Mammal MPO crystal structures were progressively acquired and encoded in PDB with partial glycosylation identification. Actually, the N-glycan composition of native MPO had been thoroughly investigated with mass spectrometry and shows 5 N-glycans at positions 323, 355, 391, 483 and 729 [1]. MPO’s enzymatic activity was shown to be modulated by hyper-truncation of 2 out of 5 N-glycosylation sites [2].

In our obtained crystal structure at 2.6 Å resolution containing 4 disulfide-linked homodimers of MPO (Fig. 1), an interesting collection of glycans have been characterized using the iterative process of crystallographic refinement and model building. We compared those with the glycans from proteomics studies and from 18 human MPO structures in the PDB. We made use of the Symbol Nomenclature for Glycans (SNFG) to illustrate congruence in the experimental data. In conclusion, we found each of the 5 glycosylation sites either non-glycosylated or glycosylated with hyper-truncated paucimannosidic, high-mannose and complex N-glycans, with the N-acetyl-β-D-glucosamine (GlcNAc) core-type asparagine-linked glycans on Asn355 or Asn391 sites [2] gate-keeping the funnel towards the ROS-activated heme group. Our results perfectly illustrate the power of protein crystallography to resolve protein glycosylation.

Figure 1. (a) Glycosylation as part of protein crystal structures (2 MPO dimers), (b) a sweet handshake holds the dimer together

[1] Van Antwerpen, P., Slomianny, M. C., et al., (2010) Glycosylation pattern of mature dimeric leukocyte and recombinant monomeric myeloperoxidase: glycosylation is required for optimal enzymatic activity. J Biol Chem 285, 16351-16359. 10.1074/jbc.M109.089748

[2] Tjondro, H. C., Ugonotti, J., et al., (2020) Hyper-truncated Asn355- and Asn391-glycans modulate the activity of neutrophil granule myeloperoxidase. J Biol Chem 10.1074/jbc.M109.089748

Keywords: myeloperoxidase; glycosylation; crystal structure, N-glycans

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14-3-3 protein dependent modulation of ubiquitin ligase Nedd4-2

Pavel Pohl1,2, Tomáš Obšil1,3, Veronika Obšilová1

1Intitute of physiology, CAS, Vestec, Czech Republic; 2Second Faculty of Medicine, Charles University in Prague, Czech Republic; 3Dept. of Physical and Macromolecular Chemistry, Faculty of Science, Charles University in Prague, Czech Republic

Neural precursor cell expressed developmentally down-regulated 4 ligase (Nedd4-2) is an E3 ubiquitin ligase that targets proteins for ubiquitination and endocytosis, thereby regulating numerous ion channels, membrane receptors and tumor suppressors. In turn, Nedd4-2 activity is regulated by autoinhibition, calcium binding, oxidative stress, substrate binding (through its WW domains), phosphorylation and 14-3-3 protein binding [1-3]. However, the structural basis of 14-3-3-mediated Nedd4-2 regulation remains poorly understood.

Here, we combined several techniques of integrative structural biology to characterize Nedd4-2 and its complex with 14-3-3. The results from our binding affinity and crystallographic analyses demonstrate that phosphorylated Ser342 and Ser448 are the key residues that facilitate 14-3-3 protein binding to Nedd4-2 and that Ser448 is the dominant site. Moreover, 14-3-3 protein binding induces a structural rearrangement of Nedd4-2 by inhibiting interactions between its structured domains, including the N- and C-lobes of the catalytic HECT domain. Overall, our findings provide the first structural glimpse into the 14-3-3-mediated Nedd4-2 regulation and highlight the potential of the Nedd4-2:14-3-3 complex as a pharmacological target for Nedd4-2-associated diseases such as hypertension, epilepsy, kidney disease and cancer.

[1] P. Goel, J. A. Manning, and S. Kumar, Gene, 557, no. 1, pp. 1–10, Feb. 2015.

[2] H. He, C. Huang, Z. Chen, H. Huang, X. Wang and J. Chen, Biomed Pharmacother, 125, no. 1, pp. 109983, Feb. 2020.

[3] J. A. Manning and S. Kumar, Trends Biochem. Sci., 43, no. 8, pp. 635–647, Aug. 2018.

This study was supported by the Czech Science Foundation (Project 20-00058S), the Czech Academy of Sciences (Research Projects RVO: 67985823 of the Institute of Physiology) and by Grant Agency of Charles University (Project 740119).

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Bacillithiol disulfide reductase Bdr - insight into a new type of FAD-containing NADPH-dependent oxidoreductases

Marta Hammerstad1, Ingvild Gudim1, Hans-Petter Hersleth1,2

1University of Oslo, Department of Biosciences, Oslo, Norway; 2University of Oslo, Department of Chemistry, Oslo, Norway

Low G+C Gram-positive Firmicutes, such as the clinically important pathogens Staphylococcus aureus and Bacillus cereus, use the low-molecular weight (LMW) thiol bacillithiol (BSH) as a defense mechanism to buffer the intracellular redox environment and counteract oxidative stress encountered by human neutrophils during infections. The protein bacillithiol disulfide reductase Bdr has recently been shown to function as an essential NADPH-dependent reductase of oxidized bacillithiol disulfide (BSSB) resulting from stress responses and is crucial in maintaining the reduced pool of BSH and cellular redox balance. We have solved the first structures of Bdrs, namely from S. aureus and B. cereus [1]. Our analyses reveal a uniquely organized biological tetramer; however, the monomeric subunit has high structural similarity to other flavoprotein disulfide reductases. The absence of a redox active cysteine in the vicinity of the FAD isoalloxazine ring implies a new direct disulfide reduction mechanism, which is backed by the presence of a potentially gated channel, serving as a putative binding site for BSSB in proximity to the FAD cofactor. We also report enzymatic activity for both Bdrs, which along with the structures presented in this work provide important structural and functional insight into a new class of FAD-containing NADPH-dependent oxidoreductases, related to the emerging fight against pathogenic bacteria.

[1] Hammerstad, M., Gudim, I. & Hersleth, H.-P. (2020). Biochemistry. 59, 4793-4798.

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Exploring Polysaccharide lyases of PL-5 family through the lens of structure, function, and dynamics

Prerana Dash1,2, Rudresh Acharya1,2

1National Institution of science education and research, Bhubaneswar, India; 2Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, Maharashtra, India

Polysaccharide lyases are the biologically and industrially important enzymes, which catalyze non-hydrolytic degradation of polysaccharides via a beta-elimination reaction mechanism. There are 40 families of PLs in the CAZY database; classified based on their secondary structure elements and the folds. The PL-5 family enzyme adopts (alpha/alpha)5,5 fold with an N-terminal lid-loop interaction giving rise to a pseudo-toroid architecture. Our research group work is focused on delineating the structure-function-dynamics for PL-5 family enzymes. To this end, the biochemical characterization has been carried on the selected among PL-5 enzymes to identify substrate specificity and enzyme efficiency. We have determined the X-ray crystal structures of the enzymes in apo and substrate-bound forms to understand structural aspects of substrate acquisition and specificity as a function of pH and the enzyme-substrate interactions. Further, the molecular dynamic simulation performed on the X-ray structures suggest the potential dynamics in loop configuration of the molecule to a closed and open state; providing mechanistic insights into functioning, and the mechanism of substrate acquisition and product expulsion in the PL-5 family enzymes.

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Structural and functional characterization of a DNA binding protein of pIP501– a broad-host-range plasmid

Tamara Margot Isamel Berger1, Nina Gubensäk1, Walter Keller1, Verena Kohler2

1University of Graz, Graz, Austria; 2University of Stockholm, Stockholm, Sweden

The spread of resistances against antibiotics in bacteria is a serious global problem. In order to prevent the transfer of resistances it is crucial to understand the involved processes. Conjugative DNA transfer is the most important means to transfer antibiotic resistance genes among bacteria. It is present in Gram- positive (G+) and in Gram- negative (G-) bacteria.

I am working on a Type IV Secretion System (T4SS) encoded on the broad-host-range plasmid pIP501 from Enterococcus faecalis. It can spread among different types of bacterial hosts and hence plays an important role in the propagation of multi drug resistant germs. Enterococci are abundant among humans and animals, which intensifies the problem. To date most of the structural information stems from G- T4SS. Deciphering the mechanisms involved and solving the structure of the pore forming complex (PFC) would be of great help in the war against multidrug resistant bacteria.
Alongside the structural elucidation of the PFC, I am working on a DNA binding protein, namely TraM, which is a putative member of the PFC. The investigation of TraM includes biophysical, biochemical and structural characterization.
We are on the way to determine the residues of TraM, which are involved in DNA binding. We designed two different N-terminal constructs varying in length, TraM94 and TraM167. The structure of TraM94 was recently solved in our group. In contrast to the monomeric TraM94 TraM167 is a trimer in solution like the C-terminal domain of TraM, whose structure was solved in our group already some years ago.

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First crystallographic study of a glutathione transferase from cyanobacteria

Eva Mocchetti1, Arnaud Hecker2, Benoît Guillot1, Sandrine Mathiot1, Franck Chauvat3, Corinne Cassier-Chauvat3, Claude Didierjean1

1CRM2, UL, CNRS, Nancy, France; 2IAM, UL, INRAE, Nancy, France; 3I2BC, UPS, CNRS, CEA, Paris-Saclay, France

Glutathione transferases (GSTs) are widespread enzymes involved in a number of catalytic and non-catalytic processes (1 and reference herein). They are mainly known as enzymes of the cellular phase II detoxification system where they catalyse the nucleophilic addition of glutathione (GSH) to a variety of small non-polar compounds. GSTs have been extensively investigated in animals and plants because of their great relevance to human health and agriculture. In contrast, studies in bacteria remain scarce, especially in the cyanobacteria phylum, which encompasses oxygenic photosynthetic prokaryotes with a wide range of morphologies and ecologies. They have key roles in global carbon and nitrogen cycles, contribute strongly to the fixation of atmospheric CO2 and to its storage in ocean sediments (carbon sinks).

The best-studied cyanobacterium Synechocystis PCC6803, which has 6 GSTs, is an attractive organism for deciphering both GST selectivity and redundancy. Preliminary studies show that these GSTs play the expected roles in stress protection. Furthermore, a knockout mutant can be restored by human GST counterparts, demonstrating the conservation of functions throughout evolution (2). SynGSTC1 is involved in the detoxication of methylglyoxal, a toxic by-product of the cellular metabolism of most organisms (3). We solved the first crystal structure of a GST from cyanobacteria, namely that of SynGSTC1. It shows the putative active site signature SRAS and belongs to the Chi class of GSTs (Figure 1) and its sequence length is shorter by about 30 residues when compared to the usual GST length (~ 220 aa). SynGSTC1 adopts the canonical GST fold that consists of two domains (Figure 1) and exhibits structural similarities with the Ure2p class of GSTs (4). The structure-function relationships of SynGSTC1 will be presented using innovative tools based on molecular dynamic simulations and charge-density of ultra-high resolution structures.

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Structural insights into the ferroxidase and iron sequestration mechanisms of ferritin from Caenorhabditis elegans

Tess R. Malcolm1, Sanjeedha Mohamed Mubarak1, Eric Hanssen2, Hamish G. Brown2, Gawain McColl3, Megan J. Maher1,4, Guy N.L. Jameson1

1Bio21 Molecular Science and Biotechnology Institute, Parkville, Australia; 2Ian Holmes Imaging Centre, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia; 3The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, Victoria, Australia; 4Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia

Iron is an essential trace element required for a multitude of cellular processes [1]. When in excess iron becomes toxic, therefore its intracellular concentration must be strictly regulated by a number of interacting mechanisms [2]. Ferritin is a ubiquitous iron-storage protein that forms a highly conserved 24-subunit spherical cage-like structure. Ferritin catalyses the oxidation of iron (II) to iron (III) by dioxygen at a di-iron site called the ferroxidase centre, and the newly oxidised iron (III) is then sequestered as a mineral core to prevent cellular damage [3]. As part of a greater study to understand iron transport we utilise the model organism, Caenorhabditis elegans, to investigate and elucidate these processes.

C. elegans contains two ferritin proteins, FTN-1 and FTN-2, that are orthologous to the human ferritins [4]. FTN-1 and FTN-2 both exhibit ferroxidase activity, although FTN-2 catalyses the oxidation of iron (II) at a rate significantly faster than FTN-1. All residues involved in catalysis are conserved between FTN-1 and FTN-2, suggesting that these mechanistic anomalies are due to structural differences at a location distinct to the ferroxidase centre. To address this, we solved the structures of both FTN-1 and FTN-2 by X-ray crystallography to 1.84 Å and 1.47 Å resolution respectively, and the structure of FTN-2 by cryo electron microscopy to 1.88 Å. FTN-1 and FTN-2 both adopt the conserved 24-subunit cage-like structure and bind one metal in the higher affinity “A site” of the di-iron ferroxidase centre of each chain [3]. Further comparative analyses using both X-ray crystallography and electron microscopy techniques, reveal the structural features that influence iron influx, catalysis and transfer to the mineral core.

These structural insights will further our understanding of the mechanisms that ferritin utilizes to regulate iron storage and its role in the iron homeostasis. These findings will have further implications for diagnosis and treatment of haemochromatosis, anaemia and other iron related diseases.

[1] Anderson, G.J. & Frazer, D.M. (2017). Am. J. Clin. Nutr. 106, 1559S-1566S.

[2] Aisen, P., Enns, C. & Wessling-Resnick, M. (2001). Int. J. Biochem. Cell Biol. 33 (10), 940-959.

[3] Ebrahimi, K.H., Hagedoorn, P. & Hagen, W.R. (2015). Chem Rev. 115 (1), 295-326.[4] Anderson, C.P. & Leibold, E.A. (2014). Front Pharmacol. 5 (113).

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Precise Redox-dependent Structural Change of the plant-type Ferredoxin revealed by X-ray structures at 0.77 Å resolution, originated and propagating from the [2Fe-2S] cluster

Yusuke Ohnishi1,2, Hideki Tanaka1, Genji Kurisu1

1Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita city, Osaka 565-0871, Japan; 2School of Pharmaceutical Sciences, Wakayama Medical University, 25-1 Shichibancho, Wakayama city, Wakayama 640-8156, Japan

Ferredoxin (Fd) is a redox protein containing the iron-sulfur cluster as the active site, and distributed in various organisms; archaea, bacteria, plants and animals. Specific Fd located in the stroma of chloroplast or cyanobacteria is called “plant-type” and possesses a [2Fe-2S] cluster ligated by four conserved cysteine residues. It carries one electron from Photosystem I reaction centre on the thylakoid membrane to several Fd-dependent enzymes. Unique feature of this plant-type Fd is its low redox-potential around -400 mV, which can reduce NADP+ to NADPH (Em = -350 mV) in vivo1. However in vitro, it means that the chemically reduced samples are easily oxidized by air and, on the other hand, the modern strong X-ray beam could reduce the oxidized form of crystallized sample2. Previous structural analyses of Ser46, Phe64 and Glu93 mutants showed the structural basis for the redox potential increase of mutants by 50~90 mV3, while these mutated residues were completely conserved among the plant-type Fds3. Furthermore, X-ray crystallography on oxidized and reduced Fd from Anabaena showed that the peptide bond next to S46 flipped upon partial reduction4. Although several X-ray structures of plant-type Fds including above were available in the PDB, their redox states were not precisely controlled and probably in the mixed states. Consequently, it is not clear how dissociation/association between the plant-type Fd and partner proteins is controlled by one electron redox on the [2Fe-2S] cluster. Here, we solved the X-ray structures of oxidized Fd with minimum X-ray dose and fully reduced Fd from cyanobacterium Thermosynechococcus elongatus (TeFd) at 0.78 and 0.77 Å resolution, respectively. Both oxidized/reduced crystals had a space group of C2 and all used crystals were isomorphous. Our high-resolution structures newly reveal the redox-linked repositioning of Ser46, Phe64 and Glu93 (Fig 1). To investigate the reason how these structural changes are originated from the small but significant structural change in the [2Fe-2S] cluster, we solved the crystal structures of the oxidized/reduced S46A or F64A mutants of TeFd at 0.95~1.05 Å resolution, independently (Fig 2). All our obtained high-resolution structures imply how the small structural changes of the cluster are spatially amplified and propagated through the peptide chain. The detail of our discussion will be presented in our presentation.

[1] Cammack, R., Rao, K. K. & Bargeron, C. P. (1977) Biochem. J. 186 (2), 205–209.

[2] Ohnishi, Y., Muraki, N., Kiyota, D., Okumura, H., Baba, S., Kawano, Y., Kumasaka, T., Tanaka, H. & Kurisu, G. (2020) J. Biochem., 167, 549–555.

[3] Holden, H. M., Jacobson, B. L., Hurley, J. K., Tollin, G., Oh, B.-H., Skjeldal, L., Chae, Y. K., Cheng, H., Xia, B. & Markley, J. L. (1994)Journal of Bioenergetics and Biomembrane, 26 (1).

[4] Morales, R., Chron, M. H., Hudry-Clergeon, G., Pétillot, Y., Norager, S., Medina, M. & Frey, M. (1999) Biochemistry 38 (48), 15764–15773.

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Crystal structure of carbohydrate esterase SmAcE1 from Sinorhizobium meliloti

Changsuk Oh1, Truc Kim1, T. Doohun Kim2, Kyeong Kyu Kim1

1Department of Precision Medicine, Sungkyunkwan University, Suwon, Korea, Republic of Korea; 2Department of Chemistry, College of Natural Science, Sookmyung Women's University, Seoul, 04310, Republic of Korea

Green chemistry paradigm has been raised to reduce environmental damages during process of products. American Chemical Society suggested 12 principals such as atom economy, safter chemicals, energy efficiency, degradable products and less hazardous chemical syntheses [1]. One of alternatives for green chemistry is using biocatalysts, whose endogenous characters are attractive in the following aspects: decrease synthesis procedures, less side products, and mild reaction condition. Microbial enzymes are one of promising sources for biocatalysts in industrial processes to produce biofuel from biomass and building blocks [2]. We identified the structure of the carbohydrate esterase, SmAcE1 from Sinorhizobium meliloti [3] . The crystal structure of SmAcE1 was determined at 2.05 Å resolution, and revealed that it belonged to an α/β hydrolase fold in GDSL superfamily. It formed a hexameric structure by dimer of trimers with supporting of size exclusion chromatography analysis. Catalytic triad (Ser15, His195 and Asp192) and an oxyanion hole-forming SGNH (Ser15, Gly57, Asn97 and His195) were also conserved in its three dimensional structure. The docking analysis to acetylate substrates showed the hydrophilic residues on its surface are important in substrate binding. The models from crystal structure and docking analysis suggest the industrially applicable potency of SmAcE1 after enhancement of its selectivity and activity by further structure-based engineering.

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Half way to hypusine. Structural characterization of human deoxyhypusine synthase.

Elżbieta Wątor, Piotr Wilk, Przemysław Grudnik

Małopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland

Deoxyhypusine synthase (DHS) is a transferase catalysing the formation of deoxyhypusine, which is the first, rate-limiting step of unique post-translational modification: hypusination. DHS catalyzes the transfer of 4-aminobutyl moiety of spermidine to a specific lysine of eIF5A precursor in an NAD-dependent manner. This modification occurs exclusively on only one protein: eukaryotic translation initiation factor 5A (eIF5A) and it is essential for cell proliferation [1]. Malfunctions of the hypusination pathway, including those caused by mutations within the DHS encoding gene, are associated with such conditions as cancer or neurodegeneration [2].

The presented study aimed to investigate substrate specificity of the first step of hypusination using macromolecular crystallography as the main tool and additionally to assess the impact of newly recognized pathological mutations in DHS coding gene on protein stability, activity and structure.

Human DHS wild type and its two mutants were expressed, purified and crystallized. Our attempts lead to six high-resolution crystal structures of DHS wt in apo form and complexes with natural substrates. Based on crystal structures and activity tests it was shown that despite almost identical binding of spermidine and spermine, probably only spermidine can serve as a proper substrate of deoxyhypusine formation. Furthermore, it was shown that against the previous studies, no conformational changes occur in the DHS structure upon spermidine-binding [3].

Availability of high-quality structural data will aid the design of novel DHS inhibitors for potential applications in cancer therapy and can significantly advance our understanding of newly recognized genetic DHS disorder.

1. Park MH, Wolff EC. Hypusine, a polyamine-derived amino acid critical for eukaryotic translation. J Biol Chem. 2018;293(48):18710-18718. 2. Ganapathi M, Padgett LR, Yamada K, et al. Recessive Rare Variants in Deoxyhypusine Synthase, an Enzyme Involved in the Synthesis of Hypusine, Are Associated with a Neurodevelopmental Disorder. Am J Hum Genet. 2019;104(2):287-298. 3. Wątor E, Wilk P, Grudnik P. Half Way to Hypusine-Structural Basis for Substrate Recognition by Human Deoxyhypusine Synthase. Biomolecules. 2020;10(4):522.

The research has been supported by National Science Centre (NCN, Poland) research grant no. 2019/33/B/NZ1/01839 to P.G and 2019/35/N/NZ1/02805 to E.W.

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On substrate binding cavity of hyoscyamine 6β-hydroxylase from devil’s trumpet

Anna Kluza1, Beata Mrugala1, Katarzyna Kurpiewska1,2, Przemyslaw J Porebski1,3, Ewa Niedzialkowska1,3, Wladek Minor3, Manfred S Weiss4, Maksymilian Chruszcz5, Tomasz Borowski1

1Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Krakow, Poland; 2Department of Crystal Chemistry and Crystal Physics, Faculty of Chemistry, Jagiellonian University, Krakow, Poland; 3Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA; 4Macromolecular Crystallography, Helmholtz-Zentrum Berlin für Materialien und Energie, Berlin, Germany; 5Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, USA

Hyoscyamine 6β-hydroxylase (H6H) is a bifunctional enzyme that catalyzes two final steps in the scopolamine biosynthesis pathway in the Solanaceae family [1]. It performs hydroxylation of (2’S)-hyoscyamine at the C6 position of the tropane moiety, which yields (6S,2'S)-6β-hydroxyhyoscyamine, and subsequent dehydrogenation of (6S,2'S)-6β-hydroxyhyoscyamine into (2’S)-scopolamine with formation of an epoxide (Figure 1). However, it was recently shown that H6H can also catalyze production of (6R, 2'S)-6β-hydroxyhyoscyamine from (2’S)-hyoscyamine at small scale [2].

