The next Annual Meeting of German Crystallographic Society (29. Jahrestagung der Deutschen Gesellschaft für Kristallographie - DGK) will take place from 15-18 March 2021.
The DGK2021 will be organised by DESY (Hamburg, Germany) as a virtual event, due to the present situation caused by the COVID-19 pandemic.
Crystallography is a modern, interdisciplinary field of research and relevant for many innovations ranging from novel pharmaceuticals to new materials. We are looking forward to meet crystallographers from different disciplines and to offer a virtual platform for a fruitful exchange of ideas at the DGK2021.
Registration deadline: 19 Mar. 2021
The participation is free of charge.
Scientific topics of the conference
The following scientific topics will be covered by the conference:
Further information will follow on this official DGK2021 conference webpage soon.
As a response to the SARS-CoV-2 pandemic we have set up a large consortium of more than one hundred scientist centered at DESY in Hamburg in order to find suitable drug candidates. In contrast to common screening techniques such as biochemical activity-based assays or X-ray fragment screening, here we employed massive X-ray crystallographic screening of two drug-repurposing libraries against the SARS-CoV-2 main protease (Mpro) as initial target. In total co-crystallization experiments of 5953 individual drugs with Mpro were setup and datasets from more than 8000 crystals were collected at the PETRA III MX beamlines. Our screening effort resulted in the identification of 37 compounds binding to Mpro. Secondary screening of these hits in a cell-based viral infection assay carried out at the Bernhard Nocht-Institute revealed antiviral activity in combination with low cytotoxicity for six compounds, which have not yet been reported as inhibitors of SARS-CoV-2. While four of these inhibitors bind to the catalytic site of the enzyme, the remaining two bind to a previously undescibed allosteric site within the dimerization domain [1]. For the two most promising compounds from our screen, Calpeptin and Pelitinib, we have intiated further preclinical testing
References:
[1] S. Günther, P. Y. A. Reinke, et al. , bioRxiv, doi:10.1101/2020.11.12.378422.
Since the worldwide outbreak of the Covid-19 pandemic in early 2020, researchers in many different parts of the world have started activities directed towards a better understanding of the SARS-CoV-2 virus life cycle or even towards medical treatment of Covid-19. Large-scale research facilities such as for instance synchrotron radiation facilities are playing a particularly important role in this respect by providing state-of-the-art Macromolecular crystallography (MX) facilities. MX has been instrumental in deciphering the first atomic resolution structure of the SARS-CoV-2 main protease (Figure 1) [1]. Several other viral protein structures have been determined following that [2]. Furthermore, owing to the manifold developments of MX towards automation and the concomitant increase in throughput, MX has also been employed as a primary screening technique for finding new substances, which might be active against SARS-CoV-2. In the presentation several user and in-house projects will be highlighted, which are directed towards this goal.
References:
[1] L. Zhang, et al., ‘Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved α-ketoamide inhibitors’, Science 368, 409-412 (2020)
[2] M. Scudellari, ‘The sprint to solve coronavirus protein structures - and disarm them with drugs’, Nature 581, 252-255 (2020)
This contribution reports reversible, single-crystal-to-single-crystal phase transitions of commensurately modulated sodium saccharinate 1.875-hydrate [Na(sac)(15/8)H2O]. The phases were studied in the temperature range 298 to 20 K. They exhibit complex disordered states. An unusual reentrant disorder has been discovered upon cooling through a phase transition at 120 K. The disordered region involves three sodium cations, four water molecules and one saccharinate anion. At room temperature, the structure is an eightfold superstructure that can be described by the superspace group C2/c(0b0)s0 with q = (0, 3/4, 0). It demonstrates maximum disorder with the disordered chemical entities having slightly different but close to 0.50:0.50 disorder component ratios. Upon cooling, the crystal tends to an ordered state, smoothly reaching a unified disorder component ratio of around 0.90:0.10 for each of the entities. Between 130 and 120 K a phase transition occurs involving a sudden increase of the disorder towards the disorder component ratio 0.65:0.35. Meanwhile, the space group and general organization of the structure are retained. Between 60 and 40 K there is another phase transition leading to a twinned triclinic phase. After heating the crystal back to room temperature its structure is the same as before cooling, indicating a complete reversibility of the phase transitions.
Correlated disorder in crystalline materials gives rise to single crystal diffuse scattering. While the average structure determination via Bragg data analysis is considered a standard procedure, disorder analysis is thought of as a lengthy and complicated process. We present a mean field approximation to model single crystal diffuse scattering in molecular materials from a simple pair-interaction Hamiltonian.
Mean filed theory is a self-consistent field theory, which is widely used in statistical physics to model high-dimensional random systems. It has proven a valuable tool in the analysis of magnetic diffuse scattering data [1]. Here, the formalism is applied to describe orientationally disordered molecular crystals.
We present a computational study based on the mean field model suggested by Naya [2] and proof its applicability to strongly correlated disorder, where the local building block geometry dictates allowed and prohibited local configurations. The system that will be analysed in detail is a two-dimensional analogue the mercury diammonium halide Hg(NH$_{3}$)$_{2}$Cl$_{2}$ as depicted in the Figure [3].
We compare the results of the diffuse scattering analysis using the mean field model as introduced by Naya [2] to the results of RMC modelling and $\Delta$PDF models based on a Warren-Cowley short range order parameter refinement (see Figure). Finally, the stability of the mean field analysis on limited data availability is demonstrated: Diffraction experiments under pressure or electric field yield a limited reciprocal space coverage. Here, we demonstrate the robustness of the proposed method against incomplete data sets.
[1] Paddison, J. A., et al. (2013). Physical review letters,110(26), 267207.
[2] Naya, S. (1974). Journal of the Physical Society of Japan,37(2), 340–347
[3] Lipscomb, W. (1953). Analytical Chemistry,25(5), 737–739.
Figure Label:
(a) Disordered structure of mercury diammonium halide Hg(NH$_{3}$)$_{2}$Cl$_{2}$ [3]. Hg in black, N in blue, Cl in light green. H atoms were omitted for clarity. The Hg is disordered over the face centres of the cubic unit cell. The ammonia groups occupy the centre of the shown cell, while the Cl is placed on the corner of the unit cell.
(b) X-ray diffuse scattering for the two-dimensional model system. Due to the fourfold symmetry of the average structure, one quadrant of the hk-layer is sufficient to represent the full data. Upper left corner: data as calculated from a model structure that fulfils the local rules; upper right corner: mean field refinement; bottom right corner: RMC refinement; bottom left corner: Warren-Cowley short range order analysis.
The group IV-VI chalcogenides have important thermoelectric applications. GeTe has emerged as a promis- ing non-toxic candidate, especially when the high-temperature cubic phase is suppressed to room tempera- ture. However, even the mechanism of phase transition is disputed, as is the presence of disorder. Here we combine ab initio MD with synchrotron X-ray and dynamic neutron pair distribution function (PDF) analysis. We show that previous reports of disorder and symmetry breaking are entirely due to highly damped and anharmonic phonons. As predicted by metavalent bonding theories, this arises due to a softening in local bonding on heating, which strengthens long-range <100>c correlations. This picture is consistent with reported changes in resistivity and dielectric constant, and shown to be ubiquitously present in other polarisable binary chalcogenides and hR6 structured elements. Our results unify the results of local probes and spectroscopy as applied to binary chalcogenides, and should inspire a re-examination of other highly anharmonic energy materials such as hybrid perovskites and ’rattling’ thermoelectrics.
R$_2$Ir$_3$Si$_5$ (R = Ho, Er, Lu) crystallize in the U$_2$Co$_3$Si$_5$ structure type at room temperature (orthorhombic space group Ibam) [1]. Upon cooling they undergo first-order charge-density-wave (CDW) phase transitions, as evidenced by anomalies with hysteresis in the temperature dependencies of the electrical resistivity ($\rho$), specific heat ($C_p$), magnetic susceptibility ($\chi$), Seebeck coefficient ($S$) and thermal conductivity ($\kappa$) [1-4]. The CDW character of the low-temperature phases is corroborated by the appearance of satellite reflections at q = (0.2495, 0.4973, 0.2483) in diffraction experiments [4,5]. Single-crystal x-ray diffraction has revealed that the incommensurate CDW is accompanied by a strong monoclinic lattice distortion, while the symmetry of the CDW phase is reduced to triclinic. Here, we discuss the microscopic mechanism of CDW formation on the basis of a superspace analysis of single-crystal x-ray diffraction data [4].
Acknowledgement: Single-crystal X-ray diffraction data were collected at Beamline P24 of PETRA-III at DESY, Hamburg, Germany.
References
[1] Y. Singh, D. Pal, S. Ramakrishnan, A. M. Awasthi and S. K. Malik, Phys. Rev. B 71, 045109 (2005).
[2] Y. K. Kuo, K. M. Sivakumar, T. H. Su and C. S. Lue, Phys. Rev. B 74, 045115 (2006).
[3] N. S. Sangeetha, A. Thamizhavel, C. V. Tomy, S. Basu, A. M. Awasthi, P. Rajak, S. Bhattacharyya, S. Ramakrishnan and D. Pal, Phys. Rev. B 91, 205131 (2015).
[4] S. Ramakrishnan, A. Schonleber, T. Rekis, N. van Well, L. Noohinejad, S. van Smaalen, M. Tolkiehn, C. Paulmann, B. Bag, A. Thamizhavel, D. Pal and S. Ramakrishnan, Phys. Rev. B 101, 060101(R) (2020).
[5] M. H. Lee, C. H. Chen, M. -W. Chu, C. S. Lue and Y. K. Kuo, Phys. Rev. B 83, 155121 (2011).
What is the complexity of a crystal structure? The definition of complexity is a challenging and similarly fascinating subject, touching different scientific disciplines such as economy, informatics, biology, math, and chemistry amongst others. Instead of defining complexity per sé, it is in practice easier to ask which system is more complex, showing that the challenge of defining complexity is closely related to the identification of an appropriate scale to measure complexity. In this contribution, the Shannon entropy is used as measuring system as defined by information theory, providing us with a framework to differentiate between the complexity of crystal structures as initially introduced by S. Krivovichev.[1]
In my presentation I discuss the opportunities and challenges that come with an information theory-based analysis of crystal structures as measure for complexity. I show that comparisons between Shannon entropy, crystal structure complexity and configurational entropy can be drawn,[2] opening intriguing opportunities for the systematic assessment of configurational entropy of crystal structures with implications in the areas of crystal growth and chemical bond theory.[3] Finally, and following on from recent developments in the field where theory development is in the centre, I introduce crystIT (crystallography & Information Theory),[4] a python-based open-access program.[5] crystIT calculates various information measures based on a *.cif file as input, providing an easy-to-use platform for an information theory-based crystal structure analysis.
[1] S. Krivovichev, Angew. Chem. Int. Ed. 2014, 53, 654.
[2] S. Krivovichev, Acta. Cryst. B 2016, 72, 274.
[3] E. S. Harper, G. v. Anders, S. C. Glotzer, Proc. Acad. Nat. Sci. 2019, 116, 16703.
[4] C. Kaußler, G. Kieslich J. Appl. Cryst. 2021, accepted.
[5] http://www.github.com/GKieslich/crystIT/
Naturally occurring single crystals of bixbyite, (Fe,Mn)2O3, from the Thomas Mountain Range in Utah, USA were studied via (scanning) transmission electron microscopy (S)TEM. With up to 5 cm edge length, these mineral specimens are the largest bixbyite crystals found worldwide. Their hexahedral shapes are often modified by {211} facets at the corners and small {211} truncations along their cube edges. Characteristic lamellar defects running parallel to the {100} planes can be observed via TEM imaging, which are, according to EDS analyses, attributed to the tetragonal manganese silicate braunite, Mn7[SiO12]. In the present study, electron nano-diffraction and atomic resolution (S)TEM were employed to verify the presence of braunite lamellae and to investigate their orientation relationship with bixbyite. The analysis confirmed an epitaxial intergrowth of both phases, with their main axes being parallel and the unique c axis of braunite always aligned perpendicularly to the lamellar plane. Moreover, small rectangular shaped precipitates, which had been, due to their almost identical chemical composition, previously interpreted as small bixbyite inclusions within the host crystal, were often observed in contact with the braunite lamellae. Electron nano-diffraction and atomic resolution (S)TEM imaging revealed these crystallites not to be bixbyite but jacobsite, a cubic iron-manganese spinel with the stoichiometric formula MnFe2O4, whose occurrence in this unique context had not been reported before. Moreover, due to the higher temperatures needed for spinel crystallization, the occurrence of jacobsite may serve as a geo-thermometer. (S)TEM in conjunction with automated crystal orientation mapping (ACOM)-TEM showed that no orientation relationship exists between the jacobsite inclusions and the bixbyite/braunite matrix. Nevertheless, their characteristic rectangular shape is typically aligned concordantly with the (001) plane of the braunite lamellae. The resulting crystal shape of jacobsite is determined by the presence of the braunite lamellae, while the respective crystallites maintain their freedom of rotation. To the authors’ knowledge, this is a novel observation of exomorphosis of jacobsite, i.e. the change in habitus of the spinel crystallites due to external conditions. Note that the term exomorphosis is used here in the mineralogical sense in contrast to the often used petrological aspect. Based on the TEM results, the formation of the jacobsite precipitates is discussed and a growth model suggested.
Metal-organic frameworks (MOFs) or porous coordination polymers (PCPs) are known for their versatile combination of inorganic building units and organic linkers, which offers immerse opportunities in a wide range of applications. Such applications are often designed by considering the inherent properties of MOFs, which in turn are governed by the crystal structures. Therefore, development of new structural characterization techniques parallels discovery of new materials.
Although single crystal X-ray diffraction (SCXRD) is the most practiced and routine method for structure determination, the acquisition of adequate data quality from weakly scattering nano- and submicro-sized crystals remains a challenge for this technique. While powder X-ray diffraction (PXRD) is more suitable technique for handling small crystals, structure determination of MOFs in particular can be challenging due to severe peak overlap as a consequence of large unit cell parameters, complexity of the structures themselves, as well as phase mixtures.
Three-dimensional electron diffraction (3DED) techniques have shown to be powerful for structural determination of 'intractable' crystals that are too small for SCXRD analysis. These techniques benefit from the strong Coulomb interaction between electrons and matter. Compared to X-ray, electrons generate much higher signal-to-noise ratios, even when the volume of the crystals are 6 or 7 orders of magnitude smaller. I will discuss applying 3DED in revealing the unique properties of MOFs for photo- and electrocatalysis. I will first present it on investigating heteroatom distribution in a photoactive MOF1. Further example will be given by applying 3DED on the study of the electrocatalyst PCN-226, where the spacing between active-sites are found crucial for its activity2. Last, I will demonstrate 3DED as a high throughput single crystal approach that can accelerate the discovery of new materials, especially in a phase mixture of nanocrystals, which makes the structure determination inaccessible to other characterization techniques. I believe 3DED as a significant development for the community of MOFs, where it allows to obtain accurate atomic information from nanocrystals, and can thus avoid the slow and arduous process of crystal growth.
(1) Yuan, S.; Qin, J.-S.; Xu, H.-Q.; Su, J.; Rossi, D.; Chen, Y.; Zhang, L.; Lollar, C.; Wang, Q.; Jiang, H.-L.; Son, D. H.; Xu, H.; Huang, Z.; Zou, X.; Zhou, H.-C. ACS Cent. Sci. 2018, 4 (1), 105–111.
(2) Cichocka, M. O.; Liang, Z.; Feng, D.; Back, S.; Siahrostami, S.; Wang, X.; Samperisi, L.; Sun, Y.; Xu, H.; Hedin, N.; Zheng, H.; Zou, X.; Zhou, H.-C.; Huang, Z. J. Am. Chem. Soc. 2020, 142, 15386−15395.
Key words: Electron Diffraction, nano-crystallography, electron diffractometer, Eldico Scientific.
Abstract: After the Science nomination for “Breakthrough of the year 2018"[1,2], 3D-Electron Diffraction (3D-ED) using the continuous rotation method and X-ray crystallographic software, is gaining a lot of attention. In the past years many achievements using electron diffraction techniques have been made in the fields of organic and inorganic molecules, polymorphism, material sciences, geological sciences, natural products, energetic materials, bio-molecules and many others [2,3]. Such experiments are done in a (modified)-Electron Microscope. Though the realization of such experiments still requires plenty of expertise and efforts and it cannot be applied on daily bases by everyone. Pioneers in the field of Electron Diffraction [4], all agree that a dedicated device for the realization of such experiments would be of great advantage to the crystallographic community. Though such a device doesn't exists (up to now) at all. Therefore, it is a necessity that such a device could be made available for the realization of this exciting field of nano-crystallography. Here will present a new device which is dedicated exclusively for such purposes. The device, an Electron Diffractometer, is built and optimized for electron diffraction experiments. Furthermore, it uses exclusively the crystallographic approach (continuous rotation method) and crystallographic software. Experimental examples carried out in this device will be showcased too.
References:
[1] See: https://vis.sciencemag.org/breakthrough2018/finalists/#rapid-structure
[2] a) T. Gruene, et al. Angew. Chem. Int. Ed., 2018, 57, 313-16317. b) C. G. Jones, et al. ACS Cent. Sci., 2018, 4, 1587−1592.
[3] Short, personal selected list of mayor achievements: a) P. Brázda, et al. Science, 2019, 364, 667-669. b) R. Bücker, et al. Nat. Commun., 2020, 11, 996. c) E. T. Broadhurst, et al. IUCrJ, 2020, 7, 5-9.
[4] Personal communication with (selected list): S. Parsons, T. Grüne, M. Gemmi, U. Kolb, among others.
The mineral khurayyimite Caenter code here Zn$_4$(Si$_2$O$_7$)$_2$(OH)$_{10}$·4H$_2$O, (IMA 2018-140) was found in small cavities in altered spurrite marbles, in the northern part of the Siwaqa pyrometamorphic rock area, Central Jordan. It is a low-temperature, hydrothermal mineral and it forms at a temperature of ca. 100 °C. It builds nearly 50 μm white or colourless, platy crystals arranged in up to 200-300 μm big spherulitic aggregates.
Single-crystal X-ray diffraction experiments at ambient conditions were performed at the X06DA beamline at the Swiss Light Source (Paul Scherrer Institute, Villigen, Switzerland). Khurayyimite crystallises in space group P21/c, with unit cell parameters (a=11.2450(8), b=9.0963(5), c=14.0679(10)Å, β = 113.237(8)º, V = 1322.25(17)Å$^3$ and Z = 2. The average structure was solved using direct methods. All H-sites are located by difference Fourier analysis. The resulting structure model was refined up to R1= 0.02. The crystal structure of khurayyimite consists of sheets perpendicular to a. Each sheet is built by very unusual loop-branched sechser single chains {lB,${1_∞^1}$}[$^6$Zn$_4$Si$_4$O$_{21}$]. Voids between chains are filled by blocks of five Ca-octahedra and two CaO$_7$ polyhedra with additional OH groups and water molecules.
The loop-branched $\textit{sechser}$ single chains {lB,${1_∞^1}$}[$^6$Zn$_4$Si$_4$O$_{21}$ ] are made of dimers of Si$_2$O$_7$ and two types of ZnO$_2$(OH)$_2$ tetrahedra connected by corners. Loops of the chain contain three tetrahedra, analogous to $\textit{dreier}$ ring. Strong repulsive forces between the tetrahedra in $\textit{dreier}$ ring are pressing connecting O atoms as far as possible forming equilateral triangle with longer ZnO$_4$ edge (≈ 3.176 Å) and two shorter two SiO$_4$ edges (≈ 2.67). These repulsive forces are, according to Libau (1985), a possible reason for why such loops have not been observed more frequent.
Different combinations of chains and frameworks made of ZnO$_4$ and SiO$_4$ tetrahedra are known. In ZnSiO$_3$ (Morimoto et al. 1975), with Zn atoms in six and four-fold coordination, two pyroxene-like chains running along the c-direction are branched with two ZnO$_4$ tetrahedra forming four-membered loops. The crystal structure of the LT and HT forms of BaZn$_2$Si$_2$O$_7$ (Lin et al. 1999) exhibit a disilicate group Si$_2$O$_7$ linked via corners with ZnO$_4$ tetrahedra in a three-dimensional framework. In such a manner are created six member rings (2×Si$_2$O$_7$, 2×ZnO$_4$), four member-rings (2×SiO$_4$, 2×ZnO$_4$) and three-membered rings (1×SiO$_4$, 2×ZnO$_4$). Still, three-membered loops, made of Si$_2$O$_7$ and ZnO$_4$, like in khurayyimite, have not been observed yet.
Libau, F. (1985) Structural chemistry of the silicates. Springer‐Verlag Berlin, Heidelberg, New York, Tokyo, 347 S.
Morimoto, N., Nakajima, Y., Syono, S., Akimoto, S. and Matsui, Y. (1975) Crystal structure of pyroxene-type ZnSiO$_3$ and ZnMgSi$_2$O$_6$. Acta Crystallographica Section B, 31, 1041-1049.
Lin, J.H., Lu, G.X., Du, J., Su, M.Z., Loong, C.-K. and Richardson. J.W (1999) Phase transition and crystal structures of BaZn$_2$Si$_2$O7. Journal of Physics and Chemistry of Solids, 60(7), 975-983.
