Acta Cryst Research Articles

Dynamical refinement with multipolar electron scattering factors.

Dynamical refinement is a well established method for refining crystal structures against 3D electron diffraction (ED) data and its benefits have been discussed in the literature [Palatinus, Petříček & Corrêa, (2015). Acta Cryst. A71, 235-244; Palatinus, Corrêa et al. (2015). Acta Cryst. B71, 740-751]. However, until now, dynamical refinements have only been conducted using the independent atom model (IAM). Recent research has shown that a more accurate description can be achieved by applying the transferable aspherical atom model (TAAM), but this has been limited only to kinematical refinements [Gruza et al. (2020). Acta Cryst. A76, 92-109; Jha et al. (2021). J. Appl. Cryst. 54, 1234-1243]. In this study, we combine dynamical refinement with TAAM for the crystal structure of 1-methyluracil, using data from precession ED. Our results show that this approach improves the residual Fourier electrostatic potential and refinement figures of merit. Furthermore, it leads to systematic changes in the atomic displacement parameters of all atoms and the positions of hydrogen atoms. We found that the refinement results are sensitive to the parameters used in the TAAM modelling process. Though our results show that TAAM offers superior performance compared with IAM in all cases, they also show that TAAM parameters obtained by periodic DFT calculations on the refined structure are superior to the TAAM parameters from the UBDB/MATTS database. It appears that multipolar parameters transferred from the database may not be sufficiently accurate to provide a satisfactory description of all details of the electrostatic potential probed by the 3D ED experiment.

The unbearable burden of peer review?

The current situation of scientific manuscript peer review is discussed, both generally and as applied to Acta Crystallographica F - Biological Research Communications.

Welcoming five new Co-editors.

Five new Co-editors are appointed to the Editorial Board of Acta Cryst. D - Structural Biology.

A note on the Hendrickson-Lattman phase probability distribution and its equivalence to the generalized von Mises distribution.

Hendrickson & Lattman [Acta Cryst. (1970), B26, 136-143] introduced a method for representing crystallographic phase probabilities defined on the unit circle. Their approach could model the bimodal phase probability distributions that can result from experimental phase determination procedures. It also provided simple and highly effective means to combine independent sources of phase information. The present work discusses the equivalence of the Hendrickson-Lattman distribution and the generalized von Mises distribution of order two, which has been studied in the statistical literature. Recognizing this connection allows the Hendrickson-Lattman distribution to be expressed in an alternative form which is easier to interpret, as it involves the location and concentration parameters of the component von Mises distributions. It also allows clarification of the conditions for bimodality and access to a simplified analytical method for evaluating the trigonometric moments of the distribution, the first of which is required for computing the best Fourier synthesis in the presence of phase, but not amplitude, uncertainty.

Private glycan investigations and public video content.

Acta Cryst. F - Structural Biology Communications plans to introduce more video content to articles and Dialpuri et al. [(2024). Acta Cryst. F80, 30-35] provide an early example.

A triclinic polymorph of miconazole

The crystal structure of the new triclinic polymorph of miconazole {MIC; C18H14Cl4N2O; systematic name: (RS)-1-[2-(2,4-dichlorobenzyloxy)-2-(2,4-dichlorophenyl)ethyl]-1H-imidazole} is reported and compared with the monoclinic form of solvent-free miconazole previously reported [Kaspiaruk & Chęcińska (2022). Acta Cryst. C78, 343–350]. A comparison shows a different orientation of imidazole and one dichlorophenyl ring between polymorphic molecules. In the crystal structure of the title compound, only weak halogen bonds and C—H...π(arene) interactions are found. Hirshfeld surface analysis and energy framework calculations complement the comparison of the two polymorphic forms of the miconazole drug.

Machine learning in crystallography and structural science.

An overview of the virtual collection on machine learning (ML) in crystallography and structural science, as represented in Acta Crystallographica Sections A, B and D, IUCrJ and Journal of Synchrotron Radiation, is presented. Some terms and concepts related to artificial intelligence and machine learning are briefly introduced and described, and a short history of ML in structural science as it appeared in these IUCr journals is given to whet the appetite for the rest of the collection.

Sidey V.I. ON THE IONIC RADIUS OF THE CYANIDE ION

Sidey V.I. ON THE IONIC RADIUS OF THE CYANIDE ION

Temperature-dependent solid-state phase transition with twinning in the crystal structure of 4-meth-oxy-anilinium chloride.

