Acta Cryst Research Articles

Periodic diffraction from an aperiodic monohedral tiling - the Spectre tiling. Addendum.

This article describes the diffraction pattern (2-periodic Fourier transform) from the vertices of a large patch of the recently discovered `Spectre' tiling - a strictly chiral aperiodic monotile. It was reported recently that the diffraction pattern of the related weakly chiral aperiodic `Hat' monotile was 2-periodic with chiral plane-group symmetry p6 [Kaplan et al. (2024). Acta Cryst. A80, 72-78]. The diffraction periodicity arises because the Hat tiling is a systematic aperiodic deletion of vertices from the 2-periodic hexagonal mta tiling. Despite the similarity of the Hat and Spectre tilings, the Spectre tiling is not aligned with a 2-periodic lattice, and its diffraction pattern is non-periodic with chiral point symmetry 6 about the origin.

Structure of face-centred icosahedral quasicrystals with cluster close packing.

A 6D structure model for face-centred icosahedral quasicrystals consisting of so-called pseudo-Mackay and mini-Bergman-type atomic clusters is proposed based on the structure model of the Al69.1Pd22Cr2.1Fe6.8 3/2 cubic approximant crystal (with space group Pa3, a = 40.5 Å) [Fujita et al. (2013). Acta Cryst. A69, 322-340]. The cluster centres form an icosahedral close sphere packing generated by the occupation domains similar to those in the model proposed by Katz & Gratias [J. Non-Cryst. Solids (1993), 153-154, 187-195], but their size is smaller by a factor τ2 [τ = (1 + (5)1/2)/2]. The clusters cover approximately 99.46% of the atomic structure, and the cluster arrangement exhibits 15 and 19 different local configurations, respectively, for the pseudo-Mackay and mini-Bergman-type clusters. The occupation domains that generate cluster shells are modelled and discussed in terms of structural disorder and local reorganization of the cluster arrangements (phason flip).

A new Section Editor for Acta Cryst. B.

Introducing the new Section Editor for Acta Cryst. B.

Influence of device configuration and noise on a machine learning predictor for the selection of nanoparticle small-angle X-ray scattering models

Small-angle X-ray scattering (SAXS) is a widely used method for nanoparticle characterization. A common approach to analysing nanoparticles in solution by SAXS involves fitting the curve using a parametric model that relates real-space parameters, such as nanoparticle size and electron density, to intensity values in reciprocal space. Selecting the optimal model is a crucial step in terms of analysis quality and can be time-consuming and complex. Several studies have proposed effective methods, based on machine learning, to automate the model selection step. Deploying these methods in software intended for both researchers and industry raises several issues. The diversity of SAXS instrumentation requires assessment of the robustness of these methods on data from various machine configurations, involving significant variations in the q-space ranges and highly variable signal-to-noise ratios (SNR) from one data set to another. In the case of laboratory instrumentation, data acquisition can be time-consuming and there is no universal criterion for defining an optimal acquisition time. This paper presents an approach that revisits the nanoparticle model selection method proposed by Monge et al. [Acta Cryst. (2024), A80, 202–212], evaluating and enhancing its robustness on data from device configurations not seen during training, by expanding the data set used for training. The influence of SNR on predictor robustness is then assessed, improved, and used to propose a stopping criterion for optimizing the trade-off between exposure time and data quality.

A recapitulation of magnetic space groups and their UNI symbols.

The mathematical structure, description and classification of magnetic space groups is briefly reviewed, with special emphasis on the recently proposed notation, the so-called UNI symbols [Campbell et al. (2022). Acta Cryst. A78, 99-106]. As illustrative examples, very simple magnetic space groups from each of the four possible types are described in detail.

Substitutional/positional disorder of biguanide and guanylurea in the structure of a decavanadate complex [(Bg)(HV10O285-)]0.4[(HGU+)(V10O286-)]0.6(H2Met2+)2(H3O+)·8H2O.