Starting from the elements, the new compounds with the composition REGaTe2 (RE = La - Nd) could be obtained, which crystallize in the non-centrosymmetric space group Pmc21. As a possible unique feature, the presence of monovalent Ga atoms can be found for these compounds, resulting in a description of these compounds according to RE(III)Ga(I)Te(-II)2. For this an investigation of the bond valence sums was carried out, which suggests the above distribution of oxidation states. Due to the relatively short atomic distances between the Ga and Te atoms, this compound can be understood as consisting of chain-like built-up polyanions [Ga(2-)Te(0)Te(1-)]3-, taking into account the Zintl concept.
Pale yellow crystals of $Ln$Sb$_2$O$_4$Br ($Ln$ = Eu – Tb) were synthesized via high temperature solid-state reactions from antimony sesquioxide, the respective lanthanoid sesquioxides and tribromides. Single-crystal X-ray diffraction studies revealed a layered structure in the monoclinic space group $P2_1/c$. In contrast to hitherto reported quaternary lanthanoid(III) halide oxoantimonates(III) [1], in $Ln$Sb$_2$O$_4$Br the lanthanoid(III) cations are exclusively coordinated by oxygen atoms in the shape of square hemiprisms. These [$Ln$O$_8]^{13−}$ polyhedra form layers parallel to the (100) plane by sharing common edges as shown in Figure 1. All antimony(III) cations are coordinated by three oxygen atoms forming ψ$^1$-tetrahedral [SbO$_3]^{3−}$ units, which have oxygen atoms in common building up meandering strands along [001] (Figure 2) according to 1D-{[SbO$^v_{2/2}$O$^t_{1/1}]^–$} (v = vertex-sharing, t = terminal). The bromide anions are located between two layers of these parallel running oxoantimonate(III) strands and have no bonding contacts with the $Ln^{3+}$ cations. Since Sb$^{3+}$ is known to be an efficient sensitizer for $Ln^{3+}$ emission, photoluminescence studies were carried out to characterize the optical properties and assess their suitability as light phosphors. Indeed, for both, GdSb$_2$O$_4$Br and TbSb$_2$O$_4$Br doped with about 1.0 – 1.5 at-% Eu$^{3+}$ efficient sensitization of the Eu$^{3+}$ emission could be detected. The resulting luminescence properties of both doped and undoped GdSb$_2$O$_4$Br and TbSb$_2$O$_4$Br are summarized in Figure 3. For TbSb$_2$O$_4$Br, in addition, a remarkably high energy transfer from Tb$^{3+}$ to Eu$^{3+}$ could be detected that leads to a substantially increased Eu$^{3+}$ emission intensity, rendering it an efficient red light emitting material [2].
References
[1] F. C. Goerigk, Th. Schleid, Z. Anorg. Allg. Chem. 2019, 645, 1079–1084.
[2] F. C. Goerigk, V. Paterlini, K. V. Dorn, A.-V. Mudring, Th. Schleid, Crystals 2020, 10, 1089–1111.
The simultaneous reaction of oxygen, its heavier homologs, and metals usually lead to the formation of substances characterized by the presence of covalent O-Ch (Ch = S, Se) bonds within complex anions like sulfates or selenides. Examples for compounds containing both, O$^{2-}$ and Ch$^{2-}$ without any attractive interaction between these species are far less known. Only a few examples for chalcogenide oxides of transition (T) and rare-earth metals (RE) are described in the literature so far, though exhibiting a relatively high variety in composition and crystal structures.
Salt-flux assisted reactions of rare-earth metals and their oxides, transition metals and selenium lead to the discovery of the mixed anionic selenide oxides RE$_2$ZrSe$_2$O$_3$ (RE = Ce-Nd, Sm) and Ce$_7$TiSe$_5$O$_7$. All these substances appear as thin needle-like crystals with diameters of 5 μm and less which are extraordinarily sensitive to mechanical stress. Consequently, structure determination had to be realized using synchrotron radiation. First investigations of Ce$_7$TiSe$_5$O$_7$ were carried out at the ESRF, beamline ID11, using micro-focused synchrotron radiation. Small crystals were pre-selected and pre-characterized using transmission electron microscopy including EDX spectroscopy [1]. The substance crystallizes with the La$_7$VSe$_5$O$_7$ structure type [2], space group Cmcm, suggesting the presence of Ti$^{3+}$ cations.
The first Zr containing selenide oxides RE$_2$ZrSe$_2$O$_3$ (= 2 RE$^{3+}$Zr$^{4+}$2Se$^{2-}$3O$^{2-}$) were investigated at PETRA III, beamline P24, and the ESRF, beamline ID11. The compounds were found to crystallize with their own structure type, space group C 2/m, characterized by the presence of large cavities extended along [010] formed by Se atoms (see Fig. 1).
Fig. 1: a-c) Crystal structure, bulk material, and SEM-SE image of Nd$_2$ZrSe$_2$O$_3$. d) TEM-BF image of the Pr$_2$ZrSe$_2$O$_3$ single-crystal investigated at ERSF, beamline ID11. The crystal part used for structure determination is emphasized.
[1] F. Fahrnbauer, T. Rosenthal, T. Schmutzler, G. Wagner, G. B. M. Vaughan, J. P. Wright, O. Oeckler, Angew. Chem. Int. Ed. 2015, 54, 10020.
[2] S. Peschke, L. Gamperl, V. Weippert, D. Johrendt, Dalton Trans. 2017, 46, 6230-6243.
The structures of the rare earth metal polychalcogenides $REX_{2-\delta}$ (X = S, Se, Te; $0 \leq \delta \leq 0.2$) share a common motive of alternating stacks of a puckered [REX] double layer and planar [X] layer, which are structurally related to the ZrSSi type. This class of compounds adopts different (super)structures, according to the chalcogen defects in their planar layers. The deficient sulfides and selenides are dominated by $X^{2-}$ and $X_{2}^{2-}$-anions, whereas a tendency to form larger anionic entities has been observed for the tellurides.[1–3]
Crystals of $RE\text{Te}_{1.875-\delta}$ (RE = Ce, Pr, Sm, Gd; $0.005 \leq \delta \leq 0.02$) have been grown by chemical transport reactions utilizing iodine and alkali halide flux reactions. All compounds crystallize in an orthorhombic unit cell, resembling a 3×4×2 supercell of the basic ZrSSi cell, with cell dimensions of about $a \approx 13.2(2)~Å$, $b \approx 17.6(2)~Å$ and $c \approx 18.0(2)~Å$. Structure solution and subsequent refinement has been performed in space group Amm2 (No. 38), in accordance with the structures of the related sulfides and selenides.[1] The generalized motif of all compounds resembles well the motif of the $\text{GdSe}_{1.875}$ type structure, as two stacks of a puckered [RE Te] and a planar [Te] layer are observed for all structures. Minor structural variations, i.e. slightly shifted atoms or additional vacancies, are observed for individual compounds within the planar [Te] layer, hinting towards marginally different ordered motifs, which can be understood as a result of structural frustration. The structural variety of the planar layer also manifests itself in a growing number of reflections violating the A-centering condition.
Quantum mechanical calculations based on DFT theory have been performed to investigate the bonding situation inside the planar [Te] layer by using the real space indicator ELI-D. The results justify the description of small anionic fragments constituting the [Te] layers, but also indicate long range order within a characteristic eight-membered Te ring. Unlike for the sulfides and selenides, these calculations suggest formally a $\text{Te}_{8}^{8-}$ anion, as bonding interactions are expected between all neighboring atoms of the ring.
[1] T. Doert, C. J. Müller, in Reference Module in Chemistry, Molecular Sciences and Chemical Engineering, Elsevier, 2016.
[2] H. Poddig, T. Donath, P. Gebauer, K. Finzel, M. Kohout, Y. Wu, P. Schmidt, T. Doert, Z. Anorg. Allg. Chem. 2018, 644, 1886–1896.
[3] K. Stöwe, Z. Kristallogr. - Cryst. Mater. 2001, 216, 215–224.
Modern instrumentation and processing techniques for single crystal X-ray diffraction enable high-quality 3D structure analysis – including absolute structure determination – often in less than an hour, faster and more comprehensively than many spectroscopic methods can even start to achieve. However, large numbers of small or highly flexible organic molecules remain intractable to even the most sophisticated crystallization methods. Our new set of chemical chaperones for co-crystallization 1 offers a new alternative to other methods, such as the crystal-sponge approach 2, 3, can significantly increase the probability of successful crystallization and provides faster access to the absolute 3D structure of an organic analyte:
We will discuss and demonstrate the features in detail along the diastereomers of Limonene including a demonstration of the crystal growth.
1 Richert, et.al, Angew. Chem. Int. Ed. 2020, 59, 15875–15879, doi.org/10.1002/anie.202004992.
2 Fujita et al, IUCrJ 2016, 3, 139-151, doi.org/10.1107/S2052252515024379.
3 Clardy, et.al, Acta Cryst. (2015), A71, 46–58 https://doi.org/10.1107/S2053273314019573.
We calculated the Gibb’s energy of all known organic and organometallic crystal structures at ambient conditions with FlexCryst (1). Firstly, the implemented data mining force field was validated for the experimental lattice energies of the reference structures. Secondly, the force field was used for the minimization of 100 structures and the error in density and energy was examined. Finally, the Gibb’s energy was calculated for all structures. After applying different filters and cleanser did remain 247 344 crystal structures.
In our analysis of the results we concentrated on crystal structures with a Gibbs energy above zero. Obviously these structures violates the second law of thermodynamics. A visualization of the intermolecular interactions did allow us to indicate poor intermolecular potentials and faulty crystal structures. The condition is fulfilled in 96.7 % of structures.
The data mining force field is integrated in the FlexCryst program suite and we tested it crystal structure prediction and in combination with XPRD for crystal structure determination. Since the obtained energies are Gibb’s energies, the energies can be used to predict reactions at ambient conditions, for instance solubility (2), co-crystal formation (3), or polymorphism.
References:
1)Hofmann, Detlef WM. "Data mining in organic crystallography." Data Mining in Crystallography. Springer, Berlin, Heidelberg, 2009. 89-134.
2)Hofmann, Detlef Walter Maria, and Ludmila Kuleshova. "New similarity index for crystal structure determination from X-ray powder diagrams." Journal of applied crystallography 38.6 (2005): 861-866.
3)Stepanovs, Dmitrijs, et al. "Cocrystals of pentoxifylline: In silico and experimental screening." Crystal Growth & Design 15.8 (2015): 3652-3660.
Figure 1: The hydrate of the ruthenium complex (CSD reference code: AMUPUU) show strong repulsive interactions between two water molecules. It indicates that water should be placed different in the correct structure.
Figure 2: The co-crystal (CSD reference code: ALARAH) of a platinum complex with methanol show strong repulsive interactions between methanol and it image. It indicates that methanol should be placed different in the correct structure.
Self-organization of biomolecular building blocks and inorganic nanoparticles into biohybrid nanomaterials
From the perturbation of crystal symmetry towards functionality
Single particle cryo electron microscopy (cryo-EM) has developed into a powerful technique to determine 3D structures of large macromolecular complexes. Due to improvements in instrumentation and computational image analysis, the number of high-resolution structures is steadily increasing. The method cannot only be used to determine high-resolution structures but also to study the dynamic behavior of macromolecular complexes and thus represents a very complementary method to X-ray crystallography. Furthermore, the maximum attainable resolution by cryo-EM has constantly improved in recent years. Most of the high-resolution structures are still in the 3 Angstrom resolution regime but some have even crossed the 2 Angstrom barrier. We have recently installed a new prototype electron microscope which is equipped with a monochromator and a next-generation spherical aberration corrector. This microscope is optically superior to the currently commercially available instruments and can therefore be used to test the resolution limits in cryo-EM. We have used the test specimen apoferritin to determine its structure at 1.25 Angstrom resolution [1] which is sufficient to visualize for the first time individual atoms clearly separated in the density map (Figure 1).
Recently, we managed to use this microscope not only to improve the resolution of the very stable and rigid protein apoferritin. We also obtained significant improvement in resolution for other more dynamic macromolecular complexes for which one could have expected that the microscope itself may not be a major resolution limiting factor.
References:
[1] Yip et al., Atomic resolution protein structure determination by cryo-EM, Nature 587, 157-161 (2020)
Cytotoxic Necrotizing Factors (CNFs) are single-chain AB-toxins and important virulence factors in pathogens such as uropathogenic E. coli (UPEC) or enteropathogenic Yersinia species. Their cytotoxic effect is based on the constitutive activation of small GTPases (Rho family) by deamidation of a glutamine residue in the switch II region, leading to cytoskeletal alterations and finally death of the host cell. Several steps are required for the toxin to fulfill its task, such as receptor binding, endocytosis and yet unknown structural changes in the B-part in order to translocate the catalytically active, toxic A-part through the endosomal membrane into the cytosol. So far, a crystal structure that could provide insight into these processes is still lacking.
Here we report on the crystal structure of full-length CNFy from Yersinia pseudotuberculosis at a resolution of 2.7 Å. The structure was solved by molecular replacement with the existing model of the C-terminal catalytic domain and the structure of the B-part, where the phases of the latter were obtained by single anomalous dispersion experiments in advance. The full-length AB-toxin comprises 1014 amino acid residues. While the two C-terminal domains (485 residues) are forming the A-part, the N-terminal B-part (529 residues) is consisting of 3 individual domains, of which all possess novel folds. From cell-biology experiments, the receptor-binding and translocation functions could be assigned to the first three domains although their mechanism(s) and the receptor of the host cell remain still unknown. The fourth domain shows structural similarity to ADP-ribosyl transferases but no similar function in CNFy could yet be detected.
Additionally, we also determined the structure of the two-domain A-part - as it should be released into the cytoplasm - alone (1.8 Å). The two domains show a different orientation towards each other than in the structure of the full-length toxin, which could hint towards activation of the catalytic domain upon release of the A-part.
Our first crystal structure of a full-length CNF-toxin lays the groundwork for further studies of the complex mechanism of this important bacterial virulence factor. CNF-toxins might not only be promising targets for future development of anti-infective drugs, the B-part might even have the potential to be exploited as delivery vehicle for large and complex drugs.
Contributed on behalf of the Hamburg SARS-CoV-2 X-ray screening initiative
As a response to the current SARS-CoV-2 pandemic we have set up a large consortium of more than one hundred scientist centered around DESY in Hamburg. In contrast to common screening techniques such as biochemical activity-based assays or X-ray fragment screening, here we employed massive X-ray crystallographic screening of two drug-repurposing libraries against SARS-CoV-2 main protease (MPro) of SARS-CoV-2 as initial target. Already in March 2020 co-crystallization experiments of 5953 individual drugs with MPro were setup. In April data from more than 8000 of these crystals were collected at the PETRA III MX beamlines. In the following weeks a data analysis pipeline for fully automatic data processing and subsequent structure refinement followed by ligand identification by pan-dataset density analysis (PanDDA) was established. Our screening effort resulted in the identification of 37 compounds binding to MPro. Secondary screening of these hits in a cell-based virus-infection assay revealed antiviral activity in combination with low cytotoxicity for six compounds which have not yet been reported as inhibitors of SARS-CoV-2. While four of these inhibitors bind to the catalytic site of the enzyme, the remaining two bind to an allosteric site within the dimerization domain(1).
To our knowledge, this is the first time X-ray crystallography has been used as a primary screen for drug discovery while using drug-like molecules rather than smaller fragments. The platform developed for this project is currently being further extended and optimized and will be available for future drug discovery efforts.
Reference
(1) S. Günther, P. Y. A. Reinke, et al. , bioRxiv, in press, doi:10.1101/2020.11.12.378422.
Figure: SARS-CoV-2 MPro dimer with hits derived from X-ray screening of drug repurposing libraries. Drug binding (stick representation) is observed across the complete MPro dimer. One MPro monomer with bound drugs is shown in white surface representation. The other monomer is shown as mixed cartoon/surface representation.
The Coronavirus Structural Task Force [1] was an ad hoc collaboration of mostly junior researchers across nine time zones, brought together by the desire to fight the pandemic.
Most of us are crystallographic methods developers and as early as February 2020, we started evaluating the structures of macromolecules in SARS-CoV and later SARS-CoV-2 as they became available from the Protein Data Bank. We found that many could be improved. A website (www.insidecorona.net) and a database containing the evaluations and revised models were set up to aid in-silico drug discovery and other downstream research. Newly deposited structures are analysed as they come out by a bespoke structure evaluation/comparison pipeline. In addition, many individual structures were revised manually, atom-by-atom. In order to spread knowledge about the structural biology of the virus, we also reviewed the literature, putting the molecular models into a larger context for the rapidly growing community of researchers - drug developers, bioinformaticians, crystallographers - tackling the COVID-19 pandemic. We established a large network of COVID-19 related research, and forged friendships and collaborations across national boundaries.
As public outreach is so important right now, we also refine structures live on Twitch, write articles and offer a 3D printable virus model for schools.
[1] Croll, T., Diederichs, K., Fischer, F., Fyfe, C., Gao, Y., Horrell, S., Joseph, A. P., Kandler, L., Kippes, O., Kirsten, F., Müller, K., Nolte, K., Payne, A., Reeves, M. G., Richardson, J., Santoni, G., Stäb, S., Tronrud, D., Williams, C. & Thorn, A. (2020). BioRxiv. doi:10.1101/2020.10.07.307546.
Protection of amino acids is an essential aspect for peptide synthesis.[1] Recently, crystals of 4-biphenylcarboxy substituted L-serine, L-tyrosine, L-alanine, L-leucine and L-phenylalanine methyl esters have been demonstrated to possess diverse supramolecular assembly governed by C–H···π and π···π interactions between biphenyl fragments and intermolecular N–H···O interactions between the amide O=C–N–H groups.[2,3] Amongst them, 4-biphenylcarxy-L-phenylalaninate is elusive because it crystallizes in monoclinic space group symmetry P21 within a pseudo-orthorhombic lattice[3] [a = 5.0748(2) Å, b = 8.7658(3) Å, c = 42.4828(13) Å, β = 90.038(3)°] at ambient conditions (phase I). The crystal comprises of two independent molecules (Z' = 2) with disparate molecular torsion and the monoclinic distortion is retained up to its melting temperature.
Temperature dependent single crystal X-ray diffraction experiments revealed a reversible structural phase transition at Tc ≈ 124 K upon cooling. Below Tc (phase II), satellite reflections in addition to main reflections were observed. q remains invariant as function of temperature that can be indexed with a modulation wave vector, q = (½, 0, ½) with respect to the basic monoclinic lattice. The crystal structure is described as a (3+1)D commensurately modulated structure in superspace group P21(σ10σ3)0 (σ1 = ½, σ3 = ½). The equivalent 3D superstructure [space group monoclinic (b–unique) B21] comprises of four independent molecules in the asymmetric unit.
Here we present the phase relations between I and II. The phase transition at Tc is primarily characterized by evolution of torsional modulation within the biphenyl fragments that are unequal for the two independent molecules. The origin of the torsional modulation is argued to lie in the competition between possible steric hindrance between the ortho-hydrogens of the biphenyl fragment that favors torsion and intermolecular C–H···π interactions that favors planar biphenyl moiety. Stabilized by weak C–H···O hydrogen bonds, short H–C···C–H interactions involving the biphenyl fragment suppresses the torsion for one independent molecule while longer H–C···C–H contacts allows larger torsional amplitude for the other.
References:
[1] Isidro-Llobet, A.; Alvarez, M. and Albericio, F. (2009) Chem. Rev. 109, 2455–2504.
[2] Sasmal, S.; Podder, D.; Debnath, M.; Nandi, S. K. and Haldar, D. (2019) ChemistrySelect 4, 10302–10306.
[3] Sasmal, S.; Nandi, S. K.; Kumar, S. and Haldar, D. (2019) ChemistrySelect 4, 11172–11176.
Single crystals often present disorder in their structure due to dopant substitution/intercalation or as an intrinsic instability of the compound. In many cases the disorder-to-order balance is responsible for key properties of the material. For example it can account for low thermal conductivity in PbTe or for the superconducting transition temperature in Sr2RuO4 where the highest Tc is obtained in disorder-free samples.
Here we present the three-dimensional mapping technique of diffuse scattering. At the Broad-Band Diffraction Swedish Material Science beamline (P21.1) at PETRA III synchrotron radiation source, total scattering measurements are possible thanks to the combination of high energy x-rays (100 keV) and large area detectors. Diffraction signal is acquired at high repetition rate allowing to operate with high incident photon flux. This is essential since the signal contains both the high intensity Bragg reflections, related to the average crystal structure, and the low intensity diffuse scattering signal accounting for the disorder. The acquired data are reconstructed in the hkl space and can be converted into the real space by Fourier transformation obtaining the three dimensional pair distribution function (3D-PDF) [1-3]. This technique is presented with the results obtained on perfect Si crystal as a standard. It is shown that 3D-PDF is sensitive to minor imperfections and/or impurities in the material.
