XXV General Assembly and Congress of the
International Union of Crystallography - IUCr 2021
August 14 - 22, 2021 | Prague, Czech Republic
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: 1st Nov 2024, 12:33:15am CET
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Session Overview |
Session | ||
MS-39: Quantum crystallography in materials science
Invited: Rebecca Scatena (UK), Cherif Matta (Canada) | ||
Session Abstract | ||
Many of the most pressing problems of our civilization, technological ones in particular, are due to the limits of the materials that are available now. Materials science and engineering are usually defined as the design and discovery of new materials, particularly solids. Thus, breakthroughs in materials science are likely to affect the future of the mankind. As quantum crystallography methods supply more accurate and precise results than routine approaches, QC and materials science is a very promising match. QC allows for a deeper understanding properties (mechanical, chemical, physical, electrical, optical, magnetic, etc), functions and performance of materials at the atomic and molecular level (structure-properties relationships). This MS will cover contributions containing applications of Quantum Crystallography methods mostly in solid state chemistry and physics including crystal engineering but also in geology, ceramics, metallurgy, biomaterials and other fields. For all abstracts of the session as prepared for Acta Crystallographica see PDF in Introduction, or individual abstracts below. | ||
Introduction | ||
Presentations | ||
10:20am - 10:25am
Introduction to session 10:25am - 10:55am
Formate-mediated Magnetic Superexchange in the Model Hybrid Perovskite [(CH3)2NH2]Cu(HCOO)3: Applicability criteria for the GKA rules 1University of Oxford, Oxford, United Kingdom; 2Polytechnic of Milan, Milan, Italy; 3University College London, London, United Kingdom We have investigated the magnetic and electronic structures of crystalline dimethylammonium copper formate [(CH3)2NH2]Cu(HCOO)3; a model compound that belongs to a wide class of hybrid organic-inorganic perovskites. We present the results of a combined experimental approach, where neutron diffraction and magnetisation measurements were used to solve the ground state magnetic structure in which the same ligand mediate antiferromagnetic and ferromagnetic interactions, while electron charge density distribution and orbital occupancy were determined by high-resolution x-ray diffraction [1]. The latter provided a microscopic analysis of the chemical bonding from which we established a detailed correlation between the structural, electronic, and magnetic properties of [(CH3)2NH2]Cu(HCOO)3, demonstrating the primary role of Cu-O bonding in establishing the nature of the exchange. Our results elucidate the mechanism of magnetic exchange mediated by formate anions, from which we examine the applicability of foundational theories of purely inorganic perovskites and define characteristics that the ligands should meet to support the use of the Goodenough-Kanamori-Anderson (GKA) rules [2]. The derived criteria for the applicability of GKA rules where used to predict the magnetic structure, then verified experimentally, of hybrid perovskites including different ligands, such as [(CH3)2NH2]Cu(HCOO)2(NO3) and Cu(HCOO)2(pyrimidine). Charge density analysis enabled us to account for qualitative and quantitative differences in the superexchange mediated by formate, nitrate and pyrimidine. [1] R. Scatena, R. D. Johnson, P. Manuel, P. Macchi, J. Mater. Chem. C 2020, 8, 12840–12847. [2] S. V. Streltsov, D. I. Khomskii, Uspekhi Fiz. Nauk 2017, 187, 1205–1235. 10:55am - 11:25am
The Electric Field of ATP-Synthase 1Département de chimie, Université Laval, Québec, QC, Canada G1V0A6; 2Department of Chemistry and Physics, Mount Saint Vincent University, Halifax, NS, Canada B3M2J6; 3Chemical Computing Group (CCG), Sherbrooke Street West, Montreal, QC, Canada H3A2R7; 4Department of Chemistry, Saint Mary's University, Halifax, NS, Canada B3H3C3 This talk will underscore the importance of developing fast Quantum Crystallographic (QCr) [1] approaches to accurately calculate the electric fields and their associated electrostatic potentials of large molecules such as proteins. Crystallographic structures of ATP synthase from five species have been used to calculate (approximately) and compare their