H6H belongs to the family of non-heme 2-oxoglutarate/Fe(II)-dependent dioxygenases that share conserved double-stranded β-helix motif, so-called jelly-roll fold, composed of eight antiparallel β-strands. Here, we present crystal structures of H6H from Datura metel and its truncated version in complexes with 2-oxoglutarate, hyoscyamine and 6β-hydroxyhyoscyamine [3]. Through analysis of the substrate binding pocket, we point out crucial residues in hyoscyamine binding and explain results of previous studies on the substrate preference of H6H.

Figure 1. Two final steps in the biosynthesis of scopolamine - both catalyzed by H6H. MarvinSketch was used to draw structures and reactions [4].

[1] Hashimoto T, Yamada Y. Plant Physiol. 1986;81(2):619–625.

[2] Pan J, Wenger ES, Matthews ML, et al. J Am Chem Soc. 2019;141(38):15153–15165.

[3] Kluza A, Wojdyla Z, Mrugala B, et al. Dalton Trans. 2020 Apr 7;49(14):4454-4469.

[4] MarvinSketch version 18.20, ChemAxon, 2018.

Keywords: hyoscyamine 6β-hydroxylase; scopolamine biosynthesis; metalloenzymes

This research project was supported by SONATA-BIS grant no.UMO-2014/14/E/NZ1/00053 from the National Science Centre, Poland. AK would like to acknowledge the support of PROM Programme – International Scholarship Exchange of PhD Candidates and Academic Staff, co-financed granted from the European Union, including the European Social Fund within the framework of the Knowledge Education Development Operational Programme, non-competitive project entitled: International Scholarship Exchange of PhD Candidates and Academic Staff, contract number PPI/PRO/2019/1/00021/U/00001.

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Control of hydroxylation regioselectivity by hyoscyamine 6β-hydroxylase as revealed by crystallographic and QM/MM studies

Zuzanna Wojdyla, Anna Kluza, Tomasz Borowski

Jerzy Haber Institute of Catalysis and Surface Chemistry Polish Academy of Sciences, Krakow, Poland

Hyoscyamine 6β-hydroxylase (H6H) is a bifunctional 2-oxoglutarate/Fe(II)-dependent dioxygenase that catalyzes the two final steps in the biosynthesis of scopolamine [1], that is a regioselective hydroxylation of hyoscyamine at the C6 position, followed by a formation of the epoxide ring utilising the installed hydroxy group [2]. The combination of crystallographic and computational studies on H6H:hyoscyamine complex provided insight into the substrate binding and the selectivity of the enzymatic reaction [3].

The QM/MM studies reveal that the regioselectivity of the hydroxylation reaction is dictated by only a few residues (i.e. Lys-129, Tyr-326, Lys-330), which promote the reaction occurring at the C6 site and at the same time hinder the alternative channel proceeding at the neighbouring (C7) position. Notably, the electronic properties of the reactants, that is hyoscyamine and the active site, do not favour any of the reaction channels, which suggests that switching regioselectivity of the oxygen rebound and thus obtaining other potentially useful alkaloids, may be achieved by targeting the residues in vicinity of the reactants.

[1] Hashimoto T., Matsuda J. & and Y. Yamada Y. (1993), FEBS Lett. 329, 35–39

[2] Li L., Van Belkum M.J. & Vederas J.C. (2012) Bioorg. Med. Chem. 20, 4356–4363

[3] Kluza A., Wojdyla Z., Mrugala B., et al. (2020) Dalton T. 49, 4454-4469

Keywords: metalloenzymes, reaction mechanisms, reaction regioselectivity, computation

This research project was supported by the National Science Centre, Poland and PL-Grid Infrastructure and in part by Project PROM - International scholarship exchange of PhD candidates and academic staff, financed by the European Social Fund implemented operational programme Knowledge Education Development, project: International scholarship exchange of PhD candidates and academic staff, contract number PPI/PRO/2019/1/00021/U/001.

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Domain movements of NADPH–cytochrome P450 oxidoreductase (CPR) are required for the smooth electron transfer from CPR to heme–heme oxygenase-1 (HO-1) complex

Masakazu Sugishima1, Junichi Taira2, Mikuru Iijima3, Hideaki Sato1, Kei Wada4, Masato Noguchi1, Keiichi Fukuyama5, Mitsunori Takano3, Hiroshi Sakamoto2, Ken Yamamoto1

1Kurume University School of Medicine, Kurume, Japan; 2Kyushu Institute of Technology, Iizuka, Japan; 3Waseda University, Tokyo, Japan; 4University of Miyazaki, Miyazaki, Japan; 5Osaka University, Toyonaka, Japan

Heme oxygenase-1 (HO-1) catalyzes the heme degradation using seven electrons supplied by NADPH–cytochrome P450 oxidoreductase (CPR) where FAD and FMN are bound as co-enzymes. Electrons flow from NADPH to heme in the redox partner via FAD and FMN. Previous biophysical analyzes such as SAXS and FRET suggest the existence of a dynamic equilibrium between the open and the closed forms of CPR in which orientations of FMN and FAD-binding domains are different [1]. We previously determined the crystal structure of the open-form stabilized CPR (ΔTGEE) in complex with heme–HO-1 at 4.3 Å resolution and demonstrated that ΔTGEE is tightly bound to heme–HO-1 while the reduction in heme–HO-1 using ΔTGEE is markedly slow because FAD is too far from FMN for electron transfer between them [2].

Here we characterized the enzymatic activity and the reduction kinetics of HO-1 using the closed-form stabilized CPR (147CC514) where the disulfide bond between FAD and FMN binding domains was introduced. We also analyzed the interaction between 147CC514 and heme–HO-1 by analytical ultracentrifugation [3]. The results indicate that HO-1 activity coupled with 147CC514 is markedly weaker than that coupled with CPR and the interaction between 147CC514 and heme–HO-1 is considerably weak. In addition, we examined the coupling of the redox and the structural states by full-scale molecular dynamics (MD) simulation of CPR (total 86.4 μs) [4]. Our MD result demonstrated that CPR has a tendency to open in the fully-reduced state while the major form of CPR is the closed form both in the fully-oxidized and fully-reduced states. We also found a correlation between the FAD-FMN distance and the predicted FMN-HO-1 distance, which is embedded in the equilibrium thermal fluctuation of CPR. Thus, the redox coupled transition between the open and the closed forms of CPR is indispensable for the smooth electron transfer from CPR to heme–HO-1 complex.

Further, we prepared the fusion protein of ΔTGEE and HO-1 referring to the previously reported structure of ΔTGEE in complex with heme–HO-1 and determined its fusion protein structure in complex with heme at 3.25 Å resolution [5]. Unexpectedly, no NADP+ was observed in the fusion protein structure although NADP+ was contained in the crystallization droplets and NADP+ was observed in the previous complex structure of ΔTGEE and heme–HO-1. Because the structural features of the NADP+-free form of CPR were also observed in the fusion protein structure, the fusion protein structure reflects the NADP+-free form of ΔTGEE–heme–HO-1 complex. Structural comparison of the NADP+-bound ΔTGEE–heme–HO-1 complex and the NADP+-free fusion protein suggests that NADP+/NADPH binding regulates the conformation change of the FAD-binding domain of CPR, which may control the efficiency of the electron transfer from FMN to heme–HO-1.

[1] Iyanagi, T., Xia, C. & Kim, J. J. P. (2012) Arch. Biochem. Biophys. 528, 72.

[2] Sugishima, M., Sato, H., Higashimoto, Y., Harada, J., Wada, K., Fukuyama, K. & Noguchi, M. (2014) Proc. Natl. Acad. Sci. USA 111, 2524.

[3] Sugishima, M., Taira, J., Sagara, T., Nakao, R., Sato, H., Noguchi, M., Fukuyama, K., Yamamoto, K., Yasunaga, T. & Sakamoto, H. (2020) Antioxidants 9, 673.

[4] Iijima, M., Ohnuki, J., Sato, T., Sugishima, M. & Takano, M. (2019) Sci. Rep. 9, 9341.

[5] Sugishima, M., Sato, H., Wada, K. & Yamamoto, K. (2019) FEBS Lett. 593, 868.

Keywords: Heme metabolism; Electron transfer; Domain motion; Cofactor binding

We acknowledged Mr. Sagara and Ms. Takemoto of Kyushu Inst. Tech., and Dr. Ohnuki and Dr. Sato of Waseda Univ. for analytical centrifugation and MD experiments, respectively. We also acknowledged beamline staffs of BL44XU, SPring-8 for crystallographic data collection. This work was partially supported by Kakenhi Grant numbers 25840026, 16K07280, and 19K06515 from JSPS, and grants from Takeda Science Foundation and Protein Research Foundation.

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Conservation of a glutamate residue in ATP-citrate lyase and succinyl-CoA synthetase

Marie Elizabeth Fraser, Ji Huang

University of Calgary, Calgary, Canada

Succinyl-CoA synthetase (SCS), the enzyme that catalyzes the only substrate-level phosphorylation in the citrate cycle, is the prototype for a family of ADP- or GDP-forming acyl-CoA synthetases that includes ATP-citrate lyase (ACLY) [1]. These enzymes catalyze the formation of a thioester bond between an organic acid and CoA, using the energy of nucleotide triphosphate (NTP) and in the presence of magnesium ions. A histidine residue is transiently phosphorylated during catalysis [2], leading to the proposed catalytic mechanism:

E + NTP ⇌ E–PO3 + NDP (1)

E–PO3 + carboxylate ⇌ Ecarboxyl–phosphate (2)

Ecarboxyl–phosphate + CoA ⇌ E + carboxyl–CoA + Pi (3)

where E represents the enzyme; –, a covalent bond; and , noncovalent interactions. For SCS, the carboxylate is succinate; for ACLY, it is citrate and there is fourth step in which citryl-CoA is cleaved to form acetyl-CoA and oxaloacetate.

A glutamate residue of ACLY, E599, was proposed to play a role in the cleavage of citryl-CoA [3]. This glutamate residue is conserved not only in ACLYs but also in SCSs (Fig. 1). The structures of SCSs and ACLYs found in the Protein Data Bank [4] are used to investigate the role of this conserved glutamate residue.

Human ACLY IRTIAIIAEGIPEALTRKLIKKA-DQKGVTIIGPATVGGIKPGCFKIGNTGGMLDNILASKLYR

Chlorobium limicola ACLY IQLVSMITEGVPEKDAKRLKKLA-QKLGKMLNGPSSIGIMSAGECRLGVIGGEFKNLKLCNLYR
Human GTPSCS α-subunit IPLVVCITEGIPQQDMVRVKHKLLRQEKTRLIGPNCPGVINPGECKIGIMPG--------HIHK
Escherichia coli
α-subunit IKLIITITEGIPTLDMLTVKVKL-DEAGVRMIGPNCPGVITPGECKIGIQPG--------HIHK
Thermus aquaticus
α-subunit IPLIVLITEGIPTLDMVRAVEEI-KALGSRLIGGNCPGIISAEETKIGIMPG--------HVFK

Figure 1. Alignment of portions of the sequences of ACLYs and SCSs. The alignment shows conservation of a glutamate residue, E599 in human ACLY, E112 in the A-subunit of Chlorobium limicola ACLY, E105a of human GTPSCS, E98a of E. coli SCS, and E97a of Thermus aquaticus GTPSCS.

[1] Sánchez, L. B., Galperin, M. Y. & Müller, M. (2000). J. Biol. Chem. 275, 5794. [2] Kreil, G. & Boyer, P. D. (1964). Biochem. Biophys. Res. Commun. 16, 551.

[3] Wei, X., Schultz, K., Bazilevsky, G. A., Vogt, A. & Marmorstein, R. (2020). Nat. Struct. Mol. Biol. 27, 33.

[4] Berman, H. M. et al. (2000). Nucleic Acids Res. 28, 235.



Monitoring the crystallization of two enzymes in real time by dynamic light-scattering

Kévin Rollet1,2, Raphaël de Wijn1, Sylvain Engilberge3, Alastair G. McEwen4, Oliver Hennig2, Heike Betet2, Mario Mörl2, François Riobé5, Olivier Maury5, Philippe Bénas1, Bernard Lorber1, Claude Sauter1

1Université de Strasbourg, ARN, CNRS UPR9002, IBMC, Strasbourg, France; 2Institute for Biochemistry, Leipzig University, Leipzig, Germany; 3Université Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France; 4Université de Strasbourg, IGBMC, CNRS UMR 7104, INSERM U 1258, Illkirch, France; 5Université Lyon 1, ENS Lyon, CNRS-UMR 5182, Lyon, France

Obtaining well-diffracting crystals is often a bottelneck of biocrystallographic studies. It is increasingly important in serial crystallography which requires a reproducible production of microcrystals that are homogneous in size and diffraction quality. In order to gain a better control over the crystallization process, we used an instrument called the XtalController. This recent technology gives access to the full monitoring of crystallization assays using dynamic light scattering and videomicroscopy, and integrates a crystallization chamber with temperature and humidity regulation, as well as piezo injectors that allow the modification of the mother liquor composition during the experiment [1]. We exploited this technology to study the crystallization of two enzymes, the CCA-adding enzyme of Planococcus halocryophilus, a cold-adapted bacterium from the permafrost, and the hen egg white lysozyme in the presence of a synthetic chemical nucleant, the crystallophore Tb-Xo4. Using the XtalController, we were able to detect early nucleation events and drive the crystallization system toward growth conditions yielding crystals with excellent diffraction properties using cycles of dissolution/crystallization [2]. This work illustrates the potential of XtalController technology for the rational production of samples for crystallography, ranging from nanocrystals for electron diffraction, microcrystals for serial or conventional X-ray diffraction, to larger crystals for neutron diffraction.

​[1] Meyer, A., Dierks, K., Hilterhaus, D., Klupsch, T., Mühlig, P., Kleesiek, J., Schöpflin, R., Einspahr, H., Hilgenfeld, R. & Betzel, C. (2012). Acta Cryst. F, 68, 994.

​[2] de Wijn, R., Rollet, K., Engilberge, S., McEwen, A.G., Hennig, O., Betat, H., Mörl, M., Riobé, F., Maury, O., Girard, E., Bénas, P., Lorber, B. & Sauter, C. (2020). Crystals, 10, 65.

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Investigating The Structural Dynamics of the Water and Proton Channels Using snap-shots of Photosystem II

Mohamed Ibrahim

HU-Berlin, Berlin, Germany

The water oxidation process in Photosystem II, a Bio-machinery that evolved nearly three billion years ago, fascinates us with its capabilities of harvesting solar energy and storing it in a chemical form. The X-ray Free Electron Lasers enabled us to study this phenomenal protein in ways that were not possible before. In the current manuscript, we introduce new approaches for XFEL data to understand better the catalytic activity, not only for PSII, via deeper analysis of the water network around the active site. Using a high-resolution 1.89 Å room temperature crystal structure of PS II and the re-processed crystallography data at various time points between the S2 to S3 transition of Kok's cycle, we identified the substrate water intake channel extends starting near O1 of the OEC to the lumenal side of the membrane. Three main well-coordinated structural events during the S2 to S3 transition occurred within the water channels, resulting in substrate insertion and proton egress. In particular, the rotation of D1-E65 and the appearance of new water before the substrate insertion likely facilitate proton removal through the Cl 1channel. While the arrival of new water near D1-E329 after the substrate insertion probably indicates the delivery via the O1 channel.

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5:10pm - 6:10pmPoster - 43 Nucleic acid: Nucleic acids and binding proteins structure and function
Session Chair: Charles Bond
Session Chair: Stephen Neidle

 

 

Poster session abstracts

Radomír Kužel



Biophysical characterization of the interaction between Forkhead Box O4 (FOXO4) and p53 transcription factors

Raju Mandal1, Klara Kohoutova1,2, Olivia Petrvalska1,2, Matej Horvath1, Václav Veverka3,4, Veronika Obsilova2, Tomas Obsil1,2

1Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, Prague, Czech Republic; 2Department of Structural Biology of Signaling Proteins, Division BIOCEV, Institute of Physiology of the Czech Academy of Sciences, 252 50 Vestec, Czech Republic; 3Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic; 4Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic

The transcription factor p53 controls numerous cellular processes including apoptosis, senescence, DNA repair, and tumor suppression [1]. The function of p53 is closely intertwined with Forkhead box O (FOXO) transcription factors and FOXO protein regulates cellular functions such as cellular homeostasis, oxidative stress resistance, metabolism, and longevity. FOXO protein family has four members: FOXO1, FOXO3, FOXO4, and FOXO6 wherein their activity is tightly regulated by post-translation modification (phosphorylation, acetylation, methylation, and ubiquitination) [2]. The previous study has demonstrated that the physical interaction between FOXO4 and p53 represses apoptosis of senescent cells by upregulating the transcription of p21 gene and maintain the viability of senescent cells [3]. However, the structural aspects of FOXO4:p53 complex formation remain unclear. Therefore, we designed several truncated constructs of FOXO4 and p53 to elucidate the structural details of this complex using analytical ultracentrifugation, NMR, chemical cross-linking, and molecular docking. Our data suggest that the transactivation domain (TAD) of p53 and DNA binding domain of FOXO4 provide overall stability of the complex along with the transient interaction from other regions of FOXO4 and p53. Furthermore, FOXO4:p53 complex formation does not affect the DNA binding affinity of FOXO4, thereby this interaction presumably allows co-localization of both FOXO4 and p53 transcription factors in the promoter region. Our finding further promotes future research for drug development aiming for the selective elimination of senescent cells.

[1] Boutelle, A.M., Attardi, L.D. (2021) Rev. Trends Cell Biology. 31, 298-310.

[2] Obsil T., Obsilova V. (2011) Rev. Biochimica et Biophysical Acta (BBA)-Molecular cell research. 1813, 1946-1953.

[3] Baar M.P., Brandt R.M.C., Putavet D.A., et al. (2017) Cell. 169, 132-147.

This study was supported by Czech Science Foundation Grant No. 21-02080S and the Grant agency of the Charles University (project number: 1002119).

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Structural basis for the specific binding between metal ion and chemically modified mismatched base pairs

Kei Hirabayashi1, Saki Adachi1, Akira Ono2, Jiro Kondo3, Hidetaka Torigoe1

1Department of Applied Chemistry, Faculty of Science, Tokyo University of Science, Tokyo 162-8601, Japan; 2Department of Material & Life Chemistry, Faculty of Engineering, Kanagawa University, Yokohama 221-8686, Japan; 3Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, Tokyo 102-8554, Japan

The interactions between metal ions and nucleic acids have attracted considerable interest for their involvement in structure formation and folding of nucleic acids, and their possible roles in catalytic activity of nucleic acids. The structural and thermodynamic properties of the binding with the perfectly matched duplex DNA have been reported for many metal ions, but few studies have been reported for the interaction of metal ions with the mismatched base pair duplex DNA. We found that the addition of Hg2+ significantly increased the thermal stability of the duplex DNA with the T:T mismatched base pair [1, 2], and the combination of Hg2+ and the duplex DNA with the T:T mismatched base pair was highly specific for metal ion-DNA interactions. Isothermal titration calorimetry (ITC) demonstrated that Hg2+ specifically bound to the T:T mismatched base pair at 1:1 molar ratio with a binding constant of 106 M-1 [2]. We also found that the addition of Ag+ significantly increased the thermal stability of the duplex DNA with the C:C mismatched base pair [3, 4], and the combination of Ag+ and the duplex DNA with the C:C mismatched base pair was highly specific for metal ion-DNA interaction. ITC demonstrated that Ag+ specifically bound to the C:C mismatched base pair at 1:1 molar ratio with a binding constant of 106 M-1 [4]. Recently, we analyzed the possibility of specific binding between metal ion and 5-fluorouracil (5-FdU)-modified mismatched base pair in duplex DNA. Thermal stability analyses revealed that Hg2+ and Ag+ could specifically bind to the T:5-FdU and the C:5-FdU mismatched base pair in duplex DNA, respectively. Here, we determined the crystal structures of two duplex DNAs including mercury-mediated T-Hg-(5F-dU) base pair and silver-mediated C-Ag-(5F-dU) base pair.

Palindromic DNA fragments designed to contain T or C:5-FdU mismatched base pair in the center were used for crystallization. Both fragments were cocrystallized with metal ions by the sitting drop vapor diffusion method, and x-ray diffraction data were collected at the Beamline BL-5A of the Photon Factory. Experimental phases of duplex DNAs containing mercury- and silver-mediated base pairs were obtained by single wavelength anomalous dispersion (SAD) phasing with mercury atoms and the molecular replacement method, respectively. The structure of duplex DNA containing mercury-mediated T-Hg-(5F-dU) base pair was determined at 2.85 Å resolution and revealed that two duplex DNA molecules present in an asymmetric unit. Hg2+ specifically bound to the T:5-FdU mismatched base pair at 1:1 ratio with taking linear coordination to N3 atoms of T and 5-FdU residues to form T-Hg-(5F-dU) base pair. The structure of duplex DNA containing silver-mediated C-Ag-(5F-dU) base pair was determined at 2.20 Å resolution and revealed that a single-stranded DNA present in an asymmetric unit; two single-stranded DNAs forming a duplex DNA in the crystal is related by crystallographic 2-fold axis. One Ag+ is specifically inserted between C:5-FdU mismatches to form a C-Ag-(5F-dU) base pair by taking linear coordination to N3 atoms of C and 5-FdU residues as same as Hg2+. In addition, a hydrogen bond is formed between O4 atom of 5-FdU and N4 atoms of C residue, implying a contribution to stability by forming a stronger bond network.

In this study, we demonstrated the structural basis for the novel interaction of metal ions with the mismatched base pair including 5-FdU. Structural information for specific binding modes between chemically modified mismatched base pairs and metal ions can be expected to be applied to various fields such as environment, medicine and nanotechnology.