[1] P. Schaub, T. Weber and W. Steurer, Philosophical Magazine 87, 2781–2787 (2007)
[2] T. Weber and A. Simonov, Z. Kristallogr. 227, 238–247 (2012)
[3] N. Roth et al., IUCrJ 5, 410–416 (2018)
Pentamers of transition metal octahedra and double semihelical chains of hydrogen bonds frame hureaulite-type oxyhydroxides (C2/c; a = 11.5 Å, b = 9.1 Å, c = 9.5 Å, beta = 96.4°) highly interesting for rich magnetic spin orders and polaron-dependent charge transport phenomena. Neutron powder diffraction data of its manganese end-member agree with that the magnetic lattice retains the (1a x 1b x1c) unit cell below the Curie temperature 7.2 K down up to 2 K, but magnetic moments of Mn2+ within MnO6 pentamers oriented predominantly parallel to the crystallographic b axis vividly change on to the (a-c) plane at lowered temperatures. The respective ferrimagnetic order corresponds to the magnetic space group C2/c at 6.5 K (Figure 1a) and C2’/c’ at 3.4 K (Figure 1b). This reflects complicated discontinuity curves of AC magnetic susceptibility. Another phase transition occurs around at 2 K, where the magnetic spins are incommensurately modulated with a propagation vector (0.545(2), 0, ~0).
We present here subtle details of a complex evolution of magnetic spin orders of the title compound along with briefing quasi- and inelastic neutron scattering studies to demonstrate mechanism for the ease with protonic superconductivity.
Ion- irradiation is an established technology to change properties of diamonds in a controlled way [1] and has been studied as a function of ion species, energy and fluence for many years [2-4]. However, little is known regarding surface effects for irradiations with high energy ions which penetrate deep into the diamond. Irradiation experiments were carried out on various synthetic diamond samples using 14 MeV Au6+ ions and a maximal fluence of 2.4 ×1015 ions/cm2. The penetration depth of such ions in diamond is about 1.7 μm [5]. The surface of the samples was characterized by atomic force microscopy (AFM), Raman spectroscopy and X-ray reflectometry (XRR).
Due to the irradiation, the formerly transparent samples darkened, which suggests partial amorphisation of the material. Raman spectroscopy revealed significant changes in the lattice dynamics and the formation of sp3 bonded amorphous carbon (Fig. 1). XRR experiments performed at beamline P08 @ PETRA III (Hamburg, Germany) revealed the formation of modified layers near the sample surface (Fig. 2). AFM provided information on changes of the surface topography including increased roughness and swelling. The surface roughness deduced from XRR data compared to AFM results will be discussed for the different diamond materials.
Fig. 1: Raman spectra of pristine (black lines) and irradiated (colored lines) diamonds for a single crystal diamond sample irradiated with 14 MeV Au-ions of different fluences.
Fig. 2: XRR curves for the experimental (black lines) and calculated (red lines) data of a single crystal diamond sample irradiated with 14 MeV Au-ions of fluence 2.4 × 1015 ions/cm2.
References:
[1] R. Kalish, Semiconductors and Semimetals, 76, (2003), 145–181.
[2] R. Kalish and S. Prawer, Nuclear Instruments and Methods in Physics Research Section B: Beam Interactions with Materials and Atoms 106, (1995), 429.
[3] J. F. Prins, Materials Science Reports 7, (1992), 275.
[4] B. A. Fairchild, S. Rubanov, D. W. Lau, M. Robinson, I. Suarez-Martinez, N. Marks, A. D. Greentree, D. McCulloch, and S. Prawer, Advanced Materials 24, (2012), 2024.
[5] J. F. Ziegler, M. D. Ziegler, and J. P. Biersack, Nuclear Instruments and Methods in Physics Research Section B: Beam Interactions with Materials and Atoms 268, (2010), 1818-1823.
Intriguing properties of mixed nitride networks have led to a range of viable applications. Nitrido(litho)aluminates, e.g. Sr[LiAl$_3$N$_4$]:Eu$^{2+}$ and Sr$_2$[MgAl$_5$N$_7$]:Eu$^{2+}$, are an important part of developments in the lightening industry due to their chemical and thermal stability and luminescence.$^{[1, 2]}$ Likewise, nitridosilicophosphates and nitridophosphates contain rare structural motifs.$^{[3, 4, 5]}$ Dense frameworks and luminescence properties that may improve the quality of specialized light-emitting diodes (LEDs) are highly sensitive to the valence state, coordination spheres, site symmetry of atoms and the concentration of activator ions. Therefore, understanding relationships between luminescent properties and crystal structures is crucial. In investigating the nitride network of nitridoalumo(oxo)phosphates, we combine these characteristics and properties and aimed at luminescent properties like low thermal quenching and a narrow emission due to the structural relationship to nitrido(litho)aluminates. Sr$_2$Al$_{10}$P$_8$N$_{20}$O$_{4.034}$F$_{5.094}$:Eu$^{2+}$ was obtained from Sr(N$_3$)$_2$, SrCO$_3$, P$_3$N$_5$, AlN, EuF$_3$ and the mineralizer NH$_4$F by mineralizer-assisted high-temperature high-pressure (HT/HP) synthesis (1400 °C, 5 GPa) with a Walker-type module.$^{[6]}$ The structure was elucidated by SCXRD (single-crystal X-ray diffraction, R1 = 0.0142, wR2 = 0.0327). BVS (bond valence sum) and CHARDI (charge-distribution) calculations indicate mixed anionic positions. The new nitridoalumofluoridooxophosphate crystallizes in space group I-4m2 [a = 11.17902(8), c = 5.1484(1) Å]. TEM SAED (transmission electron microscopy selected area electron diffraction) patterns confirmed the metric and TEM and SEM (scanning transmission electron) EDX (energy dispersive X-ray) coincide with the element ratio obtained by SCXRD. Sr$_2$Al$_{10}$P$_8$N$_{20}$O$_{4.034}$F$_{5.094}$:Eu$^{2+}$ shows a broadband emission with a maximum at 450 nm and a fwhm (full width at half maximum) of 108 nm (5315.0 cm$^{-1}$). It contains chains of face-sharing Sr(N/O/F)$_{12}$ cuboctahedra, supertetrahedra-like elements composed of ten edge-sharing Al(N/O/F)$_{6}$ octahedra where Al is positioned on three different crystallographic sites. A three-dimensional network is built by twofold and threefold vertex-sharing PN$_4$ tetrahedra.
$^{[1]}$ M. Zeuner, S. Pagano, W. Schnick, Angew. Chem.-Int. Ed. 2011, 50, 7754.
$^{[2]}$P. Wagatha, V. Weiler, P. J. Schmidt, W. Schnick, Chem. Mater. 2018, 30, 1755.
$^{[3]}$ S. Vogel, A. T. Buda, W. Schnick, Angew. Chem.-Int. Ed. 2019, 58, 3398.
$^{[4]}$ S. Vogel, M. Bykov, E. Bykova, S. Wendl, S. D. Kloß, A. Pakhomova, S. Chariton, E. Koemets, N.Dubrovinskaia, L. Dubrovinsky, W. Schnick, Angew. Chem.-Int. Ed. 2019, 58, 9060.
$^{[5]}$ S. D. Kloß, W. Schnick, Angew. Chem.-Int. Ed. 2019, 58, 7933.
$^{[6]}$ S. Merlino, C. Biagioni, E. Bonaccorsi, N. V. Chukanov, I. V. Pekov, S. V. Krivovichev, V. N. Yakovenchuk, T. Armbruster, Mineral. Mag. 2015, 79, 145.
Homonuclear dinitrogen anions are common intermediates in biological and organometallic synthetic chemistry, and play an important role in the processes of nitrogen reduction to ammonia. In extended solid-state compounds, nitrogen is typically present in the form of a nitride anion N3− and does not form catenated polyanions. However at high-pressure conditions MN2 dinitride compounds of alkali-earth metals (M = Ca, Sr, Ba), transition metals (M=Ti, Cr, Fe, Co, Ni, Cu, Ru, Rh, Pd, Re, Os, Ir, Pt) and rare earth metal (M = La) were obtained. In MN2 compounds, metals usually possess their common oxidation states, while the dinitrogen anion formally accommodates from 1 to 4 electrons. The degree of charge transfer from the metal to the nitrogen dimers significantly affects the properties of the materials (e.g. MN2 (M = Pt, Ir, Os, Ti) pernitrides with [N2]4− units are much less compressible than MN2 (M = Cr, Fe, Co, Ni, Ru, Rh) with [N2]3− units).
In this study yttrium and molecular nitrogen were compressed to 50 GPa and laser heated above 2000 K. Under these conditions, synchrotron single-crystal X-ray diffraction from multigrain samples revealed the formation of a new tetragonal yttrium nitride phase with the unusual Y5N14 composition (Fig. 1a). All nitrogen atoms form dimers, but strikingly there are three different types of nitrogen dimers in the structure with 1.24 Å, 1.28 Å and 1.36 Å nitrogen-nitrogen bond length (Fig. 1b). The bond length correlates with the multiplicity of the nitrogen-nitrogen bond and charge state of the nitrogen dimers. Our detailed analysis shows that there are six [N=N]2- dimers and one [N- ⃛N]3- dimer per Y5N14 formula unit, which corresponds to the typical Y3+ oxidation state for all yttrium atoms. Ab-initio calculations confirm that this structure is dynamically stable at such pressure.
Although [N2]2- and [N2]3- ions are known in the structures of other dinitrides, Y5N14 is the first example of the presence of two different types of charged nitrogen dimers in the same structure, which indicates more complex chemical processes of dense dinitrides formation under high pressure.
Fig. 1. a) Structure of the novel Y5N14 phase and b) different dinitrogen anions in the Y03 atom coordination environment.
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)(Bi2Te3)m (m = 0, 1, 2). (Bi, Sb)2Te3 itself and all members of its family exhibit the rhombohedral R -3 m 1 space group (No. 166) [2]. Therein interchanging sheets of (Bi, Sb) and Te build (Bi, Sb)2Te3 quintuple layers and 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) and depending on m, various stacking orders can be observed.
Our group was the first to successfully grow single crystals, and conduct an in depth study of the physical properties of MnBi2Te4, the m = 0 member of the above discussed MTI family [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 and its higher order relatives, 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.
Figure 1: The structure of Bi2Te3 [3] and the stacking variants (MnBi2Te4)(Bi2Te3)m (m = 0 - 2). For clarity, only 1/3 of the unit cell of MnBi6Te10 is displayed.
[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.
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[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.
The charge density wave (CDW) is a collective phenomenon where electrons at the Fermi level form a density wave with an additional periodicity as compared to the atomic lattice. RE$_2$Ru$_3$Ge$_5$ (RE = Pr, Sm, Dy) crystallize in the Sc$_2$Fe$_3$Si$_5$-type structure (space group $P$4/$nmc$). They show peculiar CDW-induced lattice modulations in a certain temperature range below which those modulations disappear.[1] Compared to Sm$_2$Ru$_3$Ge$_5$, Pr$_2$Ru$_3$Ge$_5$ has a higher transition temperature and no detailed structure refinements have been reported for the modulated phase for this compound. In this presentation, we will show that Pr$_2$Ru$_3$Ge$_5$ exhibits phase transitions at around 200 K from specific heat and transport property measurements. Satellite peaks have been observed in x-ray diffraction with a modulation wave vector q = (0.18,$\pm$0.18, 0). Unanticipatedly, satellite peaks disappear below 180 K. The modulated crystal structure of the CDW phase of Pr$_2$Ru$_3$Ge$_5$ will be presented on the basis of the superspace method.
[1] Bugaris, D. E et al. Charge Density Wave in the New Polymorphs of RE$_2$Ru$_3$Ge$_5$ (RE = Pr, Sm, Dy). J. Am. Chem. Soc. 2017, 139 (11), 4130-4143.
Photo-induced electron transfer reactions are crucial for many of the biological and chemical reactions that occur in nature. According to Marcus and others, electronic coupling between an electron donor and acceptor must be nonzero, for a successful electron transfer reaction. [1] Several studies are performed in order to have a better understanding of the photoinduced intramolecular electron transfer, in terms of the rate of transfer and the overall geometry of the donor-bridge-acceptor (D-B-A) system.[2] Pyrene and its derivatives, owing to their high quantum efficiency, high fluorescence lifetimes, prone to form excimers or exciplex in high concentrations and highly sensitive nature of their photophysical properties to microenvironmental changes, are considered extremely useful for photoinduced electron transfer studies.[3] We have designed a mono-substituted pyrene derivative, pyrene-(CH2)2-N, N’-dimethylaniline, where dimethylaniline (DMA) (electron donor) is connected to pyrene (electron acceptor, in this case) through alkane chain. The distance between the donor and acceptor in this molecule is expected to be suitable for electron transfer by tunneling mechanism. A serendipitous occurrence of two polymorphic crystals from two separate batches of crystallization setup, while dissolved in ethanol, provided us a unique opportunity to study these two conformational polymorphs, A and B. While, in A crystal structure pyrene and dimethylaniline are in axial orientation (P-1) with respect to each other, in B they are equatorial (P21/n). Studies on photo-induced intramolecular electron transfer has revealed the importance of conformational parameters of the molecules such as rotation around bonds that affects the distance and relative orientation of donor and acceptor which in turn can proved to be quite decisive in the photo-physical properties of charge transfer states. [4] We have performed time-resolved Laue diffraction experiments with these two polymorphic crystal forms in the ns time domain. Apart from steady-state spectroscopy, we have also measured ultrafast transient absorption with the solution, at different concentrations. A thorough crystallographic and spectroscopic investigation of this particular system, especially with the polymorphic crystals have allowed us to understand the important aspects of photo-induced electron transfer.
Figure 1. Conformation of molecules in single crystals, a) PyDMA1 and b) PyDMA2. c) Molecular superposition of PyDMA1 (black) and PyDMA2 (red) on pyrene ring with RMSD=0.0427Å. The extent of overlap between the pyrene rings belong to the symmetry related/unit translated molecules in PyDMA1/PyDMA2 in single crystals are 67% and 17%, respectively. f) Absorption (blue) and emission (red) spectra of PyDMA1, in toluene, at 0.1mM concentration.
References: [1] Jortner, J; Bixon, M. Electron Transfer-From Isolated Molecules to Biomolecules, Part 1 and Part 2; John Wiley & Sons, Inc: New York, 1999. [2] a) Paddon-Row, M. N. Acc. Chem. Res. 1994, 27, 18. b) M. D. Newton, Chem. Rev., 1991, 91, 767. [3] Stockmann,A; Kurzawa, J.; Fritz, N.; Acar, N.; Schneider, S.; Daub, J.; Engl, R. and Clark. T. J. Phys. Chem. A 2002, 106, 7958. [4] a) Bleisteiner, B.; Marian, Th.; Schneider, S.; Brouwer, A. M.; Verhoeven, J. W. Phys. Chem. Chem. Phys. 2001, 3, 2070. b) Verhoeven, J. W.; Wegewijs, B.; Scherer, T.; Rettschnik, R. P. H.; Warman, J. M.; Jäger, W.; Schneider, S. J. Phys. Org. Chem. 1996, 9, 387. (c) Wegewijs, B.; Ng, A. K. F.; Verhoeven, J. W. Recl. TraV. Chim. Pays-Bas 1995, 114, 6. (d) Jäger, W.; Schneider, S.; Lauteslager, X. Y.; Verhoeven, J. W. J. Phys. Chem. 1996, 100, 8118. (e) Lauteslager, X. Y.; van Stokkum, I. H. M.; van Ramesdonk, H. J.; Brouwer, A. M.; Verhoeven, J. W. J. Phys. Chem. 1999, 103, 653. (f) Jäger, W.; Schneider, S.; Verhoeven, J. W. Chem. Phys. Lett. 1997, 270, 50.
Due to their vast applications monometallic coordination polymers (CPs) have increasingly attracted the interest of various fields over the last years.$^{[1]}$ We focus on using heterofunctional ligands to synthesize heterobimetallic CPs, combining the properties of two metals in one homogenous material.$^{[2]}$ Our stepwise approach includes the synthesis of a metalloligand and, afterwards, its crosslinking using a second metal cation. Herein we present this approach for the ligand (3-(1,3,5-trimethyl-4-1H-pyrazolyl)acetylacetone (HacacMePz) with its heterobimetallic coordination polymer containing Fe(III) and Hg(II).
The CP crystallizes as an acetonitrile solvate in the triclinic space group $P\bar{1}$ with Z = 2. The [Fe(acacMePz)$_3$] metalloligands are linked by {Hg$_2$(µ$_2$-Cl)Cl$_3$} moieties. While the coordination sphere around the Fe(III) ion is a rather regular octahedron, the two symmetry inequivalent Hg(II) ions adopt distorted tetrahedral coordination environments ($\tau_4$ = 0.82, 0.76).$^{[3]}$ Interestingly, only one chlorido ligand is bridging and the other three are bound to one Hg(II) ion. This connectivity leads to an one-dimensional CP with a ladder-like structure as seen in Figure 1. The polymer expands in [1 −1 1] direction without any meaningful interactions between adjacent chains.
References
[1] S. R. Batten, S. M. Neville, D. R. Turner, Coordination Polymers: Design, Analysis and Application, RSC Publishing, Cambridge, 2009.
[2] M. Kremer, U. Englert, Z. Kristallogr. 2018, 233, 437-452.
[3] A. W. Addison, T. N. Rao, J. Chem. Soc., Dalton Trans. 1984, 1349-1356.
Encapsulation of inorganic nanoparticles into novel T. maritima encapsulin variants
Michael Rütten, Tobias Beck*
University of Hamburg, Institute of Physical Chemistry, Grindelallee 117
20146 Hamburg, Germany
Supported by an established synthetic strategy towards optical materials protein containers and nanoparticles are used. With protein containers as building blocks, nanoparticles will be assembled with high precision into mesoscale materials with optical properties that emerge from interactions between the components. Along the recent advances in computational redesign of protein containers, it is now possible to combine these results with nanoparticle synthesis and protein crystallography. An innovative design approach with two oppositely charged protein containers as building blocks, a new type of protein-based material will be realized (Figure 1). Surface charged protein containers can be combined with inorganic compounds to unite biological features with the chemical and physical properties of abiotic materials. In particular, protein containers, with their inherent ability to encapsulate cargo molecules, are perfect platforms for the generation of multifunctional assemblies.[1, 2] Gold nanoparticles can be decorated with a small number of encapsulin cargo-loading peptides to fill protein containers. By lock-and-key interaction between the peptides and the peptide-binding pockets on the inner container surface (Figure 2), the nanoparticles will be encapsulated with high efficiency.[3] Typically encapsulin bears a flavin that is attached to the outer surface. The flavin leads to a yellow coloured solution and its presence on the protein surface might be problematic for future applications or in crystallization. Based on the latest cryo-EM data it was possible to remove the flavin.[4] Crystalline materials are produced, which is crucial for future applications. Because the protein scaffold is independent of the nanoparticle cargo, this modular approach will enable tuning of the optical properties by choice of nanoparticle content, assembly type and protein container type. For further future applications, surface charged protein containers will be used as sustainable building blocks for bioinorganic nanomaterials.[5]
References:
[1] M. Künzle, T. Eckert, T. Beck J. Am. Chem. Soc. 2016, 138, 12731.
[2] M. Lach, M. Künzle, T. Beck Chem. Eur. J. 2017, 23, 17482.
[3] M. Künzle, J. Mangler, M. Lach, T. Beck Nanoscale 2018, 10, 22917-22926.
[4] D. Diaz et al. bioRxiv 2020, preprint
[5] M. Lach, M. Künzle, T. Beck, Biochemistry 2019, 58, 140-141.
Figure captions:
Figure 1: Strategy overview for the synthesis of highly structured optical nanomaterial.
Figure 2: Gold nanoparticle encapsulation via cargo-loading peptide into T. maritima encapsulin.
The two tartaric acid derivatives dibenzoyltartaric acid (DBTA) and di-para-toluoyltartaric acid (DPTTA) are common compounds in organic chemistry and pharmaceutical science, where they mostly function as derivatisation agents or as chiral templates. There are currently about 250 crystal structures featuring either of the acids deposited in the CCDC [1]. While the compounds are decent chelating ligands with the ability to extend bridges to neighbouring metal centres to form coordination polymers, they are hardly used in this capacity. Less than 40 structures featuring both carboxylato groups connected to a metal are deposited in the CCDC currently.
Our work focusses on the synthesis of coordination polymers with dicarboxylic acids, including tartaric acid and the titular derivatives thereof [2,3]. During these experiments, several new compounds featuring DBTA or DPTTA were synthesised, crystallized, and characterized. In this presentation we showcase several of these compounds, discuss structural similarities and differences as well as the influence of different metals, coligands or stereoisomers on the resulting structures.
[1] C. R. Groom, I. J. Bruno, M. P. Lightfoot and S. C. Ward, Acta Cryst., 2016, B72, 171-179
DOI: 10.1107/S2052520616003954
[2] M. Kremer, J. van Leusen, U. Englert, Crystals, 2020, 10, 485. DOI: 10.3390/cryst10060485
[3] M. Kremer, Dissertation, RWTH Aachen, 2020, available on the website of the RWTH University Library
The field of metal-organic frameworks (MOFs) is dominated by the chemistry of oxygen and nitrogen donor based ligands.$^{[1]}$ Next to no work revolves around polytopic ligands containing phosphorus donors.
The usage of phosphorus widens the horizon of MOF chemistry. It may broaden the structural variety, enable new applications and stabilize metal cations in low oxidation states that were previously inaccessible to MOF chemists.
The ligand 4-(3-(4-(diphenylphosphino)phenyl)-3-oxopropanoyl)benzonitrile is a prototype for the combination of the three donor atoms O, P and N. It combines a chelating beta-diketone as the oxygen donor, a nitrile representing the nitrogen donors and a triarylphosphine as a phosphorus based ligand functionality.