intrinsic electrostatic potentials and fields [2-4]. Striking consistent patterns (and differences) in the topographies of these scalar and vector fields are uncovered across the five studied ATP synthases [2]. The role of these fields in the biological function of ATP synthase will be discussed within the context of Mitchell’s chemisomotic theory. Our calculations suggest that, due to the intrinsic field of ATP synthase itself, the standard equation of chemiosmotic must be augmented by including a term that accounts for the contribution to ΔG of the difference in ATP synthase’s electrostatic potential, ΔΨATPase, between the points of entry and exit of the protons in the mitochondrion. With this inclusion, our proposed amended equation for the chemisomotic ΔG, in standard notation, becomes [2-4]: ΔG = ΔGchem.+ ΔGelec.+ (ΔGATPase (NEW TERM)) = 2.3 nRT ΔpH + nFΔΨ + nFΔΨATPase Our results can be summed-up into assigning two separate but complementary roles to ATP synthase [2]: (1) Its putative role, and that is the catalysis (i.e. lowering the ΔG‡) of the reaction: ADP + Pi ↔ ATP + H2O. (2) A novel role, that is, of altering the ΔG of the reaction of translocation of protons from the inter-membrane gap in the mitochondrion to the mitochondrial matrix, i.e. the reactions: H+inter-membrane space ↔ H+mitochondrial matrix. Said differently, due to the enzyme’s very structure and due to the chemiosmotic origin of the free energy it harnesses, ATP synthase functions over an above its role as an enzyme and is more than strictly a biological catalyst. The crucial role played by the enzyme’s own electric properties calls for their accurate and fast determinations especially with the advent of QCr [1]. An example of such approaches is the Kernel Energy Method [5-6] fragmentation whereby, given a molecular geometry, one can perform quantum calculations on fragments and obtain an approximate total electrostatic potential of the full molecules. Since this is a part of a larger project, time permitting, the talk may touch upon some of the hot current open questions such as the one we term “Mitochondrion Paradox” [7-10]. [1] Genoni, A. ; Bucinskż, L.; Claiser, N.; Contreras-Garcia, J.; Dittrich, B.; Dominiak, P. M.; Espinosa, E.; Gatti, C.; Giannozzi, P.; Gillet, J.-M.; Jayatilaka, D.; Macchi, P.; Madsen, A. Ų.; Massa, L.; Matta, C. F.; Merz Jr., K. M.; Nakashima, P.; Ott, H.; Ryde, U.; Scherer, W.; Schwarz, K.; Sierka, M.; Grabowsky, S. (2018) Chem. Eur. J. 24, 10881-10905. [2] Vigneau, J. N.; Fahimi, P.; Ebert, M.; Cheng, Y.; Tannahill, C.; Muir, P.; Nguyen-Dang, T.-T.; Matta, C. F. (2021) Submitted, in review. [3] Cheng, Y. (2019). A Computational Investigation of the Intrinsic Electric Field of ATP Synthase (M.Sc. Thesis); Saint Mary's University: Halifax, Canada. [4] Matta, C. F. (2016). Dipolar field of ATP Synthase: Unpublished results presented in a number of seminars. [5] Huang L.; Massa, L.; Karle, J. (2010). Chapter 1 in: Quantum Biochemistry: Electronic Structure and Biological Activity, Vol. I; Matta, C. F. (Ed.), Wiley-VCH: Weinheim, 2010. [6] Polkosnik, W.; Matta, C. F.; Huang, L.; Massa, L. (2019). Int. J. Quantum Chem. 119, e26095. [7] Fahimi, P. ; Matta, C. F. (2021). Phys. Biol. 18 , in press (DOI: 10.1088/1478-3975/abf7d9). [8] Fahimi, P. ; Matta, C. F. (2021) Submitted, in review. [9] Nasr, M. A.; Dovbeshko, G. I.; Bearne, S. L.; El-Badri, N.; Matta, C. F. (2019). BioEssays 41, 1900055. [10] Matta, C. F.; Massa, L. (2017). J. Phys. Chem. A 121, 9131-9135. 11:25am - 11:45am
Thermal stability of Glass forming Metal-Organic Framework: Role of metal-ligand bonding 1Center for Materials Crystallography, Department of Chemistry and iNano, Aarhus University, Aarhus 8000, Denmark; 2Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8571, Japan Melt-quenched glasses from metal-organic frameworks (MOF) represents a new class of hybrid functional materials, which have generated a lot of attention amongst the material science community due to their novel short-range structures and potential applications such as gas-mixture separations, ion conductivity, etc [1]. To improve the thermal stability window of the liquid phase of MOFs, substantial efforts are directed to lower the melting temperature of the crystalline MOF state [2, 3]. However, in this context, the relationship between chemical bonding and melting/decomposition of MOFs is still unexplored. In this