A hydrated salt of decavanadate containing diprotonated metforminium(2+) (H2Met2+), hydronium (H3O+) and either neutral biguanide (Bg) or monoprotonated guanylurea (HGU+) exhibits a previously seen complex charge-stabilized hydrogen-bonded network [Chatkon et al. (2022). Acta Cryst. B78, 798-808]. Charge balance is achieved in two ways through substitutional disorder: a 0.6 occupied HGU+ cation is paired with a V10O286- anion, and a 0.4 occupied neutral Bg molecule is paired with a HV10O285- anion, with the remaining charge in both cases balanced by two H2Met2+ dications and one H3O+ monocation. Bg/HGU+ moieties exhibit bifurcated N-H...O hydrogen bonding to the H3O+ cation and are substitutionally/positionally disordered along with the H3O+ cation about an inversion center. The HGU+ V10O286- synthon seen in the previous study occurs again. Bg exhibits bifurcated hydrogen bonding from two amino groups to two rows of cluster O atoms running diagonally across the equatorial plane of the HV10O285- anion with a return hydrogen bond from the cluster H atom to the imino N atom of the Bg. Thus, a Bg...cluster synthon similar to the HGU+...cluster synthon previously reported is found. The disordered moieties occupy spaces with excess volume in the 3-D network structure. Interestingly, when the crystallographic unit cell of the current compound, whose X-ray data was collected at 100 K, is compared with that of a previous compound exhibiting the same supramolecular framework, unit-cell parameter c does not shorten as a and b expectantly do because of the lower data collection temperature. The lack of contraction on unit-cell parameter c is possibly due to the supramolecular structure.

The challenges of growing great crystals - or at least good enough ones!

The article of Sommer [Acta Cryst. (2024), C80, 337-342] provides a concise and effective introduction to the subject of growing crystals suitable for structure determination.

Cytochrome c Oxidase Detection in Human Fibroblasts Using Scanning Electrochemical Microscopy

Cytochrome C Oxidase Deficiency (COXD) is a disorder caused by the mutation in genes encoding for the cytochrome c oxidase enzyme (COX),1 a mitochondrial multimeric enzyme which acts as the terminal electron acceptor in the electron transport chain.2 COXD causes serious health issues in affected individuals, including severe muscle weakness, brain damage and disorders in organs such as heart, liver and kidneys.1 Diagnosis is mostly performed by muscle biopsy,3,4 which is invasive and time-consuming. Finding new effective and early diagnostic strategies is therefore crucial to minimize symptoms and long-term disabilities. This research proposes the use of scanning electrochemical microscopy (SECM) as a promising method to quantify COX activity in normal and COXD fibroblasts as cell models. We explore the interaction of the redox probe N,N,N’,N’-tetramethyl-p-phenylene diamine (TMPD) with COX as an indicator of enzymatic activity.5,6 A platinum ultramicroelectrode was used to monitor electrochemical currents at different scan speeds, which were later used to determine an apparent heterogeneous rate constant (k 0) for TMPD regeneration by each cell line using numerical modelling. A significant difference in k 0 values (p < 0.1) was observed when comparing normal and COXD fibroblasts. The further treatment of normal fibroblasts with a COX inhibitor, NaN3,7 induced significant decreases in k 0 (p < 0.01). The COX activity results determined using SECM were in good agreement with a standard spectrophotometric assay. Taken together, our findings confirm SECM as an effective and rapid method to detect COXD in living tissues and provides a foundation for the development of new assays to diagnose COXD in infants. References M. Brischigliaro and M. Zeviani, Biochimica et Biophysica Acta (BBA) - Bioenergetics, 1862, 148335 (2021).A. Timón-Gómez et al., Semin Cell Dev Biol, 76, 163–178 (2018).M. L. Simard, A. Mourier, L. C. Greaves, R. W. Taylor, and J. B. Stewart, Journal of Pathology, 245, 311–323 (2018).S. B. Wortmann, J. A. Mayr, J. M. Nuoffer, H. Prokisch, and W. Sperl, Neuropediatrics, 48, 309–314 (2017).S. Kuss, E. E. L. Tanner, M. Ordovas-Montanes, and R. G. Compton, Chem Sci, 8, 7682–7688 (2017).S. Thind et al., Proc Natl Acad Sci U S A (2023). In press.M. J. Fei et al., Acta Crystallogr D Biol Crystallogr, 56, 529–535 (2000).

Tricks and tips for trips.

Finding out about sample preparation and transportation of structural biology samples in Acta Crystallographica F, Structural Biology Communications.

Synthesis and structural characterization of a new dinuclear platinum(III) complex, [Pt2Cl4(NH3)2{μ-HN=C(O)But}2], and Synthesis and structure of two novel trans-platinum complexes. Addenda and errata

This article reports changes to the authorship of two papers by Vinci &amp; Chateigner [(2022). Acta Cryst. B78, 835–841; (2023). Acta Cryst. B79, 213–219], as well as providing additional literature citations.

Pyrazine-bridged polymetallic copper-iridium clusters.