Using a stepwise approach we were able to synthesize a cationic heterobimetallic Fe$^{\text{III}}$/Ag$^{\text{I}}$ MOF with Fe$^{\text{III}}$ bound to the oxygen donors and Ag$^{\text{I}}$ bound to the P and N donors. The network can emerge in 2 different topologies while the chemical connectivity remains unchanged. Type A corresponds to the rtl network type,$^{[2]}$ Type B has not been observed yet. Both have a three dimensional pore system. The pores are large enough so a sphere with a diameter of 4 Å could move through them along all low-indexed directions.
X-ray diffraction from powders and single crystals has for decades been the key analytical tool in materials science. Bragg intensities provide information about the average crystals structure, but often it disorder and specific local structure that control key material properties. For 1D data there has been an immense growth in combined analysis of Bragg and diffuse scattering using the Pair Distribution Function (PDF), and in our group we frequently use 1D PDF analysis to study nanocrystal nucleation in solvothermal processes [1] or thin films [2], or to analyse materials under operating conditions [3]. For single crystals, diffuse scattering studies have a long history with elaborate analysis in reciprocal space, but direct space analysis of the 3D-PDF is still in its infancy. We have used 3D-PDF analysis to study the crystal structures of high performance thermoelectric materials Cu2Se (Fig 1) [4], PbTe [5], and 19-e half-heusler Nb1-xCoSb [6], where the true local structure is essential for understanding the unique properties. For frustrated magnetic materials direct space analysis of diffuse magnetic scattering provides a new route to magnetic structures [7].
[1] N. L. N. Broge et al., Auto-catalytic formation of high entropy alloy nanoparticles, Angew. Chem. Intl. Ed., 59, 21920-21924 (2020)
[2] M. Roelsgaard et al., Time-Resolved Surface Pair Distribution Functions during Deposition by RF Magnetron Sputtering, IUCrJ, 6, 299–304 (2019)
[3] L. R. Jørgensen et al., Operando X-ray scattering study of thermoelectric β-Zn4Sb3, IUCr-J, 7, 100-104 (2020)
[4] N. Roth et al., Solving the disordered structure of β-Cu2-xSe using the three-dimensional difference pair distribution function, Acta Crystallogr. Sect. A, 75, 465–473 (2019)
[5] K. A. U. Holm et al., Temperature Dependence of Dynamic Dipole Formation in PbTe, Phys. Rev. B, 102, 024112 (2020)
[6] N. Roth et al., A simple model for vacancy order and disorder in defective half-Heusler systems, IUCrJ, 7, 673-680 (2020)
[7] N. Roth et al., Model-free reconstruction of magnetic correlations in frustrated magnets, IUCr-J, 5, 410–416 (2018)
The experimental workflow of macromolecular crystallography has been improved enormously in the last two decades, especially regarding speed and throughput. One step of this workflow, namely the manipulation and harvesting of crystals, remains labour- and time-intense even though considerable efforts have been applied. In order to tackle this bottleneck, we developed a novel, low-cost device that acts as a lid for 96-well crystallization plates. It includes 96 movable parts that allow access to the individual experiment and simultaneously minimize the evaporation of the other experiments. Primary results show the successful evaporation minimization of many typical crystallization cocktails for up to six hours. The device, named EasyAccess Frame, avoids any sealing by foil and unsealing of individual wells in the process and thus facilitates easy crystal manipulation and harvesting. Therefore, the device increases throughput and is useful for a range of macromolecular crystallography experiments, especially screening campaigns. The device is successfully being used in crystallographic fragment screening campaigns at HZB and significantly reduces time and effort necessary for the crystal handling involved.
Barthel T., Huschmann F. U., Wallacher D., Feiler C. G., Klebe G., Weiss M. S., Wollenhaupt J., Facilitated crystal handling using a simple device for evaporation reduction in microtiter plates, 2021, accepted for publication in J. Appl. Cryst.
The Macromolecular Crystallography (MX) group at the Helmholtz-Zentrum Berlin (HZB) has been in operation since 2003. Since then, three state-of-the-art synchrotron beam lines (BL14.1-3) for MX have been built up on a 7T-wavelength shifter source [1-3]. Currently, the three beam lines represent the most productive MX-stations in Germany, with more than 3500 PDB depositions (Status 12/2020). BLs14.1 and 14.2 are energy tuneable in the range 5.5-15.5 keV, while beam line 14.3 is a fixed-energy side station operated at 13.8 keV. All three beam lines are equipped with state-of-the-art detectors: BL14.1 with a PILATUS3S 6M detector, BL14.2 with a PILATUS3S 2M and BL14.3 with a PILATUS 6M detector. BL14.1 and BL14.2 are in regular user operation providing close to 200 beam days per year and about 600 user shifts to approximately 100 research groups across Europe. Recently, remote beamline operation has been started successfully at BL14.1. BL14.3 is been equipped with a MD2 micro-diffractometer, a HC1 crystal dehydration device and a REX nozzle changer making it suitable for room temperature experiments. Additional user facilities include office space adjacent to the beam lines, a sample preparation laboratory, a biology laboratory (safety level 1) and high-end computing resources. Within this presentation a summary on the experimental possibilities of the beam lines and the ancillary equipment provided to the user community will be given.
[1] Heinemann U., Büssow K., Mueller, U. & Umbach, P. (2003). Acc. Chem. Res. 36, 157-163.
[2] U. Mueller, N. Darowski, M. R. Fuchs, R. Förster, M. Hellmig, K. S. Paithankar, S. Pühringer, M. Steffien, G.
Zocher & M. S. Weiss (2012). J. Synchr. Rad. 19, 442-449.
[3] Mueller, U., Forster, R., Hellmig, M., Huschmann, F. U., Kastner, A., Malecki, P., Puhringer, S., Rower, M.,
Sparta, K., Steffien, M., Uhlein, M. & Weiss, M. S. (2015). Eur. Phys. J. Plus 130, 141-150.
Beamline P11 at PETRA III in Hamburg is a versatile instrument for macromolecular crystallography (1). During ‘the Corona-year’ 2020 we operated in very exceptional conditions. Here we describe DESY responses to the pandemic situation, such as the fast-track access to the beamline, exceptional user regulations and remote access.
To date, 35 PDB depositions have arisen from P11 related to Covid-19 by our fast-track, proposal and priority access users (2-5). Additionally, P11 participates to three DESY Strategic Fund projects relating to Covid-19 research: 1) Inhibitor screening and structural characterization of virulence factors from SARS-CoV-2, 2) Multidimensional serial crystallography of Sars-CoV-2 proteins to unravel structure and dynamics of function and inhibition and 3) Automated X-ray crystallography compound screening pipeline at DESY.
In spite of the restricted user operations, the beamline had a very busy user run and the scarce commissioning time was used to employ our new Eiger2 X 16M. We successfully employed the detector for serial data collections. Dedicated nodes in our central computational cluster Maxwell will be at the disposal of our users for processing (and autoprocessing) their Eiger data next year. Inspired by the properties of our new detector, we started to streamline the serial crystallography methods available at the beamline and to integrate both the data collection and the data processing more tightly into the beamline environment.
1) Burkhardt et al. (2016) Eur. Phys. J. Plus 131 56.
2) Zhang et al. (2020) Science 368 409-412
3) Günter et al. (2020) BioRxiv (doi.org/10.1101/2020.05.02.043554)
4) Rut et al. (2020) Nat Chem Biol (doi.org/10.1038/s41589-020-00689-z)
5) Oerlemans et al. (2021) RSC Med Chem (DOI: 10.1039/D0MD00367K)
FeOCl features a simple structure built from Fe-O double layers stacked along the c-axis and separated through bi-layers of chlorine; the latter are bonded through weak van der Waals forces. On cooling, an orthorhombic-to-monoclinic lattice distortion occurs at T$_{N}$ = 81 K [1] which removes the geometric frustration of magnetic order of Fe$^{3+}$ moments, as it exists on the orthorhombic lattice [1,2]. This allows antiferromagnetic order to develop [1,2]. The quasi-two-dimensional magnetic character of FeOCl stems from the unpaired 3d electrons (Fe$^{3+}$ with 3d$^{5}$ electronic state), which results in strong intra- and interchain exchange interactions in the ab-plane of the structure [2,3]. (Quasi-)hydrostatic pressure, applied within a diamond anvil cell (DAC) up to ≈ 38 GPa, provides a way of modifying the interlayer van der Waals gap and more importantly, through geometrical modifications of the FeCl$_{2}$O$_{4}$ octahedra, a way to modify and tune the magnetic exchange interactions. These experiments have been carried out above and below the Néel temperature, which allows us to investigate the interplay of magnetic order and pressure-induced structural changes in FeOCl. Here we present one of the essential steps in this project: a detailed analysis of the pressure and temperature dependent structural evolution of FeOCl, as investigated by high-pressure low-temperature single crystal X-ray diffraction at beamline P02.2/PETRA III (Hamburg, Germany). This includes the phase transitions and an in-depth analysis of bond lengths and -angles, which sheds light on the magneto-elastic interplay in this compound. This may further contribute to the understanding of the mechanisms in exotic strongly correlated systems in general and low dimensional magnetic compounds in particular.
[1] Zhang et al., Phys. Rev. B 86, 134428 (2012).
[2] Angelkort et al., Phys. Rev. B 80, 144416 (2009).
[3] Glawion et al., Phys. Rev. B 80, 155119 (2009).
The pressure-induced solid-state amorphization found in 1985 [1] set off a series of subsequent researches on polyamorphism in SnI${}_4$. The discovery of another amorphous state [2], called Am-II to Am-I previously identified, on decompression became a breakthrough in solving the puzzle.
Later, a consistent thermodynamic argument has been given for the observed polyamorphic behaviors [3]. However, the following questions remain unanswered: The ambient crystalline phase CP-I never transforms into Am-II, which appears only on Am-I decompression. Nonetheless, CP-I can directly transform to Am-I on recompression skipping CP-II [4], the high-pressure modification of CP-I.
We reexamined the Am-I-to-Am-II process conducting high-pressure synchrotron x-ray diffraction studies with a diamond anvil cell [5]. Detailed analysis of the structural evolution revealed that the association of molecules, which are entirely dissociated, starts at around 14 GPa on decompression. About 30% of isolated Sn atoms suddenly complete the molecular formation at the Am-I-to-Am-II transition at 3.3 GPa, associated with an abrupt drop of density. Thus, the molecules formed recover their original symmetry of $T_d$ at the transition, implying the strong coupling between the global order parameter of density and the local symmetry.
Because the centers (Sn atoms) were distributed everywhere in Am-I, formed molecules' resulting location is not necessarily energetically optimized, leaving uniform distribution of shorter (2.64 Å) van der Waals I${}_2$ bonds, which play as defects. The open questions are then understandable in terms of the defects. Crystallization of Am-II to CP-I could be a defect extinction process, but the reverse process would hardly occur. It seems impossible to remove the whole defects in recovering CP-I, and the residual defects prevent defective CP-I from reordering to CP-II, which may require highly ordered stacking of Sn layers [6].
[1] Y. Fujii et al., J. Phys. C 18, 789 (1985).
[2] N. Hamaya et al., Phys. Rev. Lett. 79, 4597 (1997).
[3] K. Fuchizaki et al., J. Chem. Phys. 135, 091101 (2011).
[4] B. Grocholski et al., Phys. Rev. B 81, 094101 (2010).
[5] K. Fuchizaki et al., submitted to J. Phys.: Condens. Matter.
[6] H. Naruta et al., J. Phys.: Condens. Matter 32, 055401 (2019).
This is quite a paradox that a century after introduction of the spherical Independent Atom Model (IAM, 1914 [1]), 99.7% of all ca. 1.5mln known crystal structures, including almost all structures of minerals, have been refined using IAM which suffers from severe methodological deficiencies. Far better results can be obtained when new approaches of quantum crystallography ustilising aspherical atomic factors are applied.
A short beam wavelength (0.4Å) and a special type of Diamond Anvil Cell (DAC) with large opening angle allow us to collect data with extremaly high resolution and 100% completeness up to as high resolution as ca. 0.4 Å.
We will present details of aspherical Hansen-Coppens pseudoatom refinement of electron density which we applied in multipole modeling [2] of electron density in crystals of minerals including minerals under pressure. We have successfully refined quantitative experimental electron densities for crystals of several minerals such as fluorite, grossular and hsianghualite and others. We will present the most interesting results such as onset of F…F interactions (charge-shift bonding) in fluorite [3] and flow of charge among ions in the structure of hsianghualite, Ca3Li2(Be3Si3O12)F2, under pressure. Up to our best knowledge, these are the very first successful experimental determinations of quantitative charge density distributions in mineral crystals under high pressure. They allow for quantitative characterisation of electron density in crystals of minerals including studies of changes of electron density under pressure.
Such studies open a new field of mineralogical subatomic investigations (at the level of changes of electron density properties) of different mineralogical processes in the Earth mantle by simulating them in DAC in laboratory conditions.
KW acknowledges a financial support within the Polish National Science Centre (NCN) OPUS17 grant number DEC-2019/33/ B/ST10/02671.
References:
[1] Compton, A.H., (1915) Nature., 95, pp. 343-344.
[2] Hansen, N. K., & Coppens, P., (1978) Acta Cryst., A34, 909–921.
[3] Stachowicz, M., Malinska, M., Parafiniuk, J., &Woźniak, K., (2017) Acta Cryst., B73, 643–653.
[4] Gajda, R., Stachowicz, M., Makal, A., Sutuła, S., Parafiniuk, J., Fertey, P., & Wozniak, K., (2020) IUCRJ, 7(3), 383-392.
In recent years, we have come to appreciate the astounding intricacy of the formation process of minerals from ions in aqueous solutions. The original ‘textbook’ image of these phenomena, stemming from the adaptation of classical nucleation and growth theories, has increased in complexity due to the discovery of a variety of precursor and intermediate species [e.g. 1], including solute clusters (e.g. prenucleation clusters, PNCs), liquid(-like) phases, as well as amorphous and nanocrystalline solids etc. In general, these precursor or intermediate species constitute different, often short-lived, points along the pathway from dissolved ions to the final solids (typically crystals in this context). In this regard synchrotron-based scattering (SAXS/WAXS/HEXD) appears to be the perfect tool to follow in situ and in a time-resolved manner the crystallization pathways because of the temporal and spatial length scales that can be directly accessed with these techniques.
Here, we show how we used scattering to probe the crystallization mechanisms of calcium sulfate. CaSO4 minerals (i.e. gypsum, anhydrite and bassanite) are widespread in natural and industrial environments. During the last several years, a number of studies have revealed indeed that nucleation in the CaSO4-H2O system is non-classical. Our SAXS data demonstrate that gypsum precipitation, involves formation and aggregation of sub-3 nm primary species. These species constitute building blocks of an amorphous precursor phase [2]. Further, we show how in situ high-energy X-ray diffraction experiments and molecular dynamics (MD) simulations can be combined to derive the atomic structure of the primary CaSO4 clusters seen at small-angles [3]. We fitted several plausible structures to the derived pair distribution functions and explored their dynamic properties using unbiased MD simulations based on polarizable force fields. Finally, based on combined SAXS/WAXS, broad-q-range measurements, we show that the process of formation of bassanite, a less hydrated form of CaSO4, is very similar to the formation of gypsum: it also involves the aggregation of small primary species into larger disordered aggregates [4].
Based on these recent insights we formulated a tentative general model for calcium sulfate precipitation from solution. This model involves primary species that are formed through the assembly of multiple Ca2+ and SO42- ions into nanoclusters. These nanoclusters assemble into poorly ordered (i.e. amorphous) hydrated aggregates, which in turn undergo ordering into coherent crystalline units of either gypsum or bassanite (and possibly anhydrite). Determination of the structure and (meta)stability of the primary species is important from both a fundamental, e.g. establishing a general non-classical nucleation model, and applied perspective; e.g. allow for an improved design of additives for greater control of the nucleation pathway.
References
[1] J.J. De Yoreo; P.U.P.A. Gilbert; N.A.J.M. Sommerdijk; R. L. Penn; S. Whitelam; D. Joester; H. Zhang; J. D. Rimer,; A. Navrotsky; J. F. Banfield; et al. Science 349, aaa6760 (2015);
[2] T.M. Stawski; A.E.S. van Driessche; M. Ossorio; J. Diego Rodriguez-Blanco; R. Besselink; L.G. Benning; Nat. Commun. 7, 11177 (2016);
[3] T.M. Stawski; A.E.S. Van Driessche; R. Besselink; E.H. Byrne; P. Raiteri ; J.D. Gale; L.G. Benning; J. Phys. Chem. C 123, 37 (2019);
[4] T.M. Stawski; R. Besselink; K. Chatzipanagis; J. Hövelmann; L.G. Benning; A.E.S. Van Driessche; J. Phys. Chem. C 124, 15 (2020)
The ZnO(10-14) surface raised recent scientific interest for its outstanding stability despite its high indexed orientation, which results in a stepped mixed-terminated surface.[1] In this study, copper nanoparticles were grown via physical vapor deposition onto a ZnO(10-14) single crystalline surface and the structure and morphology was investigated using low energy electron diffraction, high energy grazing incidence x-ray diffraction, scanning electron microscopy and scanning tunneling microscopy.
Caused by anisotropic diffusion, elongated Cu particles are formed parallel to the surface steps of the substrate. They show a unique tilt of their (111) planes parallel to the (0001) terraces of the vicinal surface. This causes the generation of large, high indexed Cu facets in which their atomic steps could act as reaction sites in catalytic reactions such as methanol synthesis and CO2 activation.
Assembly of NPs into large-area monolayers on a solid substrate is fundamentally
interesting due to their unique optical and electronic properties. Furthermore, they have an impact on the creation of next-generation materials design [1] and for new devices that require monolayers with ordered structure over large areas formed with a simple method at low cost to meet the growing industrial needs. But controlling the deposition on a substrate to obtain two-dimensional and three-dimensional nanoparticle arrays is a complex process, and it occurs under specific conditions.
In this contribution, we report on the formation of large area, self assembled, highly ordered monolayers of stearyl alcohol grafted silica nanospheres of ~ 50 nm diameter on a silicon substrate based on the drop-casting method. Our novel approach to achieve improved order uses stearyl alcohol as an assistant by adding it to the colloidal NanoParticle (NP) dispersion from which the monolayers are formed. Additionally, a heat treatment step is added, to melt the stearyl alcohol in the monolayer and thereby give the particles more time to further selfassemble, leading to additional improvement in the monolayer quality. The formation of the monolayers is significantly affected by the concentration of the NPs and the stearyl alcohol, the volume of the drop as well as the time of the heat treatment. A high surface coverage and uniform monolayer film of SiO2 NPs is achieved by appropriate control of the abovementioned preparation parameters. Structural characterization of the obtained SiO2 NP monolayer was done locally by Scanning Electron Microscopy (SEM), and globally by X-ray reflectivity (XRR) and grazing incidence small-angle X-ray scattering (GISAXS), where the data was reproduced by simulation within the Distorted Wave Born Approximation (DWBA) [2]. In conclusion, our modified drop-casting method is a simple, inexpensive method, which provides highly ordered self-assembled monolayers of silica particles, if combined with a compatible additive and a heat treatment step. This method might be more general and applicable to improve the ordering between different particles in monolayers as well as multilayers after finding an appropriate additive [3].
[1] M. A. Boles, M. Engel and D. V. Talapin, Chem. Rev., 2016, 116, 11220–11289.
[2] G. Pospelov, W. Van Herck, J. Burle, J. M. Carmona Loaiza, C. Durniak, J. M. Fisher, M. Ganeva, D. Yurov and J. Wuttke, J. Appl. Crystallogr., 2020, 53, 1600–5767.
[3] A. Qdemat, E. Kentzinger, J. Buitenhuis, U. Rücker, M. Ganeva and T. Brückel, RSC Adv., 2020,10, 18339-18347.
Metallic silicides constitute an important part of current microelectronics, serving as Schottky barriers and ohmic contacts, gate electrodes, local interconnects, and diffusion barriers [1–3]. Silicide nanowires, self-organized on the Si(110) surface, are considered as building blocks of future nanoelectronics and have been intensively investigated [4]. However, the reports about their crystal structure remain contradictory, spanning cubic (s or γ) [5–7] and tetragonal (α) [8] phases. Furthermore, in nanostructures the lattice vibrational waves (phonons) deviate drastically from those in bulk crystals, giving rise to anomalies in thermodynamic, elastic, electronic, and magnetic properties. Hence, a thorough understanding of the physical properties of these materials requires a comprehensive investigation of the crystal structure and lattice dynamics as a function of the nanowire size.
Using extended x-ray absorption fine structure (EXAFS) spectroscopy and nuclear inelastic scattering (NIS) we performed a systematic study of the crystal structure and the lattice dynamics of endotaxial FeSi$_2$ nanowires, which are in-plane embedded into the Si(110) surface. The EXAFS results unveiled the formation of the metastable, surface-stabilized α phase. The Fe-partial phonon density of states, obtained by the NIS experiment, exhibits a broadening of the spectral features with decreasing nanowire width and a pronounced vibrational anisotropy that originates from the specific orientation of the tetragonal α−FeSi$_2$ unit cell on the Si(110) surface. The results from first-principles calculations are fully consistent with the experimental observations [9].
References
[1] S.P. Murarka, Intermetallics 3, 173 (1995).
[2] L. J. Chen, Silicide Technology for Integrated Circuits (Institution of Electrical Engineers, London, 2004).
[3] L.J. Chen, JOM 57, 24 (2005).