At room temperature, the title salt, C7H10NO+·Cl-, is ortho-rhom-bic, space group Pbca with Z' = 1, as previously reported [Zhao (2009 ▸). Acta Cryst. E65, o2378]. Between 250 and 200 K, there is a solid-state phase transition to a twinned monoclinic P21/c structure with Z' = 2. We report the high temperature structure at 250 K and the low-temperature structure at 100 K. In the low-temperature structure, the -NH3 hydrogen atoms are ordered and this group has a different orientation in each independent mol-ecule, in keeping with optimizing N-H⋯Cl hydrogen bonding, some of which are bifurcated: these hydrogen bonds have N⋯Cl distances in the range 3.1201 (8)-3.4047 (8) Å. In the single cation of the high-temperature structure, the NH hydrogen atoms are disordered into the average of the two low-temperature positions and the N⋯Cl hydrogen bond distances are in the range 3.1570 (15)-3.3323 (18) Å. At both temperatures, the meth-oxy group is nearly coplanar with the rest of the mol-ecule, with the C-C-O-C torsion angles being -7.0 (2)° at 250 K and -6.94 (12) and -9.35 (12)° at 100 K. In the extended ortho-rhom-bic structure, (001) hydrogen-bonded sheets occur; in the monoclinic structure, the sheets propagate in the (010) plane.

Permissible domain walls in monoclinic MAB ferroelectric phases.

The concept of monoclinic ferroelectric phases has been extensively used over recent decades for the understanding of crystallographic structures of ferroelectric materials. Monoclinic phases have been actively invoked to describe the phase boundaries such as the so-called morphotropic phase boundary in functional perovskite oxides. These phases are believed to play a major role in the enhancement of such functional properties as dielectricity and electromechanical coupling through rotation of spontaneous polarization and/or modification of the rich domain microstructures. Unfortunately, such microstructures remain poorly understood due to the complexity of the subject. The goal of this work is to formulate the geometrical laws behind the monoclinic domain microstructures. Specifically, the result of previous work [Gorfman et al. (2022). Acta Cryst. A78, 158-171] is implemented to catalog and outline some properties of permissible domain walls that connect `strain' domains with monoclinic (MA/MB type) symmetry, occurring in ferroelectric perovskite oxides. The term `permissible' [Fousek & Janovec (1969). J. Appl. Phys. 40, 135-142] pertains to the domain walls connecting a pair of `strain' domains without a lattice mismatch. It was found that 12 monoclinic domains may form pairs connected along 84 types of permissible domain walls. These contain 48 domain walls with fixed Miller indices (known as W-walls) and 36 domain walls whose Miller indices may change when free lattice parameters change as well (known as S-walls). Simple and intuitive analytical expressions are provided that describe the orientation of these domain walls, the matrices of transformation between crystallographic basis vectors and, most importantly, the separation between Bragg peaks, diffracted from each of the 84 pairs of domains, connected along a permissible domain wall. It is shown that the orientation of a domain wall may be described by the specific combination of the monoclinic distortion parameters r = [2/(γ - α)][(c/a) - 1], f = (π - 2γ)/(π - 2α) and p = [2/(π - α - γ)] [(c/a) - 1]. The results of this work will enhance understanding and facilitate investigation (e.g. using single-crystal X-ray diffraction) of complex monoclinic domain microstructures in both crystals and thin films.

Nb-Based Oxides As High Power Negative Electrode Materials

Today, one of the main challenges of lithium-ion batteries is to have the ability to charge faster and to provide high power during longer periods, thus allowing a larger development of intermittent electric power sources [1]. The actual negative electrode materials (graphite and silicon mainly) cannot sustain such high rate capabilities. In this work, we are therefore investigated some materials of the plentiful family of niobium-based oxides. A presentation of old and interesting structures will be briefly reviewed. As an example, the case of KTiNbO5 will be discussed and proposed as efficient negative electrode materials for next generation of lithium ion batteries.The layered KTiNbO5 with a two-dimensional framework represents a playground to produce a large range of closely related phases.[2] The protonated HTiNbO5 analogue is obtained by ion exchange in acidic solution and it preserves a layered structure with a smaller interlayer distance. After dehydration of HTiNbO5 at 400°C, the so-obtained Ti2Nb2O9 phase displays a 2D arrangement with empty channels unlike tunnels of H(K)TiNbO5.In this work, all the synthesized phases were studied as negative electrode materials in lithium-ion batteries. Tested in 1M LiPF6 in EC/DMC between 1.0V and 3.0V vs Li/Li+, these phases have shown different electrochemical behaviors. When HTiNbO5 exhibits a typical plateau during the charge/discharge experiment corresponding to a biphasic phenomenon, lithiation of Ti2Nb2O9 is governed by a solid—solution mechanism. For a better understanding of the charge storage mechanism, we have combined electrochemical experiments with in situ XRD measurements. We have shown that multielectron redox and corner/edge sharing system of Ti/Nb octaedra are at the origin of an interesting capacity of more than 100 mAh.g-1 at a rate of 0.2 A.g-1. A good observed cyclability (< 500 cycles) is in accordance with in situ XRD results showing a reversible behavior of the structure during cycling. Another synthesis method, using Chimie Douce techniques, leads to nanoparticules for both HTiNbO5 and Ti2Nb2O9 and allows an increase of the electrochemical performance of these materials. References : [1] Choi, C. et al, Nature Rev. Mat. 5, 5-19 (2020).[2] A. D. Wadsley, Acta Cryst. 623, 17-41 (1964).