Single crystals of the mol-ecular compound, {Cu20Ir6Cl8(C21H24N2)6(C4H4N2)3]·3.18CH3OH or [({Cu10Ir3}Cl4(IMes)3(pyrazine))2(pyrazine)]·3.18CH3OH [where IMes is 1,3-bis-(2,4,6-trimethylphen-yl)imidazol-2-yl-idene], with a unique heterometallic cluster have been prepared and the structure revealed using single-crystal X-ray diffraction. The mol-ecule is centrosymmetric with two {Cu10Ir3} cores bridged by a pyrazine ligand. The polymetallic cluster contains three stabilizing N-heterocyclic carbenes, four Cl ligands, and a non-bridging pyrazine ligand. Notably, the Cu-Ir core is arranged in an unusual shape containing 13 vertices, 22 faces, and 32 sides. The atoms within the trideca-metallic cluster are arranged in four planes, with 2, 4, 4, 3 metals in each plane. Ir atoms are present in alternate planes with an Ir atom featuring in the peripheral bimetallic plane, and two Ir atoms featuring on opposite sides of the non-adjacent tetra-metallic plane. The crystal contains two disordered methanol solvent mol-ecules with an additional region of non-modelled electron density corrected for using the SQUEEZE routine in PLATON [Spek (2015 ▸). Acta Cryst. C71, 9-18]. The given chemical formula and other crystal data do not take into account the unmodelled methanol solvent mol-ecule(s).

Following the guidelines for communicating commensurate magnetic structures: real case examples.

A few real case examples are presented on how to report magnetic structures, with precise step-by-step explanations, following the guidelines of the IUCr Commission on Magnetic Structures [Perez-Mato et al. (2024). Acta Cryst. B80, 219-234]. Four examples have been chosen, illustrating different types of single-k magnetic orders, from the basic case to more complex ones, including odd-harmonics, and one multi-k order. In addition to acquainting researchers with the process of communicating commensurate magnetic structures, these examples also aim to clarify important concepts, which are used throughout the guidelines, such as the transformation to a standard setting of a magnetic space group.

Rebuttal to the article Pathological crystal structures.

A section in the Acta Crystallographica Section C article by Raymond & Girolami [Acta Cryst. (2023), C79, 445-455] stated that the product of the reaction of [(Cp*Rh)2(μ-OH)3]+ (Cp* is 1,2,3,4,5-pentamethylcyclopentadiene) with 1-methylthymine (1-MT) at pH 10 and 60 °C, to synthesize the anionic component [RhI(η1-N3-1-MT)2]-, was not an RhI complex, but rather an AgI complex, due to the use of silver triflate (AgOTf) to remove Cl- from [Cp*RhCl2]2 to synthesize [Cp*Rh(H2O)3](OTf)2, a water-soluble crystalline complex. We will clearly show that this premise, as stated, is invalid, while the authors have simply avoided several important facts, including that Cp*OH, a reductive elimination product, at pH 10 and 60 °C, was unequivocally identified, thus leading to the RhI anionic component [RhI(η1-N3-1-MT)2]-. More importantly, AgOH, from the reaction of NaOH at pH 10 with any potentially remaining AgOTf, after the AgCl was filtered off, would be insoluble in water. Furthermore, a control experiment with the inorganic complex Rh(OH)3, reacting with 1-methylthymine at pH 10, provided no product, and this bodes well for a similar fate with AgOTf and 1-methylthymine, i.e. at pH 10, AgOTf would again be converted to the water-insoluble AgOH; therefore, no reaction would occur! Finally, a 1H NMR spectroscopy experiment was carried out with synthesized and crystallized [Cp*Rh(H2O)3](OTf)2 in D2O at various pD values; at pD 8.65 no reaction took place, while at pD 13.6, and at 60 °C for 2 h, a reductive elimination reaction caused the precipitation of Cp*OH. The subsequent 1H NMR spectrum clearly demonstrated, in the absence of any AgI complexes, that the solution structure and the X-ray crystals in D2O were similar. A postulated mechanism for this novel anionic component structure, as published previously [Smith et al. (2014). Organometallics, 33, 2389-2404], will be presented, along with the experimental data, to insure the credibility of our results. We will also answer the comments in the response of Drs Raymond and Girolami to this rebuttal.

Response to the rebuttal of the article Pathological crystal structures.

We stand fully behind our earlier suggestion [Raymond & Girolami (2023). Acta Cryst. C79, 445-455] that the claim by Fish and co-workers [Chen et al. (1995). J. Am. Chem. Soc. 117, 9097-9098; Smith et al. (2014). Organometallics, 33, 2389-2404] of a linear two-coordinate rhodium(I) species is incorrect, and that the putative rhodium atom is in fact silver.