[4] P.A. Bennett et al., Thin Solid Films 519, 8434 (2011).
[5] S. Liang et al., Appl. Phys. Lett. 88, 113111 (2006).
[6] S. Liang et al., J. Cryst. Growth 295, 166 (2006).
[7] D. Das et al., Appl. Phys. Lett. 105, 191606 (2014).
[8] Z.-Q. Zou et al., Appl. Surf. Sci. 399, 200 (2017).
[9] J. Kalt et al., Phys. Rev. B 102, 195414 (2020).
X-ray free electron lasers (XFEL) have facilitated the development of time-resolved serial femtosecond crystallography (TR-SFX) approaches to study protein structural changes [1]. This method relies upon the continuous replacement of microcrystals using micro-jet (or other) technologies and has many advantages relative to traditional time-resolved Laue diffraction methods using synchrotron radiation [2]. Photosynthetic reaction centres are integral membrane proteins which harvest the energy content of sunlight in order to power the movement of electrons. We collected TR-SFX data at the LCLS in order to observe light induced structural changes in a bacterial photosynthetic reaction centre. Our observations revealed how the light-induced movement of electrons induced a complementary structural response of the protein which stabilized the charge-separated state [3].
[1] Tenboer, J., et al. Time-resolved serial crystallography captures high-resolution intermediates of photoactive yellow protein. Science 346,1242-1246 (2014).
[2] A. Wöhri et al., Light-induced structural changes in a photosynthetic reaction center caught by Laue diffraction, Science 328, 630-633 (2010).
[3] R. Dods et al., Ultrafast structural changes within a photosynthetic reaction centre, Nature 589, 310-314 (2021)
To study the effect of high pressure on any sample property, suitable pressure devices are a fundamental requirement. Their design has to be tailored to the experimental demands regarding the intended pressure, the employed instrumentation and the expected scientific results. Our work presents the development of high pressure cells for neutron scattering on polycrystalline and single-crystalline samples at low temperatures and with applied magnetic fields.
One of the most common devices for high-pressure neutron experiments is the clamp cell [1], where the pressure is applied ex situ and which can be used independently in various setups. Our cell design [2] has been specifically developed for neutron scattering experiments at low temperatures in the closed-cycle cryostats on the instruments DNS (diffuse scattering neutron spectrometer), MIRA (cold three axes spectrometer), and POLI (polarized hot neutron diffractometer) at the Heinz Maier-Leibnitz Zentrum (MLZ) in Garching, Germany. The compact monobloc cell has been produced in two variants, the CuBe alloy and NiCrAl “Russian Alloy”, working up to about 1.1 GPa and 1.5 GPa, respectively. The low paramagnetic moment of both alloys allows also measurements of magnetic properties.
First tests of the cell with neutron radiation were performed to calibrate the load/pressure-curve of the CuBe cell (up to 1.15 GPa), to estimate its neutron absorption and background, and to measure magnetic reflections. In addition, the thermal response in the instrument cryostat was measured and the experimental findings were complemented by simulations.
Ultimately, these cells are intended as standard cells for high pressure measurements on different instruments at MLZ suitable for all available magnets and cryostats down to 1.5 K. Further tests under various conditions (temperature, pressure, magnetic field) as well as simulations are planned for both cells. The results will help both to establish the present cells and to optimise the design of subsequent cells to achieve higher pressures, to fit into smaller cryostats and to enable neutron-independent pressure calibration.
Acknowledgement: This work was supported by the Bundesministerium für Bildung und Forschung (BMBF) [grant number 05K19PA2] and by the Deutsche Forschungsgemeinschaft (DFG) [grant number GE971/5-2].
[1] Klotz, S. (2013). Techniques in High Pressure Neutron Scattering. CRC Press.
[2] Eich, A. et al. (2020). High Press. Res. Advance online publication. doi:10.1080/08957959.2020.1841759
The best crystal structures for publication require X-ray detectors with high signal-to-noise ratios and accurate intensities. The new PHOTON III detector family matches these requirements perfectly, offering mixed mode detection for the first time. Mixed mode detection simultaneously combines photon counting and integration, providing data of ultimate quality for both strong and weak reflections. Conventional photon counting detectors, like HPC or HPADs, suffer from poor linearity and count rate limitations for strong reflections, significantly degrading data quality. The mixed mode PHOTON III detector eliminates all detector noise, delivering the highest linearity and guaranteeing the highest quality data for the most challenging samples. The PHOTON III is available in three different sizes to ensure the best performance for your application needs. Users admire the detectors’ ultimate sensitivity over a wide energy range (from In-Kα to Ga-Kα), low point-spread, and parallax-free diffraction data. The PHOTON III also features high-energy event discrimination (HEED) that eliminates ubiquitous cosmic radiation artefacts making it the best detector ever developed.
Details on the function principle of the PHOTON III detector and latest application examples will be discussed.
During last decades we have been using organometallic cyclo-Pn complexes (n = 4, 5) as building blocks for the rational design of giant supramolecules, up to 4.6 nm in size [1-4]. The supramolecules consisting of hundreds of atoms frequently demonstrate weak scattering power due to the severe crystallographic disorder. In many cases, the use the high-flux synchrotron sources becomes the only remedy.
The samples of organometallic supramolecules must be permanently protected from oxygen to avoid the oxidation of cyclo-Pn fragments. Any traces of water in the organic solvents also should be avoided. Therefore, the proper sample handling requires a vacuum-argon line (Schlenk line) that protects the sample from air during the extraction of the portion of crystals for the diffraction study. Within the long-term project II-20180597 with DESY (Hamburg, Germany) we have installed such line in the sample preparation lab of P24 beamline.
To obtain quality data at dmin > 1 Å for giant supramolecules we developed optimal strategies to perform the single-crystal diffraction experiments at both P11 and P24 beamlines. For P11 beamline, the most critical is to choose radiation energy as a compromise between dmin and quantum efficiency (QE) of a PILATUS 6M detector. Higher energies improves the resolution by the cost of significantly lower QE.
The optics at the P24 beamline allows using hard X-ray radiation with E up to 44 keV. It helps in reducing the absorption and radiation damage in Ag and Ta-containing crystals. Helium open-flow cryostat provides temperature down to 10 K.
Optimization of the experimental strategy allowed us to obtain high-quality diffraction data even from weakly scattering crystals (Fig. 1) and to investigate such subtle structural effects as superstructural ordering.
This work was supported by the German Research Foundation (DFG) within the project Sche 384/44-1.
Fig. 1a) Giant cationic supramolecule [(Cp''Fe(η5-P5)12(CuNCCH3)8]8+ with an external diameter of 2.5 nm [4]. Hydrogen atoms are omitted for clarity; b) the diffraction pattern from the single crystal at P11 beamline (E = 18 keV, 0.1° scan)
[1] E. Peresypkina, C. Heindl, A. Virovets, M. Scheer (2016) Structure and Bonding 174, 321
[2] H. Brake, E. Peresypkina, C. Heindl, et al (2019) Chem. Sci. 10, 2940
[3] E. Peresypkina, M. Bielmeier, A. Virovets, M. Scheer (2020) Chem. Sci. 11, 9067
[4] J. Schiller, A.V. Virovets, E. Peresypkina, M. Scheer (2020) Angew. Chem. Int. Ed. 59, 13647
The PERCIVAL detector, a CMOS imager specifically designed for the soft X-ray regime, has served in 2020 its two first user experiments, both at a Synchrotron Radiation source (SR) and also at a Free Electron Laser (FEL). Here, we report some preliminary results of both experiments as well as future plans.
The first experiment, in collaboration with groups at the HZB and MBI, used the P04 XUV beamline at PETRA-III to perform holography imaging of topological materials (in particular skyrmions) at an energy or 780eV. The second experiment, in collaboration used the FL24 at FLASH-2 to performed ptychography imaging of plasma treated surfaces at an energy range between 92 and 462eV. Both experiments benefited from a very large dynamic range, thanks to the PERCIVAL auto-adaptative gain switching.
With its 4 x 4 cm2 active area, extendable to 8 x 8 cm2 in clover-leaf like configurations, and its 2 Megapixels, 27 um size, PERCIVAL can provide images with high spatial resolution. Moreover, its fast readout, wil be capable of speeds up to 300 frames per second. A dynamic range from ~ 14e- to 3.5 Me- is to be expected. The development, jointly carried by 5 light sources (DESY, PAL, Elettra, DLS and SOLEIL) and RAL/STFC, will enable increased science yield from today’s FEL and synchrotron light sources in the soft X-ray regime.
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) papain-like protease (PLpro) is essential for the virus replication. PLpro has the additional function of removing ubiquitin and ISG15 (Interferon-stimulated gene 15) from host-cell proteins to aid coronaviruses in their evasion of the host innate immune responses. PLpro is thus an excellent drug target for a two-fold strategy to develop antiviral compounds that both inhibit viral replication and strengthen the immune response of the host. To provide a structural framework for efficient screening of inhibitor compounds, we expressed, purified and crystallized PLpro (Fig.1). The crystals are stable, reproducible, have a high solvent content of 66% suitable for soaking experiments and diffract to a high resolution of 1.5Å (Fig.2). Bioinformatics analysis of the active site based on the PLpro crystal structure coordinates showed interestingly high similarities to the proteasome and we screened 37 proteosome inhibitors by soaking and co-crystallization experiments. The PLpro crystals complexed with these compounds diffracted in the resolution range of 1.5Å-2.5Å and structural efforts to identify new antiviral compounds to combat the coronavirus spread will be presented.strong text
Many bacteria harbor RNA-dependent nucleoside-triphosphatases of the DEAH/RHA family (1), whose molecular mechanisms and cellular functions are poorly understood (2). Here, we show that the Escherichia coli DEAH/RHA protein, HrpA, is an ATP-dependent 3’-to-5’ RNA helicase, and that the RNA helicase activity of HrpA influences bacterial survival under antibiotics treatment. Limited proteolysis, crystal structure analysis and functional assays showed that HrpA contains an N-terminal DEAH/RHA helicase cassette preceded by a unique N-terminal domain and followed by a large C-terminal region that modulates the helicase activity. Structures of an expanded HrpA helicase cassette in the apo and RNA-bound states revealed ratchet-like domain movements upon RNA engagement much more pronounced than hitherto observed in related eukaryotic DEAH/RHA enzymes (Fig. 1). Consistent with similar conformational changes supporting RNA translocation, structure-based functional analyses delineated transient inter-domain contact sites that support substrate loading and unwinding. Analogous dynamic intramolecular contacts are not possible in the related, but helicase-inactive, RNA-dependent nucleoside-triphosphatase, HrpB (3,4). Our results indicate that HrpA may be an interesting target to interfere with bacterial tolerance toward certain antibiotics and suggest possible interfering strategies.
Fig. 1. Top, Domain composition of the E. coli DEAH/RHA-type RNA helicase, HrpA. NTD, N-terminal domain; RecA1/2, RecA-like domains; WH, winged-helix domain; HB, helical bundle (“ratchet”) domain; OB, oligonucleotide/oligosaccharide-binding domain; CON, connector domain; CTR, C-terminal region. Bottom, comparison of the crystal structures of the expanded helicase cassette of E. coli HrpA in the apo (left) and RNA-bound (right) states.
References
1. Khemici, V. & Linder, P. RNA helicases in bacteria. Curr. Opin. Microbiol. 30, 58–66 (2016).
2. Redder, P., Hausmann, S., Khemici, V., Yasrebi, H. & Linder, P. Bacterial versatility requires DEAD-box RNA helicases. FEMS Microbiol. Rev. 39, 392–412 (2015).
3. Pietrzyk-Brzezinska, A. J. et al. Crystal Structure of the Escherichia
coli DExH-Box NTPase HrpB. Struct. Lond. Engl. 1993 26, 1462-1473.e4 (2018).
4. Xin, B.-G., Chen, W.-F., Rety, S., Dai, Y.-X. & Xi, X.-G. Crystal structure of Escherichia coli DEAH/RHA helicase HrpB. Biochem. Biophys. Res. Commun. 504, 334–339 (2018).
The crystal chemistry of AIBIIXO4 (AI = Alkali ion, BII = alkali-earth ion, X = P, V, As) is very rich and has been widely investigated, particularly the phosphate family [1]. In recent years, we have been investigated the crystal structures [2,3] and magnetic properties of some compositions within the AIBIIXO4 series [4]. However, despite its simple chemistry NaSrPO4 has never been reported so far. Here, we present the synthesis, crystal structure and phase transitions of this phosphate. Surprisingly, this material exhibits a complex structure (31 atoms in the asymmetric unit-cell, Z = 10) at room temperature characterized by a strongly under bonded Na atom. This under-bonded atom is responsible for the complex and rich phase diagram as function of temperature as illustrated in Figure 1. NaSrPO4 exhibits 4 phase transitions between room temperature and 750C. Besides its rich phase diagram, NaSrPO4 exhibits a re-entrant phase transition slightly below 600C before to reach a hexagonal paraelastic phase at high temperature. In addition, we show that the sequence of phase transitions is strongly driven by the history of the sample and several phases can be quenched at room temperature.
[1] V. A. Isupov, Ferroelectrics, 274(1), 203–283 (2002)
[2] G. Nénert, P. O’Meara, T. Degen, Phys Chem Minerals 44, 455–463 (2017)
[3] G. Nénert, Z. Kristallogr.; 232(10), 669–674 (2017)
[4] G. Nénert, et al., Inorg. Chem., 52, 9627−9635 (2013).
The crystal structure of the mineral tetradymite Bi2S2Te has inspired discussions about its details for a long time.[1,2] Variations of this structure led to a large family of chalcogenides composed of slabs with alternating cation and anion layers stacked in rocksalt-type fashion, which show characteristic van der Waals gaps between anion layers.[3] These compounds are of interest not only for their exact crystal structures but also for their thermoelectric properties and their high likelihood of being topologically non-trivial systems insulators.[4,5]
The rhombohedral compounds Tt1Pn2Te4 (Tt = Ge, Sn, Pb; Pn = As, Sb, Bi) feature septuple layers, in which the multiplicity of Wyckoff positions would allow complete cation ordering, which has been postulated in some cases.[6] However, more detailed studies based on single-crystal diffraction data almost always revealed cation disorder.[7] In the case of small scattering contrast, resonant X-ray diffraction corroborated the disorder.[8] Here we present a systematic investigation of these compounds with high-quality single crystal diffraction data collected with synchrotron radiation in order to establish exact site occupancy factors. As diffraction data cannot exclude short-range ordering, Z-contrast imaging by STEM-HAADF was used as a local probe, complemented by EDX spectroscopy with atomic resolution. All of these data confirm the cation disorder and could not even demonstrate short-range ordering.
The disorder observed might be explained as an interplay between charge balance at the vdW-gap and octahedron size mismatch in the layer.
[1] Harker, D. Z. Kristallogr. 1934, 89, 175-181.
[2] Pauling, L. Am. Mineral. 1975, 60, 994-997.
[3] Cook, N. J.; Ciobanu, C. L.; Stanley, C. J.; Paar, W. H.; Sundbald, K. Can. Mineral. 2007, 45, 417-435.
[4] Grauer, D. C.; Hor, Y. S.; Williams, A. J.; Cava, R. J. Mater. Res. Bull. 2009, 44, 1926–1929.
[5] Silkin, I. V.; Menshchikova, T. V.; Otrokov, M. M.; Eremeev, S. V.; Koroteev, Yu. M.; Vergniory, M. G.; Kuznetsov, V. M.; Chulkov, E. V. JETP Letters. 2012, 96, 322-325.
[6] Shu, H. W.; Jauilmes, S.; Flahaut, J. Solid State Chem., 1988, 74, 277-286..
[7] Karpinsky, O. G.; Shelimova, L. E.; Kretova, M. A.; Fleurial. J. P. J. Alloys Compd. 1998, 268, 112-117.
[8] Oeckler, O.; Schneider, M. M.; Fahrnbauer, F.; Vaughan, G. Solid State Sci. 2011, 13, 1157-1161.
Magnesium halides and pseudo-halides are essential compounds for many applications ranging from biochemistry to construction and building materials. These phases exhibit a great variety of chemical and structural properties and hence, were extensively studied. However, in the row of magnesium pseudo-halides, i.e. cyanides, cyanates etc., the thiocyanates were often overseen and are therefore still only poorly characterized.
Mg(SCN)2 · x H2O/THF coordination compounds were synthesized, characterized, their crystal structures solved ab initio from X-ray powder diffraction (XRPD) data and their thermal expansion properties investigated by temperature dependent in situ XRPD.
The recrystallization of Mg(SCN)2 · 4 H2O in THF yields the novel compounds Mg(SCN)2 · 2 (H2O, THF) and α-Mg(SCN)2 · 4 THF. By heating, α-Mg(SCN)2 · 4 THF undergoes a phase transition into β-Mg(SCN)2 · 4 THF that is associated with an increasing disorder of the THF molecules. Finally, two THF molecules are released, which leads to the formation of Mg(SCN)2 · 2 THF. The investigated compounds show a remarkable anisotropic thermal expansion and the growing disorder of THF molecules has a major impact on the expansion properties.
The coordination chemistry of Mg(SCN)2 turned out to be rich and has the potential to go beyond H2O and THF as ligands. An expansion towards other metals like nickel, cobalt or iron appears to be very feasible.
Fig. 1. Octahedral coordination of Mg2+ with SCN- and THF for a) α-Mg(SCN)2 ⋅ 4 THF; b); β-Mg(SCN)2 ⋅ 4 THF, Plots showing the variation of the thermal expansion coefficient α with the principal directions X1, X2 and X3 of c) α-Mg(SCN)2 ⋅ 4 THF, d) β-Mg(SCN)2 ⋅ 4 THF
We studied the thermo- and photo-induced phase transition between low spin (LS) and high spin (HS) states of the 2x2 grid-like iron complex: Fe4L44·C2H3N (FE4), L=4-methyl-3,5-Bis{6(2,2′-dipyridyl)}pyrazole in solid state, by using X-ray diffraction techniques. The structural analysis of the coordination geometry of the two crystallographically independent metal atoms at different temperatures demonstrates that the formation of the thermo-induced HS in one atom affects the coordination geometry of the other. The analysis of the photo-induced HS over time do not only exhibit similar structural reorganization as the thermo-induced HS state but also a relaxation from HS to LS in less than one nanosecond. The understanding of photo-switching dynamics and its relation with the thermo-induced HS under systems with strong short-range elastic coupling between small set of metal ions, such as the FE4 system, could allow for new mechanism of energy redistribution after photoexcitation and therefore, the design of new storage and processing devices.
Growing concern over resource availability and toxicity are leading to a paradigm shift towards truly sustainable materials for photovoltaics. Zn-group IV-nitrides are one potential class of materials fulfilling these criteria, which adopt a wurtzite-type derived structure. The ternary nitrides were postulated to allow a unique bandgap tuning mechanism through cation disorder$^{[1]}$ in addition to cation alloying. Fully ordered structure ZnGeN$_2$ crystallises in a ß-NaFeO$_2$ type structure in a subgroup of the wurtzite type. Interestingly, incorporating oxygen into ZnGeN$_2$ also introduces an increased degree of disorder in the material.$^{[2]}$
We present a detailed study of the degree of cation disorder in oxygen containing Zn$_{1-x}$GeN$_2$O$_x$ that is revealed through neutron powder diffraction. Studying samples with a variable degree of oxygen allows us to conclude on the role of oxygen and further comparing different samples of nominally similar composition allows to decorrelate the oxygen effect from intrinsic cation disorder. We will combine our results with optoelectronic and chemical properties of the materials and finally aim to answer the question, whether cation disorder exists independently of oxygen incorporation or is fundamentally linked to it.
[1] A.D. Martinez, A.N. Fioretti, E.S. Toberer, A.C. Tamboli, J. Mater. Chem. A, 2017, 5, 11418.
[2] J. Breternitz, Z.Y. Wang, A. Glibo, A. Franz, M. Tovar, S. Berendts, M. Lerch, S. Schorr, Phys. Status Solidi A, 2019, 1800885.
The class of transition metal phosphates (TMPs) shows a wide range of chemical compositions, variations of valence states and respective crystal structures. Among TMPs, $VO(P_2O_7)$ and $LiFePO_4$ are of special interest as the only commercially used heterogeneous catalyst for the selective oxidation of butane to maleic anhydride [1] and cathode material in rechargeable batteries [2]. Due to their structural features, TMP are considered as proton exchange-membranes in fuels cells, working in the intermediate-temperature range [2, 3]. We report on the successful ab initio structure determination of two novel titanium pyrophosphates, $NH_4Ti(III)P_2O_7$ and $Ti(IV)P_2O_7$, from X-ray powder diffraction data. Both compounds were synthesized via a new molten salt synthesis route. The low symmetry space groups $P2_1/c$ ($NH_4TiP_2O_7$) and $P\overline{1}$ ($TiP_2O_7$) complicate the structure determination, making the combination of spectroscopic, diffraction and computation techniques mandatory. In $NH_4TiP_2O_7$, titanium ions ($Ti^{3+}$) occupy the $TiO_6$ polyhedron, coordinated by five pyrophosphate groups, one as a bi-dentate ligand. This secondary coordination causes the formation of one-dimensional six-membered ring channels with a diameter $d_{max}$ of 514(2) pm, stabilized by ammonium ions. Annealing $NH_4TiP_2O_7$ in inert atmospheres results in the formation of the new $TiP_2O_7$, showing a similar framework consisting of $[P_2O_7]^{4-}$ units and $TiO_6$ octahedra as well as an empty one-dimensional channel ($d_{max}$ = 628(1) pm). The in situ X-ray diffraction study of the transformation of $NH_4TiP_2O_7$ to $TiP_2O_7$ reveals a two-step mechanism, the decomposition of ammonium ions coupled with the oxidation of $Ti^{3+}$ to $Ti^{4+}$ and a subsequent structural relaxation.