[1] Ono, A. & Togashi, H. (2004). Angew. Chem. Int. Ed. 43, 4300-4302.

[2] Torigoe, H., Ono, A. & Kozasa, T. (2010). Chem. Eur. J. 16, 13218-13225.

[3] Ono, A., Cao, S., Togashi, H., Tashiro, M., Fujimoto, T., Machinami, T., Oda, S., Miyake, Y., Okamoto, I. & Tanaka, Y. (2008) Chem. Commun. 4825-4827.

[4] Torigoe, H., Okamoto, I., Dairaku, T., Tanaka, Y., Ono, A. & Kozasa, T. (2012) Biochimie 94, 2431-2440.

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Structural and Functional Studies of TBEV Non-Structural Protein 5

Petra Havlíčková1, Joel A. Crossley1, Zdeno Gardian1,2, Ivana Kutá Smatanová1, Zdeněk Franta1

1Faculty of Science, University of South Bohemia in České Budějovice, České Budějovice, Czech Republic; 2Institute of Parasitology, Biology Center of the Czech Academy of Sciences, České Budějovice, Czech Republic

Tick-borne encephalitis virus (TBEV) is a major human pathogen, transmitted by ticks from family Ixodidae. TBEV is an enveloped virus with a ~ 11 kb positive-sense single-strand RNA genome, encoding a single 375 kDa polyprotein. During infection, the polyprotein is cleaved into three structural and seven non-structural (NS) proteins. While the structural proteins are involved in assembly of new virions, the non-structural proteins are responsible for virus replication.

Non-structural protein 5 (NS5) is a large bi-functional conserved protein comprising two domains connected by a highly flexible linker, which is important for the activity as well as determines the overall shape of the protein. N-terminal methyltransferase (MTase) domain is the capping enzyme. The C-terminal RNA-dependent RNA polymerase (RdRp) is crucial for virus replication.

This project aims at structure determination and functional studies of TBEV NS5 protein. Various gene constructs were designed and cloned: NS5 full length, RdRp domain and MTase domain. Expression and purification of individual products have been optimized and pure proteins were used for initial crystallization screening, cryo-EM analysis and functional assays.

So far, we have obtained cryo-EM data for RdRp domain, using Titan Krios equipped with Falcon 4 camera and Relion processing pipeline yielded a reconstruction of 6 Å resolution. Tiny protein crystals of RdRp grew in several crystallization conditions. Furthermore, fluorescence-based binding assays revealed substrate affinity and specificity.

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Lipopolysaccharide Recognition by human Surfactant Protein D.

William Anthony Neale1, Jens Madsen2, Howard Clark2, Annette Shrive1, Trevor Greenhough1

1Keele University, Staffordshire, United Kingdom; 2EGA Institute for Women's Health, University College London, United Kingdom

Surfactant Protein D (SP-D) is a member of the collectin family of proteins and acts as part of the innate immune system, the first line of defence, in the lung. The collectins recognise and bind specific structural features conserved amongst pathogens, particularly bacterial and fungal cell surface lipopolysaccharides (LPS) and viral glycans. SP-D can immobilise and form aggregates of pathogens that are more recognisable to neutrophils, along with triggering the rest of the immune system. High-resolution ligand-bound crystal structures of a biologically and therapeutically active recombinant homotrimeric fragment of native human SP-D (rfhSP-D) complexed with simple disaccharides have shown ligand binding to take place through the coordination of a Ca2+ ion and binding site residues to a mannose-type O3’ and O4’ pair of hydroxyls of the bound sugar[1].

Further work has taken place with fragments isolated from the lipopolysaccharide (LPS) of Haemophilus influenzae Eagan and Salmonella enterica Minnesota R5 through mild acid hydrolysis to cleave the bulky, hydrophobic lipid A[2,3]. These showed preferential binding by rfhSP-D of the LPS inner core through coordination of the calcium to the Hep O6’ and O7’ sidechain hydroxyls. These ligand-bound structures also highlight that hSP-D has the flexibility and versatility to recognise alternative LPS epitopes when the preferred core heptose is unavailable. In one subunit (subunit A) of the Salmonella LPS bound structure, the proximity of a crystal contact prevents the preferred inner core binding mode seen in the other chains, resulting in binding through the terminal glucose.

Crystals were also frozen at varying time-stages of the ligand soak, and analysis of these structures provides insight into the changes in the interaction between the protein and ligand over time as binding with the LPS progresses. The definition of the bound ligand in the electron density is seen to increases as the soaking time progresses. Comparison of the crystal structures over time also shows that in chain B the non-bound terminal glucose of the oligosaccharide, initially aligned planar with Pro319, rotates by 90° around the Glc-HepII glycosidic bond as binding progresses. There are also structural changes as depletion of the tertiary calcium site progresses over the time course of the ligand soak.

[1] Shrive AK, Tharia HA, Strong P, Kishore U, Burns I, Rizkallah PJ, et al. (2003) ‘High-resolution Structural Insights into Ligand binding and Immune Cell Recognition by Human Lung Surfactant Protein D’. J Mol Biol.; 331(2):509–23

[2] Littlejohn JR, da Silva RF, Neale WA, Smallcombe CC, Clark HW, Mackay R-MA, et al. (2018) ‘Structural definition of hSP-D recognition of Salmonella enterica LPS inner core oligosaccharides reveals alternative binding modes for the same LPS’. PLoS One. 13(6)

[3] Clark, H.W., Mackay, R.M., Deadman, M.E., Hood, D.W., Madsen, J., Moxon, R., Townsend, J.P., Reid, K.B.M., Ahmed, A., Shaw, A.J., Greenhough, T.J., Shrive, A.K. (2016). ‘Crystal Structure of a Complex of Surfactant Protein D (SP-D) and Haemophilus influenzae Lipopolysaccharide Reveals Shielding of Core Structures in SP-D-Resistant Strains’. Infection and Immunity, 84 (5), 1585 - 1592.

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5:10pm - 6:10pmPoster - 44 Art: Crystallography in art and archaeology
Session Chair: Petr Bezdicka
Session Chair: David Hradil

 

 

Poster session abstracts

Radomír Kužel



Characterization of metal carboxylates relevant for degradation of oil paintings by complementary XRPD and ssNMR

Ruslan Barannikov1,2, Silvie Švarcová1, Eva Kočí1, Petr Bezdička1, Libor Kobera3, Jan Rohlíček4, Jiří Plocek1

1Institute of Inorganic Chemistry of the Czech Academy of Sciences, ALMA Laboratory, Husinec-Řež 1001, 250 68 Husinec-Řež, Prague, Czech Republic; 2Department of Inorganic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 2030/8, 128 43 Prague 2, Czech Republic; 3Institute of Macromolecular Chemistry of the Czech Academy of Sciences, Heyrovského nám. 2, 162 06 Praha 6, Czech Republic; 4Institute of Physics of the Czech Academy of Sciences, Na Slovance 1999/2, 182 21 Praha 8, Czech Republic

Saponification occurring in paint layers represents a serious degradation process affecting the appearance and stability of paintings, leading for example to protrusions, efflorescence, darkening, delamination, exudates etc. A substantial part of saponification is formation of metal carboxylates, resulting from the interaction between metal cations (e.g., Pb2+, Zn2+) released from pigment particles (e.g., lead white, red lead, zinc white) with fatty acids (usually palmitic and/or stearic) released from triglycerides making-up oil-based binders. Metal carboxylates can adopt variable structures from ionomers to amorphous complexes to crystalline phases, and up to now the mechanism of their crystallization is not elucidated. Moreover, crystal structures of most metal carboxylates are not determined. This paucity complicates the study of the degradation process and clarifying of factors promoting or inhibiting the saponification. However, without knowledge of degradation mechanism it is impossible to find a suitable strategy to prevent it.

Within the study of miniature paintings by combination of non-destructive spectroscopic and diffraction techniques (X-ray fluorescence, infrared spectroscopy and X-ray powder diffraction), unusual patterns of crystalline metal carboxylates together with the red pigment cinnabar (HgS) were detected Fig.1 [1], indicating the possible effect of the cinnabar on the formation of these carboxylates.

Figure 1. Part of diffraction patterns of the miniature portrait J2037 with the best evidence of all important lines of metal soaps in low angle region (S lead soaps, H hydrocerussite, K kaolinite, HgS cinnabar, G gypsum, M mica, A anhydrite)

The necessity to identify metal soaps found in the paintings and to understand their formation, the synthesis of mixed mercury carboxylates was carried out. The composition of the mercury carboxylates corresponds to the formula Hg(C16)x(C18)2-x (where C16 is a palmitic acid and C18 is a stearic acid, x from 0 to 2,0 with 0,1 increments). The synthesized compounds serve as reference materials for the study of the degradation processes performed on model the paint layers. The synthesized carboxylates of the formula were investigated by X-Ray powder diffraction (XPRD), Fourier-transform infrared spectroscopy (FTIR) and ultra-wideline solid state nuclear magnetic resonance spectroscopy (ssNMR).

The structural model of selected prepared mercury carboxylates was described from the refinement of the obtained XRPD data complemented by DFT calculations from obtained ssNMR spectra. Previously reported data for lead palmitate-stearate was used as a reference. [2] We revealed that both hexadecanoate (C16) and octadecanoate (C18) chains are present in one crystal structure, creating the statistical disorder at the ethyl end of the chains.

[1] Garrappa, S., Hradil, D., Hradilová, J. et al. Non-invasive identification of lead soaps in painted miniatures. Anal Bioanal Chem 413, 263–278 (2021). https://doi.org/10.1007/s00216-020-02998-7

[2] Kočí E, Rohlíček J, Kobera L. et al. Mixed lead carboxylates relevant to soap formation in oil and tempera paintings: the study of the crystal structure by complementary XRPD and ssNMR. Dalt Trans. 2019; 48:12531–40. https://doi.org/10.1039/C9DT02040C

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Meaning of Wenzel Jamnitzer’s treatise Perspectiva corporum regularium (Nürnberg, 1568) and its relationship to history of modern science

Jan Fábry

Institute of Physics of the Czech Academy of Sciences, Praha 8, Czech Republic

The contribution aims at explanation of the meaning of Jamnitzer´s work [see also 1], especially elucidation of the relationship between the perspective, i.e. the method how the visual perception of the world can be mathematized, and five regular (Platonic) solids. Four elements, i.e. Fire, Air, Earth and Water, have been traditionally attributed to the tetrahedron, octahedron, cube and icosahedron, respectively (Plato´s Timaios). The dodecahedron symbolized the Fifth essence or Universe or God´s substance by Jamnitzer’s own words.

Jamnitzer intended to treat natural phenomena by combinations of the elements following Plato´s Timaios. It is manifested by depiction of the regular bodies and their transformations about their common symmetry elements in aesthetically appealing engravings. However, in agreement with the Christian creed, this view about the world goes beyond its visible part. Jamnitzer’s work can be interpreted that invisible world can be understood at least at part by adopting geometry and arithmetic which is a way how a human being can get closer to the Creator.

Wenzel Jamnitzer´s work was one of the treatises of this kind which were published between 15-17-th centuries [2]. This means that his work can be considered as a representative of the culture which was flourishing at that time. Among his predecessors were such important personalities like Luca Pacioli/Leonardo da Vinci (the manuscript De divina proportione, 1498-1499) and Albrecht Dürer, author of Underweysung der Messung, mit dem Zirckel und richtscheyt, in Linien, Ebnen und gantzen Corporen, Nürnberg (1525) who was also a Nürnberger citizen and a goldsmith at the very beginning of his career likewise Jamnitzer. Jamnitzer’s work shares similarities with Leonardo’s illustrations to Luca Pacioli’s treatise. It should be emphasized that Nürnberg was a centre of crafts as well as of German/transalpine humanism [1], [3] and it seems not to be coincidence that it was just there where Copernicus´s book De revolutionibus orbium coelestium libri VI was printed in 1543 by a famous printer Johannes Petreius.

The ideas which are manifested in the discussed Jamnitzer´s work have been reflected in Johannes Kepler´s books, i. a. in Mysterium cosmographicum or in Strena seu de nive sexangula (Francfurt a. M., 1611), the treatise so important for crystallography. Other examples of the applications of these ideas in architecture - see e.g. [4], [5] - and in arts - e.g. [6] will be shown. Importance of measurement as a method how to approach to the surrounding world will be emphasized in the contribution.

The author thanks the Institute of Physics for the support.

[1] Albert FLOCON (1993). Preface to translation into Spanish by Elena del Amo: Wentzel JAMNITZER, Perspectiva corporum regularium, Nürnberg 1568. Spain: Edición Siruela.

[2] Kirsti ANDERSEN (2007). The Geometry of an Art : The History of the Mathematical Theory of Perspective from Alberti to Monge, p. 212 and p. 224, New York: Springer.

[3] Martin KEMP (1990). The Science of Art. Optical themes in western art from Brunelleschi to Seraut, p. 63. New Haven and London: Yale University Press.

[4] John G. Hatch, The Science Behind Francesco Borromini's Divine Geometry, pp. 127-139 in Nexus IV: Architecture and Mathematics, eds. Kim Williams and Jose Francisco Rodrigues, Fucecchio: Florence: Kim Williams Books, 2002.

[5] George L. Hersey (2000). Architecture and Geometry in the Age of the Baroque. The University of Chicago Press: Chicago.

[6] Miguel Falomir, Lynn Roberts, Paul Mitchell (2017). Arcimboldo. Las Floras y la Primavera. Museo de Bellas Artes: Bilbao.

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5:10pm - 6:10pmPoster - 45 Minerals: Complex structures of minerals and inorganic materials
Session Chair: Marie Colmont
Session Chair: Sergey V. Krivovichev
Session Chair: Milan Rieder

 

 

Poster session abstracts

Radomír Kužel



The crystal structure of the new mineral devilliersite, Ca4Ca2Fe3+10O4[(Fe3+10Si2)O36]

Biljana Krüger1, Hannes Krüger1, Irina O. Galuskina2, Evgeny Galuskin2, Yevgeny Vapnik3

1University of Innsbruck, Innsbruck, Austria; 2University of Silesia, Sosnowiec, Poland; 3Ben-Gurion University of the Negev, Beer-Sheva, Israel

The crystal structure of the new mineral (IMA 2020-073) devilliersite Ca4Ca2Fe3+10O4[(Fe3+10Si2)O36], crystalizing in space group P–1 with cell parameters a = 10.56619(10) Å, b = 10.94969(11) Å, c = 9.08459(7) Å, α = 106.4300(8)°, β = 95.7466(7)°, γ = 124.2978(11)°, V = 786.906(16) Å3, Z=1, was solved from single-crystal diffraction data, collected at PSI(SLS). Devilliersite, as well as khesinite, Ca4Mg2Fe3+10O4 [(Fe3+10Si2)O36] [1], is a VIFe3+-analog of dorrite, Ca4Mg2Fe3+10O4[(Al10Si2)O36] [2] and synthetic SFCA (Silico-Ferrite of Calcium and Aluminium) [3]. The structural formula of minerals of the dorrite–khesinite series can be written as VII(A12A22)Σ4 VI(M1M2M32M42M52M62M72)Σ12O4[(T12T22T32T42T52T62)Σ12O36], where A are seven coordinated sites, M are octahedral sites and T are tetrahedral sites (Figure 1). The total scattering densities at the cation positions were determined using the atomic scattering factors combined with a refinement of the individual site occupancies and results of microprobe analysis.

In the structure of devilliersite all of the A-sites are fully occupied by calcium. However, chemical analyses show that additional 0.68 Ca atoms are present. For crystallochemical reasons this excess Ca has to be expected at the largest octahedral site M5, where it was placed and fixed for the refinement. The remaining scattering power at the M5 site is explained by Mg. The octahedral M1, M2, M3, M4 and M6 sites are dominated by Fe3+, their scattering power was modelled with Fe and Mg, and converged for all sites to ~93% Fe. The M7 octahedra shows the smallest level of distortion, with bond lengths ranging from 1.999(2) to 2.75(19). In the Ti-rich minerals of the rhönite-group, titanium is found at the M7 site. Therefore, we fixed Ti at this site, according to the results of the chemical analysis, and the remaining occupancy was refined as Fe vs. Mg. Scattering power indicates that the T4 site in devilliersite is fully occupied by Si. Occupancy of all other tetrahedral sites was refined as Al vs Fe. The refined chemical formula is VIICa4VI(Ca1.36Mg1.33Fe9.07Ti0.24)Σ12O4IV(Al3.24Fe6.76Si2)Σ12O36.

[1] Galuskina, I.O., Galuskin, E.V., Pakhomova, A.S., Widmer, R., Armbruster, T., Krüger, B., Grew, E.S., Vapnik, Ye., Dzierazanowski, P., Murashko, M (2017). Eur. J. Mineral, 29, 101–116

[2] Cosca, M.A., Rouse, R.R. and Essene, E.J. (1988). Am. Miner, 73, 1440-1448.

[3] Kahlenberg, V., Krüger, H., Goettgens, V.S. (2019). Acta Crystallogr. B75, 1126-1136.

Funding: European Union's Horizon 2020 research and innovation program, project CALIPSOplus, grant No. 730872.

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Formulation of clay refractory bricks: influence of the nature of chamotte and the alumina content in the clay

Moustapha SAWADOGO

Université Joseph KI ZERBO, Ouagadougou, Burkina Faso

Abstract:

Refractory materials from kaolinitic clays and clay chamotte or quartz were studied to increase the refractoriness under load at temperature above 1300°C. Two different clays mined in Burkina Faso were used and chamotte grains were obtained by preliminary firing a local clay. Fired materials at 1350-1400°C present a typical granular composite microstructure were large grains of chamotte or quartz are embedded in the clay matrix phase. Under load at high temperature, the behavior of material is influenced by the nature of the clay matrix phase that progressively melt at high temperature, the type of chamotte or quartz grains, the grain sizes of different phases and the sequence of the thermal transformations during firing. Kinetics of creep under a constant load were characterized against temperature and time. It gives the typical temperatures at fixed creep strains, that’s a well-recognized method for the refractoriness quantification. It’s shown that the kinetic of creep change with the variation of viscosity with temperature of the melted clay matrix phase, that’s related to both the chemical composition and the extend of the micro-composite nature of the heat transformed clays. Results also indicated that values of activation energy for creep are correlated to the refractoriness of materials.

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Structural analysis of ilmenite concentrates treated by acid-assisted high energy ball milling

Tania Isabel Garcia-Manzano, José Antonio Henao-Martínez, Diana Marcela Cañas-Martínez, Julio Andres Pedraza-Avella

Universidad Industrial de Santander, Bucaramanga, Colombia

La ilmenita es uno de los minerales más comunes en la corteza terrestre, a menudo se encuentra en rocas ígneas y arenas negras de depósitos aluviales y puede ubicarse en diferentes partes del mundo; se utiliza como fuente natural de TiO2 y Fe y como catalizador en procesos de fotodegradación [1]. Una investigación realizada en el Grupo de Investigación en Química Estructural - GIQUE y Grupo de Investigaciones en Minerales, Biohidrometalurgía y Ambiente - GIMBA utilizando negro rico en ilmenita de Barbacoas (Nariño, Colombia) para aplicaciones fotocatalíticas encontró que la superficie específica del mineral (2.4- 4,2 m2 / g) es bastante bajo en comparación con el de los fotocatalizadores comunes (20-50 m2 / g) [2,3]. Con el objetivo de inducir cambios morfológicos que conduzcan a un aumento de la superficie, eso implicaría más sitios activos disponibles para la reacción; Esta investigación propone someter concentrados ricos en ilmenita a molienda de bolas de alta energía asistida por soluciones ácidas de ácido acético y ácido sulfúrico, ya que los ácidos pueden provocar cambios en la distribución y estado de oxidación de los elementos en la superficie mineral, produciendo poros y grietas en la superficie del mineral. superficie [4,5]. Sin embargo, la molienda de alta energía en presencia de soluciones ácidas puede modificar significativamente la cristalografía de materiales nanoestructurados, por lo tanto, es importante evaluar el efecto de la tensión aplicada sobre el tamaño de partícula, área superficial y composición, mientras se trazan cambios en la microestructura de ilmenita. El producto del tratamiento con ácido se obtuvo evaluando la concentración de ácido en la solución 1, 3 y 5% p / v, tiempo (1-3 h), velocidad de molienda 650 rpm, relación peso bola / potencia BPR (3: 1 , 10: 1 y 20:

Particle size distribution was measured by dynamic light scattering (DLS) and the minimum average particle size of 325 nm was reached by milling for 1 h with BPR 20:1 and size of grinding medium of 4.0 mm. Qualitative analysis of the XRD pattern of the samples performed using the software Diffrac.EVA showed the presence of ilmenite, hematite and rutile as crystalline phases (Fig. 1) and the quantitative phase analysis in the XRD patterns reported ilmenite as the phase in greater proportion using Diffrac.TOPAS. although no changes were observed in the position of the peaks in the powder XRD patterns of the samples milled with neither the acid solutions, decreasing in the intensity and widening of the peaks were noticed (Fig. 1), which evidenced amorphization of the phases as a result of the stress applied. The morphology evaluated by scanning electron microscopy (SEM) ratify the decrease in particle size and showed different shapes of particle for both acid solutions however, it was noted that acetic acid slightly favours the decrease in particle size (Fig. 2). In order to further improve the properties of the material it was decided to increase the concentration of the acid solutions and milling time.