Synthesis, crystal structure and photophysical properties of a dinuclear MnII complex with 6-(di-ethyl-amino)-4-phenyl-2-(pyridin-2-yl)quinoline.

A new quinoline derivative, namely, 6-(di-ethyl-amino)-4-phenyl-2-(pyridin-2-yl)quinoline, C24H23N3 (QP), and its MnII complex aqua-1κO-di-μ-chlorido-1:2κ4 Cl:Cl-di-chlorido-1κCl,2κCl-bis-[6-(di-ethyl-amino)-4-phenyl-2-(pyridin-2-yl)quinoline]-1κ2 N 1,N 2;2κ2 N 1,N 2-dimanganese(II), [Mn2Cl4(C24H23N3)2(H2O)] (MnQP), were synthesized. Their compositions have been determined with ESI-MS, IR, and 1H NMR spectroscopy. The crystal-structure determination of MnQP revealed a dinuclear complex with a central four-membered Mn2Cl2 ring. Both MnII atoms bind to an additional Cl atom and to two N atoms of the QP ligand. One MnII atom expands its coordination sphere with an extra water mol-ecule, resulting in a distorted octa-hedral shape. The second MnII atom shows a distorted trigonal-bipyramidal shape. The UV-vis absorption and emission spectra of the examined compounds were studied. Furthermore, when investigating the aggregation-induced emission (AIE) properties, it was found that the fluorescent color changes from blue to green and eventually becomes yellow as the fraction of water in the THF/water mixture increases from 0% to 99%. In particular, these color and intensity changes are most pronounced at a water fraction of 60%. The crystal structure contains disordered solvent mol-ecules, which could not be modeled. The SQUEEZE procedure [Spek (2015 ▸). Acta Cryst. C71, 9-18] was used to obtain information on the type and qu-antity of solvent mol-ecules, which resulted in 44 electrons in a void volume of 274 Å3, corresponding to approximately 1.7 mol-ecules of ethanol in the unit cell. These ethanol mol-ecules are not considered in the given chemical formula and other crystal data.

Updating direct methods II. Reduction of the structural complexity when triplet invariants are estimated via the Patterson map

Direct methods have practically solved the phase problem for small–medium-size molecules but have substantially failed in macromolecular crystallography. They have two main limitations: a strong dependence on structural complexity and the need to work with atomic-resolution data. Many attempts have been made to broaden their field of applicability, for example the use of some a priori information to make the estimate of the triplet invariant phases more effective. Unfortunately none of these new approaches allowed the successful application of direct methods to proteins and nucleic acids. Direct methods are still a niche tool in macromolecular crystallography. In a recent publication [Giacovazzo (2019). Acta Cryst. A75, 142–157] the method of joint probability distributions has been modified to take into account new sources of prior information, one of which is relevant to this article: the Patterson map. In practice, it has been shown that with prior knowledge of the interatomic vectors one is able to modify the classic Cochran reliability parameter for estimating the triplet invariant phases. The article was essentially theoretical in nature, and no attempt was described to test the practical usefulness of the new probabilistic formulas. This work is therefore the first application of the new method. It is shown that the use of the Patterson map as prior information substantially improves the Cochran estimate of triplet phases; the phase error distribution for the new estimates, even if it is related to macromolecular structures, becomes similar to that obtained for medium-size structures. In some ways, it is as if the use of the Patterson information reduces the structural complexity, thus allowing a more general use of direct methods in macromolecular crystallography. Atomic resolution no longer seems to be a necessary ingredient for the applicability of direct methods; tests show that the apparent reduction in structural complexity also occurs in macromolecular structures with experimental data having a resolution of 2.3 Å. A number of test structures have been used to show the potential of the new technique.

TORO Indexer: a PyTorch-based indexing algorithm for kilohertz serial crystallography.