The “fluoride route”, synthesis in the presence of fluoride anions, has been established as a versatile strategy for the synthesis of all-silica zeolites. Experimental investigations of as-synthesised zeolites using diffraction and NMR methods have shown that the fluoride anions are often located in small cages and bonded to one Si atom at a cage corner, with dynamic or static disorder occurring in some, but not all systems.[1] It has also been observed that the dynamic disorder can be modulated through a variation of the organic structure-directing agent (OSDA) used in the zeolite synthesis.[2] As relatively little is known about the underlying factors determining the preferred fluoride location(s) in a given cage and the dynamic behaviour, the present work employs a combination of density functional theory (DFT) calculations and DFT-based ab-initio molecular dynamics (AIMD) simulations to contribute to the understanding of these systems.
A systematic comparison of different fluoride positions in four all-silica zeolites with different topologies (IFR, NON, STF, STT) shows excellent agreement with experiment for all systems except STF. A remarkable result is obtained for STT, where the DFT calculations predict three distinct sites to be very close in energy, in perfect correspondence with the experimentally observed disorder over these sites. The AIMD simulations do not only reproduce the dynamic disorder of fluoride anions in IFR and STT, and its absence at room temperature in NON and STF, but also allow to develop an explanation for the qualitative differences between these systems. The role of the OSDA in influencing the dynamics of the fluoride anions is investigated for MFI-type Silicalite-1. AIMD simulations for Silicalite-1 models containing different alkylammonium OSDAs show that the introduction of asymmetric organic cations with one short alkyl chain leads to a strong reduction of the fluoride mobility, agreeing with experimental observations. Further analysis shows that the heterogeneous charge distribution of these OSDAs, together with their restricted freedom of movement in the channels, enhances electrostatic interactions with the fluoride anions, reducing the dynamic motion.[3] While the primary aim of the present work is an improved fundamental understanding, similar computational approaches may, in the future, be exploited to aid the targeted synthesis of zeolites in fluoride-containing media.
Funding by the Deutsche Forschungsgemeinschaft (DFG project no. 389577027) is gratefully acknowledged.
References
[1] D. S. Wragg, R. E. Morris, A. W. Burton, Chem. Mater. 2008, 20, 1561–1570.
[2] S. L. Brace, P. Wormald, R. J. Darton, Phys. Chem. Chem. Phys. 2015, 17, 11950–11953.
[3] M. Fischer, J. Phys. Chem. C 2020, 124, 5690–5701.
During the last 50 years, relativistic quantum chemistry has undergone significant developments and methodological progress. Nowadays, it is well-known that a relativistic quantum formalism is necessary for the study of compounds with heavy elements1-3.
Within last years it has appeared that quantum crystallography is a very prospective method of refinement of crystal structures. It relies on the high-resolution and high-quality XRD data to describe crystal structure in unprecedented details4-5. Intensities of the diffracted beam are affected not only by relativistic effects but also by many other effects such as absorption6, anharmonic motion7, anomalous dispersion8, and others effects which significantly influence electron density distribution in the crystal and, in consequence, derived properties.
In this study, we validated relativistic Hirshfeld atom refinement (HAR)9 as implemented in Tonto10 by performing refinement of experimental high-resolution X-ray diffraction data for an organo-gold(I) compound. The influence of relativistic effects on statistical parameters, geometries and electron density properties was analyzed and compared to the influence of electron correlation and anharmonic atomic motions.
Acknowledgement:
Support of this work by the National Science Centre, Poland through grant PRELUDIUM no. UMO-2018/31/N/ST4/02141 is gratefully acknowledged.
The experiment was carried out at the Spring-8 with the approval of the Japan Synchrotron Radiation research Institute (Proposal Number 2019A1069).
References:
1. I. P. Grant, Advances in Physics, 1970, 19, 747–811.
2. J. P. Desclaux, Atomic Data and Nuclear Data Tables, 1973, 12, 311–406.
3. T. Ziegler, J. G. Snijders and E. J. Baerends, The Journal of Chemical Physics, 1998, 74, 1271.
4. L. J. Farrugia, C. Evans, D. Lentz and M. Roemer, Journal of the American Chemical Society, 2009, 131, 1251–1268.
5. T. S. Koritsanszky and P. Coppens, Chem. Rev., 2001, 101, 1583–1628.
6. J. Als‐Nielsen and D. McMorrow, in Elements of Modern X-ray Physics, John Wiley & Sons, Ltd, 2011, pp. 1–28.
7. R. Herbst-Irmer, J. Henn, J. J. Holstein, C. B. Hübschle, B. Dittrich, D. Stern, D. Kratzert and D. Stalke, The Journal of Physical Chemistry A, 2013, 117, 633–641.
8. S. Caticha-Ellis, Anomalous dispersion of x-rays in crystallography, University College Cardiff Press, Cardiff, Wales, 1981.
9. L. Bučinský, D. Jayatilaka and S. Grabowsky, The Journal of Physical Chemistry A, 2016, 120, 6650–6669.
10. D. Jayatilaka and D. J. Grimwood, Acta Crystallographica Section A, 2001, 57, 76–86.
EIGER2 CdTe - HPC for a wide range of X-ray energies in synchrotron and laboratory applications
Metal–organic frameworks (MOFs) are structurally diverse, porous materials comprised of metal nodes bridged by organic linkers. [1] Through careful choice of nodes and linkers, the chemical and physical properties of MOFs can be elegantly tuned and materials with very high surface area and porosity can be obtained. As a consequence, MOFs have been explored for many potential applications including, but not limited to, gas storage and release, chemical separations, catalysis, drug delivery, light harvesting and energy conversion, and the detoxification of hazardous analytes. [2] In addition to these promising potential applications, MOFs offer an interesting platform for studying fundamental concepts in inorganic materials chemistry. We are particularly interested in the study of MOFs comprised of rare-earth (RE) elements, [3] in part, because of the high and variable coordination number of these elements, which allows several unique and intricate MOF topologies to be designed and synthesized. Furthermore, RE-MOFs can be produced with diverse optical and electronic properties dictated by the 4f electron configurations of the RE-elements. In this presentation, RE-MOFs are explored from design and synthesis, to potential application.
[1] B. F. Hoskins and R. Robson, ‘Infinite polymeric frameworks consisting of three dimensionally linked rod-like segments’, J. Am. Chem. Soc. 111, 5962–5964 (1989); O. M. Yaghi and H. Li, ‘Hydrothermal Synthesis of a Metal-Organic Framework Containing Large Rectangular Channels’, J. Am. Chem. Soc. 117, 10401–10402 (1995)
[2] A. J. Howarth, Y. Liu, P. Li, Z. Li, T. C. Wang, J. T. Hupp and O. K. Farha, ‘Chemical, thermal and mechanical stabilities of metal–organic frameworks’, Nat. Rev. Mater. 1, 15018 (2016)
[3] F. Saraci, V. Quezada-Novoa, P. R. Donnarumma, ‘Rare-earth metal–organic frameworks: from structure to applications’, Chem. Soc. Rev., 49, 7949-7977 (2020)
Polarized neutron diffraction (PND) is a powerful method for investigating magnetic structures. It gives unique access to contributions from nuclear and magnetic scattering, their interference terms, and their magnetic chirality, and permits to distinct between them. In contrast to non-polarized neutron diffraction, where the scattered intensity depends on the square of the magnetic structure factor, PND has a linear nuclear–magnetic interference term as part of the scattered intensity. This increases the precision in the determination of the ordered magnetic moment by at least one order of magnitude. Recently, a first PND setup using a compact high Tc superconducting magnet and a 3He spin filter polarizer has been successfully implemented [1,2] on the hot neutrons single crystal diffractometer POLI at Maier-Leibnitz Zentrum (MLZ) in Garching b. München. Although this setup performs well and first scientific output from the measurements performed using it starts to appear [3], it suffers from the relatively low maximal available field of only 2.2 T. For studying many modern-topic (e.g quantum, topologic order, complex frustrated, etc.) magnetic materials with small ordered magnetic moment, the field-limit of about 2 T is insufficient in order to produce significant measurable signal, even for PND. To overcome this limitation, a new 8 T split-coil superconducting magnet has been procured and implemented for measurements on POLI. Although, this new magnet is actively shielded, reducing the stray field by an order of magnitude compared to the classical design, its fringe fields are still too large to be used with the sensitive 3He polarizer of the previous setup. To overcome this issue, a new large-beam-cross-section solid-state supermirror bender (SB) polarizer has been developed for POLI. It was realized by a Fe/Si multilayer coating on both sides of the thin Si wafers (m=3) by the NOB company. An additional Gd oxide layer is deposited on the convex side of each wafer to absorb the neutrons with the wrong polarization. An existing shielded Mezei-type flipper is used between the magnet and SB. A dedicated guide field construction was numerically simulated, optimized and built to link the magnetic field of the SB to the flipper and to the stray field of the magnet. The neutron beam path between the monochromator drum to the sample magnet is shown in the Fig. 1. The new setup was successfully tested using a 3He spin filter as analyzer at low fields (< 1 T), and a high quality Cu2MnAl single-crystal at high fields (> 2T). An almost loss-free spin transport within the instrument for the complete field range of the new magnet was achieved. A high polarization efficiency of above 99% even for short wavelength neutrons could be experimentally reached using the new solid-state bender (Fig.2). The new high–field PND setup is now available for precise magnetic structure investigations on POLI for the internal and external user communities.
[1] H. Thoma, H. Deng, G. Roth, V. Hutanu, “Setup for polarized neutron diffraction using a high-Tc superconducting magnet on the instrument POLI at MLZ and its applications”, J. Phys.: Conf. Ser. 1316, 012016 (2019)
[2] H. Thoma, W. Luberstetter, J. Peters & V. Hutanu, “Polarised neutron diffraction using novel high-Tc superconducting magnet on single crystal diffractometer POLI at MLZ”, J. Appl. Cryst. 51, 17-26 (2018)
[3] J. Jeong, B. Lenz, A. Gukasov, et al. “Magnetization density distribution of Sr2IrO4: Deviation from a local jeff = 1/2 picture”, Phys. Rev. Lett. 125, 097202 (2020)
The neutron single crystal diffractometer BIODIFF at the research reactor Heinz Maier-Leibnitz (FRM II) is especially designed to collect data from crystals with large unit cells. The main field of application is the structural analysis of proteins, especially the determination of hydrogen atom positions. BIODIFF is a joint project of the Jülich Centre for Neutron Science (JCNS) and the FRM II. BIODIFF is designed as a monochromatic instrument with a narrow wavelength spread of less than 3 %. To cover a large solid angle the main detector of BIODIFF consists of a neutron imaging plate in a cylindrical geometry with online read-out capability.
BIODFF is equipped with a standard Oxford Cryosystem “Cryostream 700+” which allows measurements at 100 K. A new kappa goniometer head was added recently. This allows an automated tilting of the crystal in order to increase the completeness of the data set when recording another set of frames in the tilted geometry. Typical scientific questions addressed are the determination of protonation states of amino acid side chains in proteins and the characterization of the hydrogen bonding networks between the protein active centre and an inhibitor or substrate.
Picking out some recent highlights from measurements at BIODIFF it will be shown how the method of neutron protein crystallography could be used to answer mechanistic questions in enzymatic processes or help to improve inhibitor fragment screening. New developments at the instrument will also be presented: A new collimation for the primary beam should lead to a reduction in background. It should also make it easier to align the neutron beam with the centre of the neutron imaging plate detector. Furthermore, a new single crystal x-ray diffractometer has been installed in the new MLZ lab building. It features a Molybdenum and a Copper Microfocus x-ray source and a 150° (2 ) x-ray detector. It also features also an Oxford Cryosystems 800 series Cryostream for sample temperatures between 80-400K. This x-ray diffractometer can be used to record an x-ray data set of the protein crystal after having been measured at the BIODIFF instrument. It may also be used to pre-scan the diffraction quality of the crystals the user brings for neutron beam times at MLZ instruments.
In the meantime the diffraction activities form the major portion of research at each large scale facility. Diffraction at neutron sources is exploring the full range of unique neutron properties (sensitivity to isotopes and magnetic subsystems, nuclear scattering form-factors independent on Q etc) and provides structural information complementary to X-ray or electron diffraction. Despite the different underlying physics supplementing the interaction of neutrons and photons with the matter, the ways of the data A wealth of neutron diffraction instrumentation as a probe of long-range atomic and magnetic orders from single crystal and powder samples at a variety of environmental conditions is available at MLZ, namely high-resolution and engineering diffractometers SPODI and STRESS-SPEC; hot, thermal and cold (macromolecular) single crystal diffractometers HEIDI, RESI and BioDIFF; diffuse instrument DNS and a pool of triple axis spectrometers. A number of new instrumental developments (POWTEX, SAPHIR, ERWIN) as well as new life project for FIREPOD (E9) are on their way to strengthen diffraction at MLZ even further.
There is a broad spectrum of structure-related scientific activities at MLZ e.g. (i) electrochemical energy storage systems and related materials; (ii) modern ferroelectrics; (iii) multiferroic materials and interrelation of the ferroic degrees of freedom; (iv) new generation engineering and shape memory alloys; (v) biological macromolecules; (vi) rock-forming minerals and glasses. In the current contribution an overview of the diffraction instrumentation at FRM II neutron source will be presented along with the future prospects and running developments.
M. Meven$^{*1,2}$, A. Grzechnik$^1$, V. Hutanu$^{1,2}$, K. Friese$^3$, A. Eich$^{1,3}$ and G. Roth$^1$
$^1$Institute of Crystallography, RWTH Aachen University, 52056 Aachen, Germany
$^2$Jülich Centre for Neutron Science at Heinz Maier-Leibnitz Zentrum, Forschungszentrum Jülich GmbH, 85747 Garching, Germany
$^3$Jülich Centre for Neutron Science–2/Peter Grünberg-Institute–4, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
*e-mail: martin.meven@frm2.tum.de
Due to their specific peculiarities neutrons are a very useful probe for structural studies on various hot topics related to physics, chemistry and mineralogy. The neutron single crystal diffractometer HEiDi at the Heinz Maier-Leibnitz Zentrum (MLZ) offers high flux, high resolution and large $q$ range, low absorption and high sensitivity for light elements. These properties apply in a similar way to its polarized sister diffractometer POLI, which is optimized for magnetic structure determinations.
In 2016 a project was launched in order to allow studies on tiny samples < 1 mm³ and to develop new pressure cells for HEiDi which can be combined with its existing low temperature equipment in order to study structural properties down to temperatures below 10 K, e.g. MnFe$4$Si$3$ compounds and their magnetic features [1]. As part of this project (funded by the BMBF, No. 05K16PA3), various neutron-optical components (Cu220-monochromator, solid state collimators, neutron guides) were developed and optimized in order to generate a sufficiently high flux density at the sample location at the wavelength $λ$ = 0.87 Å. Very tiny single crystal samples (< 0.1 mm³) were successfully studied using various newly developed diamond anvil cells up to several GPa, either with a panoramic pressure cell in combination with low temperatures [2] or in a transmission pressure cell, which allows simultaneous studies of the same sample using neutron, synchrotron as well as laboratory x-ray sources [3].
This project is now followed up by a second one (BMBF No. 05K19PA2) focusing on further improving the high pressure capabilities on HEiDi and POLI (including the installation of a 2-dimensional detector) and the development of optimized pressure cells for further instruments at the MLZ, namely POLI, DNS and MIRA (see contribution by A. Eich).
[1] A. Grzechnik et al.; Single-Crystal Neutron Diffraction in Diamond Anvil Cells with Hot Neutrons; J. Appl. Cryst. 51, 351-356 (2018).
[2] A. Eich et al.; Magnetocaloric Mn$_5$Si$_3$ and MnFe$_4$Si$_3$ at variable pressure and temperature; Mater. Res. Express 6, 096118 (2019).
[3] A. Grzechnik et al.; Combined X-ray and neutron single-crystal diffraction in diamond anvil cells; J. Appl. Cryst. 53(1), 1 - 6 (2020).
The oxygen mobility and exchange are fundamental properties of perovskite oxides which regulate their application in catalysis, sensing, energy conversion and information technology [1]. The increasing need of sustainable catalytic materials has driven the development of nanoporous perovskite structures with improved surface reactivity [2,3]. Although it is intuitive that enhanced specific surface area (SSA) might improve the catalytic activity, it is not clear yet how this increase influences oxygen release and mobility in nanostructured grains and what is its effect on catalysis.
In the present paper, we investigate the role of porosity on the oxygen release of mesoporous perovskite oxides and demonstrate how the combination of these two parameters affects methane and carbon monoxide oxidation. We prepared mesoporous SrTi0.65Fe0.35O3-δ perovksites with SSA ranging from 45 to 80 m2/g via a template-free approach [2]. Combining thermal analyses with in situ synchrotron X-ray diffraction under Ar-atmosphere we showed that the material with least porosity does not release surficial oxygen species as the more porous counterparts. Instead much larger desorption of lattice oxygen is observed, as result of the larger lattice strain and higher Fe(IV) concentration.
This had significant effects on the catalytic performance of the materials. For low-temperature reactions as the CO oxidation the highly porous perovskite shows better performance due to the higher SSA and larger surface defect concentration. In case of high temperature reactions as methane combustion, the contribution of lattice oxygen is more relevant and the least porous material achieves the same performance as the high porous systems.
Hence, even though nanoporosity is usually considered beneficial for catalysis applications, mere maximization of the SSA is not necessarily of help and oxygen defect location (surface, bulk) and concentration need to be taken into account for the design of nanostructured catalysts.
References:
[1] Y. Cao, M. J. Gadre, A. T. Ngo, S. B. Adler, Dane D. Morgan, Nat. Commun. 2019, 10, 1346.
[2] B. Kayaalp, S. Lee, K. Klauke, S. Jongsu, L. Nodari, A. Kornowski, W. Jung, S. Mascotto, Appl. Catal. B Environ. 2019, 245, 536–545.
[3] B. Kayaalp, S. Lee, L. Nodari, J. Seo, S. Kim, W. Jung, S. Mascotto, ACS Appl. Nano Mater. 2020, acsanm.0c02456.
ZnSnN$_{2}$ is an earth-abundant semiconductor with a predicted direct bandgap between 1.12-2.09 eV, based on DFT calculations.$^{1}$ Thus, it has been considered as a potential absorber material for solar cells. Recently, a numerical device simulation based on reported experimental material properties found a theoretical maximum efficiency of η ≈ 22% of for a ZnSnN$_{2}$ based solar cell.$^{2}$
Still, the fundamental study of structural properties of ZnSnN$_{2}$ is essential to facilitate the development of high-efficiency solar cells. Well crystallised bulk ZnSnN$_{2}$ is key to an in-depth study on its material properties, while thin-film ZnSnN$_{2}$ may hinder advanced studies due to preferred orientation and low crystallinity. However, the narrow stability region of ZnSnN$_{2}$ due to the small decomposition energy,$^{3}$ and the low decomposition temperature of ZnSnN$_{2}$$^{4}$ hamper the preparation of bulk ZnSnN$_{2}$.
In this work, we report a convenient pathway to obtain well-crystallised bulk zinc tin oxide nitrides as approximant towards ZnSnN$_{2}$ at ambient pressure and open the door to investigate structure-property relationships based on bulk samples. We achieved zinc tin oxide nitrides (Zn$_{1+x}$Sn$_{1-x}$N$_{2-2x}$O$_{2x}$) in the form of well-crystallised powder through a solid-state reaction route. This method further allows advanced characterisations that require bulk material and/or well-crystallised samples. We performed XRD experiments and interconnected it with a chemical analysis (XRF) to investigate the chemical composition and structural properties of the synthesised material. Using Raman spectroscopy, we compared the synthesised compound with reported ZnSnN$_{2}$ thin films.$^{5}$ The optical bandgap value of our powder material is in the range of the values reported by thin-film ZnSnN$_{2}$.$^{6}$ By correlating the synthesis conditions with the structural properties of the synthesised Zn$_{1+x}$Sn$_{1-x}$N$_{2-2x}$O$_{2x}$, we are now able to optimise the synthesis route. This will allow us to reduce the oxygen content in the material in a controlled way to obtain bulk ZnSnN$_{2}$ and tailor the materials properties.
Reference:
1. N. Feldberg, J. Aldous, W. Linhart, L. Phillips, K. Durose, P. Stampe, R. Kennedy, D. Scanlon, G. Vardar and R. Field III, Appl. Phys. Lett., 2013, 103, 042109.
2. A. Laidouci, A. Aissat and J. Vilcot, Sol Energy, 2020, 211, 237-243.
3. S. Chen, P. Narang, H. A. Atwater and L. W. Wang, Adv. Mater., 2014, 26, 311-315.
4. F. Kawamura, N. Yamada, M. Imai and T. Taniguchi, Cryst. Res. Technol., 2016, 51, 220-224.
5. P. C. Quayle, G. T. Junno, K. He, E. W. Blanton, J. Shan and K. Kash, Phys. Status Solidi B, 2017, 254, 1600718.
6. T. D. Veal, N. Feldberg, N. F. Quackenbush, W. M. Linhart, D. O. Scanlon, L. F. Piper and S. M. Durbin, Adv. Energy Mater., 2015, 5, 1501462.