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Investigation of structural phase transitions and superionic property of a Vanthoffite mineral, Na6Co(SO4)4

Ajana Dutta, Diptikanta Swain, T. N. Guru Row

Indian Institute of Science, Bangalore, India, Bangalore, India

There are several naturally occurring minerals that show temperature induced phase transitions, leading to a variety of materials which display specific properties such as superionic conductivityand ferroic behaviour.[1-5] Some of the minerals crystallize with different hydration levels and show phase transitions at elevated temperature.[2,3] It is important to note that superionic conductors exhibit high ionic conductivity ( ≈10-3 to 10-1 S/cm) at modest temperatures (400-600 °C) and are playing a major role to design next generation solid state batteries.[1,4] The ionic conductivity of a material and its crystal structure are highly correlated with each other. In this context, the phase behaviour of compound belongs to the Vanthoffite family, Na6Co(SO4)4.xH2O (x = 2, 4) with temperature has been investigated. Single crystals of di-and tetra-hydrates of the mineral Na6Co(SO4)4 grow concomitantly from aqueous solution containing stoichiometric molar ratio of starting materials. Both of this hydrated forms have similar morphology and crystallize in P`1 with Z=1. In fact, the elusive anhydrous crystal (Na6Co(SO4)4) [inset Fig. 1a] could be produced in situ from the tetra-hydrate/di-hydrate crystal and the transition pathway has been characterized via variable temperature single crystal X-ray diffraction analysis. Further, we have also examined the phase transitions displayed by the anhydrous phase using in situ powder X-ray diffraction and in situ Raman spectroscopy with respect to temperature [Fig. 1b]. The structural features are shown to correlate with the conductivity measurements with the super ionic behaviour (σ =1.1× 10-2 S/cm) appearing at 570 ˚C [Fig. 1a]. These observations are significant for the development and understanding of mineral based solid electrolytes.

[1] Sharma, V., Swain, D., Guru Row, T. N. (2017). Inorg. Chem. 56, 6048.

[2] Swain, D., Guru Row, T. N. (2009). Inorg. Chem. 48, 7048.

[3] Saha, D., Madras, G., Guru Row, T. N. (2011). Cryst.Growth Des. 11, 3213.

[4] Swain, D., Guru Row, T. N. (2007). Chem. Mater. 19, 347.

[5] Pradhan, G. K., Swain, D., Guru Row, T. N., Narayana, C. (2009). J. Phys. Chem. A 113, 1505.

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Raman, crystallographic and chemical characterization of roméite-group minerals.

Gerson Anderson de Carvalho Lopes1, Daniel Atencio2, Marcelo Barbosa de Andrade1

1São Carlos Institute of Physics, Av. Trabalhador São-carlense, 400, Pq. Arnold Schimidt – CEP 13566-590, São Carlos-SP - Brazil; 2Institute of Geosciensces, Rua do Lago, 562, Butantã – CEP 05508-080, São Paulo–SP - Brazil

The roméite-group [1,2] is part of the pyrochlore supergroup and comprises some cubic oxides of A2-mB2X6-wY1-n formula in which Sb5+ predominates in the B-site. Indices m, w and n indicate vacancies in A, X and Y crystallographic sites, respectively. A-site is typically occupied by cations with ionic radii greater than 1.0Å or H2O, whereas X-site is usually occupied by O2-, but smaller amounts of OH- or F- are also commonly found. Finally, Y-site is typically occupied by anions O2-, OH- or F-; however, large ionic radii monovalent cations (>1.0Å) such as K+, Cs+ and Rb+, or even H2O can occupy it. Since the predominance of Sb5+ for B site is already known, the correct A and Y main occupants determine different minerals in the group and are important for the discovery of new mineral species [3]. As a source of Sb, the roméite-group minerals are economically relevant, since Sb is present in different applications, from cosmetic industry to the metal alloy production. However, only five roméite-group mineral species, namely fluorcalcioroméite, hydroxycalcioroméite, hydroxyferroroméite, oxycalcioroméite, and oxyplumboroméite have been approved by IMA. Many others can probably be discovered from possible chemical substitutions at crystallographic sites. This study analysed three different samples and determined their chemical composition by electron microprobe analysis and Raman spectra and crystal structure obtained from single-crystal X-ray diffraction. The first sample occurs in Kalugeri Hill, Babuna Valley, Jakupica Mountains, Nezilovo,Veles, Macedonia, whereas the other two occur in Prabornaz Mine, Saint Marcel, Valle d'Aosta, Italy. Sample 1 was identified as fluorcalcioroméite, and samples 2 and 3 as hydroxycalcioroméite. These are the first descriptions of these mineral species at the mentioned occurrences.

All samples belong to the cubic crystal system, space group ??3̅?, Z = 8, where ? = 10.2881(13)Å, V = 1088.9(4)Å3 for sample 1, ? = 10.2970(13)Å, V = 1091.8(4) Å3 for sample 2, and ? = 10.289(6)Å, V = 1089.3(19)Å3 for sample 3. The crystal structure refinements led to the convergence of R-factors of the three samples: 1) R1 = 0.016. wR2 = 0.042 and Goodness-of-fit = 1.176; 2) R1 = 0.230. wR2 = 0.049 and Goodness-of-fit = 1.095; 3) R1 = 0.029. wR2 = 0.090 and Goodness-of-fit = 1.338. Bond-valence calculations validated the crystal structure refinements determining the correct valences at each crystallographic site. Discrepancies observed in the Sb5+ bond-valence calculations were solved with the use of the proper bond valence parameters revised by Mills et al. (2009) [4]. The resulting structural formulas were (Ca1.29Na0.550.11Pb0.05)Σ=2.00(Sb1.71Ti0.29)Σ=2.00(O5.73OH0.27)Σ=6.00(F0.77O0.21OH0.02)Σ=1.00 for sample 1, (Ca1.30Ce0.510.19)Σ=2.00(Sb1.08Ti0.92)Σ=2.00O6.00(OH0.61O0.21F0.18)Σ=1.00 for sample 2, and (Ca1.610.24Na0.15)Σ=2.00(Sb1.80Ti0.20)Σ=2.00O6.00(OH0.48F0.35O0.17)Σ=1.00 for sample 3. The Raman spectra of all samples exhibited the characteristic bands of chemical bonds present in roméite-group minerals - the most evident one corresponded to the stretching of Sb-O bond around 510 cm-1. Peaks around 1600 and 3600 cm-1 were observed, confirming the presence of water in the structure.

[1] Atencio, D., Ciriotti, M., Andrade, M. (2013). Mineralogical Magazine. 77, pp. 467-473.

[2] Mills, S. J. (2017). European Journal of Mineralogy. 29, pp. 307-314.

[3] Atencio, D., et al. (2010). Canadian Mineralogist. 48, pp. 673-698.

[4] Mills, S. J., et al. (2009). Zeitschrift für Kristallographie. 229, pp. 423-431.

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Cd4Te5O14, consisting of [Te5O14]-chains, a novel structure element for oxidotellurates(IV)

Felix Eder, Matthias Weil

TU Vienna, Vienna, Austria

Oxidotellurates show a vast structural diversity, especially with tellurium in the +IV oxidation state, which has been summarized and categorized recently by Christy et al. [1]. This can be attributed to the 5s2 electron lone pair of TeIV. Its large space consumption often leads to rather low symmetric and one-sided coordination polyhedra and to the formation of modular structures like clusters, chains, layers or open-framework clusters penetrated by channels [2].

Single crystals of Cd4TeIV5O14, a newly discovered compound in the Cd/TeIV/O-system, were obtained under hydrothermal conditions from a mixture of Cd(NO3)2∙4H2O and K2TeO3 (molar ratio 4:5). The educts were mixed together in a teflon vessel, which was filled with water to about ⅔ of its volume and then heated inside a steel autoclave to 483 K for a week. The title compound appeared as a minor product besides CdTeO3 [3]. Single crystals of Cd4Te5O14 are colourless and bar-shaped.

The asymmetric unit of the monoclinic unit cell (C2/c, a = 11.9074(3), b = 14.3289(3), c = 8.7169(2) Å, β = 113.629(1) °, V = 1362.58(6) ų) contains three Te, three Cd and seven O sites. With the exception of one Te and two Cd sites that are located on the 4e position (site symmetry 2), all atoms are located on the general 8f Wyckoff position. The Cd sites are all coordinated by six oxygen atoms in a range of 2.235(2)-2.539(2) Å. By edge- and corner-sharing the [CdO6]-polyhedra form an open three-dimensional framework. The TeIV sites exhibit a coordination number of 4, which is better described as 3+1 for the Te1 and Te2 sites. The [TeO4]-polyhedra have a bisphenoidal shape which is derived from a distorted [TeψO4] trigonal bipyramid where the lone pair occupies an equatorial position.

The [TeO4]-units are connected to each other by corner- and edge-sharing. This way they form helical [Te5O14]8 ̶ chains oriented parallel [203]. The sequence of the atomic sites ( ̶ Te3 ̶ Te2 ̶ Te1=Te1 ̶ Te2 ̶ ) repeats after 5 atoms which makes it a fünfer-chain. For Te-O-single-chain structures only zweier, dreier, vierer, sechser and achter-chains (repeating units of 2, 3, 4, 6 and 8 Te-atoms) have been found [1]. Using the nomenclature used by Christy et al. [1] the chains are denoted as (… ̶ ◊ ̶ ◊ ̶ ◊=◊ ̶ ◊ ̶ …). Considering the translational symmetry of the chain, a periodicity of 10 Te-atoms is found until the helix repeats itself (Fig. 1). Moving 10 Te-atoms up the chain corresponds to a translation of 2a+3c.

--- Figure 1 ---

Figure 1. [Te5O14]-chains in Cd4Te5O14; symmetry codes: i) ½-x, -½+y, ½-z; ii) ½-x, ½-y, 1-z; iii) ½+x, -½+y, 1+z; iv) 1-x, y, 1½-z; v) 1+x, -y, 1½+z

The only other known structures with the composition M4Te5O14 are two polymorphs of Ca4Te5O14 [4-5]. α-Ca4Te5O14 [4] consists of [Te8O22]-achter-single chains (…–(◊–Δ)–◊–◊–(◊–Δ)–◊–◊–…) as well as isolated [TeO3] groups. The high-pressure β-Ca4Te5O14 [5]is formed by isolated [Te3O8]- and [TeO3] groups.

[1] Christy, A. G., Mills, S. J. & Kampf, A. R. (2016). Miner. Mag. 80, 415–545. [2] Stöger, B. & Weil, M. (2013). Miner. Petrol. 107, 253–263. [3] Kraemer, V. & Brandt, G.; (1985). Acta Cryst. C41, 1152-1154. [4] Weil, M. (2004). Solid State Sci. 6, 29-37. [5] Weil, M., Heymann, G. & Huppertz, H. (2016). Eur. J. Inorg. Chem. pp. 3574-3579.

The X-ray centre of the TU Wien is acknowledged for providing access to the single-crystal and powder X-ray diffractometers. The Christiana Hörbiger foundation is acknowledged for financial support by funding the Christiana Hörbiger award.

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Water induced variety of arsenic(III) oxide intercalates with alkali chlorides

Piotr A. Gunka

Warsaw University of Technology, Warszawa, Poland

Arsenic(III) oxide has been known to form stoichiometric compounds with potassium and ammonium halides since the 19th century but they have not been structurally charaterized until the middle of the 20th century[1-4]. It was found that the compounds are intercalation compounds in which like-charged ions form alternating layers which are separated by electroneutral As2O3 layers (see Figure 1). This type of compounds have been found in nature as minerals, for instance, lucabindiite [5]. In case of intercalates with ammonium and potassium cations the layers are hexagonal and non corrugated, whereas for smaller sodium cations the arsenic(III) oxide layers are corrugated and exhibit lower symmetry. Herein, we present the synthesis methods and structural charaterization of the first As2O3 intercalates with potassium, rubidium and cesium chlorides containing water molecules in their crystal structure: MCl·As2O3·½H2O (for M = K, Rb, Cs) and KCl·As2O3·3H2O. The compounds are not only studied by single-crystal X-ray diffraction but also by solid state NMR spectroscopy and ATR-FTIR. The crystal structure determination of KCl·As2O3·½H2O permitted for a correction proposal of NH4Cl·As2O3·½H2O crystal structure.

[1] Rüdorff, F. (1886). Ber. Dtsch. Chem. Ges. 19, 2668–2679.

[2] Edstrand, M. & Blomqvist, G. (1955). Arkiv för kemi. 8, 245–256. [3] Pertlik, F. (1987). J. Solid State Chem. 70, 225–228.

[4] Pertlik, F. (1988). Monatsh. Chem. 119, 451–456.

[5] Garavelli, A., Mitolo, D., Pinto, D. & Vurro, F. (2013). Am. Mineral. 98, 470–477.

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Study of the NdO1.5-TiO2-ZrO2 ternary system of potential matrices for the immobilization of actinide wastes

Amina Sergeevna Ulanova, M S Nikolsky

IGEM, Moscow, Russian Federation

One of the defining issues in the nuclear industry's long-term development is the long-term storage of high-level waste (HLW). Preserving matrices with a complex of unique physicomechanical and chemical properties should be used to immobilization HLW. Currently, aluminophosphate and borosilicate glasses are uмsed as such matrices. Their disadvantages are low capacity for waste (4–15 wt.%), High solubility in water, rapid crystallization, deterioration of protective properties over time. It is proposed to use crystal matrices as an alternative to glasses. The study of the ternary system NdO1.5-TiO2-ZrO2 is necessary to predict the compositions of ceramics promising as matrices for the rare-earth-actinide fraction of high-level waste (HLW). By solid-phase synthesis by sintering in a muffle furnace, 6 samples were obtained with a percentage along the line of 60 wt% NdO1.5 with variable compositions of TiO2-ZrO2, and 6 samples with a percentage along the line of 35 wt% NdO1.5 with a variable composition of TiO2-ZrO2, at temperatures of 1450⁰С and 1500⁰С.
The X-ray phase analysis was carried out on an Empyrean Malvern Panalytical X-ray powder diffractometer (CuKα, 40 kV, 20 mA, 0.02 ° step), a JSM_5610LV scanning electron microscope with a ULTIM MAX 100 energy dispersive spectrometer (SEM / EDS). The phase structure was determined by comparing the experimental X-ray diffraction patterns with the standards from the database.
X-ray phase analysis of the samples showed that at a temperature of 1450⁰C for six samples with 60 wt% NdO1.5 with variable TiO2-ZrO2 compositions, the formation of phases does not occur completely and require higher temperatures, and on the 35 wt% NdO1.5 13% ZrO2 line and 52% TiO2 is assumed to form a eutectic region. A preliminary SEM analysis confirmed this. More detailed results of the analysis of samples will be shown on the stand.

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Ni2MnGa shape memory alloy studied by x-ray diffraction measured in-situ in tension

Petr Cejpek1, Kristián Mathis1, Daria Drozdenko1, Oleg Heczko2, Ladislav Straka2, Ross Colman1

1Charles University, Praha, Czech Republic; 2Institute of Physics of Czech Academy of Sciences, Praha, Czech Republic

Ni2MnGa is a widely studied system due to its interesting properties related to the magnetic shape memory phenomena. The compounds based on Ni-Mn-Ga system have also an interesting application potential as the micropumps or the sensors [1, 2]. Their shape memory properties are connected to the martensitic transformation, during which the high-temperature cubic phase (austenite) undergoes a transformation to the low-temperature phase with a lower symmetry (martensite) [3].

As a consequence of a large magnetic anisotropy and a high mobility of the internal regions (so called twin variants/twinned domains) magnetically induced reorientation could be achieved - it is more energeticaly preferable to reorient the whole unit cell than to rotate magnetic moments. A similar structural reorientation could be achieved by the application of an external mechanical force in tension or compression.

In our previous studies [3, 4], the high resolution reciprocal space mapping with x-ray diffraction proved itself as a good tool to study the structure in Ni2MnGa samples which could contain several twinned domains due to the shape memory effects. The reciprocal space mapping helps to distiguish between the Bragg reflections corresponding to individual twins. Moreover, reciprocal space mapping allows the precise study of the lattice parameters and a possible modulation in the structure.

Our goal was to study the structure during the reorientation by x-ray diffraction in-situ in the applied tension. For this purpose, we mounted the tensile stage (possible load up to 4 kN) inside the diffractometer. The studied specimen was Ni50Mn28Ga22 with martensitic structure at the room temperature. Besides the lattice parameters and volume ratios of individual twin variants in the various tension, the measurement revealed that the results differ in dependence on the way how the sample is hold inside the stage. Holding directly with clamps allows almost full structural reorientation at approximately 10 MPa, but the sample cracks when the twin boundary reached the place on the sample hold by the clamps. Holding by a glue prevented the reorientation and the full reorientation did not occur up to 20 MPa.

[1] A. R. Smith, et al., Microfluidic. Nanofluidics, 18 (2005), p. 1255, doi: 10.1007/s10404-014-1524-6

[2] A. Hobza, et al., Sensor. Actuator. A, 269 (2018), p. 137, doi: 10.1016/j.sna.2017.11.002

[3] O. Heczko, et al., Acta Mater., 115 (2016), pp. 250-258, doi: 10.1016/j.actamat.2016.05.047

[4] P. Cejpek, et al., J. Alloys Compd., 855 (2021) 157327, doi: 10.1016/j.jallcom.2020.157327

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57Fe Mössbauer spectroscopy study of the Fe-bearing, Ge,Ga-rich synthetic tourmalines

Oxana Anosova1, Kirill V. Frolov1, Tatiana V. Setkova2, Vladimir S. Balitsky2, Elena Yu. Borovikova3

1Shubnikov Institute of Crystallography of FSRC “Crystallography and Photonics” RAS, Moscow, Russian Federation; 2D.S. Korzhinskii Institute of Experimental Mineralogy RAS, Chernogolovka, Russian Federation; 3Faculty of Geology, Moscow State University, Moscow, Russian Federation

Borosilicate mineral tourmaline is one of the most widespread minerals in nature, one of the most popular gems and promising piezoelectric, adsorption material [1,2]. Synthetic Ga,Ge-rich analogue is structure model of tourmalines at high pressure. This work presents the results of Mössbauer studies of Ga,Ge-rich tourmaline crystals which contain a significant iron content. The crystals were grown in hydrothermal boric, boric-alkaline, boric-fluoride solutions at 650 ˚С and 100 MPa [3,4]. The chemical composition of the five studied tourmaline crystals in atoms per formula unit, calculated based on the 15 (T + Y + Z) atoms, is shown in Table 1.

The 57Fe Mössbauer absorption spectra were measured at room temperature on a standard MS-1104Em spectrometer with a 57Co (Rh) source. The structural and electronic states of iron ions have been studied and refined. A comparison is made with the results of X-ray diffraction measurements.

This work was supported by the Russian Ministry of Science and Higher Education under the Research Program AAAA-A18-118020590150-6 within the State assignment of D.S. Korzhinskii Institute of Experimental Mineralogy RAS - in part of crystal growth; and under the Research Program АААА-А20-120022890091-8 within the State assignment of the FSRC “Crystallography and Photonics” of RAS - in part of Mössbauer spectroscopy.

[1] Wang, C. P.; Wu, J. Z.; Sun, H. W.; Wang, T.; Liu, H. B.; Chang, Y. Adsorption of Pb(II) Ion from Aqueous Solutions by Tourmaline as a Novel Adsorbent. Ind. Eng. Chem. Res. 2011, 50 (14), 8515–8523. https://doi.org/10.1021/ie102520w.

[2] Shekhar Pandey, C.; Schreuer, J. Elastic and Piezoelectric Constants of Tourmaline Single Crystals at Non-Ambient Temperatures Determined by Resonant Ultrasound Spectroscopy. J. Appl. Phys. 2012, 111 (1). https://doi.org/10.1063/1.3673820.

[3] Setkova, T. V.; Balitsky, V. S.; Shapovalov, Y. B. Experimental Study of the Stability and Synthesis of the Tourmaline Supergroup Minerals. Geochemistry Int. 2019, 57 (10), 1082–1094. https://doi.org/10.1134/S0016702919100094.

[4] Pushcharovsky, D. Y.; Zubkova, N. V.; Setkova, T. V.; Balitskii, V. S.; Nekrasov, A. N.; Nesterova, V. A. (Ga,Ge)-Analogue of Tourmaline: Crystal Structure and Composition. Crystallogr. Reports 2020, 65 (6), 849–856. https://doi.org/10.1134/S1063774520060279.

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Co-crystal structure of a dinuclear (Zn-Y) and a trinuclear (Zn-Y-Zn) complexes derived from a Schiff base ligand

Ibrahima Elhadji Thiam1, Mohamed Lamine Gaye1, Javier Alcides Ellena2, Mamour Sarr1, Mayoro Diop1, Natalia Alvarez3, Aliou Hamady Barry4

1Université Cheikh Anta DIOP de Dakar, Dakar, Senegal; 2Instituto de Física de São Carlos, Universidade de São Paulo, CP 369, 13.560-970, São Carlos, SP, Brazil; 3Facultad de Química, General Flores 2124, UdelaR, Montevideo, 11800, Uruguay; 4Department of Chemistry, University of Nouakchott, Nouakchott, 130301, Mauritania

The present investigation describes the synthesis and structural study of a metal-zinc ligand [ZnL.H2O], which was used to generate three dimensional supramolecular complex formulated as [Y{Zn(L)(SCN)}(SCN)2].[Y{Zn(L)(SCN)}2(DMF)2].(NO3). The title compound crystallizes in the triclinic space group P-1 with the following unit cell parameters: a = 14.8987(7) Å, b = 15.6725(8) Å, c = 19.2339(10) Å, α = 94.610(4)°, β = 103.857(4)°, γ = 101.473(4)°, V = 4234.4(4) Å3, Z = 2, R1 = 0.063 and wR2 = 0.96. For this compound, the structure reveals that one heterodinuclear unit [Y{Zn(L)(SCN)}(SCN)2] is co-crystallized with a heterotrinuclear unit [Y{Zn(L)(SCN)}2(DMF)2].(NO3). In the dinuclear moiety, the organic molecule acts as a hexadentate ligand and in the trinuclear unit, it acts as a pentadentate ligand with one of the oxygen methoxy group remaining uncoordinated. In both units the coordination environment of the zinc metal can be described as distorted square pyramidal. In the dinuclear unit the Y(III) is hexacoordinated while it is octacoordinated in the trinuclear unit. The environment of the Y(III) can be described as a distorted octahedral geometry in the dinuclear and as a distorted square antiprism in the trinuclear units respectively.