work, we compare the electron density distribution of two isostructural Zeolitic Imidazole Framework (ZIF) molecules-meltable Zn-ZIF-zni with Co-ZIF-zni that undergoes thermolysis, using high-resolution synchrotron single-crystal X-ray diffraction data measured at 25 K. Several ZIFs such as ZIF-4, ZIF-1, ZIF-3, ZIF-zeg, ZIF-nog undergo thermal amorphization and recrystallization to ZIF-zni prior to melting/decomposition [4]. Charge density analysis along with derived topological parameters based on Bader’s QTAIM theory [5] shows that Zn‒N bonds are primarily closed shell ionic in nature and weaker in strength. On the other hand, Co‒N bonds are dominated by polar covalent interactions with significant electron density accumulation in bonding region and distinct π-backbonding features (Fig. 1). In situ temperature dependent Raman spectroscopy (300 K-773 K) revealed a greater degree of bond weakening in the imidazolate ligands of Co-ZIF-zni during heating. In addition, variable temperature crystallography (25 K-400 K) confirmed that Zn-ZIF-zni are less prone to framework distortion in comparison to a more rigid framework in Co-ZIF-zni. To further validate the role of metal‒ligand bonds on thermal behavior of these ZIF compounds, for the first time we prepared a set of eight novel solid solutions-CoxZn1-x-ZIF-zni where mole fraction (x) of Co ranges from 0.4 to as low as 0.003. Using differential scanning calorimetry (DSC)/ thermogravimetric analysis (TGA), we observed that a presence of very low quantity (~4%) of doped Co in Zn-ZIF-zni lattice results in thermal decomposition of the crystal framework. We identified this phenomenon as ‘butterfly effect’ of Co‒N bonds on thermal stability of these solid solution MOFs. [1] Bennett, T. D. & Horike, S. (2018). Nat. Rev Mat. 3, 431-440. [2] Frentzel-Beyme, L., Kloß, M., Kolodzeiski, P., Pallach, R. & Henke, S. (2019). J. Am. Chem. Soc. 141, 12362-12371. [3] Hou, J., Ríos Gómez, M. L., Krajnc, A., McCaul, A., Li, S., Bumstead, A. M., Sapnik, A. F., Deng, Z., Lin, R., Chater, P. A., Keeble, D. S., Keen, D. A., Appadoo, D., Chan, B., Chen, V., Mali, G. & Bennett, T. D. (2020). J. Am. Chem. Soc. 142, 3880-3890. [4] Bennett, T. D., Keen, D. A., Tan, J.-C., Barney, E. R., Goodwin, A. L. & Cheetham, A. K. (2011). Angew. Chem. Int. Ed. 50, 3067-3071. [5] Bader, R. F. (1990). Atoms in molecules. Wiley Online Library. 11:45am - 12:05pm
Chemical bonding origin of the thermoelectric power factor in Half-Heusler semiconductors Department of Materials, Imperial College London, Exhibition Road, London SW7 2AZ, United Kingdom Thermoelectric materials are able to interconvert thermal and electrical energy, and thus offer the potential to harvest waste heat through solid-state devices. A particularly interesting class of thermoelectric materials are the cubic intermetallic Half-Heusler semiconductors with XYZ stoichiometry, which show promising high temperature thermoelectric properties commonly attributed to the high degeneracy of carrier pockets in the band structure and weak electron-phonon coupling. Half-Heuslers crystallize with YZ and XY forming tetrahedrally coordinated zinc blende networks, and XZ forming a rock salt network. Stable stoichiometric Half-Heuslers have valence electron counts of 8 or 18, which has led to interpretation of their bonding and properties within Zintl chemistry [1]. Applying Zintl chemistry to Half-Heuslers, the electroposive cation, Xn+, donates all its valence electrons to the covalently bonded [YZ]n- polyanion, which then fulfils the 8- or 18-electron rule. Thus, ionic and covalent bonding patterns coexist and there is a clear distinction between the bonding within the polyanion and the bonding between formal cation and polyanion. Zintl chemistry is often applied for engineering thermoelectric materials, and for Half-Heuslers, it gives rise to predictions regarding the electronic structure and defect chemistry. Expanding on previous investigations on chemical bonding in Half-Heuslers [2,3], we present the results of computational real space chemical bonding analysis using Bader’s quantum theory of atoms in molecules and delocalization indices on a range of Half-Heusler semiconductors. This shows strong deviations from predictions from Zintl chemistry for transition metal based materials and reveal interesting relations between chemical bonding and thermoelectric and response properties [4]. We construct a map of chemical bonding in Half-Heuslers based on real space indicators [5], onto which we map important calculated thermoelectric properties. This reveals that strong covalent bonding between formal cation and polyanion results in increased carrier pocket degeneracies, and therefore improved thermoelectric properties. Thus, the materials least in line with the commonly applied Zintl concept are in fact the ones with the best thermoelectric properties. This works extends our previous studies showing the inability of Zintl chemistry to explain the unexpected isotropic properties in thermoelectric Mg3Sb2 [6], and thus presents a critical view on the simplistic chemical concepts too often applied for rational materials design. Furthermore, it highlights the potential of applying tools from chemical bonding analysis and quantum crystallography for materials design. [1] Zeier, W. G., Schmitt, J., Hautier, G., Aydemir, U., Gibbs, Z. M., Felser, C., Snyder, G. J. (2016). Nat. Rev. Mater. 1, 16032 [2] Bende, D., Grin, Y., Wagner, F. R. (2014). Chem. Eur. J. 20, 9702-9708 [3] Bende, D., Wagner, F. R., Grin., Y. (2015). Inorg. Chem. 54, 3970-3978 [4] Tolborg, K., Iversen, B.B. (2021). Submitted [5] Raty, J. Y., Schumacher, M., Golub, P., Deringer, V. L., Gatti, C., Wuttig, M. (2019). Adv. Mater. 31, 1806280 [6] Zhang, J., Song, L., Sist, M., Tolborg, K., Iversen, B. B. (2018). Nat. Commun. 9, 4716 12:05pm - 12:25pm
Towards the measurement of bonding electron densities in nanostructured materials 1Department of Materials Science, Monash University, Victoria 3800, Australia; 2Department of Physics, Norwegian University of Science and Technology (NTNU), Trondheim, Norway; 3School of Engineering and Applied Sciences, Harvard University, Cambridge, USA; 4Department of Physics, Chalmers University of Technology, Gothenburg, Sweden; 5Monash Centre for Electron Microscopy, Monash University, Victoria 3800, Australia. Quantitative convergent-beam electron diffraction (QCBED) has become established as a highly accurate and precise means of measuring bonding electrostatic potentials and electron densities [1]. To date, it has almost exclusively been performed using the Bloch-wave electron scattering formalism [2], which requires 3-dimensional periodicity throughout the scattering volume. This has restricted QCBED to bonding measurements in homogeneous, single-phased crystalline materials (just like X-ray diffraction). The multislice formalism [3] for electron scattering dispenses with the requirement of periodicity in the direction of the electron beam. Furthermore, electron probe sizes are typically of order 1 nm in dimension for QCBED, rendering even very highly curved features in nanostructured materials locally planar relative to the electron probe. This means that nanostructures that share a crystallographically coherent interface with the surrounding matrix in which they are embedded, could in principle be analysed by multislice-based QCBED. Add to this the routine sub-nanometre precision in positioning electron probes in transmission electron microscopes, and there is the potential to map bonding charge density as a function of position in nanostructured materials for the first time. We are attempting to measure bonding electron densities within a number of different nanostructures and also across their interfaces with the surrounding matrix material, using QCBED based on the multislice formalism. We will present some early results from several nanostructured materials such as those shown in Fig. 1 below. Figure 1. High angle annular dark field scanning transmission electron microscopy of an Al-Cu alloy [4] (a); a (ZnO)kIn2O3 (k = 5) thermoelectric oxide superlattice [5] (b); an Al-Cu-Sn alloy containing Sn-coated voids [6] (c & d). The figure also presents a CBED pattern (e) from the material in part b and a CBED pattern (f) taken through a void like the one shown in parts c and d. [1] Nakashima, P. N. H., Smith, A. E., Etheridge, J. & Muddle, B. C. (2011). Science 331, 1583. [2] Bethe, H. A. (1928). Ann. Phys. (Berlin) 392, 55. [3] Cowley, J. M. & Moodie, A. F. (1957). Acta Cryst. 10, 609. [4] Bourgeois, L., Zhang, Y., Zhang, Z., Chen, Y. & Medhekar, N. V. (2020). Nature Commun. 11, 1248. [5] Liang, X. & Clarke, D. R. (2018). J. Appl. Phys. 124, 025101. [6] Tan, X., Weyland, M., Chen, Y., Williams, T., Nakashima, P. N. H. & Bourgeois, L. (2021). Acta Mater. 206, 116594. We thank the Monash Centre for Electron Microscopy where all data were collected. Many thanks to A/Prof. Matthew Weyland and Prof. Joanne Etheridge for their expertise. We thank the Australian Research Council for funding (DP210100308). 12:25pm - 12:45pm