Shaping the future of Acta Crystallographica F: unveiling our vision.

One of the Editors of Acta Cryst. F - Structural Biology Communications describes what the future holds for the journal.

Electron traps and energy storage: modeling a bright path to the future.

By employing time-dependent density functional theory for solid-state chemistry, the research presented by Andrii Shyichuk [Acta Cryst. (2023), B67, 437-449] significantly contributes to the understanding of electron/hole traps in doped materials.

Mythical compounds.

There is a need for validation methods to ensure the quality and consistency of reported data, but a recent article by Raymond and Girolami [Acta Cryst. (2023), C79, https://doi.org/10.1107/S2053229623007088] will alert chemists, crystallographers, referees, and editors to not always trust the crystal structure but also to ensure that the chemistry is consistent with previous chemistry.

Using structural genomics depositions in undergraduate teaching of protein crystallography: everybody wins.

The article by Moorefield et al. [(2023), Acta Cryst. F79, 257-266] demonstrates how structural genomics depositions can be used in undergraduate teaching.

Development and Evaluation of an Efficient Second Order Non-Linear Optical Single Crystal – 2-(3-Aminopyridinium-1-yl)-3-Carboxy-Proponate Monohydrate

A slow evaporation solution approach was used to create high-quality single crystals of 2-(3-aminopyridinium-1-yl)-3-carboxyproponate monohydrate (3ACPM). The single crystal X-ray diffraction was used to determine the crystal system and lattice characteristics. Software called Krystal Shaper was used to mimic the morphology of the 3ACPM. To evaluate the optical transmittance, UV-vis spectral analysis was used. The Nd:YAG laser was used to assess the laser-induced surface damage threshold (LISDT) of 3ACPM single crystal. The presence of second harmonic generation (SHG) was evaluated using the Kurtz-Perry powder method. Full Text: PDF References Y. Zhang, H. Li, B. Xi, Y. Che,vJ. Zheng, "Growth and characterization of l-histidine nitrate single crystal, a promising semiorganic NLO material", Mater. Chem. Phys. 108, 192 (2008), CrossRef S. Draguta, M.S. Fonari, A.E. Masunov, J. Zazueta, S. Sullivan, M.Y. Antipin, T.V. Timofeeva, "New acentric materials constructed from aminopyridines and 4-nitrophenol", Cryst. Eng. Comm. 15, 4700 (2013) CrossRef G. Peramaiyan, R. Mohan Kumar, "Nonlinear optical and laser damage threshold studies of an ammonium p-toluenesulfonate crystal", Appl. Phys. A 119, 707 (2015), CrossRef G.M. Corrales, D. Morales-Morales,S. Hernandez-Ortega, J.J. Campos-Gaxiolaa, A. Cruz Enrıquez, "2-(3-Aminopyridinium-1-yl)-3-carboxypropanoate monohydrate", Acta Cryst. E68, o853 (2012), CrossRef S.K. Kurtz, T.T. Perry, "A Powder Technique for the Evaluation of Nonlinear Optical Materials", J. Appl. Phys. 39, 3798 (1968), CrossRef S. Panchapakesan, K. Subramani, B.Srinivasan, "Growth, characterization and quantum chemical studies of an organic single crystal: 3-Aminopyridine 4-Nitrophenol for opto-electronic applications", J. Mater. Sci: Mater. Electron. 28, 5754 (2017), CrossRef

Making your raw data available to the macromolecular crystallography community.

A recent editorial in the IUCr macromolecular crystallography journals [Helliwell et al. (2019), Acta Cryst. D75, 455-457] called for the implementation of the FAIR data principles. This implies that the authors of a paper that describes research on a macromolecular structure should make their raw diffraction data available. Authors are already used to submitting the derived data (coordinates) and the processed data (structure factors, merged or unmerged) to the PDB, but may still be uncomfortable with making the raw diffraction images available. In this paper, some guidelines and instructions on depositing raw data to Zenodo are given.