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Copper(II) and zinc(II) complexes based on azo Schiff base ligand: Synthesis, crystal structure and photoisomerization study

Siham SLASSI1, Abdelkrim EL-Ghayoury2, Mohammed Aarjane1, Amina Amine1

1Moulay Ismail University faculty of Science Meknes, Meknes, Morocco; 2Université d’Angers, France

Schiff base compounds have been recognized as privileged of organic molecules, because of their interesting and important properties, they are able to coordinate with various metals and stabilize them. It’s an important special centre of attraction in many areas like biological, clinical, medicinal, analytical and pharmacological field [1]. They are also used in analytical medicinal and polymer chemistry. The azomethine (C=N) linkage in Schiff bases is significant in determining the mechanism of transamination and resamination reactions in biological systems[2], and it has been suggested that the azomethine group is responsible of the biological activities of Schiff bases molecules. Schiff bases ligands with chelating abilities have been recognized as privileged ligands to form stable complexes with a large variety of transition metals [3].

Herein, newly synthesized mononuclear copper(II) and zinc(II) complexes containing an azo Schiff base ligand (L), prepared by condensation of 2-hydroxy-5 (otolyldiazenyl)benzaldehyde and propylamine, were obtained and then characterized using infrared and NMR spectroscopies, mass spectrometry and X-ray diffraction. Ligand L behaves as a bidentate chelate by coordinating through deprotonated phenolic oxygen and azomethine nitrogen. The copper and zinc complexes crystallize in triclinic and orthorhombic systems, respectively, with space groups P-1 and Pca21. In these complexes, the Cu(II) ion is in a square planar geometry while the Zn(II) ion is in a distorted tetrahedral environment. The photochemical behaviors of ligand L, [Cu(L)2] and [Zn(L)2] were investigated.

[1] P. Przybylski, A. Huczynski, K. Pyta, B. Brzezinski, and F. Bartl, “Biological Properties of Schiff Bases and Azo Derivatives of Phenols,” pp. 124–148, 2009.

[2] P. P. Dholakiya and M. N. Patel, “Synthesis and Reactivity in Inorganic and Metal- Organic Chemistry Metal Complexes : Preparation , Magnetic , Spectral , and Biocidal Studies of Some Mixed ‐ Ligand Complexes with Schiff Bases Containing NO and NN Donor Atoms,” no. April 2015, pp. 37–41, 2010.

[3] A. Corma, H. Garcia, F. X. Llabrés, and I. Xamena, “Engineering
metal organic frameworks for heterogeneous catalysis,” Chemical Reviews, vol. 110, p. 4606, 2010

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Geopolymers based on some clay from Burkina Faso : preparation and characterization

Soungalo OUATTARA1, Brahima SORGHO1, Lamine ZERBO1, Youssouf SAWADOGO1, Moustapha SAWADOGO1, Mohamed SEYNOU1, Philippe BLANCHART2

1University Joseph Ki-Zerbo, Ouagadougou, Burkina Faso; 2Institut of Research in Ceramique (IRCER)

Geopolymers based on clay materials from Burkina Faso were developed and then characterized for use in building. The results of the characterization of the clay mineral material referenced TAN as well as its calcined forms have shown by several analysis techniques (XRD, IR, ICP-AES) that TAN contains kaolinite (71%), quartz (20%), illite (4%) and goethite (2%). TAN clay and its calcined forms are each mixed with the alkaline solution (sodium hydroxide solution 8 mol. L-1) in a mass ratio (alkaline solution/clay) ranging from 0.33 to 0.36. The results of the mechanical and mineralogical tests of the geopolymers produced showed that GP-MK0 produced had the best performance favorable for its use in construction. Indeed, its linear shrinkage (3.44%) is low and the compressive strength (22.50 MPa) is greater than 4 MPa. This performance of GP-MK0 is due to the formation of a phase rich in silica and alumina (Na2(AlSiO4)6(OH)2. 2H2O).

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Impact of dopant type (Tm, Co, and Mn) and doping method on the local and statistical structure of framework whitlockite-type Ca3(VO4)2 crystals. New crystal-chemical effects.

Galina Kuz'micheva1, Irina Kaurova1, Liudmila Ivleva2

1MIREA - Russian Technological University, 78 Vernadsky ave., Moscow 119454, Russia; 2Prokhorov General Physics Institute, Russian Academy of Sciences, 38 Vavilova str., Moscow 119991, Russia

The whitlockite-type compounds have a structure favorable for the introduction of dopant ions, which led to the implementation or enhancement of functional properties. The use of different doping methods can significantly affect the concentration and structural location of activator ions in the crystal matrix, and hence the properties of the material. This was the motivation for the work. The main research methods are X-ray structural analysis (diffractometers and synchrotron, room temperature and 100 K; statistical structure) and X-ray absorption spectroscopy (synchrotron; local structure).

In the idealized whitlockite structure Ca3(PO4)2 (space group R3c, Z = 18) with the composition (Ca118Ca218Ca318)(P118P218)O144, Ca1 and Ca3 atoms are located in two-capped trigonal prisms (CN = 8; CN is a coordination number) and Ca2 atoms form mono-capped trigonal prisms (CN = 7), P1 and P2 atoms being in tetrahedra (CN = 4). In the whitlockite-type structure Ca3(VO4)2 (CVO; space group R3c, Z = 21) with the composition [Ca118Ca218Ca318Ca46(Ca52.65)(Ca5А0.35)](V118V218V36)O168, there are additional sites in the framework channels: Ca4 and Ca5A (octahedra; CN = 6), Ca5 (tetrahedron; CN = 4), Ca5 + Ca5A (distorted octahedron; CN = 6), and V3 (trigonal pyramid; CN = 3 + 1).

Dopant ions (up to 1.0 wt%) introduced into the melt (Czochralski method) over CVO stoichiometry are distributed over the Ca3 and Ca4 (light-green CVO:Tm and green CVO:Mn crystals) as well as Ca5 + Ca5A (CVO:Mn) crystallographic sites. The dopant ions form specific local environments: in the CVO:Tm structure, CN Tm3+ = 7 (octahedral coordination by O2- ions with one additional O atom) and CN V5+ = 4.4; in the CVO:Mn structure, CN Mn3+ = 6 (an elongated octahedron is a tetragonal bipyramid; Jahn-Teller effect) and CN V5+ = 4. Air annealing of CVO:Mn crystals promotes the appearance of yellow-orange crystals with Mn4+ and Mn(3+d)+ ions having octahedral coordination in the Ca3 and Ca5 sites in the structures of the lower and upper parts of the crystal boule, respectively.

High-temperature diffusion annealing of CVO crystal with the presence of Mn2O3 solid phase (blue-green CVO:Mn2O3) increases the number of sites (Ca2, Ca3, Ca4) occupied by a greater number of Mn(2+d)+ ions with variable formal charge and tetrahedral local environment. Similar annealing of CVO with the Co3O4 solid phase (violet CVO:Co3O4) leads to the appearance of Co2+ ions, which, unlike CVO:Mn2O3, partially replace the Ca2+ ions in the Ca2, Ca3, Ca4, Ca5, and Ca5A crystallographic sites.

The bands revealed on the absorption spectra were assigned to Tm, Co, and Mn ions having different formal charges and different local environments in the CVO structure.

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Understanding the structure-property relationships of lead-free piezoelectric systems

Alicia Maria Manjon Sanz1,2, Charles McLouth Culbertson2, Caitlin Berger2, Michelle Dolgos2,3

1Oak Ridge National Laboratory; 2Oregon State University; 3University of Calgary

Lead zirconate titanate, PbZr1-xTixO3 (PZT), is a ceramic perovskite material that has exceptional striking piezoelectric properties at the morphotropic phase boundary (MPB) showing a piezoelectric response (d33) of 200-600 pC/N [1]. This compound plays an important role in industry and has many commercial applications [2-3]. However, the toxicity of lead has spurred considerable interest in the discovery of Pb-free ferroelectric materials. Here, we present our results on two different Pb-free piezoelectric systems: 1) solid solutions between BaTiO3 (BT) and BiInO3 (BI), and 2) BaZr0.2Ti0.8O3 (BZT) and Ba0.7Ca0.3TiO3 (BCT).

1) Solid solutions between BaTiO3 and BiInO3: Bismuth based perovskites are established as good ferroelectric materials, but it is still necessary to improve the piezoelectric properties of Bi-based perovskites to compete with the exceptional ferroelectric properties of PZT. To fully understand the reason of these maximized physical properties at the MPB, it is crucial to study the structure in detail. For the system (1-x)BT – (x)BI, we study the electromechanical properties and the structure of the solid solution between the Bi-based material BI with orthorhombic space group Pna21 and the classical piezoelectric material BT with tetragonal structure P4mm, in the region 0.03 ≤ x ≤ 0.12. Based on a structural analysis study previously carried out by Datta et al. [4], it was predicted that there is an MPB created by a polarization extension mechanism for the system at x = 0.1. In our work, based on Rietveld analysis performed on neutron and synchrotron radiation X-ray diffraction data, we have found that a gradual structural phase transition takes place from a polar tetragonal structure (P4mm) and passes through two regions of coexisting phases: 1) P4mm + R3m in the range 0.03 ≤ x ≤ 0.075, and 2) + R3m for 0.10 ≤ x ≤ 0.12. The properties also transition from ferroelectric (x ≤ 0.03) to relaxor ferroelectric (x ≥ 0.05) as the dielectric permittivity maximum becomes temperature and frequency dependent. This transition was also confirmed via polarization-electric field measurements as well as strain-electric field measurements. At the critical composition of x = 0.065, a moderate strain of ~ 0.104%, and an effective piezoelectric coefficient (d33*) of 260 pm/V were observed. The original purpose of this study was to demonstrate the polarization extension mechanism as predicted in the literature, but due to the ferroelectric to relaxor transition, this mechanism was not found to be present in this system. However, this demonstrates that BaTiO3-based lead-free ceramics could be modified to obtain enhanced electromechanical properties for actuator applications [5].

2) Solid solutions between BaZr0.2Ti0.8O3 and Ba0.7Ca0.3TiO3: The solid solution (1-x)BZT-xBCT is the first Pb-free piezoelectric material with a significantly high enough d33 ~ 620 pC/N at the MPB at x = 0.50, that has the potential to replace the industry standard PZT in certain applications [6]. So far, lots of studies have focused mainly in investigating the physical properties. However, the two structural characterization works of the structure at the MPB for BZT-xBCT, using solely synchrotron X-ray diffraction data, yield different results [7-8]. Here, we re-investigate the phase diagram of (1-x)BZT-xBCT as a function of temperature using high quality neutron powder diffraction data collected at POWGEN at the Spallation Neutron Source and applying the Rietveld method. We study the composition x = 0.50 at the MPB, one composition in the rhombohedral range (x = 0.40), and another composition in the tetragonal range (x = 0.60). Neutron diffraction is a powerful tool to have more accurate information about the light elements such as oxygens. So, this work is crucial to investigate the octahedral tilts of (1-x)BZT-xBCT materials, and further understand how the structure has an impact on their physical properties. We expect to obtain a detailed description of the structures at different temperatures, solve the debate of the symmetry at the MPB, and build a phase diagram.

[1] Damjanovic, D., Klein, N., Li, J., Porokhonskyy, V. (2010) Funct. Mater. Lett. 3 (1):5–13.

[2] Panda, K. P. (2009) J. Mater. Sci. 44 (19):5049–5062.

[3] Roedel, J., Jo, W., Seifert, K. T. P., Anton, E. M., Granzow, T., Damjanovic, D. (2009) J. Am. Ceram. Soc. 92 (6):1153–1177

[4] Datta, K., Suard, E., Thomas, P. A. (2010) Appl. Phys. Lett. 96 (22):221902–221903.

[5] Manjon-Sanz, A., Berger, C., Dolgos, M. R., J. Mater. Sci. (2017) 52:5309–5323.

[6] Liu, W., Ren, X. B., Phys. Rev. Lett., (2009) 103, 257602.

[7] Keeble, D. S., Benabdallah, F., Thomas, P. A., Maglione, M., Kreisel, J. (2013) Appl. Phys. Lett., 102(9) 092903.

[8] Haugen, A., Forrester, J. S., Damjanovic, D., Li, B., Bowman, K. J., Jones, J. L, (2013) J. Appl. Phys., 113, 014103.

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New lead- and tellurium-free thermoelectric materials: AgSnm(SbxBi1-x)Sem+2

Daniela Delgado1, Paulina Valencia-Gálvez1, María Luisa López2, Inmaculada Álvarez-Serrano2, Silvana Moris3, Antonio Galdámez1

1Departamento de Química, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Chile; 2Departamento de Química Inorgánica, Facultad de Ciencias Químicas, Universidad Complutense, 28040 Madrid; 3Centro de investigación de estudios avanzados del Maule (CIEAM), Vicerrectoría de Investigación y Postgrado, Universidad Católica del Maule, Avenida San Miguel 3605, Talca 3480112, Chile

The global demand for energy production has intensified the interest in improving the efficiency of energy generation systems. In this context, thermoelectric materials have been used to take advantage of the conversion of residual heat into electricity [1]. High efficiencies have been obtained using lead-based nano-structured thermoelectric materials, such as (PbTe) m-AgSbTe2 systems [2]. Due to the presence of lead, a known toxic element, and tellurium, a rare element in the earth's crust, alternatives must be sought. Chemical modifications and doping of SnSe have generated interest due to its low intrinsic thermal conductivity [3]. Of such modifications, AgSnmSbSe2Tem phases with m = 2 and 10 have shown values ​​of ZT = 0.1 at RT [4]. On the other hand, to enhance the Seebeck coefficient in AgSbTe2 compounds, Bi doping has been used, which increased the ZT value by 10% [5].

Herein, we report the synthesis, characterization, and electrical properties of AgSnm(Sb1-xBix)Sem+2 compounds, with m = 1, 2. These phases were synthesized by the ceramic method at high temperatures (Figure 1A). Rietveld refinement results indicated that the selenides consisted of phases related to NaCl-type crystal structure. The powder X-ray diffraction (XRD) patterns were refined in the Pm-3m and P4/mmm space group. The backscattered image and EDS analysis of the samples revealed that the chemical compositions were uniform throughout the scanned region. The microstructural features of the samples were analysed using HRTEM. Figure 1B shows the ED patterns for the selected areas. The results suggest the presence of regions with different symmetries at the nanoscale.

Figure 1. (A) X-ray diffraction patterns (XRD) for AgSnm(Sb1-xBix)Sem+2 (B) HRTEM images showing electron diffraction patterns (ED) and fast fourier transforms (FFTs). The arrows indicate the dots of the reciprocal lattice, which violate the systematic absence of the Fm-3m space group.

[1] Zhang, X., & Zhao, L. D. (2015). Thermoelectric materials: Energy conversion between heat and electricity. Journal of Materiomics, 1(2), 92-105.

[2] Han, M. K., Androulakis, J., Kim, S. J., & Kanatzidis, M. G. (2012). Lead‐Free Thermoelectrics: High Figure of Merit in p‐type AgSnmSbTem+2. Advanced Energy Materials, 2(1), 157-161.

[3] Zhao, L. D., Lo, S. H., Zhang, Y., Sun, H., Tan, G., Uher, C., Wolverton C., Dravid V. P. & Kanatzidis, M. G. (2014). Ultralow thermal conductivity and high thermoelectric figure of merit in SnSe crystals. Nature, 508(7496), 373.

[4] Figueroa-Millon, S., Álvarez-Serrano, I., Bérardan, D., & Galdámez, A. (2018). Synthesis and transport properties of p-type lead-free AgSnmSbSe2Tem thermoelectric systems. Materials Chemistry and Physics, 211, 321-328.

[5] Mohanraman, R., Sankar, R., Chou, F. C., Lee, C. H., & Chen, Y. Y. (2013). Enhanced thermoelectric performance in Bi-doped p-type AgSbTe2compounds. Journal of Applied Physics, 114(16), 163712.

Keywords: Rietveld analysis; lead-free Thermoelectric; HRTEM, Selenides

Authors are grateful for FONDECYT Project N° 1190856

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What are the crystallographic and genetic implications of a naturally occurring polycrystal composed of two mineral phases of distinct symmetries and anionic groups? The case study of “joint-occurrence” of emerald+alexandrite polycrystals from Brazil

Teodoro Gauzzi1, Leonardo Martins da Graça2, Marco Antonio Leandro da Silva2, Erico Tadeu Fraga Freitas1, Breno Barbosa Moreira1, Karla Balzuweit3,1

1Centro de Microscopia, Universidade Federal de Minas Gerais, Belo Horizonte , Brazil; 2Departamento de Geologia, Universidade Federal de Ouro Preto, Brazil; 3Departamento de Física, Universidade Federal de Minas Gerais, Brazil

Alexandrite and emerald are two gem-quality varieties of chrysoberyl (BeAl2O4) and beryl (Be3Al2Si6O18), respectively. Chrysoberyl is a multiple oxide which crystallises within orthorhombic system and space group Pmnb. Its crystalline structure is composed of O2- anions which are distortedly arranged in a cubic closed packing together with Be2+-tetrahedra and Al3+- octahedra cations; Be2+ is an inversion Ci-type site and Al3+ is divided into inversion Al1 (Ci-type) and reflexion Al2 (Cs-type) sites. Beryl is a cyclosilicate which crystallises within orthorhombic system and space group P6/mcc. Its crystalline structure is composed of Si4+ tetrahedra which are interconnected by their vortices, forming ring-like layers that are stacked. Between the Si4+-rings, layers of Be2+-tetrahedra and Al3+-octahedra cations are alternately arranged. Moreover, the senary axis of beryl is perpendicular to the planes formed by the stacked Si4+-rings and is parallel to the channels-like voids formed by the aforementioned rings. Chrysoberyl and beryl have been extensively studied and referred not only as gemstones (i.e. the role of Cr3+ as a chromophore element) but also as materials used to manufacture lasers. Alexandrite and emerald were simultaneously approached in few studies, although studied separately. Thus, there was no study nor reference about the “joint-occurrence” of emerald and alexandrite in just one “polycrystal”. Consequently, no crystallographic relation could be established in this situation, specially all the processes that could explain the hypothetical transition from orthorhombic to hexagonal symmetry or vice versa. Two minerals that “illustrate” the crystallographic relations and the transition between the orthorhombic and hexagonal symmetries, in naturally occurring minerals, are the silicates cordierite [(Mg,Fe)2Al3(AlSi5O18); space group Cccm] and indialite [Mg2Al3(AlSi5O18); space group P6/mcc], respectively. The transition between these phases occurs above 1450 ºC and is related to Fe / (Mg + Fe) ratio during the crystallisation [1]. The transition between orthorhombic to hexagonal (no matter the order) has been mainly demonstrated by epitaxial processes which are only exemplified by synthetized materials. The phase perovskite- SrIrO3 is generally synthetized within hexagonal symmetry (space group C2/c). In conditions of high pressure, this phase symmetry becomes orthorhombic (space group Pnma) due to epitaxial processes on oxide substrates with the same crystal structure of perovskite [2]. Another example of the role of epitaxy in the transition between the aforementioned symmetries is given by multiferroics of RMnO3-type (R = rare earth elements or REE). In this case, the type of REE of R site influences the symmetry: to R = La-Dy, symmetry is orthorhombic, and to R = Ho-Lu, symmetry is hexagonal. However, with the aid of epitaxial stabilization technique, orthorhombic symmetry-materials such as TbMnO3, DyMnO3 and GdMnO3 can be synthetized within hexagonal symmetry and originate high quality magnetic materials [3]. After contextualizing the state-of-art of the crystallographic

relations and transition between orthorhombic to hexagonal symmetries, this study also proves to be novel due to the rarity of the samples: natural “joint-occurrence” alexandrite + emerald polycrystals (core of alexandrite surrounded by an emerald monocrystal) from Brazil. Apart from the transition in symmetry, other relevant questions are: how to explain the transition between a silicate (emerald) and an oxide (alexandrite), or vice versa, in the same polycrystal? Why the arrangement of the inner alexandrite monocrystals varies among the samples? Which mineral phase has crystalized first and how their genesis can be explained by chemical data? In order to answer consistently to these questions and for a better knowledge of these implications, these samples are being investigated with the aid of techniques such as electron backscattered diffraction (EBSD), transmission electron microscopy (TEM) and electronic probe microanalysis (EPMA). Preliminary TEM studies show an orientation relationship between micrometer sized grains of emerald and alexandrite.

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Effects upon Substitution in Alkali Metal Thallides: How far can X-Ray Structure Determination of Strongly Absorbing Compounds go?

Stefanie Gärtner

University of Regensburg, Institute of Inorganic Chemistry, Regensburg, Germany

Compounds including thallium in formal negative oxidation states have been known since Zintl stated the existence of NaTl in the 1930s [1]. In the 1980s and 1990s, binary materials of alkali metal and thallium have been characterized [2] but crystal structures always suffered from severe absorption effects due to very large absorption coefficients for these kinds of materials. This fact for a long time was equitable to the physical frontier of the method of structure determination for these element combinations. Nowadays, for these compounds, which were formerly assumed to behave rather as a primary beam stop, very good data sets can be realized due to highly resolving detectors and intensive x-ray sources [3]. This is the pre-condition for a renaissance of investigations on alkali metal thallides. The amount of alkali metal does not readily suggest the formed thallium sublattice. In fact, one can find transitions between different type structures in dependence of the more electropositive element involved. Looking at the already known alkali metal thallide compounds, it is striking that some gaps still have remained [4]. For example, in A15Tl27 (A= Rb, Cs) [5] and K49Tl108 [6] type structures, the ratio of alkali metal : thallium is very similar, but the respective crystal structures severely differ. While K49Tl108 is a complex cubic compound, A15Tl27 involves Tl117− clusters and two-dimensional thallium layers. Here, partially occupied alkali metal Wyckoff sites allow for the discussion of their effect on the observed thallium sublattice. Additionally, the possibility of partially replacing cesium by thallium could be demonstrated for the new binary material Cs14.53Tl28.4 in terms of an ordered substitution variant of Cs15Tl27.