Towards accurate positions of hydrogen atoms bonded to heavy metal atoms University of Warsaw, Warsaw, Poland Transition metal (TM) bound hydrides can be used as hydrogen storage materials, they also play a key role in processes of catalysis, energy conversion, and search for superconductivity. However, they are very difficult to study with the method of X-ray diffraction, on the one hand, due to the fact that hydrogen atom has only one electron with density is usually strongly shifted towards its bonding partner, on the other hand, because its weak diffraction signal is strongly screened by scattering from the electron-rich heavy metal. Moreover, it is difficult to collect high quality, let alone high resolution X-ray diffraction data for such compounds. The availability of neutron diffraction data, which are the benchmark of hydrogen positions, is even more limited. Recently, it was proven that Hirshfeld Atom Refinement (HAR), using aspherical atomic scattering factors, allows locating hydrogen atoms bonded to light elements based on standard resolution X-ray diffraction data with accuracy and precision very close to the one of neutron experiments [1]. This was a significant improvement compared to the most popular Independent Atom Model (IAM). Nevertheless, excluding this study, only 5 structures of complexes with TM-H bonds have been successfully refined with HAR [1,2] for only two of which a complementary neutron data set is available. We present the results of HAR of around 11 X-ray structures of crystals of metaloorganic compounds containing hydrogen atoms bonded to heavy metals from period IV (Fe, Co, Cu, Ni), V (Nb, Ru, Rh, Sb), and VI (Os) for which also the corresponding neutron structure is available. Refinements were performed using Olex2 with the application of atomic aspherical structure factors computed with the DiSCaMB library [3], based on Hirshfeld partition of molecular electron density calculated for the central molecule embedded in a cluster of atomic charges and dipoles centered on the atomic nuclei of the surrounding molecules within the radius of 8 Å. Additionally, HARs without a cluster of multipoles were carried out with NoSpherA2 [2]. Wave functions were calculated using the DFT method, in each case B3LYP, PBE, and M062X functionals were used. All the calculations were performed also in the version including relativistic effects as implemented in the DKH2 Hamiltonian approach. Various basis sets were tested. Overall, the DiSCaMB-HAR procedure elongates the TM-H bond lengths, bringing them closer to the neutron values [4]. The level of improvement is dependent on the quality of the experimental data and the refinement. The most prominent example of a successful refinement is the structure of a metalloorganic complex containing a Ru-H bond, which can be refined anisotropically to obtain the Ru-H distance in very high agreement with the one in the neutron structure (neutron: 1.598(3) Å, IAM: 1.56(2) Å, DiSCaMB-HAR(B3LYP/cc-pVTZ-DK): 1.593(11) Å, DiSCaMB-HAR(PBE/cc-pVTZ-DK): 1.599(11) Å). In four cases (Fe, Ru, and Rh complexes), refinement of ADPs of hydrogen atoms was feasible. In the case of the Fe complex, HAR performed with SHADE2-estimated H ADPs was feasible and was used to evaluate the H APDs refined with HAR. For two structures X-ray and neutron experiments were performed at the same temperature, thus direct comparison of HAR and neutron isotropic temperature factors of hydrogen atoms will be presented. The data sets were ranked according to various parameters describing data quality and refinement quality both for the neutron and the X-ray data sets, which lead to the final joint neutron and X-ray data-refinement quality ranking. The ranking reflects well how favorable the HAR-neutron TM-H bond length comparison is and correlates with the number of electrons in the TM. Examples showing the influence of factors such as the position in the ranking and the method of obtaining the molecular wave function on the quality of TM-H and other X-H bond lengths obtained with HAR will be presented. |
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