Serial crystallography (SX) involves combining observations from a very large number of diffraction patterns coming from crystals in random orientations. To compile a complete data set, these patterns must be indexed (i.e. their orientation determined), integrated and merged. Introduced here is TORO (Torch-powered robust optimization) Indexer, a robust and adaptable indexing algorithm developed using the PyTorch framework. TORO is capable of operating on graphics processing units (GPUs), central processing units (CPUs) and other hardware accelerators supported by PyTorch, ensuring compatibility with a wide variety of computational setups. In tests, TORO outpaces existing solutions, indexing thousands of frames per second when running on GPUs, which positions it as an attractive candidate to produce real-time indexing and user feedback. The algorithm streamlines some of the ideas introduced by previous indexers like DIALS real-space grid search [Gildea, Waterman, Parkhurst, Axford, Sutton, Stuart, Sauter, Evans & Winter (2014). Acta Cryst. D70, 2652-2666] and XGandalf [Gevorkov, Yefanov, Barty, White, Mariani, Brehm, Tolstikova, Grigat & Chapman (2019). Acta Cryst. A75, 694-704] and refines them using faster and principled robust optimization techniques which result in a concise code base consisting of less than 500 lines. On the basis of evaluations across four proteins, TORO consistently matches, and in certain instances outperforms, established algorithms such as XGandalf and MOSFLM [Powell (1999). Acta Cryst. D55, 1690-1695], occasionally amplifying the quality of the consolidated data while achieving superior indexing speed. The inherent modularity of TORO and the versatility of PyTorch code bases facilitate its deployment into a wide array of architectures, software platforms and bespoke applications, highlighting its prospective significance in SX.

Synthesis and crystal structure of the cluster (Et4N)[(Tp*)MoFe3S3(μ3-NSiMe3)(N3)3

The title compound, tetraethylammonium triazidotri-μ3-sulfido-[μ3-(trimethylsilyl)azanediido][tris(3,5-dimethylpyrazol-1-yl)hydroborato]triiron(+2.33)molybdenum(IV), (C8H20N)[Fe3MoS3(C15H22BN6)(C3H9NSi)(N3)3] or (Et4N)[(Tp*)MoFe3S3(μ3-NSiMe3)(N3)3] [Tp* = tris(3,5-dimethylpyrazol-1-yl)hydroborate(1−)], crystallizes as needle-like black crystals in space group P\overline{1}. In this cluster, the Mo site is in a distorted octahedral coordination model, coordinating three N atoms on the Tp* ligand and three μ3-bridging S atoms in the core. The Fe sites are in a distorted tetrahedral coordination model, coordinating two μ3-bridging S atoms, one μ3-bridging N atom from Me3SiN2−, and another N atom on the terminal azide ligand. This type of heterometallic and heteroleptic single cubane cluster represents a typical example within the Mo–Fe–S cluster family, which may be a good reference for understanding the structure and function of the nitrogenase FeMo cofactor. The residual electron density of disordered solvent molecules in the void space could not be reasonably modeled, thus the SQUEEZE [Spek (2015). Acta Cryst. C71, 9–18] function was applied. The solvent contribution is not included in the reported molecular weight and density.

3D ED/MicroED entering a new era.

Aragon et al. [Acta Cryst. (2024), C80, 179-189], by reporting the discussion and the final conclusions of a round table held during a symposium at the National Center for CryoEM Access and Training, well describe all the advances that have been made for the application of 3D ED/MicroED to pharmaceutical and macromolecular nanocrystals and propose possible future scenarios.

Synthesis, crystal structure and thermal properties of a new polymorphic modification of diisothiocyanatotetrakis(4-methylpyridine)cobalt(II)

The title compound, [Co(NCS)2(C6H7N)4] or Co(NCS)2(4-methylpyridine)4, was prepared by the reaction of Co(NCS)2 with 4-methylpyridine in water and is isotypic to one of the polymorphs of Ni(NCS)2(4-methylpyridine)4 [Kerr &amp; Williams (1977). Acta Cryst. B33, 3589–3592 and Soldatov et al. (2004). Cryst. Growth Des. 4, 1185–1194]. Comparison of the experimental X-ray powder pattern with that calculated from the single-crystal data proves that a pure phase has been obtained. The asymmetric unit consists of one CoII cation, two crystallographically independent thiocyanate anions and four independent 4-methylpyridine ligands, all located in general positions. The CoII cations are sixfold coordinated to two terminally N-bonded thiocyanate anions and four 4-methylpyridine coligands within slightly distorted octahedra. Between the complexes, a number of weak C—H...N and C—H...S contacts are found. This structure represent a polymorphic modification of Co(NCS)2(4-methylpyridine)4 already reported in the CCD [Harris et al. (2003). NASA Technical Reports, 211890]. In contrast to this form, the crystal structure of the new polymorph shows a denser packing, indicating that it is thermodynamically stable at least at low temperatures. Thermogravimetric and differential thermoanalysis reveal that the title compound starts to decomposes at about 100°C and that the coligands are removed in separate steps without any sign of a polymorphic transition before decomposition.