[1] E. Zintl and W. Dullenkopf, Z. phys. Chem. 1932, B16, 195-205; S. M. Tiefenthaler, M. Schlosser, F. Pielnhofer, I. G. Shenderovich, A. Pfitzner and S. Gärtner, Z.Anorg.Allg. Chem. 2020, 646, 82-87; S. Tiefenthaler, N. Korber and S. Gärtner, Materials 2019, 12.

[2] J. D. Corbett, Angew. Chem. Int. Ed. 2000, 39, 670-690.

[3] S. Gärtner, S. Tiefenthaler, N. Korber, S. Stempfhuber and B. Hischa, Crystals 2018, 8.

[4] S. Gärtner, Crystals 2020, 10(11), 1013

[5] Z. C. Dong and J. D. Corbett, Inorg. Chem. 1996, 35, 1444-1450

[6] G. Cordier, V. Müller and R. Fröhlich, Z. Kristallogr. 1993, 203, 148-149.

Keywords: x-ray structure determination; high absorption coefficients; thallides; alkali metal; Zintl phases.

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Investigation of The Relationship between Groups and Subgroups in C3S’s Structure Transition

dounia Tlamsamani, mbark ait mouha, khalid yamni

Materials, Molecular Engineering Environment Laboratory, Moulay Ismail University, Zitoune 11201, Morocco

In recent years, many studies have been carried out on cement and its phases to understand the morphology, and to control the mineralogy of this material; due to the great position it has become globally occupied. This material is formed from a synthetic rock called clinker; tricalcium silicate (Ca3SiO5 or C3S) its major constituent present a concentration from 40% to 70%, and its solid solution with various impurities is called alite. Impure C3S exhibits seven polymorphs from ambient temperature to 1500°C; three forms triclinic (T1, T2, T3), three monoclinic (M1, M2, M3) and one shape rhombohedral (R). At room temperature, impurities stabilize some of the high temperature forms of the pure compound. Those forms are related by transformation matrix determined in this article. The aim of the present paper is to investigate the structural modulations of alite.

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Synthesis and topotactic manipulation of layered oxysulfide CaSrMnO2Cu4-δS3

Viktoria Falkowski, Simon J. Clarke

University of Oxford, Inorganic Chemistry Laboratory, South Parks Rd, Oxford, OX1 3QR, UK

The utilization of transition-metal based layered compounds is already established in industrial applications. Considering a combination with mixed-anion systems creates an extended pool of materials that can be screened for superior functionality. The option for post-synthetic alterations to the system offers further possibilities to control properties and gives access to kinetically stable products.

Previous works explored the possibility to influence magnetism and reversibly insert lithium in the oxysulfides Sr2MnO2Cu2m-δSm+1 (δ ≈ 0.5).[1-3] While trying to minimize the weight of these materials the compound CaxSr2-xMnO2Cu4-δS3 (x = 1; δ ≈ 0.5) was obtained by ceramic synthesis. The compound consists of antifluorite-type copper sulfide double layers exhibiting a copper deficiency and square planar MnO2 sheets separated by the alkaline-earth cations. Magnetic susceptibility measurements show high-temperature Curie-Weiss behavior and a positive Weiss constant of 9(2) K suggests that the net exchange interactions are predominantly ferromagnetic. The effective magnetic moment of μeff = 5.63(2) μB indicates the oxidation of manganese to a (2+δ)+ state. Oxidative copper deintercalation provides control over the oxidation state of Mn, while replacing Cu+ by Li+ under reductive ion exchange conditions (sse Fig. 1) also makes the material interesting for battery applications.

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Ag, Cu, Hg, Pt, and Te substitutions in the synthetic analogue of palladseite, Pd17Se15: an experimental mineralogical study

František Laufek, Anna Vymazalová

Czech Geological Survey, Prague, Czech Republic

Palladseite, Pd17Se15 was described as a new mineral by Davis et al. [1] from residual concentrates from gold washing at Itabira, Minais Gerais, Brazil. Palladseite has an ideal chemical composition of Pd17Se15. Ag, Cu, Hg and Pt are common elements to occur in the palladseite structure and are regarded as non-essential elements for palladseite; e.g. Cabral and Lehmann [2] indicated 3.89 wt.% of Hg and 4.43 wt.% of Ag for palladseite-like mineral from Gongo Soco, Brazil. Crystal structure of synthetic Pd17Se15 was solved by Geller [3].

In order to explain the incorporation of reported significant amounts of Ag, Cu, Hg, Pt and Te and define the range of their solubility in the palladseite structure, an experimental study of solubility of above-mentioned elements in the synthetic analogue of palladseite at 400 °C was performed. Silica glass tube technique was used. To document the impact of these elements on the palladseite crystal structure, Rietveld refinement analysis of powder X-ray diffraction data of experimental products was carried out.

Palladseite (Pd17Se15) crystalizes in the Pm-3m space group (a = 10.607 Å) and contains four Pd and three Se sites. It has a framework crystal structure formed by three types of polyhedra: [PdSe6] octahedra, [PdSe4] squares and [PdSe4] flattened tetrahedra. Three way of substitution mechanism were revealed to occur in the palladseite structure. Cu, Ag and Hg enter the palladseite structure in a significant amount (e.g. up to 8.8 wt% of Hg) and occupy a new position 3d of the Pm-3m space group, which was empty in pure Pd17Se15. As a consequence, Pd occupancy of adjacent [Pd(4)Se6] octahedron is reduced to 0.5 for Cu and Ag - bearing palladseite. Incorporation of Hg cases vacancy of this [Pd(4)Se6] position. Contrary to that, Pt substitutes Pd at the Pd(2) position in the palladseite structure and shows square-planar coordination by Se atoms. This is in agreement with expected coordination preference of Pt. Te enters palladseite structure in an significant amount (6.50 wt. %) and substitutes Se atoms without further modification of the palladseite structure.

Incorporation of Cu, Ag and Hg to the palladseite causes significant changes of its powder X-ray diffraction pattern and hence can be easily detected.

Figure 1. Crystal structure of substituted palladseite (M = Ag, Cu or Hg). For Hg-bearing palladseite, the Pd(4) site is empty. Note three types of coordination polyhedra including [PdSe4] squares (yellow), [PdSe4] flattened tetrahedra (green) and [PdSe6] octahedra (orange).

[1] Davis, R.J., Clark, A.M., Criddle, A.J. (1977). Mineral Mag. 41, 123. [2] Cabral, A.R., Lehmann, B. (2007). Ore Geology Reviews, 32, 681. [3] Geller, S. (1962) Acta Cryst. 15, 713.

Keywords: Pd17Se15, palladseite, Rietlved refinement, minerals, substitutions

This work was supported by an internal project of the Czech Geological Survey no. 311020.

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Charge density in fluorapatite, Ca5(PO4)3F, from X-ray diffraction measurements on mineral and synthetic crystals

Agnieszka Huć1, Marcin Stachowicz1, D. E. Harlov2, Jan Parafiunk1, Krzysztof Woźniak3

1Institute of Geochemistry, Mineralogy and Petrology, Faculty of Geology, University of Warsaw, Żwirki i Wigury 93, Warsaw 02-089, Poland, Section 3.6; 2GeoForschungsZentrum, Telegrafenberg, 14473 Potsdam, Germany; 33Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Żwirki i Wigury 101, Warszawa 02-093, Poland

Apatite is a name currently used for a mineral supergroup which contains over 40 mineral species with a similar atomic framework structure. According to occupancy of the two metal-cation sites and the tetrahedral site in the crystal structure, the apatite supergroup is subdivided into five groups. One of these groups is the apatite group where the metal sites are occupied by the same dominant element: Ca, Pb, Mn or Sr, and the tetrahedral site is occupied by P, As, or V [1,2]. In common use, the name apatite comprises the calcium phosphate minerals in which the halogen site is occupied by the F-, Cl- or OH- anions in the form of columns along the edges of the unit cell. If the column site is dominated by F, the apatite is referred to as fluorapatite which crystallizes in space group P63/m.

On the basis of a multipole refinement from high resolution x-ray diffraction data collected up to 0.4 Å, a quantitative experimental charge density distribution has been determined for natural (n) and synthetic analog (s) of fluorapatite. The Bader charges [3] for all atoms were determined from electron density integration within atomic basins (Fig. 1), qCa(1)(n)=+1.6e; qCa(1)(s)=+1.5e; qCa(2)(n)=+1.5e; qCa(2)(s)=+1.6e; qF(n)=-0.4e; qF(s)=-0.4e; qP(n)=+3.4e qP(s)=+3.5e; qO(1)(n)=-1.5e; qO(1)(s)=-1.5e; qO(2)(n)=-1.3e; qO(2)(s)=-1.4e; qO(3)(n)=-1.3e; qO(3)(s)=-1.4e. The topological analysis of the electron density distribution showed, apart from the presence of strong Ca…F, Ca…O, P…O interactions, weak O…O interactions associated to charge-shift bonding [4,5].

The crystal structure model and the electron density distribution of fluorapatite serves as a reference for ongoing studies of the substituted F-Cl; F-OH and Cl-OH apatite series.

Figure 1. The atomic basin representation of all atoms from assymetric unit of fluorapatite. Atomic basins are surrounded by atoms from their closest neighbourhood.

[1] Pasero M., Kampf A.R., Ferraris C., Pekov I.V., Rakovan J.F., White T.J. (2010). European Journal of Mineralogy, 22, 163-179.

[2] Hughes J.M., Rakovan J.F. (2015). Elements, 11, 165-170.

[3] Bader, R. F. W. (1994). Atoms in Molecules: A Quantum Theory Clarendon Press.

[4] Shaik, S., Danovich, D., Wu, W. & Hiberty, P. C. (2009). Nat. Chem. 1, 443–449.

[5] Stachowicz, M., Malinska, M., Parafiniuk, J. & Woźniak, K. (2017). Acta Crystallogr. Sect. B Struct. Sci. Cryst. Eng. Mater. 73, 643–653.

KW acknowledges a financial support within the Polish National Science Centre (NCN) OPUS17 grant - decision DEC-2019/33/ B/ST10/02671.

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Crystal Chemistry, Phase Diagrams, and Thermoelectric Properties of the Ca-M-Co-O (M=Sr, La, Sm, Eu, Gd, and Ho) Systems

Winnie Wong-Ng1, William Laws1, Saul H Lapidus2, Qing Huang1, James A Kaduk3,4

1NIST, Gaithersburg, MD United States of America; 2APS, ANL, Argonne, IL United States of America; 3IIT, Chicago, IL United States of America; 4North Central College, Naperville, IL United States of America

Oxide materials that have high temperature stability are potential candidates for waste heat energy conversion applications. The phase diagrams of the Ca-M-Co-O (M=Sr, La, Sm, Eu, Gd, and Ho) systems were determined. These diagrams offer compatibility relationships in the ternary oxide systems that are essential for processing and for the understanding of thermoelectric properties. In these systems, in addition to the well-known (Ca, M)3Co4O9 phase (with misfit layered structure) that has excellent thermoelectric properties, other low-dimensional phases include the homologous series, An+2ConCo’O3n+3 (where A=Ca, and (Ca, Sr)). While the members of the An+2ConCo’O3n+3 series have reasonably high Seebeck coefficients and relatively low thermal conductivity, the electrical conductivity needs to be increased in order to achieve higher figure of merit (ZT) values. This paper discusses our phase equilibria/structure/property studies of selected cobaltates in the Ca-M-Co-O systems.

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Crystal chemistry of halide containing silver borates.

Sergey Volkov1, Dmitri Charkin2, Manelis Lev2, Rimma Bubnova1

1Grebenshchikov Institute of Silicate Chemistry, Saint-Petesrsburg, Russian Federation; 2Department of Chemistry, Lomonosov Moscow State University, Moscow, Russian Federation

The excellent optical properties and versatile crystal chemistry make borates outstanding candidates for application as nonlinear optical (NLO) materials. These properties are enhanced by introducing “extra” anions, halides yielding the best performances. Introducing halides increases the abundance of non-centrosymmetric structures. As constituents of ionic lattices, halide ions readily contribute to the formation of salt-inclusion structures, which are generally defined as structures comprised of two parts, of varied dimensionality, exhibiting one, covalent, and the other, ionic character of chemical bonding. The ionic part generally fills the channels and/or cavities of porous covalent networks, while the cases where these parts constitute interpenetrating frameworks are scarce.

We have successfully synthesized and characterized several new silver halide borates, Ag4B4O7X2 (X = Br, I), Ag3B6O10I, and Ag4B7O12Br, which were prepared by slow cooling stoichiometric melts jr glass crystallization. The crystal structure of Ag4B4O7X2 is non-centrosymmetric (s.g. P6122) and comprised of coalesced pentaborate groups or so-called “kernite” chains 5B : 2∆3□ : (<∆2□ >–<∆2□ >–)sharing vertices to form a framework with equal content of BO3 triangles and BO4 tetrahedra. Their thermal expansion is strongly anisotropic due to the orientation of rigid kernite chains aligned parallel to ab plane. The calculated band structures indicate that Ag4B4O7Br2 and Ag4B4O7I2 are direct semiconductors with a band gap of about 2.0 and 2.4 eV, respectively.

The crystal structure of Ag4B7O12Br is triclinic (s.g. P-1), and formed by unique layers comprised of vertex-sharing triborate and tetraborate groups. Ag3B6O10I is orthorhombic (s.g. Pnma) and isostructural to Na3B6O10Br. The structure contains two interpenetrating frameworks one of them comprised of vertex shearing B6O13 hexaborate groups; the metal-halide anti-ReO3 framework is strongly distorted towards formation of isolated Ag3I2+ groups with relatively short Ag×××Ag contacts indicative of “argentophilic” interactions.

Crystal structures of these borates are comprised of two porous interpenetrating frameworks and demonstrate a further development of the “salt-inclusion” architecture toward a “covalent-inclusion” structure. The AgX sublattices exhibit strong anharmonic vibrations. The joint-probability density function was calculated from the inverse Fourier transform of the anharmonic ADPs approximated by the third-order expansion of the Gram–Charlier series [1]. This indicates the presence of structural analogies between borate nitrates and borate halides and indicates further directions in the search for new compounds in these families.

This work was financially supported by the Russian Science Foundation through Grant 21-73-00216.

(1) Kuhs, W. F. (1992). Acta Cryst. A109, 80–98.

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Imidazole Based Ambiphilic Ligands for Anion Sensing, Metalation and Photophysical Properties

SABEEHA PARVEEN, AVINASH IRUTHAYARAJ, ANANTHARAMAN GANAPATHI

Indian Institute of Technology Kanpur, KANPUR, India

Ambiphilic molecules such as phosphine-borane and amine-borane have drawn huge interest recently. Amine borane in particular, has been widely known to be efficient in sensing of hazardous anions such as fluoride and cyanide which can monitored using the fluorimetry. In addition, the coordination properties of P-/N- donor containing borane compounds with various coinage metals had a significant impact in their luminescence properties which can be utilized for various biological or electronic applications.1,2

Erstwhile, we have reported a series of backbone heteroatom-substituted imidazoles (SPh, PPh2, SiMe3, O2BPh, I, Br) as a precursors for the synthesis of functionalized NHC-metal complexes.3 In this work, synthesis of ambiphilic ligand on metal halogen exchange with a Lewis acidic BMes2 (Mes = mesityl) at the backbone of the imidazole was achieved.4 Among them, two isomeric boron-phosphine functionalized imidazoles, monoboron-functionalized imidazoles, and its corresponding imidazolium salts were prepared and thoroughly characterized. Their solid-state structures reveals a dimeric B−N adduct that six-membered [C−B− N]2 ring, and a tetrameric B−N adduct that forms an interesting 16-membered macrocycle, among various other monomeric BMes2-substituted imidazoles. The fluoride sensing properties of the synthesised BMes2-containing imidazoles were studied using UV−vis and fluorescence spectroscopy.

The ideal separation provided by P^N-type ligand gives room for metal-metal interaction upon the coordination with coinage metals which in turn lead to bright luminescent. Here, the P^N type ligand synthesised was treated with CuX(X=Br,I) to give L2Cu4I4-type luminescent metal complexes. In addition, metalation of the P^N ligand with other coinage metal salts such as AgX (X=OTf, NO3), AuCl.SMe2 was also tried. Upon crystalisation, their solid state structures reveal the cleavage of C-5 BMes2

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Phase structure of metallothermally reduced deep-sea concretion

Jaromír Kopeček1, František Laufek2, Alena Michalcová3, Lucie Šulcová3, Alisa Tsepeleva3, Eliška Chmelíková3, David Nováček3, Nguyen Hong Vu3, Petr Dvořák3, Pavel Novák3

1FZU - Institute of Physics of the CAS, Praha, Czech Republic; 2Czech Geological survey, Praha, Czech Republic; 3University of Chemistry and Technology in Prague, Praha, Czech Republic

Metallothermally reduced deep-sea nodules from Clarion-Clipperton Zone (Pacific Ocean) are investigated in this study. The aim is to prepare “natural alloy”, to construct as simply as possible way to reduce nodules into the usable alloy without wasting the energy, mainly to avoid the purification of individual metals. Here used nodules contain manganese as the dominant element, whereas iron, nickel and copper are other major constituents besides aluminium and silicon. The deepest investigated is the aluminothermic process [1], nevertheless the other reducing metals - titanium and silicon - are investigated too.

The nodules were reduced and annealed alloys at 700 °C with various excess of aluminium (0 %, 10 %, and 20 %). Using XRD there were found three, five and eight phases, some of them not listed in databases. Some other minor phases as sulphide MnS were found using SEM with EBSD/EDS coupled detectors.

There is a couple of interesting points. The formation of main manganese rich phase, which develops from β-Mn66Ni20Si14 phase (P213 space group) at 0 % of excess to β-Mn phase (P4132 space group) at 10 % of excess and to α-Mn phase (I-43m space group) at 20 % of excess. The separation of Mn2FeSi and Mn2FeAl phases. Those phases were just recently confirmed experimentally to exist.

[1] Novák P., Nguyen H. V., Šulcová L., Kopeček J., Laufek F., Tsepeleva A., Dvořák P. & Michalcová A. (2021) Materials 14, 561.

Keywords: deep-sea nodules, metal reduction, aluminothermy, EBSD, manganese

We acknowledge Czech Science Foundation project 20-15217S for support and CzechNanoLab Research Infrastructure (LM2018110) by MEYS CR for SEM infrastructure support.

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Structural Landscape of Lanthanide coordinated Polyoxometalates

Shailabh Tewari, Arunachalam Ramanan

Indian Institute of Technology Delhi, Ghaziabad, India

What should be investigated to comprehend a journey, life, or any dynamic phenomenon? Apart from the input and outcome, the observable steps in-between are pivotal in understanding the whole process and getting perspectives for further utilization. The struggle in rationalizing crystallization, a supramolecular reaction, for the targeted design of functional materials is to recognize the underlined possible pathways. The task is significantly challenging due to the obscurity of well-defined links between synthesis, structure, and property. However, Polyoxometalates (POM), the intermediate soluble molecular analogues of the bulk oxides, may provide some insights. These anionic oxo-clusters, typically of V, Mo, and W, have been of interest to researchers in the field of solid-state and materials chemistry not only due to their promising potential in near-future applications but also for the fundamental acumens they can provide into surface properties of bulk oxides. Out of many possible POM architectures, our choice of the Anderson Evans archetype was based on its structural versatility tunable at the molecular level. Our interest further strengthened upon noticing the ruby-like emission from the Cr-analogue of the archetype {Cr(OH)6Mo6O18}3-, even when other luminescent species were present. We then ventured on the quest of incorporating luminescent lanthanide counter cations into {Cr(OH)6Mo6O18}3- as well as the photo-physically silent {Al(OH)6Mo6O18}3- for understanding the variations in properties of the landscape of structures associated with changes in synthetic parameters. The poster presents a multidimensional structural landscape of lanthanide coordinated solids based on the Anderson-Evans cluster and the investigation of its photoluminescent properties.

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5:10pm - 6:10pmPoster - 46 SAXS: SAXS, SANS
Session Chair: Semra IDE
Session Chair: Jan Ilavsky

 

 

Poster session abstracts

Radomír Kužel



Structural characterization of liposomes using integrated methods of HPLC/AF4, UV-Vis absoprtion, Refractive Index, MALLS, DLS, and SAXS

TingWei Hsu1, Kuei-Fen Liao1, Yi-Qi Yeh1, Orion Shih1, U-Ser Jeng1,2

1National Synchrotron Radiation Research Center, Hsinchu Science Park, Hsinchu 30076, Taiwan;; 2Department of Chemical Engineering, National Tsing Hua University, Hsinchu 30013,

Liposome are increasingly better developed as efficient drug carriers. Structural characterization of the functional liposomes with and without drug-uptake and the consequent drug-transport and conditional drug-delivery, is of interest yet not well-stablished. Here, we report an established combined methods using high-performance liquid chromatography(HPLC), asymmetric flow field-flow fractionation (AF4), UV-Vis absorption, refractive index (RI), multi-angle laser light scattering (MALLS), dynamic light scattering (DLS), and small-angle X-ray scattering for structural characterization of liposome solutions. We will demonstrate an example of using the integrated system to successfully determine hydrodynamic radius and its distribution, molecular mass, lipid aggregation number, of a model liposome system. The radius of gyration and detailed bilayer structures of the liposome system are determined using simultaneous small- and wide-angle X-ray scattering, incorporated with HPLC/UV-vis/RI, at the high-flux 13A BioSAXS undulator beamline of the 3.0 GeV Taiwan Photon Source. We expect this fast structural characterization system would contribute greatly on drug screening of biomedical industrials.