In data we trust: X-ray diffraction experiments for charge density investigations.

A short commentary is given on the paper by Vosegaard et al. [Acta Cryst. (2023), 79, https://doi.org/10.1107000/S205252062300776X], which compares charge density models derived from four datasets measured on conventional diffractometers with the results of a high-quality dataset from SPring-8.

Low Temperature Niobium Tungsten Oxides as Anodes for Fast Charging Li-Ion Batteries

The development of fast-charging Li-ion batteries is one of the important steps in building electric vehicles that need high power and fast charging. The reduction in the particle size to the nanometre length scale drastically improves the charging rate by increasing the surface area but lowers the volumetric energy density and can potentially result in more rapid degradation of the electrolyte via electrode-catalysed reactions. Recent reports show that niobium tungsten oxides (NbWOs) with µm sized particles serve as good anode materials for Li-ion batteries having high volumetric capacity with good cyclability at high rates while avoiding solid electrolyte interphase formation (SEI). The high rate performance of NbWOs is attributed to the topochemical charge storage mechanism that exhibits (i) minimal, highly reversible structural changes during the charge-discharge cycles, (ii) high Li-ion diffusion coefficients due to the presence of fast conducting tunnels, and (iii) high electronic conductivity upon lithiation.1,2 The NbWOs are known to crystallize into two families of different crystal structures depending on the composition and synthesis conditions. The NbWOs phases can either have tungsten bronze-type structures or block-type structures (commonly referred to as Wadsley-Roth phases). Different NbWO phases are reported in the literature3 which could serve as potential anode materials with better performance.In this work, a series of new NbWO phases have been synthesized at reduced annealing temperatures and the structure of these phases has been established using X-ray and neutron diffraction data. The electrochemical properties of NbWO/Li half cells were examined through a series of galvanostatic (dis)charge tests at varying current rates ranging from 0.2 C to 20 C. The NbWO phases delivers a high reversible capacity of 200 and 130 mAh/g at 0.2C and 10 C respectively vs. Li metal. Here we use operando powder X-ray diffraction to investigate the structural changes occurring at the anode during the charge-discharge process in the newly synthesised NbWO phases. Reference s : 1 K. J. Griffith, K. M. Wiaderek, G. Cibin, L. E. Marbella and C. P. Grey, Nature, 2018, 559, 556–563.2 C. P. Koçer, K. J. Griffith, C. P. Grey and A. J. Morris, Chem. Mater., 2020, 32, 3980–3989.3 N. C. Stephenson, Acta Crystallogr. Sect. B Struct. Crystallogr. Cryst. Chem., 1968, 24, 637–653. Figure 1

Combinatorial aspects of the Löwenstein avoidance rule. Part III: the relational system of configurations.

This paper introduces a new method of determining the independence ratio of periodic nets, based on the observation that, in any maximum independent set of the whole net, be it periodic or not, the vertices of every unit cell should constitute an independent set, called here a configuration. For 1-periodic graphs, a configuration digraph represents possible sequences of configurations of the unit cell along the periodic line. It is shown that maximum independent sets of the periodic graph are based on directed cycles with the largest ratio. In the case of 2-periodic nets, it is necessary to draw a different configuration digraph for each crystallographic direction defining a linkage between neighbouring cells, a concept known as a binary relational system. The two possible systems are analysed in this paper: \overrightarrow{\bf{sql}} is associated to nets displaying linkages between unit cells along the directions 10 and 01, and \overrightarrow{\bf{hxl}} is associated to nets also displaying linkages between cells along the direction 11. For both kinds of nets, a maximum independent set is obtained as a homomorphic image from \overrightarrow{\bf{sql}} or \overrightarrow{\bf{hxl}} to the respective configuration system. The method is illustrated with some of the 2-periodic nets listed on the Reticular Chemistry Structure Resource site; it is shown that it provides a rigorous solution to the case of the net sdh that was not satisfactorily solved in Part II [Moreira de Oliveira, de Abreu Mendes & Eon (2022). Acta Cryst. A78, 115-127]. The method is extended to relational systems based on non-translational symmetry operations. The successive steps are then summarized and a simple application to the 3-periodic net qtz is discussed; analysis of zeolites and aluminosilicates may proceed along the same lines. It is shown that the new method enables the analysis of disordered distributions in periodic nets.