Our quest to find new materials to be utilised in technological applications leads us more and more towards solid solutions between different materials. These solid solutions allow for the fine-tuning of desired material properties, but also pose additional problems in experimental characterisation and theoretical modelling. While we’re able to deal with fractional occupancies of Wyckoff positions in experimental investigations, this is not the case for theoretical materials modelling based on density functional theory, and we have to resort to additional methods to properly model the structural, electronic, and optical properties of solid solutions.
Here, we’re using first-principles calculations based on density functional theory to shed some light into the structure-property relations in the (Cu,Ag)$_2$ZnSnSe$_4$ and (FA,Cs)PbI$_3$ solid solutions (FA: formamidinium). While (Cu,Ag)$_2$ZnSnSe$_4$ only requires the mixing over different Wyckoff positions, in (FA,Cs)PbI$_3$ we additionally have to account for the rotations of the FA cation. For both systems, in order to simulate the different concentrations within the solid solution, we’re employing a supercell approach. All our structure models are geometry optimised employing the recently developed SCAN exchange and correlation functional. In order to obtain more reliable electronic and optical properties, selected optimised structures are subjected to one-shot calculations employing the more accurate hybrid functional HSE06.
This work made use of computational resources provided by the North-German Supercomputing Alliance (HLRN).
Zirconium dioxide (ZrO2) has been of major industrial and scientific interest over the past decades for its wide range of applications, in particular thanks to its catalytic properties. Regardless the multiple synthesis routes employed, undoped bulk ZrO2 is stabilized in the monoclinic structure (m-ZrO2) at ambient temperature and atmospheric pressure. However, these last years, studies showed that it was also possible to stabilize pure t-ZrO2 without cationic substitution. To do so, three main effects are identified in the literature: (i) the presence of oxygen vacancies, (ii) the existence of structural similarities, and (iii) the size effect, with the existence of a critical size below which pure t-ZrO2 is formed.
In this presentation we will introduce the synthesis of quasi pure t-ZrO2 nanocrystals in supercritical fluids using borderline nonhydrolytic sol−gel (B.N.H.S.G.) conditions. The term borderline is used to express the nuance from nonhydrolytic sol−gel (N.H.S.G.) reactions when small amounts of water molecules are generated in situ from solvent (alcohols) decomposition to trigger hydrolysis/condensation. This amount of water being controlled, the reaction kinetics can be tuned and slow down. This enabled us to performed in situ total scattering measurements in order to catch the various stages of the nanocrystal formation upon various conditions (temperature, nature of the alcohols and presence of surfactants). These observations where combined to various ex situ characterizations (Raman, PDF, EXAFS, HR-TEM, XRD, etc.) to discuss the existence of a critical size below which pure t-ZrO2 is formed, as reported in literature and propose a formation mechanism in this specific synthesis route.
2D materials are considered as unique class of modern materials. Understanding the mechanisms behind the exfoliation processes enables us to significantly enhance processing potential of 2D materials. In-situ synchrotron X-ray characterization is employed to study the temporal changes of hexagonal-boron nitride (h-BN) while its initial processing from bulk 3D crystalline material towards its 2D counterpart. In situ X-ray powder diffraction (XPDF) experiment is conducted with thermal cycle that heating bulk h-BN up to 1273 K and subsequent cooling. The results show a linear expansion in c-axis direction of h-BN crystals as commonly understanding, however a contraction behaviour in a-axis direction is observed up to around 750 K during heating process, followed by an expansion behaviour when temperature over 750 K. Characterization particularly indicates structural changes of long-range order favourable for exfoliation between the range of 750 K to 950 K. With the consideration of thermal oxidation studies also, a hypothesis of thermal assisted exfoliation with oxygen interstitial and substitution of nitrogen at high temperature is proposed through our studies to drive the exfoliation mechanisms.
Oxide-supported nanoparticles are important heterogeneous catalysts. The nanoparticles shapes and type of facets are decisive for the catalyst activity and lifetime. During a catalytic reaction, the nanoparticle may be subject to shape changes, and segregation in alloys may adjust the termination of the surface to a changing gas environment.
Here we report on the evolution of the 3D strain state in a single alloy PtRh nanoparticle operando followed by coherent X-ray diffraction imaging (CXDI). At a temperature of T=700 K the nanoparticle environment was switched between the gas compositions (I) inert Ar, (II) CO+Ar, (III) CO+O$\textrm{}_{2}$+Ar and (IV) CO+Ar resembling different adsorption and catalytic reaction scenarios on the nanoparticle surface.
SrTiO$\textrm{}_{3}$ supported nanoparticles were grown by co-deposition of Pt and Rh and annealed in UHV to induce the equilibrium shape. A single nanoparticle was pre-selected in an SEM and subsequently, hierarchical Pt fiducial markers were deposited in the vicinity of the selected nanoparticle and used to re-locate the same particle in the X-ray beam.
The nanoparticle exhibited solely low index <100> and <111> type facet surfaces, intriguingly showing distinct, facet-family specific strain states. Under the catalytic reaction condition (III) we observed significant strain relaxations for all facets accompanied with a preferential segregation of Rh to the nanoparticle surface, in line with density functional theory calculations (DFT). The Rh enrichment on the facets turned out to be non-reversible under the subsequent CO reduction condition (IV) as compared to the identical previous gas condition (II).
Tracking the dynamics of facet-specific structural reorganizations of the nanoparticle is one key for the future design of heterogeneous catalysts with optimized efficiency and selectivity.
Selective in-situ exsolution of catalytically active metals from doped perovskites during methane dry reforming
Florian Schrenk, Lorenz Lindenthal, Hedda Drexler, Raffael Rameshan, Christoph Rameshan
Institute of Materials Chemistry, Technische Universität Wien, Austria
Perovskite type oxides, doped with catalytically active metals, have shown great potential to catalyse MDR (Methane Dry Reforming) [1]. These materials can undergo exsolution, the formation of metallic nanoparticles on the surface, of B-site elements if reducing conditions are applied [2]. These exsolved nanoparticles are leading to an increase in catalytic activity. A Ni-doped perovskite (Nd0.6Ca0.4Fe0.97Ni0.03O3) and a Co-doped perovskite (Nd0.6Ca0.4Fe0.9Co0.1O3) were investigated in MDR conditions with a CH4 excess of 2:1 over CO2. To investigate the changes the catalyst undergoes during the reaction in situ NAP XPS (Near Ambient Pressure X-ray Photoelectron Spectroscopy) as well as in situ XRD (X-Ray Diffraction) experiments were performed. The XRD data showed the formation of a bcc phase at higher temperatures which cannot be assigned to Fe or the dopant (Ni/Co) due to the bad signal to noise ratio (Figure 1). The XPS data reveals that Ni is exsolving before Fe, as the Ni2p signal is shifting from the oxidized state into a metallic state between 600 °C and 650 °C and the Fe2p signal does not show a metallic component even at 700 °C, as seen in Figure 2. For the Co-doped catalyst, the formation of a metallic Co component was observed while no metallic Fe was detected.
Figure 1: in-situ XRD diffractograms of the Ni-doped catalyst with a CH4:CO2 ratio of 2:1 and temperature steps from 500 °C to 700 °C. The phases observed could be assigned to a perovskite phase (blue) as well as a brownmillerite phase with ordered oxygen vacancies (grey) during all temperatures. Forming at higher temperatures a CaCO3 (violet) and a bcc Phase, stemming ether from Ni or Fe (green), could be detected.
Figure 2: Comparison of the Fe2p and Ni2p transitions in the in-situ NAP XPS experiment of the Ni-doped catalyst. The sample was oxidized at 1 mbar O2 before the reaction, afterwards an atmosphere of 1 mbar CH4 and CO2 in a ratio of 2:1 was set and temperature steps between 500 °C and 700 °C were performed. A metallic component (blue) is forming between 600°C and 650 °C for Ni, whereas the Fe transition does not so such a component even at 700 °C.
References:
[1] D. Pakhare and J. Spivey, "A review of dry (CO2) reforming of methane over noble metal catalysts," Chemical Society Reviews, vol. 43, no. 22, pp. 7813-7837, Nov 2014, doi: 10.1039/c3cs60395d.
[2] L. Lindenthal et al., "Modifying the Surface Structure of Perovskite-Based Catalysts by Nanoparticle Exsolution," Catalysts, vol. 10, no. 3, Mar 2020, Art no. 268, doi: 10.3390/catal10030268.
Doping is a well-known method for improving gas sensing responses by metal oxide based functional materials.[1] And the plausible explanations provided in justification of using a specific dopant have been changes in material crystallinity, particle size, morphology and so on; but these ideas alone aren’t able to clearly highlight the fundamental changes and intricacies of a system that exhibits improved performance by virtue of doping.[2] In this context, we have tried to analyze improved ammonia sensing responses by vanadium doped tin oxide nano-particles of formula Sn1-xVxO2 with respect to crystal structure and surface structural aspects.[3] While the doped samples showed a nearly four-fold improved response as compared to pure SnO2, the sample Sn0.696V0.304O2 showed 1.2 times improved response than Sn0.857V0.343O2. Structural analyses by Rietveld refinement[4] revealed reduction of unit cell volume in doped samples, leading to generation of surface active sites up to 1019/mm3 of doped sample, explaining improved response by increase in surface interaction. Surface structure analyses by XPS reveal presence of 1.2 times excess surface positive charge in Sn0.857V0.343O2 as compared to Sn0.696V0.304O2. Considering the concept of charge immobilization by surface electronic states in the former, the variable sensing responses amidst the doped samples can be explained. The specific role of vanadium ion in improving ammonia sensing responses by pure SnO2 has been delineated.
References:
[1] Morrison, S. R. Mechanism of Semiconductor Gas Sensor Operation Sensors and Actuators 1987, 11, 283 – 287.
[2] Mirzaei, A.; Lee, J. H.; Majhi, S. M.; Weber, M.; Bechelany, M.; Kim, H. W.; Kim, S. S. Resistive gas sensors based on metal-oxide nanowires J. Appl. Phys. 2019, 126, 241102.
[3] Rietveld, M. H. A profile refinement method for nuclear and magnetic structures J. Appl. Crystallogr. 1969, 2, 65-71.
[4] N. Chakraborty, A. Sanyal, S. Das, D. Saha, S. K. Medda and S. Mondal, Ammonia Sensing by Sn1-xVxO2 Mesoporous Nanoparticles, ACS Appl. Nano Mater. 2020, 3, 8, 7572-7579.
Heteroanionic hydrides are an emerging class of compounds with representatives showing hydride ion conductivity [1] or catalytic activity [2]. Their properties are fundamentally linked to their anionic substructure; for example, might a difference between ordered and disordered anions change their behavior from a conducting to an isolating behavior [3].
From the solid-state reaction of Li2O, LaN and LaH3, we obtained the new nitride hydride oxide LiLa2NH2O as a black powder. It crystallizes in the K2NiF4 structure type (I4/mmm, a = 3.65431(6) Å, c = 13.3570(3) Å) and can be described as an aliovalent substitution product (2 O2- → N3- + H-) of the hydride ion conductor LiLa2HO3 [1]. The analysis of the anion substructure demanded the combination of different methods. We therefore performed neutron powder diffraction measurements on both hydride LiLa2NH2O and deuteride LiLa2ND2O (coherent scattering lengths bc(H) = -3.7 fm, bc(D) = 6.7 fm) in addition to powder X-ray diffraction and nuclear magnetic resonance spectroscopic analysis.
H/D and N/O show a separation on two crystallographic sites 4d and 4e with only slight but significant mixing. Additionally, both sites are significantly underoccupied, resulting in a charge imbalanced composition. H/D occupies favorably the Li-rich site 4d, while N and O share the La-rich 4e position (Figure 1). Both sites are coordinated in a distorted octahedral fashion with Li situated on opposite vertices of the H-rich polyhedron with short Li-H distances (1.83 Å; LiH: 2.04 Å).
Figure 1. Crystal structure of LiLa2NH2O (left) and coordination polyhedra of the H-rich site (4d, middle) and N/O-rich site (4e, right).
[1] G. Kobayashi et al., Science 2016, 351, 1314-7.
[2] M. Kitano et al., J. Am. Chem. Soc. 2019, 141, 20344-53.
[3] H. Nawaz et al., Chem. Commun. 2020, 56, 10373-6.
The development of second-generation short-pulse laser-driven radiation sources requires a mature understanding of the relativistic laser-plasma processes such as heating and transport of relativistic electrons as well as the development of plasma instabilities. Accessing these dynamic effects occurring on femtosecond and nanometer scales experimentally is very difficult but it is crucial to understand the behavior of matter under the extreme conditions, which follow the interaction of solids with ultra-intense laser irradiation.
In a first experiment in 2014 at the Matter of Extreme Conditions facility at LCLS we demonstrated that Small Angle X-ray Scattering (SAXS) of femtosecond x-ray free electron laser pulses is able to make these fundamental processes accessible on the relevant time and length scales in direct in-situ pump-probe experiments [Kluge et al., Phys. Rev. X 8, 031068 (2018)]. Here we report on a follow-up experiment with significantly higher pump intensity reaching the relativistic intensity domain, improved targetry, XFEL shaping, and particle diagnostics. We give an overview of the new capabilities in combining a full suite of particle and radiation diagnostics and SAXS. In particular, probing at resonant x-ray energies has shown to give new insight into the ionization process, plasma opacity and density by studying asymmetries in SAXS patterns from nanostructured grating targets [Gaus et al., arXiv: 2012.07922 (under review)].
Scientific advances are often enabled by either new emerging techniques or a previously unconsidered combination of existing methods. Particularly synchrotron X-ray diffraction (XRD) has led to large advances in our understanding of materials under high pressure and temperature conditions. Especially its combination with diamond anvil cells (DAC) has been very fruitful and, therefore, almost every 3rd generation synchrotron source in the world has now one or several beamlines dedicated to high pressure DAC research.
On the other hand, in the regime of X-ray free-electron lasers (XFEL), which provide previously unprecedented brightness in a single X-ray pulse, high-pressure and temperature XRD experiments as of today are mainly conducted with a combination of laser driven shock. The absence of DAC research at these facilities is mainly due to a combination of two factors: either the XFEL sources provide only a relatively low photon energy (<11 keV) leading to strong absorption of the X-rays in the diamond anvils as well as a small angular XRD coverage; or if the pulse energy is high enough (e.g. SACLA up to 25 keV on the fundamental) repetition rate on the order of only 10 to 120 Hz is not fast enough to provide significant advantage over 3rd generation synchrotron sources for time-resolved studies, such as the dynamic piezo-driven DAC.
The European XFEL (EuXFEL) in Schenefeld, Germany, is now capable of providing X-ray photons with energies up to 25 keV and a repetition rate of 4.5 Mhz and thus, facilitates the opportunity of combining DAC-XRD experiments with the unique properties of XFEL radiation sources.
Here we want to present the new DAC setup dedicated to XRD studies at the high energy density (HED) instrument of the EuXFEL. This setup has been provided through the Helmholtz International Beamline for Extreme Fields (HiBEF) user consortium and is situated in the interaction chamber 2 of the HED instrument. Currently, two sample platforms are available in the vacuum chamber: the first is a combination of standard or membrane DACs, for use with time resolved optical spectroscopy as well as pulsed laser heating, and the second provides capabilities and space for dynamic DACs with ultrafast piezo driven compression drivers.
The primary goal of both setups is to utilize the high brightness of the EuXFEL source, which permits good quality XRD images, comparable to several seconds of exposure in a 3rd generation synchrotron, even from a single X-ray pulse. The EuXFEL provides bursts of X-ray pulses within a so-called pulse-train with a frequency of 4.5 MHz, equating to 220 ns between each pulse. In combination with an AGIPD detector currently commissioned at the instrument, images will be collected with 4.5 MHz, facilitating the study of physical phenomena by XRD with a unique time resolution.
In the standard DAC setup, the thermal response due to single laser heating pulses or heating by intense X-ray pulses can be investigated by a combination of spectroradiometric measurements (utilizing a streak camera) and XRD on a submicrosecond timescale without the need of collecting multiple iterations in a pump-probe experiment, as performed previously at 3rd generation synchrotron facilities. The dynamic DAC setup enables the study of materials under fast compression and closes the strain rate gap between these type of experiments at synchrotron facilities and shock compression experiments further.
First experiments utilizing the standard DAC setup have been conducted during a community assisted commissioning beamtime in October 2019 (Proposal number 2292, PI R.S. McWilliams). Many exciting new results have been obtained, but also challenges arising from the nature of an XFEL source have been identified.
We will present the setup, its capabilities and some of the first interesting results in this contribution.
Acknowledgments: The authors are indebted to the HiBEF UC for the provision of instrumentation and Staff that enabled this experiment. We acknowledge European XFEL in Schenefeld, Germany, for provision of X-ray free-electron laser beamtime at Scientific Instrument HED (High Energy Density Science) and would like to thank the staff for their assistance.
Magnetic materials, in particular molecular magnets, can display remarkable, aesthetically pleasing and elegant structures, although most promising properties have been detected in simple mononuclear compounds [1]. The highly interdisciplinary field of molecular magnetism has been defined by Oliver Kahn as study of "magnetic properties of isolated molecules and/or assemblies of molecules” [2]. Applications of molecular magnets are foreseen in high-density data storage and quantum computing. The latter might be significant not only for on-ground, but also for space applications (e.g. satellite quantum communications).
Crystal structures of molecular magnets, although not fully representative of the targeted applications, play an important role in resolution of magnetostructural correlations [3]. These correlations may be retrieved via special setups, such as high-pressure crystallography [4]. For polynuclear metal complexes (Figure 1) often problems with diffraction data quality and solvent disorder are faced [5].
References:
[1] A. Castro-Alvarez et al. 'High performance single-molecule magnets, Orbach or Raman relaxation suppression?' Inorg. Chem. Front. 7, 2478 (2020).
[2] O. Kahn 'Molecular Magnetism', VCH (1993).
[3] C. J. Milios et al. 'Hexanuclear manganese(III) single-molecule magnets ' Angew. Chem. 43, 210 (2004).
[4] A. M. Thiel et al., 'High-Pressure Crystallography as a Guide in the Design of Single-Molecule Magnets', Inorg. Chem. 59, 1682−1691 (2020).
[5] A. J. Tasiopoulos et al. 'Giant Single‐Molecule Magnets: A {Mn84} Torus and Its Supramolecular Nanotubes' Angew. Chem. Int. Ed. 43, 2117 –2121 (2004).
[6] M. Holynska et al. '[MnIII6O3Ln2] single-molecule magnets: Increasing the energy barrier above 100 K' Chem. Eur. J. 35, 9605-9610 (2011).
[7] M. Holynska et al. 'A Defect Supertetrahedron Naphthoxime-Based [Mn9(III)] Single-Molecule Magnet' Inorg. Chem. 52, 13, 7317–7319 (2013).
Hybrid halide perovskites are a new class of solution-processed semiconductors that combine low-temperature (<100 °C) synthesis, high charge carrier diffusion length and low defect density. The past few years, hybrid halide perovskites such as $CH_{3}NH_{3}PbI_{3}$ have shown promising results for the detection of high-energy ionizing radiation (X- and Gamma-rays).[1] Their large-scale commercialization is however hindered by their poor stability, owing to the volatility of the small organic cation $CH_{3}NH_{3}^{+}$.
2D layered hybrid halide perovskites $(R-NH_{3})_{2}PbX_{4}$ (R = organic chain, X = $Cl^{-}$, $Br^{-}$, $I^{-}$) have recently shown an increasing interest in the fields of solar cells and LEDs. This sub-class of perovskite crystallizes in a natural, self-assembled quantum well structure and possess several interesting features, among which a much better stability than their 3D counterparts.[2,3] We will present in this work the first solid-state ionizing radiation detector based on a 2D layered hybrid perovskite. This material can be deposited from solution in the form of micro-crystalline thin films that display a single crystalline orientation. We will expose the direct integration of this material onto a pre-patterned flexible substrate and demonstrate the effective detection of X-Rays with sensitivity values as high as 757 uC.Gy-1.cm-2 and a Limit of Detection (LoD) of 8 nGy.s-1, which is among the lowest reported value for solid-state detectors. 2D perovskites offers the prospects of flexible solid-state detectors capable of working at low radiation flux for real-time X-Ray dosimetry.
[1] L. Basiricò, S. P. Senanayak, A. Ciavatti, M. Abdi-Jalebi, B. Fraboni and H. Sirringhaus, Adv. Funct. Mater., 2019, 9.
[2] D. B. Mitzi, Journal of the Chemical Society, Dalton Transactions, 2001, 0, 1–12.
[3] J. V. Passarelli, D. J. Fairfield, N. A. Sather, M. P. Hendricks, H. Sai, C. L. Stern and S. I. Stupp, J. Am. Chem. Soc., 2018, 140, 7313–7323.
Figure caption. (a) Schematic of the device structure. Bottom: graphical representation of the $(R-NH_{3})_{2}PbX_{4}$ crystal structure projected along the direction <010> showing the stacking of the 2D layers. (b) Photograph (left) and microscope image (right) showing the crystal grains morphology close to the pixel area.