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Solution Structures of Intrinsically Disordered Dipeptide-Repeats Studied by SAXS and Molecular Structure Simulation

Tien-Chang Lin1, U-Ser Jeng1,2, Yun-Ru Chen3, Bing-Jun Lian1, Kai-Tai Lin1, Yu-Jen Chang3, Orion Shih2, Yi-Qi Yeh2, Kuei-Fen Liao2

1Department of Chemical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan; 2National Synchrotron Radiation Research Center, Hsinchu,Taiwan; 3Genomics Research Center, Academia Sinica, 115, Taiwan

Often found in the gene chromosome 9 open reading frame 72 (C9ORF72) in the patients of familial frontotemporal dementia (a progressive disorder of the brain) and amyotrophic lateral sclerosis (muscles decreasing in size, resulting in difficulty in speaking, swallowing, and eventually breathing) are segments of abnormal dipeptide repeats, which serve as a signature of the diseases mentioned. Such dipeptide repeating of 10 – 1000 times can be found in the brain or spinal cord of the patients, including toxic Glycine-Arginine (GR)n. Using the biological small-angle X-ray scattering beamline 13A at the Taiwan Photon Source (TPS), covering a wide range of scattering vector q = 0.01 to 1.0 Å-1, we observed gradually ordered solution structures of (GR)n (n = 5, 10, 15, 20, 25, 30) when the n value increases over 20. The model structures of the dipeptide repeats reconstructed based on the SAXS data analysis combined with molecular simulation suggest a possible formation mechanism of the ordered structures. Effect of intervening Prolines into the GR dipeptide repeats is also observed. We note that up to date, there are no crystal structures available for the intrinsically disorder dipeptide repeats.

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Nanostructural changes in commodity polyethylene during environmental exposure

Christoper Garvey1,2,3, Ron Demjaha2, Michael Weir4, Peter Halley5, Bronwyn Laycock5, Yu-Chieh Hsu5, Marianne Impéror-Clerc1, Stéphan Rouzière1

1Technical University Munich, Garching, Germany; 2Lund Institute for Advanced Neutron and X-ray Science, 223 70 Lund, Sweden; 3Heinz Maier-Leibnitz Zentrum (MLZ), Lichtenbergstrasse 1 85747, Garching, Germany; 4School of Physics and Astronomy, University of Nottingham, University Park, Nottingham, NG7 2RD, United Kingdom; 5School of Chemical Engineering, The University of Queensland, St Lucia, Qld. 4067, Australia

Incomplete recrystallization after the melt processing of thermoplastics leads to a kinetically frustrated state in plastic packaging. Release of this frustration by random chain scission during environmental exposure and the associated structural relaxation is a mechanism in the embrittlement and fragmentation for these materials.[1] This mechanism is therefore a major route of physical degradation for the majority of plastic waste. The loss of mechanical properties and barrier properties of the material may catalyse further oxidation of microplastic waste and ultimately limit the lifetime of waste in the environment. After establishing the important role of nanostructure in embrittlement and further degradation we discuss the characterization of this process by X-ray scattering, both in the wide (WAXS) and small angle (SAXS) domains using semi-crystalline polyethylene as a model. These two experimental techniques characterize the packing of polymer chains into crystallites and the arrangement of these crystallites into lamellae respectively. These non-destructive bulk characterization techniques with a minimum of sample preparation offers a rapid and convenient access to relevant nanostructural parameters in order to define the temporal relationship between environmental exposure and structural relaxation.[2,3] Thus the perspective of X-ray scattering provides important insight into the lifetime of thermoplastics in the environment and will allow the engineering of more sustainable materials with optimized and controlled degradation, and thus impact on the environment.

Keywords: commodity plastics; plastic packaging; wide angle X-ray scattering; small angle X-ray scattering

C.J.G. acknowledges the CNRS and Université Paris-Sud for financial support during his sabbaticals. We would like to thank the Cooperative Research Centre for Polymers for funding parts of this study under project 2.4, Polyolefin-Biopolymer Films for More Sustainable Agricultural Production.

[1] Garvey, C. J., Impéror-Clerc, M., Rouzière, S., Gouadec, G., Boyron, O., Rowenczyk, L., Mingotaud, A. F. & ter Halle, A. (2020). Environmental Science & Technology 54, 11173-11181.

[2] Hsu, Y. C., Truss, R. W., Laycock, B., Weir, M. P., Nicholson, T. M., Garvey, C. J. & Halley, P. J. (2017). Polymer 119, 66-75.

[3] Hsu, Y. C., Weir, M. P., Truss, R. W., Garvey, C. J., Nicholson, T. M. & Halley, P. J. (2012). Polymer 53, 2385-2393.

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Investigations of the precipitation microstructure in the alloys, hard metal composites, and powders using SANS

Vasyl Ryukhtin1, Pavel Strunz1, Ahmet Bahadir Yildiz2, Pavel Zháňal3,4, Kazuki Ohishi5, Yukihiko Kawamura5, Premysl Beran6, Snejana Bakardjieva7

1Nuclear Physics Institute Řež, Řež, Czech Republic; 2Department of Materials Science and Engineering, KTH Royal Institute of Technology, SE-100 44 Stockholm, Sweden; 3Material and Mechanical Properties, Research Centre Řež Ltd., Řež, Czech Republic; 4Charles University in Prague, Faculty of Mathematics and Physics, Ke Karlovu 3, 12116, Prague, Czech Republic; 5Neutron Science and Technology Center, CROSS, Tokai, Ibaraki 319-1106, Japan; 6ESS AB, Lund, Sweeden; 7Institute of Inorganic Chemistry CAS, 250 68 Husinec-Rez, Czech Republic

In this study, we present the microstructure of various materials, obtained by using small-angle neutron scattering (SANS) in combination with different complementary scattering techniques. SANS resolution enables the investigation of inhomogeneities or precipitates in mesoscopic range with excellent statistics through sample bulk, moreover, it can be applied in-situ. For an example of precipitation of ω and α phases in the β matrix of the metastable β titanium alloy (Ti with 15 wt.% Mo), we show how SANS data can describe temperature resolved evolution of these phases at various heating rates [1]. Small-angle scattering, in this example, allow to overcome detection limits of the neutron diffraction due to the small size of the nanoparticles, and, it helped to demonstrate the coexistence of all three phases at about 550 °C, and to explain the abnormal behaviour of resistivity during constant rate heating.

SANS is an effective tool for the investigation materials containing heavy elements such as W and Co. In vanadium (V)-doped tungsten carbide (WC)-Co composite material system, in-situ and ex-situ SANS and ultra-small-angle neutron scattering (USANS) experiments helped us to delineate how additions of V affect the nano- and microstructure during sintering and result in smaller WC grains [2, 3]. Whereas SANS quantified the nano-scale interfacial layers responsible of grain coarsening inhibition, USANS was applied to study microstructural refinement.

SANS was also applied for the investigation of the Sc-doped TiO2 anatase as material for photocatalysis. Growth of Sc precipitations was observed with increasing aging temperature (Fig. 1) due to its expelling from anatase crystallites. It was proved by SANS, neutron diffraction, and electron microscopy measurements that whole scandium content at 800 °C was driven out of grains and formed particles at TiO2 grain boundaries.

[1] Zháňal, P., Ryukhtin, V., Farkas, G., Kadletz, P., Keiderling, U., Wallacher, D., Harcuba, P, (2020) MATEC Web of Conf. 321, 12027. [2] Yildiz A. B., Weidow, J., Ryukhtin, V., Norgrend, S., Wahnström, G., Hedström, P. (2019). Scripta Mat. 173, 106-109.

[3] Yildiz A. B. et al (2021) Materials & Design, 109825, In Press

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R&D Studies on metal oxide-based nanoparticles: Structure dependent physical and chemical properties

Gözde Bayazit Sekitmen1, Rukiye Babaca Tosun1, Süleyman Ali Tuncel2, Semra İde3

1Department of Nanotechnology and Nanomedicine,Hacettepe University, ANKARA, Turkey; 2Department of Chemical Engineering,Hacettepe University, ANKARA, Turkey; 3Department of Physics Engineering,Hacettepe University, ANKARA, Turkey

Metal oxide-based porous nanomaterials are widely synthesized and used for several technological developments based on energy storage, catalytic chemistry, and medical applications [1-3]. In the present study, the newly designed MeOx (Me: Ce, Mn, Si, Ti) nanoparticles were prepared and structurally investigated in molecular, nanoscopic, and microscopic scales by using several complementary experimental (SAXS, SEM) methods. The form factors for elliptical, core-shell oblate, and fractal models were used in SAXS analyses (it can be shown in Figure 1) to characterize the morphologies. Thermal processes were activated at T= 410, 450, and 500 °C to investigate nanostructural properties. The focused targets with the present R&D studies were increasing the surface area of the nanoparticles and reaching the stabilized monodispersed morphologies and uniform distributions. As a result of the study, it was obtained that, the size, shape, and distribution controlled synthesizing processes are possible with thermal treatments. Especially, a critical temperature value of about 400°C is effective on the nanomorphologies of MnO2 particles. Ellipsoidal fractal units come together to form larger and more compact core-shell oblate shape nanoparticles. Electrochemical measurements were also performed by using a conventional three-electrode system to determine the physicochemical properties. So, it was obtained that, the larger electrochemical capacitance than the commercial electrolytic metal dioxides may be prepared with these nanoparticles. On the other hand, it was also determined that the larger surface area and high porosity of the synthesized TiO2 nanoparticles besides their well-determined monodispersed and uniformly distributed nanomorphologies may cause various immunomodulatory effects when they are exposed to cells with the purpose of several biochemical and biophysical applications. The in-vitro and in-vivo examinations were also started on the determined nanoparticles made by choice according to their properties to investigate their potential usages in medical applications.

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Revealing the Metal-Ligand Coordination effects on the Structure modifications for Balanced Tensile Modulus and Self-Healing of Polyurethane Films

Yu Sheng Lin1, Chun-Hsiu Lin1, Wei-Ru Wu2, Chun-Jen Su2, Ho-Hsiu Chou1, An-Chung Su2, U-Ser Jeng1,2

1National Tsing Hua University, Hsinchu , Taiwan; 2National Synchrotron Radiation Research Center, Hsinchu,Taiwan

Polyurethane (PU) films are potential candidate substrate for next-generation stretchable electron devices that attract much attention. Both tensile modulus and self-healing of PU films are anticipated yet seemingly mutual excluded properties. Here, metal-ligand coordination is proposed to modify the crystalline and nanostructural features of PU films for concomitantly improved tensile modulus and self-healing. PU films of bpyPTD are prepared from reaction of bpy with PTD of different polarity of solvents such as THF or DMF/THF. Metal precursors solutions of Zn, Ni, were selectively mixed into the bpyPTD solution for cast of the final product films of M-bpyPTD, with M = Ni, Zn. X-ray absorption is used to elucidate how the critical metal-ligand coordination between Zinc (II)/Nickel (II) and bipyridine (bpy) could effectively crosslink the segmented PTD into network structures of Zn-bpyPTD and Ni-bpyPTD.

The network structures of the M-bpyPTD are tested under film stretching at low temperatures and high humidity, using concomitant small- and wide-angle X-ray scattering (SAXS and WAXS). Density (or mean spacing) of the metal-ligand coordination cites could be enriched with the higher polarity solvent for improved tensile modulus. By contrast. improvement of the self-healing capability is reached with enhanced metal-ligand coordination strength of bpy with Ni. Accordingly, Ni-bpyPTD could be fabricated into pyramidal pressure sensors, showing characteristic pressure response with good cyclability for promising applications as electronic skins.

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Development of reference standard for small angle scattering measurement q calibration

R. Joseph Kline

NIST, Gaithersburg, United States of America

We report on the development of a reference standard for q calibration of small angle scattering measurements. The standard consists of a 100 nm pitch line grating on a silicon nitride membrane. The grating is 100 nm tall and 40 nm wide tungsten lines. Tungsten was selected to give strong scattering intensity while not having absorption features around the carbon k-edge. The silicon nitride membrane allows measurements over a large range of beam energies. The test structure has a 1 µm two-dimensional grating super-imposed on the 100 nm line grating. The superlattice provides additional scattering peaks that can only be resolved in high-resolution configurations. The test structure allows evaluation of q-resolution in addition to calibration of q.

The prototype structure was tested between 250 eV and 24.5 keV and provided strong scattering at all energies. Figure 1 shows an example scattering pattern collected in a 60 s exposure on a laboratory SAXS system using Ga Kalpha. The scattering pattern allows calibration between 0.0006 Å-1 and 0.1 Å-1. We will also discuss measurements made at SAXS beamlines and at soft X-ray scattering beamlines.

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Towards a better understanding of structure-performance relation in PEMFC fuel cells based on ptychography X-ray nanotomography and scanning small angle X-ray scattering

Christian Appel1, Katharina Jeschonek2, Kai Brunnengräber2, Bastian Etzold2, Marianne Liebi3,4, Manuel Guizar-Sicairos1

1Paul Scherrer Institut, Villigen, Switzerland; 2Technische Universität Darmstadt, Darmstadt, Germany; 3EMPA, St. Gallen, Switzerland; 4Chalmers University of Technology, Gothenburg, Sweden

Advanced composite materials will play a big role to meet growing challenges for future energy solutions. In the transportation sector polymer electrolyte membrane fuel cells (PEMFCs) are promising alternatives to combustion engines to reduce CO2 emissions. PEMFC generate electricity by electrochemical reactions that take place in a complex environment within a so-called catalyst layer. In recent years, fundamental and applied PEMFC research has continuously been trying to improve its understanding of structure-performance relation of these layers. PEMFC catalyst layers are porous materials built from three different components; chemically active sites, electron conducting support and proton conducting binder. This study focusses on investigating Pt nanoparticles on carbon black support (PtC, HiSPEC3000) spray-coated on a polymer membrane (Nafion 211). We investigate three different samples with varying amounts of binder (PTFE) but an equal loading of catalyst (mPt = 0.2 mg/m2).

Scanning SAXS was performed at the cSAXS beamline of the Swiss Light Source (SLS) to study the meso and nanoscale of the samples based on simultaneous measurements of X-ray scattering and fluorescence (XRF) spectroscopy from small regions of 10x10 µm2 within the catalyst layers. Figure 1A shows an exemplarily SAXS curve revealing statistical information of the nanostructure by e.g. evaluating the power law scaling at low q. The corresponding XRF spectroscopy data from XRF is particular interesting due to its ability to measure the distribution of Pt in the catalyst layer based on the Pt Mα emission line at 2.05 keV. A major advantage of scanning SAXS is also its capability to probe the data illustrated in Figure 1A/B on a macroscopic length scales, to possibly use these two features, power law scaling exponent at low q (Figure 1C) and the intensity of the Pt Mα (Figure 1D), to generate 2D scattering maps for a 1x1 mm2 area. Based on the results obtained from these maps, specific areas were chosen to mill out cylindrical µm-sized pillars using FIB/SEM (see Figure 1F). These pillars were then investigated with the OMNI setup [1] at cSAXS to reveal the 3D nanostructure with ptychography X-ray nanotomography (PXCT) down to a resolution of 26 nm. Figure 1E shows the rendered pore network from one of the catalyst layer color-coded with the pore size distribution (threshold segmented). Currently, we explore different approaches to correlate the imaging data (PXCT) with the statistical data (SAXS and XRF). Our vision is to obtain 3D representative models for the catalyst layers based on the real structure (3D nanostructure PXCT, resolution 26nm), complemented with statistical data from SAXS and XRF down to single nanometer length scale.

[1] M. Holler, M. Guizar-Sicairos, et. Al. (2017). Rev. Sci. Instrum. 88(11),113701.

Keywords: IUCr2020; abstracts; PXCT; SAXS; PEMFC

This project has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No 701647 (PSI-FELLOW-III-3i) and funding from the Chalmers initiative for advancement of neutron and x-ray techniques. The authors acknowledge the funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement No. 681719). We also acknowledge the Paul Scherrer Institut, Villigen, Switzerland for provision of synchrotron radiation beamtime at beamline cSAXS of the SLS.

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Structural analysis of antibody complexes by inverse contrast-matching small-angle neutron scattering combined with size exclusion chromatography (SEC-iCM-SANS)

Nobuhiro Sato1, Rina Yogo2,3,4, Saeko Yanaka2,3,4, Anne Martel5, Lionel Porcar5, Ken Morishima1, Rintaro Inoue1, Taiki Tominaga6, Takao Arimori7, Junichi Takagi7, Masaaki Sugiyama1, Koichi Kato2,3,4

1Institute for Integrated Radiation and Nuclear Science, Kyoto University, Osaka, Japan; 2Institute for Molecular Science (IMS), National Institutes of Natural Sciences, Okazaki, Aichi, Japan; 3Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Aichi, Japan; 4Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Aichi, Japan; 5Institut Laue–Langevin, Grenoble, France; 6Neutron Science and Technology Center, Comprehensive Research Organization for Science and Society (CROSS), Tokai, Ibaraki, Japan; 7Institute for Protein Research, Osaka University, Suita, Osaka, Japan

Small-angle neutron scattering (SANS) has been effectively utilized for structural analysis of biomacromolecular complex in solution because each component can be distinguished by using contrast matching method with selectively deuterated molecules. In particular, inverse contrast matching (iCM) method is quite useful because it can suppress incoherent scattering from hydrogen of solvent water by measuring nearly 75% deuterated biomolecules in 100% heavy water. Meanwhile, SEC-SAS, a combination of inline size-exclusion chromatography (SEC) and small-angle scattering measurements (SAS), has recently been developed to address the problem that undesirable contamination of aggregates and dissociated fragments prevent the precise analysis of target molecules. Currently SEC-SAS has become a popular option for small-angle X-ray scattering (SAXS), but not widely available yet for SANS. In this study, we applied the SEC-SAS technique to the iCM-SANS measurements (SEC-iCM-SANS) of antibody interaction systems: Immunoglobulin G (IgG) or its Fc fragment and 75% deuterated Fc-binding proteins. As a result, we could confirm that bound species were successfully fractionated by SEC excluding aggregates and unbound molecules and immediately subsequent iCM-SANS measurements provided the scattering profiles of the target complexes alone, in which hydrogenated components in the complexes were selectively observable.

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Small-angle X-ray scattering beamlines at the photon factory

Nobutaka Shimizu, Hideaki Takagi, Yasuko Nagatani, Kento Yonezawa, Takeharu Mori, Keiko Yatabe, Masatsuyo Takahashi, Keishi Oyama, Noriyuki Igarashi

Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki, Japan

Three small-angle X-ray scattering (SAXS) beamlines, BL-6A, BL-10C, and BL-15A2, are in operation at the Photon Factory, a synchrotron radiation facility in Japan, and are commonly utilized for versatile application to carry out the structural analysis and the structure-property correlation studies for soft and hard materials including biological macromolecules. The light source of BL-6A is a bending magnet, and the available X-ray energy is fixed at 8.3 keV (1.5 Å). The maximum camera length is 2.5 m, and SAXS/WAXS (wide-angle X-ray scattering) measurements are performed using PILATUS3 1M (Dectris) for SAXS and PILATUS 100K for WAXS as detectors, respectively. BL-10C is also the bending magnet beamline, and the available X-ray energy range is generally 7.0-14.0 keV (0.89-1.77 Å). The Max. camera length is 3.0 m, and SAXS/WAXS measurements can be performed with PILATUS3 2M for SAXS and PILATUS3 200K for WAXS. BL-15A is the short-period undulator beamline, and 15A1 and 15A2 are dedicated to XAFS and SAXS, respectively. BL-15A2 has two dedicated diffractometers, one for hard X-rays (5.7-15 keV, Max. camera length: 3.5 m) and the other for tender X-rays (2.1-5.4 keV, Max. camera length: 0.8 m), and these are tandemly installed against the beam in BL-15A2. PILATUS3 2M for SAXS and PILATUS3 300K-W for WAXS are installed as detectors. Because this PILATUS3 2M is vacuum compatible, it can be directly connected to the dedicated vacuum diffractometer for tender X-rays use under the vacuum condition. We have also installed a special setting to connect the hard X-ray system to the tender X-ray system. The max. camera length is 6.5 m at that time, and the SAXS resolution reaches 1500 nm using 2.1 keV. The devices for BioSAXS are installed in BL-10C and BL-15A2, which can be used not only for SEC-SAXS but also for titration-SAXS and time-resolved SAXS using microfluidic cells. We will introduce the latest measurement and analysis environment at these beamlines in this presentation.

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A pipeline for time-resolved small-angle X-ray scattering data analysis on amyloid fibrils formation in solution

Taja Cheremnykh1, Mohsin Shafiq2, Stefano Da Vela1, Markus Glatzel2, Dmitri Svergun1

1EMBL Hamburg, Hamburg, Germany; 2UKE, Hamburg, Germany

Structural and functional biophysical studies often require temporal resolution to explore the kinetics of processes in macromolecular systems. The processes like amyloid fibrils formation and protein aggregation involve rapid consequent chemical reactions happening at native conditions [1]. Conformational changes caused by changing conditions have impact on the functionality of biological macromolecules and their complexes. Small-angle X-ray scattering (SAXS) is a structural method allowing one to capture conformational changes and measure kinetics of the macromolecules and complexes in near native solutions [2].

For functional biological complexes, it is important not only to observe structural changes, but also to recognise their biological implications with the help of additional information about the system. The sources if information can be e.g. an atomic model of a given state from cryo-electron microscopy or X-ray crystallography and/or simulated behaviour of the complex (molecular dynamics) under conditions of the time-resolved SAXS experiment [2, 3].

As the analysis of one dimensional SAXS data in terms of three-dimensional (3D) models is an ill-posed problem, and the analysis of kinetics needs the detection of time-dependent changes, characteristic times of the structural changes to need to be defined to analyse large amounts of time-resolved data. To do this, linear methods of reducing the dimensionality of data are being applied for obtaining time dependencies; statistical methods are utilised for the assessment of the importance of the contributing components and machine learning is used for data classification. The ATSAS software [4] is a powerful tool for small-angle scattering data analysis capable to extract rich structural information from the experimental data and also to fit the data with the available 3D models provided by other methods. This allows one to combine the structural information into a biophysical and biochemical evidence.

Although all the available ATSAS tools are straightforward to use, the data analysis still requires significant level of expertise to interactively utilize the tools when dealing with time-resolved studies. In order to optimise and simplify the data analysis procedures for the analysis of processes occurring in biomacromolecular systems, a new pipeline has been developed. The pipeline allows one to perform a comprehensive analysis and incorporates relevant components of ATSAS for the analysis of time-resolved. Its capacity is illustrated by the application to the time-resolved data on amyloid fibrils formation in solution.

[1] Michaels, T. C., et al. (2020) Nature chemistry, 12(5), 445-451.

[2] Svergun, D.I., et al. (2013), Small angle X-ray and neutron scattering from solutions of biological macromolecules. Vol. 19. Oxford University Press.

[3] Vestergaard, B. (2016), Archives of biochemistry and biophysics 602: 69-79.

[4] Manalastas-Cantos, K., et al. (2021) J. Appl. Cryst. 54, 343-355

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5:10pm - 6:10pmPoster - 47 Synchrotron and XFEL: Synchrotron and XFEL facilities
Session Chair: Sofia Diaz-Moreno
Session Chair: Makina Yabashi

 

 

Poster session abstracts

Radomír Kužel



Beam heating from a fourth-generation synchrotron source

Eleanor Lawrence Bright, Carlotta Giacobbe, Jonathan Wright

European Synchrotron Radiation Facility, Grenoble, France

Fourth-generation synchrotron X-ray sources bring increasing levels of flux and coherence, allowing unprecedented levels of resolution for a wide range of techniques, but with increasing risk of radiation damage. The high flux achievable at synchrotrons has been well known to cause damage in biological samples at around 5-20 keV, however, with increasing flux we have found that radiation effects become significant even for metal samples and high-energy X-rays through beam heating.

Beam heating effects were investigated at the ID11 beamline at the newly upgraded European Synchrotron Radiation Facility-Extremely Brilliant Source, using thermal lattice expansion to perform in-situ measurements. Results showed significant increases in temperature for metal and ceria samples in a focussed 43.44 keV beam, as displayed in Fig. 1. These temperature increases may affect sample properties and drive significant chemical or physical changes, such as the rapid recrystallisation of copper wire shown here.

Aluminium and Copper wire samples were investigated and compared to a lumped thermodynamic model. By designing samples to maximise effects and simplify the thermodynamics of the system, we facilitate quantitative comparison to the modelled beam heating, helping to understand the severity of the problem. With these results we show that radiation beam heating is a potential issue for all samples, not only soft matter, and provide information needed to consider, predict, and mitigate its effects.

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Azimuthal integration and crystallographic algorithms on field-programmable gate arrays

Zdeněk Matěj1, Kenneth Skovhede1,2, Carl Johnsen2, Artur Barczyk1, Clemens Weninger1, Andrii Salnikov1, Brian Vinter2

1MAX IV Laboratory, Lund University, Sweden; 2Niels Bohr Institute, University of Copenhagen, Denmark

With the onset of next generation synchrotron light sources and X-ray free electron lasers, accompanied by developments of future photon detectors, delivering mega-pixel diffraction images at frame rates over 10 kHz, production of data from crystallography experiments is rapidly increasing. Crystallographers were utilizing various types of computing hardware from the early beginning. Algorithms and computing devices were constantly developing. Nowadays even quantum computers are available in commercial clouds. A potential of Field-Programmable Gate Arrays (FPGAs) – a more classical computing accelerators, is explored and demonstrated in this work on a task of Azimuthal Integration (AZINT) of area-detector data from powder diffraction and small angle scattering. Beside these two most known application cases, where among other data volumes are reduced by a factor of 1000, the underlaying procedure i.e. bin-counting has applications in data analysis tasks as background estimation in conventional single crystal diffraction images or data reduction from diffraction anomalous fine structure. The new potential of FPGAs for big data science and complex data analysis originates from recent progress in tools allowing scientific software developers to easily program FPGAs, prototype and implement algorithms on them with complexity fitting the scientific requirements. It is demonstrated that AZINT can process 600 Gb/s of uncompressed data stream, i.e. about 20–40 Gpixels/s, on a single commercial FPGA available at photon and neutron facilities or compute clouds, however energy and cost-effective commodity hardware FPGAs can be used as well. FPGAs are usually more energy-efficient in comparison to widely known graphical processing units (GPUs) and they are very flexible so they can better fit a specific problem and outperform GPUs in many relevant applications, in particular AZINT here. Beside high throughput required for big data analysis FPGAs allow data reduction and filtering with well-defined and low latencies. This enables experiments with X-rays as a real-time probe. Development of crystallographic code for big data handling on FPGAs may have additional synergies. FPGAs can be radiation tolerant and operate under some extreme conditions. It makes them ideal components for extra-terrestrial crystallography (e.g. Mars rovers). AZINT was developed at MAX IV synchrotron Laboratory however similar activities are present on other photon sources. It is worth to mention at least data acquisition and spot-finding project [1] for macromolecular crystallography at SLS/PSI.

[1] Leonarski, F., Mozzanica, A., Brückner, M., Lopez-Cuenca, C., Redford, S., Sala, L., Babic, A., Billich, H., Bunk, O., Schmitt, B., Wang, M. (2020). Structural Dynamics 7, 014305. https://doi.org/10.1063/1.5143480

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High-resolution synchrotron powder diffraction with the use of scanning 2D detector

Roman Svetogorov, Pavel Dorovatovskii, Vladimir Lazarenko

NRC Kurchatov Institute, Moscow, Russian Federation

Simultaneous recording of diffraction patterns in a large solid angle with the subsequent conversion of a two-dimensional histogram into a one-dimensional intensity – diffraction angle dependence [I (2θ)] is obviously a highly efficient data collection method for polycrystalline samples, the diffraction pattern of which is axially symmetric. This approach provides a high measurement rate with the required statistical accuracy. Shooting time is smaller by orders of magnitude compared to a point or linear detector. The negative effect of graininess and preferential orientation (texture) on data quality is reduced. However, due to the limited size of two-dimensional detectors, the resulting angular range is very limited and insufficient to obtain accurate structural information about the studied objects. In this regard, the principle of a scanning two-dimensional detector was used at the X-ray structural analysis beamline (XSA) mounted on a beam from a bending magnet of Kurchatov Synchrotron Radiation Source. The optical scheme is standard and includes a monochromator with a sagittal bend of the second crystal to focus the beam in the horizontal plane to obtain maximum intensity values [1].

The goniometer provides rotation of the test sample (placed in a special cryoloop or thin-walled capillary) around the horizontal axis φ, to ensure averaging of diffraction patterns over the orientations of the sample, as well as rotation of the detector around the 2θ axis, which allows high quality data to be obtained up to large values ​​of sinθ / λ. The use of such a scheme made it possible to obtain the following parameters of the diffraction experiment:

  • an angular range of up to 140⁰ in 2θ (q = 14.8 Å-1)
  • instrumental contribution to the peak broadening from 0.039⁰
  • angular accuracy Δ2θ = 0.001 °,
  • the accuracy of determining the intensities of the Bragg peaks of the standard – 0.5%,
  • the range of recorded intensities of the Bragg peaks Imax / Imin = 105.

[1] Svetogorov R.D., Dorovatovskii P.V., Lazarenko V.A. (2020) Cryst. Res. Tech. in press

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The APS upgrade: New Opportunities for Materials and Applied Science

Uta Ruett

Argonne National Laboratory, Lemont, United States of America

The Advanced Photon Source (APS) at Argonne National Laboratory has played a major role in the materials and applied science research for 25 years. Now the source will be upgraded starting in April 2023 [1,2]. In 2024, users can expect an ultra-bright source operated at 6 GeV with high fraction of coherence even at high-energy x-ray. There will be 9 new feature beamlines built to take full advantage of the new source parameter, and many beamlines will become enhanced including insertion devices, optics, and instrumentation.

11-ID-D operated by the Structural Science group at the APS is one of the enhanced beamlines, which will enable a combination of total scattering with small angle scattering and focusing into the submicrometer range. Here, we can close the gap between the resolution in reciprocal and real space to provide a complete picture of the structure of materials. Multimodal setups and photon energies between 26 keV and 120 keV with highest flux will enable complex in situ and operando experiments. An emphasis will be on the understanding and discovery of new materials covering in situ synthesis and manufacturing to studies during functionality.

[1] https://www.aps.anl.gov/APS-Upgrade

[2] Advanced Photon Source Upgrade Project Preliminary Design Report https://doi.org/10.2172/1423830

Keywords: synchrotron radiation; powder diffraction; total scattering; nanomaterials; materials science

Acknowledgement: This 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.

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Conceptual design of a scattering/diffraction beamline for the Russian synchrotron Ultimate Source for Synchrotron Radiation

Melanie Nentwich1, Dmitri Novikov1, Oliver Seeck1, Timur V. Kulevoy2, M. M. Borisov2, Ilya A. Subbotin2, Roman A. Senin2

1DESY Photon Science, Hamburg, Germany; 2NRC “Kurchatov Institute” – Institute for Theoretical and Experimental Physics, Moscow, Russia

The arrival of the 4th Generation Synchrotron Rings (4GSR) facilitates a crucial step forward in the application range of modern X-ray methods. The 4GSR sources pave a way for time resolved experiments at nanometer and nanosecond resolution level and beyond. Their development therefore allows for moving the established scattering, diffraction and spectroscopy methods to the nanoscale, to combine them with microscopy at mesoscopic levels and to investigate dynamics at nanosecond time scales. The Russian national flagship Ultimate Source for Synchrotron Radiation (USSR) facility will be one of the world leading synchrotrons once it starts operation.

A major part of the existing 4GSR beamlines is dedicated to nanobeam experiments. The intended X-ray research methods must be capable of obtaining the information of the real structure at nanometer resolution levels. The required spatial resolution on the objects can vary from several interatomic spaces in modern microelectronic devices, lithium-based batteries and catalytic materials and up to tens of micrometers e. g. in research on mechanical fails or stress propagation. Moreover, the key interest concentrates on the evolution of the objects, under external influences or in the cause of device operation. Because of this great interest in nanobeam experiments, the conceptual design of nano-diffraction beamlines is of primary interest in the preparation phase of USSR.

Here, we present an analysis of the scientific cases and developments of conceptual and technical solutions for the design of a scattering/diffraction beamline. This study includes a broad overview of recent scientific cases investigated at nowadays beamlines with similar focus. Additionally, we present an extensive comparison of Nanoprobe Beamlines at 4GSR that are already operating or under construction. From those key data, we derive a model beamline for nanoprobe experiments at USSR. This generic beamline consists of (1) a double-crystal monochromator Si(111) with a bandwidth of 10-4, covering an energy range of 5 keV to 40 keV, (2) a 4m long tunable undulator (see Fig. 1), (3) two different combinations of focusing elements and (4) a 4+2 circle diffractometer. The beam properties of these concepts were modelled with the x-ray tracing software xrt at different positions of the beamline. The minimal beam size at the sample position is 220nm x 70nm (FWHM), see Fig. 2.

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The BioMAX beamline for macromolecular crystallography at MAX IV

Ana Gonzalez, Oskar Aurelius, Monika Bjelčić, Mikel Eguiraun, Ishkhan Gorgisyan, Elmir Jagudin, Sandesh Kanchugal, Tobias Krojer, Mirko Milas, Jie Nan, Thomas Ursby

MAX IV Laboratory, Lund, Sweden

As the first macromolecular crystallography (MX) beamline at a fourth-generation synchrotron source, BioMAX [1] is also the first MX beamline at the MAX IV Laboratory. The primary usage case has targeted high sample throughput and robustness, using the performance of the MAX IV source to achieve a 20 x 5 μm2 beam focus with few beam shaping elements. Operation of the KB-mirror pair used for focusing, is automated to also deliver a defocused beam size of 50 x 50 or 100 x 100 μm2. Using a double crystal Si(111) monochromator, an energy range of 5 to 25 keV is user accessible and a photon flux of 5 x 1012 photon/s is routinely achieved at a ring current of 250 mA and a photon energy of 13 keV.

The beamline endstation has been based around well-established components such as the MD3 diffractometer from Arinax, a Dectris Eiger 16M photon counting detector and an IRELEC ISARA sample changer. The beamline is accommodating to a wide range of experiment types, including: cryogenic data collection, humidity-controlled room temperature data collection, optimised SAD/MAD capability, serial crystallography by fixed-target supports or injectors [2], helical data collection, rapid-feedback mesh scans and with a suite of auto-processing pipelines.

Also associated with the beamline is the FragMAX fragment screening program at MAX IV [3]. Beamline control is provided through the web-technology based MXCuBE3 [4] and with the ISPyB database [5] for LIMS functionality via the EXI user interface.

[1] 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 Radiat. 27, 1415. DOI:10.1107/s1600577520008723

[2] Shilova, A., Lebrette, H., Aurelius, O., Nan, J., Welin, M., Kovacic, R., Ghosh, S., Safari, C., Friel, R. J., Milas, M., Matej, Z., Högbom, M., Brändén, G., Kloos, M., Shoeman, R. L., Doak, B., Ursby, T., Håkansson, M., Logan, D. T. & Mueller, U. (2020). J. Synchrotron Radiat. 27, 1095. DOI: 10.1107/S1600577520008735

[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. 76, 771. DOI: 10.1107/S205979832000889X

[4] Mueller, U., Thunnissen, M., Nan, J., Eguiraun, M., Bolmsten, F., Milàn-Otero, A., Guijarro, M., Oscarsson, M., de Sanctis, Daniele. & Leonard, G. A. (2017). Synchrotron Radiat. News 30, 22. DOI: 10.1080/08940886.2017.1267564

[5] Delagenière, S., Brenchereau, P., Launer, L., Ashton, A. W., Leal, R., Veyrier, S., Gabadinho, J., Gordon, E. J., Jones, S. D., Levik, K. E., McSweeney, S. M., Monaco, S., Nanao, M., Spruce, D., Svensson, O., Walsh, M. A. & Leonard, G. A. (2011). Bioinformatics 27 (22), 3186. DOI: 10.1093/bioinformatics/btr535

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The Chemical Crystallography Beamline P24 - Status and Future Developments

Christian W. Lehmann1, Christian Schäfer1, Carsten Paulmann2

1MPI für Kohlenforschung, Mülheim an der Ruhr, Germany; 2Universität Hamburg, Hamburg, Germany

Since 2016 the Chemical Crystallography beamline P24 at the synchrotron Petra III located at DESY Hamburg is offering user operation. The two experimental hutches EH1 and EH2 are equipped with a large kappa-geometry diffractometer and a four circle eulerian-craddle diffractometer respectively. In recent years serveral improvements have been added in order to facilitate small molecule chemical crystallography in particular the determination of routine crystal structures from extremely small single crystals unsuitable for home laboratory X-ray diffractometers.

At present the available energies (wavelengths) encompasses an small window at 8 keV (1.54 Å) and the range from 17 to 30 keV (0.73 to 0.41 Å). Higher energies up to 40 keV are technically possible. A Pilatus 3R 1M cadmiumtelluride hybridpixel detector in addition to a Mar 165 CCD are available in either experimental hutch, together with low temperature gas flow coolers, down to helium temperatures. A set of recently installed compound refractive lenses (CRLs) allows to focus the beam to below 100 μm. Presently in EH1 a sample changing collaborative robot is being tested, together with a new fixed Chi sample stage, which allows for omega scans exceeding 180° in combination with predefined Phi-settings. An automated goniometer head allows to centre the crystal remotely.

A low temperature sample storage accessible for the robot is planned for the near future. This will complete the setup for possible remote operation of the beamline by EH1 users including a mail-in service for air, humidity and temperature sensitive samples.

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Possibilities at the Polar beamline at APS

Joerg Strempfer, Steven Kearney, Altaf Khan, Daniela Capatina, Deming Shu, Ruben Reininger, Luca Rebuffi, Yongseong Choi, Gilberto Fabbris, Daniel Haskel

Argonne National Laboratory, Lemont, United States of America

In 2024, the upgrade of the Advanced Photon Source at Argonne National Laboratory to an MBA reverse bent lattice will be completed. APS-U will offer extremely brilliant and highly coherent beam through the new low emittance source [1] to the user community. This will enable a variety of exciting new possibilities for dichroic scattering and spectroscopy experiments by pushing towards extreme pressures and high spatial resolution. Polar, the beamline for polarization modulation spectroscopy at sector 4 of the APS will make use of these new possibilities in terms of small focus sizes, coherence and polarization.

Fast polarization flipping between left and right circular as well as between horizontal and vertical linear polarization will be possible with the new Superconducting Arbitrarily Polarizing Emitter (SCAPE) undulators which are currently being designed for the Polar beamline. Two in-line SCAPE undulators will produce horizontal and vertical linear polarization as well as left and right circular polarization in the energy range from 2.7 to 27 keV, thanks to the implementation of small diameter round ID vacuum chambers enabled by on-axis injection at APS-U. Two experimental setups will make use of this new source and will allow diffraction (XRD, REXS, XRMR) as well as absorption spectroscopy (XMCD, XMLD) experiments covering all relevant absorption edges.

The beamline will make accessible especially the energy range above 14 keV for magnetic spectroscopy experiments, normally not reachable at conventional hard-x-ray beamlines using phase plates for polarization manipulation and will enable investigation of magnetic properties of materials at the 5f L- and 4d K-edges using spectroscopic methods. Small focused and coherent beams down to 100 nm will allow reaching new areas in terms of resolution, by employing direct imaging or ptychographic methods, at low temperature, high magnetic fields and high pressures. Beamline optics are designed to reduce vibrations to guarantee small focus sizes.

A low vibration, large bore superconducting magnet with 9 T longitudinal and 1 T transversal fields will allow XMCD and XMLD measurements at extreme pressures using the small beam focused by KB optics. A horizontal diffractometer with an optional 2 T superconducting magnet will allow dichroic diffraction and spectroscopy experiments in moderate fields and at high pressures. An interchangeable high-precision sample stage will allow for 3D dichroic imaging experiments using highly focused beam.

[1] https://www.aps.anl.gov/Beamline-Selection/Technical-Information/Storage-Ring-Parameters

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6:10pm - 7:00pmKN-31: The contribution of crystallography to new vaccine formulations
Location: Terrace 2A
Session Chair: Graciela Carlota Díaz de Delgado

Marcia Fantini

 

Using crystallography tools to improve vaccine formulations

Márcia Carvalho de Abreu Fantini1, Cristiano Luis Pinto Oliveira1, José Luiz de Souza Lopes1, Tereza da Silva Martins2, Milena Apetito Akamatsu3, Aryene Góes Trezena4, Milene Tino de Franco4, Viviane Fongaro Botosso5, Osvaldo Augusto Brazil Esteves Sant´Anna6, Nikolay Kardjilov7, Martin Kjaerulf Rasmussen8, Heloísa Nunes Bordallo8

1University of São Paulo, Physics Institute, São Paulo - SP, Brazil; 2Chemistry Department, Federal University of São Paulo, Diadema - SP, Brazil; 3Innovation Division, Butantan Institute, São Paulo - SP, Brazil; 4Imunogenetic Laboratory, Butantan Institute, São Paulo - SP, Brazil; 5Virology Laboratory, Butantan Institute, São Paulo - SP, Brazil; 6Imunochemistry Laboratory, Butantan Institute, São Paulo - SP, Brazil; 7HZB für Materialien und Energie, Helmholtz-Zentrum Berlin, Berlin, Germany; 8Niels Bohr Institute, University of Copenhagen,

This work summarizes developments attained in oral vaccine formulations based on the encapsulation of antigens inside porous silica matrices. These vaccine vehicles protect the proteins from the harsh acidic stomach medium, allowing them to reach the Peyer´s patches, inducing immunity. Focusing on the pioneer research conducted at Butantan Institute, in Brazil, the results report the optimization of the antigens´ encapsulation yield, as well as their homogeneous distribution inside the meso and macro porous network. The characterization plus modelling of pure antigens having different dimensions and their complexes, like silica with hepatitis B virus like particles and diphtheria anatoxin, were performed by Small Angle X-ray Scattering (SAXS), X-ray Absorption Spectroscopy (XAS), X-ray Phase Contrast Tomography (XPCT) and neutron and X-ray imaging. The association of these techniques with complementary ones provided a clear picture of the proposed vaccines. Mice with variable high and low humoral responses presented significant levels of antibodies, proving the efficacy of the proposed oral immunogenic complex.

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6:10pm - 7:00pmKN-32: Crystallography and cultural heritage - On beauty, science and passion
Location: Terrace 2B
Session Chair: Jose Miguel Delgado

Gilberto Artioli

 

Crystallography and cultural heritage - On beauty, science and passion

Gilberto Artioli

Università di Padova, Padova, Italy

Crystallography has many traditional and intuitive links with cultural heritage. The most scholar one is the description and analysis of symmetry in art and architecture [1-2]. The most natural is the fascination that crystals induce on human mind, as light- and color-capturing gems [3]. However virtually all artistic forms and all products derived from human activity are made of materials. The fundamental contribution that crystallography provides to our knowledge of matter is being rapidly transferred into our ability to better interpret archaeological evidence of past human activities (Fig. 1), and to manage and preserve artworks for future generations. The science of cultural heritage materials is profiting greatly of the state-of-the-art crystallographic methods and techniques, and in turns poses new and unexpected challenges to future crystallographers.

[1] MacGillavry, C.H. (1965) Symmetry aspects of M.C. Escher’s periodic drawings. Utrecht: Oosthoek

[2] Makovicky, E. (2016). Symmetry: through the eyes of old masters. Berlin/Boston: Walter de Gruyter GmbH & Co KG.

[3] Garcia-Ruiz, J.M. (2018). 2001: The Crystal Monolith. Substantia, 2, 19-25.

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6:10pm - 7:00pmKN-33: Overview of Global Neutron Sources, Instruments and Initiatives
Location: Club A
Session Chair: Jiri Kulda

Ken Andersen

 

Overview of Global Neutron Sources, Instruments and Initiatives

Ken Andersen

Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America

Neutron scattering is an essential element in the materials science toolkit, providing unique structural and dynamic information. It relies on an ecosystem of facilities and smaller sources, which provide access to researchers covering a vast range of scientific problems. This talk will provide an overview of the current global neutron landscape, both today and in the near future. I aim to demonstrate the scientific impact, diversity and vitality of this ecosystem, highlighting the important role that neutron scattering plays in addressing a number of societally-impactful grand challenges.

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8:00pm - 11:55pmDinner: Conference dinner
Location: National House

extra fee


 
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