Research interest has increasingly focused on hybrid perovskites MABX3 like [CH3NH3]+ (MA), B = Pb and X = I or Cl as a future photovoltaic material. There is a strong demand to better understand the possible impact of various entropy contributions (stochastic structural fluctuations, anharmonicity and lattice softness) on the optoelectronic properties of halide perovskite materials and devices.1 There are essentially two sources of dynamic disorder in halide perovskites. One is the motion of the organic cations. FTIR [2] and quasi-elastic neutron scattering (QENS) [2] studies showed that chlorine substitution has a large influence on the rotational dynamics of the MA molecule in MAPbI3-xClx perovskites[3] since the chlorine substitution leads to a weakening of the hydrogen bridge bonds (these bonds connect the MA molecules with the [PbX6]- octahedra host structure).[3] Another source of dynamic disorder is the anharmonic motion of the halide atom. The analysis of the Pb L3-edge EXAFS Debye-Waller factor of chlorine-substituted MAPbI3 allows a direct determination of the influence of chlorine substitution on the anharmonicity of the lead-halide bond. This allows quantitative statements to be made about the effective pair potentials of the bond. The experimentally determined potential parameters can then be compared with computational results obtained, for example, from ab initio molecular dynamics simulations.
[1] Katan, C. et al, Nature Materials 2018, 17, 377
[2] G. Schuck, et. al., J. Phys. Chem. C, 2018, 122, 5227
[3] G. Schuck, et. al., J. Phys. Chem. C, 2019, 123, 11436
We report the fabrication of SrTiO3 thin films doped by Ni and its influence on the electronic structure. The SrTiO3 thin films were deposited by magnetron sputtering which is suitable for mass-production of samples adapted for nanoelectronic applications. The structure of the STO:Ni was investigated by XRD phase analysis. We evaluated the influence of Ni on crystallinity, the size of coherent diffract areas, and micro-stress in the lattice of STO as a function of Ni concentration[1]. The second part of the presentation deals with the study of the electronic band structure of STO films doped with Ni, high-quality ordered pristine and SrTiO3:Nix films with x=0.06 and 0.12 were prepared by pulsed laser deposition. Electronic band structure calculations for the ground state, as well as one-step model photoemission calculations performed by using the Korringa-Kohn-Rostoker Greens's function method, predicted the formation of localized 3d-impurity bands in the bandgap of SrTiO3 close to the valence band maxima. The measured valence bands at the resonance Ni2p excitation and band dispersion are in agreement with theory[2].
References:
1. Z. Jansa, L. Prusakova, F. Alarab, P. Sutta; Structural analysis of Ni-doped SrTiO3: XRD study, AIP Conference Proceedings 2131(1):020022, July 2019
2. F. Alarab, K. Hricovini, B. Leikert, L. Nicolai, M. Fanciulli, O. Heckmann, Ch. Richter, L. Prušáková, Z. Jansa, P. Šutta, J. Rault, P. Lefevre, M. Muntwiller, R. Claessen, and J. Minár; Photoemission study on pristine and Ni-doped SrTiO3 thin films, Materials Science, arXiv:2011.12684, November 2020
The ability to selectively take up and store gases is one of the promising properties of metal–organic frameworks (MOFs) already implemented for industrial applications. Judicious choice of secondary building units can allow for further catalyzing reactions with stored content; for example, much research is currently pursuing their use for filtration of chemical warfare agents. Recently, the Zr-based MOF UiO-67 was shown to effectively adsorb and decompose the nerve-agent simulant, dimethyl methylphosphonate (DMMP).
Various methods are available for probing the gas sorption and reaction pathway, but quantitative structural information on the localized binding is difficult to obtain. A better understanding of the binding behavior is necessary to improve the performance of these MOFs for chemical agent neutralization. Here, we demonstrate the quantitative tracking of both framework and binding component structures using in situ X-ray total scattering measurements of UiO-67 under DMMP exposure, pair distribution function analysis, and theoretical calculations. The adsorption and desorption of DMMP within the pores, association with linker-deficient Zr6 cores, and decomposition to irreversibly bound methyl methylphosphonate were directly observed and analyzed with atomic resolution.
Going forward, wider access to powerful synchrotron beamlines and robust in situ capabilities will allow for comprehensive investigations into the structural implications of the full processing procedure from activation to adsorption, reaction, and re-activation. The procedures developed in this study could help guide further investigations into processes in other MOF/functional systems.
Metal-organic frameworks (MOFs) are known for their versatile combination of inorganic building units and organic linkers, which offers immense opportunities in a wide range of applications. However, many MOFs are typically synthesized as multiphasic polycrystalline powders, which are challenging for studies by X-ray diffraction. Therefore, developing new structural characterization techniques is highly desired in order to accelerate discoveries of new materials. Here, we report a high-throughput approach for structural analysis of MOF nano- and sub-microcrystals by three-dimensional electron diffraction (3DED). A new zeolitic-imidazolate framework (ZIF), denoted ZIF-EC1, was first discovered in a trace amount during the study of a known ZIF-CO3-1 material by 3DED. The structures of both ZIFs were solved and refined using 3DED data. ZIF-EC1 has a dense 3D framework structure, which is built by linking mono- and bi-nuclear Zn clusters and 2-methylimidazolates (mIm-). The discovery of this new MOF highlights the power of 3DED in developing new materials and their applications.
Several metal-organic frameworks (MOF) excel in harvesting water from the air or as heat pumps as they show a steep step in the water isotherm at 10-30 RH%c [1]. Yet, a precise understanding of the water structure within the confined space of such MOF is still lacking. Here, we unravel the structural properties of CAU-10-H under various water content. We show that the water content can be tuned using the relative humidity, temperature and history of the sample. Previous studies have shown a structural phase transition from hydrated (non-centrosymmetric structure) to dry (centrosymmetric structure) [2]. Here in this contribution, we show that high resolution powder diffraction can allow to locate water molecules and the existence of various states of hydrated phases including centrosymmetric one.
This study besides bringing further insight into the water clusters present in this MOF enlights also the powerfulness of powder diffraction in the study of MOF materials.
[1] Wentao Xu, Omar M. Yaghi, ACS Cent. Sci. 2020, 6, 8, 1348–1354
[2] Dominik Fröhlich et al. J. Mater. Chem. A, 2016,4, 11859-11869
In the artificial self-assembling systems based on metal atoms and spacing ligands small variations of reagents, stoichiometry, solvents or concentration may cause drastic changes in the structure of the resulting supramolecular architectures [1,2]. Methodologically based rational supramolecular design requires the systematic study of the effects of variation of one of the parameters when other controllable synthetic conditions are kept as close as possible.
Having experience in using pentaphosphaferrocenes [CpRFe(η5-P5)] (CpR = η5-C5R5, R = Me, CH2Ph) as building blocks to construct coordination polymers and giant supramolecules via coordination of the cyclo-P5 ligand to coinage metal cations [3,4], we systematically investigated how the direction of one-pot self-assembly reaction of [Cp*Fe(η5-P5)] (A) with AgSbF6 and flexible aliphatic dinitriles NC(CH2)xCN (DNx) [5] depends on the length of the aliphatic chains in a range x = 1 – 10. We found that this reaction can lead to two distinct types of the products, namely, 1D–3D simple coordination polymers (CPs), or 3D supramolecular coordination polymers (SCPs), where huge polycationic nano-sized supramolecules are linked by the DNx spacers into 3D networks (Fig.). The value of x = 7 marks the borderline: for x < 7 the self-assembly leads to various 1D–3D CPs, while at x = 7 the system discontinuously switches to 3D SCP (SbF6)@(A)9Ag11(DN7)610 with huge, supramolecules of ø2.21 nm in size as nodes. For x = 8 – 10 the self-assembly leads to 3D SCPs (A)@(A)12Ag12(DNx)612 with spherical cationic supramolecules of 2.40 – 2.44 nm in size acting as nodes. The SCPs specifically encapsulate guests, SbF6- anion or A, inside the nodes, while the voids between the nodes in the 3D network are filled with solvent molecules and SbF6- counterions. All products are characterized by NMR spectroscopy, MS spectrometry and single-crystal X-ray diffraction at 10-90 K.
The research was partly performed at P11 and P24 beamlines on PETRA III at DESY. This work was supported by the German Research Foundation (DFG) within the project Sche 384/44-1.
[1] T. Schnitzer, G. Vantomme (2020) ACS Cent. Sci. 6, 2060.
[2] Y. Sun, C. Chen, P. J. Stang (2019) Acc. Chem. Res. 52, 802.
[3] E. Peresypkina, C. Heindl, A. Virovets, M. Scheer (2016) Structure and Bonding 174, 321.
[4] J. Schiller, A. V. Virovets, E. Peresypkina, M. Scheer (2020) Angew. Chem. Int. Ed., 59, 13647.
[5] E. Peresypkina, M. Bielmeier, A. Virovets, M. Scheer, Chem. Sci. (2020) 11, 9067–9071.
The targeted control of particle/crystallite size, crystallinity, and polymorphism is of crucial importance for many functional materials, in particular quantum materials$^\text{1}$. They are frequently synthesized by the facile sol-gel method which in a broader sense can be described as the conversion of molecular precursors in solution into inorganic solids via hydrolysis, condensation, and aggregation$^\text{2}$. The synthesis of pure nanocrystalline samples, however, can be very difficult if various stable and metastable phases exist often leading to co-crystallization. In this study, we use in situ total scattering and Pair Distribution Function (PDF) analysis to follow the transformation of molecular precursors into multiferroic Bi$_\text{2}$Fe$_\text{4}$O$_\text{9}$ with a second-scale time resolution. The precursors were synthesized by the sol-gel process using the respective metal nitrates and meso-erythritol as the complexing agent. We show how the crystallization pathways and kinetics of the target compound can dramatically be changed by variation of the synthesis medium and ratio of metal nitrate to the complexing agent and relate this to the precursor structure. As an example, using small amounts of complexing agent leads to a crystalline precursor which first gets amorphous at 613 K, crystallizes into BiFeO$_\text{3}$ at 706 K, and subsequently transforms into Bi$_\text{2}$Fe$_\text{4}$O$_\text{9}$ at 815 K. On the other hand, bigger amounts of complexing agent produce an amorphous precursor which directly crystallizes into Bi$_\text{2}$Fe$_\text{4}$O$_\text{9}$ at 762 K. Using PDF we reveal the importance of the initial gel structure in the overall crystallization behaviour of the system.
$^\text{1}$ Samarth, N. Nat. Mater., 2017, 16, 1068.
$^\text{2}$ Niederberger, M. Acc. Chem. Res., 2007, 40, 793.
The performance of magnetite-based devices and catalysts crucially depends on their surface structure and stoichiometry [1]. While annealing in ultra high vacuum and the adsorption of small molecules (partially) lift the subsurface cation vacancy reconstruction on Fe$_3$O$_4$ (001) surfaces [3,4,5], annealing under oxidising conditions results in the growth of new Fe$_3$O$_4$ layers involving near-surface cation transport [6].
To study the influence of O$_2$ pressure on cation transport in the Fe$_3$O$_4$ near-surface region, the homoepitaxial growth of Fe$_3$O$_4$ by molecular beam epitaxy was observed in-situ by surface X-ray diffraction (SXRD) at different pressures and growth rates.
Details about the grown structures and the growth process obtained from crystal truncation rods and X-ray intensity growth oscillations will be complemented by low energy electron diffraction and X-ray reflectivity data. These results will be presented in relation with their implications for cation transport in Fe$_3$O$_4$ [7].
References:
[1] Parkinson, G., Surf. Sc. Rep. 71, 272 (2016); [2] Bliem, R. et al., Science 346, 1215 (2014); [3] Arndt, B. et al., Chem. Comm. 1, 92 (2019); [4] Arndt, B. et al., Surf. Sci. 653, 76 (2016) [5] Arndt, B. et al., PCCP 22, 8336 (2020); [6] Nie, S. et al., J. Am. Chem. Soc. 135, 10091 (2013), [7] Dieckmann, R. et al., Ber. Bunsenges. Phys. Chem. 81, 344 (1977)
Caption:
Fig. 1: Growth oscillations observed by SXRD at (4 0 1.97) (blue), (4 0 1) (green) and (2 2 0.97) (yellow) indicating a layer by layer growth of half unit cells. Growth at 4$\times 10^{-6}$ mbar O$_2$ and a flux of 30 nA.
Misfit strain in crystalline core-shell nanowires can be elastically released by nanowire curvature in case of inhomogeneous shell growth around the nanowires 1. In this work, we performed time-resolved in-situ XRD investigations of the evolution of GaAs nanowires bending during the asymmetric growth of InxGa1-xAs shell without substrate rotation. By means of micro X-ray beam at beamline P23 and P09 at PETRA-III at DESY and a portable molecular beam epitaxy chamber (pMBE)2, this study gives insight into the temporal development of the bending as well as the strain in the core-shell nanowire. In particular, different bending directions of nanowires grown on Si with native oxide and thermal oxide were observed and the demonstration of the nanowire curvature as function of shell thickness showed nonlinear dependency.
References
1 Lewis R B, Corfdir P, Küpers H, Flissikowski T, Brandt O and Geelhaar L 2018, Nano Lett. 18 2343–50
2 Slobodskyy T, Schroth P, Grigoriev D, Minkevich A A, Hu D Z, Schaadt D M and Baumbach T 2012, Review of Scientific Instruments vol 83
Platinum electrocatalyst degradation forms a large barrier for the wide-spread application of electrolysers and fuel cells, which are crucial for a sustainable energy society. A detailed understanding of the catalyst surface structure during the chemical reaction is required to design more stable catalysts. We have developed a Rotating Disk Electrode (RDE) setup that enables a structural characterization by synchrotron High-Energy Surface X-Ray Diffraction (HE-SXRD) experiments while maintaining well-defined diffusion conditions and high catalytic reaction rates (current densities). With this setup we followed the oxidation of Pt(111) and Pt(100) model electrodes, from the Place-Exchange surface oxidation occurring around 1.1V until the formation of a (bulk) oxide at potentials relevant for the oxygen evolution reaction. In contrast with heterogenous oxidation experiments, no ordered oxide structures are observed.
Ferroelectric materials possess a spontaneous polarisation that can be electrically switched between different orientations. Compared to ferromagnetics, the domain walls are small, allowing memory cells of higher storage density. Thin films of ferroelectric materials allow to increase the storage density even further. Exemplarily, incipient ferroelectricity is found in strontium titanate SrTiO3 (STO) at a low transition temperature. This ferroelectricity can be stabilized by a variety of external factors such as doping, strain, electric field, isotope substitution etc., even up to room temperature.
Recently, we studied the effect of the electroformation of STO and the accompanied creation of the migration-induced field-stabilized polar (MFP) phase [1] extensively, i.e. with the newly developed approach of Resonantly Suppressed Diffraction (RSD) [2] at Beamline P23 of PETRA III. Because of the breakdown of Friedel's law under resonant conditions, RSD can be used to obtain information about the polarization state of polar materials, namely by monitoring the Bragg intensity while scanning the energy of the incident beam through the absorption edge of strontium.
Here, we transferred this methodology to ferroelectric STO thin films and measured the energy dependent intensities for different Bragg reflections. As underlying structure model, we combined the structure of the low temperature antiferrodistortive (AFD) phase and of a generalized MFP phase. The resulting structure is ferroelectric and rather unknown within the perovskites. The energy dependent intensities of the chosen reflections of simulated data were fitted against the experimental values. Additionally, we performed Density Functional Theory (DFT) calculations to determine the atomic displacements from the lattice parameters at the different low temperatures. The results show that the major structural components within those STO thin films are the AFD displacements, while the MFP displacements are negligible.
[1] J. Hanzig, M. Zschornak, F. Hanzig, E. Mehner, H. Stöcker, B. Abendroth, C. Röder, A. Talkenberger, G. Schreiber, D. Rafaja, S. Gemming, D. C. Meyer: Migration-induced field-stabilized polar phase in strontium titanate single crystals at room temperature, Physical Review B 88, 024104 (2013).
[2] C. Richter, M. Zschornak, D. Novikov, E. Mehner, M. Nentwich, J. Hanzig, S. Gorfman, D. C. Meyer: Picometer polar displacements in strontium titanate determined by a new approach of resonant x-ray diffraction, Nature Communications 9, 178 (2018).
While the silicon-rich members of the series Cu2Zn(Ge,Si)Se4 crystallize in wurtz-kesterite type structure [1], germanium-rich samples adopt a tetrahedral structure of the kesterite type [2]. Identification of the silicon site is straightforward from regular X-ray diffraction, as Si4+ is a light element and has less electrons than the other cations. However, Cu1+, Zn2+, and Ge4+ are all isoelectronic and have very similar form factors. The kesterite type of the cation distribution has been established by neutron diffraction [2].
We now applied anomalous X-ray diffraction to this system, using Rietveld refinement and Multiple Edge Anomalous Diffraction (MEAD) [1] with data taken at the K-absorption edges of Cu, Zn, and Ge. These energies are accessible at beamline KMC-2, BESSY II, Berlin [3]. In contrast to previous studies, where Sn4+ was the M(IV) species in the structure [1], in Cu2ZnGeSe4 all cations have very similar scattering power under normal conditions. This results in superstructure peaks (with respect to the cubic ZnS parent structure) that are very weak. For Rietveld analysis this is a drawback, as the optimization will be dominated by the main peaks of the parent structure. In MEAD, however, it increases the effect of the changing scattering power close the absorption edges. As a result, not only are Kesterite and Stannite types clearly distinguishable at the Cu-K edge (figure 1), also the Cu/Zn ordering within the Kesterite structure is clearly detectable and quantifiable at the Zn-K edge. The structure of the MEAD spectrum at the Ge-K edge was found to be very sensitive to the presence of vacancies at the Ge 2b site of the structure at the Si-free composition. Within the compositional range, Si4+ has very similar influence.
[1] D. M. Többens et al., Cation distribution in Cu2ZnSnSe4, Cu2FeSnS4 and Cu2ZnSiSe4 by multiple-edge anomalous diffraction. Acta Crystallographica B76, 1027-1035 (2020)
[2] G. Gurieva et al., Cu-Zn disorder in Cu2ZnGeSe4. A complementary neutron diffraction and
Raman spectroscopy study. Journal of Physics and Chemistry of Solids 99, 100-104 (2016)
[3] Helmholtz-Zentrum Berlin für Materialien und Energie, KMC-2: an X-ray beamline with dedicated diffraction and XAS endstations at BESSY II. Journal of large-scale research facilities, 2, A49 (2016)
Figure 1: Observed and simulated MEAD spectra of Bragg peak 011 of Cu2.03Zn1.060Ge0.947Se4. The structure is highly ordered Kesterite. The peak at the Ge-edge indicates ≤10% vacancies at the Ge 2b site.
Resonant X-ray elastic scattering (REXS) is a unique element, site, and valence specific probe to study the charge, spin and orbital degrees of freedom and multipole orders in solids and thin films [1,2]. This technique, which combines X-ray diffraction with X-ray absorption spectroscopy, has been successful in unraveling different order parameters and solving magnetic structures.
REXS is complementary to neutron techniques for magnetic structure determination. Several situations make it essential: when the magnetic species involved present a neutron absorption cross-section too large, like Eu, Dy, Gd… [3], when the magnetic moments cannot be determined unambiguously with neutron experiments [4], or when more than one magnetic species is involved.
Different types of data can be collected during a REXS experiments: intensities of a set of magnetic reflections, full linear polarization analysis of a specific magnetic reflection, or its azimuthal dependence. The analysis of these data is highly complex and no crystallographic software has been developed yet to enable users to solve magnetic structures from a REXS experiment.
MagStREXS is a crystallographic software dedicated to the determination of Mag-netic St-ructures through R-esonant E-lastic X-ray S-cattering and the preparation of magnetic diffraction experiments. It is under development since mid-2017 at beamline P09 [5] at PETRA III at DESY and based on CrysFML, a library developed to facilitate the creation of crystallographic software that includes some resources especially oriented to deal with magnetic structures.
Hereby, we will present an overview of MagStREXS, its current status and some of the magnetic structures which have already been solved with it in the field of highly correlated systems.
References
[1] J. P. Hill and D. F. Mc Morrow, Acta Cryst. A 52, 236-244 (1996)
[2] Y. Murakami and S. Ishihara, “Resonant X-Ray Scattering in Correlated Systems”, Springer Tracts in Modern Physics 269 (2017)
[3] T. Kurumaji, et al., “Skyrmion lattice with a giant topological Hall effect in a frustrated triangular-lattice magnet”,Science, 365, 914-918 (2019)
[4] J. Sears et al., “Ferromagnetic Kitaev interaction and the origin of large magnetic anisotropy in $\alpha$-RuCl$_3$”, Nature Physics 16, 837-840 (2020)
[5] J. Strempfer, S. Francoual, et al. Synchrotron Rad. 20, 541-549 (2013)
Agenda:
15:00 Willkommen
Sprecher: Prof. Ute Kolb (Uni Mainz) und Prof. Hans-Joachim Kleebe (TU Darmstadt)
15:10 Neubesetzung des AK Sprecheramts
Wahlvorschläge
15:40 Diskussion des AK3-Titels
Es wird vorgeschlagen, den Titel des AK3 von "Elektronenmikroskopie" auf "Elektronenmikroskopie und -kristallographie" zu erweitern.
16:00 Diskussion von möglichen Aktivitäten im AK3 (auch zu Pandemie-Zeiten)
17:00 Sitzungsende